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Faculty Publication (2019)

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1. Abdulmalik-Labe, O. P., & Quilang, J. P. (2019). DNA barcoding of fishes from Lake Lanao, Philippines. Mitochondrial DNA Part B: Resources, 4 (1), Pages 1890–1894.more

Abstract:

Lake Lanao, the second largest lake in the Philippines and one of the 15 ancient lakes in the world, used to contain 20 endemic cyprinid species, which had attracted the attention of evolutionary biologists in the past. Over the years, there has been a steady decline in the abundance and diversity of endemic fishes in the lake because of overfishing and introduction of non-native species. This study represents the first molecular survey of the ichthyofauna of Lake Lanao. A total of 75 specimens of 12 different species belonging to nine genera, eight families, and five orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Average Kimura 2-parameter genetic distances were 0.24% (within species), 8.31% (between species), 9.69% (within family), and 24.86% (between families). Possible hybrids between Oreochromis species were detected. Glossogobius spp. was highlighted for further taxonomic investigation because barcoding indicated unidentified species of this genus. The partial sequence of mitochondrial COI gene was found to be a good DNA barcode for fast and accurate species identification of fishes in Lake Lanao and for tagging species that warrant further taxonomic investigation.

 

2. Abdulmalik-Labe, O. P., & Quilang, J. P. (2019). Genetic diversity among the endemic barb Barbodes tumba (Teleostei: Cyprinidae) populations from Mindanao, Philippines. Journal of Threatened Taxa, 11 (7), Pages 13822–13832.more

Abstract:

Barbodes tumba is an important fishery resource in Lake Lanao and nearby areas in Mindanao, Philippines. It is one of only two remaining endemic cyprinids out of 20 endemic species originally reported in the lake. In this study, specimens were obtained from fishermen and fish vendors from the lake and from three other sites in Mindanao, namely, Nunungan Lake in Lanao del Norte, Dagoyanan Lake in Lanao del Sur, and Pulangi River in Bukidnon. Eighty-seven haplotypes were recovered from the 122 complete mitochondrial DNA control region sequences analysed. All four populations showed high levels of haplotype (0.662–0.976) and nucleotide (0.552–2.736 %) diversities. Pairwise FST values showed high genetic divergence between populations. Maximum likelihood tree and median-joining network showed geographic separation of Bukidnon population from the three other populations. Lanao Lake specimens also formed a distinct group, which clustered with nine specimens from Dagoyanan Lake. All the other specimens from Dagoyanan clustered with specimens from Nunungan Lake. Despite the high intra- and inter-population genetic variation found in the species, its populations need to be protected and managed so that it will not suffer the same fate as that of the other endemic cyprinids which are now reported to be extinct.

 

3. Adao, D. E. V., Ronquillo, I. D. J., Dela Cruz, Y. K. M., Pagoso, E. J. A., & Rivera, W. L. (2019). Molecular characterization of giardia duodenalis and blastocystis SP in livestock from animal farms in Bulacan, Philippines. Southeast Asian Journal of Tropical Medicine and Public Health, 50 (3), Pages 450–460.

Abstract:

Gastrointestinal protozoa such as Giardia duodenalis and Blastocystis sp pose risks to health of both farm workers and livestock. However, there are little data on G. duodenalis and Blastocystis sp prevalence and genotypes in livestock in the Philippines. A survey of G. duodenalis genotypes and Blastocystis sp subtypes (STs) collected from fecal samples of livestock in animal farms of Bulacan Province, Philippines revealed positive results only from porcine specimens, 6% and 73% infected with G. duodenalis and Blastocystis sp, respectively. Only G. duodenalis assemblage B was identified while ST5 was predominant among Blastocystis sp specimens. These data should help shed light on the possible risk of cross-trans-mission between humans and livestock posed by these two important zoonotic protozoa in Bulacan Province and elsewhere in the Philippines.

 

4. Aya, F.A., Nillasca, V.S.N., Sayco, M.J.P., Garcia, L.M.B. (2019). Improved survival, prey selectivity and diel feeding cycle of silver therapon Leiopotherapon plumbeus (Perciformes: Terapontidae) larvae reared in tanks with substrate. Ichthyological Research, 66 (2), Pages 239-248.more

Abstract:

Physical substrates in the rearing environment can influence the early survival and feeding patterns of captive-reared fish. In this study, we determined whether substrates affect the survival and growth of hatchery-reared silver therapon Leiopotherapon plumbeus larvae as well as examined their prey selectivity and diel feeding cycle. Newly hatched larvae [1.92 mm total length (TL)] were reared for 40 days in triplicate 4 m3 tanks with or without tropical almond Terminalia catappa leaves as substrate. Prey selectivity of larvae reared in tanks with substrate for 35 days from the yolk-sac stage was measured by the Chesson’s selectivity index (αi). Diel feeding cycle of 3-4 days post-hatch (dph) silver therapon larvae reared in tanks exposed to natural light cycle and fed wild zooplankton was also studied. Larvae reared in tanks with substrate had significantly higher survivorship (48.44 ± 7.85%) than those reared in tanks without substrate (26.73 ± 1.60%). However, total length, specific growth rate and body weight of silver therapon larvae from tanks with or without substrate were not significantly different. Silver therapon larvae are generalist predator, demonstrating a degree of prey selectivity in some prey items during early ontogeny. Prey selectivity of silver therapon larvae varied during larval ontogeny, with higher Chesson’s selectivity index for copepod nauplii among the smaller fish larvae (2–5 dph; 2.94–5.17 mm TL), cladocerans (Moina micrura and Bosmina coregoni) among intermediate (6–11 dph; 5.72–9.60 mm TL), and ostracod, cladoceran and insect larvae among larger fish (12–35 dph; 10.28–20.96 mm TL). Larvae showed a diel feeding cycle where they actively fed during daylight hours, with a peak in the late afternoon, and reached a minimum at dark. Together, these findings advance our understanding of the feeding predatory behavior and efficiency of silver therapon larvae and preference for tanks with substrate that improve their survival.

5. Bascos, E.M.A., Rodriquez, L.J.V., Duya, M.V., Fernando, E.S., Ong, P.S. (2019). Philippine rafflesia: emerging patterns in floral morphology and distribution. Flora: Morphology, Distribution, Functional Ecology of Plants, 257, Article number 151409.more

Abstract:

The Philippines is one of the centers of diversity of the genus Rafflesia(Rafflesiaceae). At present, 13 Rafflesia species have been recorded in the country. Prior to 2013, only 10 species of Rafflesia were found in the Philippines. Afterwards, two species have been described while one species has been resurrected. Morphological characteristics of the 13 species of Rafflesia in the Philippines were synthesized, from which an updated identification key is provided. Based on an analysis of the emerging patterns in morphology and distribution of Philippine Rafflesia, floral diameter remained a key differentiating trait in Rafflesia taxonomy. There is a significant inverse relationship between floral diameter and latitudinal distribution. The distribution map of all Philippine Rafflesia species, with their floral diameters drawn to scale, is presented wherein all species, except R. speciosa, occurred in only one island. Of the more than 7100 islands that make up the Philippine Archipelago, Rafflesia had been found in only five islands, which corresponded to three Pleistocene islands: the Greater Luzon, Greater Mindanao and the Greater Negros Panay.

 

6. Chan, A. F. O., Luczon, A. U., Fontanilla, I. K. C., Ong, P. S., Santos, M. D., Willette, D. A., & Quilang, J. P. (2019). DNA barcoding cannot discriminate between Sardinella tawilis and S. hualiensis (Clupeiformes: Clupeidae). Mitochondrial DNA Part B, 4 (2), Pages 2499–2503.more

Abstract:

Sardinella tawilis, the only known freshwater sardinella in the world, is endemic to Taal Lake, Philippines. Previous studies found the Taiwan sardinella, S. hualiensis, to be morphologically very similar to S. tawilis and identified it as the marine sister species of S. tawilis. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase I (COI) gene was carried out to analyze species demarcation in the Sardinella genus, focusing primarily on the relationship between S. tawilis and S. hualiensis. The neighbour-joining (NJ) tree that was constructed using Kimura 2-parameter (K2P) model showed a single clade for the two species with 100% bootstrap support. K2P interspecific genetic divergence ranged from 0% to 0.522%, which is clearly below the suggested 3–3.5% cutoff for species discrimination. Recombination activating gene 1 (RAG1), mitochondrial control region (CR), cytochrome b, 16S rRNA, and S7 markers were used to further validate the results. Sardinella tawilis and S. hualiensis clustered together with a bootstrap support of 99–100% in each of the NJ trees. Low interspecific genetic distances between S. tawilis and S. hualiensis for all the markers except CR could be attributed to incipient allopatric speciation.

7. Claveria, R. J. R., Perez, T. R., Apuan, M. J. B., Apuan, D. A., & Perez, R. E. C. (2019). Pteris melanocaulon Fée is an As hyperaccumulator. Chemosphere, 236, Art No.124380.more

Abstract:

Pteris melanocaulon is noted to thrive very well in selected Cu-Au mines in the Philippines such as the Carmen Cu mine in Cebu and the Manila Mining Cu-Au mine in Surigao. Soil and plant samples were collected from field surveys as well as potted experiments. The computed bioaccumulation factor (BF) and translocation factor (TF) values from the analyses of As contents of the soil and the belowground and above ground components of the plant, apparently were comparable to known As hyperaccumulators Pteris vittata and Pityrogramma calomelanos. It is inferred with probability that the factors that influence the bioavailability of As as well as the uptake mechanisms for P. melanocaulon would be similar to the 2 known As hyperaccumulators. Previous works have noted P. melanocaulon as a very good Cu accumulator with very high Cu values in the belowground components and this study further identified it to be an excellent As hyperaccumulator with high As values in the above ground components.   

8. Duytschaever, G., Janiak, M.C., Ong, P.S., Wells, K., Dominy, N., Melin, A.D. (2019). Opsin genes of select treeshrews resolve ancestral character states within Scandentia. Royal Society Open Science, 6 (4), Article number 182037. more

Abstract:

Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted by ca 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew (Tupaia everetti, the senior synonym of Urogale everetti). We found that the opsin genes are under purifying selection and that D. murina shares the same substitution as its congener, a result that distinguishes Dendrogale from other treeshrews, including T. everetti. We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.

9. Khaing, T. T., Pasion, B. O., Lapuz, R. S., & Tomlinson, K. W. (2019). Determinants of composition, diversity and structure in a seasonally dry forest in Myanmar. Global Ecology and Conservation, 19, Article number e00669.more

Abstract:

Seasonally dry forest with a deciduous canopy is a widespread ecosystem in Southeast Asia. Debate continues about whether this vegetation is forest or savanna. Savannas have tree cover <60%, C4-dominated ground vegetation, and frequent fires. Forests have tree cover >70%, C3-dominated ground vegetation, and infrequent fires. We studied three community types previously identified in seasonally dry forests in Myanmar, High Indaing, Low Indaing (both types of deciduous Dipterocarp-dominated forest) and Mixed Deciduous Forest (usually dominated by non-Dipterocarp species). We wanted to know whether their herbaceous layer communities were also compositionally distinctive, whether their structure (% tree cover, C4 abundance) identified them as savannas or forests, and whether they differed with respect to soil nutrients, and fire frequency. We sampled fifteen 50 m × 50 m plots thought to represent the 3 community types (5 plots of each community type). In each plot we measured basal area, abundance and richness of trees with DBH ≥5 cm, and percentage cover, abundance and richness of herbaceous layer species, and classified each species as C3/C4. We estimated tree cover along four 50 m line transects recording canopy openness/closure every 1 m. We pooled six 0–15 cm soil cores to estimate soil parameters (N, P, K, pH). We recorded fire frequency in each plot using MODIS fire products for 2001–2017.

 

10. Li, H., Guinto, S. K. P., Papa, R. D. S., Han, B. P., Magbanua, F. S., Rizo, E. Z. C., Lin, Q. (2019). On Filipinodiaptomus Lai, Mamaril Sr. & Fernando, 1979 (Calanoida, Diaptomidae): Redescription and re-Allocation of the Philippine endemic Diaptomus vexillifer Brehm, 1933. Crustaceana, 92 (5), Pages 513–536.more

Abstract:

The original description of Diaptomus vexillifer Brehm, 1933, endemic to Lake Danao (Leyte Island), was elementary and lacking taxonomically satisfactory characters. In this paper, we redescribe the Philippine-endemic genus Filipinodiaptomus Lai, Mamaril Sr. & Fernando, 1979 and the species D. vexillifer collected from its type locality, using light and scanning electron microscopy and an analysis of the mtCOI gene and the ITS of the nuclear 18S operon. We found that D. vexillifer is the second species under this endemic genus. A neotype and paraneotypes are hereby designated. Also a detailed morphological comparison is made between Filipinodiaptomus vexillifer (Brehm, 1933) comb. nov. and Filipinodiaptomus insulanus (Wright, 1928). Their taxonomic characters, interspecies relationship, and biogeography are likewise discussed.

 

11. Mendoza, M.V., Rivera, W.L. (2019). Identification of Leptospira spp. from environmental sources in areas with high human leptospirosis incidence in the Philippines. Pathogens and Global Health, 133 (3), Pages 109-116.more

Abstract:

Leptospira is the causative agent of leptospirosis, which is considered an emerging major threat to public health due to its increasing frequency reported worldwide. In the Philippines, the prevalence of the disease continuously rises, particularly in urban areas. Because leptospirosis is commonly transmitted through contact with contaminated environment, water and soil samples were collected in regions in the Philippines where high incidence of human leptospirosis cases was reported recently. Of the 54 samples screened for the presence of Leptospira, 35% were found positive through 23S rRNA gene PCR-based detection. None were found positive when primers targeting lipL32, lipL41, and ompL1 genes were used. Most of these isolates were collected from rural areas. However, 16S rRNA gene sequencing identified all isolates to be L. yanagawae and L. meyeri, which are nonpathogenic. Despite the lack of evidence of the presence of pathogenic species in the environmental sources, the results still suggest that leptospires persist in these areas. These data are crucial for environmental monitoring and identification of contaminated areas where humans may be at risk of infection.

12. Navas, A.L.A., Osei, F., Leonardo, L.R., Magalhaes, R.J.S., Stein, A. (2019). Modeling schistosoma japonicum infection under pure specification Bias: Impact of environmental drivers of infection. International Journal of Environmental Research and Public Health, 16 (2), Article number 176.more

Abstract:

Uncertainties in spatial modeling studies of schistosomiasis (SCH) are relevant for the reliable identification of at‐-risk populations. Ecological fallacy occurs when ecological or group-level analyses, such as spatial aggregations at a specific administrative level, are carried out for an individual‐-level inference. This could lead to the unreliable identification of at‐-risk populations, and consequently to fallacies in the drugs’ allocation strategies and their cost‐-effectiveness. A specific form of ecological fallacy is pure specification bias. The present research aims to quantify its effect on the parameter estimates of various environmental covariates used as drivers for SCH infection. This is done by (i) using a spatial convolution model that removes pure specification bias, (ii) estimating group and individual‐-level covariate regression parameters, and (iii) quantifying the difference between the parameter estimates and the predicted disease outcomes from the convolution and ecological models. We modeled the prevalence of Schistosoma japonicum using group‐-level health outcome data, and city‐-level environmental data as a proxy for individual‐-level exposure. We included environmental data such as water and vegetation indexes, distance to water bodies, day and night land surface temperature, and elevation. We estimated and compared the convolution and ecological model parameter estimates using Bayesian statistics. Covariate parameter estimates from the convolution and ecological models differed between 0.03 for the nearest distance to water bodies (NDWB), and 0.28 for the normalized difference water index (NDWI). The convolution model presented lower uncertainties in most of the parameter estimates, except for NDWB. High differences in uncertainty were found in night land surface temperature (0.23) and elevation (0.13). No significant differences were found between the predicted values and their uncertainties from both models. The proposed convolution model is able to correct for a pure specification bias by presenting less uncertain parameter estimates. It shows a good predictive performance for the mean prevalence values and for a positive number of infected people. Further research is needed to better understand the spatial extent and support of analysis to reliably explore the role of environmental variables.

 

13. Quibod, M. N. R. M., Alviola, P. A., de Guia, A. P. O., Cuevas, V. C., Lit, I. L., & Pasion, B. O. (2019). Diversity and threats to cave-dwelling bats in a small island in the southern Philippines. Journal of Asia-Pacific Biodiversity, (xxxx), Pages 1–7.more

Abstract:

More than 2,000 caves have been documented in the Philippines, yet cave research is very limited. This study was conducted to provide benchmark information on the diversity and ecology of cave-dwelling bats from Samal Island, a small island in the southern Philippines. Bats were surveyed from thirty caves of varying physical features and disturbances. Fifteen species of bats were identified in the island; 14 of which are new records for the island, increasing the island distribution of the identified bats in the country. The abundance of cave-dwelling bats varied from low to high density, with some caves estimated to harbor more than 10,000 individuals. Abundance and richness of cave-dwelling bats positively increased with longer cave length, higher ceilings, bigger and multiple entrances, and presence of water. The Bat Cave Vulnerability Index (BCVI) revealed three high priority caves, 12 medium priority caves and 15 low priority caves, indicating the importance of standardized method in assessing cave disturbance. Traces of tourism and hunting were the most common disturbance factors. The results of this study highlight the need for fundamental data on the distribution, diversity, and ecology of cave-dweling bats in the Philippines.

 

14. Ragasa, L.R.P., Dinglasan, J.L.N., Felipe, I.R.E., Basiao, Z.U, Velarde, M.C. (2019). Exposure to aeromonas hydrophila induces inflammation and increases expression of the gene encoding for a putative dual CTLD-containing lectin in milkfish liver. Comparative Biochemistry and Physiology Part – B : Biochemistry and Molecular Biology, 230, Pages 37-47.more

Abstract:

Milkfish (Chanos chanos Forsskal) is an important aquaculture product and is the sole extant species of the family Chanidae (order Gonorynchiformes). While there are already several reports regarding milkfish aquaculture, studies on milkfish immunity and gene expression are very limited. In this study, we showed that Aeromonas hydrophila induces inflammation in milkfish liver. We identified a milkfish C-type lectin-like domain containing proteins (CTLDcps) gene, designated as CcClec, which was upregulated in respond to A. hydrophila. Full-length sequencing was performed using Rapid Amplification of cDNA Ends (RACE PCR) to produce a complete Coding DNA Sequence (CDS) of the gene. The CcClec gene encoded a predicted protein of 340 amino acids containing two CTLDs that may potentially bind carbohydrates, especially sucrose and cellobiose. The CcClec mRNA transcript was expressed highest in the liver, followed by head kidney, brain, heart, gills, spleen, and midgut. CcClec transcripts were upregulated in damaged liver upon exposure to A. hydrophila. Overall, these findings demonstrated that CcClec is implicated in milkfish innate immunity, and is most highly expressed in the liver, suggesting a role of the liver in the milkfish immune system.

 

15. Santos, B.S., Basiao, Z.U., Quilang, J.P. (2019). Genetic diversity and patterns of demographic expansion in natural populations of milkfish, Chanos chanos (Forsskål, 1775), in the Philippines. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 30 (2), Pages 312-324.

Abstract:

The milkfish, Chanos chanos (Forsskål, 1775) is an important aquaculture species produced in the tropical Pacific region. Milkfish aquaculture is heavily reliant on seedstock; thus, there is a need to assess the genetic diversity of wild populations to identify areas that could be sources of high quality seedstock and broodstock. In this study, 631 milkfish specimens from 11 Philippine and, for comparison, two Indonesian wild populations were analysed for their genetic diversities using mitochondrial control region and cytochrome b. High genetic diversity indices were found for Sarangani, Claveria, and Camarines Sur populations in the Philippines. Philippine samples had either comparable or higher genetic diversity values than Indonesian samples from Medan and Sulawesi. Based on neutrality tests and mismatch distribution analysis, Philippine samples exhibited population expansion. Such pattern was not observed among Indonesian specimens. Genetic structure among populations was weak based on analysis of molecular variance (AMOVA). Correlation between genetic distance and geographic distance was not significant. Differentiation among marine biogeographic regions was small based on hierarchical AMOVA. High gene flow due to natural dispersal and influx of haplotypes brought about by importation may have contributed to the patterns observed, but diversification events within the Philippines were still evident.

 

16. Sato, M.O., Adsakwattana, P., Fontanilla, I.K.C., Kobayashi, J., Sato, M., Pongvongsa, T., Fornillos, R.F.C. (2019). Odds, challenges and new approaches in the control of helminthiasis, an Asian study. Parasite Epidemiology and Control, 4, Article number e00083.more

Abstract:

The time is passing, and the worms are still a major struggle for local people in Asian countries, especially the less empowered and in a situation of social vulnerability. We are working in the field in Laos, Thailand, and the Philippines where the usual control programs based only on human treatment are partially effective. Areas with mass drug administration could diminish, but not eliminate STHs of endemic areas. The persistence of helminthic NTDs in the environment and animal hosts makes the eradication a very difficult task. Great changes in the landscapes of endemic areas, such as construction of dams, can change the fauna and the lifestyle of local people. Those changes can improve infrastructure, but it can also lead to social vulnerability. The challenge, then, is to conceive new and directed control programs for helminthiasis based on multi- and transdisciplinary approaches diminishing the health gap in a globalized world. In this short review, we summarize the actual scenario concerning the main helminths in Southeast Asia and how an environmental DNA approach and the use of GIS could contribute to surveillance and control programs.

17. Schreiber, K. H., Arriola Apelo, S. I., Yu, D., Brinkman, J. A., Velarde, M. C., Syed, F. A., … Lamming, D. W. (2019). A novel rapamycin analog is highly selective for mTORC1 in vivo. Nature Communications, 10 (1), Pages 1–12.more

Abstract:

Rapamycin, an inhibitor of mechanistic Target Of Rapamycin Complex 1 (mTORC1), extends lifespan and shows strong potential for the treatment of age-related diseases. However, rapamycin exerts metabolic and immunological side effects mediated by off-target inhibition of a second mTOR-containing complex, mTOR complex 2. Here, we report the identification of DL001, a FKBP12-dependent rapamycin analog 40x more selective for mTORC1 than rapamycin. DL001 inhibits mTORC1 in cell culture lines and in vivo in C57BL/6J mice, in which DL001 inhibits mTORC1 signaling without impairing glucose homeostasis and with substantially reduced or no side effects on lipid metabolism and the immune system. In cells, DL001 efficiently represses elevated mTORC1 activity and restores normal gene expression to cells lacking a functional tuberous sclerosis complex. Our results demonstrate that highly selective pharmacological inhibition of mTORC1 can be achieved in vivo, and that selective inhibition of mTORC1 significantly reduces the side effects associated with conventional rapalogs.

 

18. Tun, J.O., Salvador-Reyes, L.A., Velarde, M.C., Saito, N., Suwanborirux, K., Concepcion, G.P. (2019). Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells. Marine Drugs, 17 (9), Page 536.more

Abstract:

Renieramycin M (RM) is a KCN-stabilized tetrahydroisoquinoline purified from the blue sponge Xestospongia sp., with nanomolar IC50s against several cancer cell lines. Our goal is to evaluate its combination effects with doxorubicin (DOX) in estrogen receptor positive MCF-7 breast cancer cells. MCF-7 cells were treated simultaneously or sequentially with various combination ratios of RM and DOX for 72 h. Cell viability was determined using the MTT assay. Synergism or antagonism was determined using curve-shift analysis, combination index method and isobologram analysis. Synergism was observed with pharmacologically achievable concentrations of DOX when administered simultaneously, but not sequentially. The IC95 values of RM and DOX after combination were reduced by up to four-fold and eight-fold, respectively. To gain insights on the mechanism of synergy, real-time profiling, cell cycle analysis, apoptosis assays, and transcriptome analysis were conducted. The combination treatment displayed a similar profile with DNA-damaging agents and induced a greater and faster cell killing. The combination treatment also showed an increase in apoptosis. DOX induced S and G2/M arrest while RM did not induce significant changes in the cell cycle. DNA replication and repair genes were downregulated commonly by RM and DOX. p53 signaling and cell cycle checkpoints were regulated by DOX while ErbB/PI3K-Akt, integrin and focal adhesion signaling were regulated by RM upon combination. Genes involved in cytochrome C release and interferon gamma signaling were regulated specifically in the combination treatment. This study serves as a basis for in vivo studies and provides a rationale for using RM in combination with other anticancer drugs. 

