IPA Recipients for February 2020

Romnick S. Baliton1 , Leila D. Landicho2, Rowena Esperanza D. Cabahug2, Roselyn F. Paelmo3, Roberto G. Visco1 and Arnold Karl A. Castillo2
1Institute of Renewable Natural Resources, College of Forestry and Natural Resources (UP Los Baños)
2Institute of Agroforestry, College of Forestry and Natural Resources (UP Los Baños)
3Institute of Crop Science, College of Agriculture and Food Science (UP Los Baños)

Ecological Services of Agroforestry Systems in Selected Upland Farming Communities in the Philippines,  Biodiversitas, 21(2): 701-717, 2020

Project team conducts biodiversity assessment in Molawin-Dampalit Sub-watershed, MMFR

Project team conducts biodiversity assessment in Way Betung Watershed, Indonesia

This article highlights the results of the study which assessed the ecological contributions of agroforestry landscapes in Molawin-Dampalit Sub-Watershed in the Philippines, and in Way Betung Watershed in Indonesia. Specifically, the assessment centered on the biodiversity assessment and carbon stock assessment of the different agroforestry systems in two watersheds, as well as the socioeconomic assessment of the upland farmers within the said landscapes. A total of 106 farmers in the Molawin-Dampalit Sub-Watershed and 261 farmers in Way Betung Watershed were interviewed, while about 27 and 14 agroforstry plots were considered for biodiversity and carbon stock assessment, respectively. Research results indicated that the total carbon found among the crop components was 52.32 MgC/ha in Molawin Dampalit siub-Watershed and 244.26 MgC/ha in Way Betung Watershed, which suggest a high carbon sequestration potential of woody perennials and understorey crops in an agroforestry system. The farmlots being cultivated by the smallholder farmers were found to contribute to biodiversity conservation have a moderate biodiversity index of 2.59 and 2.53, respectively. These findings suggest that agroforestry should always be an integral part of all initiatives toward ecological restoration with the smallholder farmers as potential partners.

The research provided empirical data and evidences about the ecological services of agroforestry, particularly its potentials in ensuring biodiversity and providing carbon stock, which are all important considerations in climate change mitigation and adaptation. This article/creative work will serve as a relevant reference of research and extension institutions in promoting agroforestry as the main production technology in upland farming communities.

Link to the article: http://journal.biotrop.org/index.php/biotropia/issue/archive
Impact factor: Not Applicable

Rhenish C. Simon1, Jenny Lou B. Sagisi1, Niña Angelica F. Zambale1 and Nathaniel P. Hermosa II1
1National Institute of Physics, College of Science (UP Diliman)

Is a Single Layer Graphene a Slab or a Perfect Sheet?,  Carbon, 157: 486-494, 2020

Cartooned drawing of a single layer graphene on top of an SiO2/Si substrate

The different crossing angle curves from three different models, M1 (solid), M2 (dotted), and M3 (dashed)

Graphene, despite being a monolayer crystal, exhibits desirable mechanical, electrical, thermal, and optical properties for electronic and photonic applications. The construction of graphene-based materials is also being ventured nowadays for its potential in bio-related and medical applications.

Currently, there are three different models for graphene which are, the slab model (a thin film with finite thickness), conducting perfect sheet (graphene is infinitesimally thin), and a polarizable-conducting perfect sheet (graphene is infinitesimally thin and polarizable). The model that is best suited for a single layer graphene is a slab of finite thickness. We identified this by measuring the reflectivity of a graphene on an SiO2 /Si system using the 633 nm, 612 nm, 604 nm, 594 nm and 543 nm wavelengths. In this paper, we define a parameter called the crossing angle of the degree of polarization (intersection to the incident angle axis) which discriminates the three models better compared to the pseudo-Brewster angle and reflectivity magnitude. The experimental values of the crossing angles were determined at different wavelengths available to us and we have compared them with the predictions of the three models. The slab model, which assumes the graphene to be a film of finite thickness and with a complex refractive index, gives the nearest predictions for the crossing angle positions. The implications of a single graphene having a finite thickness must be considered in calculations for photonic applications.

In our paper, we have identified that among the three models for graphene the most suitable model is to treat graphene as a slab of finite thickness. Our results suggest that the graphitic refractive index is enough to describe the optical properties of graphene. This means that the refractive index of graphite is independent of thickness which holds from bulk down to a monolayer. This finite thickness and refractive index of graphene must be considered in calculations for photonic applications.

Link to the article: https://www.sciencedirect.com/science/article/pii/S0008622319310590
Impact factor: (2018/2019) 7.466

Dave Eldon B. Olano1, Lilibeth A. Salvador-Reyes1, Marco Nemesio E. Montaño1 and Rhodora V. Azanza1
1Marine Science Institute, College of Science (UP Diliman)

Sorption of Paralytic Shellfish Toxins (PSTs) in Algal Polysaccharide Gels,  Algal Research, 45: 101655, 2020

Fig. 1. Time-course monitoring of STX reduction using algal polysaccharide gels at (A) 25°C and (B) 37°C. Data presented as mean ± SD, n=3.

Fig. 3. Pseudo-first-order kinetic modeling of A. STX and B. neo-STX on algal polysaccharide gels at 25°C and 37°C. Data presented as mean log (qe-qt) from triplicate runs.

Seaweed or algal extracts namely 1) Semi Refined Carrageenan (SRC), 2) Refined Carrageenan (RC) and 3) alginates and 4) agar, were used in laboratory experiments and chemistry modeling to learn about their capabilities to possibly absorb Paralytic Shellfish Toxins (PSTs). These toxins are produced by microalgae like Pyrodinium species and Gynodinium species that often grow in high density in many coastal areas in the country and other tropical countries and can cause Paralytic Shellfish Poisoning (PSP).

The experiment have shown that the PSTs i.e. Saxitoxin (STx) and Neo-Saxitoxins (Neo-STx) are absorbed differentially by the abovementioned seaweed polysaccharides and sorption was affected by temperature, contact time and their surface chemistry. For the first time these mechanisms/chemistry models have been elucidated in this paper.

This original and pioneering work has shown the science and potential for technology development and innovation on the use of seaweed or algal extracts in relation to the current problems and needs in toxic algal bloom events which negatively impact public health and coastal economy/fisheries.

