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Faculty Publication (2020)

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1. Almerio, F.M., Asi, R.J.L., Jacinto, S.D., Mazahery, A.R.F. (2020). Reducing mitomycin-C-induced ROS levels in mouse feeder cells improves induced pluripotent stem cell colony growth. Biotechniques, 68 (5). more

Abstract:

Chemically defined stem cell culture media are often costly, and the use of mitotically arrested mouse embryonic fibroblasts (MEFs) as feeder cells is a popular and cost-efficient way to maintain induced pluripotent stem cells (iPSCs). However, the commonly used mitotic inhibitor mitomycin-C (MMC) is known to cause cellular metabolic stress. Therefore, our aim was to determine whether such stress in feeder cells indirectly affects iPSC growth during coculture. We report that prolonged exposure to MMC causes metabolic stress in MEFs in the form of oxidative dysregulation. Through optimization of MMC exposure time, we show how to effectively arrest MEFs without inducing oxidative stress, thus promoting significantly better colony growth rates (p < 0.05), improved viability and longer periods between passages of iPSCs in coculture.

 

2. Bejar, S.G.F., Duya, M.R.M., Duya, M.V., Galindon, J.M.M., Pasion, B.O., Ong, P.S. (2020). Living in small spaces: Forest fragment characterization and its use by Philippine tarsiers (Tarsius syrichta Linnaeus, 1758) in Mindanao Island, PhilippinesPrimates, 61, Pages 529-542. https://doi.org/10.1007/s10329-020-00798-2 more

Abstract:

The Philippine tarsier (Tarsius syrichta) is a charismatic species that is threatened by illegal hunting and deforestation. Although they occur in forest and disturbed habitats, ecological information about them is still considerably lacking, which consequently hampers our ability to effectively protect tarsiers from further endangerment. Here, we characterized a 36-ha forest fragment in Mindanao Island where a population of tarsiers persist, and assessed the factors that could have influenced their distribution within the area. We sampled trees (> 1 cm DBH) within 10 × 10-m sampling plots (N = 54), which were established within 1-ha grids (N = 32) and locations where tarsiers were captured (N = 22). The habitat was characterized as a regenerating forest over limestone, with a generally homogeneous structure in terms of tree species richness, abundance, mean DBH, and height. In both sampling plots, we found an abundance of trees below 5 cm in DBH (> 50%) and between 2.6 and 5 m in height (> 40%), which, accordingly, the tarsiers appeared to prefer to use when foraging or sleeping. Lianas were among the most important features of the forest, possibly being a keystone structure in such habitats. Community assemblage, species richness, and mean height of trees, as well as distance to the forest edge, were found to be significant factors that influenced tarsier distribution in the fragment. Our study provides basic yet critical information on the habitat and ecology of Philippine tarsiers in Mindanao, and highlights the importance of forest fragments with rich flora diversity to the survival of the species.

 

3. Fidelino, J.S., Duya, M.R.M., Duya, M.V., Ong, P.S. (2020). Fruit bat diversity patterns for assessing restoration success in reforestation areas in the Philippines. Acta Oecologica, 108, 103637.more

Abstract:

In response to extensive deforestation in the Philippines in the last century, reforestation initiatives have been developed, setting area- or seedling count-based success criteria. However, to sufficiently assess reforestation as an approach to conserving biodiversity and protecting habitats, restoration of ecosystem integrity must be evaluated. Increased recognition of the role of fauna in ecological restoration has led to the evaluation of the role of different groups in assisting recovery and as potential metrics of success. In this study, we used mist netting data to evaluate how richness, abundance, diversity, and composition of fruit bats differ between reforestation areas and nearby secondary forest, and their potential as measures of restoration success. We captured 6564 fruit bats representing 15 species from a sampling effort of 1,994,366 m2·h. Estimated species richness and Simpson indices did not differ significantly between habitat types. Overall abundance was only significantly different in Palinpinon, with more individuals in the reforestation area, while Shannon indices only differed significantly in BacMan. Differences in composition were all found to be statistically significant, based on non-metric multidimensional scaling ordination biplots and permutational MANOVA. Of the three most abundant species captured across all reservations, the generalists Cynopterus luzoniensis and Macroglossus minimus were more abundant in reforestation areas. On the other hand, the forest specialists Haplonycteris fischeri, Harpyionycteris whiteheadi, and Ptenochirus minor showed lower abundances in reforestation areas. While univariate biodiversity metrics did not differ between secondary forests and reforestation areas, the abundance of particular species and the species composition of fruit bats remained distinct between these habitats. We identified specific aspects of the fruit bat assemblage with the potential as metrics of restoration success. To facilitate evaluation of restoration success using changes in faunal assemblage, we recommend the development of sampling protocols and metrics that would standardize this process.

 

4. Francisco, J.C.E., Rivera, W.L., Vital, P.G. (2020). Influences of carbohydrate, nitrogen, and phosphorus sources on the citric acid production by fungal endophyte Aspergillus fumigatus P3I6Preparative Biochemistry and Biotechnology, 50 (3), Pages 292-301. DOI: 10.1080/10826068.2019.1689510 more

Abstract:

Fungi are ecologically ubiquitous organisms on earth and regarded as one of the prolific sources of natural products. Fungal endophytes may provide essential prerequisite molecules to plant biochemical pathways which allow the efficient synthesis of primary and secondary metabolites. This study characterized the influences of various combinations of process parameters namely, carbohydrate, nitrogen, and phosphorus sources on citric acid (CA) production by the isolated fungal endophyte Aspergillus fumigatus P3I6 from Citrus microcarpa. Aspergillus fumigatus P3I6 had higher CA concentration of 9.2 (± 0.9) g L−1 and 9.0 (± 5.0 × 10−15) g L−1 when supplemented with sucrose and white refined sugar, respectively, than A. niger NRRL 599. Response Surface Methodology (RSM) had shown that A. fumigatus P3I6 produced the highest CA (23.8 g L−1) in Combination 4 (18.0% sucrose, 0.3 g L−1 ammonium sulfate, and 5.0 g L−1 dipotassium phosphate (K2HPO4)). Analysis of variance showed that when K2HPO4 concentrations were increased, CA content in fermentation media was significantly elevated. Hence, K2HPO4 was the most critical variable in the quadratic model (p < 0.05); however, sucrose concentration still has its role in production. Aside from using A. niger in most fermentation processes, this discovered fungal strain can be potentially used in biotechnological applications.

 

5. Garcia, L.M.B., Sayco, M.J.P., Aya, F.A. (2020). Point-of-no-return and delayed feeding mortalities in first-feeding larvae of the silver therapon Leiopotherapon plumbeus (Kner) (Teleostei: Terapontidae)Aquaculture Reports, 16, Article number 100288. https://doi.org/10.1016/j.aqrep.2020.100288 more

Abstract:

This study examined the incidence of mortalities among first-feeding post-yolk sac silver therapon Leiopotherapon plumbeus (Kner) larvae deprived of live food in the hatchery. Starting after their yolk was consumed at 40 h post-hatch (hph) and every 2 h thereafter until 54 hph, larvae were fed and exposed to live food for an hour only and their performance was observed after initial feeding at 25 °C. Feeding incidence progressively increased until 48 hph as larval mouth gape increased during exogenous feeding, but oil globule volume progressively declined until full exhaustion at 52 hph. All starved larvae fed at 48 hph but feeding incidence progressively declined until larvae ceased to feed at 54 hph to coincide with a significant reduction in survivorship, indicating that larvae have reached their point-of-no-return (PNR) at 50 hph despite the availability of food. Delayed initial feeding of un-fed post-yolk sac larvae starting at 46 hph until 54 hph resulted in significantly higher feeding incidence among 46−48 hph larvae than those fed after 50 hph, which did not survive longer than 10 h after initial feeding. These results demonstrate that silver therapon larvae have a very brief transitional or mixed-feeding period of 12 h after yolk exhaustion so that initial feeding beyond 50 hph when larvae have reached their PNR results in early onset of death.

 

6. Hereward, J.P.Cai, X.Matias, A.M.A.Walter, G.H.Xu, C.Wang, Y. (2020). Migration dynamics of an important rice pest: The brown planthopper (Nilaparvata lugens) across Asia—Insights from population genomicsEvolutionary Applications, 132449– 2459.https://doi.org/10.1111/eva.13047more

Abstract:

Introduction

Brown planthoppers (Nilaparvata lugens) are the most serious insect pests of rice, one of the world's most important staple crops. They reproduce year‐round in the tropical parts of their distribution, but cannot overwinter in the temperate areas where they occur, and invade seasonally from elsewhere. Decades of research have not revealed their source unambiguously.

Methods and Results

We sequenced the genomes of brown planthopper populations from across temperate and tropical parts of their distribution and show that the Indochinese peninsula is the major source of migration into temperate China. The Philippines, once considered a key source, is not significant, with little evidence for their migration into China. We find support for immigration from the west of China contributing to these regional dynamics.

Discussion

The lack of connectivity between the Philippine population and the mainland Chinese populations explains the different evolution of Imidacloprid resistance in these populations. This study highlights the promise of whole‐genome sequence data to understand migration when gene flow is high—a situation that has been difficult to resolve using traditional genetic markers.

 

7. Labrador, K.L., Nacario, M.A.G., Malajacan, G.T., Abello, J.J.M., Galarion, L.H., Rensing, C., Rivera, W.L. (2020). Selecting rep-PCR markers to source track fecal contamination in Laguna Lake, Philippines. Journal Water & Health, 18 (1), Pages 19-29. more

Abstract:

Fecal contamination is one of the factors causing deterioration of Laguna Lake. Although total coliform levels are constantly monitored, no protocol is in place to identify their origin. This can be addressed using the library-dependent microbial source tracking (MST) method, repetitive element sequence-based polymerase chain reaction (rep-PCR) fingerprinting. Serving as a prerequisite in developing the host-origin library, we assessed the discriminatory power of three fingerprinting primers, namely BOX-A1R, (GTG)5, and REP1R-1/2-1. Fingerprint profiles were obtained from 290 thermotolerant Escherichia coli isolated from sewage waters and fecal samples of cows, chickens, and pigs from regions surrounding the lake. Band patterns were converted into binary profiles and were classified using the discriminant analysis of principal components. Results show that: (1) REP1R-1/2-1 has a low genotyping success rate and information content; (2) increasing the library size led to more precise estimates of library accuracy; and (3) combining fingerprint profiles from BOX-A1R and (GTG)5 revealed the best discrimination (average rate of correct classification (ARCC) = 0.82 ± 0.06) in a two-way categorical split; while (4) no significant difference was found between the combined profiles (0.74 ± 0.15) and using solely BOX-A1R (0.76 ± 0.09) in a four-way split. Testing the library by identifying known isolates from a separate dataset has shown that a two-way classification performed better (ARCC = 0.66) than a four-way split (ARCC = 0.29). The library can be developed further by adding more representative isolates per host source. Nevertheless, our results have shown that combining profiles from BOX-A1R and (GTG)5 is recommended in developing the MST library for Laguna Lake.

 

8. Leonardo, L., Hernandez, L., Magturo, T.C., Palasi, W., Rubite, J.M., de Cadiz, A., Moendeg, K., Fornillos, R.J., Tabios, I.K., Mistica, M., Fontanilla, I.K. (2020). Current status of neglected tropical diseases (NTDs) in the PhilippinesActa Tropica, 203, Article number 105284. https://doi.org/10.1016/j.actatropica.2019.105284 more

Abstract:

In the Philippines, ten NTDs are prevalent, but only six namely LF, schistosomiasis, STH, food-borne trematodiases, rabies and leprosy are considered to be of public health importance. The 81 provinces in the country are endemic for at least one of these NTDs. Others may be endemic for two or even more of these diseases. Since 2000, after the Philippines accepted and implemented the WHO guidelines for NTDs prevention, control and elimination, significant progress has been achieved in reducing the magnitude of NTDs endemic in the country. Since 2009, out of 46 filariasis-endemic provinces, the number of provinces that has eliminated LF has progressively increased so that by 2015, 76% are already LF-free. By 2019, only four provinces remain endemic for LF. For schistosomiasis, as of 2012, report from the Department of Health (DOH) put the number of high endemic provinces at 10, moderately endemic at 6 and low to elimination levels at 12. For STH, results of the National Parasite Survey in the Philippines among school-aged children conducted in 2015 by the Research Institute for Tropical Medicine, the research arm of the Philippine DOH, however, showed that the overall cumulative prevalence was 28.4% with a prevalence range between 7.1% and 67.4%. The figures are way above the <20% prevalence standard set by the World Health Organization. Control and prevention efforts for FBTs just gained traction with the call of WHO for elimination of NTDs in 2015. There is an urgent need to update information by an intensive national baseline survey that can validate previous data as well as generate new information on the magnitude of the FBT problem in the Philippines. For leprosy, elimination activities have been intensified in high prevalence areas and from 2009 to 2013, case detection and prevalence were sustained at <1.0 per 10,000 population. Rabies elimination activities have been effective that by 2011, only five regions out of 16 remained with the highest number of rabies cases. In a period of seven years from 2010 to 2017, the number of rabies-free provinces and municipalities increased from 3 to 49. Problems continue to hound the NTD programmes in the Philippines as priorities shift to more urgent health problems in a country that is weighed down not only by the triple burden of disease but serious health consequences of emergencies and disasters and the fast-growing population itself. Paradigm shifts are suggested to replace the traditional and conventional perspectives of control. These include change from disease approach to intervention approach to allow for integration of strategies targeting several NTDs and multisectoral, multidisciplinary approach requiring strong, viable and sustainable partnerships involving various agencies of the government, public and private sector, pharmaceuticals, academe, researchers, local government units and the endemic communities themselves.

 

9. Leonardo, L., Varonab, G., Fornillos, R.J., Manalo, D., Tabios, I.K.,  Moendeg, K., De Cadiz, A., Kikuchi, M., Chigusa, Y., Mistica, M., Hernandez , L., Palasi, W., Fontanilla, I.K. (2020). Oncomelania hupensis quadrasi: Snail intermediate host of Schistosoma japonicum in the Philippines. Acta Tropica, 210, 105547.more

Abstract:

Oncomelania hupensis quadrasi is the snail intermediate host of Schistosoma japonicum in the Philippines. It was discovered by Dr. Marcos Tubangui in 1932 more than two decades after the discovery of the disease in the country in 1906. This review, the first for O. h. quadrasi, presents past and present works on the taxonomy, biology, ecology, control, possible paleogeographic origin of the snail intermediate host and future in research, control and surveillance of the snail. Extensive references are made of other subspecies of O. hupensis such as the subspecies in China for which majority of the advances has been accomplished. Contrasting views on whether the snail is to be considered an independent species of Oncomelania or as one of several subspecies of Oncomelania hupensis are presented. Snail control methods such as chemical methods using synthetic and botanical molluscicides, environmental manipulation and biological control are reviewed. Use of technologies such as Remote Sensing, Geographical Information System and landscape genetics is stressed for snail surveillance. Control and prevention efforts in the Philippines have consistently focused on mass drug administration which has proved inadequate in elimination of the disease. An integrated approach that includes snail control, environmental sanitation and health education has been proposed. Population movement such as migration for employment and economic opportunities and ecotourism and global climate change resulting in heavy rains and flooding challenge the gains of control and elimination efforts. Concern for possible migration of snails to non-endemic areas is expressed given the various changes both natural and mostly man-made favoring habitat expansion.

10. Peralta, E.M., Batucan, L.S., Jr., De Jesus, I.B.B., Trino, E.M.C., Uehara, Y., Ishida, T., Kobayashi, Y., Ko, C.Y., Iwata, T., Borja, A.S., Briones, J.C.A., Papa, R.D.S., Magbanua, F.S., Okuda, N. (2020). Nutrient loadings and deforestation decrease benthic macroinvertebrate diversity in an urbanised tropical stream system. Limnological, 80. more

Abstract:

Lotic ecosystems in urban areas are severely impacted by anthropogenic environmental stressors, such as deforestation and nutrient pollution, due to socioeconomic activities in the catchment. To work out measures for identification and mitigation of concurrent multiple stressors to a stream system, it is necessary to assess the relative importance of impacts by the individual stressors. Here we aimed to discriminate the covarying effects of nutrient pollution and deforestation on benthic macroinvertebrate communities in an urbanised tropical stream system. In the Silang-Santa Rosa Subwatershed (SSRS) of Laguna de Bay, benthic macroinvertebrates and physicochemical environments were investigated at 13 sites varying in human population density, riparian canopy, and land-use pattern as indicated by geographic information systems in the catchment. Regression and multivariate analyses were performed to identify the drivers of the biodiversity loss and understand its underlying mechanisms. In the SSRS, where rapid economic growth took place without updating poorly installed wastewater treatment plants (WWTPs), domestic activity indicated by human population density in the catchment was the primary factor in generating heavy phosphorous loadings (mean total phosphorus = 0.91; range = 0–1.50 mg/l) that caused hypoxia (mean dissolved oxygen = 2.98; range = 0.13–6.27 mg/l) in stream waters and subsequently reduced macroinvertebrate diversity (mean H’ = 0.91; SD ± 0.61). Nutrient and organic pollution and riparian deforestation explained 53.5% and 9.7% of the variation of benthic macroinvertebrate communities in SSRS, respectively. Given such scenario, additional WWTPs servicing urban developments and improved riparian canopy cover in the SSRS can be both strategic and cost-effective in the initial steps of environmental mitigation in urbanised streams, especially in rapidly developing countries.

 

11. Perez, G.J., Comiso, J.C., Aragones, L.V., Merida, H.C., Ong, P.S. (2020). Reforestation and Deforestation in Northern Luzon, Philippines: Critical Issues as Observed from SpaceForests, 11, 1071. https://doi.org/10.3390/f11101071more

Abstract:

Among the richest in biodiversity globally has been the Philippine rainforest, which used to cover about 90% of the country’s land area. During the last few decades, the forest cover has been reduced to less than 10% of the original, only a fraction of which is old-growth forest. The negative impacts of deforestation led to the launching of the National Greening Program (NGP) that involved the planting of more than a billion seedlings over a few million hectares of land from 2011 to 2016. To assess the success of the NGP, satellite data from Landsat and the Moderate Resolution Imaging Spectroradiometer (MODIS) were analyzed before, during, and after the NGP. Reforestation in the NGP sites was examined concurrently with observed deforestation in Luzon using forest loss data derived from Landsat for the period 2001 to 2018. The results show that losses declined from 2011 to 2015 but increased from 2016 to 2018. Because of such losses, the net effect is a balance of reforestation and deforestation or no significant gain from the NGP. Case studies were done in three sites in the Sierra Madre forest, where half of the remaining old-growth forest is located, using a combination of Landsat and Very High Resolution (VHR) data. The Landsat data were classified into closed forest, open forest, and other vegetation cover types. The conversion from one vegetation cover type to another was evaluated through the use of the Sankey Diagram. While some non-forest types became open or closed forests, the loss of open or closed forests is more pronounced. VHR data reveal critical issues happening within the NGP sites during the NGP period. More comprehensive data from MODIS also confirm that there was no significant increase in the forest cover in Luzon, Sierra Madre, and Cordillera from 2001 to 2018.

12. Saguyod, S.U., Alhallak, I., Simmen, R.C., & Velarde, M.C. (2020). Metformin regulation of progesterone receptor isoform‑B expression in human endometrial cancer cells is glucose‑dependent. Oncology Letters, 20, 249. https://doi.org/10.3892/ol.2020.12112more

Abstract:

Metformin (MET) constitutes the first‑line treatment against type 2 diabetes. Growing evidence linking insulin resistance and cancer risk has expanded the therapeutic potential of MET to several cancer types. However, the oncostatic mechanisms of MET are not well understood. MET has been shown to promote the expression of progesterone receptor (PGR) and other antitumor biomarkers in patients with non‑diabetic endometrial cancer (EC) and in Ishikawa EC cells cultured in normal glucose (5.5 mM) media. Therefore, the present study aimed to assess the effects of MET on EC cells under conditions simulating diabetes. Ishikawa cells treated with 10 nM 17β‑estradiol (E2) and/or 100 µM MET and exposed to normal and high (17.5 mM) concentrations of glucose were evaluated for proliferative and PGR expression status. Under normal glucose conditions, MET attenuated E2‑induced cell proliferation and cyclin D1 gene expression, and increased total PGR and PGR‑B transcript levels. MET inhibited Ishikawa cell spheroid formation only in the absence of E2 treatment. In E2‑treated cells under high glucose conditions, MET showed no effects on cell proliferation and spheroid formation, and increased total PGR but not PGR‑B transcript levels. Transfection with Krüppel‑like factor 9 small interfering RNA increased PGR‑A transcript levels, irrespective of glucose environment. Medroxyprogesterone acetate downregulated PGR‑A expression more effectively with metformin under high compared with normal glucose conditions. To evaluate the potential mechanisms underlying the targeting of PGR by MET, E2‑treated cells were incubated with MET and the AMPK inhibitor Compound C, or with the AMPK activator 5‑aminoimidazole‑4‑carboxamide ribonucleotide (AICAR), under normal glucose conditions. Compound C abrogated the effects of MET on PGR‑B while AICAR increased PGR‑B transcript levels, albeit less effectively compared with MET. The present results demonstrate the glucose‑dependent effects of MET on PGR‑B isoform expression, which may inform the response to progestin therapy in diabetic women with EC.

 

13. Sajo, M.E.J.V, Teves, J.M.Y., Corachea, A.J.M., Diaz, L.A., Chan, A.F.O., Valparaiso, A.P., Dy Echo, A.V.A., Macalindong, S.S., Uy, G.L.B., Dofitas, R.B., Habana, M.A.E., Gerona, R.R., Irwin, J.C., Gaudice, L.C., and Velarde, M.C. (2020). A Pilot Cancer-Phenome Biobanking System in a Low-Resource Southeast Asian Setting: The Philippine General Hospital Biobank Experience. Biopreservation and Biobanking, 18 (3), Pages 180-188.more

Abstract:

Biobanking has become an indispensable tool for translational research and health innovations. While the field of biobanking has progressed and evolved globally, biobanking in developing Association of Southeast Asian Nations (ASEAN) countries such as the Philippines remains underrepresented because of several challenges often encountered in these low- and middle-income countries. Recently, the Philippine government has undertaken enormous efforts to advancing research and development in the country, and one of the current research pursuits is the establishment of biobanks, with the hope of attaining more discoveries and innovations in the future. Given that cancer remains a leading cause of death in the Philippines, the Philippine government supported the establishment of a cancer biobank at the Philippine General Hospital (PGH). In this study, we present a specific use case of biobanking activity at the PGH Biobank, to build a cohort of biospecimens from Filipino patients with breast, endometrial, and ovarian cancer. This initiative is part of a biomonitoring study (1) to assess environmental exposures and possible risk factors in the Philippine population and (2) to develop a system of culturing human cells from Filipino patients for subsequent in vitro studies. We discuss issues faced and the solutions developed during the implementation of the biobank. Strong research collaboration, a funding source, basic infrastructure, and appropriate technology helped initiate this pilot biobank in the Philippines. Overall, the experiences of establishing the PGH Biobank may help other institutions in low-resource countries to set up cancer biobanks.

 

14. Santos, B.S., Torres, S.K.M. (2020). Species identification among morphologically-similar caranx speciesTurkish Journal of Fisheries and Aquatic Sciences, 20 (2), Pages 159-169. http://doi.org/10.4194/1303-2712-v20_2_08 

Abstract:

Accurate identification of species is important in assessing biodiversity and in conservation and population management strategies. Species with similar morphology, however, could be difficult to identify correctly. Published papers have reported on Caranx species that have been incorrectly identified and careful analysis is needed when identifying these species. In this study, 21 specimens from the genus Caranx were identified using DNA barcoding. Specimens were collected from Batangas, Philippines, where freshwater Caranx, which are about 50% more expensive, are present. Using morphological characteristics, C. ignobilis and C. sexfasciatus were identified correctly while one C. papuensis specimen was identified as C. sexfasciatus. Barcodes for three species, namely C. ignobilis, C. sexfasciatus, and C. papuensis, were detected based on cytochrome c oxidase I (COI) sequences. With the addition of Caranx COI sequences from GenBank, the calculated average K2P distance among species (8.19%), was higher than the average K2P distance within species (0.30%). Analysis of all available COI sequences of C. sexfasciatus from GenBank showed multiple cases of likely misidentification in other studies. Geometric morphometric analyses revealed morphological differences between specimens barcoded as C. papuensis and C. sexfasciatus that could aid in identifying the species. 

 

15. Santos, P.D.M., Widmer, K.W., Rivera, W.L. (2020). PCR-based detection and serovar identification of Salmonella in retail meat collected from wet markets in Metro Manila, Philippines. PLoS ONE, 15 (9): e0239457. https://doi.org/10.1371/journal.pone.0239457more

Abstract:

This study aimed to detect Salmonella from retail meat collected from nine wet markets in Metro Manila, and identify the subtypes of Salmonella isolates using molecular serotyping assays from previously developed primers. Of the 720 collected meat samples, 57.64% were found to be Salmonella-contaminated. The most predominant serogroup was Salmonella O:3, and Salmonella serogroups O:4, O:6,7, O:8, O:9, and undetermined serogroups were also found. Most frequently detected isolates in bovine meat were S. 3:e,h:1,6 (putative identity: S. Anatum) and S: 4:e,h:1,2 (putative identity: S. Saintpaul), in porcine meat was S. 3:e,h:1,6 (putative identity: S. Anatum), and S. 8:i:z6 (putative identity: S. Kentucky) was common in poultry products. This study also demonstrated retail meat samples were contaminated with multiple Salmonella serogroups and serovars. This is the first Philippine study that utilized PCR-based assays to characterize Salmonella isolates down to a serovar level and provides baseline information regarding Salmonella prevalence and serovar distribution in retail meat. Molecular serotyping performed in this study can be used as an alternative approach to traditional serotyping in surveillance of Salmonella in the Philippines since the latter is expensive, time-consuming, and requires skilled technicians.