19. Vital, P.G., Rivera, W.L., Abello, J.J.M., Francisco, J.C.E. (2019). Microbiological assessment of fresh, minimally processed vegetables from open air markets and supermarkets in Luzon, Philippines, for food safety. Environment, Development and Sustainability, 21 (1), Pages 51-60.more

Abstract:

A wide-range investigation of the microbiological quality of fresh produce from different open air markets and supermarkets in Luzon, Philippines was performed. Different vegetables which are usually consumed raw (bell pepper, carrot, lettuce, mung bean sprout, and tomato) had been screened for the presence and amount of contamination of enteric microorganisms, namely Escherichia coli, Salmonella spp., and somatic bacteriophages (or viruses). Phenotypic characterization was employed using selective and differential media such as eosin methylene blue agar and xylose lysine deoxycholate agar. Viable plate count (colony-forming units or CFU) and most probable number (MPN) methods were used to estimate the cell numbers of E. coli and Salmonella spp., respectively. Double agar assay was used to detect and quantify somatic phages as plaque-forming units (PFU). Polymerase chain reaction was also done to confirm the identity of the isolates using species-specific primers. From a total of 410 vegetable samples collected, 44 bacterial (prevalence of 5.85% E. coli and 5.12% of Salmonella spp.) and 21 (prevalence of 5.12%) viral isolates were obtained. It is alarming to note that samples contaminated with Salmonella spp. were significantly higher in counts (3.751 ± 0.60 log MPN/g) as compared to E. coli (1.472 ± 0.25 log CFU/g), while samples with coliphage (0.316 ± 0.12 log PFU/g) were the least in numbers. The degree of contamination in the samples can cause great risks on the health of individuals especially in developing countries such as the Philippines. Thus, monitoring on the handling of different produce is important to improve the country’s food quality and safety.

 

20. Yason, J. A., Liang, Y. R., Png, C. W., Zhang, Y., & Tan, K. S. W. (2019). Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies. Microbiome, 7 (1), Page 30.more

Abstract:

Background: Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota. Results: Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus. Conclusions: This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.

 

 Chemistry logo

1. Acuram, L.K. and Hernandez, C.L.C. (2019). Anti-hypertensive effect of Moringa oleifera Lam. Cogent Biology 5:1596526.more

Abstract:

Bioassay-guided fractionation of the crude extracts of Moringa oleifera Lam. using in-vitro angiotensin-converting enzyme inhibition assay was employed to purify the two compounds, namely: quercetin-3-O-glucoside (1) and kaempferol-3-O-glucoside (2). Compound 1 has a significant % of inhibition at varying concentrations: 7 ug/ml (56.37 ± 0.0059%), 15 ug/ml (59.16 ± 0.0137%) and 28 ug/ml (75.74 ± 0.0161%). The methanol extract was found to contain 180.15 ug/ml of compound 1 for every 2 mg/ml of methanol extract after standardization. Furthermore, oral administration of M. oleifera crude extracts did not present acute toxicity in mice. Methanolic and ethyl acetate extracts have significantly reduced systolic blood pressure in Nω-nitro-L-arginine methyl ester or L-NAME induced hypertensive mice (90.97 ± 0.7975 mm Hg in methanolic extract treated mice; 87.71 ± 0.9623 mm Hg in ethyl acetate-treated mice versus 89.21 ± 0.8025 mm Hg in control group).

2. Babela, D.L.D.T. and Lamorena, R.B (2019). Effect of humidity and organic vapors on water absorption of metal oxides. Chemical Papers, Pages 1-11.more

Abstract:

Water plays a vital role in atmospheric heterogeneous chemistry by inducing particle surface speciation resulting in enhanced surface chemistry and reactivity. In this study, selected metal oxides (CdO, CuO, MnO2 and ZnO) were synthesized and characterized using UV–Vis spectroscopy for their λmax. The oxide particle sizes were found to fall within the 1–3 µm size range with satisfactory monodispersity. Particles were subjected to ambient (60–70%) and high (99%) relative humidity (%RH) levels at 28 °C—the average ambient temperature. Water adsorption of metal oxides in the presence of low-molecular-weight gas-phase organic compounds (formic acid, acetic acid, formaldehyde and acetaldehyde) was also evaluated. ATR-FTIR analyses were done by subjecting samples to dry, ambient and high % RH conditions in the presence and absence of volatilized organic compounds. Presence of infrared (IR) bands at 1600–1590 cm−1 and 3600–3100 cm−1 in sample IR spectra indicated water adsorption, the possible speciation of oxides into hydroxyl groups and the H bonding of water to hydroxyl groups, respectively. Surface roughness of dry and “wet” samples was also analyzed using atomic force microscopy (AFM) for supplementary surface characterization. Results show that increasing the %RH levels and presence of volatile organic compounds (VOCs) lead to increase in metal oxide water adsorption.

3. Crisostomo, B.A., Atis, A.A.G., Mirano-Bascos, D.N.R. and Hernandez, C.C. (2019). Identification of cysteine knot peptides in four Philippine plant species using mass spectrometry and transcriptome analysis. Philippine Science Letters, 12 (1), Pages 39-61.more

Abstract:

Knottins are small proteins with at least three disulfide bridges that form a cysteine knot, giving them exceptional stability. These molecules are candidates for developing peptide-based drugs that are envisioned to fill the gap between small-molecule drugs and biologics as they are bioavailable, like small-molecule drugs, and target-specific, like biologics. Plant-derived knottins are able to preserve their stable conformation in the presence of mutations and peptide grafts, making them potential drug scaffolds. Through LC/MS screening of 185 plant extracts from 180 plant species, we identified 6 Philippine plants that produce disulfide-rich peptides structurally related to knottins. Four of these plants were further analyzed using transcriptome screening and we confirmed that Alstonia scholaris, Wrightia pubescens and Tabernaemontana pandacaqui from the Apocynaceae family produce knottin-like peptides similar to previously reported Apocynaceae alpha amylase inhibitors. Given the novelty of their sequences, it is possible that these peptides possess novel functions as well. This is the first report of cysteine knot peptides from W. pubescens and T. pandacaqui. Finally, we showed that LC/MS screening followed by transcriptome analysis is a more efficient workflow for identifying cysteine knot peptides as opposed to LC/MS screening alone.

4. dela Cruz, J.B., Ruamps, M., Arco, S.D. and Hung, C.H. (2019). Ni and Pd N-confused porphyrin complexes as catalysts for the synthesis of cyclic carbonates from epoxides and CO2. Dalton Transactions, 48, Pages 7527-7531.more

Abstract:

We have demonstrated the design of a novel bifunctional catalyst that is based on an N-confused tetraphenylporphyrin (NCTPP) motif for the cycloaddition of an epoxide to carbon dioxide via cooperative activation of the epoxide through a Pd(II) or Ni(II) metal center and a peripheral benzoate moiety with percent conversions of up to 99% and TON = 7000.

5. Gaza, J.T., Sampaco, AR.B., Custodio, K.K.S. and Nellas, R.B. (2019). Conformational dynamics of α -conotoxin PnIB in complex solvent systems. Molecular Diversity, Pages 1-9.more

Abstract:

Cone snails are slow-moving animals that secure survival by injecting to their prey a concoction of highly potent and stable neurotoxic peptides called conotoxins. These small toxins (~ 10–30 AA) interact with ion channels and their diverse structures account for various variables such as the environment and the prey of preference. This study probed the conformational space of α-conotoxin PnIB from Conus pennaceus by performing all-atom molecular dynamics simulations on the conotoxin in complex solvent systems of water and octanol. Secondary structure analyses showed a uniform conformation for the pure (C100Oc, C100W) and minute (C95Oc, C5Oc) systems. In C50Oc, however, structural changes were observed. The original helices were converted to turns and were shown to happen simultaneously with the elongation of the helix and shortening of end-to-end distance. The transitions complement the orientation of the peptide at the interface. The shift to the broken helix conformation is marked by the rearrangement of solvent molecules to a framework that favors the accumulation of water molecules at residues 6–11 of the H2 region. This promotes specific protein–solvent interactions that facilitate secondary structure transitions. As PnIB has shown favorable binding toward neuronal nicotinic acetylcholine receptors, this study may provide insights on this conotoxin’s therapeutic potential.

 

6. Gili, M. and Conato, M. (2019). Synthesis and characterization of mordenite -type zeolite via hydrothermal method using silica gel and sodium aluminate as Si and Al sources at varying temperature. Journal of Physics: Conference Series, 1191, 012038.more

Abstract:

Mordenite-type zeolites were prepared via hydrothermal method using silica gel and sodium aluminate as Si and Al sources respectively. The temperature was varied from 150 °C up to 190 °C to determine the minimum temperature to obtain crystalline mordenite using a 23 mL Teflon-lined stainless-steel autoclave. The samples were characterized using XRD, FTIR and SEM. With the given experimental conditions, mordenite-type zeolites with good crystallinity and excellent purity were produced at 190 °C. Amorphous materials with notable peaks that correspond to mordenite planes were produced at 170 °C. The sample produced at 150°C was completely amorphous. FTIR revealed that all the three samples contain bands associated to aluminosilicate vibrational groups. However, a significant decrease in the intensities of vibration bands associated to hydroxyl (HO−) stretching and water bending were observed as the temperature is decreased. From the SEM, the sample treated at 190°C was composed of particles with strikingly linear edges having an average grain size of ~38.0 µm. Most particles are hexagonal in shape. Particle components of the samples synthesized at 170 °C and 150 °C have irregular sizes and shapes.

7. Gili, M.B.Z. and Conato, M.T. (2019). Synthesis and characterization of mordenite-type zeolites with varying Si/Al ratio. Materials  Research Express, 6 (1), article no.  015515.more

Gili, M.B.Z and Conato, M.T. (2019). Corrigendum: Synthesis and characterization of mordenite-type zeolites with varying Si/Al ratioMaterials Research Express, 6 (3), 039501. more

Abstract:

One factor that makes mordenite-type zeolites attractive in adsorption applications is its high cation exchange capacity (CEC) that can further be improved by controlling its Si/Al ratio (SAR). Mordenite-type zeolites with SAR of 25, 20, 15, 10 and 5 were attempted to synthesize via hydrothermal method using silica gel and sodium aluminate as Si and Al sources respectively. The SAR was varied by changing the molar composition of the starting gel solution. The starting solution with theoretical SAR of 15 and 10 successfully produced mordenite with high degree of crystallinity and purity. At high SAR equal to 20, the product was found to be amorphous with significant peaks indexed to mordenite. Amorphous materials were mostly formed from the starting solution with theoretical SAR of 25. On the other hand, the starting solution with theoretical SAR of 5 yielded analcime-type zeolites. FTIR confirms the presence of vibrational bands that are typical to zeolites and/or aluminosilicates for all samples. The synthesized crystalline mordenites have prismatic, hexagonal shapes while others have fibrous or needle-like structures. XRF analysis shows that the synthetic mordenites indeed have varying actual SAR, though the values are lower than expected.

8. Gili, M.B.Z. and Conato, M.T. (2019). Adsorption uptake of mordenite-type zeolites with varying Si/Al ratio on Zn2+ ions in aqueous solution. Materials Research Express, 6 (4), 045508.more

Abstract:

The adsorption uptake of synthetic mordenite-type zeolites with varying Si/Al ratio was investigated for Zn2+ ions in aqueous solution to determine the influence of Si/Al ratio in removing heavy metals. Synthetic mordenites were hydrothermally synthesized from gel solutions with Si/Al ratio of 10, 15 and 20 as denoted by samples SAR10, SAR15 and SAR20 respectively. The samples were characterized using XRD, SEM, XRF, and TG-DTA. The adsorption kinetic and thermodynamic behaviour of the synthetic mordenites were examined. From the kinetic study, the pseudo-second-order kinetic model best fit the kinetic data among other models (i.e. pseudo-first order and intraparticle-diffusion models). It was found that cation-exchange was the most dominant adsorption mechanism. Further, it was observed that the pH level significantly affects the sorption of Zn2+ ions. The uptake of crystalline mordenite increases more than threefold from 7.19 mg Zn2+/g at pH = 3 to 24.27 mg Zn2+/g at pH = 7 using feed solution of 100 mg Zn2+/L. With regards to the equilibrium data, the adsorption isotherm generated from Langmuir model fits better than that of Freundlich model. Accordingly, the theoretical maximum adsorption capacities of SAR10, SAR15 and SAR20 are 39.97, 48.90, 32.48 mg Zn2+/g respectively. The lower the Si/Al ratio, the higher the negative charge density of zeolites resulting to a higher cation exchange capacity (CEC). However, lower Si/Al ratio do not automatically mean higher maximum adsorption capacity of mordenites to heavy metal ions especially Zn2+, as demonstrated in this study.

 

9. Gili, M.B., Olegario-Sanchez, L. and Conato, M. (2019). Adsorption uptake of Philippine natural zeolite for Zn2+ ions in aqueous solution. Journal of Physics: Conference Series, 1191, 012042.more

Abstract:

The Philippine natural zeolite (PNZ) was characterized and subjected to Zn2+ adsorption tests in aqueous solutions to determine its adsorption uptake and to understand its adsorption behaviour. The PNZ was characterized using XRD, SEM, BET-analysis and TG-DTA. XRD showed significant peaks indexed to natural mordenite-type zeolite along with other natural zeolites and minerals. SEM micrographs revealed a rough and corrugated surface morphology of the sample. BET physisorption analysis showed a surface area of 222.63 m2/g. From the analytical tests report given by the supplier, the Si/Al ratio (SAR) was computed to be equal to 4.29 based on the silica and alumina content of the PNZ. Adsorption kinetic and thermodynamic studies were done to determine the adsorption mechanism and adsorption capacity of PNZ for Zn2+ ions in aqueous solution. From the adsorption kinetic curve, the PNZ attained chemical equilibrium after 50 min. Pseudo-second-order kinetic model was the most applicable kinetic model providing the highest correlation with the data. Langmuir model better described the adsorption isotherm of the PNZ than Freundlich model. The theoretical maximum cation exchange capacity of PNZ was computed as 27.17 mg Zn2+/g according to the Langmuir model.

 

10. Gorospe, A.E.B., Buenviaje, S.C., Edañol, Y.D.G., Cervera, R.B.M. and Payawan, L.M. Jr. (2019). One-step co-preciptiation synthesis of water-stable poly (Ethylene-glycol)-coated magnetite nanoparticles. Journal of Physics: Conference Series, 1191, 012059.more

Abstract:

Magnetite is one of the important materials used in drug delivery systems, magnetic resonance imaging, and cancer therapy due to its low toxicity, durability, high biocompatibility, and low cost. Among the different methods of synthesizing magnetite, co-precipitation presents a facile route for synthesizing nanoparticles. Since rapid crystallization occurs in this method, a coating agent is essential to prevent the aggregation of the nanoparticles and increase its water-stability. In this study, PEG-coated and uncoated magnetite nanoparticles were synthesized by one-step co-precipitation. FeSO4centerdot7H2O, FeCl3centerdot6H2O, and PEG were used as the precursors for the magnetite nanoparticles. Addition of NH4OH while maintaining the reaction in an N2 environment at 80 ° C completed the synthesis of the nanoparticles. XRD analysis confirmed the structure of the synthesized nanoparticles is magnetite. The addition of PEG coating results in generally weaker diffraction peaks as well as the absence of some peaks, indicating a decrease in the crystallinity of the sample. AFM and SEM measurements reveal a spherical morphology for both PEG-coated and uncoated magnetite nanoparticles. DLS measurements showed that the PEG-coated magnetite nanoparticles had a lower average particle diameter (73.95 ± 0.786 nm) compared to that of the uncoated magnetite nanoparticles (143.72 ± 1.60) nm. The observed values are lower compared to the results of a previous study. DLS also showed that both the uncoated and PEG-coated magnetite nanoparticles are monodisperse. Zeta potential analysis reveals that the PEG-coated magnetite nanoparticles are more stable in water than the uncoated magnetite nanoparticles. Addition of the polymer coating reduces the particle size and enhances the water-stability of the magnetite nanoparticles, making it useful for biomedical applications.

11. Lin, H.S., Kue, K.Y., Claudio, G.C. and Hsu, C.P. (2019). First principle prediction of intramolecular singlet fission and triplet triplet annihilation rates. Journal of Chemical Theory and Computation, 15 (4), Pages 2246-2253.more

Abstract:

Intramolecular singlet fission and triplet–triplet annihilation (TTA) has been experimentally observed and reported. However, problems remain in theoretically accounting for the corresponding intramolecular electronic couplings and their rates. We used the fragment excitation difference (FED) scheme to calculate the coupling with states from restricted active-space spin-flip configuration interaction. We investigated three covalently linked pentacene dimers via a phenyl group in an ortho-, meta-, and para-arrangement. The singlet fission and TTA couplings were enhanced when two chromophores were covalently linked. With the Fermi golden rule, both the estimated singlet fission and TTA rates were in line with the experimental results. For systems with significant singlet-fission coupling, charge-transfer components were observed in the excited states involved, and charge-transfer states were also seen within 1 eV above the singlet excited states. Our approach allows for an analysis of through-bond versus through-space singlet fission in the full electronic wave functions. The FED scheme is useful for calculating intramolecular singlet-fission and TTA couplings.

12. Malto, Z.B.L., Bacal, C.J.O., Diaz, M.J.S. and Yu, E.T. (2019). Local fungal endophyes as rich sources of Chitinase genes. Philippine Journal of Science,148 (3), Pages 575-582.more

Abstract:

The ability of three fungal endophytes (JB10, JB11, and D12 isolates) to degrade chitin, and their potential as microbial sources of chitinases was investigated. Amplification and sequencing of the ITS regions revealed the identity of the fungal isolates: JB10 (Fomitopsis sp.), JB11 (Aspergillus tubingensis), and D12 (Daldinia eschscholzii). All three fungi were able to grow on minimal media with colloidal chitin as sole carbon source, albeit at different rates. Isolates JB11 and D12 are observed to have comparable or faster growth rates in chitin as compared to the simpler potato dextrose carbon source. Turbidimetric measurements show that the fungal cultures are able to degrade chitin with 3–5 d of incubation. While the crude, secreted proteins from these three fungi show comparable total chitinolytic activities (~0.35 U/mL), JB11 was found to have the highest exochitinase activity (~0.25 U/mL). Bioinformatic analysis of the chitinase (GH18) genes for A. tubingensis (JB11) and D. eschscholzii (D12) revealed variability in the GH18 chitinase sequences in terms of the amino acid sequences of the canonical DXXDXDXE catalytic motif as well as the presence of additional domain architectures, which make these fungi ideal sources for chitinases for both biotechnology applications and chitinase enzyme mechanistic studies.

 

13. Mayuga, G. P., Favila, C., Oppus, C., Macatulad, E., & Lim, L. H. (2019). Airborne particulate matter monitoring using UAVs for smart cities and urban areas. Paper presented at the IEEE Region 10 Annual International Conference, Proceedings/TENCON, Jeju, Korea (South), 2018. Pages 1398-1402.more

Abstract:

In smart cities and urban areas, localized weather monitoring will be a readily available feature. Checking the air quality in small area urban motifs, specifically schools and universities situated near a national primary road and mid to high-rise condominiums with increasing sources of pollutants, e.g. particulate matter (PM), becomes a need for risk assessment. An aerial sensor system, consisting of an unmanned aerial vehicle (UAV) and a sensor payload, is designed and implemented. Measurements for PM concentration are taken at various elevations, and during heavy and light traffic conditions. Results show trends relating PM concentration with elevation and traffic conditions.

14. Mendoza, C.B., Masacupan, D.J.M., Batoctoy, D.C.R., Yu, E.T., Lluisma, A.O. and Salvador-Reyes, L.A.(2019). Conomarphins cause paralysis in mollusk: critical and tunable structual elements of bioactivity. Journal of  Peptide Science, 25 (7), e3179.more

Abstract:

Two conomarphins were purified as the major component of the venom of Conus eburneus. Conomarphins Eb1 and Eb2 showed biological activity in the mollusk Pomacea padulosa, causing sluggishness and retraction of siphon, foot, and cephalic tentacles. To further probe the effects of conserved amino acids and posttranslational modifications in conomarphins, we prepared four synthetic analogues: conomarphin Eb1 Hyp10Pro, Hyp10Ala, d‐Phe13Ala, and l‐Phe13 variants. Structure‐activity relationship analysis indicated that d‐Phe13 is critical to the biological activity of conomarphins. In contrast, amino acid changes at position 10 and removal of posttranslational modification in Hyp10Pro can be tolerated. The high expression level and observed mollusk activity of conomarphins may suggest their potential role as defensive arsenal of Conoidean snails against other predatory gastropods.

 

15. Ortiz, C.L., Matel, H.D., and Nellas, R.B. (2019). In Silico insights on enhancing thermostability and activity of a plant Fructosyltransferase from Pachysandra terminalis via introduction of disulfide bridges. Journal of Molecular Graphics and Modelling, 89, Pages 250-260.more

Abstract:

Drawbacks of industrially-used fructosyltransferases (FTs) such as low optimum temperature and low fructooligosaccharides (FOS) yield necessitates the search for engineered FTs that are highly thermostable and active. With the availability of the first plant FT crystal structure from Pachysandra terminalis (PDB ID: 3UGH), computer-aided protein engineering of plant FT is now feasible. To obtain insights on the effect of specific mutations i.e. disulfide bridge introduction, wild-type and mutant FTs were subjected to a 15 μs Martini Coarse-grained Molecular Dynamics (CGMD) simulations at 303 K and 334 K. We report here the five mutants, M31C-Q49C, L144C-S193C, P34C-W300C, S219C-L226C and V470C-S498C with enhanced thermostabilities and/or activities relative to the wild type. Interestingly, M31C-Q49C, which is located within the catalytic-carrying blade of the catalytic domain, has an activity enhancement at both temperatures. At 334 K, three mutations, L144C-S193C, P34C-W300C and V470C-S498C, achieved thermostability relative to the wild type. Intriguingly, both activity and stability enhancement exhibited only at 334 K can be achieved provided that the mutation is located either on the catalytic-carrying residue blade of the catalytic domain or on the non-catalytic domain. Our results suggest that V470C-S498C and L144C-S193C are promising mutants and that domain-specific approach may be exploited to customize enzyme properties.