Link to the article: https://www.sciencedirect.com/science/article/pii/S2211926419302735
Impact factor: (2018/2019) 3.723

Patrick R. Pata1 and Aletta T. Yñiguez1
1Marine Science Institute, College of Science (UP Diliman)

Larval Connectivity Patterns of the North Indo-West Pacific Coral Reefs, PLOS ONE, 14(7), https://doi.org/10.1371/journal.pone.0219913, 2019

This study explored how coral reefs in the North Indo-West Pacific are connected to each other using a computer model that tracks the larvae (early stage) of a coral, sea urchin and reef fish as they go with the flow of ocean currents before settling onto a reef (or not surviving) when their time in this stage is up. We explored if the different organism types, the season (amihan or habagat), and year affected the pattern of connection. What we found was that although these can change the patterns somewhat, the connections were all quite similar across the factors and can be explained more by where the reefs are geographically located.

Reef critters like corals, sea urchins and fishes can be transported a thousand kilometers from where they were born while in their larvae (baby) phase, but most end up settling in reefs a few hundred kilometers nearby. The pattern of these connections between coral reefs in the North Indo-West Pacific is highly influenced by how the reefs are arranged, and they can be grouped into reef clusters that are most similar in connections. This connectivity information is important for managing marine resources and conservation planning

Link to the article: https://doi.org/10.1371/journal.pone.0219913
Impact factor: (2018/2019) 2.776

Hidelisa D. de Chavez1 , Efren B. Villavicencio2, Virgilio T. Villancio2, Jose Nestor M. Garcia2, Mary Jean G. Bulatao2 and Maria Lea H. Villavicencio1
1National Plant Genetic Resources Laboratory, College of Agriculture and Food Science (UP Los Baños)
2Agricultural Systems Institute, College of Agriculture and Food Science (UP Los Baños)

Propagation Techniques for Rapid Establishment and Production of Cocoyam (Xanthosoma sagittifolium (L.) Schott),  Journal of International Society for Southeast Asian Agricultural Sciences, 25 (2): 83-94, 2019

Cocoyam (Xanthosoma sagittifolium) plant showing the whole plant and the different parts used as planting materials, (a) whole plant, (b) whole corm, (c) cormels, (d) bottom half corm, (e) top half corm and (f) setts.

Cocoyam or Gabing San Fernando (GSF) is an important crop both for food (like sinigang) and feed (particularly swine) due to its superiority in terms of energy, protein and mineral elements compared to other rootcrops like cassava. Despite its growing importance, its large scale production is limited by the production of planting material. Headsett (consist of cut corm with attached cut petiole) is the planting material used widely in the Philippines. But a GSF plant will only produce one headsett for a period of 7 to 8 months. This research was undertaken to find out how to produce more planting materials that will give better yield and determine the optimum size of headsett as planting material.

Using whole corm or top half of corm produce higher corm yield than using the bottom half of corm or whole cormel. Alternatively, using small headsetts with 15 and 30 cm petiole and big headsett with 30 cm petioles produce higher corm yield, longer corm and bigger petioles. Using small headsetts with 15 cm petiole and big headsett with 30 cm petiole produce higher cormel yield. The petiole should always be cut to produce longer and more number of cormels.

Cocoyam (Xanthosoma sagittifolium) (L.) Schott locally known in the Philippines as Gabing San Fernando, Galiang, Takudo, and Butig is a staple crop in parts of Ghana, Nigeria, Japan, and Hawaii. In the Philippines, they are widely grown in dry and marginal environments for their corms, cormels and young leaves for household food and feeds for pigs. Cocoyam is now gaining more importance due to the superiority of their corms and cormels in terms of energy, proteins and mineral elements.

In spite of its growing importance, the production of cocoyam has been stagnant for many years due to limited availability of traditional planting material (corm cuttings. Planting material acquisition is a big challenge especially for commercial or large scale production due to the inherent low multiplication ratio of the corms. The production technologies for cocoyam for large scale production are not yet well established in the Philippines and are greatly based on small-scale production. Thus, there is a need to develop the component technologies for large scale planting to get the potential benefits from this crop. Thus, this study was conducted to determine the most practical and effective propagation technique using different plant parts of cocoyam as planting materials that will give early establishment and higher yield.

Link to the article: http://issaasphil.org/wp-content/uploads/2019/11/8.-De-Chavez-et-al.-2019-Cocoyam-production-FINAL.pdf
Impact factor: Not Applicable

May Anne E. Mata1 , Cleto L. Nanola Jr.2 and Merlene E. Elumba2
1Department of Mathematics, Physics, and Computer Sciences, College of Science and Mathematics (UP Mindanao)
2Department of Biological Sciences and Environmental Studies, College of Science and Mathematics (UP Mindanao)

Age-based Growth Variation of Green-Blotched Parrotfish Scarus quoyi in Southern Philippine Sea,  Philippine Journal of Science, 148(2): 411-417, 2019

Comparison of von Bertalanffy growth curves for three populations of Scarus quoyi showing 95% confidence regions around least squares estimate of K and L∞, following Kimura (1980).

There has been a growing interest in studying the characteristics of the green-blotched parrotfish (Scarus quoyi) as these provide information on coral reefs biota and diversity. Examples of these characteristics, of which the study is focused on, are the age and size. In our research, we ask the question: “Are their differences among the age-based growth of parrotfish populations in three different areas of the Southern Philippines, namely, the Davao Gulf, Pujada Bay, and Sarangani Bay, given the proximity of the areas and the common current influencing the regions?” To answer this question, we collected fish individuals from different local markets in the three sampling sites between April 2013 and May 2016. Sagittal otoliths of the fish were extracted and examined to determine its age. The size (length) of each fish was also measured. The data were used to fit a von Bertalanffy model for age-based growth to estimate the limiting length and the limiting growth rate of the fish in each region (see photo 1). Our findings reveal that the parrotfish populations in three locations vary significantly in terms of their growths. It is recommended that differences in habitat structure, fishing pressure, fish density, and food availability should be examined further as they can potentially influence the growth patterns of Scarus quoyi in the Southern Philippine seas.

Scarus quoyi or locally known as “molmol” is a commercially important reef fish. Understanding the growth of this organism in various bays and gulf in southern Mindanao can promote or enhance its fishery management. In this study, it was found that the bays/gulf examined has different growth rates. This may mean that fish populations are different. One is almost independent to another. In terms of management, all three populations must be managed/conserved well for this species to survive/flourish in each bay/gulf. The unregulated continuous harvesting of this species in an area may result to localize extinction or extirpation of the said species.