 

16. Singer, G.A., Loya, F.P., Lapsley, W.D., Tobar, B.Z., Carlos, S., Carlos, R.S., Carlos, E.T., Adao, D.E.V., Rivera, W.L., Jaffe, D.A., Mazet, J.A.K., Chomel, B.B. (2020). Detection of Bartonella infection in pet dogs from Manila, the PhilippinesActa Tropica, 205, Article number 105277. http://doi.org/10.1016/j.actatropica.2019.105277more

Abstract:

Dogs can be infected by a wide range of Bartonella spp., but studies regarding the prevalence of Bartonella infection in dogs in the Philippines have not been conducted. This study aimed at determining the prevalence of Bartonella infection in pets dogs from two veterinary clinics in Metro Manila, The Philippines, using both serology and polymerase chain reaction (PCR). Blood samples from 116 dogs from two different groups, one of 60 mainly “healthy dogs” and the other one of 56 dogs enrolled in a tick-borne disease suspect group, were tested for presence of B. henselae antibodies and to detect Bartonella DNA using primers specific for the citrate synthase gene. Seroprevalence for B. henselae was very low (2.6%), as the only three (5%) seropositive dogs (titer 1:64) where among the healthy pet dog group. Following subsequent sequencing, 13 samples, all from the tick-borne disease group, were determined positive for B. henselae (11.2%). This is the first study to report dog infection with B. henselae in the Philippines. 

 

 Chemistry logo

1. Agulto, V., Empizo, M.J., Inguito, J.M., Magallanes, B.J., Nalayog, M., Shinohara, K., Umeno, D., Salazar, K., Solibet, E.J.C., Ibus-Armonia, J., Judicpa, M.A., Somintac, A., Yamanoi, K., Shimizu, T., Yago, A.C., Sarmago, R. and Sarukura, N. (2020). Spectroscopic investigations of ZnO-polymer composites grown via wet chemical method. Proceedings of the Samahang Pisika ng Pilipinas. 38, SPP-2020-2C-04.more

Abstract:

Composites are made from a synergy of different materials, hence they exhibit improved properties compared to their individual constituents. With interest in ZnO as an optical material, our primary focus is to determine how the incorporation of polymers can improve the optical properties of ZnO microstructures. This paper presents the material properties of ZnO-polymer composites investigated using x-ray diffraction (XRD) spectroscopy, Raman spectroscopy, and photoluminescence (PL) spectroscopy. A combination of wet chemical methods was used to synthesize the composites—hydrothermal growth of ZnO microrods and dip-coating in different aqueous polymer solutions. The findings show that the composites have the same structural properties as the base ZnO material, but the photoluminescence properties differ depending on the type of polymer used. Selecting appropriate polymers can then be used to yield ZnO-based materials with different luminescence characteristics.

 

2. Amor, E.C., Attanayake, A.P., Nicolas, M.G., Yu, G.F.B., Macaulay, J.O. (2020). Undergraduate education in biochemistry and molecular biology: A parallel session at the IUBMB/PSBMB 2019 “Harnessing Interdisciplinary Education in Biochemistry and Molecular Biology” conferenceBiochemistry  and  Molecular  Biology Education (early view).more

Abstract:

Although science education, including biochemistry and molecular biology education, starts before students commence university, for many students, undergraduate programs are their first real introduction to biochemistry and molecular biology. Students often report that biochemistry and molecular biology are relatively difficult topics hence the use of varied and well‐thought‐out approaches are critical to fully engage students. This session provided insights into undergraduate curriculum design.

 

3. Buenaventura, A.G.E. and Yago, A.C. (2020). Electrochemical Reversible Copper Oxide (CuO) System on Multiwalled Carbon Nanotube Paste Electrode (CPE) as Sensor for Hydrogen Peroxide in Wound Cleaning Solution. Philippine Journal of Science, 149 (3-a), Pages 801-813.more

Abstract:

An electrochemical sensor for hydrogen peroxide (H2O2) was prepared and optimized in this study. The sensor recognition element consisted of mainly copper oxide (CuO) particles electrodeposited on an anodized multiwalled carbon nanotube paste electrode (MWCPE), which is composed of multiwalled carbon nanotubes (MWCNT) and polydimethylsiloxane (PDMS). Chronoamperometry (CA) was used as the electrodeposition technique both for Cu deposition and oxidation to CuO. The layer of CuO was shown to react with H2O2, which lead to measurable voltammetric current at varying concentrations of H2O2. Different parameters were optimized as follows: Cu deposition time, Cu oxidation time, and equilibration time. Differential pulse voltammetry (DPV) was used as the main sensing technique for CuO-CPE. DPV measurements showed that the average peak current (ave. Ip) was found to be increasing linearly with increasing H2O2 concentration. Two H2O2 concentration ranges, low concentration (20 μM – 100 μM) and high concentration (400 μM – 1200 μM), were observed to have a linear correlation with ave. Ip. The limits of detection (LODs) were calculated to be equal to 11.40 µM using the low concentration range, while 13.04 μM using the high concentration range. The H2O2 measurements using CuO-CPE were found to be reproducible and repeatable. Real sample analysis was also performed on a wound cleaning solution (aqua oxigenada, 6% H2O2 w/w) as a sample. From the measurements, the H2O2 concentration of the analyte was found to be 6.16% w/w; the calculated % error was equal to 2.67%. Overall, CuO-CPE composite was shown to be an effective electrochemical sensor for H2O2 analysis.

 

4. Buenviaje, S.C. Jr., Usman, K.A.S., Edanol, Y.D.G, Maylem, G.T. and Payawan, L.M. Jr. (2020). One-Pot Photochemical Synthesis of Solution-Stable TiO2- Polypyrrole Nanocomposite for the Photodegradation of Methyl Orange. Key Engineering Materials, 853, Pages 217-222.more

Abstract:

Photocatalysis is a promising technology used in wastewater treatment. However, the practical application of this approach has been hindered by several factors. One issue is the aggregation of the photocatalyst in solution which leads to significant decrease in catalytic efficiency. Recent innovations in photochemical research have geared towards improving the colloidal stability of well-known photocatalysts such as titanium dioxide (TiO2). In this study, a simple method of imparting colloidal stability to TiO2, through one-pot photo-polymerized polypyrrole (PPy) nanoparticle coatings were demonstrated. The resulting TiO2-PPy (TP) dispersions exhibited excellent resistance to aggregation as evident in their uniform particle size distribution (diameter = 81.40 ± 6.58 nm, polydispersity index = 0.412 ± 0.037) and stable zeta-potential values (ζ = 33.15 ± 4.35). The optimum TiO2 to polymer ratio also resulted to significant lowering in band-gap energy (from 3.54 eV to 3.15 eV) which is an indicator of improved photocatalytic properties. Photodegradation of a model pollutant, methyl orange (MO) performed at optimal lightning condition and 4TP dosage showed 35% /hour photocatalytic efficiency. Lastly, kinetic studies suggest that the catalytic performance is dependent on the pollutant concentration as shown by a second-order MO degradation with rate constant of 306.856 x 10-7 M-1 s-1 and proposed rate law of R = k[MO]2. The study had also indicated the chemical conversion of MO to CO2 by measuring about 43% decrease in total organic carbon in an hour.  

 

5. Custodio, K.K.S., Claudio, G.C. and Nellas, R.B.(2020). Structural Dynamics of Neighboring Water Molecules of N-Isopropylacrylamide PentamerACS Omega, 5 (3), Pages 1408-1413. more

Abstract:

Poly(N-isopropylacrylamide) (PNIPAM) is a popular polymer widely used in smart hydrogel synthesis due to its thermo-responsive behavior in aqueous medium. Aqueous PNIPAM hydrogels can reversibly swell and collapse below and above their lower critical solution temperature (LCST), respectively. The present work used molecular dynamics simulations to explore the behavior of water molecules surrounding the side chains of a NIPAM pentamer in response to temperature changes (273-353 K range) near its experimental LCST (305 K). Results suggest a strong inverse correlation of temperature with water density and hydrophobic hydration character of the first coordination shell around the isopropyl groups. Integrity of the first and second coordination shells is further characterized by polygon ring analysis. Predominant occurrence of pentagons suggests clathrate-like behavior of both shells at lower temperatures. This predominance is eventually overtaken by 4-membered rings as temperature is increased beyond 303 and 293 K for the first and second coordination shells, respectively, losing their clathrate-like property. It is surmised that this temperature-dependent stability of the coordination shells is one of the important factors that controls the reversible swell-collapse mechanism of PNIPAM hydrogels.

 

6. Elatico, A.J.J. and Nellas, R.B.(2020). Computational reverse engineering of the lipase from Pseudomonas aeruginosa PAO1: α-helices. Journal of Molecular Graphics and Modelling, 100: 107657. more

Abstract:

Lipases are important enzymes in many biochemical industries, thus making them attractive targets for protein engineering to improve enzymatic properties. In this work, a ‘‘reverse engineering’’ approach was explored: disrupt secondary structures to determine their contribution to enzyme stability and activity. All the α-helices of the lipase from Pseudomonas aeruginosa PAO1 (PAL) were systematically disrupted using computational proline mutagenesis and molecular dynamics (MD) simulations. This method identified the mutant (R89P), located within the vicinity of the active site, to be significantly important for stability and activity. In addition, the system (L159P), part of the ‘‘cap’’ domain that regulates substrate entry into the active site, was found to be critical for activity as it pushed the lipase to adopt a completely closed conformation. The perturbation introduced by the proline mutations resulted in increased backbone flexibility that significantly decreased protein stability. Moreover, mutations within the cap domain helices — (A115P), (S132P, G139P), (L159P), and (R169P) — resulted in increased flexibility of the N-terminal region of the helix, the mobile ‘‘lid’’ helix, that pushes the gorge into a partially closed conformation. The mutation (L159P) further increased the flexibility of the helix–loop region at the C-terminal end of the helix to push the lid into the fully closed state. Therefore, the and helices could be ‘‘hot spots’’ for stabilizing mutations that could improve the overall enzyme stability and activity this lipase. The insights obtained in this work may be validated experimentally in future works.  

 

7. Espiritu, R, Tan, JL, Lim, LH, Arco, S. (2020). Density functional theory study on the degradation of fuel cell anion exchange membranes via removal of vinylbenzyl quaternary ammonium head groupJournal of Physical Organic Chemistry. e4049. more

Abstract:

The alkaline stability of different tethered amine functional groups of fuel cell anion exchange membranes (AEMs), namely, trimethyl amine (TMA), 1‐azabicyclo[2.2.2]octane (ABCO), 1,4‐diazabicyclo[2.2.2]octane (DABCO), and N‐methylpiperidine (NMP), is investigated using density functional theory (DFT). Among the amine functional groups investigated, ABCO emerged as the most stable exhibiting the highest energy of barrier (EOB) of 33.5 kcal/mol, while DABCO has the lowest EOB of 30.0 kcal/mol due to the presence of an additional electron‐withdrawing nitrogen. The calculated lowest unoccupied molecular orbital (LUMO) energy revealed the trend of increasing alkaline stability against nucleophilic attack, consistent with their measured barrier energies: DABCO < TMA < NMP < ABCO. Most importantly, the DFT calculations confirmed the proposed multistep AEM degradation mechanism via the detachment of the whole vinylbenzyl quaternary ammonium group through the following steps: (1) nucleophilic attack leading to the loss of aromaticity with subsequent transformation to a quinodimethane moiety, (2) detachment of the quinodimethane‐like intermediate from the polymer backbone by the attack of superoxide and/or peroxy radicals via oxidative cleavage, and (3) the rearomatisation of the reaction intermediate.

 

8. Garcia, J.L., Yu, E., and Tapang, G. (2020). Triplet-based-correlation pattern matching for de novo sequencing of conopeptides. Proceedings of the Samahang Pisika ng Pilipinas 38, SPP-2020-1C-06.more

Abstract:

Conopeptides are small peptides produced by predatory marine snails belonging to the conoidean family. The development of tools for conopeptide sequencing is necessary due to increasing interest in conopeptides as potential therapeutic drugs. Peptides are sequenced by performing tandem mass spectrometry (MS) followed by transcriptome-guided analysis of the resulting mass spectra. To maximize the utility of MS in conopeptide sequencing, de novo sequencing tools which do not rely on transcriptome data are needed. In this study, a triplet-based-correlation algorithm for de novo sequencing is tested on a theoretical MS/MS spectrum with sequence GWVYHAHPEANSFWT. Due to the algorithm's naïve approach, it can be applied to any peptide MS/MS spectrum.

 

9. Gregorio, C.G.C., Yu, K.L.B., Singson, F.V.T., Alas, C.A.R., and Balbuena, J.W. (2020). Towards the Establishment of Baseline Scientific Information Based on the Volatile Organic Compounds (VOCs) of Philippine Traditional Alcoholic Beverages.  Philippine Journal of Science 149 (3-a), Pages 869-885.more

Abstract:

Investigations on four Philippine traditional alcoholic beverages – namely, lambanog, tapuy, basi, and tuba – were carried out by determining volatile organic compounds (VOCs) in these beverages. Headspace gas chromatography with flame ionization detection (HS-GC-FID) is employed in this study to quantify four compounds – namely, ethanol, ethyl acetate, isoamyl alcohol, and isobutyl alcohol. Mean concentration values for the these VOCs within each beverage type were found to be as follows: 35.69% (v/v) ethanol, 329.67 mg/L ethyl acetate, 145.03 mg/L isoamyl alcohol, and 51.86 mg/L isobutyl alcohol for lambanog; 10.86% (v/v) ethanol, 212.87 mg/L ethyl acetate, 175.82 mg/L isoamyl alcohol, and 37.98 mg/L isobutyl alcohol for tapuy; 11.06% (v/v) ethanol, 114.18 mg/L ethyl acetate, 247.45 mg/L isoamyl alcohol, and 66.54 mg/L isobutyl alcohol for basi; and 8.79% (v/v) ethanol, 351.77 mg/L ethyl acetate, 68.74 mg/Lisoamyl alcohol, and 16.23 mg/L isobutyl alcohol for tuba. Results showed that there is wide variability in the VOCs quantified in the four beverages, possibly on account of the sampling site, raw material used, and manufacturing process. Preliminary gas chromatography – mass spectrometry (GC-MS) studies qualitatively confirm the presence of other families of VOCs. The results from this study are envisioned to serve as new baseline information on Philippine traditional beverages.

 

10. Hipol, R.M., Hipol, R.B., Fabian, M.C.P., Sasotona, J.S. and Hernandez, C.C. (2020). HMG-CoA Reductase Inhibitory Activity of Leaf-associated Fungi. Acta Medica Philippina, 54 (5), Pages 498-502.more

Abstract:

Cholesterol   is   an   important   biomolecule   for   cells.   However,   because   of   certain   lifestyle,   the   amount  of  cholesterol  can  increase  beyond  what  our  bodies  can  consume.  Increased  intake  may  result  in  the  accumulation  of  cholesterol  in  the  blood  leading  to  atherosclerosis  that  can  lead  to  congestive  heart  failure. With the use of statins, cholesterol levels are reduced therefore lowering the risk for this disease. It does so by inhibiting the hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase, the first committed enzyme in cholesterol biosynthesis.  In  light  of  the  increasing  cases  of  hypercholesterolemia,  there  is  a  need  to  discover  novel  classes  of HMG-CoA inhibitors.

 

11. Itang, C.E.M.M., Gaza, J.T., Masacupan, D.J.M., Batoctoy, D.C.R., Chen, Y.-J., Nellas, R.B., Yu, E.T. (2020) Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations. Marine Drugs, 18 (10), Page 503.more

Abstract:

Marine cone snails belonging to the Conidae family make use of neuroactive peptides in their venom to capture prey. Here we report the proteome profile of the venom duct of Conus eburneus, a cone snail belonging to the Tesseliconus clade. Through tandem mass spectrometry and database searching against the C. eburneus transcriptome and the ConoServer database, we identified 24 unique conopeptide sequences in the venom duct. The majority of these peptides belong to the T and M gene superfamilies and are disulfide-bonded, with cysteine frameworks V, XIV, VI/VII, and III being the most abundant. All seven of the Cys-free peptides are conomarphin variants belonging to the M superfamily that eluted out as dominant peaks in the chromatogram. These conomarphins vary not only in amino acid residues in select positions along the backbone but also have one or more post-translational modifications (PTMs) such as proline hydroxylation, C-term amidation, and γ-carboxylation of glutamic acid. Using molecular dynamics simulations, the conomarphin variants were predicted to predominantly have hairpin-like or elongated structures in acidic pH. These two structures were found to have significant differences in electrostatic properties and the inclusion of PTMs seems to complement this disparity. The presence of polar PTMs (hydroxyproline and γ-carboxyglutamic acid) also appear to stabilize hydrogen bond networks in these conformations. Furthermore, these predicted structures are pH sensitive, becoming more spherical and compact at higher pH. The subtle conformational variations observed here might play an important role in the selection and binding of the peptides to their molecular targets.

12. Ocampo, A.B., Braza, M.K.E. and Nellas, R.B. (2020). The interaction and mechanism of monoterpenes with tyramine receptor (SoTyrR) of rice weevil (Sitophilus oryzae). SN Applied Sciences, 2: 1592.more

Abstract:

Rice weevils (Sitophilus oryzae) are pests that feed on grain products. One strategy employed in the safe pest management is the use of essential oils from plant materials as biopesticide. Monoterpene compounds, present in essential oils, are generally less acutely toxic than other conventional insecticides and are known to possess biopesticide activity against octopaminergic receptors (OAR). Tyramine receptor (TyrR) is a desired biopesticide target due to its absence in vertebrates and its role in insect’s physiological and cellular response. In this study, the biochemical basis of monoterpenes and SoTyrR interactions were determined using in silico methods: ensemble docking, 3DQSAR analysis, and toxicity prediction. Ensemble docking results showed that the lead compounds has binding affinity of − 4.2 to − 6.8 kcal/mol. Four monoterpene compounds: terpinolene, carvacrol, carene, and pulegone were considered top hits based on their favorable binding affinity. Furthermore, hydrophobic interactions of monoterpenes with residues Asp114, Val404, Lys189, Leu190, Tyr196, Phe397, and Tyr401 stabilized the observed docking poses. Upon consolidation of docking and 3DQSAR results, we functionalized top hit ligands and showed significant increase in the average binding affinity of candidate compounds, ranging from − 4.7 to − 8.3 kcal/mol. A carene derivative exhibited the highest binding energy of − 8.3 kcal/mol with a calculated Ki of 0.547 μM which surpassed the known activators of OAR. The top hit modified ligands were also clear of toxicity risks as predicted by Osiris Property Explorer. This work could provide insights in the development of effective biopesticides for rice weevils that is less toxic than conventional pesticides.

13. Panghulan, G.R., Vasquez, M.R Jr.,  Edañol, Y.D., Chanlek, N., and Payawan, L.M. Jr. (2020). Synthesis of TiN/N-doped TiO2 composite films as visible light active photocatalystJournal of Vacuum Science & Technology B, 38 (6): 062203.more

Abstract:

Titanium nitride/nitrogen-doped titanium oxide (TiN/N-doped TiO2) composite films were synthesized for visible light photodegradation applications. Thin films of TiN were sputter-deposited on precleaned glass substrates in an admixture of argon and nitrogen gases. The grown TiN films were subsequently oxidized in air at 350 ∘C at 15, 30, and 60 min. Raman spectral analysis revealed the formation of TiO2 with anatase structure at 15 min and transitioned to the rutile structure at longer oxidation times. X-ray photoelectron spectral analysis revealed the formation of N-doped TiO2 from the oxidized Ti. Visible light-induced photodegradation of methylene blue as test analyte showed 30% removal efficiency after exposure to visible light after 2.5 h. The highest degradation efficiency was observed when the anatase phase of TiO2 is the dominant phase in the film. Moreover, N-doping realized the visible light sensitivity of TiO2. This makes the composite film ideal for solar light-driven photodegradation of organic contaminants in wastewater.

 

14. Patricio, J. N., Perez, S. J. L. P., & Arco, S. D. (2020). Carboxylate-Functionalized Imidazolium-Based Binary Ionic Liquids as Electrolytes for Symmetric Carbon-Based Supercapacitors. Materials Science Forum, 998, Pages 233–238.more

Abstract:

Ionic liquids (ILs) containing 1-ethyl-3-methylimidazolium (EMIM) cations and carboxylate anions were prepared using solventless sonochemical synthesis followed by a facile halide-to-anion exchange method and were characterized for their structural and electrochemical properties. The structures of the synthesized ILs were found to significantly affect their electrochemical window (EW) and varied anions exhibited different reductive and oxidative limits. Ionic conductivity and cyclic voltammetry measurements revealed that [EMIM]hexanoate and [EMIM]2[oxalate] offered relatively high ionic conductivity values and wide EWs. A 1:1 binary IL mixture based on the synthesized ILs was prepared and its EW was found to significantly vary as compared with the EWs of the individual component ILs. Supercapacitor prototypes were then fabricated with edge-oxidized graphene sheets as conductive additives for the electrodes and electrospun nanofibers as separator membranes. An electric-double layer capacitive behaviour associated to the ion diffusion process of the electrolyte ions onto the porous electrode surface was shown and quasi-rectangular curves were observed having no redox peaks at any point in the generated repetitive voltammograms. These considerable results have shown valuable insights for further development of binary IL electrolytes for energy storage devices. 

 

15. Pelagio, M.C., Navarro, D.A., Janik, L.J. and Lamorena, R.B. (2020). Potential application of laser‐Induced breakdown spectroscopy (LIBS) data for the determination of cation exchange capacity (CEC) of agricultural soils. Chemistry Select, 5 (13), Pages 3798-3804. more

Abstract:

The potential for Laser Induced Breakdown Spectroscopy (LIBS) technique to predict cation exchange capacity (CEC) values in agricultural soils, based on a partial least square (PLS) regression model, was investigated by analysing soils (N= 225) using a portable LIBS system. The prediction from the validation set was 0.75 and the RMSE was 5.4 cmol+/kg. Analysis of the PLS loading weights showed that emission lines that correlate with the exchangeable cations (Ca, Mg, K and Na) and clay (Al and Si) are significant. Good quality predictions could be obtained from the model as described by the ratio of performance to deviation (RPD) values calculated for calibration (RPDc =1.99) and validation (RPDv=2.02). The ratio of performance to interquartile distance (RPIQ) for calibration (RPIQc=3.20) and validation (RPIQv=3.32) indicated excellent prediction capability. It has been demonstrated that LIBS spectra coupled with multivariate data analysis could be used to predict CEC of agricultural soils which is considered fast and a chemical‐free technique. 

 

16. Perez, S.J.LP., Atayde, E.C. and Arco, S.D. (2020). Synthesis and biological evaluation of some novel 1‐alkyl‐3‐methylimidazolium carboxylate ionic liquids as potential antifungal agentsJournal of the Chinese Chemical Society. https://doi.org/10.1002/jccs.201900366 more

Abstract:

In an effort to discover lead compounds that may be of importance as potent antifungal agents, a series of novel 1‐alkyl‐3‐methylimidazolium carboxylate ionic liquids were efficiently synthesized through a solvent‐free ultrasound‐assisted quaternization reaction of 1‐methylimidazole and alkyl bromides RBr (R = hexyl, octyl) followed by an anion exchange process with selected carboxylate anions (cinnamate, salicylate, crotonate, and oxalate). Quantitative yields obtained were in the range of 86–94%. Structure characterization was done using FT‐IR, 1H‐NMR, and 13C‐NMR spectroscopic techniques. All the synthesized compounds showed in vitro antifungal activity against the fungus Candida albicans with the minimum inhibitory concentrations found to be less than or equal to 1%. Preliminary cytotoxicity assays (trypan blue exclusion and MTT) were performed on all ionic liquids and findings revealed higher lymphocyte viability in 1‐hexyl‐3‐methylimidazolium carboxylate ionic liquids than in 1‐octyl‐3‐methylimidazolium counterparts. No extensive toxicity effect was observed with the carboxylate anion variation. Among the tested compounds, 1‐hexyl‐3‐methylimidazolium crotonate and 1‐hexyl‐3‐methylimidazolium oxalate exhibited the lowest cytotoxicity in the trypan blue exclusion and MTT assays, respectively. Together, our results highlight the potential of carboxylate‐based ionic liquids in the development of next‐generation antifungal drugs.

 

17. Perez, S.J.L.P. and Claudio, G.C. (2020). Molecular dynamics simulations of two double-helical hexamer fragments of iota-carrageenan in aqueous solution. Journal of Molecular Graphics and Modelling,  98: 107588.more

Abstract:

The gelation of anionic carrageenans is known to occur through a coil-to-helix transition followed by further aggregation or association on which positive counterions play a significant role. In the present work, molecular dynamics (MD) simulations were performed on two double-helical iota-carrageenan hexamer fragments along with their sodium counterions using the Carbohydrate Solution Force Field (CSFF) in an aqueous (TIP4P) solution with the GROMACS molecular dynamics package. Results showed a counterion condensation between the two double helices and that the subsequent forces of interaction between them were predominantly attractive. By varying the distance separating the two double helices, the effect of distance on the counterion distribution and the forces of attraction was also investigated. In the presence of counterions, an increase in the forces of attraction was observed as the distance between the two double helices decreases which can be attributed to the greater counterion density between the two like-charged oligosaccharides.  

  

18. Regulacio, M.D., Yang, D.-P. and Ye, E. (2020). Toward greener methods of producing branched metal nanostructuresCrystEngComm, 22 (3), Pages 399-411. more

Abstract:

The continuous drive to develop green and sustainable production methods has prompted scientists into exploring the use of biogenic resources (e.g. plant extracts, microorganisms, and biomolecules) as environmentally benign reagents for the synthesis of functional metal nanomaterials. An emerging class of metal nanomaterials is branched metal nanostructures, which display tremendous potential in diverse technological areas, including biomedicine, catalysis, and sensing. In the biogenic synthesis of branched metal nanostructures, biological systems often take on multiple roles as reducing, capping, and shape-directing agents. Furthermore, the reaction typically proceeds at relatively lower temperatures, sometimes even at room temperature, and water is conveniently used as a solvent. This greatly simplifies the synthetic procedure, aside from lowering the production cost and rendering the process greener. Herein, we review different biogenic methods of preparing metal nanostructures having distinctively branched architectures (e.g. flowers, stars, and dendrites). We highlight reports that provide critical insights that are pertinent to the elucidation of the formation mechanisms. However, a more rigorous understanding is still necessary to establish exact mechanisms, and so, further research on this matter is encouraged. Advancing our mechanistic understanding will help us improve existing bioinspired methodologies to create high-quality branched metal nanostructures with optimal performance for envisioned applications.