16. Pineda, E.G.S. and Villaraza, A.J.L. (2019). Effect of Solvent on Gd (DOTA)–Complex Formation: A Preliminary Investigation. Philippine Journal of Science, 148 (1), Pages 167-182.more

Abstract:

The thermodynamic stability and kinetic inertness of gadolinium-based MRI contrast agents remains an important research topic in the field of radiological contrast agent development. In this study, the kinetics and thermodynamics of Gd3+-complex formation with the macrocyclic ligand DOTA (i.e., 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) was investigated under aqueous (acetate buffer pH 5.8) and non-aqueous (MeOH) conditions. Using Job’s method of continuous variation, solutions were prepared of increasing mole fraction of Gd3+ relative to xylenol orange (XO, i.e., 3,3′-bis[N,N-bis(carboxymethyl)aminomethyl]-o-cresolsulfonephthalein) in MeOH, and their absorbances were measured at 582 nm.The kinetics of complex formation via ligand substitution of DOTA and DO3A (i.e., 1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid) with Gd-XO under aqueous and non-aqueous conditions were determined using UV-Vis spectrophotometry. Furthermore, the thermodynamic parameters of DOTA complexation with Gd3+ for both solvent conditions were compared by measuring the heats of injection using isothermal titration calorimetry. Results of this study demonstrate that XO forms a well-defined 1:1 stoichiometry with Gd3+ regardless of solvent polarity. Meanwhile, the rate of ligand substitution between Gd-XO and the macrocyclic ligand is effectively minimized under non-aqueous conditions (kobs, buffer= 33.9 ± 1.0 x 10–3 s–1; kobs,MeOH = 5.62 ± 2.22 x 10–3 s–1). The binding reaction of Gd3+ with DOTA has comparable negative ΔG values in the two solvents (ΔGbuffer= ‒9.28 ± 0.57 kcal/mol; ΔGMeOH = ‒8.19 ± 0.14 kcal/mol), suggesting that the reaction is equally spontaneous under both conditions. However, computation of global thermodynamic properties demonstrate that the reaction is entropically-driven in acetate buffer in comparison with MeOH where the reaction is enthalpy-driven. Finally, the nature of solvent has an effect on the metal-to-ligand stoichiometry (N) of the resulting complex, which in acetate buffer (N = 1:1) is lower than that in MeOH (N = 1:2). These results are important in the context of optimizing reaction conditions in the preparation of related MRI contrast agents.

17.Pontillas, S. M., Marquez, M., Sumera, F., & Advincula, R. (2019). Optimizing the property of cross-linked carbazole-based polymer for efficient hole transport in bulk-heterojunction photovoltaic device. KIMIKA, 30 (1), Pages 13-17.more

Abstract:

Thin films made of cross-linked carbazole pendants of poly(ethylmethacrylate) deposited on indium tin oxide (ITO) was assessed for potential use as hole transport layer (HTL) in a fabricated photovoltaic cell configuration (ITO/PCDTBT/PCBM/Al). Before measurement, the film was designed to have uniform molecular weight, cross-linked carbazole for high electron mobility, high transmittance at the visible wavelength range and smoothness in morphology. Results showed that the film  provided 70 times more of current value at open circuit voltage than without the film under light illumination, at optimized thickness from 15 to 25 cycles of deposition at  25 mV/s using cyclic voltammetry.

18. Sakamoto, K., Ozaki, T., Yen-Chun, K., Tsai, C.F., Gong, Y., Morozumi, M., Ishikawa, Y., Uchimura, K., Nadanaka, S., Kitagawa, H., Zulueta, M.M.L., Bandaru, A., Tamura, J., Hung, S.C., and Kadomatsu, K. (2019). Glycan sulfation patterns define autophagy flux at axon tip via PTPRσ-cortactin axis. Nature Chemical Biology,15, Pages 699-709.more

Abstract:

Chondroitin sulfate (CS) and heparan sulfate (HS) are glycosaminoglycans that both bind the receptor-type protein tyrosine phosphatase PTPRσ, affecting axonal regeneration. CS inhibits axonal growth, while HS promotes it. Here, we have prepared a library of HS octasaccharides and, together with synthetic CS oligomers, we found that PTPRσ preferentially interacts with CS-E—a rare sulfation pattern in natural CS—and most HS oligomers bearing sulfate and sulfamate groups. Consequently, short and long stretches of natural CS and HS, respectively, bind to PTPRσ. CS activates PTPRσ, which dephosphorylates cortactin—herein identified as a new PTPRσ substrate—and disrupts autophagy flux at the autophagosome–lysosome fusion step. Such disruption is required and sufficient for dystrophic endball formation and inhibition of axonal regeneration. Therefore, sulfation patterns determine the length of the glycosaminoglycan segment that bind to PTPRσ and define the fate of axonal regeneration through a mechanism involving PTPRσ, cortactin and autophagy.

 

19. Wang, C.I., Braza, M.K.E., Claudio, G.C., Nellas, R.B. and Hsu, C.P. (2019). Machine learning for predicting electron transfer coupling. The Journal of Physical Chemistry A, 123 (36), Pages 7792-7802.more

Abstract:

Electron transfer coupling is a critical factor in determining electron transfer rates. This coupling strength can be sensitive to details in molecular geometries, especially intermolecular configurations. Thus, studying charge transporting behavior with a full first-principle approach demands a large amount of computation resources in quantum chemistry (QC) calculation. To address this issue, we developed a machine learning (ML) approach to evaluate electronic coupling. A prototypical ML model for an ethylene system was built by kernel ridge regression with Coulomb matrix representation. Since the performance of the ML models highly dependent on their building strategies, we systematically investigated the generality of the ML models, the choice of features and target labels. The best ML model trained with 40 000 samples achieved a mean absolute error of 3.5 meV and greater than 98% accuracy in predicting phases. The distance and orientation dependence of electronic coupling was successfully captured. Bypassing QC calculation, the ML model saved 10–104 times the computation cost. With the help of ML, reliable charge transport models and mechanisms can be further developed.

 

20. Yeh, C.J., Ku, C.C., Lin, W.C., Fan, C.Y., Zulueta, M., Manabe, Y., Fukase, K., Li, Y.K. and Hung, S.C. (2019). Single-step per-O-sulfonation and 1,6-Anhydro-bridge formation of sugar oligomers for fibroblast growth factor interactions. Chembiochem. 20 (2), Pages 237-240.more

Abstract:

Many circulating cancer‐related proteins, such as fibroblast growth factors (FGFs), associate with glycosaminoglycans—particularly heparan sulfate—at the cell surface. Disaccharide analogues of heparan sulfate had previously been identified as the shortest components out of the sugars that bind to FGF‐1 and FGF‐2. Taking note of the typical pose of l‐iduronic acid, we conceived of per‐O‐sulfonated analogues of such disaccharides, and devised a single‐step procedure for per‐O‐sulfonation of unprotected sugars with concomitant 1,6‐anhydro bridge formation to achieve such compounds through direct use of SO3Et3N as sulfonation reagent and dimethylformamide as solvent. The synthesized sugars based on the oligomaltose backbone bound FGF‐1 and FGF‐2 mostly at the sub‐micromolar level, although the tetrasaccharide analogue achieved low‐nanomolar binding with FGF‐2.

 

IESM logo

1. Bagtasa, G. (2019). 118-year climate and extreme weather events of Metropolitan Manila in the Philippines. International Journal of Climatology.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. Hagad, H.R., Cayetano, M.G. (2019). PM10 and surface dust source characterization in Baguio City Central Business District (CBD), Philippines. Environmental Geochemistry and Health, 41 (1), pages 427-446.more

Abstract:

This study measured both PM 10 and surface dust concentrations at roadside in the Central Business District of Baguio City. A total of 66 PM 10 filters and 25 surface dust samples were analyzed for 14 metals (Na, Mg, Al, Ca, Cr, Mn, Co, Ni, Cu, Zn, As, Sr, Cd and Pb) using inductively coupled plasma mass spectrometer ICP-MS to characterize sources of airborne particulate matter (APM). Calculation of enrichment factors indicated elements Zn, Cd, Pb and As to be enriched in both PM 10 and surface dust samples. The compositional signature of local surface dust was found to be strongly correlated with that of PM 10 particles. Enrichment Factor, Conditional Probability Function (CPF), Correlation Analysis and Principal component analysis were applied to determine sources affecting the Baguio CBD area, and results indicate three APM contributing sources (1) soil sources and (2) soil–road dust resuspension and vehicular emissions (3) vehicular emissions. The NE and SW wind sectors were dominant for most of the identified sources.

 

3. Kecorius, S., Madueño, L., Löndahl, J., Vallar, E., Galvez, M.C., Idolor, L.F., Cayetano, M.G., Müller, T., Birmili, W., Wiedensohler, A. (2019). Respiratory tract deposition of inhaled roadside ultrafine refractory particles in a polluted megacity of South-East Asia. Science of the Total Environment, 663, pages 265-274.more

Abstract:

Recent studies demonstrate that Black Carbon (BC) pollution in economically developing megacities remain higher than the values, which the World Health Organization considers to be safe. Despite the scientific evidence of the degrees of BC exposure, there is still a lack of understanding on how the severe levels of BC pollution affect human health in these regions. We consider information on the respiratory tract deposition dose (DD) of BC to be essential in understanding the link between personal exposure to air pollutants and corresponding health effects.

In this work, we combine data on fine and ultrafine refractory particle number concentrations (BC proxy), and activity patterns to derive the respiratory tract deposited amounts of BC particles for the population of the highly polluted metropolitan area of Manila, Philippines. We calculated the total DD of refractory particles based on three metrics: refractory particle number, surface area, and mass concentrations. The calculated DD of total refractory particle number in Metro Manila was found to be 1.6 to 17 times higher than average values reported from Europe and the U.S. In the case of Manila, ultrafine particles smaller than 100 nm accounted for more than 90% of the total deposited refractory particle dose in terms of particle number.

This work is a first attempt to quantitatively evaluate the DD of refractory particles and raise awareness in assessing pollution-related health effects in developing megacities. We demonstrate that the majority of the population may be highly affected by BC pollution, which is known to have negative health outcomes if no actions are taken to mitigate its emission. For the governments of such metropolitan areas, we suggest to revise currently existing environmental legislation, raise public awareness, and to establish supplementary monitoring of black carbon in parallel to already existing PM10 and PM2.5 measures.

 

4. Smith, A.B., Pacini, A.F., Nachtigall, P.E., Laule, G.L., Aragones, L.V., Magno, C., Suarez, J.A. (2019). Transmission beam pattern and dynamics of a spinner dolphin (Stenella longirostris). The Journal of the Acoustical Society of America, 145 (6).more

Abstract:

Toothed whales possess a sophisticated biosonar system by which ultrasonic clicks are projected in a highly directional transmission beam. Beam directivity is an important biosonar characteristic that reduces acoustic clutter and increases the acoustic detection range. This study measured click characteristics and the transmission beam pattern from a small odontocete, the spinner dolphin (Stenella longirostis). A formerly stranded individual was rehabilitated and trained to station underwater in front of a 16-element hydrophone array. On-axis clicks showed a mean duration of 20.1 μs, with mean peak and centroid frequencies of 58 and 64 kHz [standard deviation (s.d.) ±30 and ±12 kHz], respectively. Clicks were projected in an oval, vertically compressed beam, with mean vertical and horizontal beamwidths of 14.5° (s.d. ± 3.9) and 16.3° (s.d. ± 4.6), respectively. Directivity indices ranged from 14.9 to 27.4 dB, with a mean of 21.7 dB, although this likely represents a broader beam than what is normally produced by wild individuals. A click subset with characteristics more similar to those described for wild individuals exhibited a mean directivity index of 23.3 dB. Although one of the broadest transmission beams described for a dolphin, it is similar to other small bodied odontocetes.

5. Tinio, M.M.R., Rollon, A.P., Moya, T.B. (2019). Synergy in the urban solid waste management system in Malolos city, Philippines. Philippine Journal of Science, 148 (1), Pages 73-79.more

Abstract:

The paper demonstrates through system dynamics modelling how the following variables work together in the urban solid waste management (USWM) system: population, city income, public participation, composting and recycling, and greenhouse gas emissions. Malolos City, Philippines, is used as a case study for three ten-year model scenarios: (1) USWM with no composting and recycling, (2) USWM with an operational materials recovery and composting facility (MRCF), and (3) USWM with operational MRCF and incorporated effects of public participation towards solid waste management practices. The operation of the MRCF in Scenario 2 reduced total volume of disposed solid waste by about 25,000 tons but increased total expenses for solid waste management by about Php 37M. The incorporation of the effects of public participation in Scenario 3 further reduced the volume of disposed solid waste by about 103,900 tons; reduced the volume of generated solid waste by around 101,000 tons; and allowed the informal collection of 9,966 tons of recyclables. Estimates of CH4 and CO2 emissions also decreased in Scenario 3. The results revealed how composting and recycling and public participation affects the USWM through reduced waste volumes and increased savings.

6. Uldo, D.A., Feliciano, C., Cayetano, M., De Guzman, Zenaida. (2019). Gamma irradiation for the inactivation of Aspergillus niger in aged cotton fabric. Radiation physics and chemistry, 165, 108399.more

Abstract:

To address the problem of biodegradation of fiber-based museum natural textiles, several decontamination methods are being used; the most common of which is chemical fumigation. However, the use of toxic chemicals presents not only occupational health hazards, but also challenges in terms of legal restrictions regarding environmental release and waste disposal. Methods that eliminate toxic pollutant release while offering low resource (energy and water) requirements and faster and effective treatment are desirable. This study investigated the use of gamma irradiation as an alternative fungal decontamination method for aged undyed 100% cotton fabric. Fabric samples inoculated with Aspergillus niger were irradiated at increasing doses of gamma radiation from a Co-60 source in the irradiation facility of the Philippine Nuclear Research Institute to determine its radiation sensitivity. The decimal reduction value (D10) was determined to be 0.21 kGy, which is sufficient to inactivate 90% of the total colony forming units initially obtained. The minimum dose required for high level disinfection (6-log reduction) of the textile material is 1.26 kGy. To determine the effects of gamma radiation to strength and color properties, fabric samples were irradiated at doses 0.1–25 kGy then subjected to breaking strength and elongation and color measurement tests. Physical property testing reveals that cotton fabrics of similar composition and construction as the one used in the study do not undergo significant degradation in terms of breaking strength up to 10 kGy dose. This may be regarded as the maximum dose of irradiation, which is well above the minimum dose of 1.26 kGy required to effectively decontaminate the textile material from A. niger. Gamma irradiation with cobalt-60 is an effective decontamination method for cotton fabrics that may be used for museum applications.

 

7. Villanueva, J.C.B., Ringor, C.L., Pascua, C.S., Miyazawa, K. (2019). Size, structure, and conductivity of plant oil-derived carbon nanospheres synthesized by atmospheric ionization CVD. Materials Chemistry and Physics, 225, Pages 84-90.more

Abstract:

Particle size of the as-deposited carbon spheres (CSs) from plant-derived oil precursor was modified through the addition of a corona discharge ionizer as an attachment to the conventional atmospheric chemical vapor deposition (CVD) setup. Influences of synthesis parameters such as temperature, solvent-oil concentration, and the presence of ionization on the particle size distribution, graphitization, and conductivity of the CSs were also investigated. The addition of pyridine as a solvent to the Calophyllum inophyllum (CI) oil improved precursor atomization, breaking down the viscous oil into finer vapor intermediates and consequently, the process of decomposition. Measured particle size distribution from scanning electron microscope (SEM) and atomic force microscope (AFM) images show a decrease in mean particle diameter, from >180 nm without ionization to <100 nm with ionization. This relates mostly to the decrease in Brownian motion of particles within the system during deposition due to the presence of opposing electrostatic forces brought about by particles having the same electric charge. TEM images confirm the presence of concentrically-wrapped layers of carbon at the surface. Raman spectra also show the presence of graphitic layering within the carbon spheres, with two primary peaks located at 1350 cm−1 and 1580 cm−1 pertaining to both the D and the G bands of all in-plane bonded carbon atoms, respectively. Ionized samples have higher ID/IG ratios, suggesting a short order graphitization compared to non-ionized samples. However, samples prepared at higher temperatures show a slight improvement in the level of graphitization with a decreased ID/IG ratio. Currentvoltage measurements from conductive AFM have a general ohmic behavior for all non-powdered CSs. Ionized samples show lower sheet resistance (23.13160.72kΩ) possibly due to reduced particle size. The nanometer size may have resulted to lower void fraction, allowing efficient electron flow. This study emphasizes nanometer size control of conducting carbon spheres from sustainable resources.

 

IM

1. Akiyama, S., Caalim, J., Imai, K., & Kaneko, H. (2019). Corona Limits of Tilings: Periodic Case. Discrete and Computational Geometry, 61 (3), Pages 626–652.more

Abstract:

We study the limit shape of successive coronas of a tiling, which models the growth of crystals. We define basic terminologies and discuss the existence and uniqueness of corona limits, and then prove that corona limits are completely characterized by directional speeds. As an application, we give another proof that the corona limit of a periodic tiling is a centrally symmetric convex polyhedron [see Zhuravlev (St Petersbg Math J 13(2):201–220, 2002) and Maleev and Shutov (Layer-by-layer growth model for partitions, packings, and graphs, Tranzit-X, Vladimir, 2011)].

2. Arceo, Carlene P.C., Jose, Editha C., Lao, Angelyn R., Mendoza, Eduardo R. (2019). Chemical Reaction Networks: Filipino Contributions to Their Theory and Its ApplicationsPhilippine Journal of Science, 148 (2), Pages 249-261.more

Abstract:

This paper reviews the theory of chemical reaction networks and the contributions of Filipino scientists to it. The modern theory of chemical reaction networks began in the early 1970´s with the work of American chemical engineers and chemists from Canada and Russia. The field was reshaped at the turn of the century with the emergence of systems biology and biologists, computer scientists, mathematicians, and researchers from other disciplines joining the collaborative efforts. Luis F. Razon, a chemical engineer, and Baltazar D. Aguda, a chemist, were the first Filipinos to contribute to the theory with their Ph.D. theses in 1985 and 1986, respectively. Over twenty-five years later in 2014, mathematicians from several Philippine universities revived the research – focusing on power law kinetic systems and biological applications – and contributing nine international publications since. The paper concludes with a description of their current research and some promising perspectives.

 

3. Almocera, A. E. S., Hsu, S.-B., & Sy, P. W. (2019). Extinction and uniform persistence in a microbial food web with mycoloop: Limiting behavior of a population model with parasitic fungi. Mathematical Biosciences and Engineering, 16 (1), Pages 516–537.more

Abstract:

It is recently known that parasites provide a better picture of an ecosystem, gaining attention in theoretical ecology. Parasitic fungi belong to a food chain between zooplankton and inedible phytoplankton, called mycoloop. We consider a chemostat model that incorporates a single mycoloop, and analyze the limiting behavior of solutions, adding to previous work on steady-state analysis. By way of persistence theory, we establish that a given species survives depending on the food web configuration and the nutrient level. Moreover, we conclude that the model predicts coexistence under bounded nutrient levels.

 

4. Aricheta, V. M. (2019). Supersingular Elliptic Curves and Moonshine. Symmetry, Integrability and Geometry: Methods and Applications, 15, Article number 7.more

Abstract:

We generalize a theorem of Ogg on supersingular j-invariants to supersingular elliptic curves with level. Ogg observed that the level one case yields a characterization of the primes dividing the order of the monster. We show that the corresponding analyses for higher levels give analogous characterizations of the primes dividing the orders of other sporadic simple groups (e.g., baby monster, Fischer's largest group). This situates Ogg's theorem in a broader setting. More generally, we characterize, in terms of supersingular elliptic curves with level, the primes arising as orders of Fricke elements in centralizer subgroups of the monster. We also present a connection between supersingular elliptic curves and umbral moonshine. Finally, we present a procedure for explicitly computing invariants of supersingular elliptic curves with level structure.

 

5. Canlubo, C. R. (2019). Weak algebra bundles and associator varieties. Philippine Journal of Science, 148 (2), Pages 309–316.more

Abstract:

Algebra bundles, in the strict sense, appear in many areas of geometry and physics. However, the structure of an algebra is flexible enough to vary non-trivially over a connected base – giving rise to a structure of a weak algebra bundle. We will show that the notion of a weak algebra bundle is more natural than that of a strict algebra bundle by illustrating that the classifying object of algebra bundles and, consequently, of weak algebra bundles is a weak algebra bundle. We will give necessary and sufficient conditions for weak algebra bundles to be locally trivial. The collection of non-trivial associative algebras of a fixed dimension forms a projective variety called associator varieties. We will show that these varieties play the role the Grassmannians play for principal O(n)-bundles.

 

6. Damasco, J. R. C. G., Frettlöh, D., & Loquias, M. J. C. (2019). Fundamental domains for rhombic lattices with dihedral symmetry of order 8. Electronic Journal of Combinatorics, 26 (3), Article number P3.5.more

Abstract:

We show by construction that every rhombic lattice Γ in R2 has a fundamental domain whose symmetry group contains the point group of Γ as a subgroup of index 2. This solves the last open case of a question raised in a preprint by the authors on fundamental domains for planar lattices whose symmetry groups properly contain the point groups of the lattices.

 

7. Dela Cruz, R.B. and Ol, S. (2019). Cheating-immune secret sharing schemes from maiorana-mcfarland boolean functions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 11396 LNCS, Pages 233-247.more

Abstract:

We consider cheating-immune secret sharing schemes proposed by Pieprzyk and Zhang. This type of secret sharing sheme keeps dishonest participants from having a better chance (over the honest ones) of knowing the secret using incorrect shares. We show that the class of Maiorana-McFarland Boolean functions can be used to construct such schemes. Consequently, new cheating-immune secret sharing schemes are presented.

 

8. Escaner JM IV, Rabajante J, Tabornal R. (2019). Mathematical Modeling on Competition and Cooperation of Species Using Hill-type Function. Proceedings of the 11th International Conference on Computer Modeling and Simulation, March 2019, Pages 8–18.more

Abstract:

Competition and cooperation play an important role in society. It drives the species to survive and it enables to balance and maintain the biodiversity in communities. These concepts are important in many fields, such as in ethology, economics, ecology, and evolutionary theory. In this paper, we develop a mathematical model that describes the dynamics of the population of a species that simultaneously interact with a competitor and/or with a cooperator. This modeling study uses a Hill-type function rather than the classical Lotka-Volterra equations. Numerical simulations are done on this model. Heat maps are used to describe different cases by varying the competition coefficient δ and cooperation coefficient γ. Our model has demonstrated not just coexistence but also exclusion or extinction of the population of species. This means that even if competition and cooperation are done simultaneously by a species, it is not a guarantee that they will always survive in the long run. It depends on how much the strength of competition and cooperation they exerted towards its co-competitor or co-cooperator. Moreover, cooperating species are most likely to survive as compared to the competing species. This modeling study enables us to look possibly for ways to control δ and γ, and consequently, control populations in our ecosystem. This will be useful not only for biologists and ecologists but also for researchers who are interested in studying the competitive and cooperative interactions of species in societies.

 

9. Gonzales K., Celeste R., & Corcino R. (2019). Staircase Tableaux and an Alternative Matrix Formula for Steady State Probabilities in the Asymmetric Exclusion Process (q = 1). Discrete Math. Lett., 2, Pages 26–31.more

Abstract:

We derive an alternative matrix formula for steady state probabilities in the asymmetric exclusion process where particles hop at equal rates inside a one-dimensional finite lattice. The result is derived using the combinatorial properties of staircase tableaux and alternative tableaux.

10. Hambric, C.L., Li, C.K. Pelejo, D.C. & Shi, J. (2019). Minimum number of non-zero-entries in a 7x7 stable matrix. Linear Algebra and its Applications, 572, Pages 135-152. more

Abstract:

We prove that if a 7×7 sign pattern matrix is potentially stable, then it has at least 11 non-zero entries. The results for n×n matrix with n up to 6 are known previously. We prove the result by making a list of possible associated digraphs with at most 10 edges, and then use algebraic conditions to show all of these digraphs or matrices cannot be potentially stable. In relation to this, we also determine the minimum number of edges in a strongly connected digraph depending on its circumference.