Link to the article: http://philjournalsci.dost.gov.ph/images/pdf/pjs_pdf/vol148no2/aged_based_growth_variation_.pdf
Impact factor: Not Applicable

Marish S. Madlangbayan1 and Marloe B. Sundo1
1Department of Civil Engineering, College of Engineering and Agro-Industrial Technology (UP Los Baños)

Pedestrian Simulation of Metro Rail Transit (MRT) Line 7 Station 1-North Avenue Station, Quezon City, Philippines , International Journal of Geomate, 18(66): 156-162, 2020

Simulation of pedestrian flow represents an advanced approach in modeling and evaluating train stations. In this study, the pedestrian simulation was done using the simulation software Simio to assess the passenger capacity of MRT 7 Station 1-North Avenue Station through level of service (LOS), queuing system, and train facility utilization. This paper presents the actual situation inside the train station while predicting the behavior of queuing pedestrians and provides an accurate estimate of the volume-to-capacity ratio of passengers entering the station. The study’s approach debugged the conventional assignments of pedestrians currently used in the field. The constructed three-dimensional building of the North Avenue Station served as framework for the simulation. Sources, sinks, servers, and paths of the software were the main elements of the simulation. Each library was defined by their time usage based on data gathered. Time usages of 1.21 sec. and 240 sec. for sources and sinks, respectively, were used in the simulation. Servers were defined by the train facilities utilized in the simulation, namely, automatic ticketing machines with time usage of 43 seconds, ticketing toll gates with 1.4 seconds, and manual ticketing windows with 20 seconds. In addition to the libraries, paths that provided the flow, direction, and distribution of pedestrians were calibrated. Simulation results showed that the new proposed plan has a higher passenger capacity than the original plan.

The railway system is one of the easiest and most convenient ways of traveling from one place to another. However, rail transport causes heavy pedestrian traffic and severe congestion in train stations, which has become an object of growing public concern. Since the increasing number of commuters is unavoidable, the only solution is to improve train station infrastructures and facilities. An approach is to adopt a pedestrian simulation technique in order to systematically assess and estimate the actual movements and activities of commuters inside train stations. In this study, pedestrian simulation will be conducted as part of the preliminary study for the design and construction of Metro Rail Transit (MRT) Station. The study will be essential in debugging the conventional subjective assignments of pedestrians over train stations with more sophisticated planned paths.

Link to the article: https://doi.org/10.21660/2020.96320
Impact factor: Not Applicable

Gladys Maria V. Pangga1 and Theresa Marie A. Collantes1
1Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine (UP Los Baños)

Morphological and Growth Characteristics of Primary Cell Cultures Derived from Philippine Native Banaba and Rhode Island Red Chicken (Gallus gallus domesticus L.), Philippine Journal of Veterinary Medicine, 56(1): 47-56, 2019

Morphology of Philippine Native Banaba chicken fibroblasts

Mature Philippine Native Banaba Chicken.

The Philippine native Banaba chicken, an indigenous breed from the Quezon province known for its good resistance against respiratory diseases, was successfully preserved at a cellular level. This was established by conducting primary cell culture establishment and subsequent cryogenic technology.

Initially, 11-day old chicken embryos were subjected to chemical disintegration to isolate fibroblast cells and consequently grown in cell culture plates and flasks with artificial media. The properties of the cells were monitored for 6 days and were determined to be comparable with the standard cells derived from Rhode Island Red, which is a common commercial breed used for laying purposes. This mainly includes the typical fibroblastic appearance of the cells and steady sigmoid growth rates, both indicating good health of the preserved cells and the success of the experimentation.

Overall, the study has preserved genetic resources of Banaba chicken in which both applied methodology and image results can be used in future molecular research studies to further explore the special characteristics of this breed.

This research studied the feasibility of in vitro preservation of the Philippine Native Banaba chicken, which was considered as an endangered indigenous type of chicken in the country. This is relevant as anecdotal evidence shows that this breed is inherently resistant and/or less susceptible to economically important infectious diseases in poultry. Thus, the main objective of study was to characterize and preserve the genetic resources of the chicken at a cellular level, which was achieved through the establishment of primary cell culture fibroblasts; and in the future, may be used for further applied molecular research.

The study also explored its comparability with a commonly used commercial breed Rhode Island Red chicken as a cell culture substrate. In doing so, we have determined that there were no significant differences in terms of morphology and growth rate. This result may then indirectly indicate that virology testing using this cell culture may be similar to virology testing of standard breeds such as Rhode Island Red. The shown images and the adapted methodology followed may also be used for future studies and of molecular biology courses as reference images of healthy chicken cell fibroblasts and for independent cell culture researches.

Link to the article: https://www.researchgate.net/profile/Gladys_Maria_Pangga/publication/338421963_Morphological_and_growth_characteristics_of_primary_cell_cultures_derived_from_Philippine_native_Banaba_and_Rhode_Island_Red_Chicken_Gallus_gallus_domesticus_L/links/5e4125bd299bf1cdb91c381f/Morphological-and-growth-characteristics-of-primary-cell-cultures-derived-from-Philippine-native-Banaba-and-Rhode-Island-Red-Chicken-Gallus-gallus-domesticus-L.pdf
Impact factor: Not Applicable

Andrew D. Montecillo1, Nacita B. Lantican1and Asuncion K. Raymundo1
1Institute of Biological Sciences, College of Arts and Sciences (UP Los Baños)

Archaeal Community Profiling of a Mixed Culture from Mud and Water Slurry from Solfataric Mudspring as Revealed by a Community Proteome Approach, Philippine Science Letters, 12(SI): 001-010, 2019

In this paper, we describe the use of community proteome approach to study the Archaeal community in cellulose-enriched mud and water slurry from a double-extreme environment of Mt. Makiling Mudspring. Total proteins were extracted from the set-up and the resulting peptides were analyzed by a very-sensitive set-up called liquid chromatography-electrospray ionization coupled with tandem mass spectrometry. Majority of the proteins sampled and identified appear to be largely from extremophilic Sulfolobus, several which are known to be able to utilize highly recalcitrant cellulosic substrates. Proteins with high similarity to those from other extremophilic Archaea such as Caldivirga maquilingensis, Acidianus, Metallosphaera sedula, Desulforococcus, Pyrococcus furiosus, and Pyrodictium occultum were identified, suggesting their presence in the sample. Many of these Archaea were not detected in earlier reports of DNA-based Mudspring microbial community analysis. Using multi-faceted approach in the study of Mudspring microbial community will foster an understanding of the microbial diversity in such ecological niches and may enable isolation of thermally stable proteins of commercial value in the future. Our approach allowed functional and taxonomic survey of the Mudspring microbial community structure.