 

19. Sacdal, R., Madriaga, M., and Espino, M.P. (2020). Overview of the analysis, occurrence and ecological effects of hormones in lake waters in AsiaEnvironmental Research, 182, (109091). more

Abstract:

Hormones are natural and synthetic compounds that are now being detected in the aquatic environment. Many lakes in Asia are important water sources that may be affected by these emerging contaminants. Lakes are drains and reservoirs of watersheds that are altered by changing land use and environmental conditions. While there are several studies on the detection of hormones in lakes, these studies were mostly done in China. Limited information is available on the presence of these contaminants in the lakes in other Asian countries. Hormones in the lake water come from discharge waters in urban areas, farm runoffs, and effluents of wastewater and sewage treatment plants. Hormones contamination in water has been shown to affect the reproduction and growth of certain aquatic organisms. In this review, a background on the chemical nature and physiological functions of hormones is provided and the existing knowledge on the occurrence and ecological impacts of hormones in lakes is described. The available analytical methods for sampling, analyte extraction and instrumental analysis are outlined. This overview provides insights on the current conditions of lakes that may be impacted by hormones contamination. Understanding the levels and possible ecological consequences will address the issues on these emerging contaminants especially in the Asian environment. This will elicit discussions on improving guidelines on wastewater discharges and will drive future research directions.

 

20. Sta. Ana, K.M. and  Espino, M.P. (2020). Occurrence and distribution of hormones and bisphenol A in Laguna Lake, Philippines. Chemosphere 256, 127122 more

Abstract: 

The occurrence of hormones and hormone-like compounds in water has been regarded as an emerging environmental concern. These water contaminants are known to cause endocrine disruption that may affect aquatic organisms. In this study, hormones and phenolic xenoestrogens were investigated and measured in the surface waters of Laguna Lake, Philippines. Laguna Lake is the largest lake in the country that has many uses including fish cultivation and source for potable water production. The hormones estrone, 17-beta-estradiol, 17-alpha-ethynylestradiol, progesterone and testosterone as well as the plasticizer bisphenol A in the lake water were determined by solid phase extraction and LC-MS/MS. The extraction method exhibited good recoveries (75–90% in spiked lake water) while the instrumental method of analysis has low detection limits (0.01–0.24 μg/L) and good linear response (>99% in the 0–50 μg/L concentration range). In the nine sampling sites across the lake, estrone was found in concentrations between 0.03 and 0.30 ng/L. 17-Beta-estradiol, testosterone and progesterone were detected in some of the sites in concentrations up to 0.36, 0.22, and 2.05 ng/L, respectively. Bisphenol A was detected in all sites in higher concentrations of 0.71–47.40 ng/L. Although there are no local guidelines yet, the determination and monitoring of these emerging water contaminants are important because of their potential environmental impacts. Further to this initial study, investigations on point sources spanning the tributary rivers, long-term determination of locational and temporal variations, and assessment of ecotoxicological risks are needed. These are crucial in the regulation and mitigation of discharges into the lake.

 

21. Tiongson, J.K. A., Aganda , K. C. C., Bruzon, D. A. V., Guevara, A. P., Basilia, B. A., Tapang, G. A. and Martinez I. S. (2020). Exploring the corrosion inhibition capability of FAP-based ionic liquids on stainless steel. Royal Society Open Science, 7 (7) : 200580.more

Abstract:

Corrosion is clearly one of the more common causes of materials failure in stainless steel. To manage corrosion, chemical inhibitors are often used for prevention and control. Ionic liquids due to their hydrophobic and corrosion-resistant property are being explored as alternative protective coatings and anti-corrosion materials. In this particular study, ionic liquids containing functionalized imidazolium cations and tris(pentafluoroethyl)trifluorophosphate (FAP) anions were investigated for their ability to inhibit corrosion on stainless steel surfaces in acidic environment. Using surface characterization techniques, specifically scanning electron microscopy and energy-dispersive X-ray (EDX), the morphology and the elemental composition of the steel surfaces before and after corrosion were determined. Contact angle measurements were also performed to determine how these ionic liquids were able to wet the stainless steel surface. In addition, potentiodynamic studies were carried out to ensure that corrosion inhibition has occurred. Results show that these ionic liquids were able to inhibit corrosion on the stainless steel surfaces. This indicates promise in the use of these FAP-based ionic liquids for corrosion management in stainless steel.

 

22. Usman, K.A.S., Maina, J.W., Seyedin, S., Conato, M.T., Payawan, L.M. Jr., Dumee, L.F., and Razal, J.M. (2020). Downsizing metal–organic frameworks by bottom-up and top-down methods. NPG Asia Materials, 12:58.more

Abstract:

Downsizing metal–organic framework (MOF) crystals into the nanoregime offers a promising approach to further benefit from their inherent versatile pore structures and surface reactivity. In this article, downsizing is referred to as the deliberate production of typical large MOF crystals into their nanosized versions. Here, we discuss various strategies towards the formation of crystals below 100 nm and their impact on the nano-MOF crystal properties. Strategies include an adjustment of the synthesis parameters (e.g., time, temperature, and heating rate), surface modification, ligand modulation, control of solvation during crystal growth and physical grinding methods. These approaches, which are categorized into bottom-up and top-down methods, are also critically discussed and linked to the kinetics of MOF formation as well as to the homogeneity of their size distribution and crystallinity. This collection of downsizing routes allows one to tailor features of MOFs, such as the morphology, size distribution, and pore accessibility, for a particular application. This review provides an outlook on the enhanced performance of downsized MOFs along with their potential use for both existing and novel applications in a variety of disciplines, such as medical, energy, and agricultural research.

 

23. Usman, K.A.S, Edanol, Y.D.G., and Conato, M.T. (2020). In Memoriam – Dr. Leon M. Payawan Jr. KIMIKA 31 (2), Pages 62-67.more

Abstract:

On September 25, 2020, the Philippine chemistry society lost one of its most eminent members. Herein we reflect on the life and work of Dr. Leon M. Payawan Jr., referred to as Leon by his close friends and colleagues. We highlight some of his contributions that left a huge impact, not only to his students and cohorts, but also to the Philippine research community in general, both locally and internationally.

 

24. Yeh, C.J., Zulueta, M.M.L., Li, Y.K., Hung, S.C. (2020). Synthesis of hyaluronic acid oligosaccharides with a GlcNAc-GlcA repeating pattern and their binding affinity with CD44. Organic Biomolecular Chemistry,18 (28), Pages 5370-5387.more

Abstract:

Hyaluronic acid (HA) is a ubiquitous glycosaminoglycan in the extracellular matrix and a ligand of CD44, a transmembrane glycoprotein that is important in cell migration. Crystal and NMR studies found a hexasaccharide of the pattern (GlcA–GlcNAc)3 as the shortest HA that could bind to CD44, but molecular dynamics simulations indicated that a tetrasaccharide of the pattern (GlcNAc–GlcA)2 is the key structure interacting with CD44. Access to oligomers with such a repeat pattern is crucial in binding studies with CD44. Here we developed a synthetic procedure to afford the HA oligosaccharides with the GlcNAc–GlcA repeating unit and measured the binding interaction between these sugars and human CD44 by isothermal titration calorimetry (ITC). During the chemical synthesis, we successfully generated the β-glycosidic bond in the absence of neighbouring group participation and overcome the issues in the oxidation step. In addition, ammonia-free dissolving metal reduction for debenzylation and azido reduction has been applied in carbohydrate synthesis for the first time. ITC analysis revealed that the HA tetrasaccharide (GlcNAc–GlcA)2 could indeed interact and bind to the human CD44.

 

 

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1. Bagtasa, G. (2020). 118-year climate and extreme weather events of Metropolitan Manila in the PhilippinesInternational Journal of Climatology, 40 (2), Pages 1228-1240. more

Abstract:

Metropolitan Manila, the Philippines, is a megacity with a population of 12.9 million people. Unabated urbanization and disorganized infrastructure build‐up, coupled with a large urban poor population have made many of its population vulnerable to climate change. This study presents the 118‐year urban climate and extreme weather events of Metropolitan Manila. Daily average and minimum temperature are on the rise comparable to countrywide trends. Consequently, there are more warm and less cold nights. Total annual precipitation is also increasing at a rate of 77.99 mm/decade. Decreasing simple daily intensity index implies that higher observed precipitation is due to the increase in wet days count rather than intensity. Tropical cyclones (TCs) are critical in producing most extreme rainfall events in the metropolis. Extreme precipitation is induced either by a TC's immediate rainbands or remote precipitation effects by enhancing the prevailing summer monsoon flow. TC‐induced rain modulates annual rainfall variability and is estimated to contribute 45.2% to Metropolitan Manila mean total rainfall.

 

2. Castro, E., Ishida, T., Takahashi, Y., Kubota, H., Perez, G.J., Marciano, J.S., Jr. (2020). Determination of Cloud-top Height through Three-dimensional Cloud Reconstruction using DIWATA-1 Data. Scientific Reports, (10) 1, Article number 7570. more

Abstract:

Cloud-top height is a useful parameter with which to elucidate cloud vertical growth, which often indicates severe weather such as torrential rainfall and thunderstorms; it is widely used in meteorological research. However, general cloud-top height estimation methods are hindered by observational and analytical constraints. This study used data from DIWATA-1, the Philippines’ first microsatellite, to overcome these limitations and successfully produce sophisticated three-dimensional cloud models via stereo-photogrammetry. High-temporal snapshot 200-ms-interval imaging of clouds over Iloilo, Philippines, is performed. Two types of telescopes were used to capture 30 stereoscopic cloud images at ~60- and ~3-m ground sampling resolutions; these were used to construct three-dimensional cloud models with 40- and 2-m vertical resolutions, respectively. The imaged clouds have heights of 2.0 to 4.8 km, which is below freezing level for the Philippines and typical of stratocumulus and cumulus clouds. The results are validated using cloud-edge heights determined by measuring the distance from the clouds to their ground shadows. An RMSE of 0.32 km and a maximum difference of 0.03 km are found for the low- and high-resolution telescopes, respectively. For further validation, the results are compared with cloud-top heights estimated from HIMAWARI-8 images captured on the same day, yielding an average vertical difference of 0.15 km and a maximum difference of 1.7 km.

3. Manuel, A., C. Blanco, A.C., Tamondong, M.,  Jalbuena, R., Cabrera, O., Gege, P. (2020). Optimization of Bio-Optical model parameters for turbid lake water quality estimation using LANDSAT8 and WASI-2DInternational Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences - ISPRS Archives, 42 (3/W11), Pages 67-72. more

Abstract:

Laguna Lake, the Philippines’ largest freshwater lake, has always been historically, economically, and ecologically significant to the people living near it. However, as it lies at the center of urban development in Metro Manila, it suffers from water quality degradation. Water quality sampling by current field methods is not enough to assess the spatial and temporal variations of water quality in the lake. Regular water quality monitoring is advised, and remote sensing addresses the need for a synchronized and frequent observation and provides an efficient way to obtain bio-optical water quality parameters. Optimization of bio-optical models is done as local parameters change regionally and seasonally, thus requiring calibration. Field spectral measurements and in-situ water quality data taken during simultaneous satellite overpass were used to calibrate the bio-optical modelling tool WASI-2D to get estimates of chlorophyll-a concentration from the corresponding Landsat-8 images. The initial output values for chlorophyll-a concentration, which ranges from 10–40 μg/L, has an RMSE of up to 10 μg/L when compared with in situ data. Further refinements in the initial and constant parameters of the model resulted in an improved chlorophyll-a concentration retrieval from the Landsat-8 images. The outputs provided a chlorophyll-a concentration range from 5–12 μg/L, well within the usual range of measured values in the lake, with an RMSE of 2.28 μg/L compared to in situ data. 

 

4. Palermo, J.D.H.,  Labrador, K.L.,  Follante, J.D.,  Agmata, A.B.,  Pante, M.J.R.,  Rollon, R.N.,  David, L.T. (2020). Susceptibility of Sardinella lemuru to emerging marine microplastic pollution. Global Journal of Environmental Science and Management, 6 (3), Article number 07, Pages 373-384. more

Abstract:

Marine microplastics are emerging pollutants that impact across levels of marine food chain at a global scale. Its presence was determined on Sardinella lemuru, a commercial pelagic fish that are harvested generally in the Northern Mindanao, consumed locally, and exported worldwide as bottled or canned sardine products. The stomach contents of 600 sardines were examined visually under a microscope, stained with Rose Bengal, and tested with hot needle technique to identify ingested microplastics. These anthropogenic particles were measured and physically classified into fibers, fragments, and films. Results of this study showed that 85% of S. lemuru were already contaminated with 3.74 ± 3.92 # of microplastics even before being processed into various sardine products. These microplastics ranged from 0.12 to 21.30 mm and 80 % were mostly < 2.5 mm size classes. The dominant microplastics were 97.94 % in the form of fibers while 1.52 % and 0.54 % were respectively classified into fragments and films. Method validation by isolating microplastics from spiked samples (n = 30) with three retrieval attempts showed 100% recovery efficiency. While results from Canonical Correspondence Analysis of ingested microplastic data had no relationship with the standard lengths of the sardine and the masses of ingested food materials at varying size classes, the total number of ingested microplastics from 2014 to 2016 were directly correlated (r2=0.91, p=0.003) with the human population at the landing sites along the coastline of northern Mindanao.

 

5. Perez, G.J., Felix, M.J., Namuco, S., Felicio, F., Merida, H., Vergel, K.K., Castro, E., Marciano, J.J.S., Jr. (2020). Environmental monitoring using Philippines' DIWata-2: A case study in Laguna de Bay40th Asian Conference on Remote Sensing, ACRS 2019, 40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea, Code 157736.

Abstract:

The Philippines extensive coastline, fertile land and high species diversity makes the country abundant in natural resources. Protection of the environment and sustainable use of resources is of paramount importance, especially with the continuous increase in population and exposure of the country to natural hazards. This has been one of the primary motivations for the development of the Philippines' microsatellites, Diwata-1 and Diwata-2, with missions focusing on environmental monitoring and disaster assessment. This paper highlights the improvements made in the second satellite mission which makes it more effective for spatiotemporal change analysis. Launched in 29 October 2018, Diwata-2 is deployed at 621 km sun-synchronous orbit with 8°inclination, allowing 11-day revisit period and 3 to 5 years expected mission lifetime. This, together with wider image swaths and improved signal-to-noise ratio of its imaging cameras, make Diwata-2 capable for more in-depth studies of water quality in high-value coastal and inland waters. This is demonstrated through the retrievals of turbidity in Laguna de Bay, which at ~900 km2 area, is considered as the largest lake in the country. Using Diwata-2 Spaceborne Multispectral Imager (SMI) with Liquid Crystal Tunable Filter (LCTF), series of images of the lake were captured within the period of March to June 2019. The highest turbidity values were observed in April, which coincides with the peak months of dry season. The turbidity of the lake then gradually drops at the end of the dry season. Large spatial variability is also observed across the lake's major bays. This detailed information is valuable to fish pen and cage operators, lake managers, local and national government, and other stakeholders in ensuring the sustainable use of the lake. Through the improved capabilities of Diwata-2, images can be captured and analyzed to track the spatiotemporal changes of different geophysical variables that are relevant for the management of the country's natural resources and environment.

 

6. Veloria, A., Perez, G.J., Tapang, G., Comiso, J. (2020). Comparison between GPM and gridded precipitation product from interpolated rain gauge measurements40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea, Code 157736.

Abstract:

Due to sparsely distributed synoptic stations in the Philippines, representation of precipitation is inadequate. Satellite-derived products, such as the Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Measurement (GPM), are available to complement synoptic data for more precise and robust measurements. However, these products tend to over- or underestimate rainfall depending on the season. Precipitation measurements from a dense network of rain gauges in the Philippines are available courtesy of the Department of Science and Technology - Advance Science and Technology Institute (DOST-ASTI). This study aims to create a gridded precipitation data over the Philippines from interpolated rain gauge measurements and validate its performance through comparison with GPM. Comparison of rain gauge data with overlapping synoptic measurements in a 0.25° grid showed distance-dependent likelihood. Thus, inverse distance weighting (IDW) was performed to combine multiple rain gauge measurements representative of precipitation over 0.1° grid. Strong positive correlations (r = 0.58 to 0.97) were obtained from comparing IDW values and monthly synoptic measurements suggesting that rain gauge measurements may be used as complimentary ground data. IDW values were then subjected to kriging and iterative method to create a monthly gridded precipitation. Results showed that the interpolated precipitation follows the wet and dry season as well as monsoon seasonality in the Philippines. The calculated differences between the interpolated precipitation and GPM monthly product revealed that the interpolated precipitation have lower estimates with respect to GPM regardless of season. This is in contrast with the strong positive relationship between monthly synoptic measurements and GPM (r = 0.856). Low estimates from the interpolated precipitation is due to isolated zero measurements from various rain gauges. This may be attributed to maintenance issues of the sensors where the data do not report broken and erroneous instruments. Further filtering of the dataset and regular maintenance of the sensors must be done to better incorporate the use of dense rain gauge network for the creation of a Philippine gridded precipitation.

 

7. Valete, M.A.P., Perez, G.J.P., Enricuso, O.B., Comiso, J.C. (2020). Spatiotemporal evaluation of historical drought in the Philippines40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea, Code 157736.

Abstract:

Negative impacts of drought on agriculture and water resources vary according to different timescales and intensity. In this paper, the historical droughts in the Philippines were examined using the Standardized Precipitation Index (SPI) at different timescales (SPI-1, SPI-3, and SPI-12). SPI is derived from the monthly rainfall data of Tropical Rainfall Measuring Mission (TRMM) 3B43 v7 from 1998 to 2018. A total of 384 TRMM grids in the Philippines were used in the time series analysis to investigate the spatiotemporal dynamics of drought. Results showed that the Philippines was frequently hit by different types of drought. It also showed that the spatial distribution of the past drought events varied through timescales. Particularly, more variation was observed in the entire land area using the shorter SPI timescales, i.e. SPI-1 and SPI-3. With longer timescales, values tend to be more similar and closer to each other resulting in smoother trends. The affected areas in terms of percentage were also examined. Each drought event's severity, duration, and intensity for the areal average of the Philippines was also investigated. These results demonstrate the viability of satellite-derived SPI for drought evaluation at a national level, which is important in the decision-making for drought mitigation in the Philippines.

 

IM

1. Afable, E. A., de la Cruz, R. J., Paras, A. T., & Segui, M. E. (2020). Diagonalizability with respect to perplectic and pseudo-unitary similarity transformations. Linear Algebra and its Applications, 591, Pages 61-71. doi:10.1016/j.laa.2020.01.010 more

Abstract:

Let Rn be the n-by-n backward identity matrix and let Ln,k:=Ik−In−k. Suppose ACn×n is nonsingular. We say that A is perplectic if RnATRn=A−1; and A is pseudo-unitary if Ln,kALn,k=A−1. We give necessary and sufficient conditions for a matrix to be diagonalizable via a perplectic or a pseudo-unitary matrix.

 

2. Agapito, T. D., & Paras, A. T. (2020). ψS-orthogonal matrices and ψS-symmetries. Linear Algebra and its Applications, 584, Pages 185-196. doi:10.1016/j.laa.2019.09.017 more

Abstract:

Let GLn(C) denote the set of n-by-n nonsingular matrices with entries from the field C of complex numbers. For any SGLn(C), define the map ψS:GLn(C)→GLn(C) by ψS(A)=SA−1‾S−1. A matrix AGLn(C) is said to be ψS-orthogonal if ψS(A)=A−1. A ψS-orthogonal H is called a ψS-symmetry if rank(H−I)=1. We give conditions on S so that ψS-symmetries exist. Moreover, we determine conditions on S such that the ψS-symmetries generate the ψS-orthogonal matrices, and the minimum number of ψS-symmetries needed to express a ψS-orthogonal.

 

3. Alota, C. P., Pilar-Arceo, C. P. C., & de los Reyes V, A. A. (2020). An edge-based model of SEIR epidemics on static random networks. Bulletin of Mathematical Biology, 82 (7). doi:10.1007/s11538-020-00769-0

Abstract:

Studies have been done using networks to represent the spread of infectious diseases in populations. For diseases with exposed individuals corresponding to a latent period, an SEIR model is formulated using an edge-based approach described by a probability generating function. The basic reproduction number is computed using the next generation matrix method and the final size of the epidemic is derived analytically. The SEIR model in this study is used to investigate the stochasticity of the SEIR dynamics. The stochastic simulations are performed applying continuous-time Gillespie’s algorithm given Poisson and power law with exponential cut-off degree distributions. The resulting predictions of the SEIR model given the initial conditions match well with the stochastic simulations, validating the accuracy of the SEIR model. We varied the contribution of the disease parameters and the average degree of the network in order to investigate their effects on the spread of disease. We verified that the infection and the recovery rates show significant effects on the dynamics of the disease transmission. While the exposed rate delays the spread of the disease, increasing it towards infinity would lead to almost the same dynamics as that of an SIR case. A network with high average degree results to an early and higher peak of the epidemic compared to a network with low average degree. The results in this paper can be used as an alternative way of explaining the spread of disease and it provides implications on the control strategies applied to mitigate the disease transmission.

4. Arias, J. C. H., & Loquias, M. J. C. (2020). Similarity isometries of point packings. Acta Crystallographica.Section A, Foundations and Advances, 76, Pages 677-686. doi:10.1107/S2053273320011547 more

Abstract:

A linear isometry R of {\bb R}^{d} is called a similarity isometry of a lattice \Gamma\subseteq{\bb R}^{d} if there exists a positive real number β such that βRΓ is a sublattice of (finite index in) Γ. The set βRΓ is referred to as a similar sublattice of Γ. A (crystallographic) point packing generated by a lattice Γ is a union of Γ with finitely many shifted copies of Γ. In this study, the notion of similarity isometries is extended to point packings. A characterization for the similarity isometries of point packings is provided and the corresponding similar subpackings are identified. Planar examples are discussed, namely the 1 × 2 rectangular lattice and the hexagonal packing (or honeycomb lattice). Finally, similarity isometries of point packings about points different from the origin are considered by studying similarity isometries of shifted point packings. In particular, similarity isometries of a certain shifted hexagonal packing are computed and compared with those of the hexagonal packing.

 

5. Awa, D., & de la Cruz, R. J. (2020). Every real symplectic matrix is a product of real symplectic involutions. Linear Algebra and its Applications, 589, Pages 85-95. doi:10.1016/j.laa.2019.12.003 more

Abstract:

A 2n-by-2n matrix A is symplectic if AT[0I−I0]A=[0I−I0]. It is known that if n>1, then every 2n-by-2n complex symplectic matrix is a product of four symplectic involutions. We consider the real case. We give an example of a real symplectic matrix which is a product of two complex symplectic involutions but is not a product of two real symplectic involutions. We show that every 4-by-4 real symplectic matrix is a product of four real symplectic involutions. We use this result to show that for n>1, every 2n-by-2n real symplectic matrix is a product of a finite number of real symplectic involutions. 

 

6. Balmaceda, J. M. P., & Datu, J. P. P. (2020). Idempotents in certain matrix rings over polynomial rings. International Electronic Journal of Algebra, 27, Pages 1-12. doi:10.24330/ieja.662942 more

Abstract:

We determine the forms of the nontrivial idempotents in the ring of 2 × 2 matrices over the polynomial rings Zpq[x] and Zp2[x], where p and q are any primes. Any such idempotent in the stated rings will be of a form in our list. Our work generalizes the results of Kanwar, Khatkar and Sharma (2017) who identified the forms of idempotents in M2(Z2p [x]) and M2(Z3p [x]).

 

7. Balmaceda, J.M.P. (2020).  Building bridges through mathematics.  AIP Conference Proceedings 2268,030001more

Abstract:

In this rapidly changing world, mathematicians are increasingly being relied upon to provide insightful analysis, theory and tools to address current and emerging problems. These problems include highly complex issues such as vulnerability to natural disasters, economic uncertainties, and environmental and health hazards. These are among the many pressing challenges to our region that require multi- and trans-disciplinary approaches. In addition, the advent of the Fourth Industrial Revolution, marked by data-driven technology and economy, and the pervasiveness of social media, are changing the landscape of academia. As we develop our research capabilities and improve instruction at all levels, a deeper engagement with different sectors and stakeholders becomes imperative. We need to strengthen connections with individuals and institutions, both within and beyond our discipline and respective communities. By building these bridges, we widen our influence, expand our horizons, increase our relevance, and collectively, achieve more. In this paper, I will reflect on these connections including the role of national mathematical societies and international organizations such as the Southeast Asian Mathematical Society and the International Mathematical Union.

 

8. Caalim, J. V., Futorny, V., Sergeichuk, V. V., & Tanaka, Y. (2020). Isometric and selfadjoint operators on a vector space with nondegenerate diagonalizable form. Linear Algebra and its Applications, 587, Pages 92-110. doi:10.1016/j.laa.2019.11.004 more

Abstract:

Let V be a vector space over a field F with scalar product given by a nondegenerate sesquilinear form whose matrix is diagonal in some basis. If F=C, then we give canonical matrices of isometric and selfadjoint operators on V using known classifications of isometric and selfadjoint operators on a complex vector space with nondegenerate Hermitian form. If F is a field of characteristic different from 2, then we give canonical matrices of isometric, selfadjoint, and skewadjoint operators on V up to classification of symmetric and Hermitian forms over finite extensions of F.

 

9. Caalim, Jonathan & de la Cruz, R.J. (2020). 2n2n-by-2n2n symplectic completions of matrices of order 2n−1.  Asian-European Journal of Mathematics.  DOI: https://doi.org/10.1142/S1793557121500650more

Abstract:

Let F𝔽 be a field. Set J:=[0InIn0]J:=0In−In0. A matrix XF2n×2nX∈𝔽2n×2n is symplectic if XJ1XTJ=IXJ−1XTJ=I. We say that a matrix PF2n1×2n1P∈𝔽2n−1×2n−1 has a symplectic completion of order 2n2n if there exist x,yF2n1×1x,y∈𝔽2n−1×1 and a scalar αFα∈𝔽 such that [PyTxα]PxyTα is symplectic. If PP is nonsingular, we give necessary and sufficient conditions such that PP has a symplectic completion of order 2n2n. We give an implicit characterization of all matrices of order 3 which have symplectic completions of order 4.

 

10. Cajayon, Raquel C., Lucilo, Jayson A., Pilar-Arceo, Carlene PC., & Mendoza, Eduardo R. (2020). Comparison of Two Nature-Inspired Algorithms for Parameter Estimation of S-system Models.  Philippine Journal of Science, 149 (1), Pages 63-78. more

Abstract:

Parameter estimation for models of biochemical systems is computationally expensive due to the nonlinearity and high dimensionality of the coupled systems of ordinary differential equations underlying the models. Hence, it is important to apply novel methods to the problem and evaluate their performance. We consider the Bat algorithm (BA) and the Firefly algorithm (FA) with respect to parameter estimation of S-system models. Using three S-systems of increasing complexity from the MADMan benchmarking framework, we assess and compare the relative performance of the two algorithms relative to various data sets, initial conditions, and noise levels. Simulation results show that both algorithms can be effectively used in estimating parameters of the S-system models. In particular, in all three S-systems used, the FA performed better than the BA based on the final cost function values and relative estimate errors. The introduction of noise to data significantly affected the convergence of both algorithms.

