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Faculty Publication (2019)

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1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

 

6. 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.

 

7. 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.

 

8. 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.

9. 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.

 

 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. 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.

3. 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.

4. 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.

5. 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.

 

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

 

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1. 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.

 

2. 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.

 

3. 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.

4. 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.

5. 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. Amarra, Carmen, Jin, Wei, & Praeger, Cheryl E. (2019). On locally n x n grid graphs. arXiv, arXiv:1903.07931. more

Abstract:

We investigate locally n×n grid graphs, that is, graphs in which the neighbourhood of any vertex is the Cartesian product of two complete graphs on n vertices. We consider the subclass of these graphs for which each pair of vertices at distance two is joined by sufficiently many paths of length 2. The number of such paths is known to be at most 2n by previous work of Blokhuis and Brouwer. We show that if each distance two pair is joined by at least n−1 paths of length 2 then the diameter is bounded by O(log(n)), while if each pair is joined by at least 2(n−1) such paths then the diameter is at most 3 and we give a tight upper bound on the order of the graphs. We show that graphs meeting this upper bound are distance-regular antipodal covers of complete graphs. We exhibit an infinite family of such graphs which are locally n×n grid for odd prime powers n, and apply these results to locally 5×5 grid graphs to obtain a classification for the case where either all μ-graphs have order at least 8 or all μ-graphs have order c for some constant c.

 

2. Dela Cruz, R.B. and Ol, S. Cheating-immune secret sharing schemes from maiorana-mcfarland boolean functions (2019). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Paper presented at the 21st International Conference on Information Security and Cryptology, ICISC 2018, Seoul, South Korea, 28-30 November 2018. Volume 11396 LNCS, Pages 233-247. DOI:10.1007/978-3-030-12146-4_15.

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.

3. 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.

 

4. Hernandez, Bryan S., Mendoza, Eduardo R., de los Reyes, Aurelio (2019). A Computational Approach to Multistationarity of Power-Law Kinetic SystemsarXiv, arXiv:1902.02306.more

Abstract:

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

 

5. 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.

 

6. Tabornal, Racquel U., Escaner IV, Jose Maria, Rabajante, Jomar F.  (2019). Mathematical Modeling on Competition and Cooeration of Species Using Hill-type FunctionICCMS 2019 Proceedings of the 11th International Conference on Computer Modeling and Simulation, 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.

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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. 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.

 

3. 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.

 

4. 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.

 

5. 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

6. 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.

 

7. 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.

 

8. 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.

9. 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. 

 

10. 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.

 

11. 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.

 

12. 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.

13. 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.

14.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. 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.

3. 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 population. BMC Pregnancy and Childbirth. doi.org/10.1186/s12884-018-2152-z. 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.

 

4. Bascos, N.A.D., Jimenez, E.C. (2019). Molecular dynamics simulations of the conformational states of a D-tryptophan-containing conus venom peptide and its all-l-amino acid analog. Current Topics in Peptide & Protein Research, 19, Pages 27 - 41.more

Abstract:

Molecular dynamics (MD) simulation is a powerful method for examining the conformational states of biomolecular systems. In the present work, MD simulations were employed to probe into the dynamic modes and conformational states of contryphan-Sm (a Conus venom peptide with D-Trp4) and its analog, [L-Trp4]contryphan-Sm, specifically focusing on the investigation of their structural differences. Molecular modeling showed that the basic cyclic structures of contryphan-Sm and [L-Trp4]contryphan-Sm were similar, with no steric clashes occurring among the amino acid residues. The MD simulations showed that contryphan-Sm assumed a more compact conformation compared to [L-Trp4]contryphan-Sm based on their maximum peptide dimensions and radii of gyration. After ~ 20 ns of MD simulations, the root-mean-square deviation (RMSD) values were lower for almost all of the amino acid residues in contryphan-Sm, with its D-Trp4 showing the highest difference in RMSD from L-Trp4 in [L-Trp4]contryphan-Sm, suggesting that contryphan-Sm had less structural variability. Energy measurements supported this finding, with contryphan-Sm consistently exhibiting lower kinetic energy values compared to [L-Trp4]contryphan-Sm throughout the MD simulations. The Ramachandran plots showed greater variations in phi or psi angles in L-Trp4, Gln5, Pro6 and Trp7 in [L-Trp4]contryphan-Sm than the corresponding residues in contryphan-Sm at the start and end of the MD simulations. Contryphan-Sm showed less solvent accessibility than [L-Trp4]contryphan-Sm as shown by the measurements of their solvent-activated surface areas. Decreased solvent accessibility may be linked to the stacked conformation adopted by contryphan-Sm, aligning D-Trp4, Pro6 and Trp7. Despite the observed motions of the Trp side chains, both contryphan-Sm and [L-Trp4]contryphan-Sm structures do not support the occurrence of intramolecular covalent crosslinking between D/L-Trp4 and Trp7. The observed differences in dynamic modes and conformational states of contryphan-Sm and [L-Trp4]contryphan-Sm are correlated with the greater structural stability of the D-Trp-containing contryphan.

 

5. Dy, R.L., Rigano, L.A., Fineran, P.C. (2019). Phage-based biocontrol strategies and their application in agriculture and aquaculture. Biochemical Society Transactions, 46 (6), Pages 1605-1613.more

Abstract:

Meeting global food demands for a growing human population with finite natural resources is a major challenge. Aquaculture and agriculture are critical to satisfy food requirements, yet suffer significant losses from bacterial diseases. Therefore, there is an urgent need to develop novel antimicrobial strategies, which is heightened by increasing antibiotic resistance. Bacteriophages (phages) are viruses that specifically infect bacteria, and phage-derived therapies are promising treatments in the fight against bacterial diseases. Here, we describe multiple ways that phages and phage-based technologies can be used as antimicrobials. Antimicrobial activity can be achieved through lysis of targeted bacteria by virulent phages or lytic enzymes. Alternatively, phages can be engineered for the delivery of lethal genes and other cargoes to kill bacteria and to manipulate the bacterial response to conventional antibiotics. We also briefly highlight research exploring phages as potential biocontrol agents with examples from agriculture and aquaculture.

6. 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.

 

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. 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.

 

5. 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.

 

 

6. 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.

 

7. 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.

 

 

8. 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. 

 

9. 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.

 

10. 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.

 

11. 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. 

 

12. 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.