 

11.  Jung, E., De Los Reyes, A. A., Pumares, K. J., & Kim, Y. (2019). Strategies in regulating glioblastoma signaling pathways and anti-invasion therapy. PLoS ONE, 14 (4), Pages 1–34.more

Abstract:

Glioblastoma multiforme is one of the most invasive type of glial tumors, which rapidly grows and commonly spreads into nearby brain tissue. It is a devastating brain cancer that often results in death within approximately 12 to 15 months after diagnosis. In this work, optimal control theory was applied to regulate intracellular signaling pathways of miR-451–AMPK–mTOR–cell cycle dynamics via glucose and drug intravenous administration infusions. Glucose level is controlled to activate miR-451 in the up-stream pathway of the model. A potential drug blocking the inhibitory pathway of mTOR by AMPK complex is incorporated to explore regulation of the down-stream pathway to the cell cycle. Both miR-451 and mTOR levels are up-regulated inducing cell proliferation and reducing invasion in the neighboring tissues. Concomitant and alternating glucose and drug infusions are explored under various circumstances to predict best clinical outcomes with least administration costs.

 

12. Lope, J. E. C., Sato, R., & Vernescu, B. (2019). Well-posedness of steady state Navier–Stokes equations with slip boundary conditions. Applicable Analysis, 98 (1–2), Pages 295–309.more

Abstract:

We study the motion of a viscous incompressible fluid in a bounded region of R3 containing finitely many rigid solid particles of small size. On the boundary of the particles, we prescribe the slip boundary condition of the form developed in Fujita H. [A mathematical analysis of motions of viscous incompressible fluid under leak or slip boundary conditions. Mathematical fluid mechanics and modeling (Kyoto, 1994). Srikaisekikenkysho Kkyroku No. 888; 1994. p. 199–216] and Le Roux C, Tani A. [Steady solutions of the Navier–Stokes equations with threshold slip boundary conditions. Math Methods Appl Sci. 2007;30(5):595–624]. We derive a weak formulation of the problem and obtain an equivalent variational inequality formulation. Sufficient conditions for existence, uniqueness, and continuous dependence on data are obtained.


13. Palen, D. I., Almarinez, B. J. M., Amalin, D. M., Legaspi, J. C., & David, G. (2019). A Host-Parasitoid Model for Aspidiotus rigidus (Hemiptera: Diaspididae) and Comperiella calauanica (Hymenoptera: Encyrtidae). Environmental Entomology, 48 (1), Pages 134–140.more

Abstract:

The outbreak of the coconut scale insect Aspidiotus rigidus Reyne (Hemiptera: Encyrtidae) posed a serious threat to the coconut industry in the Philippines. In this article, we modeled the interaction between A. rigidus and its parasitoid Comperiella calauanica Barrion, Almarinez, Amalin (Hymenoptera: Encyrtidae) using a system of ordinary differential equations based on a Holling type III functional response. The equilibrium points were determined, and their local stability was examined. Numerical simulations showed that C. calauanica may control the population density of A. rigidus below the economic injury level. 

 

14. Pilar-Arceo, C. P. C., Jose, E. C., Lao, A. R., & Mendoza, E. R. (2019). Chemical reaction networks: Filipino contributions to their theory and its applications. Philippine Journal of Science, 148 (2), Pages 249–261.   

Abstract:

This paper reviews the theory of chemical reaction networks and the contributions of Filipino scientists to it. The modern theory of chemical reaction networks began in the early 1970 ́s with the work of American chemical engineers and chemists from Canada and Russia. The field was reshaped at the turn of the century with the emergence of systems biology and biologists, computer scientists, mathematicians, and researchers from other disciplines joining the collaborative efforts. Luis F. Razon, a chemical engineer, and Baltazar D. Aguda, a chemist, were the first Filipinos to contribute to the theory with their Ph.D. theses in 1985 and 1986, respectively. Over twenty-five years later in 2014, mathematicians from several Philippine universities revived the research – focusing on power law kinetic systems and biological applications – and contributing nine international publications since. The paper concludes with a description of their current research and some promising perspectives.

 

15. Pelejo, Diane Christine and Abagat, Jean Leonardo. (2019). On Sign Pattern Matrices that Allow or Require Algebraic PositivityElectronic Journal of Linear Algebra, 35, Pages 331-356.more

Abstract:

A square matrix M with real entries is algebraically positive (AP) if there exists a real polynomial p such that all entries of the matrix p(M) are positive. A square sign pattern matrix S allows algebraic positivity if there is an algebraically positive matrix M whose sign pattern is S. On the other hand, S requires algebraic positivity if matrix M, having sign pattern S, is algebraically positive. Motivated by open problems raised in a work of Kirkland, Qiao, and Zhan (2016) on AP matrices, all nonequivalent irreducible 3 by 3 sign pattern matrices are listed and classify into three groups (i) those that require AP, (ii) those that allow but not require AP, or (iii) those that do not allow AP. A necessary condition for an irreducible n by n sign pattern to allow algebraic positivity is also provided.

 

16. Rabajante, J. F., Custodio, C. J. D. M., Babierra, A. L., Collera, J. A., De Los Reyes, A. A., del Rosario, R. C. H., … Tubay, J. M. (2019). Birthing a mathematical biology community in the Philippines. Philippine Science Letters, 12 (2), Pages 104–106.  

Abstract:

The International Workshop on Mathematical Biology, or IWOMB, has already been held for two consecutive years in the Philippines. The first workshop was held on January 7-10, 2018 at Costabella Tropical Beach Resort, Cebu City, Philippines [1]. The second workshop was held on January 6-10, 2019 at Bohol Bee Farm, Bohol, Philippines [2]. Like a mother bearing a child, the IWOMB has been thought of as an avenue to organize and build a strong mathematical biology community dedicated to the training and mentoring of young researchers. IWOMB participants include emerging researchers and graduate students from different provinces of the Philippines and neighboring countries, who are interested in diverse topics on mathematical biology. The workshop also aims to explore research breakthroughs and give birth to fresh ideas from scientific discussions between Filipino and foreign mathematical biology enthusiasts.

 

17. Recio, Kristine Rey O. and Mendoza, Renier (2019). Three-step Approach to Edge Detection of TextsPhilippine Journal of Science, 148 (1), Pages 193-211.more   

Abstract:

We proposed a three-step image segmentation approach to determine the edges of images containing old texts. In general, texts from old books and articles tend to be very noisy. Thus, we first employed a suitable denoising method to obtain a smooth approximation I_s of a given image I ̃. Then, the fuzzy edge map E ̃ was obtained using the gradient of I_s. This gradient map gave an estimate of the edges of the texts. For the second step, the method of k-means++ with two clusters was employed to separate the edges from rest of the image. Because a smooth approximation of the image was used, the edges obtained are "thick." And so, in the last step of the method, the binary image generated from the previous step was post-processed using a thinning algorithm. We implemented our method to images containing Baybayin texts from the National Museum of the Philippines.

 

18. Riñon, J. B. E., Mendoza, R. G., & Mendoza, V. M. P. (2019). Parameter Estimation of an S-system Model Using Hybrid Genetic Algorithm with the Aid of Sensitivity Analysis. PCSC 2019: Proceedings of the 19th Philippine Computing Science Congress, Pages 94-102.more

Abstract:

A biochemical system is a biological system consisting of a collection of chemical compounds interacting with each other. One way to model and analyze a biochemical system is by using S-systems, which are coupled ordinary differential equations based on power-law formalism. In this paper, we do a parameter estimation on an S-system model called HS96. This model, proposed by Hlavacek and Savageau in 1996, describes a simple genetic network consisting of five states Xi, i = 1, 2, 3, 4, 5. As a preliminary method, sensitivity analysis of HS96 is conducted to investigate the change in model outputs with respect to the changes in model parameters. Usual model outputs are Xi and Xi, i = 1, 2, 3, 4, 5. From the results of the sensitivity analysis, model outputs are selected which are then used to estimate the parameters of the HS96 model. A hybrid of genetic algorithm with a local minimizer is used in the parameter estimation.

 

19. Rivero, Rachelle & David, G. (2019). Modeling Structural Breakpoints in Volatility of Philippine Peso-US Dollar Currency Exchange Rate.  Edited by Rahmawati, Y.  Empowering Science and Mathematics for Global Competitiveness: Proceedings. London: CRC Press.more

Abstract:

This work presents a novel method to determine structural breakpoints in volatility of a time series.  The proposed method called the breakpoint-search algorithm, utilizes the log-likehood function value derived from the fitted Generalized Auto-Regressive Conditional Heteroskedasticity (GARCH) model of the given data.  In many time series models, volatility is approximated to be constant over a period of time or moving from one regime to another.  In such cases, it is important to determine when shifts in volatility patterns occur, in order to capture the behavior of the data very well.  The proposed model, together with the GARCH model, are used to identify periods of high and low volatility, and to assess the long-term volatility of the time series.  To test the efficacy of the proposed algorithm, the method is applied to a real-world time series data, such as the Philippine Peso-US-Dollar currency exchange rate.  Empirical results agree with the events in Philippine history indicating periods of economic instability.  

 

20. Rivero, R., Onuma, Y., & Kato, T. (2019). Threshold Auto-Tuning Metric Learning. IEICE Transactions on Information and Systems, E102D (6), Pages 1163–1170.more

Abstract:

It has been reported repeatedly that discriminative learning of distance metric boosts the pattern recognition performance. A weak point of ITML-based methods is that the distance threshold for similarity/dissimilarity constraints must be determined manually and it is sensitive to generalization performance, although the ITML-based methods enjoy an advantage that the Bregman projection framework can be applied for optimization of distance metric. In this paper, we present a new formulation of metric learning algorithm in which the distance threshold is optimized together. Since the optimization is still in the Bregman projection framework, the Dykstra algorithm can be applied for optimization. A nonlinear equation has to be solved to project the solution onto a half-space in each iteration. Naïve method takes O (LMn 3) computational time to solve the nonlinear equation. In this study, an efficient technique that can solve the nonlinear equation i n O (Mn 3 ) has been discovered. We have proved that the root exists and is unique. We empirically show that the accuracy of pattern recognition for the proposed metric learning algorithm is comparable to the existing metric learning methods, yet the distance threshold is automatically tuned for the proposed metric learning algorithm.

21. Villar, J. J. S., Lubenia, P. V. N., Mendoza, E. R., & Pilar-Arceo, C. P. C. (2019). Structural Stability Analysis of Models of Dopamine Synthesis and D1 Receptor Trafficking in RPT Cells using CRNT. Philippine Journal of Science, 148 (3), Pages 523–533.more

Abstract:

Dopamine plays an important role in different physiological and metabolic functions, including the control of sodium excretion in the kidney. Studies have shown that there is a positive correlation between a defect in dopamine synthesis and/or dopamine receptor function, and a defect in renal sodium excretion – which may lead to the development of essential hypertension. Specific receptors for dopamine, such as the D1 receptor, have been identified in the various regions within the kidney. It is observed that errors regarding dopamine receptor-G protein coupling and changes in the signaling components may be responsible for the failure of dopamine to increase sodium excretion in hypertensive subjects. In this paper, two symbolic kinetic models of dopamine synthesis and one of dopamine D1 receptor trafficking are presented. The three models are chemical reaction networks constructed and analyzed using Chemical Reaction Network Theory (CRNT), a framework that provides different insights on the static properties of a chemical reaction network regarding the existence of steady states, their multiplicity, and structural stability. It is found that all three networks do not support multiple steady states.

  

 

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1. Bardolaza, H.,  Afalla, J.,  De Los Reyes, A.,  Lumantas, D.A.,  Vasquez, J.D.,  Muldera, J.,  Mag-usara, V.K.,  Somintac, A.,  Salvador, A.,  Tani, M.,  Estacio, E. (2019). Efficacy of proposed 2DEG-based photoconductive antenna using magnetic bias-controlled carrier transport. Current Applied Physics, 19 (6), Pages 756-761.more

Abstract:

An externally applied magnetic field was used to induce increased photocarrier transport along the high mobility channel in GaAs/AlGaAs modulation-doped heterostructures (MDH). The terahertz (THz) emission from GaAs/AlGaAs MDH increases with increasing magnetic field, applied parallel to the heterojunction. The THz emission enhancement factors due to the magnetic field in MDH are higher than in undoped GaAs/AlGaAs heterojunction and in bulk SI-GaAs. This demonstrates that properly utilizing the high-mobility channel for carrier transport promises to be a viable design consideration for efficient THz photoconductive antenna (PCA) devices. Moreover, it was observed that for MDH, as well as for an undoped GaAs/AlGaAs heterojunction, the enhancement for one magnetic field direction is greater than the enhancement for the opposite direction. This is in contrast to the symmetric enhancement with magnetic field direction observed in a bulk SI-GaAs. An analysis of photocarrier trajectories under an external magnetic field supports the explanation that the enhancement asymmetry with magnetic field direction in MDH is due to the cycloid motion of electrons as affected by the GaAs/AlGaAs interface.

2. Gili, M.B.Z., Conato, M.T. (2019). Adsorption uptake of mordenite-type zeolites with varying si/al ratio on zn2+ ions in aqueous solution. Materials Research Express, 6 (4).more

Abstract:

The adsorption uptake of synthetic mordenite-type zeolites with varying Si/Al ratio was investigated for Zn2+ ions in aqueous solution to determine the influence of Si/Al ratio in removing heavy metals. Synthetic mordenites were hydrothermally synthesized from gel solutions with Si/Al ratio of 10, 15 and 20 as denoted by samples SAR10, SAR15 and SAR20 respectively. The samples were characterized using XRD, SEM, XRF, and TG-DTA. The adsorption kinetic and thermodynamic behaviour of the synthetic mordenites were examined. From the kinetic study, the pseudo-second-order kinetic model best fit the kinetic data among other models (i.e. pseudo-first order and intraparticle-diffusion models). It was found that cation-exchange was the most dominant adsorption mechanism. Further, it was observed that thepH level significantly affects the sorption of Zn2+ ions. The uptake of crystalline mordenite increases more than threefold from 7.19 mg Zn2+/g at pH?=?3 to 24.27 mg Zn2+/g atpH?=?7 using feed solution of 100 mg Zn2+/L. With regards to the equilibrium data, the adsorption isotherm generated from Langmuir model fits better than that of Freundlich model. Accordingly, the theoretical maximum adsorption capacities of SAR10, SAR15 and SAR20 are 39.97, 48.90, 32.48 mg Zn2+/g respectively. The lower the Si/Al ratio, the higher the negative charge density of zeolites resulting to a higher cation exchange capacity (CEC). However, lower Si/Al ratio do not automatically mean higher maximum adsorption capacity of mordenites to heavy metal ions especially Zn2+, as demonstrated in this study.

 

3. Gili, M.B.Z., Conato, M.T. (2019). Synthesis and characterization of mordenite-type zeolites with varying Si/Al ratio. Materials Research Express, 6 (1), article number 015515.more

Abstract:

One factor that makes mordenite-type zeolites attractive in adsorption applications is its high cation exchange capacity (CEC) that can further be improved by controlling its Si/Al ratio (SAR). Mordenite-type zeolites with SAR of 25, 20, 15, 10 and 5 were attempted to synthesize via hydrothermal method using silica gel and sodium aluminate as Si and Al sources respectively. The SAR was varied by changing the molar composition of the starting gel solution. The starting solution with theoretical SAR of 15 and 10 successfully produced mordenite with high degree of crystallinity and purity. At high SAR equal to 20, the product was found to be amorphous with significant peaks indexed to mordenite. Amorphous materials were mostly formed from the starting solution with theoretical SAR of 25. On the other hand, the starting solution with theoretical SAR of 5 yielded analcime-type zeolites. FTIR confirms the presence of vibrational bands that are typical to zeolites and/or aluminosilicates for all samples. The synthesized crystalline mordenites have prismatic, hexagonal shapes while others have fibrous or needle-like structures. XRF analysis shows that the synthetic mordenites indeed have varying actual SAR, though the values are lower than expected. 

 

4. Jose, A.,  Montecillo, A.,  De Los Reyes, A.,  Bacaoco, M.,  Lopez, J.,  Cafe, A.,  Faustino, M.A.,  Husay, H.A.,  Vasquez, J.D.,  Gonzales, K.C.,  Catindig, G.A.,  Afalla, J.P.,  Mag-usara, V.K.,  Kitahara, H.,  Tani, M.,  Somintac, A.,  Salvador, A.,  Estacio, E. (2019). Enhanced terahertz emission of a gallium arsenide thin film on a porous silicon distributed Bragg reflector designed at 800nm wavelength. Optical Materials, 92, Pages 335-340.more

Abstract:

Enhanced terahertz (THz) radiation was generated from a gallium arsenide thin film integrated on top of porous silicon distributed Bragg reflector (GaAs/PSi DBR). The film's thickness was designed to be less than the penetration depth of the 800 nm excitation source, while the PSi DBR was centered at the laser wavelength to reflect the transmitted photons at the film-substrate interface. Reflection-geometry THz time-domain spectroscopy measurement revealed enhancement in THz peak to peak amplitude by 1.67 and 5.7 times as compared to the same thickness of GaAs on silicon (GaAs/Si) and bulk semi-insulating (SI) GaAs, respectively. In comparison with the bulk SI-GaAs, both thin film samples showed an order of magnitude improvement in the THz output power. The excitation-wavelength study also revealed a maximum increase near the design wavelength. The enhancement was attributed to the high reflectivity at the film-substrate interface and optical cavity effect in GaAs. These factors contributed to an effective optical confinement within the film's THz generation region.

5. Santos-Putungan, A.B., Stojić, N., Binggeli, N., Paraan, F.N.C. (2019). Strong chemisorption of CO2 on B10–B13 planar-type clusters. Journal of Physics Condensed Matter, 31 (14), Article number 145504.more

Abstract:

An ab initio density functional study was performed investigating the adsorption of CO2 on neutral boron B n (n  =  10–13) clusters that are characterized by planar and quasiplanar ground-state atomic structures. For all four clusters, we found large chemisorption binding energies, reaching 1.6 eV between CO2 and B12, with the adsorbed molecule oriented in the plane of the cluster and adsorbed along the cluster edge. A configuration with chemisorbed dissociated CO2 molecule also exists for B11 and B13 clusters. The strong adsorption is due to the bending of the CO2 molecule, which provides energetically accessible fully in-plane frontier molecular orbitals matching the edge states of the clusters. At the same time, the intrinsic dipole moment of a bent CO2 molecule facilitates the transfer of excess electronic charge from the cluster edges to the molecule.

6. Villanueva, J.C.B., Ringor, C.L., Pascua, C.S., Miyazawa, K. (2019). Size, structure, and conductivity of plant oil-derived carbon nanospheres synthesized by atmospheric ionization CVDMaterials Chemistry and Physics225, Pages 84-90.more

Abstract:

Particle size of the as-deposited carbon spheres (CSs) from plant-derived oil precursor was modified through the addition of a corona discharge ionizer as an attachment to the conventional atmospheric chemical vapor deposition (CVD) setup. Influences of synthesis parameters such as temperature, solvent-oil concentration, and the presence of ionization on the particle size distribution, graphitization, and conductivity of the CSs were also investigated. The addition of pyridine as a solvent to the Calophyllum inophyllum (CI) oil improved precursor atomization, breaking down the viscous oil into finer vapor intermediates and consequently, the process of decomposition. Measured particle size distribution from scanning electron microscope (SEM) and atomic force microscope (AFM) images show a decrease in mean particle diameter, from >180 nm without ionization to <100 nm with ionization. This relates mostly to the decrease in Brownian motion of particles within the system during deposition due to the presence of opposing electrostatic forces brought about by particles having the same electric charge. TEM images confirm the presence of concentrically-wrapped layers of carbon at the surface. Raman spectra also show the presence of graphitic layering within the carbon spheres, with two primary peaks located at 1350 cm−1 and 1580 cm−1 pertaining to both the D and the G bands of all in-plane bonded carbon atoms, respectively. Ionized samples have higher ID/IG ratios, suggesting a short order graphitization compared to non-ionized samples. However, samples prepared at higher temperatures show a slight improvement in the level of graphitization with a decreased ID/IG ratio. Currentvoltage measurements from conductive AFM have a general ohmic behavior for all non-powdered CSs. Ionized samples show lower sheet resistance (23.13160.72kΩ) possibly due to reduced particle size. The nanometer size may have resulted to lower void fraction, allowing efficient electron flow. This study emphasizes nanometer size control of conducting carbon spheres from sustainable resources.

 

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1. Altamia M.A., Shipway J.R., Concepcion G.P., Haygood M.G., Distel D.L. (2019). Thiosocius teredinicola gen. nov., sp. nov., a sulfur-oxidizing chemolithoautotrophic endosymbiont cultivated from the gills of the giant shipworm, Kuphus polythalamius. International Journal of Systematic and Evolutionary Microbiology, Pages 1-7.more

Abstract:

A chemolithoautotrophic sulfur-oxidizing, diazotrophic, facultatively heterotrophic, endosymbiotic bacterium, designated as strain 2141T, was isolated from the gills of the giant shipworm Kuphus polythalamius (Teredinidae: Bivalvia). Based on its 16S rRNA sequence, the endosymbiont falls within a clade that includes the as-yet-uncultivated thioautotrophic symbionts of a marine ciliate and hydrothermal vent gastropods, uncultivated marine sediment bacteria, and a free-living sulfur-oxidizing bacterium ODIII6, all of which belong to the Gammaproteobacteria. The endosymbiont is Gram-negative, rod-shaped and has a single polar flagellum when grown in culture. This bacterium can be grown chemolithoautotrophically on a chemically defined medium supplemented with either hydrogen sulfide, thiosulfate, tetrathionate or elemental sulfur. The closed-circular genome has a DNA G+C content of 60.1 mol% and is 4.79 Mbp in size with a large nitrogenase cluster spanning nearly 40 kbp. The diazotrophic capability was confirmed by growing the strain on chemolithoautotrophic thiosulfate-based medium without a combined source of fixed nitrogen. The bacterium is also capable of heterotrophic growth on organic acids such as acetate and propionate. The pH, temperature and salinity optima for chemolithoautotrophic growth on thiosulfate were found to be 8.5, 34 °C and 0.2 M NaCl, respectively. To our knowledge, this is the first report of pure culture of a thioautotrophic animal symbiont. The type strain of Thiosocius teredinicola is PMS-2141T.STBD.0c.01aT (=DSM 108030T).

 

2. Bangi H.G.P., Juinio-Meñez M.A. (2019). Resource allocation trade-offs in the sea urchin Tripneustes gratilla under relative storminess and wave exposure. Marine Ecology Progress, 608, Pages 165-182.more

Abstract:

Increased temperature and storminess will render nearshore tropical organisms more vulnerable to climate change. The sea urchin Tripneustes gratilla lives in a wide range of habitats and can survive even in harsh conditions, but the mechanisms underlying its resilience are not well understood. We investigated the somatic and reproductive phenotypic traits of adults (66.78 ± 0.22 mm test diameter) from seagrass- and seaweed-dominated sites during 2 monsoon seasons in a location frequently disturbed by strong cyclones and northeasterly winds in the northeastern Philippines (NE Phil). These were compared with seagrass sites in a less exposed location in the northwest portion of the islands (NW Phil). Populations from NE Phil had significantly thicker and heavier body walls, but significantly smaller Aristotle’s lanterns, guts and gonads regardless of season compared to those from NW Phil. Moreover, the body walls in individuals from the seaweed-dominated sites were thicker and heavier. Allocation of the body wall to body weight was 62.2 and 53.7% in the NE Phil seaweed and seagrass sites, respectively, both of which were significantly greater than those from the NW Phil seagrass sites (44.74%). In contrast to other studies, plasticity in the Aristotle’s lantern was not related to food availability. The differences in the Aristotle’s lantern, gonad and body wall weights indicate a trade-off in resource allocation for feeding (growth) and reproduction in favor of maintenance. Comparative analysis of multiple phenotypic traits of T. gratilla populations provides substantive empirical field evidence and insights into the resilience of tropical species to increased storminess and wave exposure.