 

11. de la Cruz, R. J., & Paras, A. T. (2020). The sums of symplectic, hamiltonian, and skew-hamiltonian matrices. Linear Algebra and its Applications, 603, Pages 84-90. doi:10.1016/j.laa.2020.05.036

Abstract:

A complex 2n×2n matrix A is called skew-Hamiltonian, Hamiltonian, and symplectic if AJ=A, AJ=−A, and AJ=A−1, respectively, in which J=[0In−In0] and AJ=J−1ATJ. We prove that each 2n×2n matrix is a sum of type “symplectic + Hamiltonian”. A 2n×2n matrix A is a sum of type “symplectic + symplectic” if and only if AAJ is similar to AJA. A 2n×2n matrix A is a sum of type “symplectic + skew-Hamiltonian” if and only if the Jordan blocks of A−AJ with eigenvalue 2i and size k≥ 2 come in pairs of the form Jk(2i)Jk(2i) and Jk(2i)Jk+1(2i).

12. de la Cruz, R.J. & Reyes, Edgar (2020). On the Iwasawa decomposition of a perplectic matrix. Journal of Communications in Algebra.more

Abstract:

Let M be the backward identity matrix. A complex matrix G is perplectic if G is an isometry of the symmetric scalar product (x,y)→xTMy,(x,y)→xTMy, that is, (x,y)=(Gx,Gy)(x,y)=(Gx,Gy) for all column vectors x and y. The set of perplectic matrices P(n) forms a noncompact and nonconnected group. We show an Iwasawa-like decomposition for P(n), that is, we write every element G as a product KAN, where K is perplectic unitary, A is perplectic and diagonal having positive diagonal entries, and N is perplectic unipotent having a special block upper triangular structure.

   

13. De la Cruz, Ralph John (2020). On sums, products, and commutators of symplectically diagonalizable matrices. Journal of the Mathematical Society of the Philippines, 43 (1), ISSN 0115-6926more

Abstract:

Set J =  0 In −In 0  . Let A ∈ C 2n×2n and define A J = J −1A T J. The matrix A is skew-Hamiltonian if A J = A; The matrix A is Hamiltonian if A J = −A; The matrix A is symplectic if A J = A −1 ; and the matrix A is symplectically diagonalizable if there exists a symplectic P such that P AP −1 is diagonal. We show that every (skew)- Hamiltonian matrix A is a sum of two diagonalizable (skew)-Hamiltonian matrices. We show that every even-sized matrix is a sum of four symplectically diagonalizable matrices. We show that every even-sized matrix is a product of symplectically diagonalizable matrices. We also show that every even-sized matrix with zero trace is a sum of matrices of the form XY − Y X, where both X and Y are symplectically diagonalizable matrices and that every even-sized matrix with unit determinant is a product of matrices of the form XY X−1Y −1 , where both X and Y are symplectically diagonalizable matrices.

 

14. Dela Rosa, K. L., & Woerdeman, H. J. (2020). Location of ritz values in the numerical range of normal matrices. Linear and Multilinear Algebra, doi:10.1080/03081087.2020.1761280

Abstract:

Let (Formula presented.) be a complex number in the numerical range (Formula presented.) of a normal matrix A. In the case when no eigenvalues of A lie in the interior of (Formula presented.), we identify the smallest convex region containing all possible complex numbers (Formula presented.) for which (Formula presented.) is a 2-by-2 compression of A. 

 

15. Dimabayao, J. T. (2020). Jeśmanowicz’ conjecture for polynomials. Periodica Mathematica Hungarica, doi:10.1007/s10998-020-00339-w 

Abstract:

Let (a, b, c) be pairwise relatively prime integers such that a2+ b2= c2. In 1956, Jeśmanowicz conjectured that the only solution of ax+ by= cz in positive integers is (x, y, z) = (2 , 2 , 2). In this note we prove a polynomial analogue of this conjecture. 

16. Dimabayao, J. T. (2020). The torsion subgroup of a family of elliptic curves over the maximal abelian extension of . Czechoslovak Mathematical Journal, doi:10.21136/CMJ.2020.0082-19

Abstract:

We determine explicitly the structure of the torsion group over the maximal abelian extension of and over the maximal p-cyclotomic extensions of for the family of rational elliptic curves given by y2 = x3 + B, where B is an integer. © 2020, Mathematical Institute, Academy of Sciences of Cz.

17. Donato, P. & Fulgencio, R. (2020). Some properties of an elliptic periodic problem with an interfacial resistance. ZAMM Zeitschrift Fur Angewandte Mathematik Und Mechanik, doi:10.1002/zamm.202000065

Abstract:

In the homogenization of quasilinear elliptic problems, it is crucial for the homogenized matrix to have some kind of Lipschitz continuity in order to provide the uniqueness of the solution of the limit problem. In this paper, we prove that some estimates providing the uniqueness for a class of quasilinear problems in a periodic two-component domain, remains valid after the homogenization process. To do that, we first prove a suitable Meyers type estimate for the periodic cell problem describing the homogenized matrix, which is posed in a two-component cell, with a jump of the solution proportional to the flux prescribed on the interface. We also complete the study by a boundedness result for this periodic solution.

 

18. Ferrolino, A. R., Lope, J. E. C., & Mendoza, R. G. (2020). Optimal location of sensors for early detection of tsunami waves. doi:10.1007/978-3-030-50417-5_42 

Abstract:

Tsunami early detection systems are of great importance as they provide time to prepare for a tsunami and mitigate its impact. In this paper, we propose a method to determine the optimal location of a given number of sensors to report a tsunami as early as possible. The rainfall optimization algorithm, a population-based algorithm, was used to solve the resulting optimization problem. Computation of wave travel times was done by illustrating the kinematics of a wave front using a linear approximation of the shallow water equations.

 

19. Galvez, L., & Kim, J. (2020). Projection decoding of some binary optimal linear codes of lengths 36 and 40. Mathematics, 8 (1). doi:10.3390/MATH8010015 more

Abstract:

Practically good error-correcting codes should have good parameters and efficient decoding algorithms. Some algebraically defined good codes, such as cyclic codes, Reed–Solomon codes, and Reed–Muller codes, have nice decoding algorithms. However, many optimal linear codes do not have an efficient decoding algorithm except for the general syndrome decoding which requires a lot of memory. Therefore, a natural question to ask is which optimal linear codes have an efficient decoding. We show that two binary optimal [36,19,8] linear codes and two binary optimal [40,22,8] codes have an efficient decoding algorithm. There was no known efficient decoding algorithm for the binary optimal [36,19,8] and [40,22,8] codes. We project them onto the much shorter length linear [9,5,4] and [10,6,4] codes over GF(4) , respectively. This decoding algorithm, called projection decoding, can correct errors of weight up to 3. These [36,19,8] and [40,22,8] codes respectively have more codewords than any optimal self-dual [36,18,8] and [40,20,8] codes for given length and minimum weight, implying that these codes are more practical.

 

20. Galvez, L. E., & Kim, J. (2020). Construction of self-dual matrix codes. Designs, Codes, and Cryptography. doi:10.1007/s10623-020-00740-z more

Abstract:

Matrix codes over a finite field FqFq are linear codes defined as subspaces of the vector space of m×nm×n matrices over FqFq. In this paper, we show how to obtain self-dual matrix codes from a self-dual matrix code of smaller size using a method we call the building-up construction. We show that every self-dual matrix code can be constructed using this building-up construction. Using this, we classify, that is, we find a complete set of representatives for the equivalence classes of self-dual matrix codes of small sizes. In particular we have classifications for self-dual matrix codes of sizes 2×42×42×52×5 over F2F2, of size 2×32×32×42×4 over F4F4, of size 2×22×22×32×3 over F8F8, and of size 2×22×22×32×3 over F13F13, all of which have been left open from K. Morrison’s classification.

 

21. Galvez, Lucky Erap, Betty, Rowena Alma & Nemenzo, Fidel (2020). Self-orthogonal Codes over Fq + uFq and Fq + uFq + u 2FqEuropean Journal of Pure and Applied Mathematics, 13 (4), Pages 873-892. DOI:https://doi.org/10.29020/nybg.ejpam.v13i4.3838more

Abstract:

In this paper, we establish a mass formula for Euclidean and Hermitian self-orthogonal codes over the finite ring Fq + uFq, where Fq is the finite field of order q and u2 = 0. We also establish a mass formula for Euclidean self-orthogonal codes over the finite ring Fq + uFq + u2Fq, with u3 = 0 and characteristic of Fq is odd. These mass formulas are used to give a classification of Euclidean and Hermitian self-orthogonal codes over F2 + uF2 and F3 + uF3 of small lengths.

22. Gonda, Erwin J.& Paras, Agnes T.  (2020). The Jordan Canonical Form of a product of elementary S-unitary matricesScience Diliman, 32 (1).more

Abstract:

Let S be an n-by-n, nonsingular, and Hermitian matrix. A square complex matrix Q is said to be S-unitary if Q*SQ = S. An S-unitary matrix Q is said to be elementary if rank(Q - l) = 1. It is known what form every elementary S-unitary can take, and that every S-unitary can be written as a product of elementary S-unitaries. In this paper, we determine the Jordan canonical form of a product of two elementary S-unitaries.

23. Hernandez, B.S. (2020). On the Independence of Fundamental Decompositions of Power-Law Kinetic Systems. MATCH Communications in Mathematical and in Computer Chemistry, 84 (2020), Pages 57-84.more

Abstract:

The fundamental decomposition of a chemical reaction network (CRN) is induced by partitioning the reaction set into “fundamental classes”. It was the basis of the Higher Deficiency Algorithm for mass action systems of Ji and Feinberg, and the Multistationarity Algorithm for power-law kinetic systems of Hernandez et al. In addition to our previous work, we provide important properties of the independence (i.e., the network’s stoichiometric subspace is the direct sum of the subnetworks’ stoichiometric subspaces) and the incidence-independence (i.e., the image of the network’s incidence map is the direct sum of the incidence maps’ images of the subnetworks) of these decompositions. Feinberg established the essential relationship between independent decompositions and the set of positive equilibria of a network, which we call the Feinberg Decomposition Theorem (FDT). Moreover, Fari˜nas et al. recently documented its version for incidence-independence. Fundamental decomposition divides the network into subnetworks of deficiency either 0 or 1 only. Hence, available results for lower deficiency networks, such as the Deficiency Zero Theorem (DZT), can be used. These justify the study of independent fundamental decompositions. A MATLAB program which (i) computes the subnetworks of a CRN under the fundamental decomposition and (ii) is useful for determining whether the decomposition is independent and incidence-independent is also created. Finally, we provide the following solution for determining multistationarity of CRNs with the following steps: (1) the use of the program, (2) the application MATCH Communications in Mathematical and in Computer Chemistry MATCH Commun. Math. Comput. Chem. 84 (2020) 57-84 ISSN 0340 - 6253 of available results for CRNs with deficiency 0 or 1 (e.g., DZT), and (3) the use of FDT. We illustrate the solution by showing that the generalization of a subnetwork of Schmitz’s carbon cycle model by Hernandez et al., endowed with mass action kinetics, has no capacity for multistationarity.

 

24. Hernandez, B. S., Mendoza, E. R., & Reyes V, A. A. (2020). A computational approach to multistationarity of power-law kinetic systems. Journal of Mathematical Chemistry, 58 (1), Pages 56-87. doi:10.1007/s10910-019-01072-7 more

Abstract:

This paper presents a computational solution to the multistationarity problem for any power-law kinetic system, i.e., to determine if such a system can have multiple positive equilibria within a stoichiometric class. The approach combines (i) the extension of the "Higher Deficiency Algorithm" of Ji and Feinberg for mass action systems to power-law kinetic systems with reactant-determined interactions (i.e., reactions branching from the same reactant complex have identical kinetic order vectors) and (ii) the CF-RM method which transforms any power-law system to a dynamically equivalent one with reactant-determined interactions. We apply the approach to models of anaerobic yeast fermentation and monolignol biosynthesis in populus xylem, both in the GMA (generalized mass action) format of Biochemical Systems Theory. We establish their monostationarity, i.e., for any set of rate constants, the systems have at most one positive steady state. We also provide examples of the broader scope of our approach for deficiency one power-law kinetic systems in comparison to the extension of Feinberg's Deficiency One Algorithm to such systems. Such examples have the capacity for multistationarity for particular rate constants.

 

25. Hernandez, B.S., Mendoza, E.R. & de los Reyes, A.A. V. (2020). Fundamental decompositions and multistationarity of power-law kinetic systemsMATCH Communication in Mathematical  and in Computer Chemistry, 83, Pages 403-434.more

Abstract:

The fundamental decomposition of a chemical reaction network (also called its “F-decomposition”) is the set of subnetworks generated by the partition of its set of reactions into the “fundamental classes” introduced by Ji and Feinberg in 2011 as the basis of their “higher deficiency algorithm” for mass action systems. The first part of this paper studies the properties of the F-decomposition, in particular, its independence (i.e., the network’s stoichiometric subspace is the direct sum of the subnetworks’ stoichiometric subspaces) and its incidence-independence (i.e., the image of the network’s incidence map is the direct sum of the incidence maps’ images of the subnetworks). We derive necessary and sufficient conditions for these properties and identify network classes where the F-decomposition coincides with other known decompositions. The second part of the paper applies the abovementioned results to improve the Multistationarity Algorithm for power-law kinetic systems (MSA), a general computational approach that we introduced in previous work. We show that for systems with non-reactant determined interactions but with an independent F-decomposition, the transformation to a dynamically equivalent system with reactant-determined interactions – required in the original MSA – is not necessary. We illustrate this improvement with the subnetwork of Schmitz’s carbon cycle model recently analyzed by Fortun et al.

 

26. Jamilla, C. Mendoza, R., Mezo, I.  (2020).  Solutions of neutral delay differential equations using a generalized Lambert W function. Applied Mathematics and Computation, 382.  Doi: 10.1016/j.amc.2020.125334 more

Abstract:

The Lambert W function is defined by W(a)eW(a)−a=0. One of the many applications of the Lambert W function is in solving delay differential equations (DDEs). In 2003, Asl and Ulsoy provided a solution of some DDEs in terms of the Lambert W functions Asl et al. (2003)[1]. However, the solutions are limited to differential equations with delay in the state variable. Scott et al. (2006)[2] introduced a generalized Lambert function which was further studied by Mező and Baricz (2017)[3]. In our work, we show that this generalization of the Lambert W function provides an analytical solution to neutral delay differential equations (NDDEs). NDDEs are DDEs with time delay not only in the state variables but also in the derivative terms. This analytical solution is advantageous such that it is similar to the general solutions of linear ODEs. Also, one can identify how the parameters affect the solution of the equation since our proposed solution is written in terms of these parameters. We then propose a new numerical method to solve linear NDDEs using the generalized Lambert W function. We test our method to examples with known solutions. We also provide a real-world application by solving an NDDE model of the population growth of an E. coli culture using our proposed approach.

27. Jamilla, C.U., Mendoza, R.G., Mendoza, V.M.P. (2020). Explicit solution of a Lotka-Sharpe-McKendrick system involving neutral delay differential equations using the r-Lambert W function. Mathematical Biosciences and Engineering, 17 (5), Pages 5686-5708. doi: 10.3934/MBE.2020306more

Abstract:

Structured population models, which account for the state of individuals given features such as age, gender, and size, are widely used in the fields of ecology and biology. In this paper, we consider an age-structured population model describing the population of adults and juveniles. The model consists of a system of ordinary and neutral delay differential equations. We present an explicit solution to the model using a generalization of the Lambert W function called the r-Lambert W function. Numerical simulations with varying parameters and initial conditions are done to illustrate the obtained solution. The proposed method is also applied to an insect population model with long larval and short adult phases.

 

28. Jaming, P., Kellay, K., & Perez, R. (2020). Phase retrieval for wide band signals. Journal of Fourier Analysis and Applications, 26 (4). doi:10.1007/s00041-020-09767-1

Abstract:

This study investigates the phase retrieval problem for wide-band signals. We solve the following problem: given f L2(R) with Fourier transform in L2(R,e2c|x|dx), we find all functions g L2(R) with Fourier transform in L2(R,e2c|x|dx), such that | f(x) | = | g(x) | for all x R. To do so, we first translate the problem to functions in the Hardy spaces on the disc via a conformal bijection, and take advantage of the inner-outer factorization. We also consider the same problem with additional constraints involving some transforms of f and g, and determine if these constraints force uniqueness of the solution. 

 

29. Li, C. -., Liu, Y. U. E., Ma, C., & Pelejo, D. C. (2020). A note on parallel distinguishability of two quantum operations. Electronic Journal of Linear Algebra, 36 (1), Pages 198-209. doi:10.13001/ela.2020.4957

Abstract:

In this work, the authors consider a homogeneous system of linear equations of the form AN α x = 0 arising from the distinguishability of two quantum operations by N uses in parallel, where the coefficient matrix Aα depends on a real parameter α. It was conjectured by Duan et al. that the system has a non-trivial nonnegative solution if and only if α lies in a certain interval RN depending on N. The authors affirm the necessity part of the conjecture and establish the sufficiency of the conjecture for N ≤ 10 by presenting explicit non-trivial nonnegative solutions for the linear system.

30. Luy, Jasmin Mae S. (2020). A Test of the Generalized Yunus Equation and its Implications for Microcredit in the Philippines. DLSU Business & Economics Review, 29 (2), Pages 117-127.more

Abstract:

Microcredit is one of the most important financial services offered by microfinance institutions (MFIs) in the Philippines. Loan repayment by frequent installments faces the challenge of possible random delays, which leads to random interest rates. Such randomness affects both microlenders and borrowers. This research utilizes a mathematical model called the generalized Yunus equation (GYE) to study the microloan repayment process in the Philippine setting. Using this model, an explicit formula was formulated expressing the effective interest rate involved in repayment as a function of the time when the delay takes place, which closely approximates the actual values of the rate that microlenders receive. The model can potentially help lenders identify how much interest they gain or lose, which is a viable part of their operation’s sustainability.

 

31. Magdalena, I., Atras, M. F., Sembiring, L., Nugroho, M. A., Labay, R. S. B., & Roque, M. P. (2020). Wave transmission by rectangular submerged breakwaters. Computation, 8 (2). doi:10.3390/COMPUTATION8020056

Abstract:

In this paper, we investigate the wave damping mechanism caused by the presence of submerged bars using the Shallow Water Equations (SWEs). We first solve these equations for the single bar case using separation of variables to obtain the analytical solution for the wave elevation over a rectangular bar wave reflector with specific heights and lengths. From the analytical solution, we derive the wave reflection and transmission coefficients and determine the optimal height and length of the bar that would give the smallest transmission coefficient. We also measure the effectiveness of the bar by comparing the amplitude of the incoming wave before and after the wave passes the submerged bar, and extend the result to the case of n-submerged bars. We then construct a numerical scheme for the SWEs based on the finite volume method on a staggered grid to simulate the propagation of a monochromatic wave as it passes over a single submerged rectangular bar. For validation, we compare the transmission coefficient values obtained from the analytical solution, numerical scheme, and experimental data. The result of this paper may be useful in wave reflector engineering and design, particularly that of rectangle-shaped wave reflectors, as it can serve as a basis for designing bar wave reflectors that reduce wave amplitudes optimally. 

 

32. Manejero, James Lee & Mendoza, Renier (2020). Variational approach to data graduation. Philippine Journal of Science, 149 (2), Pages 431-449.more

Abstract:

The Whittaker-Henderson graduation is a data smoothing method commonly used in actuarial science for mortality table computation. This method is a finite-dimensional minimization problem, which aims to give a smooth approximation of the crude data. Our goal is to treat the Whittaker-Henderson method as a minimization problem in a Sobolev space. We take advantage of some results in the study of Sobolev spaces to analyze the solution to the graduation problem. Solving the arising minimization problem is equivalent to solving a partial differential equation (PDE). To solve the PDE numerically, we use the finite element method (FEM). We apply this variational approach to the data sets found in the literature. In particular, we test our method to check for patterns in (1) mortality rates for Filipino males, (2) global average temperature anomaly, and (3) monthly eBay share price. We also compare the results with that of the Whittaker-Henderson method.

33. Marfil, Ramon Iñigo D. & David, Guido (2020). On the Placing Probabilities for the Four-Tower Problem Using Recursions Based on MultigraphsJournal of the Mathematical Society of the Philippines, 43 (1), Pages 19-32.more

Abstract:

The Four-Tower Problem is a four-player gambler’s ruin model where two players are involved in an even-money bet during each round. In this problem, the objective is to solve for each player’s ruin and final placing probabilities given their initial wealths. Weighted directed multigraphs were constructed to model the transitions between chip states. Linear systems are constructed based on the connections between nodes in these graphs. Solutions for the placing probabilities of each player are obtained from these linear systems. A numerical algorithm is developed to solve the Four-Tower Problem for any positive integer chip total. The solution leads to exact values, and results show that the equities in this model depend on the number, not just proportion, of chips each player holds.

 

34. Mendoza, Renier & Keeling, Stephen (2020). Existence of solution for a segmentation approach to the impedance tomography problemElectronic Journal of Differential Equations, 2020 (93), Pages 1–30.

Abstract:

In electrical impedance tomography (EIT), image reconstruction of the conductivity distribution of a body can be calculated using measured voltages at the boundary. This is done by solving an inverse problem for an elliptic partial differential equation (PDE). In this work, we present some sensitivity results arising from the solution of the PDE. We use these to show that a segmentation approach to the EIT inverse problem has a unique solution in a suitable space using a fixed point theorem.

 

35. Fuchs, M., Lee, C.H. and Paningbatan, A.R. (2020). Distributional analysis of the extra-clustering model with uniformly generated phylogenetic trees. Electronic Communications in Probability, 25 (13), Page 13.more

Abstract:

The extra-clustering model for the group formation process of social animals was introduced by Durand, Blum and François. The model uses the relatedness of the animals, which is described by phylogenetic trees. If these trees are drawn from the Yule-Harding model, it was analyzed in recent work. Here, we analyze it for the uniform model, which is the other widely-studied model on phylogenetics trees. More precisely, we derive moments and limit laws for the number of groups, the number of groups of fixed size and the largest group size. Our results show that, independent of the probability of extra-clustering, there is on average only a finite number of groups, one of which is very large whereas all others are small. This behavior considerably differs from the Yule-Harding case, where the finiteness of the number of groups is dependent on the extra-clustering probability.

 

36. Fuchs, M. and Paningbatan, A.R. (2020). Correlation between Shapley values of rooted phylogenetic trees under the beta-splitting model. Journal of Mathematical Biology, 80 (3), Pages 627-653.more

Abstract:

In recent years, several different versions of the Shapley value have been introduced in phylogenetics for the purpose of ranking biodiversity data in order to decide whether to preserve the data or not. Two of these Shapley values are the rooted and unrooted Shapley value which have been compared with the fair proportion index since this index is easier to compute. In particular, it was proved for the former that it is identical with the fair proportion index and numerical data was presented by several authors that the latter is strongly correlated with the fair proportion index. In this paper, we will prove a theoretical result which supports this observation. More precisely, we will prove that in random phylogenetic trees under the ββ-splitting model, the correlation coefficient between the unrooted Shapley value and the fair proportion index indeed tends to one for all ββ with β>−1β>−1. We also present data which suggests that the convergence worsens as ββ is approaching 1−1.

 

37. Paras, A. T., & Salinasan, J. R. (2020). The product of an involution and a skew-involution. Linear Algebra and its Applications, 584, Pages 431-437. doi:10.1016/j.laa.2019.09.035 more

Abstract:

We give necessary and sufficient conditions for a matrix over a field to be the product of an involution (A2=I) and a skew-involution (A2=−I).

38. Rolando Perez III Perez, R. (2020). A note on the phase retrieval of holomorphic functions. Canadian Mathematical Bulletin, 1-8. DOI:10.4153/S000843952000082Xmore

Abstract:

We prove that if f and g are holomorphic functions on an open connected domain, with the same moduli on two intersecting segments, then f=gf=gup to the multiplication of a unimodular constant, provided the segments make an angle that is an irrational multiple of ππ. We also prove that if f and g are functions in the Nevanlinna class, and if |f|=|g||f|=|g|on the unit circle and on a circle inside the unit disc, then f=gf=gup to the multiplication of a unimodular constant.

 

39. Velasco, Arrianne Crystal, Darbas, Marion, Mendoza, Renier, Bacon, Monica, & de Leon, John Cedrick (2020). Comparative study of heuristic algorithms for electrical impedance tomography. Philippine Journal of Science, 149 (3-a), Pages 747-772.more

Abstract:

Based on electrical measurements from electrodes placed around the boundary of a body, electrical impedance tomography (EIT) is an imaging procedure that recovers the spatial distribution of the conductivities in the interior of a body. Recent studies have shown promising results in reconstructing EIT images using heuristic algorithms. This work presents a study of the applicability of six heuristic algorithms – firefly algorithm (FA), novel bat algorithm (NBA), genetic algorithm with new multi-parent crossover (GA-MPC), success history-based adaptive differential evolution with linear population size reduction with semiparameter adaptation hybrid with covariance matrix adaptation evolutionary strategy (LSHADE-SPACMA), ensemble sinusoidal differential covariance matrix adaptation (LSHADE-cnEpSin), and effective butterfly optimizer with covariance matrix adapted retreat phase (EBOwithCMAR) – for the EIT image reconstruction problem. These algorithms have never been employed to solve the EIT inverse problem. Series of numerical tests were carried out to compare the performance of the selected algorithms.

 

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1. Afalla, J., Catindig, G., De Los Reyes, A., Prieto, E., Faustino, M.A.,  Vistro, V., Gonzales, K.C., Bardolaza, H., Mag-Usara, V.K., Husay, H.A., Muldera, J., Cabello, N.I., Ferrolino, J.P., Kitahara, H., Somintac, A., Salvador, A., Tani, M., Estacio, E. (2020). Ultrafast carrier dynamics and THz conductivity in epitaxial-grown LT-GaAs on silicon for development of THz photoconductive antenna detectorsJournal of Physics D: Applied Physics, 53 (9), article number 095105. more

Abstract:

Carrier dynamics and photoconductivity in epitaxial-grown low-temperature GaAs on nominal and vicinal Si(1 0 0) substrates ('LT-GaAs/Si') were studied to predict their actual performance as THz photoconductive antenna (PCA) detectors. An optical-pump terahertz-probe technique was used to obtain the transmittance, carrier lifetime and photoconductivity of two LT-GaAs/Si samples, grown using different substrates and different growth protocols. The LT-GaAs grown on Si(1 0 0) substrate with a 4° tilt to 1 1 0 has better crystallinity, in agreement with other reports; while the LT-GaAs layer grown on nominal Si(1 0 0) substrate, though more structurally defective, has a much faster electron trapping time. Fabricated test PCAs with either dipole or bowtie geometries confirm the characterization results. The photoconductivity and carrier lifetime results manifest in the PCA performance, in responsivity, and in detection bandwidth. The prototypes' sensitivities, bandwidths and dynamic ranges show that with some growth optimization, LT-GaAs/Si can be tailored to create economical, broadband THz detectors.