The application of metaproteomics to more complex microbial communities such as those in Mt. Makiling Mudspring still presents a considerable challenge. For complex environments (e.g., seawater, soil, and other water environments) that are of great interest to microbial ecologists, one can expect to resolve only a minute fraction (less than 1%) of the metaproteome with the methods that are currently available. These limitations necessitate improvements in the protein extraction, separation, and identification technologies. Via database analysis using the level of homology to other species, the proteomics method has the potential to reveal the identity of the active microorganisms in an environment. It can also be used as a decision tool in prioritizing the investigation of elusive functional genes from large metagenomic datasets.

Link to the article: http://dx.doi.org/10.5958/0974-0112.2019.00061.6
Impact factor: Not Applicable

Emmanuel Bonifacio S. Timog1, Renerio P. Gentallan Jr.1, Nestor C. Altoveros1, Teresita H. Borromeo1, Leah E. Endonela1 and Antonio G. Lalusin1
1Institute of Crop Science, College of Agriculture and Food Science (UP Los Baños)

Cross-species Amplification of Selected SSR Markers to Jackfruit and its Related Species , Indian Journal of Horticulture, 76(3): 377-381, 2019

Fig. 2. UPGMA dendrogram of Artocarpus accessions based on Dice’s similarity coefficient using 7 cross-amplified SSR markers.

In the Philippines, jackfruit (Artocarpus heterophyllus) is considered as a high value crop regarded for its great economic potential and an important component of subsistence farming systems. The study aimed to increase the number of microsatellite markers in jackfruit, noting the importance of microsatellites or simple sequence repeats (SSRs) markers high potential for genetic mapping, marker-assisted selection and genotyping; particularly for species with limited to no SSR markers. The study tested cross-species amplification of twenty-eight (28) SSR primers from sweet potato (Ipomoea), cassava (Manihot) and sugarcane (Saccharum). Seven (25%) markers were found to be stable, reproducible and highly polymorphic amplifications in 16 Artocarpus heterophyllus accessions and 5 related species. The number of alleles per marker ranged from 6 to 17 with a PIC per marker ranging from 0.73 to 0.89. The haplotype also showed unique banding patterns in the 21 accessions of Artocarpus across the seven primers with 67% similarity. This denotes a potentially successful interfamilial amplification and transferability of the selected SSR markers to jackfruit.

The study tested cross-species amplification of twenty-eight (28) SSR primers from sweet potato (Ipomoea), cassava (Manihot) and sugarcane (Saccharum) to increase the number of microsatellite markers in jackfruit (Artocarpus heterophyllus). This will facilitate further genetic studies of Artocarpus species.

Link to the article: http://dx.doi.org/10.5958/0974-0112.2019.00061.6
Impact factor: (2018/2019) 0.108

Vachel Gay V. Paller
Institute of Biological Sciences
College of Arts and Sciences
UP Los Baños

Soil-transmitted Helminth (STH) Eggs Contaminating Soils in Selected Organic and Conventional Farms in the Philippines, Parasite Epidemiology and Control, https://doi.org/10.1016/j.parepi.2019.e00119, 2019

Fig. 1 STH eggs found in soil farms from Northern and Southern Luzon Provinces: A) Ascaris sp.; B) Hookworm; C) Trichuris sp.; D) Toxocara sp. (Scale bar: 10 μm)

Fig. 2 Map showing the collection sites in Northern and Southern Luzon Provinces, Philippines

Soils from selected organic and conventional farms in the Philippines were examined for parasite contamination. A total of 600 soil samples from twenty organic and conventional farms were collected and processed for the presence of parasites. Results revealed that 41% of soil samples were contaminated with parasite eggs. Parasites recovered were Ascaris, whipworms, hookworm/strongylid, Toxocara, tapeworms which could be coming from animals or human excreta. Both organic and conventional farms were found to be contaminated with parasites. Some farming practices were documents through surveys and results revealed that the use of manure as fertilizer in farms and wash water used contribute significantly to parasite contamination in soils. These findings have implications on food safety and could be used to help the agriculture sector and other stakeholders in their efforts to improve food safety policies.

In the Philippines, some studies reported the contamination of parasites in soils from selected urban and rural areas in Southern Luzon (Paller and de Chavez, 2014; Horiuchi et al., 2013). However, there are still no reports regarding parasite contamination in soils from agricultural farms and the comparison of parasite contamination between organic and conventional farms. There are also no reports about the association of farming practices with the extent of parasite soil contamination in agricultural lands. Thus, this study generally aimed to determine the extent of contamination of soil with STH eggs and determine the association between some farming practices and contamination rate in soils from selected organic and conventional farms in the Philippines.

Agriculture is one of the major sources of livelihood in the Philippines. However, the findings of the present study revealing the occurrence of STH in soil farms pose a threat to public health. In fact, this study reinforced the recent findings of Ordoñez et al. (2018) regarding the parasite contamination of vegetables collected from the same sites. Most of the helminths found in this study were zoonotic parasites that are potentially capable of infecting humans. Some of the current farm practices by both conventional and organic farms, such as the use of untreated manure and contaminated wash water, greatly pose threats for further parasite transmission to humans, animals and the environment. Consumers of farm produce may also be at risk of infection.

Agricultural systems, both conventional and organic farming, embrace the idea of a sustainable approach for agricultural production. It aims to maintain and increase the soil fertility to ensure a healthy environment. However, based on the findings of the current study, there is a need to review some of the guidelines on farming systems to ensure that not only the integrity of the environment but also the health of the farmers and consumers are being addressed.