 

3. Benico, G.A., Takahashi, K. Lum, W.M., Yñiguez, A.T., Azanza, R.V., Leong, S.C.Y., Lim, P.T., Iwataki, M. (2019). First report of Biecheleriopsis adriatica in Bolinao, Northwestern Philippines and its wide distribution in Southeast Asia and adjacent waters. Philippine Journal of Natural Sciences, 24, Pages 34-41.

Abstract:

Morphology and phylogeny of the marine woloszynskioid dinoflagellate Biecheleriopsis adriatica, collected from Philippines, Singapore, Palau and Japan, were examined by using light and scanning electron microscopy (SEM), and molecular phylogeny based on rDNA sequences. Cells of these cultures were ovoid to spherical, measured 11.5–17.3 μm in length, with a displaced cingulum, a sigmoid sulcus and an eyespot. Cells have an elongate apical vesicle (EAV) mostly 3.1–3.8 μm in length with globular knobs up to 32, and straight lower cingular margin in the dorsal side. These morphological characters were identical to those of B. adriatica previously reported from the Adriatic Sea, China, Japan and Korea. Molecular phylogeny based on sequences of ITS and LSU rDNA revealed that the culture isolated from Bolinao, Philippines positioned in a clade with B. adriatica. Cultures isolated from Japan, Palau and Singapore had the identical morphological characters under light microscopy, and cultures investigated were positioned in B. adriatica clade in the phylogenetic tree of ITS and LSU rDNA. B. adriatica co-occurred with a bloom of Takayama sp. associated with mass mortality of farmed milkfish in May 2016 in Bolinao, Philippines. Based on existing data, this species is unlikely the culprit responsible for the massive fish kill event but the results suggest the need for further study to clarify its role in the overall dynamics of algal blooms in Bolinao. The results also show the wide distribution of B. adriatica in Southeast Asia and adjacent waters.

 

4. Hirabayashi S., Yokohama Y., Suzuki A., Esat T., Miyari Y., Aze T., Siringan F.P., Maeda Y. (2019). Local marine reservoir age variability at Luzon Strait in the South China Sea during the Holocene. Nuclear Instruments and Methods in Physics Research. Article in Press, Pages 1-7.more

Abstract:

Here, we report new estimates of local marine radiocarbon reservoir ages from northwestern Luzon Island in the Philippines, on the east side of the South China Sea. Data for two periods, through the 1940’s and the mid-Holocene, were derived from modern and fossil corals. Our results from Luzon Island show variable ΔR values, from −39 ± 25 to 337 ± 27 14C yr over the past 6000 years and highlight the importance of understanding temporal ΔR changes to obtain accurate radiocarbon dates for mid-Holocene samples. An abrupt shift in ΔR at 5.5 ka BP, in the east side of the South China Sea, can be attributed to changes in the intensity of the upwelling, in the eastern Pacific, and to the East Asian Monsoon. Additional reservoir age data from the Pacific is likely to reveal details of oceanographic and climate changes at this time.

5. Labrador K., Agmata A., Palermo J.D., Follante J., Pante M.J. (2019). Authentication of processed Philippine sardine products using Hotshot DNA extraction and minibarcode amplification. Food Control, 95, Pages 150-155.more

Abstract:

In lieu of the importance of species authentication of processed fishery products, no reports have been made on sardine products in the Philippines. This is partly because of the challenges in dealing with biological material that has been subjected to extreme conditions during the process. Although molecular tools are now within reach, they are often reliant on proprietary kits which make the process expensive. In this paper, we used hot sodium hydroxide and tris (HotSHOT) DNA extraction protocol and cytochrome oxidase I (COI) minibarcode amplification to genotype and identify selected brands of locally-produced canned and dried sardines. To validate, fresh representatives based on advertised and suspected identities of the processed samples were genotyped as well. Success rate of amplification has gone from 0% to 64% when the minibarcode was amplified, as opposed to using the full-length COI barcoding region. Phylogenetic analysis allowed for the successful identification of processed Sardinella lemuru. Species substitution was detected on samples marketed as dried tawilis; however, the resolving power of minibarcode was not enough to discriminate the samples up to the species level. Regardless, coupling HotSHOT extraction with minibarcode amplification proved to be effective with processed sardines. Using this method to authenticate other processed fishery products that have underwent extreme postharvest processing warrants further exploration.

 

6. Liang X, Luo D, Yan J-L, Rezzaei MA, Salvador-Reyes LA, Gunasekera SP, Li C, Ye T, Paul VJ, Luesch H. (2019). Discovery of amantamide, a selective CXCR7 agonist from marine cyanobacteria. Organic Letters, Article in Press, Pages 1-5.more

Abstract:

CXCR7 plays an emerging role in several physiological processes. A linear peptide, amantamide (1), was isolated from marine cyanobacteria, and the structure was determined by NMR and mass spectrometry. The total synthesis was achieved by solid-phase method. After screening two biological target libraries, 1 was identified as a selective CXCR7 agonist. The selective activation of CXCR7 by 1 could provide the basis for developing CXCR7-targeted therapeutics and deciphering the role of CXCR7 in different diseases.

 

7. Lum, W.M., Azanza, R.V., Furio, E., Lim, P.T., Lim, H.C., Takahashi, K., Iwataki, M. (2019). Morphology and molecular phylogeny of the harmful raphidophyte Chattonella subsalsa isolated from Bolinao, Philippines. Philippine Journal of Natural Sciences, 24, Pages 50-56.

Abstract:

Morphology and phylogenetic position of the marine harmful raphidophyte Chattonella isolated from Bolinao, Pangasinan, Philippines in 2013 and 2017 were examined using light microscopy and molecular phylogeny inferred from LSU rDNA and ITS sequences. Cells of Chattonella were variable in shape and typically teardrop- shaped with a roundish antapical end, 26.0–49.5 μm in length, with an anterior flagellum directing swimming direction and a posterior flagellum trailing backward. Cell surface was covered by numerous small granules and several larger button-like rounded bodies. Discharge of transparent tubular mucocysts was also observed from cells just before collapse. Numerous brownish chloroplasts were located peripherally, each with a pyrenoid. Two Chattonella strains isolated in 2017 had identical LSU rDNA and ITS sequences and branched in the clade of Chattonella subsalsa, and were closely related especially to strains isolated from the Gulf of Mexico and East coast of USA. This is the first report of C. subsalsa based on morphological and phylogenetic information from the Philippines.

 

8. Moncada C., Hassenruch C., Gardes A., Conaco C. (2019). Microbial community composition of sediments influenced by intensive mariculture activity. FEMS Microbiology Ecology. Article in Press, Pages 1-12.more

Abstract:

Marine aquaculture is a major industry that supports the economy in many countries, including the Philippines. However, excess feeds and fish waste generated by mariculture activities contribute an immense nutrient load to the environment that can affect the underlying sediment. To better understand these impacts, we compared the physicochemical characteristics and microbial community composition of sediments taken at a fish cage and an off cage site in Bolinao, Philippines. Sediments and pore water at the fish cage site showed evidence of greater organic enrichment relative to the off cage site. Under these conditions, we found lower relative abundance of dissimilatory sulfate reductase and nitrite reductase genes, suggesting shifts in prevalent nutrient cycling processes. This is further supported by 16S rRNA gene sequencing that revealed differences in the community composition between sites. Fish cage sediments favored the growth of taxa that thrive in anaerobic, organic carbon-enriched environments, such as members of class Anaerolineae, which can potentially serve as bioindicators of eutrophication in sediments. This study demonstrates that intensive mariculture activity can cause eutrophic sediment conditions that influence microbial community structure and function.

 

9. Onda D.F.L., Santos M.A.G., dela Cruz-Papa D., Yñiguez A.T., Azanza R.V., Siringan M.A.T. (2019). Microbial oceanography studies in the context of climate change in the Philippines. Philippine Science Letters, 12 (1), Pages 9-23.more

Abstract:

Studying ocean microbiomes is important in understanding the effects of the changing environment on our seas. The Philippines, being an archipelago, has been regarded as one of the most vulnerable regions under climate change scenarios, and understanding of the functions and diversity of microbial communities is a paramount step toward mitigating and adapting to the impact of globally or locally catastrophic environmental changes. We explore the current state, challenges, and potentials for microbial oceanography or marine microbial studies in the Philippines, particularly in the context of climate change, and suggest measures on how we can best move forward to upgrade and contribute to the development of this field in the country. Despite the great diversity in the marine provinces in the country and the answers they hold in unlocking the secrets of microbial communities, this review highlights that Philippine-based microbial or marine research in general has been limited. Previous microbial studies focused on applications in aquaculture and fisheries, while more basic aspects such as on diversity and ecological interactions and functioning are sorely lacking. Limited recognition and support for basic research, lack of expertise, and insufficient infrastructure (e.g., properly equipped oceangoing research vessels) were identified as critical bottlenecks in the progress of ocean research in general. The heightened national interest in the country’s oceans and greater awareness of climate change threats can be a means further to spur Philippine oceanographic research that can be strengthened through the mobilization of research networks around the country.

 

10. Ravago-Gotanco R., Kim K.M. (2019). Regional genetic structure of Holuthuria (Metriatyla) scabra populations across the Philippine archipelago. Fisheries Research, 209, Pages 143-155.more

Abstract:

The sandfish, Holothuria (Metriatyla) scabra Jaeger, 1833 is a commercially-valuable tropical sea cucumber species which is overexploited throughout much of its distributional range, the Philippine archipelago included. The need for management interventions to sustain the fishery is recognized. However, the lack of knowledge on the genetic structure of natural populations needs to be addressed to guide management initiatives. The present study examined genetic diversity and spatial patterns of genetic structure of sandfish populations across the Philippine archipelago. Population genetic analysis using 11 microsatellite markers revealed weak yet significant regional genetic structure among 15 H. scabra populations across the Philippine archipelago (FST = 0.016; P <  0.0001). Six genetic groups broadly concordant with marine biogeographic regions were identified. Genetic connectivity was strongest among populations situated in the center of the archipelago (internal seas; FST = 0.002, P >  0.05). Peripheral locations exhibited limited gene flow (Philippine Sea, South China Sea, Sulu Sea and Celebes Sea; mean FST = 0.023, P <  0.0001), with significant genetic relatedness further suggesting relative isolation or high levels of self-recruitment. Excluding the two most divergent Sulu Sea populations, there was a significant signal of isolation-by-distance for the rest of the Philippine populations, suggesting that geographic distance between coastal habitats coupled with oceanographic circulation largely influence genetic structure. There was no signature of genetic bottlenecks for any population, although effective population sizes (Ne) were larger for central populations compared to peripheral populations. This study provides information on genetic stocks which has important implications to genetic resource management of Philippine sandfish populations to support sustainability of the fishery.

 

11. Repollo, C.L.A., Flores-Vidal, X., Chavanne, C., Villanoy, C.L., Flament, P. (2019). Low-Frequency Surface Currents and Generation of an Island Lee Eddy in Panay Island, Philippines. Journal of Physical Oceanography, Pages 1-58.more

Abstract:

High-frequency Doppler radar (HFDR) and acoustic Doppler current profiler (ADCP) time-series observations during the Philippine Straits Dynamics Experiment (PhilEx) were analyzed to describe the mesoscale currents in Panay Strait, Philippines. Low-frequency surface currents inferred from three HFDR (July 2008–July 2009), reveal a clear seasonal signal concurrent with the reversal of the Asian monsoon. A mesoscale cyclonic eddy west of Panay Island is generated during the winter northeast (NE) monsoon. This causes changes in the strength, depth, and width of the intraseasonal Panay coastal (PC) jet as its eastern limb. Winds from QuikSCAT and from a nearby airport indicate that these flow structures correlate with the strength and direction of the prevailing local wind. An intensive survey in 8–9 February 2009 using 24 h of successive cross-shore conductivity–temperature–depth (CTD) sections, which in conjunction with shipboard ADCP measurements, show a well-developed cyclonic eddy characterized by near-surface velocities of 50 cm s−1. This eddy coincides with the intensification of the wind in between Mindoro and Panay Islands, generating a positive wind stress curl in the lee of Panay, which in turn induces divergent surface currents. Water column response from the mean transects show a pronounced signal of upwelling, indicated by the doming of isotherms and isopycnals. A pressure gradient then is set up, resulting in the spin up of a cyclonic eddy in geostrophic balance. Evolution of the vorticity within the vortex core confirms wind stress curl as the dominant forcing.

 

12. Roleda M.Y., Marfaing H., Desnica N., Jónsdóttir R., Skjermo J., Rebours C., Nitschke U. (2019). Variations in polyphenol and heavy metal contents of wild-harvested and cultivated seaweed bulk biomass: health risk assessment and implication for food applications. Food Control, 95, Pages 121-134.more

Abstract:

Seaweeds are increasingly used in European cuisines due to their nutritional value. Many algal constituents, such as polyphenols, are important antioxidants and thus considered beneficial to humans. However, many seaweed species can accumulate heavy metals and exhibit potential health risks upon ingestion. We investigated temporal and spatial variations in polyphenol and heavy metal (As, Cd, Hg, Pb) concentrations of three edible seaweed species. The brown algae Saccharina latissima and Alaria esculenta, and the red alga Palmaria palmata were sourced from natural populations and aquaculture in the NE Atlantic and processed as bulk biomass mimicking industrial scales. The mean polyphenol content was species-specific (Alaria > Saccharina > Palmaria), and highest in winter (for Alaria and Saccharina) and spring (for Palmaria); inter-annual and spatial variations were marginal. Heavy metal concentrations varied between species and depended on collection site, but seasonal variations were minimal. Our data suggest that all three species are good sources of antioxidants, and the heavy metal concentrations are below the upper limits set by the French recommendation and the EU Commission Regulation on contaminants in foodstuffs. A health risk assessment indicated that consumption of these seaweed species poses a low risk for humans with regard to heavy metals. However, an EU-wide regulation on maximal concentration of heavy metals in seaweeds should be established.

 

13. Santiago V.S., Manzano G.G., Yu C.C., Aliño P.M., Salvador-Reyes L.A. (2019). Mariculture potential of renieramycin-producing Philippine blue sponge Xestospongia sp. (Porifera : Haplosclerida). Aquaculture, 502, Pages 356-364.more

Abstract:

Open-sea mariculture of the Philippine blue sponge Xestospongia sp. was established as a route for the production of the biomedically-important renieramycins. We assessed the effects of harvesting regime, culture period or periodicity, sponge translocation and farming methods to sponge survival, sponge growth, chemistry and bioactivity of sponge extracts. During the 12-month culture, sponge growth, renieramycin M content and antiproliferative activity of sponge extracts showed significant differences, depending on the culture period and location. Growth and renieramycin biosynthesis were minimally affected by temperature and may be driven by thermal-independent processes in the coral reef. Multiple harvesting of Xestospongia sp. was also favorable to growth and consequently, provided higher biomass and renieramycin M yields.

 

14. Santiañez W.J.E., Wynne M.J. (2019). Evidence for the treatment of Talarodictyon tilesii as an older taxonomic synonym of Hydroclathrus stephanosorus (Scytosiphonaceae, Phaeophyceae). Phycological Research, 67, Pages 82-85.more

Abstract:

Morphological and anatomical evidence is presented to support the taxonomic judgment that Talarodictyon tilesii Endlicher is conspecific with Hydroclathrus stephanosorus Kraft in Kraft & Abbott. Because the former name has nomenclatural priority over the latter name, Hydroclathrus tilesii (Endlicher) comb. nov. is proposed.

 

15. Santiañez W.J.E., Kogame K. (2019). Proposals to recognize Petalonia tenella comb. nov. and to resurrect Hapterophycus canaliculatus(Scytosiphonaceae, Phaeophyceae). Botanica Marina, 62 (2), Pages 149-153.more

Abstract:

The brown algal family Scytosiphonaceae has recently received considerable attention resulting in the description of several new genera and species. However, members of the genus Scytosiphon and Petalonia remain polyphyletic. By integrating multi-gene phylogenetic data (mitochondrial cox3 and plastid psaA and rbcL genes) with their known morpho-anatomies and life histories, we herein resurrect Hapterophycus canaliculatus, currently considered a member of genus Scytosiphon, and transfer Scytosiphon tenellus to the genus Petalonia.

 

16. Shipway, J.R, Altamia, M.A., Rosenberg, G., Concepcion G.P., Haygood M.G., Distel D.L. (2019). Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines. PeerJ, Pages 1-18.more

Abstract:

Here we describe an anatomically divergent wood-boring bivalve belonging to the family Teredinidae. Specimens were collected off the coast of Mabini, Batangas, Philippines, in February 2018, from sunken driftwood at a depth of less than 2 m. A combination of characteristics differentiates these specimens from members of previously named teredinid genera and species. Most notable among these include: an enlarged cephalic hood which extends across the posterior slope of the shell valves and integrates into the posterior adductor muscle; a unique structure, which we term the 'cephalic collar', formed by protruding folds of the mantle immediately ventral to the foot and extending past the posterior margin of the valves; a large globular stomach located entirely posterior to the posterior adductor muscle and extending substantially beyond the posterior gape of the valves; an elongate crystalline style and style sac extending from the base of the foot, past the posterior adductor muscle, to the posteriorly located stomach; calcareous pallets distinct from those of described genera; a prominently flared mantle collar which extends midway along the stalk of the pallets; and, separated siphons that bear a pigmented pinstripe pattern with highly elaborate compound papillae on the incurrent siphon aperture. We used Micro-Computed Tomography (Micro-CT) to build a virtual 3D anatomical model of this organism, confirming the spatial arrangement of the structures described above. Phylogenetic analysis of the small (18S) and large (28S) nuclear rRNA gene sequences, place this bivalve within the Teredindae on a branch well differentiated from previously named genera and species. We propose the new genus and species Tamilokus mabinia to accommodate these organisms, raising the total number of genera in this economically and environmentally important family to 17. This study demonstrates the efficacy of Micro-CT for anatomical description of a systematically challenging group of bivalves whose highly derived body plans are differentiated predominantly by soft tissue adaptations rather than features of calcareous hard-parts.

 

17. Yap, H.T. (2019). One-ecosystem analysis for environmental conservation and sustainable livelihood. F1000 Research, 8, Pages 1-21.more

Abstract:

In order to achieve the objectives of resource conservation, it is important to recognize that habitats are connected by material and energy flows, and that humans often play a central role, directly or indirectly. Hence, ecological research should be designed that treats all interlinked habitats, including human populations, as one ecosystem. Examples would be coastal habitats that are impacted by effluent from the upland, which in turn can be generated by deforestation and harmful agricultural practices. All of these aspects, including the river systems that deliver run-off, should be included in the investigation. This approach entails a carefully articulated hypothesis or set of hypotheses drawing on the natural as well as social sciences, and an appropriate sampling and statistical design. It clearly imposes high demands on resources, financial and otherwise. But the continued compartmentalization of efforts along disciplines and specializations will likely slow down progress in environmental conservation.

 

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1. Buena, A. E., Villaplaza, B. R. B., Payot, B. D., Gabo-Ratio, J. A. S., Ramos, N. T., Faustino-Eslava, D. V. , Queaño, K. L., Dimalanta, C. B., Padrones, J. T., Tani, K., Brown, W. W., Yumul, G. P. Jr. (2019). An evolving subduction-related magmatic system in the Masara Gold district, Eastern Mindanao, Philippines. Journal of Asian Earth Sciences. doi.org/10.1016/j.jaesx.2019.100007.more

Abstract:

The Masara Gold District in Eastern Mindanao, Philippines, is one of the most prolific gold provinces in the Philippines. Recent district-scale mineral exploration makes it possible to undertake geologic and geochemical studies and thus to yield better insights about the mineralization environment of the Masara Gold District.

In the Masara Gold District, mineralization is hosted in andesitic rocks and multiple stocks of diorite intrusions. New U-Pb and whole rock K-Ar age dating of these host rocks reveal Eocene to Plio-Pleistocene ages for the magmatic suites. A new lithologic unit is proposed to accommodate the composite diorite phases associated with mineralization. Major and trace element geochemistry of these host rocks show that the Eocene magmatic suite exhibits a tholeiitic character while the diorite and subvolcanic andesite pulses of the Miocene are calc-alkaline in composition. Adakitic rocks were emplaced during the Late Miocene and Plio-Pleistocene. Mineralization in eastern Mindanao is associated with several intrusive events formed during the Oligocene to the Pliocene. The majority of these mineralization events is associated with calc-alkaline magmatic suites. Based on this study, epithermal gold mineralization in the Masara Gold District is closely related to the Late Miocene magmatic rocks which exhibit calc-alkaline and adakitic signatures.

2. Catane, S. G., Veracruz, N.A.S., Flora, J.R.R., Go, C.M.M., Enrera, R.E., Santos, E.R.U. (2019). Mechanism of a low-angle translational block slide: evidence from the September 2018 Naga landslide, Philippines. Landslides, 16 (9), Pages 1709–1719.more

Abstract:

There is a general lack of understanding on the detailed processes and mechanism of low-angle translational block slides. The September 20, 2018 Naga landslide, with a volume of 27 M m3 and a runout distance of 1.34 km, provided new insights on the initiation, transport, and deposition mechanisms of this type of landslide. Drone photogrammetry, video footage, satellite images, slope stability analyses, and field evidence revealed that the landslide occurred as multiple block detachments along a series of tension cracks that formed and grew progressively prior to the main failure. Predominance of intact upright blocks traceable to the distal end of the deposit indicates dominant translational motion. Facies within the Naga landslide deposit revealed that at least three processes (slide, dry flow, and fall) occurred during the main movement. Post-slide processes immediately after emplacement included small avalanches and rockfalls related to the instability of the landslide deposit and the main scarp. Preliminary slope stability analyses showed that the slopes were marginally unstable (FoS 0.67–3.96) even in dry conditions. The low-angle profile of the slip surface (6°) favors stability, but low shear strength of the limestone bedrock and unsupported cut slopes may have contributed to the failure.


3. de Vera, F.I., Bardolaza, H., Arcilla, C., Sarmago. R. (2019). Effect of In2O3 on the grain connectivity and superconducting behavior of Bi2Sr2−xInxCaCu2O8+d. SN Applied Sciences, 1:96. doi.org/10.1007/s42452-018-0109-5.more

Abstract:

The effect of In2O3 on grain connectivity and superconducting properties of Bi-2212 was investigated. Indium was intentionally doped on the Sr-site of BSCCO at doping levels from x = 0 to x = 0.8. Accessing the Sr lattice site in BSCCO provides useful control on the possible effect of indium on its superconducting behavior and microstructural proper-ties. Results show that the superconductivity persists in BSCCO even at high indium concentration (x = 0.8). However, secondary phases form at x ≥ 0.4 indium concentration affecting normal resistivity, magnetic susceptibility response and superconducting transition temperature of BSCCO. Formation of secondary phases weakens the diamagnetic intergrain coupling. An apparent increase in the formation of micron-sized grains is related to the increased sinterability of BSCCO with indium doping. The enhanced sinterability of BSCCO with indium provides possibility of synthesizing thin films with reduced thermal heat treatment.

 

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. (2019). Characterization of the proto-Philippine Sea Plate: Evidence from the emplaced oceanic lithosphere fragments along eastern Philippines. Geoscience Frontiers. 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 archipelago. In 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. Fernando, A. G. S. & Sy, E. Y. (2019). Red-tailed Green Ratsnake Gonyosoma oxycephalum predation on White-bellied Woodpecker in the Philippines. Southeast Asia Vertebrate Records, 2019: 033-034.more

Abstract:

Description of record: A green snake was observed hanging from a horizontal branch approximately three meters above the ground, whilst constricting a White-bellied Woodpecker. Another White-bellied Woodpecker nearby was making non-stop alarm calls. The bird ceased struggling after three minutes and the snake started its attempt to swallow it head first. The snake was able to swallow the head of the bird, but regurgitated it after a few minutes. It made another attempt to swallow the bird, but this was also unsuccessful. The two swallowing attempts lasted for 17 minutes. Observation was discontinued immediately after the second regurgitation, thus the actual consumption of the bird by the snake was not observed.