 

2. De Los Reyes, A., Bardolaza, H., Vasquez, J. D., Cabello, N. I., Lopez, L., Chang, C. Y., Somintac, A., Salvador, A., Jang, D. J., & Estacio, E. (2020). Temperature-dependent terahertz time-domain spectroscopy of 3D, 2D, and 0D semiconductor heterostructuresJournal of Materials Science: Materials in Electronics0123456789. https://doi.org/10.1007/s10854-020-03188-y more

Abstract:

Carrier transport in semiconductors with different dimensionalities, i.e., 3D (bulk), 2D (QW), and 0D (QD), were investigated via temperature-dependent terahertz time-domain spectroscopy (THz-TDS). The optical properties and recombination dynamics in the samples were probed via photoluminescence spectroscopy. The temperature-dependence of the THz emission from the samples was explained in the context of the drift-diffusion model using the dominant THz radiation mechanism. The THz emission from diffusion-type THz emitters such as p- and n-InAs decreases as temperature increases due to mobility decrease. Conversely, the THz emission from drift-type THz emitters such as SI-GaAs, GaAs QW, and InAs QD was found to increase with temperature due to the increase in the driving electric field. In summary, THz-TDS can be utilized to gain qualitative insights on the temperature-dependent transport characteristics and establish dominant THz radiation mechanisms.

 

3. De Los Reyes, A.E., Vasquez, J.D., Bardolaza, H.R., Lopez, L.P., Jr., Chang, C.-Y., Somintac, A.S., Salvador, A.A., Jang, D.-J., Estacio, E.S. (2020). Low-temperature carrier dynamics in MBE-grown InAs/GaAs single-and multi-layered quantum dots investigated via photoluminescence and terahertz time-domain spectroscopyOptical Materials Express, 10 (1), Pages 178-188. more

Abstract:

The photocarrier dynamics in molecular beam epitaxy (MBE)-grown single-(SLQD) and multi-layered (MLQD) InAs/GaAs quantum dots were studied. Photoluminescence (PL) spectroscopy has shown that the MLQD has more uniform QD size distribution as compared to the bimodal SLQD. Correlation between PL and THz-TDS has shown that photocarrier transport is more favored in the MLQD owing to this uniform QD size distribution, resulting to higher THz emission. The THz emission from the QD samples were found to be proportional to temperature. A drift-related photocarrier transport mechanism is proposed, wherein photocarriers generated in the QDs are accelerated by an interface electric field.

 

4. Escaño, M.C., Balgos, M.H., Nguyen, T.Q., Prieto, E.A., Estacio, E.,  Salvador, A., Somintac, A., Jaculbia, R., Hayazawa, N., Kim, Y.b., Tani, M. (2020). True bulk As-antisite defect in GaAs(1 1 0) identified by DFT calculations and probed by STM/STS measurementsApplied Surface Science, Volume 511, Article number 145590. more

Abstract:

We reveal the As-antisite (AsGa) defect close to the surface of GaAs(1 1 0) with bulk characteristics using first-principles methods with experimental verifications. We found that the AsGa in the third-layer mimics the geometry, partial charge density and more importantly, the density of states of AsGa in bulk GaAs. Notably, the mid-gap state induced by AsGa in bulk GaAs is well-reproduced by the AsGa in the third layer of GaAs(1 1 0). Simulated and experimental STM images show an “asymmetric two-lobe” feature in the region around the defect. Using local density of states (LDOS) and STS spectra, we propose three prominent peaks with characteristic energy levels corresponding to the third layer AsGa. The above results present the first report of surface electronic signatures of true bulk defect near the surface of GaAs(1 1 0).

 

5. Sanchez, J.R.G.,  Joson, P.R.S., Vega, M.M. (2020). Studying absorbance properties and mercury remediation capabilities of gold–graphene oxide–iron oxide (Au–GO–Fe3O4) nanoparticle systemsJournal of Environmental Science and Health - Part A Toxic/Hazardous Substances and Environmental Engineering, 55 (3), Pages 216-223. more

Abstract:

Mercury pollution is a rampant problem in many economically significant Philippine freshwater ecosystems. Communities dependent on these freshwater sources are therefore at risk for exposure to harmful levels of mercury. Various formulations of a novel gold–graphene oxide–iron oxide (Au–GO–Fe3O4) hybrid nanoparticle system were created and subjected to UV–Vis spectroscopy to determine optimal formulations that would best serve as potential substrates for Surface-Enhanced Raman Spectroscopy (SERS) detection of mercury. Optimal formulations of Au–GO–Fe3O4 were also introduced into mercury-polluted environments to evaluate its ability to remove mercury from both water and biological tissues. Spectroscopic analysis revealed that Fe3O4-rich formulations of Au–GO–Fe3O4 had the greatest potential to boost Raman signal intensities of mercury due to red shifting of absorbance peaks and overall increased absorbance across visible wavelengths resulting in the inclusion of greater areas underneath absorbance peaks. Mercury remediation experiments likewise demonstrated Au–GO–Fe3O4 to significantly reduce average concentrations of mercury from 1.67 to 0.82 ppm in polluted water samples–corresponding to a mercury removal efficiency of 50.9% and a mercury adsorption capacity of 5.89 mg/g. The results highlight the viability of Au–GO–Fe3O4 to function as both substrate for SERS detection of mercury and as effective adsorbent for mercury remediation.

 

6. Santos-Putungan, A.B., Stojić, N., Binggeli, N., Paraan, F.N.C. (2020). Selective capture of CO2 over N2 and CH4: B clusters and their size effectsMaterials Today Communications, 22, article number 100712. more

Abstract:

Using density-functional theory (DFT), we investigate the selectivity of adsorption of CO2 over N2 and CH4 on planar-type B clusters, based on our previous finding of strong chemisorption of CO2 on the B10−13 planar and quasiplanar clusters. We consider the prototype B8 and B12 planar-type clusters and perform a comparative study of the adsorption of the three molecules on these clusters. We find that, at room temperature, CO2 can be separated from N2 by selective binding to the B12 cluster and not to the B8 cluster. Selective adsorption of CO2 over CH4 at room temperature is possible for both clusters. Based on our DFT-adsorption data (including also a semi-infinite Boron sheet) and the available literature-adsorption value for N2 on the planar-type B36 cluster, we discuss the selectivity trend of CO2 adsorption over N2 and CH4 with planar-cluster size, showing that it extends over sizes including B10-13 clusters and significantly larger.

 

 

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1. Cardenas, M. B., Rodolfo, R. S., Lapus, M. R., Cabria, H. B., Fullon, J., Gojunco, G. R., . . . Zhang, T. (2020). Submarine groundwater and vent discharge in a volcanic area associated with coastal acidificationGeophys Res Lett, 47 (1), e2019GL085730. more

Abstract:

We investigated submarine groundwater discharge (SGD) in a volcanic coastal area that hosts the world's most biodiverse reefs. Measurements of 222Rn activity in coastal seawater, a tracer for groundwater, indicated prevalent SGD. In areas where seawater 222Rn activity was generally higher, we discovered hydrothermal springs emitting acidic waters (pH ~5.4–6.0) and venting magmatic CO2 that brought local pCO2 levels up to 95,000 ppm. The collection of vents raised CO2 and lowered pH over 1–2 km of coastline. The hydrogen and oxygen isotope compositions of water and chloride concentration revealed that the springs discharge recirculated seawater mixed variably with terrestrial groundwater. Shallower springs and pore water have a higher proportion of terrestrial groundwater than deeper springs, which emit mostly recirculated seawater. This suggests that different SGD mechanisms are present. The SGD could be contributing to the evolution and function of the biodiverse ecosystem, but it also represents myriad pathways for contamination.

 

2. Conaco C, Cabaitan PC. (2020). Influence of salinity and temperature on the surivival and settlement of Helipora coerulea larvae. Mar. Pollut. Bull., 150: 110703. more

Abstract:

Recurrent thermal stress events and intensified precipitation alter the ocean environment resulting in the decline of coral populations. However, the influence of these changes on larval survival and settlement is not well understood. We examined the effect of salinity (15, 20, 25, 30, 35, and 40 ppt) and temperature (27 °C, 30 °C, and 33 °C) on settlement and survival of larvae of the octocoral, Heliopora coerulea. Larvae settled successfully at salinities from 25 to 30 ppt. On the other hand, larval survival and settlement decreased with increasing temperature. A combination of 25–35 ppt and 27–30 °C resulted in highest survival and settlement. These results indicate that early life stages of H. coerulea are negatively impacted by thermal stress but may be able to survive at reduced salinity. The wider tolerance range of H. coerulea larvae compared to most scleractinian larvae may thus contribute to the success of this coral on disturbed reef ecosystems.

 

3. Jackisch D, Yeo B-X, Switzer AD, He S, Cantarero DLM, Siringan FP, Goodkin NF. (2020). Precipitation stable isotopic signatures of tropical cyclones in Metropolitan Manila, Philippines show significant negative isotopic excursionsEarth Syst. Sci. Discuss. DOI: https://doi.org/10.5194/nhess-2019-352. Article in Review. more

Abstract:

Tropical cyclones have devastating impacts on the environment, economies, and societies, and may intensify in the coming decades due to climate change. Stable water isotopes serve as tracers of the hydrological cycle, as the fractionation process may leave distinct precipitation isotopic signatures. Here we present a record of daily precipitation isotope measurements from March 2014 to October 2015 for Metropolitan Manila, which is a first of a kind dataset for the Philippines and Southeast Asia, and analyze if there is an isotopic response to tropical cyclones. The most negative shift in δ18O value (−13.84 ‰) leading to a clear isotopic signal was caused by Typhoon Rammasun, which directly hit Metropolitan Manila. The average δ18O value of precipitation associated with tropical cyclones is −10.24 ‰, whereas the mean isotopic value for rainfall associated with non-cyclone events is −5.29 ‰. Further, the closer the storm track to the sampling site, the more negative the isotopic values, indicating that in-situ isotope measurements can provide a direct linkage between isotopes and typhoon activities in the Philippines.

 

4. Li T, Lin X, Yu L, Lin S, Rodriguez IB, Ho T-Y. (2020). RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metalsSci Total Environ, 705, 135767.more

Abstract:

A healthy symbiotic relationship between corals and Symbiodiniaceae relies on suitable temperature and adequate nutrients including trace metals. Besides global warming, trace metal deficiency has been shown to cause coral bleaching, a phenomenon responsible for extensive coral reef degradation around the world. How trace metal deficiency impacts Symbiodiniaceae and coral symbiosis is poorly understood, however. In this study, we applied RNA-seq to investigate how Fugacium kawagutii responds to the deficiency of five trace metals (Fe2+, Zn2+, Cu2+, Mn2+, Ni2+). We identified 685 to 2805 differentially expressed genes (DEGs) from these trace metal deficiency conditions, among which 372 were commonly regulated by all the five trace metals and were significantly enriched in energy metabolism (e.g. fatty acid synthesis). Furthermore, genes associated with extracellular matrix (ECM), cell surface structure and cell adhesion were impacted, suggesting that the ability of recognition and adhesion of F. kawagutii may be altered by trace metal deficiencies. In addition, among the five metals, Fe2+ deficiency exhibited the strongest influence, with Fe-rich redox elements and many antioxidant synthesis genes being markedly down-regulated, indicative of adaptive reduction of Fe demand but a compromised ability to combat oxidative stress. Overall, deficiency of trace metals (especially Fe) seems to repress growth and ability of ROS scavenging, elevate energy metabolism and innate immunity, and alter cell adhesion capability, with implications in symbiosis disruption and coral bleaching.

 

5. Ligson CA, Tabalanza TD, Villanueva RD, Cabaitan PC. (2020). Feasibility of early outplanting of sexually propagated Acropora verweyi for coral reef restoration demonstrated in the PhilippinesRestoration Ecology, 28 (1), Pages 244-251. more

Abstract:

Over the last 20 years, coral sexual propagation techniques for reef restoration have been steadily developed and improved. However, these techniques involve considerable time and costs to grow coral propagules. There is a need to examine the optimal size of juvenile corals for outplantation. Here, we outplanted sexually propagated small (3–5 mm diameter) and large (10–15 mm diameter) Acropora verweyi corals at 4 months after fertilization at two sites in northwestern Philippines, and compared their survival and radial growth rate after a year. A. verweyi coral juveniles (n  = 240) exhibited an overall mean survival of 29.5% and growth rate of 11.12 ± 6.2 mm/year (mean ± SD). Large colonies had a significantly higher growth rate than smaller colonies. Although survivorship of large juveniles was significantly better than that of the smaller ones at one site, it did not differ significantly at the other. Each 4‐month‐old coral cost US$1.52 to produce, while the cost of each of the outplanted juveniles (n  = 240) was about US$2.67, whereas the cost of each survivor about a year after outplantation was US$11.47. Results suggest that A. verweyi reared in ex situ nurseries for only 4 months can survive reasonably well when outplanted onto coral reefs.

 

6. Millwer BW, Torres JP, Flores MS, FOrteza I, Rosenber G, Haygood MG, Schmidt EW, Concepcion GP. (2020). Synergistic anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and absolute stereochemistry of 7,8-dideoxygriseorhodin CJournal of Antibiotics, 73, Pages 290-298. more

Abstract:

The emergence of antibiotic resistance necessitates not only the identification of new compounds with antimicrobial properties, but also new strategies and combination therapies to circumvent this growing problem. Here, we report synergistic activity against methicillin-resistant Staphylococcus aureus (MRSA) of the β-lactam antibiotic oxacillin combined with 7,8-dideoxygriseorhodin C in vitro. Ongoing efforts to identify antibiotics from marine mollusk-associated bacteria resulted in the isolation of 7,8-dideoxygriseorhodin C from a Streptomyces sp. strain cultivated from a marine gastropod tissue homogenate. Despite the long history of 7,8-dideoxygriseorhodin C in the literature, the absolute configuration has never been previously reported. A comparison of measured and calculated ECD spectra resolved the configuration of the spiroketal carbon C6, and 2D ROESY NMR spectroscopy established the absolute configuration as 6s,6aS. The compound is selective against Gram-positive bacteria including MRSA and Enterococcus faecium with an MIC range of 0.125–0.5 μg ml−1. Moreover, the compound synergizes with oxacillin against MRSA as observed in the antimicrobial microdilution and time-kill assays. Simultaneous treatment of the compound with oxacillin resulted in an approximately tenfold decrease in MIC with a combination index of <0.5, indicating synergistic anti-MRSA activity.

 

7. Olano DEB, Salvador-Reyes LA, Montaño MNE, Azanza RV. (2020). Sorpiton of paralytic shellfish toxins (PSTs) in algal polysaccharide gelsAlgal Research 45: 101655. more

Abstract:

Sorption mechanics of the paralytic shellfish toxins (PSTs), saxitoxin (STX) and neo-saxitoxin (neo-STX), on algal polysaccharide gels was characterized using surface chemistry models. Refined (RC), semi-refined (SRC) carrageenan and alginate showed sorption of STX and neo-STX. The sorption of PSTs on RC, SRC and alginate was affected by contact time and in part, temperature. From surface chemistry models, alginate followed a spontaneous endothermic physical monolayer sorption of STX and neo-STX. SRC and RC favoured the concurrence of physical and chemical monolayer sorption, being endothermic for SRC and exothermic for RC.

 

8. Onda DFL, Gomez NC. (2020). Marine microbes and plastic debris research status and opportunities in the PhilippinesPhilippine Journal of Science, 149 (1), Pages 89-100.more

Abstract:

Marine plastics have been shown to affect all organisms across the trophic levels including the microbial communities, influencing their community assembly, composition, metabolic processes, and ecosystem functions. Thus, studying plastic-microbe interactions in the marine environment is important in understanding its implications alongside the growing issue of plastic pollution. The Philippines, despite being suggested as the third-largest contributor to marine plastic debris, currently does not have any existing national research programs on basic plastics research, resulting in our limited understanding of the extent and implications in the country. This paper then reviews the current status and knowledge of the plastic-microbe association focusing on how plastic surfaces serve as a new environment for marine microbes, how this system could become dispersal mechanisms of unwanted microorganisms, and how microbes possibly contribute to the biodegradation of plastics in the marine environment. These also translate to possible research opportunities for Filipino scientists to work on the topic.

 

9. Quimpo TJR, Cabaitan PC, Hoey AS. (2020). Detachment of Porites cylindrica nubbins by herbivorous fishesRestor Ecol, 28 (2), Pages 418-426. more

Abstract: 

A form of active restoration for coral assemblages involves culturing coral nubbins at nursery sites before transplantation to recipient reefs. Incidental grazing and/or directed predation by local fish assemblages are major sources of dislodgement and mortality for coral nubbins in nurseries. However, the rate of coral nubbin detachment, how this varies across fish taxa, and whether nubbin size affects rates of detachment warrant further investigation. We used field and aquaria experiments to examine the effect of incidental grazing and predation on the detachment of Porites cylindrica nubbins of different sizes (0.5, 1, 2, 3, 4, and 5 cm height). Short‐term (6 hours) exposure of nubbins to local fish assemblages at Lucero Reef, northwestern Philippines, caused higher detachment (1.93% ± 0.53 SE) compared to caged controls (0.16% ± 0.16 SE), with no detectable effect of nubbin size. To identify the impact of individual fish species, nubbins were exposed to one of four locally abundant herbivorous and corallivorous fish species in aquaria for 8 hours. Nubbin detachment was greater when exposed to Chlorurus spilurus (1.20–36.2%) and Siganus fuscescens (0.00–15.0%) than Chaetodon lunulatus (0.00–4.00%) and Chaetodon kleinii (0.00–1.20%), with the smallest nubbins (0.5 cm) being the most vulnerable. Our results suggest that incidental grazing by herbivorous fishes, especially parrotfishes, may potentially be an important source of detachment and likely mortality of nubbins. Optimizing coral nursery protocols should consider potential trade‐offs between excluding grazing fishes and the accumulation of algal material on caging structures to minimize nubbin mortality and improve coral restoration success.

 

10. Quimpo TJR, Ligson CA, Manogan DP, Requilme JNC, Albelda RL, Conaco C, Cabaitan PC. (2020). Fish farm effluents alter reef benthic assemblages and reduce coral settlement. Mar. Pollut. Bull., 153:111025. more

Abstract:

Fish farming in coastal areas is a rapidly growing industry. However, unregulated fish farming practices that release massive amounts of unconsumed feed and fecal material into the water column, can result in a nutrient-enriched environment that extends to nearby reef systems. To understand the impact of fish farm effluent on coral settlement, we tested the settlement rate of Pocillopora acuta larvae on artificial substrates conditioned for 12 weeks at three sites with increasing distance (2–10 km) from fish farms in Bolinao, Philippines. Sites far from the fish farms had higher biofilm and crustose coralline algae cover. In contrast, the site closest to the fish farms, where nutrient levels were higher, had greater sediment and turf algae cover. Tiles conditioned at the farther sites promoted higher (6–8%) larval settlement whereas tiles from the nearer site had lower settlement (3%). These findings show that fish farm effluents can indirectly affect coral settlement on adjacent reefs by promoting growth of other biota that may inhibit larval settlement and by reducing the availability of suitable substrate.

 

11. Reich HG, Rodriguez IB, LaJeunesse TC, Ho T-Y. (2020). Endosymbiotic dinoflagellates pump iron: differences in iron and other trace metal needs among the SymbiodiniaceaeCoral Reefs. Article in Review. DOI:10.1007/s00338-020-01911-z more

Abstract:

Iron (Fe) is essential to the physiology and growth of marine phytoplankton. It remains unclear how important iron is to the functional ecology of symbiotic dinoflagellates in the family Symbiodiniaceae, and whether limitations in iron ultimately affect the health and productivity of coral hosts, especially during episodes of ocean warming. Five Symbiodiniaceae species (spanning three genera) were used to investigate the effects of reduced iron availability on cell growth and the acquisition of other trace metals. When grown under iron replete conditions, intracellular iron quotas (content) reflected a large biochemical demand and ranged from 7.8 to 23.1 mmol Fe mol Phosphorus−1. Symbiodinium necroappetens was the only species that acclimated and maintained high growth rates while subjected to the lowest iron treatment (250 pM Fe′). Cultures surviving under low iron concentrations experienced changes in cellular concentrations (and presumably their use as cofactors) of other trace metals (e.g., zinc, copper, cobalt, manganese, nickel, molybdenum, vanadium), in ways that were species-specific, and possibly related to the natural ecology of each species. These changes in trace metal contents may have cascading effects on vital biochemical functions such as metalloenzyme activities, photosynthetic performance, and macronutrient assimilation. Furthermore, these species-specific responses to iron limitation provide a basis for investigations on how iron availability effects cellular processes among species and genera of Symbiodiniaceae, and ultimately how metal shortages modulate the response of coral–algal mutualisms to physiological stressors.

 

12. Tabalanza TD, Jamodiong EA, Diaz LA, Tañedo MCS, Leriorato JC, Villanueva RD, Cabaitan PC. (2020). Successfully cultured and reared coral embryos from wild caught spawn slick in the Philippines. Aquaculture, 525: 734354 more

Abstract:

Various coral propagation techniques, including utilization of spawn slicks, have been developed to help restore degraded coral communities. Although, it has been demonstrated that embryos from spawn can be used for sexual propagation of corals, few have quantified fertilization, survival, settlement, post-settlement mortality, and long term survival of transplanted corals, grown from spawn slick. Spawn slicks were collected at night off Anda, northwestern Philippines, following a mass spawning of Acropora spp. The collected spawn, which contained ~4,100,000 developing embryos, was highly viable (96% actively dividing) at 12 h post-mixing. Based on assays, 2-day old larvae exhibited high survival in culture (87.9%), and subsequent settlement competency (92%). All 3330 settlement substrates (coral plug-ins), seeded with approximately 2,100,000 3-day old coral larvae, had at least one settled coral after one month. Forty-five pieces of these plug-ins, which were randomly tagged, had settled coral spats ranging from 3 to 88 spats per plug-in (26.7 ± 3.4 spats per plug-in, mean ± SE). Two and four months after the initial settlement on plug-ins, 76.3 ± 1.2% and 42.5 ± 1.2% of the spats survived, respectively. Two hundred seventy (270) coral plug-ins were then transplanted at six sites. Transplanted corals exhibited varying survival in different sites, from 11 to 62%, five months post-transplantation. Thirty-one months post-transplantation, only two of the six sites had surviving transplanted corals, i.e., four colonies of Acropora millepora, three A. divaricata, and one A. cf. austera. However, setbacks in the survival of transplants highlight the need to further examine drivers affecting long term performance of coral transplants, which is vital in establishing different generations of parent colonies that can be used for sustainable mariculture of corals.

 

13. Torres JP, Lin Z, Fenton DS, Leavitt LU, Niu C, Lam P-Y, Robes JM, Pterson RT, Concepcion GP, Haygood MG, Olivera BM, Schmidt EW. (2020). Boholamide A, an APD-Class, Hypoxia-Selective CyclodepsipeptideJournal of Natural Products, 83 (4), Pages 1249-1257. more

Abstract:

Calcium homeostasis is implicated in some cancers, leading to the possibility that selective control of calcium might lead to new cancer drugs. On the basis of this idea, we designed an assay using a glioblastoma cell line and screened a collection of 1000 unique bacterial extracts. Isolation of the active compound from a hit extract led to the identification of boholamide A (1), a 4-amido-2,4-pentadieneoate (APD)-class peptide. Boholamide A (1) applied in the nanomolar range induces an immediate influx of Ca2+ in glioblastoma and neuronal cells. APD-class natural products are hypoxia-selective cytotoxins that primarily target mitochondria. Like other APD-containing compounds, 1 is hypoxia selective. Since APD natural products have received significant interest as potential chemotherapeutic agents, 1 provides a novel APD scaffold for the development of new anticancer compounds.

 

14. Tuo S -, Rodriguez IB, Ho T-. (2020). H2 accumulation and N2 fixation variation by ni limitation in cyanotheceLimnology and Oceanography, 65 (2), Pages 377-386. more

Abstract: 

Ni is an essential cofactor in NiFe‐uptake hydrogenase, an enzyme regulating H2 metabolism in diazotrophic cyanobacteria, the major H2 producers in the surface ocean globally. Here, we investigated the effect of Ni supply on H2 production and N2 fixation by using a model marine cyanobacterial diazotroph, Cyanothece . By mediating total dissolved Ni concentrations from 100 to 0.03 nmol L−1 in a trace metal‐defined culture medium, we demonstrated that Ni deficiency results in H2 accumulation, coupled with decreasing Ni quotas, growth rates, and occasionally relatively low N2 fixation rates. These results indicate that Ni deficiency limits the growth of the Cyanothece to some extent, considerably decreases H2 uptake by hydrogenase and leads to H2 accumulation and N2 fixation variation in the diazotroph. The findings show that Ni availability is a critical factor on controlling H2 production and N2 fixation in marine diazotrophic cyanobacteria. The information of Ni bioavailability for diazotrophic cyanobacteria is thus essential to evaluate the importance of Ni for H2 cycling and N2 fixation in oceanic surface waters.