Link to the article: https://www.sciencedirect.com/science/article/pii/S2405673119300820?via%3Dihub
Impact factor: Not Applicable

Vachel Gay V. Paller
Institute of Biological Sciences
College of Arts and Sciences
UP Los Baños

Histopathological Features and Prevalence of Capillaria hepatica Infection in Rattus spp. in Philippine Mount Makiling Forest Reserve and its Adjacent Areas, Journal of Parasitic Diseases, https://doi.org/10.1007/s12639-019-01189-1, 2020

Rats are recognized as reservoir hosts of several pathogens that pose a threat to human health. Although rats are reported to be hosts of a large number of pathogens, a survey of Capillaria hepatica carried by rats in the Philippines has not been fully understood. A total of 90 rats from three different species were collected through trapping in selected residential, agroforestry, and agricultural areas in Los Banos Laguna, Philippines. The overall infection rate of C. hepatica among rats was 21.11%. Rats from residential areas showed the highest prevalence of C. hepatica infection (50%) while agroforestry and agricultural areas at 6.7% each. Most of the infected rats were moderately infected and few were lightly and severely infected. Lastly, the presence of C. hepatica in liver is suggestive of presence of lymphocytes, amyloid, granuloma, and the occurrence of necrosis, hypertrophy, fibrosis, and cholestasis in the liver of the host. Capillariasis could be occurring in Philippine human populations, hence there is need for screening the population with appropriate means and to create awareness of this emerging zoonotic disease.

Rats play an important ecological role in terrestrial ecosystems. However, due to anthropogenic impacts such as land use, habitat and biodiversity loss, these animals tend to move to human habitations. Rattus spp. are known as agricultural pests which feed on crops and damage properties. They are also known as vectors of many pathogenic bacteria and serve as carriers of ectoparasites, and reservoir hosts of zoonotic parasites. The commonly widespread rats and continuously growing in number in the Philippines are Brown rats (Rattus norvegicus), Pacific rats (Rattus exulans), and Asian house rats (Rattus tanezumi). These rats are categorized as least concern in International Union for Conservation of Nature (IUCN) (Salibay and Luyon 2008). Rats are capable of transmitting Capillaria hepatica which causes hepatic capillariasis with no specific signs or symptoms in the host, but can manifest as acute or subacute hepatitis, hypereosinophilia, anemia, chronic fever which can even become fatal without proper treatment (Aghdam et al. 2015).

Capillaria hepatica is a parasitic nematode known to have a complex life cycle since eggs are known to be liberated and infective via the decay of an infected host (natural death) or through digestion of the liver of an infected host either by another organism or the same species (cannibalism) (Farhang-Azad 1977). Since C. hepatica symptoms are commonly misdiagnosed, it is important to evaluate its epidemiology, particularly its prevalence in rat hosts that now co-inhabit with humans. Although C. hepatica infection is reported to be common among rats, C. hepatica infection among Rattus spp. found in the Philippines has not been fully understood. Furthermore, there were no reported cases of C. hepatica infections in humans in the country although this absence could either be a result of underreporting or misdiagnosis. Horiuchi et al. (2013), however, reported the presence of Capillaria sp. eggs in soil from the Philippines. Hence, the present study was conducted to contribute as baseline information on C. hepatica infection and its histopathological features in Rattus spp. collected in the Philippines.

Link to the article: https://link.springer.com/article/10.1007%2Fs12639-019-01189-1#citeas
Impact factor: Not Applicable

Mark Angelo O. Balendres
Institute of Plant Breeding
College of Agriculture and Food Science
UP Los Baños

Confirmed Record of Spongospora subterranea subsp. subterranea in Potato cv. Igorota in Northern Philippines and the Susceptibility of Tomato cv. Yellow Plum to Spongospora Root Infection, Archives of Phytopathology and Plant Protection, https://doi.org/10.1080/03235408.2020.1717252, 2020

Potato is an important staple crop in the Philippines, more popular in the highlands of Benguet and Bukidnon. Potato production has been hampered by problems that include the occurrence of soil-borne plant diseases. Powdery scab and common scab are two tuber diseases that affect the marketability of potato tubers. Although they are caused by two different pathogens of varying biology, the symptoms in potato tubers are sometimes indistinguishable. This research identified powdery scab from different samples of potato showing scab-like diseases. This is the first time that the 1990’s report was validated. It was noteworthy, however, that most of the samples are common scab, which indicates that powdery scab is not common in the field. Nevertheless, the photomicrographs provided a more detailed characteristic of the Philippine collection of Spongospora subterranea subsp. subterranea, the powdery scab pathogen. Powdery scab is quite relatively a neglected disease in the country with little to know studies of its causal agent. Test on tomato indicates that the pathogen can also cause root infection. This indicates that the pathogen can also become an important problem of tomato.

The findings from this study will help establish the relative importance of powdery scab and Spongospora root infection in potato and tomato production, respectively, in the country. The information presented here could also improve research on Spongospora disease monitoring and management in the country.

Link to the article: https://www.tandfonline.com/doi/full/10.1080/03235408.2020.1717252
Impact factor: Not Applicable

Renerio P. Gentallan Jr.1, Nestor C. Altoveros1, Teresita H. Borromeo1 and Cherray Gabrielle A. Macabecha1
1Institute of Crop Science, College of Agriculture and Food Science (UP Los Baños)

Antimicrobial and Phytochemical Properties of Atuna racemosa Raf. Kernel Extract, Indian Journal of Agricultural Research, 53: 733-736, 2019

Atuna racemosa Raf., commonly known as tabon-tabon is a forest tree species used to season raw fish (kinilaw) dish in the Philippines, is proven to have antibacterial properties. The study aimed to help explain the significance of using its kernel as a condiment and consequently, increase its value by assessing its antimicrobial and phytochemical properties. The antimicrobial activity of its ethanolic extracts were screened against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Salmonella enterica ser. Typhimurium, Aspergillus niger, Saccharomyces cerevisiae and Candida albicans using agar disc diffusion technique. Qualitative phytochemical screening was done, and total phenolic content was determined at a concentration of 100 mg dry sample per 1 mL solvent. The extract showed bacterial growth inhibition in Staphylococcus aureus, Pseudomonas aeruginosa and Bacillus cereus while a mild antifungal activity against Aspergillus niger was observed. Phytochemical analysis detected the presence of cardiac glycosides, tannins, phenolic compounds and saponins in the extract. It yielded a total phenolic content of 42.7 mg GAE/100 g. This denotes that the kernel of A. racemosa has the potential to be classified as a natural food preservative and functional food.

