Faculty Publication (2020)

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract: 

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

6. Veloria, A., Perez, G.J., Tapang, G., Comiso, J. (2020). Comparison between GPM and gridded precipitation product from interpolated rain gauge measurements. 40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea, Code 157736.

Abstract:

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

 

7. Valete, M.A.P., Perez, G.J.P., Enricuso, O.B., Comiso, J.C. (2020). Spatiotemporal evaluation of historical drought in the Philippines. 40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea, Code 157736.

Abstract:

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

 

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

Abstract:

Let R_n be the n-by-n backward identity matrix and let L_n,k:=I_k⊕−I_n−k. Suppose A∈C^n×n is nonsingular. We say that A is perplectic if R_nA^TR_n=A⁻¹; and A is pseudo-unitary if L_n,kA^⁎L_n,k=A⁻¹. We give necessary and sufficient conditions for a matrix to be diagonalizable via a perplectic or a pseudo-unitary matrix.

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

We determine the forms of the nontrivial idempotents in the ring of 2 × 2 matrices over the polynomial rings Z_pq[x] and Z_p2[x], where p and q are any primes. Any such idempotent in the stated rings will be of a form in our list. Our work generalizes the results of Kanwar, Khatkar and Sharma (2017) who identified the forms of idempotents in M₂(Z_2p [x]) and M₂(Z_3p [x]).

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

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.

 

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

Abstract:

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

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

Abstract:

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

 

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

Abstract:

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

 

2. De Los Reyes, A., Bardolaza, H., Vasquez, J. D., Cabello, N. I., Lopez, L., Chang, C. Y., Somintac, A., Salvador, A., Jang, D. J., & Estacio, E. (2020). Temperature-dependent terahertz time-domain spectroscopy of 3D, 2D, and 0D semiconductor heterostructures. Journal of Materials Science: Materials in Electronics, 0123456789. https://doi.org/10.1007/s10854-020-03188-y 

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract: 

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract: 

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

 

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

Abstract: 

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

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

Abstract: 

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

 

 

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

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.

 

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

Abstract:

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

 

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

Abstract:

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

4. Ratio, M. A., Gabo-Ratio, J. A., Fujimitsu, Y. (2020). Exploring public engagement and social acceptability of geothermal energy in the Philippines: A case study on the Makiling-Banahaw Geothermal Complex. Geothermics, 85: 101774. 

Abstract:

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

 

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

Abstract:

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

 

6. Tiauzon, A., Peterson, J., Robles, E. C., Neri, L. A., Forestier, H., Titton, S., Manipon, D. R., Fernando, A. G., Mijares, A., Paz, V., Dizon , E. (2020). Unfolding the technological production strategies of the large toolkits across Philippine Paleolithic sites with specific reference to northern Mindanao.  Quaternary International,  535: 69-87. 

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.

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract: 

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

8. Mapalo, M.A., Arakawa, K., Baker, C.M., Persson, D.K., Mirano-Bascos, D., Giribet, G. (2020). The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across Ecdysozoa. G3: Genes, Genomes, Genetics, 10 (1), DOI: 10.1534/g3.119.400734 

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

 

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

Abstract:

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

 

2. Afalla, J., Catindig, G., Delos Reyes, A., Prieto, E., Faustino, M. a., Vistro, V., Gonzales, K. C., Bardolaza, H., Mag-usara, V., Husay, H. A., Muldera, J., Cabello, N., Ferrolino, J. P., Kithara, H., Somintac, A., Salvador, A., Tani, M., & Estacio, E. (2020). Ultrafast carrier dynamics and THz conductivity in epitaxial-grown LT-GaAs on silicon for development of THz photoconductive antenna detectors. Journal of Physics D: Applied Physics, 53 (9). https://doi.org/10.1088/1361-6463/ab5aa7 

Abstract:

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

3. Bernardo, R. C., Celestial, J., & Vega, I. (2020). Stealth black holes in shift symmetric kinetic gravity braiding. Physical Review D, 101 (2), 24036. https://doi.org/10.1103/PhysRevD.101.024036 

Abstract:

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

 

4. De Los Reyes, A., Bardolaza, H., Vasquez, J. D., Cabello, N. I., Lopez, L., Chang, C. Y., Somintac, A., Salvador, A., Jang, D. J., & Estacio, E. (2020). Temperature-dependent terahertz time-domain spectroscopy of 3D, 2D, and 0D semiconductor heterostructures. Journal of Materials Science: Materials in Electronics, 0123456789. https://doi.org/10.1007/s10854-020-03188-y 

Abstract:

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

 

5. De Los Reyes, A. E., Vasquez, J. D., Bardolaza, H. R., Lopez, L. P., Chang, C.-Y., Somintac, A. S., Salvador, A. A., Jang, D.-J., & Estacio, E. S. (2020). Low-temperature carrier dynamics in MBE-grown InAs/GaAs single- and multi-layered quantum dots investigated via photoluminescence and terahertz time-domain spectroscopy. Optical Materials Express, 10 (1), 178. https://doi.org/10.1364/ome.380909 

Abstract:

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

 

6. Flores, M., Kar, D., & Kim, J. S. (2020). Constraining Stealth SUSY with illuminated fat jets at the LHC. Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics, 801, 135151. https://doi.org/10.1016/j.physletb.2019.135151 

Abstract:

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

 

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

Abstract:

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

 

8. Manaoat, N. M., Bantang, J. Y., & Bo-ot, L. M. (2020). Diurnal Temperature Variation in an Idealized Room for Different Wall Materials Using a Thermal Load Model in the Philippine Setting. 1st International Conference on Human Interaction and Emerging Technologies, IHIET 2019; Nice; France; 22 August 2019 through 24 August 2019; Code 229139, 110–116. 

Abstract:

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

 

9. Pablico, D. A. L., & Galapon, E. A. (2020). Quantum traversal time across a potential well. Physical Review A, 101 (2), Pages 1–13. https://doi.org/10.1103/PhysRevA.101.022103 

Abstract:

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

 

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

Abstract:

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

 

11. Simon, R. C., Sagisi, J. L. B., Zambale, N. A. F., & Hermosa, N. (2020). Is a single layer graphene a slab or a perfect sheet? Carbon, 157, Pages 486–494. https://doi.org/10.1016/j.carbon.2019.10.044 

Abstract:

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

 

12. Veloria, A., Perez, G.J., Tapang, G., Comiso, J. (2020). Comparison between GPM and gridded precipitation product from interpolated rain gauge measurements. 40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019; Daejeon Convention Center (DCC)Daejeon; South Korea; 14 October 2019 through 18 October 2019; Code 157736

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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

 

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

Abstract:

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