 

15. Yñiguez AT, Lim PT, Leaw CP, Jipanin SJ, Iwataki M, Benico G. (2020). Over 30 years of HABs in the Philippines and Malaysia: What have we learned? Harmful Algae, 101776. Article in Press. more

Abstract: 

In the Southeast Asian region, the Philippines and Malaysia are two of the most affected by Harmful Algal Blooms (HABs). Using long-term observations of HAB events, we determined if these are increasing in frequency and duration, and expanding across space in each country. Blooms of Paralytic Shellfish Toxin (PST)-producing species in the Philippines did increase in frequency and duration during the early to mid-1990s, but have stabilized since then. However, the number of sites affected by these blooms continue to expand though at a slower rate than in the 1990s. Furthermore, the type of HABs and causative species have diversified for both toxic blooms and fish kill events. In contrast, Malaysia showed no increasing trend in the frequency of toxic blooms over the past three decades since Pyrodinium bahamense was reported in 1976. However, similar to the Philippines, other PST producers such as Alexandrium minutum and Alexandrium tamiyavanichii have become a concern. No amnesic shellfish poisoning (ASP) has been confirmed in either Philippines or Malaysia thus far, while ciguatera fish poisoning cases are known from the Philippines and Malaysia but the causative organisms remain poorly studied. Since the 1990s and early 2000s, recognition of the distribution of other PST-producing species such as species of Alexandrium and Gymnodinium catenatum in Southeast Asia has grown, though there has been no significant expansion in the known distributions within the last decade. A major more recent problem in the two countries and for Southeast Asia in general are the frequent fish-killing algal blooms of various species such as Prorocentrum cordatum, Margalefidinium polykrikoides, Chattonella spp., and unarmored dinoflagellates (e.g., Karlodinium australe and Takayama sp.). These new sites affected and the increase in types of HABs and causative species could be attributed to various factors such as introduction through mariculture and eutrophication, and partly because of increased scientific awareness. These connections still need to be more concretely investigated. The link to the El Niño Southern Oscillation (ENSO) should also be better understood if we want to discern how climate change plays a role in these patterns of HAB occurrences.

16. Yñiguez AT, Ottong ZJ. (2020). Predicting fish kills and toxic blooms in an intensive mariculture site in the Philippines using a machine learning model. Sci Total Environ, 707, 136173. more

Abstract: 

Harmful algal blooms (HABs) that produce toxins and those that lead to fish kills are global problems that appear to be increasing in frequency and expanding in area. One way to help mitigate their impacts on people's health and livelihoods is to develop early-warning systems. Models to predict and manage HABs typically make use of complex multi-model structures incorporating satellite imagery and frequent monitoring data with different levels of detail into hydrodynamic models. These relatively more sophisticated methods are not necessarily applicable in countries like the Philippines. Empirical statistical models can be simpler alternatives that have also been successful for HAB forecasting of toxic blooms. Here, we present the use of the random forest, a machine learning algorithm, to develop an early-warning system for the prediction of two different types of HABs: fish kill and toxic bloom occurrences in Bolinao-Anda, Philippines, using data that can be obtained from in situ sensors. This site features intensive and extensive mariculture activities, as well as a long history of HABs. Data on temperature, salinity, dissolved oxygen, pH and chlorophyll from 2015 to 2017 were analyzed together with shellfish ban and fish kill occurrences. The random forest algorithm performed well: the fish kill and toxic bloom models were 96.1% and 97.8% accurate in predicting fish kill and shellfish ban occurrences, respectively. For both models, the most important predictive variable was a decrease in dissolved oxygen. Fish kills were more likely during higher salinity and temperature levels, whereas the toxic blooms occurred more at relatively lower salinity and higher chlorophyll conditions. This demonstrates a step towards integrating information from data that can be obtained through real-time sensors into a an early-warning system for two different types of HABs. Further testing of these models through times and different areas are recommended.

 

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1. Armada, L., Dimalanta, C., Parcutela, N., Austria, R., Padrones, J., Payot, B., Queaño, K., and Yumul, G. Jr. (2020). Bouguer Anomaly of Central Cebu, Philippines. Journal of Maps,16 (2), Pages 577-584. DOI: 10.1080/17445647.2020.1791270more

Abstract:

Cebu Island in Central Philippines consists of a Cretaceous basement complex capped by mostly Tertiary sedimentary units. Recent mapping conducted in Central Cebu revealed limited exposures of lithologies, especially those comprising the basement complex. The gravity method was utilized to generate Bouguer anomaly maps for Central Cebu. These geophysical maps provide the first images of the subsurface extent of the basement units. A prominent nearly circular gravity anomaly high is consistently observed in the Bouguer anomaly maps coinciding with the location of dense basement and intrusive rocks. However, field mapping revealed the very limited surface exposure of these units. The gravity highs recognized in the residual anomaly maps may correspond to the larger extent of the intrusive units at depth. The broad gravity high observed in the regional anomaly map may define the extent of the subsurface distribution of the Cretaceous basement complex. 

2. Capule, M. C., David, C. P., Geronia, M.C. (2020). Estimating the long term leaching potential of PCBs in soil. Eurasian Journal of Soil Science, 9 (3), Pages 282-291. DOI: 10.18393/ejss.753279more

Abstract:

Polychlorinated Biphenyls (PCBs) are a group of man-made organic chemicals known as chlorinated hydrocarbons. PCBs were banned in 1979 due to its toxicity and persistence in the environment. Variations of PCBs were determined in soils and plants. Degradation of PCB Aroclors and congener patterns were investigated from known contaminated site at a former Military Air Base. PCB concentrations ranged between 17 - 1,040 µg L-1 at 0 - 0.5 m depth, between 36 - 898 µg L-1 at 1.0 - 1.5 m depth, between 20 - 73 µg L-1 at 4 m depth and 21 µg L-1 at 8 m depth. There is also a negative correlation between the mean of the Toxicity Characteristic Leaching Procedure (TCLP) of PCBs versus the sampling depth. Linear regression analyses were used to determine the correlation of the factors such as depth, Octanol/Water Partition Coefficient (Kow) and solubility affected Soil/Water Distribution Coefficient (Kd). Effects were found only when the soil depth is at 0.3 - 0.5 m (at 95% confidence level). Kd is positively correlated with Kow while Kd has some level of negative correlation with solubility. No effect was found at 1.0 - 1.5 m, 4.0 m, and 8.0 m. Organic Carbon/Water Partition Coefficient (Koc) showed high results exceeding the log Koc criteria of 4.5; as a result, this is now a matter of concern on the potential adverse effects of the substance on terrestrial organisms within its vicinity.

3. Castro, A. L.., Fernando, A. G. S., Peleo-Alampay, A. M., Javellana, G. R. R., Marquez, D. J. D., Nogot, J. R. C. P. (2020). Rare occurrence of Nautilus sp. Fossils from Batangas, PhilippinesPhilippine Journal of Science, 149 (3), Pages 495-501.more

Abstract:

Two nautilid (Cephalopoda, Mollusca) fossils are discovered from an exposure of the late Miocene – early Pliocene Calatagan Formation in Talim Point, Lian, Batangas, southwestern Luzon. They were identified as Nautilussp. because of the similarity in conch shape and sutures to those of extant species of Nautilus. The two Nautilus specimens were found in a fine- to medium-grained sandstone unit and observed to be associated with other macrofossils such as corals, gastropods, bivalves, brachiopods, and echinoids. The age of the Nautilus specimens was determined through the analysis of the planktonic foraminifera in the sandstone matrix. These specimens represent the oldest fossil record of Nautilus in the Philippines.

 

4. Dimalanta, C. B., Faustino-Eslava, D. V., Gabo-Ratio, J. A. S., Marquez, E. J., Padrones, J. T., Payot, B. D., Queaño, K. L., Ramos, N. T., Yumul, G. P. Jr. (2020). Characterization of the proto-Philippine Sea Plate: Evidence from the emplaced oceanic lithosphere fragments along eastern PhilippinesGeoscience Frontiers, 11 (1), Pages 3-21. https://doi.org/10.1016/j.gsf.2019.01.005 more

Abstract:

The proto-Philippine Sea Plate (pPSP) has been proposed by several authors to account for the origin of the Mesozoic supra-subduction ophiolites along the Philippine archipelagoIn this paper, a comprehensive review of the ophiolites in the eastern portion of the Philippines is undertaken. Available data on the geology, ages and geochemical signatures of the oceanic lithospheric fragments in Luzon (Isabela, Lagonoy in Camarines Norte, and Rapu-Rapu island), Central Philippines (Samar, Tacloban, Malitbog and Southeast Bohol), and eastern Mindanao (Dinagat and Pujada) are presented. Characteristics of the Halmahera Ophiolite to the south of the Philippines are also reviewed for comparison. Nearly all of the crust-mantle sequences preserved along the eastern Philippines share Early to Late Cretaceous ages. The geochemical signatures of mantle and crustal sections reflect both mid-oceanic ridge and supra-subduction signatures. Although paleomagnetic information is currently limited to the Samar Ophiolite, results indicate a near-equatorial Mesozoic supra-subduction zone origin. In general, correlation of the crust-mantle sequences along the eastern edge of the Philippines reveal that they likely are fragments of the Mesozoic pPSP.

 

5. Jabagat, K. D., Gabo-Ratio, J. A., Queaño, K. L., Yonezu, K., Dimalanta, C. B., Lee, Y-H., Yumul, G. P., Jr. (2020). Petrogenetic constraints on magma fertility in the Baguio Mineral District, Philippines: Probing the mineralization potential of the igneous host rocks in the Sangilo epithermal deposit. Ore Geology Reviews, 125, 103703. https://doi.org/10.1016/j.oregeorev.2020.103703more

Abstract:

In the Baguio Mineral District (BMD), porphyry Cu ± Au deposition and associated epithermal mineralization are attributed to the highly evolved magmatism during the Pliocene. It has been well-documented that the interaction between silicic crustal melts and primitive mantle melts formed water-rich, oxidized magmas that resulted to hydrothermal mineralization. However, there are very few studies on the Early to Middle Miocene calc-alkaline magmatism which is considered to be barren of mineralization. This magmatic event is represented by phases of the Central Cordillera Diorite Complex (CCDC), which also serve as host rocks to the Sangilo epithermal deposit. The Sangilo quartz-carbonate veins in the BMD are hosted by an Early Miocene hornblende diorite (22.33 ± 0.63 Ma) intruded by a Middle Miocene quartz diorite (15.91 ± 0.6 Ma) which are, in turn, penetrated by Pliocene basaltic andesite dikes. The Miocene magmatic units with hybrid crust-mantle source affinity were formed from varying degrees of interaction within the MASH (mixing, assimilation, storage, and homogenization) zone during the formation of the CCDC. The basaltic andesite dikes, part of the Pliocene Mafic Dike Complex, represent direct differentiates of basaltic melts that experienced ponding at the base of the lower crust before ascending to shallow crustal levels. Based on the assessment of the physico-chemical conditions, three distinct magmatic events were identified: a barren Early Miocene event, a fertile Middle Miocene event and a fertile Pliocene event. The Middle Miocene fertile magmatism is attributed to further development of the MASH zone under the Luzon arc from the Early to Middle Miocene. On the other hand, the enhanced fertility during the Pliocene is associated with the subduction of the Scarborough Ridge.

 

6. Labis, F. A.C., Payot, B. D., Valera, G. T. V., Pasco, J. A., Dycoco, J. M. A., Tamura, A., Morishita, T., & Arai, S. (2020). Melt-rock interaction in the subarc mantle: records from the plagioclase peridotites of the southern Palawan Ophiolite, Philippines. International Geology Reviewhttps://doi.org/10.1080/00206814.2020.1746930 more

Abstract:

The interaction between migrating melts and the upper mantle largely affects the composition of the ascending melt and residual peridotites. In island arcs, melt-rock interactions and products which involved highly depleted mantle peridotites are still largely undocumented despite their petrological importance. In this contribution, the petrographic and geochemical signatures of refractory and refertilized peridotites comprising the mantle section of the southern Palawan Ophiolite, Philippines are investigated. The peridotites are dominantly comprised of residual spinel harzburgites with minor dunite and plagioclase peridotites. Spinel harzburgites are similar to other highly depleted residual mantle materials of other suprasubduction zone ophiolites. Plagioclase peridotites, which are cut by gabbroic intrusions, preserve distinct petrological characteristics indicating melt-rock interaction. The melts preserved as gabbroic dikes have signatures transitional between mid-ocean ridge and island arc, and are comparable to back-arc basin lavas. We therefore propose that the plagioclase peridotites were formed due to the reaction between highly depleted mantle peridotites beneath an intraoceanic arc and migrating BABB-like magmas possibly during the incipient stages of back-arc rifting

 

7. Liu, H.-Q,, Yumul, G. P., Jr., Dimalanta, C. B., Queaño, K. Xia, X.-P., Peng, T.-P., Lan, J.-B., Xu, Y.-G., Guotana, J.M.R., Olfindo, V. S. (2020). Western Northern Luzon isotopic evidence of transition from Proto-South China Sea to South China Sea fossil ridge subductionTectonics, (39) 2, e2019TC005639. https://doi.org/10.1029/2019TC005639more

Abstract:

Temporal geochemical comparisons are conducted for representative magmatism from western Northern Luzon to reconstruct the Cenozoic tectonics. Oligo‐Pleistocene magmas from western Northern Luzon display elemental and Sr‐Nd‐Hf‐Pb‐O isotope geochemistry similar to intraoceanic arc magmatism, consistent with derivation from the mantle wedge, coupled with fractional crystallization. Specifically, the Oligo‐Miocene (~26.8–15.6 Ma) Central Cordillera diorite complex samples exhibit a negative correlation between Sr‐Nd isotopes, consistent with mantle metasomatism by fluids/melts released from pelagic sediments. The Mio‐Pleistocene samples (<~9 Ma) exhibit consistent 87Sr/86Sr ratios with variable εNd and partially overlap with those of Scarborough seamount basalts, consistent with mantle metasomatism by fluids/melts released from the Scarborough seamount basalts, which are being subducted beneath Northern Luzon with the South China Sea fossil ridge. Temporal changes in Sr‐Nd‐Hf‐Pb isotopes are also observed for the Taiwan‐Luzon arc magmatism. The Oligo‐Miocene (>~9 Ma) magmatism exhibit intraoceanic arc isotopic signatures, suggestive of a chemical imprint from subducted pelagic sediments. The Mio‐Pleistocene (<~9 Ma) lavas display enriched mantle‐type isotope compositions, consistent with an input of terrigenous sediment in the mantle. The temporal variations in Sr‐Nd‐Hf‐Pb isotopes for the Taiwan‐Luzon magmatism, combined with paleomagnetic evidence, mirror a transition from the Proto‐South China Sea to the South China Sea fossil ridge subduction beneath western Northern Luzon at ~9 Ma. In addition, this study also highlights the importance of relatively enriched components in the lower plate in the maturation of overriding juvenile oceanic crust in an arc‐continent collision system.

 

8. Lumongsod, R. M., Ramos, N. T. and Ramos, R. V. (2020). GIS-based spatial analysis of sinkholes in Cebu City, Philippines: Insights on sinkhole occurence and development. In Land, L., Kromhout, C. and Byle, M. J. (Eds.), Proceedings of the Sixteenth Multidisciplinary Conference on Sinkholes and the Engineering and Environmental Impacts of Karst (first edition) (pp. 362-370) National Cave and Karst Research Institute. more

Abstract:

In 2017, at least 770 sinkholes were reported to occur in Cebu City, a populated town in the Philippines dominantly underlain by karstic formations. In this study, the genesis and development of these sinkholes were related to various geomorphologic, geologic, and hydrologic factors in order to determine their influence on sinkhole distribution in the area using GIS-based spatial analyses. Results show that the sinkhole frequency varies with respect to the relative age of the underlying karstic formation, slope, and elevation. Most sinkholes occur on younger bedrock, low slope, and low elevation areas. However, sinkholes that occur on younger bedrock are significantly smaller in area than those in older bedrock; in terms of total area, the sum of the areas of sinkholes are greater on relatively older bedrock. Other factors found to influence sinkhole occurrence were lineaments and streams. GIS-based analyses of sinkholes such as those presented in this study are useful for sinkhole-susceptibility prediction and disaster risk reduction management efforts of communities.

9. Parcuela, N. E., Dimalanta, C.B., Armada, L. T., Yumul, G. P., Jr. (2020). PHILCRUST3.0: New constraints in crustal growth rate computations for the Philippine arc. Journal of Asian Earth Sciences, X, 100032.  https://doi.org/10.1016/j.jaesx.2020.100032more

Abstract:

A revised crustal thickness map for the Philippine island arc, PHILCRUST3.0, has been generated using new gravity data from the EGM2008. The gravity-derived crustal thickness is compared with crustal thickness estimates obtained using the Sr/Y ratios. PHILCRUST3.0 shows that crustal thickness in the Philippines varies from 13 to 33 km. The Philippine arc appears to be at its thinnest in areas underlain by ophiolites and young magmatic arcs. The resulting crustal thickness values are used to revisit the growth rates of the Philippine arc from magmatic and amagmatic contributions. Arc magmatism contributes more significantly to the growth of Philippine crust with rates from specific volcanoes varying from 5 to 35 km3/km/m.y. Despite being relatively young, magmatism associated with the volcanoes of the East Philippine Arc displayed a higher growth rate (32 km3/km/m.y.) compared to volcanoes belonging to older magmatic arcs in the archipelago. This is attributed to the more hydrated oceanic lithosphere subducting beneath the Philippine Trench. PHILCRUST3.0 provides the most complete crustal thickness map of the Philippines to date. This will enable the computation of crustal growth rate in areas within the Philippines where point gravity or geochemical data is not available.

 

10. Ratio, M. A., Gabo-Ratio, J. A., Fujimitsu, Y. (2020). Exploring public engagement and social acceptability of geothermal energy in the Philippines: A case study on the Makiling-Banahaw Geothermal Complex. Geothermics, 85: 101774. https://doi.org/10.1016/j.geothermics.2019.101774 more

Abstract:

The Makiling-Banahaw Geothermal Complex was one of the first two geothermal projects for exploration and development in the Philippines. The study aims to identify critical issues and supporting factors for geothermal energy projects in the Philippines by collecting and analyzing qualitative and quantitative data from various stakeholders of the Makiling-Banahaw Geothermal Complex. The case study reveals that stakeholders of barangays with geothermal facilities were agreeable to geothermal energy. Frequent periodic and strategic public engagement initiated by geothermal resource developers and local government can develop trust and improve integration of geothermal energy with the local communities.

 

11. Rodrigo, J. D., Gabo-Ratio, J. A. S., Queaño, K. L., Fernando, A. G. S., de Silva, L.P. Jr., Yonezu, K. Zhang, Y. (2020). Geochemistry of the late Cretaceous Pandan formation in Cebu Island, Central Philippines: sediment contributions from the Australian plate margin during the MesozoicThe Depositional Record (The journal of the International Association of Sedimentologists. https://doi.org/10.1002/dep2.103more

Abstract:

The Late Cretaceous Pandan Formation in Cebu Island is one of the oldest sedimentary units in the Central Philippines. The inconsistencies in geological descriptions and interpretation of the depositional environment of the Pandan Formation complicated efforts to determine the origin and tectonic history of the basement of Cebu Island. This study therefore looks into the petrological and geochemical characteristics of the Pandan Formation and their implications for the tectonic development of the Philippine Arc during the late Mesozoic. Petrographic analyses indicate significant contribution from mafic sources with additional inputs from felsic rocks, siliciclastics and metamorphic sources. Enrichment of detrital quartz from felsic volcanic and plutonic rocks, as well as from siliciclastic and metamorphic sources, has shifted the SiO2 composition of the Pandan clastics from a mafic to a more intermediate source. Whole‐rock geochemical analyses revealed low SiO2/Al2O3 = 4.21, low K2O/Na2O = 1.16, low Th/Sc = 0.13, low Th/U = 2.78, high La/Th = 4.51, significantly low REEs = ca 76.45 ppm and low LaN/YbN = 4.28. A slight negative chondrite‐normalized Eu/Eu* (0.91) anomaly and significantly high PAAS‐normalized positive Eu/Eu* (1.39) values are consistent with derivation from a young undissected magmatic arc terrane. Tectonic discrimination diagrams suggest formation in an oceanic island arc to active margin/collision zone modelled to be located at the oceanic leading edge of Australia. Rapid uplift and erosion of the magmatic arc and older allochthonous blocks gave way to the rapid deposition of the Pandan Formation in the Late Cretaceous at the subequatorial region.

 

12. Tiauzon, A., Peterson, J., Robles, E. C., Neri, L. A., Forestier, H., Titton, S., Manipon, D. R., Fernando, A. G., Mijares, A., Paz, V., Dizon , E. (2020). Unfolding the technological production strategies of the large toolkits across Philippine Paleolithic sites with specific reference to northern MindanaoQuaternary International,  535: 69-87. https://doi.org/10.1016/j.quaint.2018.10.037 more

Abstract:

For more than a half-century of research, the Philippine Paleolithic toolmaking has shown the persistence of the small-based flake tools. The bulk of the evidence comes from the excavation in caves and rock shelters. This paper presents the discovered open-sites in northern Mindanao that have large stone artifacts such as choppers and picks. These tools were produced with direct percussion on hard hammer initiated by wedge-flaking. Locally available cobble-sized materials were reduced with very low intensity led to the provisioning of the various tool forms. They are equipped with multiple functional edges trimmed as convex pointed and straight, intended for the heavy-duty tasks. The assemblage bears a striking resemblance to the core tools found in the Cagayan Valley Open Sites and to the well-known Paleolithic sites throughout Island Southeast Asia. This paper examines and describes the production sequences of the large stone tools as well as behavioral patterns in the reduction process.

 

13. Tupaz, C. A. J., Watanabe, Y., Sanematzu, K., Echigo, T., Arcilla, C., and Ferrer, C. (2020). Ni-Co mineralization in the Intex laterite deposit, Mindoro, Philippines. Minerals, 7 (10), Page 579. DOI:10.3390/min10070579more

Abstract:

The Intex laterite deposit in Mindoro, Philippines is derived from the weathering of the ultramafic rocks under a tropical climate. This study investigates the several types of serpentines and the effect of the degree of chemical weathering of ultramafic rocks and laterites on the enrichment of Ni in the deposit. The five types of serpentines are differentiated based on their textural features and Raman spectral data. Type I, type II, type III, and type IV serpentines contain a low amount of NiO (average 0.15 wt%), and their formation is linked to the previous exhumation of the ultramafic body. Conversely, type V serpentines show the highest NiO contents (average 1.42 wt%) and have the composition of serpentine-like garnierites, indicating a supergene origin. In the limonite horizon, goethite is the main ore mineral and shows high NiO contents of up to 1.68 wt%, whereas the Mn-oxyhydroxides (i.e., asbolane and lithiophorite–asbolane intermediate) display substantial amounts of CoO (up to 11.3 wt%) and NiO (up to 15.6 wt%). The Ultramafic Index of Alteration (UMIA) and Index of Lateritization (IOL) are used to characterize the different stages of weathering of rocks and laterites. The calculated index values correspond to a less advanced stage of weathering of the Intex laterites compared with the Berong laterites. The Berong deposit is a Ni-Co laterite deposit in the Philippines, which is formed from the weathering of the serpentinized peridotite. The less extreme degree of weathering of the Intex laterites indicates less advanced leaching, and thereby the re-distribution of Ni, Si, and Mg from the limonite towards the saprolite horizon may have resulted in the poor precipitation of talc-like (kerolite-pimelite) and sepiolite-like (sepiolite-falcondoite) phases in the studied saprolite horizon. Nickel in the Intex deposit has undergone supergene enrichment similar to other humid tropical laterite deposits.

 

14. Well-Accardo, J., Feuillet, N., Satake, K., Goto, T., Harada, T., Kayanne, H., Nakamura, M., Ramos, N., Saurel, J.-M., Sowa, K., Liu, S.-C., Yu, T.-L., Shen, C.-C. (2020). Relative sea-level changes over the past centuries in the Central Ryukyu Arc inferred from coral microatolls. Journal of Geophysical Research: Solid Earth 125(2): Article number e2019JB018466. https://doi.org/10.1029/2019JB018466 more

Abstract:

This study focuses on Okinawa and Yoron islands, in order to better understand tectonics in the Ryukyu Arc related to the subduction zone. We used coral microatolls—known for their centimetric accuracy in the record of relative sea-level (RSL) changes—to reconstruct RSL changes over the last century from living microatolls. A fossil microatoll in Yoron was used to discuss possible RSL changes beyond the last century. The signal consists of emergence whose rate varies through time, interrupted by decadal to multidecadal periods of sudden and/or gradual submergence and by interannual sea-level falls. Comparison with other existing RSL records in the arc highlights RSL variability along the arc. This pattern contrasts with the homogeneous and linear absolute regional sea-level rise, implying that this latter signal cannot fully explain our observations and that an additional process is required. We suggest the subduction zone as a possible source for generating centimetric scale RSL changes observed in coral microatolls. We tested how the Ryukyu megathrust could explain our observations with elastic dislocation modeling. The emergence trend could be explained by interseismic loading on the plate interface with a minimum coupling rate of 25%, which is higher than previous estimates based on short instrumental records. As for the submergence events that occurred regularly in the coral record, we show that they could be explained by slow slip events on the shallower part of the megathrust or in the transition zone. Such process could accommodate a significant part of the total convergence.

 

15. Yu, M., Dilek, Y., Yumul, G. P., Jr., Yan, Y., Dimalanta, C. B., Huang, C.-Y.(2020). Slab-controlled elemental-isotopic enrichments during subduction initiation magmatism and variations in forearc chemostratigraphy. Earth and Planetary Science Letters, 538: 11617. DOI: 10.1016/j.epsl.2020.116217 more

Abstract:

Supra-subduction zone (SSZ) ophiolites formed in forearc settings and the Izu–Bonin–Mariana (IBM) in-situ forearc show conversions from normal mid-ocean ridge basalt (MORB) to boninitic affinities, which are widely interpreted as rules for the evolving chemical geodynamics of subduction initiation magmatism (SIM). Nevertheless, forearc sequence generated by subduction initiation need not always include boninitic rocks. Here we reconstruct a forearc chemostratigraphy without boninitic affinity based on the Central Palawan and Amnay (CPA) ophiolites of the west Philippines to show diversity in melt evolution of SIM. Zircon U–Pb dating on the MORB-type Amnay gabbros reveal a 10 m.y. of seafloor spreading from 33 to 23 Ma. These ages together with the progressively enriched zircon in-situ oxygen isotopes (δ18O= 1.62–10.1‰) and whole rock elemental and Nd–Hf isotopic signatures ([La/Yb]N= 0.19–3.45; Nb/Yb= 0.07–5.24; εNd= 2.1–10.2; εHf= 11.2–24.1) indicate that the depleted MORB mantle (DMM)-type source of the Amnay ophiolite was getting enriched by fluxing of aqueous slab fluid in the early stage followed by addition of adakitic and Nb-enriched slab melts in the later stage. This distinct mantle evolution together with higher εHf at a given εNd of the Amnay mafic samples than the contemporaneous South China Sea (SCS) oceanic samples do not support previous interpretation that the Amnay ophiolite was a fragment of the SCS. However, the 33–23 Ma Amnay ophiolite can be the younger part of the 34 Ma forearc-type Central Palawan ophiolite, and both (i.e. the CPA ophiolites) represent on-land fragments of the NW Sulu Sea. We propose that the 34–23 Ma CPA ophiolites and the NW Sulu Sea constitute forearc basin of the late Oligocene–middle Miocene island arc–backarc basin duo of the Cagayan Ridge and SE Sulu Sea, associated with subduction of the Cretaceous to Eocene Proto-SCS since 34 Ma. The CPA ophiolites lack boninite but show geochemical progression from normal to enriched MORB affinities, whose melt evolution differs from that of the IBM SIM. We attribute the differences in SIM and variations in forearc chemostratigraphy to the subduction of a younger slab with thick terrigenous sediment cover of the Proto-SCS versus an older slab with thin pelagic sediment cover of the Pacific Plate.