Aside from the toxicity studies conducted, no reports on the total phenolic content and antifungal properties of Atuna racemosa seed extracts were made. Furthermore, earlier studies did not use ethanol as an extracting solvent for phytochemical analysis and no broad-spectrum antibacterial screening was conducted. Hence, the study screened the antimicrobial and phytochemical properties of A. racemosa kernel ethanolic extracts to help elucidate the significance of using kernel as a condiment and, consequently, increase its value.

Link to the article: https://doi.org/10.18805/IJARe.A-415
Impact factor: Not Applicable

Alvin Karlo G. Tapia
Institute of Mathematical Sciences and Physics
College of Arts and Sciences
UP Los Baños

Investigation on Performance of Epoxy-coated Steels with Nano-SiO2 and Polyaniline Composite Using Complex Impedance Spectroscopy, International Journal of Geomate, 17(64): 49-54, 2019

Photos during the evaluation of the effects of Nanosilica-PANI composite coating

Coated Metal Specimens during Drying

In this study, the effects of the application of Nanosilica-Polyaniline nanocomposite epoxy coating on 3.5% NaCl induced corrosion of carbon steel. The epoxy coating was modified using a varying concentration of silica combinations. Briefly, coated steels were dipped in 3.5 wt% NaCl solution to induce corrosion after coating application. Impedances spectroscopy, an electrochemical technique, was utilized to evaluate the performance of applied coatings on the metal surface and its effects on the progress of corrosion on carbon steel samples.
The electrical characterization was related to the coating performance of epoxy coating with varying concentrations. The Nyquist and Bode plots were displayed and related to the graphs with the coating resistance and capacitance. Based on these plots, 40-60% combination of Nano-SiO2 and PANI has the largest semi-circle curve while on Bode plots, still, the 40-60% combination has the largest magnitude of impedance and phase angles. The equivalent circuit model was fitted to measure directly the coating resistance and coating capacitance of the coated steel. Based on the equivalent circuit model, the 40-60% of Nano-SiO2 to PANI combination had the highest coating resistance. Based on the results, all combinations showed increased anti-corrosion protection as compared to epoxy alone. This indicates that incorporation of nanosilica into PANI-epoxy network enhances its anti-corrosion performance.

Until today, corrosion is considered one of the major problems of several industries as well as in the household. Despite its poor resistance to corrosion, carbon steel or mild steel is commonly used as a construction material because of its abundance, easy availability, low cost, good formability, workability and remarkable strength. Corrosion inhibitors are substances that are added in small amounts to the metal to reduce and/or inhibit corrosion. Epoxy coatings represent the most important engineered polymer that piqued the interest of researchers due to its wide applications including protection of structural materials and anti-corrosion coatings. In recent years, introduction of additives into epoxy polymers has gained attention to enhance their properties as well as improve their mechanical strength. Several studies have shown that incorporation of these additives significantly modify and improved the characteristics of these epoxy coatings. In the advent of nanotechnology, various nanomaterials such as, TiO2, ZnO, ZrO2, CeO2, CaCO3, Fe2O3 and SiO2 nanoparticles have been incorporated as reinforcements in order to improve coatings’ performance as a barrier for corrosive environments. Nanosilica is a multipurpose nanoparticle utilized to produced multifunctional nanocomposite coatings. Previously conducted researches on nanosilica-reinforced epoxy coatings often rely on the use of tetraethoxyorthosilicate (TEOS) as general source of nanosilica particles. However, TEOS does not come cheap and various researchers have increased interest in finding alternative source of silicate materials. Rice hull ash (RHA) is a good source of silicates reportedly containing 90% silica, which makes it an economical silica source.

In this study, the nanosilica used was sourced-out from rice hull and combined with polyaniline (PANI) to create an anti-corrosive coating to prevent chloride ingress that can be applied to steel metals. Also, we investigate and characterized the effectiveness of the coating in steel using low impedance spectroscopy by determining the coating capacitance and coating resistance. Based on the results, incorporation of nanosilica into PANI polymer network showed better corrosion protection performance compared to that of pure epoxy coated steel.

Link to the article: https://www.geomatejournal.com/sites/default/files/articles/49-54-42047-Marish-Dec-2019-64g.pdf
Impact factor: Not Applicable

Mark Angelo O. Balendres1 and Christian Joseph R. Cumagun2
1Institute of Plant Breeding, College of Agriculture and Food Science (UP Los Baños)
2Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science (UP Los Baños)

Mycotoxigenic Fungi and Mycotoxins in Agricultural Crop Commodities in the Philippines: A Review, Foods, 8(7): 249, doi: 10.3390/foods8070249, 2019

Detection of mycotoxins in crops and in various regions in the country.

Mycotoxigenic fungi are pathogens of global importance. They damage the quality of agricultural crop commodities and impact negatively on food safety. In the Philippines, several Aspergillus, Fusarium, and Penicillium species have been detected in crop by-products and were found to contaminate major crop commodities (e.g. corn, peanut, rice, etc.). There are five mycotoxin groups (aflatoxin, fumonisin, ochratoxin, nivalenol, and zearalenone) that have been detected in both the raw form and the by-products of major crops grown in the country. Since the first scientific report of aflatoxin contamination in the Philippines in 1972, new information has been generated on mycotoxins and mycotoxigenic fungi, but little has been known of other mycotoxins until the last two decades. Nevertheless, the increase of scholarly output indicates a growing interest by researchers on these fungi. In the last decade, there have been additional studies on Fusarium species and fumonisins. Research outputs in the future could assist policy-makers in developing or improving standards and policies.

This paper reviews the existing knowledge of mycotoxigenic fungi in the Philippines and the mycotoxin contamination in major agricultural crop commodities and their by-products. The information presented updates our understanding of the impact of these fungi and mycotoxins to food security and food safety. The paper also highlights the lack of effective control measures and the need for further studies in the plant-mycotoxin pathosystem to develop effective, sustainable, and environment-friendly control against mycotoxigenic fungi and mycotoxins.

In our research, we were able to determine the individual’s susceptibility to asthma via utilizing the genomic profile, i.e. single nucleotide polymorphism (SNP). This research demonstrated the capability of machine learning algorithms in the field of personal medicine. The translation of the research work into actual solution would empower early diagnosis, risk assessments, and personalized treatments. Ultimately, it paves the way to the advancement of research in understanding the biological nature of complex diseases.