 

6. Frias, S. M. P., Imai, A., Takahashi, R., Balangue-Tarriela, M. I. R., Arcilla, C. Blamey, N. (2019). Geology, alteration, and mineralization of the Kay Tanda Epithermal Gold Deposit, Lobo, Batangas, Philippines. Resource Geology, Pages 1-34.more

Abstract:

The Kay Tanda epithermal Au deposit in Lobo, Batangas is one of the Au deposits situated in the Batangas Mineral District in southern Luzon, Philippines. This study aims to document the geological, alteration, and mineralization characteristics and to determine the age of the mineralization, the mechanism of ore deposition, and the hydrothermal fluid characteristics of the Kay Tanda deposit. The geology of Kay Tanda consists of (i) the Talahib Volcanic Sequence, a Middle Miocene dacitic to andesitic volcaniclastic sequence that served as the host rock of the mineralization; (ii) the Balibago Diorite Complex, a cogenetic intrusive complex intruding the Talahib Volcanic Sequence; (iii) the Calatagan Formation, a Late Miocene to Early Pliocene volcanosedimentary formation unconformably overlying the Talahib Volcanic Sequence; (iv) the Dacite Porphyry Intrusives, which intruded the older lithological units; and (v) the Balibago Andesite, a Pliocene postmineralization volcaniclastic unit. K‐Ar dating on illite collected from the alteration haloes around quartz veins demonstrated that the age of mineralization is around 5.9 ± 0.2 to 5.5 ± 0.2 Ma (Late Miocene). Two main styles of mineralization are identified in Kay Tanda. The first style is an early‐stage extensive epithermal mineralization characterized by stratabound Au‐Ag‐bearing quartz stockworks hosted at the shallower levels of the Talahib Volcanic Sequence. The second style is a late‐stage base metal (Zn, Pb, and Cu) epithermal mineralization with local bonanza‐grade Au mineralization hosted in veins and hydrothermal breccias that are intersected at deeper levels of the Talahib Volcanic Sequence and at the shallower levels of the Balibago Intrusive Complex. Paragenetic studies on the mineralization in Kay Tanda defined six stages of mineralization; the first two belong to the first mineralization style, while the last four belong to the second mineralization style. Stage 1 is composed of quartz ± pyrophyllite ± dickite/kaolinite ± diaspore alteration, which is cut by quartz veins. Stage 2 is composed of Au‐Ag‐bearing quartz stockworks associated with pervasive illite ± quartz ± smectite ± kaolinite alteration. Stage 3 is composed of carbonate veins with minor base metal sulfides. Stage 4 is composed of quartz ± adularia ± calcite veins and hydrothermal breccias, hosting the main base metal and bonanza‐grade Au mineralization, and is associated with chlorite‐illite‐quartz alteration. Stage 5 is composed of epidote‐carbonate veins associated with epidote‐calcite‐chlorite alteration. Stage 6 is composed of anhydrite‐gypsum veins with minor base metal mineralization. The alteration assemblage of the deposit evolved from an acidic mineral assemblage caused by the condensation of magmatic volatiles from the Balibago Intrusive Complex into the groundwater to a slightly acidic mineral assemblage caused by the interaction of the host rocks and the circulating hydrothermal waters being heated up by the Dacite Porphyry Intrusives to a near‐neutral pH toward the later parts of the mineralization. Fluid inclusion microthermometry indicates that the temperature of the system started to increase during Stage 1 (T = 220–250°C) and remained at high temperatures (T = 250–290°C) toward Stage 6 due to the continuous intrusion of Dacite Porphyry Intrusives at depth. Salinity slightly decreased toward the later stages due to the contribution of more meteoric waters into the hydrothermal system. Boiling is considered the main mechanism of ore deposition based on the occurrence of rhombic adularia, the heterogeneous trapping of fluid inclusions of variable liquid–vapor ratios, the distribution of homogenization temperatures, and the gas ratios obtained from the quantitative fluid inclusion gas analysis of quartz. Ore mineral assemblage and sulfur fugacity determined from the FeS content of sphalerite at temperatures estimated by fluid inclusion microthermometry indicate that the base metal mineralization at Kay Tanda evolved from a high sulfidation to an intermediate sulfidation condition

7. Lagmay, A. M. F., Racoma, B. A. (2019). Lessons from tropical storms Urduja and Vinta disasters in the Philippines. Disaster Prevention and Management: An International Journal, 28 (2), Pages 154-170.more

Abstract:

Purpose

Tropical storms Urduja and Vinta battered the Philippines in December 2017. Despite advances in disaster risk reduction efforts of the country, the twin December storms caused numerous deaths in the Visayas and Mindanao regions. Analysis of these events shows that alerts raised during the Pre-Disaster Risk Assessment (PDRA) for both storms were largely ineffective because they were too broad and general calling for forced evacuations in too many provinces. Repeated multiple and general warnings that usually do not end up in floods or landslides, desensitize people and result in the cry-wolf effect where communities do not respond with urgency when needed. It was unlike the previous execution of PDRA from 2014 to early 2017 by the National Disaster Risk Reduction and Management Council (NDRRMC), which averted mass loss of lives in many severely impacted areas because of hazard-specific, area-focused and time-bound warnings. PDRA must reinstate specific calls, where mayors of communities are informed by phone hours in advance of imminent danger to prompt and ensure immediate action. Mainstreaming Climate Change Adaptation and Disaster Risk Reduction information using probabilistic (multi-scenario) hazard maps is also necessary for an effective early warning system to elicit appropriate response from the community. The paper aims to discuss these issues.

Design/methodology/approach

Methods of early warning through the PDRA of the National Disaster Mitigation and Management Council (NDRRMC) of the Philippines during tropical storm Urduja and Typhoon Vinta were assessed in this study and compared to the previous PDRA system from 2014 to early 2017.

Findings

It was found out that the numerous casualties were due to inadequate warning issued during the approach of the tropical cyclones. During an impending hazard, warnings must be accurate, reliable, understandable and timely. Despite the availability of maps that identified safe zones for different communities, warnings raised during the PDRA for both tropical cyclones were deemed too general calling for evacuations of whole provinces. As such, not all communities were evacuated in a timely manner because of failure in the key elements of an effective early warning system.

Originality/value

To avoid future disasters from happening, it is recommended that the PDRA reinstate its hazards-specific, area-focused and time-bound warnings. Similarly, to increase the resilience of communities, more work on mainstreaming of Climate Change Adaptation and Disaster Risk and Vulnerability Reduction systems for communities must be done as well. Learning from the lessons of these previous disasters will enable communities, their leaders and every stakeholder, not to repeat the same mistakes in the future.

 

8. Li, H., Kong, H., Zhou, Z-K., Wu, Q.-H., Xi, X.-S., Gabo-Ratio, J. A. S. (2019). Ore-forming material sources of the Jurassic Cu–Pb–Zn mineralization in the Qin–Hang ore belt, South China: Constraints from S–Pb isotopes. Geochemistry. doi.org/10.1016/j.geoch.2018.12.008.more

Abstract:

The Qin–Hang ore belt in South China, which serves as the boundary between the Yangtze and Cathaysia blocks, is marked by extensive Jurassic porphyry-skarn-metasomatic Cu–Pb–Zn polymetallic mineralization. In this contribution, S and Pb isotopic compositions of the Baoshan Cu–Pb–Zn deposit in the western portion of the Qin–Hang ore belt were analyzed to determine the ore-forming material sources in the area. This is coupled by the first systematic collection, compilation and interpretation of previously published S and Pb isotopic data of multiple sulfide minerals to reveal the metal origin and accumulation mechanism of the Cu–Pb–Zn mineralization from the significant deposits in the region (i.e., Dexing, Qibaoshan, Shuikoushan, Baoshan, Huangshaping, Tongshanling and Dabaoshan). The results show that Cu mineralization is characterized by low and narrow δ34S (‰) range of values (–5 to 6) and Pb isotopic ratios (208Pb/204Pb = 38.0–39.0, 207Pb/204Pb = 15.4–15.8, and 206Pb/204Pb = 17.7–18.7), which are consistent with those of local porphyries. In contrast, the Pb–Zn mineralization reveals higher and more variable δ34S (‰) values (–4 to 18) and Pb isotopic ratios (208Pb/204Pb = 38.0–39.5, 207Pb/204Pb = 15.3–16.0, and 206Pb/204Pb = 18.0–19.0) that correspond to wall-rock and basement rock compositions in the region. This indicates that the sulfur and lead that formed the Cu mineralization in the Qin–Hang ore belt was mainly sourced from regional magmatism with mantle contributions, whereas the sulfur and lead for the Pb–Zn mineralization was likely derived from the host sedimentary rocks and Proterozoic metamorphic basement rocks, respectively. The S and Pb isotopic data, combined with the geochemical signatures of mineralization-related porphyries, suggest that the Cu was sourced from the deeper levels along with mantle-derived magmas. In contrast, the Pb–Zn probably originated from the crust, with partial melting of the crystalline basement in the Cathaysia Block. Consequently, a three-stage genetic model is proposed to explain the ore-forming processes of the Qin–Hang Cu-polymetallic belt in South China.

 

9. Mendoza, J. P. A., Balangue-Tarriela, M. I. R., Reed, M. H. (2019). Modeling adiabatic boiling in the Biliran Geothermal Wells usung CHIM-XPT (2016). Philippine Journal of Science, 148 (4), Pages 117-124.more

Abstract:

Boiling is a common process in geothermal wells where the primary water quickly ascends to the surface and liquid water is converted to steam due to depressurization and cools downs (i.e., no heat exchange with surrounding rocks). An assumption in the present study is that there is no heat exchange between wall rock and boiling water; thus, the process is isenthalpic. This study presents the results of changes in the chemical composition of fluid from a geothermal system as it ascends to the surface together with the description of minerals precipitating out of the solution at certain temperature conditions. The results of the study will contribute significantly to the assessment of scaling potentials in a geothermal field. Using FORTRAN Programs SOLVEQ and CHIM-XPT, adiabatic boiling was simulated for the normal enthalpy wells of Biliran geothermal field. Results of theoretical geothermometry for the wells are consistent with the reported chemical geothermometers. Aside from a steam phase dominated by water vapor and CO2, Well BN-1 formed chlorite, calcite (up to 170 °C) and talc in the initial boiling model. Well BN-2 precipitated mostly talc and calcite almost all throughout its ascent. The occurrence of calcite calculated from the model is consistent with the abundance of calcite scales and veins in BN-1 while BN-2 is dominated by aragonite. Minor differences in the mineralogy of the wells is mainly due to the significant difference in the fluid and gas chemistry amongst wells in the field. The partitioning of CO2 into a gas phase drives the increase in pH for both wells. Both the formation of the gas phase and the fractionated minerals reflect changes occurring in the total concentration of the aqueous phase wherein species fractionated into the gas or solid phase decrease in the total aqueous concentration.

 

10. Meyer-Dombard, D.R., Osburn, M.R., Cardace, D. and Arcilla, C.A. (2019). The effect of a tropical climate on available nutrient resources to springs in ophiolite-hosted, deep biosphere ecosystems in the Philippines. Frontiers in Microbiology, 10:761.  doi: 10.3389/fmicb.2019.00761.more

Abstract:

Springs hosted in ophiolites are often affected by serpentinization processes. The characteristically low DIC and high CH4 and H2 gas concentrations of serpentinizing ecosystems have led to interest in hydrogen based metabolisms in these subsurface biomes. However, a true subsurface signature can be difficult to identify in surface expressions such as serpentinizing springs. Here, we explore carbon and nitrogen resources in serpentinization impacted springs in the tropical climate of the Zambales and Palawan ophiolites in the Philippines, with a focus on surface vs. subsurface processes and exogenous vs. endogenous nutrient input. Isotopic signatures in spring fluids, biomass, and carbonates were examined to identify sources and sinks of carbon and nitrogen, carbonate geochemistry, and the effect of seasonal precipitation. Seasonality affected biomass production in both low flow and high flow spring systems. Changes in meteorological precipitation affected δ13CDIC and δ13CDOC values of the spring fluids, which reflected seasonal gain/loss of atmospheric influence and changes in exogenous DOC input. The primary carbon source in high flow systems was variable, with DOC contributing to biomass in many springs, and a mix of DIC and carbonates contributing to biomass in select locations. However, primary carbon resources in low flow systems may depend more on endogenous than exogenous carbon, even in high precipitation seasons. Isotopic evidence for nitrogen fixation was identified, with seasonal influence only seen in low flow systems. Carbonate formation was found to occur as a mixture of recrystallization/recycling of older carbonates and rapid mineral precipitation (depending on the system), with highly δ13C and δ18O depleted carbonates occurring in many locations. Subsurface signatures (e.g., low DOC influence on Cbiomass) were most apparent in the driest seasons and lowest flow systems, indicating locations where metabolic processes divorced from surface influences (including hydrogen based metabolisms) are most likely to be occurring.

11. Ratio, M. A., Gabo-Ratio, J. A., Tabios-Hillebrecht, A. L. (2019). The Philippine Experience in Geothermal Energy DevelopmentGeothermal Energy and Society, Pages 217-238. DOI: 10.1007/978-3-319-78286-7_14. more

Abstract:

Situated along the Pacific Ring of Fire, the Philippines has a total installed capacity of 1916 MW geothermal energy, which makes it one of the world’s top producers. The Philippine Government aims to increase its renewable energy capacity to an estimated 15,304 MW by 2030 comprising of 1495 MW for geothermal capacity. In order to reach its interim targets for increasing geothermal installed capacity, the government must work closely with the private resource developers to expedite permit related-processes and avoid project delays, thereby supporting timely geothermal exploration and construction activities. With decades of experience in geothermal energy development, the Philippines has learned valuable lessons from its various and unique geothermal energy projects from the lowland accessible Makiling-Banahaw geothermal complex to the socio-culturally and environmentally sensitive Mindanao geothermal complex. The past controversies and successful stakeholder resolutions have shed light on the complicated connection between geothermal energy and stakeholders particularly that of the indigenous cultural communities and indigenous people. 

 

12. Shin, C. P., Yasuhara, M., Iwatani, H., Kase, T., Fernando, A. G. S., Hayashi, H., Kurihara, Y., and Pandita, H. (2019). Neogene marine ostracod diversity and faunal composition in Java, Indonesia: Indo-Australian Archipelago biodiversity hotspot and the Pliocene diversity jump. Journal of Crustacean Biology. doi.org/10.1093/jcbiol/ruy110.more

Abstract:

Neogene diversity history in the world center of biodiversity known as the Indo-Australian Archipelago (IAA) or the Coral Triangle remains poorly understood. Of particular interest is the recently reported Pliocene diversity jump that is considered to have established the present-day biodiversity level of the region needs rigorous inspections. We investigated Neogene fossil marine ostracods from Java, Indonesia and evaluate and test the Pliocene Diversity Jump hypothesis. We found a significant diversity increase from the late Miocene to the Pliocene, supporting the hypothesis. At the same time, there are considerable differences in depositional environments between the Miocene and Pliocene samples. Although it is unlikely that the main reason of the diversity increase is due to this paleoenvironmental difference, further samples and data from the IAA hotspot region are needed for more rigorous inspections. Our comparison between species-level and genus-level data indicated that species-level data are better to detect detailed macroevolutionary diversity histories, and genus level data are more useful for paleoenvironmental and paleoceanographic reconstructions.

 

13. Sun, H.-S., Li, H., Algeo, T. J., Gabo-Ratio, J. A. S., Yang, H., Wu, J.-H., & Wu, P. (2018). Geochronology and geochemistry of volcanic rocks from the Tanjianshan Group, NW China: Implications for the early Palaeozoic tectonic evolution of the North Qaidam Orogen. Geological Journal, 54 (3), Pages 1769-1796.more

Abstract:

The widely exposed Tanjianshan volcanic rocks in the North Qaidam Orogen (NW China) encode abundant information about early Palaeozoic magma origin and tectonic evolution. This research utilizes petrological, geochemical, and geochronological methods to investigate the last volcanic cycle (Formation d) of the Tangjianshan Group, aiming to reveal the tectonic evolutionary processes of the North Qaidam Orogen. Formation d can be further divided into two major volcanic sequences, that is, Formation d‐1/d‐4 and Formation d‐3. Formation d‐1/d‐4 is a set of intermediate–basic volcaniclastic rocks intercalated with volcanic lava and contemporary hypabyssal diabase–gabbro intrusive rocks. The rocks are characterized by high average concentrations of Al2O3, K2O, Na2O, and P2O5, pronounced differentiation of light (LREE) and heavy rare earth elements (HREE) and enrichment of LREEs and light‐ion lithophile elements (LILE), showing continental arc affiliation and enriched mid‐ocean‐ridge basalt (E‐MORB) characteristics. They have positive zircon εHf (t) values (7.5 to 16.1) and variable whole‐rock εNd (t) values (−2.7 to 7.0), with crustal Hf model ages (TDMC) and two‐stage Nd model ages (T2DM) ranging from 428 to 970 Ma and from 618 to 1,410 Ma, respectively. The magma may have originated from an enriched mantle source and experienced crustal contamination in a continental back‐arc basin. In contrast, Formation d‐3 is composed of volcaniclastic rocks intercalated with layered basaltic andesite and basalts. It has higher average concentrations of CaO, FeOT, and MgO, lower ΣREE and flatter REE patterns, lower average 87Sr/86Sr ratios (0.70557), higher average 143Nd/144Nd ratios (0.51285), and exclusively positive εNd (t) values (1.3 to 5.0), consistent with normal mid‐ocean‐ridge basalt (N‐MORB) influence. The magma may have been derived from a normal mantle source without significant modification, which probably formed in a rift‐related tectonic setting or even a mid‐ocean ridge that developed within a back‐arc basin. Magmatic zircons from Formation d‐1/d‐4 yield U–Pb ages mostly at 460–440 Ma, whereas zircons modified by continental exhumation‐related orogenic fluids are mainly dated at 430–420 Ma. Magmatic zircons from Formation d‐3 mainly have U–Pb ages of 440–430 Ma. Integrating the magma genesis and rock affiliation interpretations of this study with geological information for the study area and adjacent regions, a four‐stage tectonic evolutionary model is proposed for the early Palaeozoic North Qaidam Orogen: (a) oceanic subduction with arc magmatism (520–460 Ma), (b) continental collision with back‐arc magmatism (Formation d‐1/d‐4) (460–440 Ma), (c) mid‐ocean ridge extension with rift‐related magmatism (Formation d‐3) (440–430 Ma), and (d) continental exhumation with orogenic fluid modification (430–420 Ma).

 

14. 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. (2019). Unfolding the technological production strategies of the large toolkits across Philippine Paleolithic sites with specific reference to northern Mindanao. Quaternary International. (In Press, Corrected Proof)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.

 

15. Tsai, C.-H., Shyu, J. B. H., Chung, S.-L., Ramos, N.T. and Lee, H.-Y. (2019). Detrital zircon record from major rivers of Luzon Island: implications for Cenozoic continental growth in SE Asia. Journal of the Geological Society. https://doi.org/10.1144/jgs2019-003.more

Abstract:

The significance of continental crustal growth in the Phanerozoic has long been debated. As an active accretionary orogenic belt, SE Asia has been proposed to be one of the best archives for studying juvenile continental growth in the Cenozoic, despite the limited availability of data. Therefore, we conducted for the first time a comprehensive U–Pb and Hf isotopic analysis of detrital zircons separated from major rivers of Luzon Island, the largest landmass of the Philippine Archipelago. U–Pb ages of these zircons are predominantly <50 Ma, consistent with literature zircon U–Pb ages or whole-rock K–Ar ages. A sample from the central Sierra Madre, however, contains zircons with age clusters at 110–70 and 180–140 Ma, supporting the presence of Mesozoic basement rock units in that area. All dated zircons show positive and high εHf(T) values that plot close to the depleted mantle. Therefore, we argue that pre-Cenozoic continental materials played insignificant roles in the construction of Luzon Island, and that this part of the southeastern Eurasian margin consists predominantly of a juvenile terrane where substantial continental crustal growth occurred in the Cenozoic.

16. Valera, G.T.V., Payot, B. D., Arai, S. Takeuchi, M., Ishimaru, S. Tamura, A. (2019). Petrologic nature of the active subarc crust -mantle boundary: Mixed magmatic-metasomatic process recorded in xenoliths from Sabtang Island, Luzon arc. Journal of Volcanology and Geothermal Research, 374, Pages 80-99.more

Abstract:

Some arc magmas reside in the uppermost mantle and the lower crust. Their deep-seated behavior determines the composition of magmas that erupt at the surface. Mafic-ultramafic xenoliths newly found in Sabtang island, Batanes group of islands of the Luzon arc record subarc processes. The xenolith suite is comprised mainly of dunites, orthopyroxenites, clinopyroxenites, hornblendites, and gabbros, all hosted in basaltic to andesitic lavas. Petrographic characteristics suggest the metasomatic formation of orthopyroxenites and hornblendites from dunites and clinopyroxenites, respectively. The apparently primary minerals are homogeneous in composition. Olivine is relatively magnesian (Fo 82–90 ) and chromian spinel is rich in Cr# (=Cr/[Cr + Al], around 0.7) in dunites. Clinopyroxene is relatively magnesian (Mg# = Mg/[Mg + Fe 2+ ] = 0.73–0.93) in clinopyroxenites and gabbros, and plagioclase is highly anorthitic (An 89–98 ) in the gabbros. The primary mineral assemblage reflects crystallization of olivine and spinel followed by clinopyroxene all occurring in the uppermost mantle and lower crust of the Luzon arc. The orthopyroxenes and amphiboles were metasomatically produced at the expense of olivine and clinopyroxene, respectively. Clinopyroxene in the xenoliths is in equilibrium with the magmas that formed the Sabtang volcanics. They have relatively elevated contents of large-ion lithophile elements and light-rare-earth elements, which suggest derivation from an enriched mantle. The Sabtang xenoliths evidence the very active modification of the subarc mantle-crust boundary zone by mantle-derived magmas and slab-derived melts/fluids so that the mineral assemblage of the resultant rocks is similar to that of the predominant recent magma.

17. Vallalar, B., Meyer-Dombard, D. R., Cardace, D., Arcilla, C. A. (2019). Multimetal resistant, alkalitolerant bacteria isolated from serpentinizing fluid-associated sediments and acid mine drainage in the Zambales Ophiolite, the Philippines. Geomicrobiology Journal. DOI:  10.1080/01490451.2019.1628132.more

Abstract:

Weathering in ophiolitic exposure settings often produces fluids and sediments that have elevated concentrations of various toxic heavy metals such as chromium, nickel, cobalt, copper, and zinc. Microorganisms inhabiting these environments (e.g., serpentinite soils or sediments) are likely adapted to tolerate these metals along with other physicochemical extremes. The purpose of this study is to isolate bacteria capable of tolerating extremely high concentrations of multiple metals and to assess the various tolerance mechanisms exhibited by different organisms. Sediment samples for microbial culturing were collected from Manleluag Spring National Park and Barlo Mine located on the island of Luzon, the Philippines. Luria-Bertani (LB) agar medium was supplemented with increasing concentrations of five trace elements – Cu, Cr, Co, Ni, and Zn. Over 20 isolates were obtained from media with concentrations ranging from 25 mg/L to 400 mg/L of each metal. Most isolates were identified as belonging to the genus Bacillus. Adaptation mechanisms, including potential biomineralization, were considered for select strains using inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction (XRD). ICP-OES analysis suggests that the primary resistance mechanism used by most isolates is cellular efflux, although it was determined that some organisms were able to reduce aqueous Cu concentration by up to 40%. Most strains exhibited growth at pH 12, demonstrating that alkalitolerant, highly metal resistant organisms are found in these ophiolite-associated environments. These organisms may be exploited for bioremediation, secondary metabolite production, and other industrial applications.