 

16. Yumul, Graciano P., Jr., Armada, L. T., Gabo-Ratio, J. A. S., Dimalanta, C. B., Austria, R. S. P. (2020).  Subduction with arrested volcanism: Compressional regime in volcanic arc gap formation along east Mindanao, Philippines. Journal of Asian Earth Sciences: X: 10030. https://doi.org/10.1016/j.jaesx.2020.100030 more

Abstract:

The eastern portion of the Philippine island arc system, from the Bicol Peninsula through Leyte island to the Pacific Cordillera of east Mindanao, is the overriding plate underneath which the West Philippine Basin (part of the Philippine Sea Plate) and Palau Basin oceanic plates subduct along the Miocene-Pliocene to present-day Philippine Trench. Southward younging of the trench, coupled with the presence of the left-lateral Philippine Fault Zone parallel to it, is recognized. Young volcanic centers (<7Ma to present) are well-developed in the Bicol Peninsula and in Leyte island but not in the Pacific Cordillera. There are only two volcanic centers that are exposed in the Pacific Cordillera, the Paco volcanic center in the north and the Leonard Kniassef in the south. There is a 250 km volcanic arc gap distance between the two volcanic centers. Reported inland and offshore geologic structures, from onramp structures to thrust faults, and strain rate computations suggest a predominantly compressional regime in the Pacific Cordillera from the Miocene to the present. This is consistent with the hinge advance character of the Philippine Trench and the recognized E-W directed σ1 in this part of the island arc system. It is forwarded that the prevailing compressional regime inhibited the extrusion of lavas leading to the non-formation of surficial volcanic centers between the Paco and Leonard Kniassef volcanic centers. Furthermore, the compression can also partly account for the presence of porphyry copper deposits in this part of Mindanao.

 

17. Yumul. G. P. Jr., Dimalanta, C. B., Gabo-Ratio, J. A. S., Armada, L. T., Queaño, K. L., Jabagat, K. D. (2020). Mineralization parameters and exploration targeting for gold – copper deposits in the Baguio (Luzon) and Pacific Cordillera (Mindanao) Mineral Districts, Philippines: A reviewJournal of Asian Earth Sciences, 191.  https://doi.org/10.1016/j.jseaes.2020.104232more

Abstract:

The Baguio Mineral District in Luzon, Philippines is known to host several world-class epithermal gold – porphyry copper deposits. The interplay of tectonic setting, magma composition, structural control and hydrothermal systems contributed to the generation of these deposits. Ridge subduction (Scarborough seamount) resulting to flat subduction and a transpressional regime could also be related to the formation of epithermal gold - porphyry copper deposits in Baguio. Subduction processes leading to the formation of calc-alkaline rocks associated with high water pressure, oxygen fugacity and late sulfur saturation are almost always associated with the gold-copper deposits in the district. Compared to the Baguio Mineral District, less exploration work, mine development and production were done in the Pacific Cordillera Mineral District, Mindanao in southern Philippines. It is worth noting, however, that both mineral districts show similarities and overlapping features in terms of geological, geophysical and geochemical characteristics. This leads one to conclude that the Pacific Cordillera Mineral District has ore deposits waiting to be discovered.

 

18. Yumul, G.P., Jr., Dimalanta, C.B., Gabo-Ratio, J.A. S., Queaño, K. L., Armada, L. T., Padrones, J. T., Faustino-Eslava, D. V., Payot, B. D., Marquez, E. J. (2020). Mesozoic rock suites along western Philippines: Exposed proto-South China Sea fragments. Journal of Asian Earth Sciences: X: 100031. https://doi.org/10.1016/j.jaesx.2020.100031 more

Abstract: 

An ancient oceanic crustal leading edge east of mainland Asia, the proto-South China Sea crust, must have existed during the Mesozoic based on tectonic reconstructions that accounted for the presence of subducted slabs in the lower mantle and the exposed oceanic lithospheric fragments strewn in the Philippine and Bornean regions. Along the western seaboard of the Philippine archipelago, numerous Mesozoic ophiolites and associated lithologies do not appear to be genetically associated with the younger Paleogene-Neogene ocean basins that currently surround the islands. New sedimentological, paleomagnetic, paleontological, and isotopic age data that we generated are presented here, in combination with our previous results and those of others, to reassess the geological make-up of the western Philippine island arc system. We believe that the oceanic lithospheric fragments, associated melanges, and sedimentary rocks in this region are exhumed slivers of the proto-South China Sea ocean plate.

 

19. Yumul, G. P., Jr., Dimalanta, C. B., Salapare, R. C., Queño, K. L., Faustino-Eslava, D. V., Marquez, E. J., Ramos, N. T., Payot, B. D., Guotana, J. M. R., Gabo-Ratio, J. A. S., Armada, L. T., Padrones, J. T., Ishida, K., Suzuki, S. (2020). Slab rollback and microcontinent subduction in the evolution of the Zambales Ophiolite Complex (Philippines): A reviewGeoscience Frontiers, 11 (1), Pages 22-36. https://doi.org/10.1016/j.gsf.2018.12.008more

Abstract:

New radiolarian ages show that the island arc-related Acoje block of the Zambales Ophiolite Complex is possibly of Late Jurassic to Early Cretaceous age. Radiometric dating of its plutonic and volcanic-hypabyssal rocks yielded middle Eocene ages. On the other hand, the paleontological dating of the sedimentary carapace of the transitional mid-ocean ridge – island arc affiliated Coto block of the ophiolite complex, together with isotopic age datings of its dikes and mafic cumulate rocks, also yielded Eocene ages. This offers the possibility that the Zambales Ophiolite Complex could have: (1) evolved from a Mesozoic arc (Acoje block) that split to form a Cenozoic back-arc basin (Coto block), (2) through faulting, structurally juxtaposed a Mesozoic oceanic crust with a younger Cenozoic lithospheric fragment or (3) through the interplay of slab rollback, slab break-off and, at a later time, collision with a microcontinent fragment, caused the formation of an island arc-related ophiolite block (Acoje) that migrated trench-ward resulting into the generation of a back-arc basin (Coto block) with a limited subduction signature. This Meso-Cenozoic ophiolite complex is compared with the other oceanic lithosphere fragments along the western seaboard of the Philippines in the context of their evolution in terms of their recognized environments of generation.

 

nimbb

1. Barbosa, C.F.C., Koh, R.B.L., Aquino, V.M. and Galvez, L.C. (2020). Accurate Diagnosis of Multicomponent Babuviruses Infecting Abaca by Simultaneous Amplification of their Genome Segments. Philippine Journal of Science, 149 (2), Pages 373-382.more

Abstract:

Abaca bunchy top virus and banana bunchy top virus (ABTV and BBTV; genus Babuvirus; Family: Nanoviridae) are two of the most destructive abaca viruses. Uniplex polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) are nucleic acid amplification techniques (NAATs) currently being used for their detection and diagnosis. However, the multicomponent nature of these bunchy top viruses has been documented to affect the diagnostic sensitivity of the aforementioned techniques, resulting in false-negative detection. This study, therefore, aimed to develop an assay that is strategic for accurate diagnosis of these multicomponent viruses. The multiplex PCR method was optimized at 56.5 °C annealing temperature (TA), and was evaluated to have 91–100% diagnostic sensitivity and diagnostic specificity (CI = 95%, n = 60) against ABTV and BBTV – more accurate than LAMP and uniplex PCR. This paper provides evidence on the effect of the multicomponent nature of ABTV and BBTV in their detection even on techniques with superior analytical sensitivity such as LAMP.  Moreover, it provides a strategic diagnostic tool to circumvent difficulties in the diagnosis of multicomponent abaca viruses.

 

2. Bascos, N.A.D.,  Craig, P.A.,  Lapeña, J.F.F. Jr.,  Ortiz, P.,  Yu, G.F.B.,  Macaulay, J.O.  (2020). Publishing in education: A parallel session at the IUBMB/PSBMB 2019 “Harnessing Interdisciplinary Education in Biochemistry and Molecular Biology” conferenceBiochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.21455more

Abstract:

Ensuring currency with trends, knowledge, and understanding of teaching and learning is essential for all educators. Researching learning and teaching is an enormous field which can range from examining the practical impact of new classes to research into the processes of learning. The “Publishing in Education” conference session discussed some of the approaches and outcomes of researching and publishing in education.

 

3. Boonchuen, P., Maralit, B.A., Jaree, P., Tassanakajon, A., Somboonwiwat, K. (2020). MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticusScientific Reports, 10 (787), https://doi.org/10.1038/s41598-019-57409-4 more

Abstract:

While Vibrio parahaemolyticus (VPAHPND) has been identified as the cause of early mortality syndrome (EMS) or acute hepatopancreatic necrosis disease (AHPND) in shrimp, mechanisms of host response remain unknown. Understanding these processes is important to improve farming practices because this understanding will help to develop methods to enhance shrimp immunity. Pre-treatment of shrimp with 5-minute chronic non-lethal heat stress (NLHS) for 7 days was found to significantly increase Litopenaeus vannamei survival against VPAHPND infection. To elucidate the mechanism involved, mRNA and miRNA expression profiles from the hemocyte of L. vannamei challenged with VPAHPND after NLHS with corresponding control conditions were determined by RNA-Seq. A total of 2,664 mRNAs and 41 miRNAs were differentially expressed after the NLHS treatment and VPAHPND challenge. A miRNA-mRNA regulatory network of differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) was subsequently constructed and the interactions of DEMs in regulating the NLHS-induced immune-related pathways were identified. Transcriptomic data revealed that miRNA and mRNA interactions contribute to the modulation of NLHS-induced immune responses, such as the prophenoloxidase-activating system, hemocyte homeostasis, and antimicrobial peptide production, and these responses enhance VPAHPND resistance in L. vannamei.

 

4. Gibbons, J.A., Garcia, R.L., Craig, P.A., Yu, G.F.B., Macaulay, J.O. (2020). Laboratory classes in biochemistry and molecular biology: A parallel session at the IUBMB/PSBMB 2019 “Harnessing Interdisciplinary Education in Biochemistry and Molecular Biology” conference. Biochemistry and Molecular Biology Education. DOI: 10.1002/bmb.21436more

Abstract:

Laboratory classes are a central element of all biochemistry and molecular biology programs. These play a role in developing students' hands‐on and technical skills and also offer much more. The design of laboratory classes depends on many factors including the programs the students are enrolled in, the level they are at, employment destinations, and learning outcomes. This conference session considered the design and outcomes of laboratory experiences for undergraduate students.

 

5. Itang, L.A.M., Stec, D., Mapalo, M.A., Mirano-Bascos, D. & Michalczyk, L. (2020). An integrative description of Mesobiotus dilimanensis, a new tardigrade species from the Philippines (Eutardigrada: Macrobiotidae: furciger group)Raffles Bulletin of Zoology, 68, Pages 19–31 DOI:10.26107/RBZ-2020-0003 more

Abstract:

In this study, a new species of the Mesobiotus furciger group from Diliman, Quezon City, Philippines was identified using an integrative taxonomy approach. Morphological and morphometric data obtained through phase and Nomarski contrast microscopy and scanning electron microscopy along with molecular analyses of the DNA sequences of four molecular markers (18S rRNA, 28S rRNA, ITS-2, and COI) support the erection of Mesobiotus dilimanensis, new species. The new species is the third limno-terrestrial tardigrade species from the Philippines described as new to science and is the first member of the Mesobiotus furciger species complex described using an integrative taxonomy approach in the country.

 

6. Galvez, L.C., Barbosa, C.F.C., Koh, R.B.L., Aquino, V.M. (2020). Loop-mediated isothermal amplification (LAMP) assays for the detection of abaca bunchy top virus and banana bunchy top virus in abacaCrop Protection, 131. DOI: 10.1016/j.cropro.2020.105101 more

Abstract:

Abaca bunchy top virus (ABTV) and banana bunchy top virus (BBTV) are pathogens that infect abaca in the Philippines causing significant reduction in abaca fiber yield and quality. In this study, a sensitive loop-mediated isothermal amplification (LAMP) assay was developed for detecting ABTV and BBTV in abaca, Musa textilis Nee. Five primer sets were designed and tested to detect ABTV while three primer sets were designed and tested to detect BBTV. Out of which only one primer set for each virus was specific to their respective targets that is DNA-N for ABTV and DNA-S for BBTV for successful LAMP based detection applications. The concentrations of Bst DNA polymerase, dNTPs, incubation time and temperature were optimized for both viruses using either GelRed™ or SYBR™ Green I as detection dyes. The ABTV and BBTV LAMP assays were more sensitive than conventional PCR and were able to detect ABTV or BBTV in asymptomatic abaca samples. The developed LAMP protocols provide a simple, fast and accurate detection method that will be indispensable for the production of ABTV- and BBTV-free abaca tissue cultured plantlets. This is the first report of a LAMP-based assay for detection of ABTV and BBTV in abaca.

 

7. Galvez, L. C., Koh, R. B. L., Barbosa, C. F. C., Aquino, V. M. (2020). Multiplex reverse transcription-polymerase chain reaction for simultaneous detection of banana bract mosaic virus (BBrMV) and sugarcane mosaic virus (SCMV) in abacaCanadian Journal of Plant Pathology, DOI: 10.1080/07060661.2019.1708810 more

Abstract:

The abaca (Musa textilis Nee) is an important fibre crop in the Philippines. Its fibre yield and quality is severely impacted by two potyviruses, namely, banana bract mosaic virus (BBrMV) and sugarcane mosaic virus (SCMV). A multiplex RT-PCR assay was developed for the simultaneous detection of these two RNA viruses in abaca. Primer sets were designed to amplify fragments of BBrMV coat protein (743 bp), SCMV coat protein (595 bp) and Musa sp. elongation factor 1 (219 bp) as an internal control. The specificity of each primer pair was confirmed by cloning and sequencing of the RT-PCR products. The multiplex RT-PCR assay was optimized by varying primer concentration combinations, dNTP concentration, Mg2+ concentration, Taq polymerase concentration, annealing temperature and extension temperature. The developed multiplex RT-PCR protocol has the same level of sensitivity and specificity when compared with uniplex RT-PCR detection for each virus and internal control. The inclusion of internal control amplification eliminates the risk of obtaining false negative results. The use of the optimized multiplex RT-PCR in simultaneous detection of BBrMV and SCMV from field samples proves that it is reliable, robust and faster than uniplex RT-PCR detection of each virus. This method will be useful for large-scale surveys of these two RNA viruses in abaca and will be vital for epidemiological studies and disease prevention.

 

8. Ghodsinia, A.A., Lego, J.M.T, and Garcia, R.L. (2020). Mutation-Associated Phenotypic Heterogeneity in Novel and Canonical PIK3CA Helical and Kinase Domain Mutants. Cells, 9 (5), 1116; https://doi.org/10.3390/cells9051116 more

Abstract:

Phosphatidylinositol 3-kinase, catalytic subunit alpha (PIK3CA) is an oncogene often mutated in colorectal cancer (CRC). The contribution of PIK3CA mutations in acquired resistance to anti-epidermal growth factor receptor (EGFR) therapy is well documented, but their prognostic and predictive value remain unclear. Domain- and exon-specific mutations are implicated in either favorable or poor prognoses, but there is paucity in the number of mutations characterized outside of the mutational hotspots. Here, two novel non-hotspot mutants—Q661K in exon 13 and C901R in exon 19—were characterized alongside the canonical exon 9 E545K and exon 20 H1047R mutants in NIH3T3 and HCT116 cells. Q661K and E545K both map to the helical domain, whereas C901R and H1047R map to the kinase domain. Results showed variable effects of Q661K and C901R on morphology, cellular proliferation, apoptosis resistance, and cytoskeletal reorganization, with both not having any effect on cellular migration. In comparison, E545K markedly promoted proliferation, survival, cytoskeletal reorganization, migration, and spheroid formation, whereas H1047R only enhanced the first three. In silico docking suggested these mutations negatively affect binding of the p85 alpha regulatory subunit to PIK3CA, thereby relieving PIK3CA inhibition. Altogether, these findings support intra-domain and mutation-specific variability in oncogenic readouts, with implications in degree of aggressiveness.

 

9. Koh, R.B.L., Barbosa, C.F.C., Aquino, V.M., Galvez, L.C. (2020). Rapid, simple detection of banana bract mosaic virus in abaca using a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Journal of General Plant Pathology. https://doi.org/10.1007/s10327-020-00949-9more

Abstract:

Banana bract mosaic virus (BBrMV) causes one of the major viral diseases of the fiber crop abaca at a great economic loss in the Philippines. A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect BBrMV. A set of six primer pairs was designed based on the conserved coat protein gene sequences of BBrMV. The RT-LAMP can be completed in 30 min and was 100,000-fold more sensitive than RT-PCR. The RT-LAMP assay is suitable for field detection of BBrMV using crude RNA extracts and fluorescent DNA intercalating dyes that produce easily visualized results.

 

10. Koh, R.B.L., Zaulda, F.A.D.L.C.,  Barbosa, C.F.C., Aquino, V.M., Galvez, L.C. (2020). Immunodiagnosis of bunchy top viruses in abaca with polyclonal antibodies against their recombinant coat proteinsArchives of Phytopathology and Plant Protection, DOI: 10.1080/03235408.2020.1727106 more

Abstract:

Polyclonal antibodies against abaca bunchy top virus (ABTV) and banana bunchy top virus (BBTV) proteins are necessary for immuno-based detection of these two viruses in abaca (Musa textilis Nee). In this study, recombinant bunchy top viral coat proteins fused with a 6xHis tag at the N-terminus were expressed in E. coli BL21StarTM(DE3)pLysS strain and purified under denaturing conditions. Purified recombinant ABTV and BBTV coat proteins were used as antigens for the production of rabbit polyclonal antibodies. IgG was purified and evaluated by Direct Antigen Coating (DAC)-ELISA and further optimized by testing primary to secondary antibody dilution combinations. Analysis of ABTV and BBTV-infected abaca samples using the optimized DAC-ELISA assay showed that the anti-ABTV CP IgG can react to BBTV and that anti-BBTV CP IgG can react to ABTV, hence, a cross-reaction. The study demonstrates the advantage of using recombinant DNA technology for mass production of antigens for antibody production. Although specificity of the polyclonal antibodies may have been compromised when renatured recombinant proteins were used as immunogens, the ability of the purified IgGs to detect positive abaca samples reveals that the DAC-ELISA can be routinely used for screening disease-free abaca planting materials.

 

11. Kregel, S., Bagamasbad, P., He, S., LaPensee, E., Raji, Y., Brogley, M., Chinnaiyan, A., Cieslik, M., Robins, D.M. (2020). Differential modulation of the androgen receptor for prostate cancer therapy depends on the DNA response elementNucleic Acids Research, gkaa178, https://doi.org/10.1093/nar/gkaa178 more

Abstract:

Androgen receptor (AR) action is a hallmark of prostate cancer (PCa) with androgen deprivation being standard therapy. Yet, resistance arises and aberrant AR signaling promotes disease. We sought compounds that inhibited genes driving cancer but not normal growth and hypothesized that genes with consensus androgen response elements (cAREs) drive proliferation but genes with selective elements (sAREs) promote differentiation. In a high-throughput promoter-dependent drug screen, doxorubicin (dox) exhibited this ability, acting on DNA rather than AR. This dox effect was observed at low doses for multiple AR target genes in multiple PCa cell lines and also occurred in vivo. Transcriptomic analyses revealed that low dox downregulated cell cycle genes while high dox upregulated DNA damage response genes. In chromatin immunoprecipitation (ChIP) assays with low dox, AR binding to sARE-containing enhancers increased, whereas AR was lost from cAREs. Further, ChIP-seq analysis revealed a subset of genes for which AR binding in low dox increased at pre-existing sites that included sites for prostate-specific factors such as FOXA1. AR dependence on cofactors at sAREs may be the basis for differential modulation by dox that preserves expression of genes for survival but not cancer progression. Repurposing of dox may provide unique opportunities for PCa treatment.

 

12. Mapalo, M.A., Arakawa, K., Baker, C.M., Persson, D.K., Mirano-Bascos, D., Giribet, G. (2020). The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across EcdysozoaG3: Genes, Genomes, Genetics, 10 (1), DOI: 10.1534/g3.119.400734 more

Abstract:

Tardigrades are microscopic animals known to withstand unfavorable abiotic conditions. These animals are also constantly exposed to biotic stresses, including parasites and internal microbiomes. However, the tardigrade immune mechanisms against these biotic stresses are largely uncharacterized. Due to the contentious phylogenetic position of tardigrades, it is not intuitive whether they possess an immune system more similar to that of arthropods (e.g., Toll, Imd, and JNK pathways of the Drosophila melanogaster antimicrobial response) or to that of nematodes (e.g., the Tir-1/Nsy-1/Sek-1/Pmk-1/Atf-7 signaling cassette [called Tir-1 pathway here]) in Caenorhabditis elegans). In this study, comparative genomic analyses were conducted to mine homologs of canonical D. melanogaster and C. elegans immune pathway genes from eight tardigrades (Echiniscoides cf. sigismundi, Echiniscus testudo, Hypsibius exemplaris, Mesobiotus philippinicus, Milnesium tardigradum, Paramacrobiotus richtersi, Richtersius cf. coronifer, and Ramazzottius varieornatus) and four non-arthropod ecdysozoans (two onychophorans: Epiperipatus sp. and Opisthopatus kwazululandi; one nematomorph: Paragordius varius; and one priapulan: Priapulus caudatus) in order to provide insights into the tardigrade antimicrobial system. No homologs of the intracellular components of the Toll pathway were detected in any of the tardigrades examined. Likewise, no homologs of most of the Imd pathway genes were detected in any of the tardigrades or any of the other non-arthropod ecdysozoans. Both the JNK and Tir-1 pathways, on the other hand, were found to be conserved across ecdysozoans. Interestingly, tardigrades had no detectable homologs of NF-κB, the major activator of antimicrobial response gene expression. Instead, tardigrades appear to possess NF-κB distantly related NFAT homologs. Overall, our results show that tardigrades have a unique gene pathway repertoire that differs from that of other ecdysozoans. Our study also provides a framework for future studies on tardigrade immune responses.

 

13. Maruyama, H., Prieto, E., Nambu, T., Mashimo, C., Kashiwagi, K., Okinaga, T., Atomi, H. and Takeyasu, K. (2020). Different Proteins Mediate Step-Wise Chromosome Architectures in Thermoplasma acidophilum and Pyrobaculum calidifontis. Front. Microbiol. 11, 1247. doi: 10.3389/fmicb.2020.01247 more

Abstract:

Archaeal species encode a variety of distinct lineage-specific chromosomal proteins. We have previously shown that in Thermococcus kodakarensis, histone, Alba, and TrmBL2 play distinct roles in chromosome organization. Although our understanding of individual archaeal chromosomal proteins has been advancing, how archaeal chromosomes are folded into higher-order structures and how they are regulated are largely unknown. Here, we investigated the primary and higher-order structures of archaeal chromosomes from different archaeal lineages. Atomic force microscopy of chromosome spreads out of Thermoplasma acidophilum and Pyrobaculum calidifontis cells revealed 10-nm fibers and 30–40-nm globular structures, suggesting the occurrence of higher-order chromosomal folding. Our results also indicated that chromosome compaction occurs toward the stationary phase. Micrococcal nuclease digestion indicated that fundamental structural units of the chromosome exist in T. acidophilum and T. kodakarensis but not in P. calidifontis or Sulfolobus solfataricus. In vitro reconstitution showed that, in T. acidophilum, the bacterial HU protein homolog HTa formed a 6-nm fiber by wrapping DNA, and that Alba was responsible for the formation of the 10-nm fiber by binding along the DNA without wrapping. Remarkably, Alba could form different higher-order complexes with histone or HTa on DNA in vitro. Mass spectrometry detected HTa and Rad50 in the T. acidophilum chromosome but not in other species. A putative transcriptional regulator of the AsnC/Lrp family (Pcal_1183) was detected on the P. calidifontis chromosome, but not on that of other species studied. Putative membrane-associated proteins were detected in the chromosomes of the three archaeal species studied, including T. acidophilum, P. calidifontis, and T. kodakarensis. Collectively, our data show that Archaea use different combinations of proteins to achieve chromosomal architecture and functional regulation.

 

14. Mojica, C.A.R., Ybañez, W.S., Olarte, K.C.V., Poblete, A.B.C., Bagamasbad, P.D. (2020). Differential Glucocorticoid-Dependent Regulation and Function of the ERRFI1 Gene in Triple-Negative Breast Cancer. Endocrinology, 161 (7), bqaa082. https://doi.org/10.1210/endocr/bqaa082 more

Abstract:

Glucocorticoids (GCs; eg, hydrocortisone [CORT]) are routinely used as chemotherapeutic, anti-emetic, and palliative agents in breast cancer (BCa) therapy. The effects of GC signaling on BCa progression, however, remain a contentious topic as GC treatment seems to be beneficial for receptor-positive subtypes but elicits unfavorable responses in triple-negative BCa (TNBC). The mechanistic basis for these conflicting effects of GC in BCa is poorly understood. In this study, we sought to decipher the molecular mechanisms that govern the GC-dependent induction of the tumor suppressor ERRFI1 gene, an inhibitor of epidermal growth factor receptor (EGFR) signaling, and characterize the role of the GC-ERRFI1 regulatory axis in TNBC. Treatment of TNBC cell lines with a protein synthesis inhibitor or GC receptor (GR) antagonist followed by gene expression analysis suggests that ERRFI1 is a direct GR target. Using in silico analysis coupled with enhancer-reporter assays, we identified a putative ERRFI1 enhancer that supports CORT-dependent transactivation. In orthogonal assays for cell proliferation, survival, migration, and apoptosis, CORT mostly facilitated an oncogenic phenotype regardless of malignancy status. Lentiviral knockdown and overexpression of ERRFI1 showed that the CORT-enhanced oncogenic phenotype is restricted by ERRFI1 in the normal breast epithelial model MCF10A and to a lesser degree in the metastatic TNBC line MDA-MB-468. Conversely, ERRFI1 conferred pro-tumorigenic effects in the highly metastatic TNBC model MDA-MB-231. Taken together, our findings suggest that the progressive loss of the GC-dependent regulation and anti-tumorigenic function of ERRFI1 influences BCa progression and may contribute to the unfavorable effects of GC therapy in TNBC.