Link to the article: https://doi.org/10.3390/foods8070249
Impact factor: (2018/2019) 3.011

Maria Ellenita G. De Castro
Department of Forest Biological Sciences
College of Forestry and Natural Resources
UP Los Baños

Phytoremediation Potential and Copper Uptake Kinetics of Philippine Bamboo Species in Copper Contaminated Substrate, Heliyon, 5: e02440, 2019

Figure 1. Layout of the experiment showing the randomized distribution of the 3 bamboo species used in the study (Photo by ME De Castro).

Figure 2. Propagule of two-week old Dendrocalamus asper utilized in the study (Photo by ME De Castro).

Phytoremediation is an emerging field of study that focuses on the ability of some plant species to absorb and hyperaccumulate heavy metals above the threshold level. This unique potential to absorb metals is species-dependent, which means certain plant species are more adaptive to absorb specific heavy metals like nickel, copper, iron, and manganese. Copper is an important engineering element but considered as a potentially toxic since its non-biodegradable and can persist in the environment for a long period of time. The present work is a preliminary attempt to determine the potential of the tallest grass in the world for copper phytoremediation using hydroponic culture. Bambusa merilliana, Bambusa blumeana and Dendrocalamaus asper are the three locally-available bamboo species tested in the study and were exposed to varying concentrations of copper (40, 80 and 120 µM) to determine their uptake mechanism. D. asper proved to be the most efficient in terms of Cu phytoremediating potential with a constant positive uptake of 80µM concentrated in its massive root system. Such result suggests the potential of D. asper for two types of phytoremediation strategies—rhizofiltration and phytostabilization. And because of their large root biomass, D. asper can be recommended as erosion control agent near contaminated bodies of water or soils. The kinetics of copper uptake in the plant tissues was also determined to be at it optimum level at Day 7 suggesting that if it will be used in the clean-up of contaminated substrate, D. asper must not be harvested beyond this period.

Preliminary evidences on the Copper phytoremediation potential of 3 locally available bamboo species, namely Bambusa merillana, Bambusa blumeana and Dendrocalamus asper using hydroponic culture was highlighted in the study. Among the three promising bamboo species however, D. asper proved to be the most efficient in terms of copper phytoremediation potential with a consistent uptake of 80µM and bioconcentration factor of 50.57. This result only reveals that D. asper can tolerate high Cu concentrations, which bodes well for its potential utilization in phytoremediation strategies. Furthermore, the present work also found out that copper were highly retained in the root system of the tested bamboo species indicating its importance as phytostabilization and rhizofiltration capacity. With regards to the kinetics of contaminant removal within the plant tissue, the current work proved that the Cu concentration decreased with time though the best fit was obtained at day 7.

Link to the article: https://doi.org/10.1016/j.heliyon.2019.e02440
Impact factor: Not Applicable

Jason R. Albia1, Allen L. Nazareno1, Joverlyn D. Gaudillo1, Lei Rigi P. Baltazar1, Jae Joseph Russell B. Rodriguez2 and Julianne A. Vilela3
1Institute of Mathematics and Physical Sciences, College of Arts and Sciences (UP Los Baños)
2Institute of Biological Sciences, College of Arts and Sciences (UP Los Baños)

3Philippine Genome Center Program for Agriculture, Office of the Vice Chancellor for Research and Extension (UP Los Baños)

Machine Learning Approach to Single Nucleotide Polymorphism-based Asthma Prediction, PLOS ONE, 14(12): e0225574, doi: 10.1371/journal.pone.0225574, 2019

Complex diseases, e.g. asthma, diabetes, and hypertension, are influenced by a combination of genetic and environmental factors. At the genomic level, mutations occur that change the biological composition of an individual leading to the development of diseases. In our study, we utilized single nucleotide polymorphisms (SNPs), a single change or variation in the genomic sequence, to ascertain the possible occurrence of a disease or phenotype. Understanding the nature of the complex disease at the genomic level allowed us to discover its primitive cause before its physical manifestation, thus granting us the capability to determine an individual’s susceptibility to a disease.

SNPs occur throughout the genome; few are considered biomarkers that are highly associated to a disease. The high dimensionality of the data proves to be a challenge; hence, machine learning algorithms were used in our study to analyze SNP data. Machine
Learning provides computers with the ability to learn without being explicitly programmed. In our case, we programmed a machine learning model to learn from SNP data in order to identify biomarkers that are highly associated to asthma. This model can now be used to ingest an individual’s SNP profile and provide a likelihood of asthma susceptibility.

With the feats of technology, high-throughput sequencing platforms are rapidly advancing with its cost lowering, leading to personal genome sequencing. In consequence, volume of genomic data is exponentially generated along with hidden patterns and unknown associations. In order to take advantage of the growing data, big data analytics is utilized to study complex and high-dimensional data.

In our research, we were able to determine the individual’s susceptibility to asthma via utilizing the genomic profile, i.e. single nucleotide polymorphism (SNP). This research demonstrated the capability of machine learning algorithms in the field of personal medicine. The translation of the research work into actual solution would empower early diagnosis, risk assessments, and personalized treatments. Ultimately, it paves the way to the advancement of research in understanding the biological nature of complex diseases.

Link to the article: https://doi.org/10.1371/journal.pone.0225574
Impact factor: (2018/2019) 2.776

Renerio P. Gentallan Jr.1, Nestor C. Altoveros1, Teresita H. Borromeo1, Leah E. Endonela2, Antonio G. Lalusin1 and Consorcia E. Reaño1
1Institute of Crop Science,College of Agriculture and Food Science (UP Los Baños)
2Institute of Plant Breeding, College of Agriculture and Food Science (UP Los Baños)

An Objective Method of Shape Descriptor State Establishment Using Elliptic Fourier Analysis (EFA), Plant Genetic Resources: Characterization and Utilization, 17(6): 480-487, 2019

Elliptic Fourier Analysis (EFA) analyses closed contours immaterial of the size and configuration and describes mathematically the overall shape of an object by transforming outline information into Fourier coefficients. The study systematically established shape descriptor states EFA using pili (Canarium ovatum Engl.) kernel as a model. Kernel images of 53 pili accessions from the National Plant Genetic Resources Laboratory (NPGRL), University of the Philippines Los Baños were acquired using VideometerLab 3. Shape features, such as roundness, compactness and elongation, were extracted from the images. Shapes outlines were characterized using elliptic Fourier coefficients calculated from SHAPE version 1.3 software. Principal component analysis and cluster analysis were used to explain clusters representing the shape descriptor states. The Fourier coefficients were also able to represent the variation observed from the physical properties of shape. The method may be used in establishing shape descriptors of all plant parts of all crop species.