18.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. (2019). Slab rollback and microcontinent subduction in the evolution of the Zambales Ophiolite Complex (Philippines): A review. Geoscience Frontiers. doi.org/10.1016/j.gsf.2018.12.008.more

Abstract:

New radiolarian ages show that the island arc-related Acoje block of the Zambales Ophiolite Complex is possibly of Late Jurassicto 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. Alcantara, Krizelle Mae M. and Garcia, Reynaldo L. (2019). MicroRNA92a promotes cell proliferation, migration and survival by directly targeting the tumor suppressor gene NF2 in colorectal and lung cancer cells. Oncology Reports, 41 (4), Pages 2103-2116.more

Abstract:

Inactivation of the tumor suppressor protein Merlin leads to the development of benign nervous system tumors in neurofibromatosis type2 (NF2). Documented causes of Merlin inactivation include deleterious mutations in the encoding neurofibromin2 gene (NF2) and aberrant Merlin phosphorylation leading to proteasomal degradation. Rare somatic NF2 mutations have also been detected in common human malignancies not associated with NF2, including colorectal and lung cancer. Furthermore, tumors without NF2 mutations and with unaltered NF2 transcript levels, but with low Merlin expression, have been reported. The present study demonstrated that NF2 is also regulated by microRNAs (miRNAs) through direct interaction with evolutionarily conserved miRNA response elements (MREs) within its 3'untranslated region (3'UTR). DualLuciferase assays in human colorectal carcinoma (HCT116) and lung adenocarcinoma (A549) cells revealed downregulation of NF2 by miR92a3p via its wildtype 3'UTR, but not NF23'UTR with mutated miR92a3p MRE. HCT116 cells overexpressing miR92a3p exhibited significant downregulation of endogenous NF2 mRNA and protein levels, which was rescued by cotransfection of a target protector oligonucleotide specific for the miR92a3p binding site within NF23'UTR. miR92a3p overexpression in HCT116 and A549 cells promoted migration, proliferation and resistance to apoptosis, as well as altered Factin organization compared with controls. Knockdown of NF2 by siRNA phenocopied the oncogenic effects of miR92a overexpression on HCT116 and A549 cells. Collectively, the findings of the present study provide functional proof of the unappreciated role of miRNAs in NF2 regulation and tumor progression, leading to enhanced oncogenicity.

 

2. Amosco, Melissa D., Tavera, Gloria R., Villar, Van Anthony M., Naniong, Justin Michael A., David-Bustamante, Lara Marie G., Williams, Scott M., Jose, Pedro A., Saloma, Cynthia P. (2019). Non-additive effects of ACVR2A in preeclampsia in a Philippine populationBMC Pregnancy and Childbirth, 19 (11).more

Abstract:

Background

Multiple interrelated pathways contribute to the pathogenesis of preeclampsia, and variants in susceptibility genes may play a role among Filipinos, an ethnically distinct group with high prevalence of the disease. The objective of this study was to examine the association between variants in maternal candidate genes and the development of preeclampsia in a Philippine population.

Methods

A case-control study involving 29 single nucleotide polymorphisms (SNPs) in 21 candidate genes was conducted in 150 patients with preeclampsia (cases) and 175 women with uncomplicated normal pregnancies (controls). Genotyping for the GRK4 and DRD1 gene variants was carried out using the TaqMan Assay, and all other variants were assayed using the Sequenom MassARRAY Iplex Platform. PLINK was used for SNP association testing. Multilocus association analysis was performed using multifactor dimensionality reduction (MDR) analysis.

Results

Among the clinical factors, older age (P <  1 × 10–4), higher BMI (P <  1 × 10–4), having a new partner (P = 0.006), and increased time interval from previous pregnancy (P = 0.018) associated with preeclampsia. The MDR algorithm identified the genetic variant ACVR2A rs1014064 as interacting with age and BMI in association with preeclampsia among Filipino women.

Conclusions

The MDR algorithm identified an interaction between age, BMI and ACVR2A rs1014064, indicating that context among genetic variants and demographic/clinical factors may be crucial to understanding the pathogenesis of preeclampsia among Filipino women.

 

3. Angeles, A.K.J., Yu, R.T.D., CutiongcoDe la Paz, E.M., Garcia, R.L. (2019). Phenotypic characterization of the novel, nonhotspot oncogenic KRAS mutants E31D and E63K. Oncology Letters, 18 (1), Pages 420-432.more

Abstract:

KRAS protooncogene, GTPase (KRAS) functions as a molecular switch at the apex of multiple signaling pathways controlling cell proliferation, differentiation, migration, and survival. Canonical KRAS mutants, such as those in codons 12 and 13, produce constitutively active oncoproteins that shortcircuit epidermal growth factor receptor (EGFR)initiated signaling, resulting in dysregulated downstream effectors associated with cellular transformation. Therefore, antiEGFR therapy provides little to no clinical benefit to patients with activating KRAS mutations. Current genotyping procedures based on canonical mutation detection only account for ~40% of nonresponders, highlighting the need to identify additional predictive biomarkers. In the present study, two novel nonhotspot KRAS mutations were functionally characterized in vitro: KRAS E31D was identified from a genetic screen of colorectal cancer specimens at the UPNational Institutes of Health. KRAS E63K is curated in the Catalogue of Somatic Mutations in Cancer database. Similar to the canonical mutants KRAS G12D and KRAS G13D, NIH3T3 cells overexpressing KRAS E31D and KRAS E63K showed altered morphology and were characteristically smaller, rounder, and highly refractile compared with their nontransformed counterparts. Filamentous actin staining also indicated cytoplasmic shrinkage, membrane ruffling, and formation of pseudopod protrusions. Further, they displayed higher proliferative rates and higher migratory rates in scratch wound assays compared with negative controls. These empirical findings suggest the activating impact of the novel KRAS mutations, which may contribute to resistance to antiEGFR therapy. Complementary studies to elucidate the molecular mechanisms underlying the transforming effect of the rare mutants are required. In parallel, their oncogenic capacity in vivo should also be investigated.

 

4. Bagamasbad, P. D., Espina, J. E. C., Knoedler, J. R., Subramani, A., Harden, A. J., & Denver, R. J. (2019). Coordinated transcriptional regulation by thyroid hormone and glucocorticoid interaction in adult mouse hippocampus-derived neuronal cells. Plos One, 14 (7), Article number e0220378.more

Abstract:

The hippocampus is a well-known target of thyroid hormone (TH; e.g., 3,5,3’-triiodothyronine—T3) and glucocorticoid (GC; e.g., corticosterone—CORT) action. Despite evidence that TH and GC play critical roles in neural development and function, few studies have identified genes and patterns of gene regulation influenced by the interaction of these hormones at a genome-wide scale. In this study we investigated gene regulation by T3, CORT, and T3 + CORT in the mouse hippocampus-derived cell line HT-22. We treated cells with T3, CORT, or T3 + CORT for 4 hr before cell harvest and RNA isolation for microarray analysis. We identified 9 genes regulated by T3, 432 genes by CORT, and 412 genes by T3 + CORT. Among the 432 CORT-regulated genes, there were 203 genes that exhibited an altered CORT response in the presence of T3, suggesting that T3 plays a significant role in modulating CORT-regulated genes. We also found 80 genes synergistically induced, and 73 genes synergistically repressed by T3 + CORT treatment. We performed in silico analysis using publicly available mouse neuronal chromatin immunoprecipitation-sequencing datasets and identified a considerable number of synergistically regulated genes with TH receptor and GC receptor peaks mapping within 1 kb of chromatin marks indicative of hormone-responsive enhancer regions. Functional annotation clustering of synergistically regulated genes reveal the relevance of proteasomal-dependent degradation, neuroprotective effect of growth hormones, and neuroinflammatory responses as key pathways to how TH and GC may coordinately influence learning and memory. Taken together, our transcriptome data represents a promising exploratory dataset for further study of common molecular mechanisms behind synergistic TH and GC gene regulation, and identify specific genes and their role in processes mediated by cross-talk between the thyroid and stress axes in a mammalian hippocampal model system.

 

5. Bautista, M. A. M., & Llames, J. S. (2019). Draft Genome Sequences of Ralstonia solanacearum Isolated from Banana and Tomato in the Philippines. Philippine Journal of Science, 148 (S1), Pages 115–126.more

Abstract:

Ralstonia solanacearum causes bacterial wilt of several plant species, including banana and tomato. With limited options for control, understanding the molecular mechanism of pathogenicity is warranted. Herein, we report the draft genome sequences of two R. solanacearum isolates from the Philippines infecting banana and tomato. R. solanacearum 10314 was isolated from banana while R. solanacearum 10154 was isolated from tomato. Pathogenicity tests indicated that 10314 can infect both banana and tomato while 10154 can only infect tomato. In an effort to investigate the molecular basis of virulence and differential host-specificity of the isolates, whole genome sequencing was performed using the Ion Torrent Proton platform. Draft assemblies were generated using three assemblers, and the quality was evaluated using assembly metrics. Standard genome annotation was performed allowing for identification of important virulence- and host-specificity-related genes for the bacterial isolates, which provided clues underlying their differential capacity to infect banana and tomato. The availability of these data in public repositories will complement the existing data from several R. solanacearum strains, including those isolated from the Philippines; thus, it can provide essential platforms for studying R. solanacearum pathogenicity and help in the control of bacterial wilt.

6. Crisostomo, B.A., Atis, A.A.G., Mirano-Bascos, D.N.R. and Hernandez, C.C. (2019). Identification of cysteine knot peptides in four Philippine plant species using mass spectrometry and transcriptome analysisPhilippine Science Letters, 12 (1), Pages 39-61.more

Abstract:

Knottins are small proteins with at least three disulfide bridges that form a cysteine knot, giving them exceptional stability. These molecules are candidates for developing peptide-based drugs that are envisioned to fill the gap between small-molecule drugs and biologics as they are bioavailable, like small-molecule drugs, and target-specific, like biologics. Plant-derived knottins are able to preserve their stable conformation in the presence of mutations and peptide grafts, making them potential drug scaffolds. Through LC/MS screening of 185 plant extracts from 180 plant species, we identified 6 Philippine plants that produce disulfide-rich peptides structurally related to knottins. Four of these plants were further analyzed using transcriptome screening and we confirmed that Alstonia scholaris, Wrightia pubescens and Tabernaemontana pandacaqui from the Apocynaceae family produce knottin-like peptides similar to previously reported Apocynaceae alpha amylase inhibitors. Given the novelty of their sequences, it is possible that these peptides possess novel functions as well. This is the first report of cysteine knot peptides from W. pubescens and T. pandacaqui. Finally, we showed that LC/MS screening followed by transcriptome analysis is a more efficient workflow for identifying cysteine knot peptides as opposed to LC/MS screening alone.

 

7. Lazaro, J. E. H., Bascos, N. A. D., Tablizo, F. A., Abes, N. S., Ivy, R., Paynaganan, D. G., … Saloma, C. P. (2019). Genome-wide Analysis for Variants in Philippine Trypanosoma evansi Isolates with Varying Drug Resistance Profiles. Philippine Journal of Science, 148 (S1), Pages 219–233.more

Abstract:

Surra, a parasitic disease transmitted by hematophagous flies and caused by Trypanosoma evansi, affects many domesticated animals – including water buffaloes, camels, horses, pigs, dogs, and other carnivores – throughout the world. When left untreated, this disease can cause anemia, significant loss of weight, abortion, and death in affected animals. Among Philippine isolates of T. evansi, variability has been reported in terms of virulence as well as response to drug treatment. In this study, trypanosoma-positive blood was obtained from 15 Philippine water buffalo samples from different sites in the country. The collected T. evansi strains were propagated in mice then subjected to in vivo virulence, in vitro drug sensitivity testing, and whole genome sequencing.  One strain (O14) was found to be highly virulent in vivo, and was found to be resistant to three commonly used drugs [i.e., isometamidium chloride (IC), diminazene diaceturate (DD), and melarsamine hydrochloride (CY for Cymelarsan®)] in vitro. This highly resistant sample was compared with two less-virulent strains using genome-wide analysis of single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels) relative to the reference strain STIB 805. Variant analysis between O14 and the less virulent strains (M4 and C117) identified a number of distinctive SNPs, many of which corroborate previous data. Genes with relatively high copy numbers were observed in mutation hotspots. These included genes that code for variant surface glycoproteins (VSGs), expression site-associated genes (ESAGs), retrotransposon hot spot (RHS) proteins, and leucine rich repeat proteins. Notable mutations were also predicted from genes coding for membrane transporters and cysteine peptidases, as well as those involved in RNA degradation. The whole genome sequences acquired from the Philippine isolates (O14, M4, and C117) vary greatly from the reference strain (STIB 805). These WGS data serve as a good resource for the discovery of genetic and phenotypic features that may be translated to effective treatment strategies, relevant to the Philippine setting.

 

8. Prieto , E.I., Maeshima, K. (2019). Dynamic chromatin organization in the cell. Essays in Biochemistry, 63 (1), Pages 133-145.more

Abstract:

The organization and regulation of genomic DNA as nuclear chromatin is necessary for proper DNA function inside living eukaryotic cells. While this has been extensively explored, no true consensus is currently reached regarding the exact mechanism of chromatin organization. The traditional view has assumed that the DNA is packaged into a hierarchy of structures inside the nucleus based on the regular 30-nm chromatin fiber. This is currently being challenged by the fluid-like model of the chromatin which views the chromatin as a dynamic structure based on the irregular 10-nm fiber. In this review, we focus on the recent progress in chromatin structure elucidation highlighting the paradigm shift in chromatin folding mechanism from the classical textbook perspective of the regularly folded chromatin to the more dynamic fluid-like perspective.

 

9. Punzalan, M. R., Cabria, G. L., Bautista, M. A., Emmanuel, E., Rivera, R., Rivera, S., & Saloma, C. (2019). Differential Expression Analysis in High-yielding and Low-yielding Philippine Coconut through Transcriptome Sequencing. Philippine Journal of Science, 148 (S1), Pages 83–95.more

Abstract:

The demand for coconut oil (CNO) continues to rise in the global market. This puts pressure for coconut-producing countries such as the Philippines to increase CNO and copra production. Baybay Tall (BAYT) is known to have the highest copra yield among the tall coconut varieties in the Philippines. However, traditional breeding techniques that rely on the use of morphological markers are very limited, laborious, and time-consuming. In order to improve breeding strategies for increased copra production, differential gene expression analysis was performed on coconut shell and kernel of high-yielding and low-yielding palms. High-quality RNA was isolated from the endosperm (ES or kernel) and endocarp (EC or shell) of nut tissues followed by transcriptome sequencing using Illumina HiSeq2000. De novo transcriptome assembly was performed using Trinity. Read abundance was estimated using Corset and differentially expressed genes were identified using edgeR. In total, 1,945 genes were found to be differentially expressed (FDR < 0.05) from the nut tissues. Annotation of the transcripts revealed that only 82 of the differentially expressed genes have significant annotation. Potential gene-targeted markers (GTMs) were designed for 64 candidate genes, which can be further validated for possible use in the marker-assisted selection of high-yielding palms. Microsatellite (SSR) sequences were identified in 19,147 unigenes in the EC and 17,394 in the ES. However, only two SSRs were found among differentially expressed genes in the EC and only one in the ES. Functional analysis revealed that high nut yield could arise from concerted actions of several transcription activators and regulatory proteins leading to increased cell division, secondary cell wall formation, enhanced energy metabolism, and activated stress response. Taken together, these processes contribute to increased kernel volume and thus increase in copra yield. Identified genes in this study can be used as potential targets in improving productivity in the Philippine coconut.

 

10. Punzalan, M. R., Bautista, M. A., Emmanuel, E., Rivera, R., Rivera, S., & Saloma, C. (2019). Transcriptome of the Traditional Coconut Variety Laguna Tall. Philippine Journal of Science, 148 (S1), Pages 153–164.more

Abstract:

Coconut, Cocos nucifera L., is widely cultivated for its edible and non-edible products. In the Philippines, the traditional coconut variety, Laguna Tall (LAGT), exhibits good genetic potential as a pure population or as open-pollinated variety (OPV).  It was the male parent of the first PCA-recommended hybrid. Because of its importance in agronomic breeding, efforts are geared towards increasing genetic resources through genome and transcriptome sequencing. Here, pooled total RNA from leaves, nuts, and flowers of mature stage LAGT was sequenced using Illumina HiSeq 2000, followed by de novo assembly using four different transcriptome assemblers: Trinity, SOAPdenovo-Trans, Trans-Abyss, and Velvet-Oases. Each assembly was evaluated for accuracy using RSEM-EVAL, a reference-free evaluation method for transcript abundance data. Trans-Abyss outperformed the other three assemblers, but to have a better representation of the LAGT transcriptome, assemblies generated by the four programs were combined using the Evidential Gene tr2aacds pipeline. A total of 79,263 transcripts were generated from the combined transcriptomes. Also, Fragments Per Kilobase of transcript per Million mapped read (FPKM) units were used to quantify in silico gene expression. A total of 68,147 transcripts were generated by RSEM and compared against the CDD, Trembl, and UniProt databases. Gene ontology (GO) analysis and KEGG classification revealed that up to 33.8% of LAGT genes are involved in protein modification. The top 20 expressed genes were annotated using the nr database, which revealed that the most highly expressed transcript is a novel transcript. Microsatellite markers were also obtained for future use as breeding tools. Overall, this study provides a comprehensive assembly of the Cocos nucifera L. transcriptome useful as a molecular toolbox to identify key factors involved in important biological and cellular processes in coconut.

 

 

nip 

1. Abella, A.P., Soriano, M.N. (2019). Detection and visualization of water surface three-wave resonance via a synthetic Schlieren method. Physica Scripta, 94 (3).more

Abstract:

Three-wave resonance is one of the most fundamental energy-transfer mechanisms that can occur among weakly nonlinear surface waves. Here we show experimentally that if two source waves are propagating at an angle to each other, the conditions for three-wave resonances are satisfied and a third resultant wave is produced. We present 3D visualization of surface waves using the Free-Surface Synthetic Schlieren method, which removes the need for the addition of a light-diffusing agent, thereby retaining the surface tension and viscous properties of water. For three triad frequencies, we compute the average temporal power spectral density (PSD) of the wave heights. The direction of wave propagation is visualized by integrating the temporal PSD and by obtaining the average spatial PSD for each triad. Our results are in good agreement with the theory.

 

2. Afalla, J., Gonzales, K.C., Prieto, E.A., Catindig, G., Vasquez, J.D., Husay, H.A., Tumanguil-Quitoras, M.A., Muldera, J., Kitahara, H., Somintac, A., Salvador, A., Estacio, E., Tani, M. (2019). Photoconductivity, carrier lifetime and mobility evaluation of GaAs films on Si (100) using optical pump terahertz probe measurements. Semiconductor Science and Technology, 34 (3), Article number 035031.more

Abstract:

The carrier lifetimes and electron mobility values were estimated for 2 μm thick GaAs films grown on Si (100) substrates by means of optical pump terahertz probe (OPTP) technique. The GaAs/Si films measured were epitaxial grown at different substrate temperatures (T S = 520 °C or T S = 630 °C). From x-ray diffraction measurements and Raman spectroscopy, the GaAs/Si films were shown to experience minimum strain at room temperature, and crystal misorientation in the (111) or (110) direction. With no measureable photoluminescence at room temperature, carrier lifetimes were measured via OPTP and found to be 20 and 35 ps for a fluence of 4 μJ cm -2 , which is in the same order of magnitude as a reference bulk GaAs grown on SI-GaAs (T S = 630 °C) having a lifetime of 70 ps. From OPTP photoconductivity measurements, the estimated GaAs/Si films' electron mobility are 2900 cm 2 V -1 s -1 (T S = 520 °C) and 3500 cm 2 V -1 s -1 (T S = 630 °C) at a pump-probe delay time of Δt = 50 ps, in which the bulk GaAs electron mobility is 5200 cm 2 V -1 s -1.

 

3. Bardolaza, H., Afalla, J., De Los Reyes, A., Lumantas, D.A., Vasquez, J.D., Muldera, J., Mag-usara, V.K.,  Somintac, A.b, Salvador, A., Tani, M., Estacio, E. (2019). Efficacy of proposed 2DEG-based photoconductive antenna using magnetic bias-controlled carrier transport. Current Applied Physics, 19 (6), Pages 756-761.more

Abstract:

An externally applied magnetic field was used to induce increased photocarrier transport along the high mobility channel in GaAs/AlGaAs modulation-doped heterostructures (MDH). The terahertz (THz) emission from GaAs/AlGaAs MDH increases with increasing magnetic field, applied parallel to the heterojunction. The THz emission enhancement factors due to the magnetic field in MDH are higher than in undoped GaAs/AlGaAs heterojunction and in bulk SI-GaAs. This demonstrates that properly utilizing the high-mobility channel for carrier transport promises to be a viable design consideration for efficient THz photoconductive antenna (PCA) devices. Moreover, it was observed that for MDH, as well as for an undoped GaAs/AlGaAs heterojunction, the enhancement for one magnetic field direction is greater than the enhancement for the opposite direction. This is in contrast to the symmetric enhancement with magnetic field direction observed in a bulk SI-GaAs. An analysis of photocarrier trajectories under an external magnetic field supports the explanation that the enhancement asymmetry with magnetic field direction in MDH is due to the cycloid motion of electrons as affected by the GaAs/AlGaAs interface.

 

4. Bernardo, R.C., Vega, I. (2019). Hair-dressing Horndeski: An approach for obtaining hairy solutions in cubic Horndeski gravity. Physical Review D, 99 (12), Article number 124049.more

Abstract:

In obtaining exact solutions in gravitational theories containing arbitrary model functions, such as Horndeski gravity, one usually starts by prescribing the model functions of the theory and then goes on to solve their corresponding field equations. In this paper, we explore the extent to which the reverse procedure can be useful, whereby one starts with desired solutions and then determines the models that support them. Working within the phenomenologically interesting cubic and shift-symmetric sector of Horndeski gravity, we develop a method for obtaining exact static and spherically symmetric solutions, one of which happens to be a new hairy black hole. We study this black hole and its properties. We also discuss the limitations of the method and its possible extension to other Horndeski sectors. 

5. Dailisan, D.N., Lim, M.T. (2019). Vehicular traffic modeling with greedy lane-changing and inordinate waiting. Physica A: Statistical Mechanics and its Applications, 521, Pages 715-723.more

Abstract:

Lane changing and vehicular slowdowns are known to impact traffic flow. Using a modified Nagel–Schreckenberg cellular automata model for two vehicle types: blocking (e.g. cars) and non-blocking (e.g. motorcycles), we determined the thresholds at which the interplay of lane changing, random and non-random slowdowns strongly impact vehicle speeds. Lane changing improves speed with diminishing returns as vehicles opt to change lanes. At the same time, lane changing is detrimental to the overall speed when lane straddling occurs. Increasing random slowdowns beyond a critical value (in the case of motorcycles, slowdown values of pslow≈[0.2,0.3,0.4] for densities ρ=[0.20,0.15,0.10] respectively) can force crossover from free flowing traffic into a state where interactions between vehicles reduce the average speed.