 

15. Roquid, K.R., Alcantara, K.M., Garcia, R.L. (2020). Identification and validation of mRNA 3'untranslated regions of DNMT3B and TET3 as novel competing endogenous RNAs of the tumor suppressor PTENInternational Journal of Oncology, 56, Pages 544-558. https://doi.org/10.3892/ijo.2019.4947 more

Abstract:

PTEN inactivation is a frequent event in oncogenesis. Multiple regulatory mechanisms such as promoter hypermethylation, antisense regulation, histone modifications, targeting by microRNAs (miRNAs/miRs) and regulation by transcription factors have all been shown to affect the tumor suppressor functions of PTEN. More recently, the functional involvement of competing endogenous RNAs (ceRNAs) in miRNA‑dependent and coding‑independent regulation of genes shed light on the highly nuanced control of PTEN expression. The present study has identified and validated DNA methyltransferase 3β (DNMT3B) and TET methylcytosine dioxygenase 3 (TET3) as novel ceRNAs of PTEN, with which they share multiple miRNAs, in HCT116 colorectal cancer cells. miR‑4465 was identified and characterized as a miRNA that directly targets and regulates all 3 transcripts via their 3'untranslated regions (3'UTRs) through a combination of luciferase reporter assays, abrogation of miRNA response elements (MREs) via site‑directed mutagenesis, target protection of MREs with locked nucleic acids, RT‑qPCR assays and western blot analysis. Competitive miRNA sequestration was demonstrated upon reciprocal 3'UTR overexpression and siRNA‑mediated knockdown of their respective transcripts. Overexpression of DNMT3B or TET3 3'UTR promoted apoptosis and decreased migratory capacity, potentially because of shared miRNA sequestration and subsequent activation of PTEN expression. Knockdown of TET3 and DNMT3B decoupled their protein‑coding from miRNA‑dependent, coding‑independent functions. Furthermore, the findings suggested that the phenotypic outcome of ceRNAs is dictated largely by the number of shared miRNAs, and predictably, by the existence of other ceRNA networks in which they participate. Taken together, the findings of the present study identified DNMT3B and TET3 as novel ceRNAs of PTEN that may impact its dose‑sensitive tumor suppressive function.

 

16. Tan, A.P.S., Hedreyda, C.T. (2020). Sequence Analysis and Cloning of Alkane 1-monooxygenase and Catechol 1,2-dioxygenase Genes from Acinetobacter baumannii Isolated from the Philippine Pasig River. Philippine Journal of Science, 149 (1), Pages 159-168. more

Abstract:

Accidental fuel oil spills and improper disposal of toxic waste oil into waterways have caused serious pollution problems worldwide. This study is focused on the use of microorganisms and enzymes they produce to address problems of waste oil pollution. Complete genes for enzymes alkane 1-monooxygenase (AlkM) and catechol 1,2-dioxygenase (CatA) implicated in bunker oil degradation were amplified and sequenced from two new strains of Acinetobacter baumannii (S341 and S354) isolated from the polluted Pasig River in the Philippines. Genes for both AlkM and CatA enzymes and predicted proteins exhibited almost identical sequences with the type strain A. baumannii (ATCC 19606). Sequence identity (80%) of alkM genes is lower than the sequence identity (90%) of predicted enzymes between A. baumannii environmental strains and most of the other species under the same genus. Genes for AlkM (or for enzymes with equivalent functions as AlkM like AlkB) and CatA from species that do not belong to the genus Acinetobacter exhibited very low gene and protein sequence identities (49.8–54.6%) with corresponding genes and proteins in strains S341 and S354. Stretches of conserved amino acids in the predicted protein sequences (eight histidine motifs in AlkM/AlkB) and a ferric ion ligated by four amino acids (Tyr164, Tyr200, His224, and His226) in the CatA protein were observed, consistent with previous reports. These conserved regions may be crucial in protein function. The study also reports the successful cloning, in the correct orientation, of complete alkM and catA genes from A. baumannii strains S341 and S354 in pBAD Thio-TOPO plasmid for future expression of the recombinant proteins in non-pathogenic host cells.

17. Yu, R.T.D. and Garcia, R.L. (2020). NRAS mutant E132K identifed in young‑onset sporadic colorectal cancer and the canonical mutants G12D and Q61K afect distinct oncogenic phenotypes. Scientific Reports, 10, 11028. https://doi.org/10.1038/s41598-020-67796-8 more

Abstract:

Recent data show a global increase in colorectal cancer (CRC) cases among younger demographics, which portends poorer prognosis. The cause of rising incidence is uncertain, and its mutational landscape remains largely unexplored, including those in genes of the epidermal growth factor receptor pathway. Among these are NRAS mutants where there is paucity of functional studies compared to KRAS. Here, the novel NRAS mutant E132K, identified in three tumor samples from Filipino young-onset, sporadic colorectal cancer patients, was investigated for its effects on different cancer hallmarks, alongside the NRAS canonical mutants G12D and Q61K which are yet poorly characterized in the context of CRC. The novel NRAS mutant E132K and the canonical G12D and Q61K mutants show resistance to apoptosis, cytoskeletal reorganization, and loss of adhesion. In contrast to activating KRAS mutations, including the analogous KRAS G12D and Q61K mutations, all three NRAS mutants have no apparent effect on cell proliferation and motility. The results highlight the need to characterize isoform- and mutation-specific oncogenic phenotypes which can have repercussions in disease management and choice of therapeutic intervention. Further analyses of young-onset versus late-onset CRC datasets are necessary to qualify NRAS E132K as a biomarker for the young-onset subtype.

 

nip 

1. Abella, A.P., Soriano, M.N. (2020). Spatio-Temporal Analysis of Surface Waves Generating Octupole Vortices in a Square Domain. J. Exp. Theor. Phys. 130 (3), Pages 452–462. https://doi.org/10.1134/S1063776120030085 more

Abstract:

In this study, we examine the underlying surface wave dynamics forming an octupole structure of vortices on the air–water interface. The surface waves are generated by a square wavemaker made of four cylindrical edges half-submerged on the interface. These waves direct the motion of floaters into gyrating trajectories, forming two counter-rotating vortices along each edge of the wavemaker and generating the overall octupole pattern. We 3D reconstruct the wave heights and describe the underlying flow through spatio-temporal analysis. Specifically, we decompose the overall wave field into components coming from the edges and corners of the wavemaker. To our knowledge, we are first to obtain a closed-form solution for a velocity potential, via a superposition of edge and phase-shifted oblique progressive waves produced by the wavemaker, to qualitatively model these octupole vortices. The methodology outlined provides a phenomenological approach to characterize the flow that may be useful for characterizing waves inside arbitrary finite-sized domains.

 

2. Afalla, J., Catindig, G., Delos Reyes, A., Prieto, E., Faustino, M. a., Vistro, V., Gonzales, K. C., Bardolaza, H., Mag-usara, V., Husay, H. A., Muldera, J., Cabello, N., Ferrolino, J. P., Kithara, H., Somintac, A., Salvador, A., Tani, M., & Estacio, E. (2020). Ultrafast carrier dynamics and THz conductivity in epitaxial-grown LT-GaAs on silicon for development of THz photoconductive antenna detectorsJournal of Physics D: Applied Physics53 (9). https://doi.org/10.1088/1361-6463/ab5aa7 more

Abstract:

Carrier dynamics and photoconductivity in epitaxial-grown low-temperature GaAs on nominal and vicinal Si(1 0 0) substrates ('LT-GaAs/Si') were studied to predict their actual performance as THz photoconductive antenna (PCA) detectors. An optical-pump terahertz-probe technique was used to obtain the transmittance, carrier lifetime and photoconductivity of two LT-GaAs/Si samples, grown using different substrates and different growth protocols. The LT-GaAs grown on Si(1 0 0) substrate with a 4° tilt to 1 1 0 has better crystallinity, in agreement with other reports; while the LT-GaAs layer grown on nominal Si(1 0 0) substrate, though more structurally defective, has a much faster electron trapping time. Fabricated test PCAs with either dipole or bowtie geometries confirm the characterization results. The photoconductivity and carrier lifetime results manifest in the PCA performance, in responsivity, and in detection bandwidth. The prototypes' sensitivities, bandwidths and dynamic ranges show that with some growth optimization, LT-GaAs/Si can be tailored to create economical, broadband THz detectors.

 

3. Balmeo, M.M., Dizon, J.S.C., Empizo, M.J.F., Solibet, E.J.C.D., Agulto, V.C., Salvador, A.A., Sarukura, N., Nakanishi, H., Kasai, H., Padama, A.A.B. (2020). Density functional theory-based investigation of hydrogen adsorption on zinc oxide (101¯0) surface: Revisited. Surface Science, 703, Article number 121726. https://doi.org/10.1016/j.susc.2020.121726more

Abstract:

Density functional theory based calculations with Hubbard correction (DFT + U) were performed to investigate the effects of varying coverage and different adsorption sites on hydrogen (H) adsorption on zinc oxide (ZnO) (101¯0) surface. Results show that H adsorption on top of oxygen (O) at low coverage (0.25 monolayer, ML) shifts the conduction band below the Fermi level and narrows the band gap. These phenomena are attributed to the charge transfer between H and the surface zinc (Zn) and O atoms. On the other hand, the H adsorption on top of Zn at low coverage (0.25 ML) shows an overlapping of H, Zn, and O states while maintaining the semiconductor nature of the system. At high coverage (1.0 ML), a charge accumulation layer on the surface forms, and the mechanisms that govern the interactions of H atoms when adsorbed exclusively on top of Zn or top of O are found to be similar with the low coverage cases. Lastly, at full coverage (2.0 ML), the effect of H on top of Zn is more evident as the system retained its semiconducting property. The adsorption energy is enhanced due to the reinforced overlapping of the H, Zn, and O states and due to the possible attraction between the adsorbed H atoms. The properties and stability of full-coverage adsorption were explained based on the findings on high- and low- coverages adsorption. The findings of the study will aid in understanding the interaction of H with the ZnO surface toward the further development of ZnO's optoelectronic applications.

 

4. Bardolaza, H., Faustino-Lopez, M.A., Bacaoco, M., Ferrolino, J.P., Verona, I.C., Vistro, V.D.C.A., Cabello, N.I., Lopez, L., De Los Reyes, A., Somintac, A., Salvador, A., Estacio, E. (2020). Observation of enhanced terahertz emission in two-dimensional metal line arrays on GaAs surfaces. Japanese Journal of Applied Physics, 59 (7), Article number 070907. https://doi.org/10.35848/1347-4065/ab9ba0more

Abstract:

Enhanced terahertz (THz) emission was observed from semi-insulating GaAs with square and diamond two-dimensional metal line arrays (2DMLA's) of subwavelength periodicity. An externally-applied magnetic field was used to generate elliptically-polarized THz radiation from the samples and the THz emission characteristics were measured using a THz time-domain spectroscopy setup in transmission geometry. Finite difference time-domain simulations verified the enhancement as due to confinement of the THz electric field at the 2DMLA apertures. These results demonstrating spoof plasmonic enhancement effects may be useful for future photoconductive antenna emitter designs incorporating 2D micro-scale integrated optics, THz metamaterials, without the need for expensive electron beam nanolithography.

 

5. Bernardo, R. C., Celestial, J., & Vega, I. (2020). Stealth black holes in shift symmetric kinetic gravity braidingPhysical Review D101 (2), 24036. https://doi.org/10.1103/PhysRevD.101.024036 more

Abstract:

We derive all hairy stealth black holes in the most general second-order, shift symmetric, scalar-tensor theory with luminally propagating gravitational waves, often called kinetic gravity braiding. Our approach exploits a loophole in a recently obtained no-go statement which claims shift symmetry breaking to be necessary for stealth solutions to exist in kinetic gravity braiding. We highlight the essential role played by a covariantly constant kinetic density in obtaining these solutions. Lastly, we propose a parametrization of the theories based on the asymptotics of its stealth solutions and comment on the intriguing singular effective metric for scalar perturbations in stealth black holes.

 

6. De Los Reyes, A., Bardolaza, H., Vasquez, J. D., Cabello, N. I., Lopez, L., Chang, C. Y., Somintac, A., Salvador, A., Jang, D. J., & Estacio, E. (2020). Temperature-dependent terahertz time-domain spectroscopy of 3D, 2D, and 0D semiconductor heterostructuresJournal of Materials Science: Materials in Electronics, 31 (8), Pages 6321-6327. https://doi.org/10.1007/s10854-020-03188-y more

Abstract:

Carrier transport in semiconductors with different dimensionalities, i.e., 3D (bulk), 2D (QW), and 0D (QD), were investigated via temperature-dependent terahertz time-domain spectroscopy (THz-TDS). The optical properties and recombination dynamics in the samples were probed via photoluminescence spectroscopy. The temperature-dependence of the THz emission from the samples was explained in the context of the drift-diffusion model using the dominant THz radiation mechanism. The THz emission from diffusion-type THz emitters such as p- and n-InAs decreases as temperature increases due to mobility decrease. Conversely, the THz emission from drift-type THz emitters such as SI-GaAs, GaAs QW, and InAs QD was found to increase with temperature due to the increase in the driving electric field. In summary, THz-TDS can be utilized to gain qualitative insights on the temperature-dependent transport characteristics and establish dominant THz radiation mechanisms.

 

7. De Los Reyes, A. E., Vasquez, J. D., Bardolaza, H. R., Lopez, L. P., Chang, C.-Y., Somintac, A. S., Salvador, A. A., Jang, D.-J., & Estacio, E. S. (2020). Low-temperature carrier dynamics in MBE-grown InAs/GaAs single- and multi-layered quantum dots investigated via photoluminescence and terahertz time-domain spectroscopyOptical Materials Express10 (1), 178. https://doi.org/10.1364/ome.380909 more

Abstract:

The photocarrier dynamics in molecular beam epitaxy (MBE)-grown single- (SLQD) and multi-layered (MLQD) InAs/GaAs quantum dots were studied. Photoluminescence (PL) spectroscopy has shown that the MLQD has more uniform QD size distribution as compared to the bimodal SLQD. Correlation between PL and THz-TDS has shown that photocarrier transport is more favored in the MLQD owing to this uniform QD size distribution, resulting to higher THz emission. The THz emission from the QD samples were found to be proportional to temperature. A drift-related photocarrier transport mechanism is proposed, wherein photocarriers generated in the QDs are accelerated by an interface electric field.

 

8. Flores, M., Kar, D., & Kim, J. S. (2020). Constraining Stealth SUSY with illuminated fat jets at the LHCPhysics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics801, 135151. https://doi.org/10.1016/j.physletb.2019.135151 more

Abstract:

We investigate the discovery potential of a Stealth SUSY scenario involving squark decays by reconstructing the lightest neutralino decay products using a large-radius jet containing a high transverse momentum photon. Requirements on the event topology, such as photon and large-radius jet multiplicity result in less background than signal. We also estimated the sensitivity of our analysis and found that it has a better exclusion potential compared to the strongest existing search for the specific benchmark points considered here.

 

9. Hayasaka, T., Lin, A., Copa, V.C., Lopez, L.P., Jr., Loberternos, R.A., Ballesteros, L.I.M., Kubota, Y.a, Liu, Y., Salvador, A.A., Lin, L. (2020). An electronic nose using a single graphene FET and machine learning for water, methanol, and ethanol. Microsystems and Nanoengineering, 6 (1), Article number 50. https://doi.org/10.1038/s41378-020-0161-3 more

Abstract:

The poor gas selectivity problem has been a long-standing issue for miniaturized chemical-resistor gas sensors. The electronic nose (e-nose) was proposed in the 1980s to tackle the selectivity issue, but it required top-down chemical functionalization processes to deposit multiple functional materials. Here, we report a novel gas-sensing scheme using a single graphene field-effect transistor (GFET) and machine learning to realize gas selectivity under particular conditions by combining the unique properties of the GFET and e-nose concept. Instead of using multiple functional materials, the gas-sensing conductivity profiles of a GFET are recorded and decoupled into four distinctive physical properties and projected onto a feature space as 4D output vectors and classified to differentiated target gases by using machine-learning analyses. Our single-GFET approach coupled with trained pattern recognition algorithms was able to classify water, methanol, and ethanol vapors with high accuracy quantitatively when they were tested individually. Furthermore, the gas-sensing patterns of methanol were qualitatively distinguished from those of water vapor in a binary mixture condition, suggesting that the proposed scheme is capable of differentiating a gas from the realistic scenario of an ambient environment with background humidity. As such, this work offers a new class of gas-sensing schemes using a single GFET without multiple functional materials toward miniaturized e-noses.

 

10. Manaoat, N. M., Bantang, J. Y., & Bo-ot, L. M. (2020). Diurnal Temperature Variation in an Idealized Room for Different Wall Materials Using a Thermal Load Model in the Philippine Setting1st International Conference on Human Interaction and Emerging Technologies, IHIET 2019; Nice; France; 22 August 2019 through 24 August 2019; Code 229139, 110–116. 

Abstract:

A simple thermal model is used to simulate the heat load received by an idealized room incorporating climatological factors and daily weather patterns in the Philippine setting. The model provides diurnal temperature variation of the idealized room with varying wall materials situated in Quezon City during the cool-dry and hot-dry seasons in the country. The model was used to calculate the heat load to keep the temperature of the room less than 25 °C. Rooms with walls made of bamboo and oak were demonstrated to perform better than those which are made of concrete, bricks and sandstone. The room with oak walls were shown to provide up to 3 × savings in terms of computed daily energy consumption during the hot-dry season. This study can help us provide design and structural considerations in relation to energy utilization and possibly conservation.

 

11. Pablico, D. A. L., & Galapon, E. A. (2020). Quantum traversal time across a potential wellPhysical Review A101 (2), Pages 1–13. https://doi.org/10.1103/PhysRevA.101.022103 more

Abstract:

We consider the quantum traversal time of an incident wave packet across a potential well using the theory of quantum time of arrival (TOA) operators. This is done by constructing the corresponding TOA operator across a potential well via quantization. The expectation value of the potential-well TOA operator is compared to the free-particle case for the same incident wave packet. The comparison yields a closed-form expression of the quantum well traversal time which explicitly shows the classical contributions of the positive and negative momentum components of the incident wave packet and a purely quantum-mechanical contribution significantly dependent on the well depth. An incident Gaussian wave packet is then used as an example. It is shown that for shallow potential wells, the quantum well traversal time approaches the classical traversal time across the well region when the incident wave packet is spatially broad and approaches the expected quantum free-particle traversal time when the wave packet is localized. For deep potential wells, the quantum traversal time oscillates from positive to negative, implying that the wave packet can be advanced or delayed.

 

12. Santos-putungan, A. B., Binggeli, N., & Paraan, F. N. C. (2020). Selective capture of CO 2 over N 2 and CH 4 : B clusters and their size effects. Materials Today Communications, 22Article number 100712. https://doi.org/10.1016/j.mtcomm.2019.100712 more

Abstract:

Using density-functional theory (DFT), we investigate the selectivity of adsorption of CO2 over  and  on planar-type B clusters, based on our previous finding of strong chemisorption of  on the B planar and quasiplanar clusters. We consider the prototype B and B planar-type clusters and perform a comparative study of the adsorption of the three molecules on these clusters. We find that, at room temperature,  can be separated from  by selective binding to the B cluster and not to the B cluster. Selective adsorption of  over CH4 at room temperature is possible for both clusters. Based on our DFT-adsorption data (including also a semi-infinite Boron sheet) and the available literature-adsorption value for  on the planar-type B36 cluster, we discuss the selectivity trend of  adsorption over  and CH4 with planar-cluster size, showing that it extends over sizes including B10-13 clusters and significantly larger.

 

13. Simon, R. C., Sagisi, J. L. B., Zambale, N. A. F., & Hermosa, N. (2020). Is a single layer graphene a slab or a perfect sheetCarbon157, Pages 486–494. https://doi.org/10.1016/j.carbon.2019.10.044 more

Abstract:

We show that graphene is best described as a slab with finite thickness based on our reflectivity analysis for five different wavelengths. We perform fine-scan angular reflectivity on a single layer graphene on top of SiO2/Si and determine its crossing angle. The experimental data were then compared to the predictions of the three most common models for a single layer graphene. We find that the slab model gives good predictions for the crossing angle in all our experiments. This implies that (1) the real part of the electric permittivity of graphene has a crucial role in the electromagnetic wave propagation, (2) the field across a single layer graphene is continuous, and (3) the dispersionless refractive index of graphite can describe the optical index of graphene in the visible regime.

 

14. Veloria, A., Perez, G.J., Tapang, G., Comiso, J. (2020). Comparison between GPM and gridded precipitation product from interpolated rain gauge measurements40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea; 14 October 2019 through 18 October 2019; Code 157736

Abstract:

Due to sparsely distributed synoptic stations in the Philippines, representation of precipitation is inadequate. Satellite-derived products, such as the Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Measurement (GPM), are available to complement synoptic data for more precise and robust measurements. However, these products tend to over- or underestimate rainfall depending on the season. Precipitation measurements from a dense network of rain gauges in the Philippines are available courtesy of the Department of Science and Technology - Advance Science and Technology Institute (DOST-ASTI). This study aims to create a gridded precipitation data over the Philippines from interpolated rain gauge measurements and validate its performance through comparison with GPM. Comparison of rain gauge data with overlapping synoptic measurements in a 0.25° grid showed distance-dependent likelihood. Thus, inverse distance weighting (IDW) was performed to combine multiple rain gauge measurements representative of precipitation over 0.1° grid. Strong positive correlations (r = 0.58 to 0.97) were obtained from comparing IDW values and monthly synoptic measurements suggesting that rain gauge measurements may be used as complimentary ground data. IDW values were then subjected to kriging and iterative method to create a monthly gridded precipitation. Results showed that the interpolated precipitation follows the wet and dry season as well as monsoon seasonality in the Philippines. The calculated differences between the interpolated precipitation and GPM monthly product revealed that the interpolated precipitation have lower estimates with respect to GPM regardless of season. This is in contrast with the strong positive relationship between monthly synoptic measurements and GPM (r = 0.856). Low estimates from the interpolated precipitation is due to isolated zero measurements from various rain gauges. This may be attributed to maintenance issues of the sensors where the data do not report broken and erroneous instruments. Further filtering of the dataset and regular maintenance of the sensors must be done to better incorporate the use of dense rain gauge network for the creation of a Philippine gridded precipitation.

 

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1. De Ungria, M. C. A. and Jose, J. M. (2020). The war on drigs, forensic science and the death penalty in the Philippines. Forensic Science International: Synergy, 2, Pages 32-34. https://doi.org/10.1016/j.fsisyn.2019.11.002 more

Abstract:

The effectiveness of the death penalty to deter heinous crimes remains a contentious issue even though it has been abolished in many countries. Three years into President Rodrigo Duterte’s administration, the push to re-impose the death penalty is being taken seriously. There is urgency in providing options to the drug problem other than killing drug suspects in the streets or sentencing them to death. The drug problem is a complex issue and exposes the human vulnerability of its users for criminal exploitation. We propose here that addressing these vulnerabilities in a balanced and comprehensive manner through health-focused, rights-based criminal justice responses, conducting forensic science-based drug investigations and determining the social causes of drug abuse is an alternative solution that demands cooperation across different sectors of society as well as underscores the fundamental value of human life.

 

2. Francisco, J. C. E., Rivera, W. L.  & Vital, P. G. (2020). Influences of carbohydrate, nitrogen, and phosphorus sources on the citric acid production by fungal endophyte Aspergillus fumigatus P3I6. Preparative Biochemistry & Biotechnology, 50 (3), Pages 292-301. DOI: 10.1080/10826068.2019.1689510 more

Abstract:

Fungi are ecologically ubiquitous organisms on earth and regarded as one of the prolific sources of natural products. Fungal endophytes may provide essential prerequisite molecules to plant biochemical pathways which allow the efficient synthesis of primary and secondary metabolites. This study characterized the influences of various combinations of process parameters namely, carbohydrate, nitrogen, and phosphorus sources on citric acid (CA) production by the isolated fungal endophyte Aspergillus fumigatus P3I6 from Citrus microcarpaAspergillus fumigatus P3I6 had higher CA concentration of 9.2 (± 0.9) g L−1 and 9.0 (± 5.0 × 10−15) g L−1 when supplemented with sucrose and white refined sugar, respectively, than A. niger NRRL 599. Response Surface Methodology (RSM) had shown that A. fumigatus P3I6 produced the highest CA (23.8 g L−1) in Combination 4 (18.0% sucrose, 0.3 g L−1 ammonium sulfate, and 5.0 g L−1 dipotassium phosphate (K2HPO4)). Analysis of variance showed that when K2HPO4 concentrations were increased, CA content in fermentation media was significantly elevated. Hence, K2HPO4 was the most critical variable in the quadratic model (p < 0.05); however, sucrose concentration still has its role in production. Aside from using A. niger in most fermentation processes, this discovered fungal strain can be potentially used in biotechnological applications.

 

3. Singer, G. A., Loya, F. P., Lapsley, W. D., Tobar, B. Z., Carlos, S., Carlos, R. S., Carlos, E. T., Adao, D. E. V., Rivera, W. L., Jaffe, D. A., Mazet, J. A.K., Chomel, B. B. (2020). Detection of Bartonella infection in pet dogs from Manila. Acta Tropica, 205. https://doi.org/10.1016/j.actatropica.2019.105277. more

Abstract:

Dogs can be infected by a wide range of Bartonella spp., but studies regarding the prevalence of Bartonella infection in dogs in the Philippines have not been conducted. This study aimed at determining the prevalence of Bartonella infection in pets dogs from two veterinary clinics in Metro Manila, The Philippines, using both serology and polymerase chain reaction (PCR). Blood samples from 116 dogs from two different groups, one of 60 mainly “healthy dogs” and the other one of 56 dogs enrolled in a tick-borne disease suspect group, were tested for presence of B. henselae antibodies and to detect Bartonella DNA using primers specific for the citrate synthase gene. Seroprevalence for B. henselae was very low (2.6%), as the only three (5%) seropositive dogs (titer 1:64) where among the healthy pet dog group. Following subsequent sequencing, 13 samples, all from the tick-borne disease group, were determined positive for B. henselae (11.2%). This is the first study to report dog infection with B. henselae in the Philippines.