 

6. De Leon, K., Vega, I. (2019). Weak gravitational deflection by two-power-law densities using the Gauss-Bonnet theorem. Physical Review D, 99 (12), Article number 124007.more

Abstract:

We study the weak deflection of light by nonrelativistic mass distributions described by two-power-law densities ρ(R)=ρ0R-α(R+1)β-α, where α and β are non-negative integers. New analytic expressions of deflection angles are obtained via the application of the Gauss-Bonnet theorem to a chosen surface on the optical manifold. Some of the well-known models of this two-power-law form are the Navarro-Frenk-White (NFW) model (α,β)=(1,3), Hernquist (1,4), Jaffe (2,4), and the singular isothermal sphere (2,2). The calculated deflection angles for Hernquist and NFW agree with that of Keeton and Bartelmann, respectively. The limiting values of these deflection angles (at zero or infinite impact parameter) are either vanishing or similar to the deflection due to a singular isothermal sphere. We show that these behaviors can be attributed to the topological properties of the optical manifold, thus extending the pioneering insight of Werner and Gibbons to a broader class of mass densities.

7. De Vero, J., Jasmin, A., Dasallas, L., Garcia, W., & Sarmago, R. (2019). Synthesis of Iron Oxide Nanostructures via Carbothermal Reaction of Fe Microspheres Generated by Infrared Pulsed Laser Ablation. Coatings, 9 (3), Page 179.more

Abstract:

Iron oxide nanostructures were synthesized using the carbothermal reaction of Fe microspheres generated by infrared pulsed laser ablation. The Fe microspheres were successfully deposited on Si(100) substrates by laser ablation of the Fe metal target using Nd:YAG pulsed laser operating at λ = 1064 nm. By varying the deposition time (number of pulses), Fe microspheres can be prepared with sizes ranging from 400 nm to 10 µm. Carbothermal reaction of these microspheres at high temperatures results in the self-assembly of iron oxide nanostructures, which grow radially outward from the Fe surface. Nanoflakes appear to grow on small Fe microspheres, whereas nanowires with lengths up to 4.0 μm formed on the large Fe microspheres. Composition analyses indicate that the Fe microspheres were covered with an Fe<sub>3</sub>O<sub>4</sub> thin layer, which converted into Fe<sub>2</sub>O<sub>3</sub> nanowires under carbothermal reactions. The apparent radial or outward growth of Fe<sub>2</sub>O<sub>3</sub> nanowires was attributed to the compressive stresses generated across the Fe/Fe<sub>3</sub>O<sub>4</sub>/Fe<sub>2</sub>O<sub>3</sub> interfaces during the carbothermal heat treatment, which provides the chemical driving force for Fe diffusion. Based on these results, plausible thermodynamic and kinetic considerations of the driving force for the growth of Fe<sub>2</sub>O<sub>3</sub> nanostructures were discussed.

8. Dingle, C. A. M., Jecong, J. F. M., Hila, F. C., Ramo, M. E. S. V., Guillermo, N. R. D., Vasquez Jr, M. R., & Samson, V. A. I. (2019). Determination of the REE content, geological age, and absorbed alpha dose of allanite mineral from Palawan, Philippines. X-Ray Spectrometry, 48 (5), Pages 513-521.more

Abstract:

Allanite is a common accessory mineral in igneous rocks that contains significant amounts of rare‐earth elements (REEs), thorium (Th), and uranium (U). The presence of Th and U in the allanite exposes it to radiation resulting in radiation damage in its crystal structure and further leads to metamictization. Hence, allanite can be used as a natural analogue to assess the long‐term radiation effects in materials for high‐level nuclear waste disposal. It provides information on the effect of α‐decay on the crystal structure including the stability and integrity of the material. In this study, the absorbed α‐dose of allanite from Ombo, Palawan, Philippines, was estimated from the Th and U content and geological age of the mineral using X‐ray fluorescence and gamma‐ray spectrometry. The amount of Th and REE was measured to be around 1.37 and ~30.4 wt.%, respectively. Radiometric dating using gamma‐ray spectrometry estimated the age of the allanite mineral to be around 24–35 million years. Having obtained the amount of radioactivity and the time of exposure, the corresponding absorbed α‐dose was estimated to be at 2.84 × 1014 α‐decays/mg. Results suggest that the allanite mineral studied has not accumulated significant radiation damage to cause amorphization and still exhibit a crystalline structure. This study may provide data on the properties of allanite or silicate matrices as part of the ongoing studies on silicate minerals as natural analogues.

9. Flores, P.C.M., Galapon, E.A. (2019). Quantum free-fall motion and quantum violation of the weak equivalence principle. Physical Review A, 99 (4), Article number 042113.more

Abstract:

The weak equivalence principle (WEP) in the quantum regime has been the subject of many studies with a broad range of approaches to the problem. Here, we tackle the problem anew through the time of arrival (TOA) operator approach. This is done by constructing the TOA operator for a nonrelativistic and structureless particle that is projected upward in a uniform gravitational field with an intended arrival point below the classical turning point. The TOA operator is constructed under the constraint that the inertial and gravitational masses are equivalent and that Galilean invariance is preserved. These constraints are implemented by Weyl quantization of the corresponding classical TOA function for the projectile. The expectation value of the TOA operator is explicitly shown to be equal to the classical time of arrival plus mass-dependent quantum correction terms, implying incompatibility of the WEP with quantum mechanics. The full extent of the violation of the WEP is shown through the mass dependence of TOA distribution for the projectile.

 

10. Improso, W.D.G.D., Hilario, P.L.A.C., Tapang, G.A. (2019). Spurious Transmission in Liquid Crystal Tunable Filter Operation in Microscopy(Conference Paper). 2018 Conference on Lasers and Electro-Optics Pacific Rim, Article number 8699371.

Abstract:

We investigate the effect of incidence angle to the transmitted power of a liquid crystal tunable filter (LCTF) with a 632nm laser source. Spurious transmission in other wavelengths was observed in non-normal incidence angles.

 

11. Improso, W. D. G. D., Tapang, G. A., & Saloma, C. A. (2019). Suppression of Zeroth-Order Diffraction in Phase-Only Spatial Light Modulator. Springer Series in Optical Sciences, Pages 1-30.more

Abstract:

A correction beam is created using a spatial light modulator (SLM) to suppress the zeroth-order diffraction (ZOD) that is produced by the unmodulated light coming from the dead areas of the said SLM. The correction beam is designed to interfere destructively with the undesirable ZOD that degrades the overall quality of the propagated SLM signal. Two possible techniques are developed and tested for correction-beam generation: aperture division and field addition. With a properly-calibrated SLM, ZOD suppression is demonstrated numerically and experimentally at sufficiently high area factor (AF) values where suitable matching is achieved between the correction beam and the ZOD profiles to result in a 39% reduction of the ZOD intensity via angular aperture division, 32% reduction via annular aperture division, and 24% reduction via vertical aperture division. At low AF values however, meaningful ZOD suppression is not obtained. With the field addition method, a ZOD reduction as high as 99% is gained numerically which was not realized experimentally using an SLM with a fill factor of 0.81 due to limitations posed by an iterative phase-recovery algorithm (ghost image) as well as unwanted signal contributions from the SLM anti-reflection coating, SLM surface variations, optical misalignment and aberrations.

 

12. Jose, A., Montecillo, A., De Los Reyes, A., Bacaoco, M., Lopez, J., Cafe, A., Estacio, E. (2019). Enhanced terahertz emission of a gallium arsenide thin film on a porous silicon distributed Bragg reflector designed at 800nm wavelength. Optical Materials, 92 (May), Pages 335–340.more

Abstract:

Enhanced terahertz (THz) radiation was generated from a gallium arsenide thin film integrated on top of porous silicon distributed Bragg reflector (GaAs/PSi DBR). The film's thickness was designed to be less than the penetration depth of the 800 nm excitation source, while the PSi DBR was centered at the laser wavelength to reflect the transmitted photons at the film-substrate interface. Reflection-geometry THz time-domain spectroscopy measurement revealed enhancement in THz peak to peak amplitude by 1.67 and 5.7 times as compared to the same thickness of GaAs on silicon (GaAs/Si) and bulk semi-insulating (SI) GaAs, respectively. In comparison with the bulk SI-GaAs, both thin film samples showed an order of magnitude improvement in the THz output power. The excitation-wavelength study also revealed a maximum increase near the design wavelength. The enhancement was attributed to the high reflectivity at the film-substrate interface and optical cavity effect in GaAs. These factors contributed to an effective optical confinement within the film's THz generation region.

 

13. Manaoat, N.M., Bantang, J., Bo-ot, L.M. (2019). Diurnal temperature variation in an idealized room for different wall materials using a thermal load model in the Philippine setting (Conference Paper). Advances in Intelligent Systems and Computing, 1018, Pages 110-116.more

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. 

14. Narag, J.P.C., Hermosa, N. (2019). Probing Higher Orbital Angular Momentum of Laguerre-Gaussian Beams via Diffraction through a Translated Single Slit. Physical Review Applied, 11 (5), Article number 054025.more

Abstract:

Laguerre-Gaussian (LG) beams and their orbital angular momentum (OAM) have found a plethora of applications - from quantum information to gravitational-wave detection. In this work, we probe the OAM of LG beams by using a digital micromirror device programmed as a single slit. We observe the diffraction patterns of the beams through the slit and we show that we can determine the OAM of the incoming beams from the changes in the diffraction pattern as the slit is moved transversely. Moreover, we demonstrate that we can access higher OAM modes compared to previous works involving slit diffraction. Our results are valuable in the study of OAM especially for beams where the current technology for detection is not yet mature, for example, beams whose wavelengths are in the terahertz regime or beams of higher energy such as, electron vortex beams.

 

15. Narag, M. J. G., & Soriano, M. N. (2019). Identifying the painter using texture features and machine learning algorithmsACM International Conference Proceeding Series, Pages 201–205.more

Abstract:

Every artist has their own unique style of painting. The quantitative analysis of artworks is therefore essential to better understand the statistical differences between the paintings of different artists. In this study, we test if we can distinguish the works of Juan Luna from other Filipino painters using features derived from different sections of their paintings - foreground, background, foreground and background. We extracted texture features from the Gray Level Co-occurrence Matrix (GLCM) of the patches obtained from these sections and apply neural networks and Support Vector Machine (SVM) on duplets and triplets of features. From k-fold validation, the SVM on duplet of features from the background section of the paintings gave the highest accuracy of 83% for 375 dpi and 82% for 100 dpi. We have therefore shown that our approach can distinguish the works of Juan Luna from other Filipino painters.

 

16. Oca, G.M., Almoro, P.F.  (2019). Enhanced schlieren imaging applied in heat and air jet visualizations: A wave propagation-based model. Proceedings of SPIE - The International Society for Optical Engineering, 11052.more

Abstract:

Refractive index variations caused by temperature or pressure gradients in transparent fluids are invisible to the naked eye. Schlieren effect reveals this variation using refraction and the knife-edge method. High contrast schlieren images are important in the analyses of fluid flow, gas density, shockwaves, heat transfer, flames, ballistics, leak detection and other applications. The neglect of physical or wave theory in schlieren technique leads to erroneous results in some circumstance. Specifically, a study had mathematically shown that illumination is fairly uniform over large part of the field but suddenly increases at the edge and is fairly appreciable for some way outside the actual physical boundary of the aperture. This bright edge is noticeable in all schlieren systems whereas a geometrical optics would lead to a uniformly illuminated field. Geometric ray-tracing codes are useful for optical design, but they cannot describe the key role of diffraction in the formation of schlieren image. In this study, a wave propagation-based model of the schlieren technique is proposed. Compared to the ray optics approach, the proposed model provides valuable insights and visualization of fluid flow dynamics. Some predictions of the model will be confirmed through experimental demonstrations. Setup parameters are also optimized resulting in enhanced resolution of schlieren images. 

 

17. Revilla, M., Lorenzo, J.C., Hermosa, N.  (2019). A paraxial cloak with four lenses of different focal lengths. European Journal of Physics, 40 (3), Article number 035303.more

Abstract:

We demonstrate cloaking with four lenses of different focal lengths. To achieve this, we compute the separation distances between lenses such that the effective ABCD matrix is equal to just a propagation in free space. Previously, calculations using this method have been restricted to two pairs of lenses with equal focal lengths. Our computations, on the other hand, have no such restrictions: we generalize even with an asymmetric case. We derive expressions that show the dependence of the distances on the lenses and their focal lengths. Furthermore, we propose a way to minimize the length of this cloak. Our equations reduce to the Rochester cloak when its restriction is imposed. A general paraxial cloak could be useful in advanced undergraduate experiments in optics because (i) the limit imposed by the focal length has been lifted, and (ii) there is a pedagogical benefit of doing experiments with lenses beyond the usual imaging experiments, such as reinforcing concepts in Gaussian optics.

 

18. Santos-Putungan, A.B., Stojić, N.c, Binggeli, N., Paraan, F.N.C. (2019). Strong chemisorption of CO 2 on B 10 -B 13 planar-type clusters. Journal of Physics Condensed Matter, 31 (14).more

Abstract:

An ab initio density functional study was performed investigating the adsorption of CO 2 on neutral boron B n (n = 10-13) clusters that are characterized by planar and quasiplanar ground-state atomic structures. For all four clusters, we found large chemisorption binding energies, reaching 1.6 eV between CO 2 and B 12 , with the adsorbed molecule oriented in the plane of the cluster and adsorbed along the cluster edge. A configuration with chemisorbed dissociated CO 2 molecule also exists for B 11 and B 13 clusters. The strong adsorption is due to the bending of the CO 2 molecule, which provides energetically accessible fully in-plane frontier molecular orbitals matching the edge states of the clusters. At the same time, the intrinsic dipole moment of a bent CO 2 molecule facilitates the transfer of excess electronic charge from the cluster edges to the molecule.

 

19. Tica, C.D., Galapon, E.A. (2019). Finite-part integration of the generalized Stieltjes transform and its dominant asymptotic behavior for small values of the parameter. II. Non-integer orders. Journal of Mathematical Physics, 60 (1).more

Abstract:

This paper constitutes the second part on the subject of finite part integration of the generalized Stieltjes transform Sλ[f]=â0âžf(x)(ω+x)-λdx about ω = 0, where now λ is a non-integer positive real number. Divergent integrals with singularities at the origin are induced by writing (ω + x) as a binomial expansion about ω = 0 and interchanging the order of operations of integration and summation. The prescription of finite part integration is then implemented by interpreting these divergent integrals as finite part integrals which are rigorously represented as complex contour integrals. The same contour is then used to express Sλ[f] itself as a complex contour integral. This led to the recovery of the terms missed by naïve term-wise integration which themselves are finite parts of divergent integrals whose singularity is at the finite upper limit of integration. When the function f(x) has a zero at the origin of order m = 0, 1, such that m-λ < 0, the correction terms missed out by the naïve term by term integration give the dominant contribution to Sλ[f] as ω → 0. Otherwise, the correction term is sub-dominant to the leading convergent terms in the naïve term by term integration. We apply these results by obtaining exact and asymptotic representations of the Kummer and Gauss hypergeometric functions by evaluating their known Stieltjes integral representations. We then apply the method of finite part integration to obtain the asymptotic behavior of a generalization of the Stieltjes integral which is relevant in the calculation of the effective index of refraction of a shallow potential well. 

 

20. Yumang, A. N., Dimaunahan, E. D., Cruz, J. Dela, Talisic, G. C., Sampedro, G. A. R., & Soriano, M. N. (2019). Real-Time Plasmodium Falciparum Parasitemia using Natural Neighbor Interpolation. 2018 IEEE 10th International Conference on Humanoid, Nanotechnology, Information Technology,Communication and Control, Environment and Management (HNICEM), Pages 1–6.more

Abstract:

This paper focuses on the development of an attachment to an Olympus CX21 microscope capable of automating the process of the parasitemia of P. Falciparum, one of the most common parasitic strains of malaria. The device uses a camera module attached to the eyepiece of the microscope to analyze the slide, and a set of stepper motors attached to the stage control to adjust the position of the mechanical stage. The flood-fill algorithm is used to analyze each field of view (FOV) of the slide to count the number of red blood cells and infected cells. Furthermore, while manual differential counting includes the analysis of hundreds of fields of views, the device uses the numerical method, natural neighbor interpolation (NNI), to reduce the number of slides to be examined, thereby making the process much more efficient. The results of the various tests yielded an accuracy rate of more than 90% for the automation of the process and a percent difference of no more than 20% for the application of NNI.

 

21. Zambale, N.A.F., Sagisi, J.L.B., Hermosa, N.P. (2019). Goos-Hänchen shifts due to graphene when intraband conductivity dominates. Optics Communications, 433, Pages 25-29.more

Abstract:

The conductivity of a monolayer graphene at intraband transitions is sensitive on the Fermi level and on the wavelength of the incident beam. Changing conductivity values through these parameters thus may offer better control of light impinging on graphene. In this paper, we investigate reflection, the simplest interaction of light on such surface, by looking at the Goos-Hänchen (GH) shift experienced by the incident light where the wavelength is at terahertz range. With this wavelength range, we assume that the carriers in graphene undergo intraband transition. We calculate that spatial and angular GH shifts can be present. For both GH shifts in general, we find that increasing the Fermi level changes the incident angle at which the maximum GH shifts arise. Moreover, we see that at higher frequencies, the amount of beam shift decreases with the Fermi level. At lower frequencies on the other hand, the shift becomes proportional to the Fermi level. Upon obtaining the measurable shifts, we find that the magnitude of the physical shifts can be easily detected given appropriate experimental parameters. Our results may increase the utility of graphene in optoelectronics devices and applications. 

 

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1. Mendoza, M.V., Rivera, W.L. (2019). Identification of Leptospira spp. from environmental sources in areas with high human leptospirosis incidence in the Philippines. Pathogens and Global Health, 133 (3), Pages 109-116.more

Abstract:

Leptospira is the causative agent of leptospirosis, which is considered an emerging major threat to public health due to its increasing frequency reported worldwide. In the Philippines, the prevalence of the disease continuously rises, particularly in urban areas. Because leptospirosis is commonly transmitted through contact with contaminated environment, water and soil samples were collected in regions in the Philippines where high incidence of human leptospirosis cases was reported recently. Of the 54 samples screened for the presence of Leptospira, 35% were found positive through 23S rRNA gene PCR-based detection. None were found positive when primers targeting lipL32, lipL41, and ompL1 genes were used. Most of these isolates were collected from rural areas. However, 16S rRNA gene sequencing identified all isolates to be L. yanagawae and L. meyeri, which are nonpathogenic. Despite the lack of evidence of the presence of pathogenic species in the environmental sources, the results still suggest that leptospires persist in these areas. These data are crucial for environmental monitoring and identification of contaminated areas where humans may be at risk of infection.

2. Rodriguez, J.J.R.B., Bright, J.-A., Salvador, J.M., Laude, R.P., De Ungria, M.C.A. (2019). Probabilistic approaches to interpreting two-person DNA mixtures from post-coital specimens. Forensic Science International, 300, Pages 157-163.more

Abstract:

Biological samples submitted for sexual assault investigation typically involve mixtures of DNA from the victim and the assailant/s. Providing a statistical weight to such evidence may be mathematically complex and may be affected by subjective judgment of a human analyst. Software tools have been developed to address these issues. To contribute towards improving the system for routine DNA testing of sexual assault cases, we evaluated two likelihood ratio (LR) approaches: a semi-continuous model using LRmix Studio and a fully continuous approach employed in STRmix™ for interpreting two-person DNA mixtures. LRs conditioned on the presence of the receptive partner’s DNA were calculated for a total of 102 two-person DNA samples from simulated mixtures and various post-coital samples. Our results highlight the importance of maximising information provided into the LR calculation to generate strong support for the true hypothesis. This can be achieved by recovering sufficient DNA from a sample to minimise risk of drop-out and increase peak intensities and by implementing a statistical model that utilises as much of the electropherogram information as possible. LRmix is open-source and can handle profiles with allelic drop-out and drop-ins, however stuttering is not modelled and requires manual removal by a DNA analyst especially for mixtures with low template components. STRmix™ makes effective use of all available information by incorporating into its biological model complicating aspects of a DNA profile such as degradation, allele drop-out and drop-in, stutters, and peak height variability.

3. Sales, P.R.L., Ferrer, D.E.C., Calacal, G.C., Salvador, J.M., De Ungria, M.C.A. (2019). Validation of two extraction methods for human DNA from cigarette butts. Science Diliman, 31 (1), Pages 25-36.

Abstract:

Cigarette butts found in crime scenes may be used to identify persons and link them to a crime through DNA profiling of epithelial cells from saliva stains on these materials. Downstream analysis of cigarette butts poses some challenges because these are often exposed to chemical contaminants and environmental conditions which lead to DNA degradation. In this study, several factors were tested to compare the amount and quality of DNA obtained from cigarette butts extracted using an organic procedure and the QIAamp® DNA Micro Kit (QIAGEN). Results show that exposure to an outside environment had a significant effect on DNA yield and amplifiability for both extraction procedures. Prolonged storage of cigarette butts of up to six months affected the amount of DNA that can be extracted using the QIAamp® DNA Micro Kit. However, complete DNA profiles can be generated from cigarette butts stored for six months provided that these samples are stored indoors under controlled temperature conditions and with minimal exposure to contaminants.

4. Sato, M.O., Adsakwattana, P., Fontanilla, I.K.C., Kobayashi, J., Sato, M., Pongvongsa, T., Fornillos, R.F.C. (2019). Odds, challenges and new approaches in the control of helminthiasis, an Asian studyParasite Epidemiology and Control, 4, Article number e00083.more

Abstract:

The time is passing, and the worms are still a major struggle for local people in Asian countries, especially the less empowered and in a situation of social vulnerability. We are working in the field in Laos, Thailand, and the Philippines where the usual control programs based only on human treatment are partially effective. Areas with mass drug administration could diminish, but not eliminate STHs of endemic areas. The persistence of helminthic NTDs in the environment and animal hosts makes the eradication a very difficult task. Great changes in the landscapes of endemic areas, such as construction of dams, can change the fauna and the lifestyle of local people. Those changes can improve infrastructure, but it can also lead to social vulnerability. The challenge, then, is to conceive new and directed control programs for helminthiasis based on multi- and transdisciplinary approaches diminishing the health gap in a globalized world. In this short review, we summarize the actual scenario concerning the main helminths in Southeast Asia and how an environmental DNA approach and the use of GIS could contribute to surveillance and control programs.

 

5. Vital, P.G., Rivera, W.L., Abello, J.J.M., Francisco, J.C.E. (2019). Microbiological assessment of fresh, minimally processed vegetables from open air markets and supermarkets in Luzon, Philippines, for food safety. Environment, Development and Sustainability, 21 (1), Pages 51-60.more

Abstract:

A wide-range investigation of the microbiological quality of fresh produce from different open air markets and supermarkets in Luzon, Philippines was performed. Different vegetables which are usually consumed raw (bell pepper, carrot, lettuce, mung bean sprout, and tomato) had been screened for the presence and amount of contamination of enteric microorganisms, namely Escherichia coli, Salmonella spp., and somatic bacteriophages (or viruses). Phenotypic characterization was employed using selective and differential media such as eosin methylene blue agar and xylose lysine deoxycholate agar. Viable plate count (colony-forming units or CFU) and most probable number (MPN) methods were used to estimate the cell numbers of E. coli and Salmonella spp., respectively. Double agar assay was used to detect and quantify somatic phages as plaque-forming units (PFU). Polymerase chain reaction was also done to confirm the identity of the isolates using species-specific primers. From a total of 410 vegetable samples collected, 44 bacterial (prevalence of 5.85% E. coli and 5.12% of Salmonella spp.) and 21 (prevalence of 5.12%) viral isolates were obtained. It is alarming to note that samples contaminated with Salmonella spp. were significantly higher in counts (3.751 ± 0.60 log MPN/g) as compared to E. coli (1.472 ± 0.25 log CFU/g), while samples with coliphage (0.316 ± 0.12 log PFU/g) were the least in numbers. The degree of contamination in the samples can cause great risks on the health of individuals especially in developing countries such as the Philippines. Thus, monitoring on the handling of different produce is important to improve the country’s food quality and safety.