Oftentimes, the formal characterization of plant genetic resources is limited due to subjective assessment using formulated descriptor lists. Particularly for traits with irregular shapes, there is difficulty in accurately identifying clear and definable states due to ambiguity in the process of representation. The method described by the authors will facilitate the systematic establishment of a descriptor list and the subsequent objective delineation of the shape descriptor states by elliptic Fourier analysis. The study uses Canarium ovatum as a model plant but the protocol established may be used in any plant part of all plant species.

Link to the article: https://doi.org/10.1017/S1479262119000285
Impact factor: (2018/2019) 0.717

Percival P. Sangel
Institute of Animal Science
College of Agriculture and Food Science
UP Los Baños

Importin-β Proteins Expression Modulation in Embryonic Stem Cells and Embryonic Fibroblasts of Mouse, Philippine Journal of Science, 149(1): 21-26, 2020

Figure 1. Phase contrast images of siRNA treated mouse embryonic stem cells (EB3) after 96 h incubation.

Figure 2. Reprogramming efficiency of MEFs 14 days post infection. Representative images of plates after alkaline phosphatase staining.

Importin-β proteins are transport proteins important in the shuttling of cargo proteins by binding to either nuclear localization signal (NLS) or nuclear export signal (NES). This study investigated the in vitro expression modulation of selected Importin-βs. Specifically, this study characterized the culture behavior of mouse embryonic stem cells after knockdown (suppression of synthesis) of selected Importin- β proteins like Cse1L, IPO7, KPNB1, RanBP16, RanBP17 or XPO4. Also, this study assessed the effects of overexpressing (production of more than the normal levels in the cell) RanBP17 or IPO7 during cellular reprogramming of mouse embryonic fibroblasts. Results showed that Cse1L and KPNB1 are essential for the viability of mouse embryonic stem cells since knockdown of either one of these proteins resulted to death of mouse embryonic stem cells. Meanwhile, the growth characteristics of RanBP17, XPO4, IPO7 or RanBP16 knockdown mouse embryonic stem cells were comparable with the control. Aside from round colonies, the appearance of flat cells and spreading growth characteristics in some colonies were observed which indicated early signs of differentiation (development into a more definitive cell type). On the other hand, the number of colonies with overexpressed Oct4, Sox2, Klf4, cMYC (OSKM) + RanBP17 or OSKM+ IPO7 was comparable to OSKM+Flag or OSKM (controls). This suggests that RanBP17or IPO7 have limited application in the generation of induced pluripotent stem cells.

This work has contributed information to the further understanding of the role of some importin beta proteins in the nucleocytoplasmic transport system of mouse embryonic stem cells since there are limited reports available for these proteins. These proteins partake in the control and transport of protein cargoes in and out nucleus; hence, they are bilogically important. This research also investigated the potential use of some of these importin beta proteins in the generation of induced pluripotent stem cells (iPS cells) from mouse embryonic fibroblasts.

Link to the article: http://philjournalsci.dost.gov.ph/publication/regular-issues/next-issue/96-vol-149-no-1-march-2020/1151-importin-proteins-expression-modulation-in-embryonic-stem-cells-and-embryonic-fibroblasts-of-mouse
Impact factor: Not yet available

Rodolfo A. Aguirre Jr.
Department of Electrical Engineering
College of Engineering and Agro-Industrial Technology
UP Los Baños

Determination of Hosting Capacity of Solar and Wind Distributed Generation (DG) Using Stochastic Approach , TENCON IEEE Region 10 Conference Proceedings, 1960-1965, 2019

Nowadays, the rising global economic growth has influenced the energy sector to engage in distributed generation. It is a small-scale technology that produces electricity close to the end-users, thus eliminating the need for new transmission lines and additional power plants. However, integration of DGs can cause voltage fluctuations and damage to the system if not properly planned. Using probabilistic approach, this paper determines the maximum allowable penetration level of solar and wind DGs and its effects to power losses in the distribution network. The methodology involved optimal siting of DG using genetic algorithm, load flow analysis considering the varying nature of solar and wind, and simulations performed in IEEE-37 bus test system. Results showed that the hosting capacity of solar and wind DG are 142 units and 136 units, respectively. The smaller hosting capacity of wind DG may be attributed to the additional reactive support given by its installation. The effect of the penetration level of DG to the power loss in the system also exhibited an inverse linear relationship – as the penetration level increases, the power loss decreases. This is true for both solar and wind DGs. However, increasing the number of wind DG units after reaching its lowest point resulted to increased level of power loss.

The study of the hosting capacity will provide energy planners a different perspective about the increasing utilization of renewable energies nowadays. With the technical challenges incorporated by the integration of solar and wind generators, this study will give distribution system operators an alternative on how to properly determine the maximum rating of the renewable energy technologies without compromising the integrity of the system. In addition, these resources can be accurately placed depending on the topology and components of the distribution network. Finally, this work will be beneficial to all the electricity consumers since the electricity rates will be lowered due to the reduction of the system loss.

Link to the article: https://ieeexplore.ieee.org/document/8650071
Impact factor: Not yet available

Andrew D. Montecillo
Institute of Biological Sciences
College of Arts and Sciences
UP Los Baños

Characterization of Bacterial Nanocellulose Produced by Isolates from Philippine Nata Starter and its Biocompatibility, Journal of Biomaterials Applications, 34(3): 339-350, 2019

The material properties of nanocellulose membranes were characterized using scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray dispersive spectroscopy, Calcofluor staining and water retention. The biocompatibility of the nanocellulose membranes was evaluated using MC3T3 pre-osteoblast cells and was analyzed using CCK-8 cell viability assay. The macroscopic appearance and chemical nature of BNCs produced by the two isolates were generally similar regardless of the isolate and/or substrate used in this study. The differences in the BNC yield and fiber microstructure were related to the variation of organism-substrate combination. Therefore, these factors must be optimized in order to maximize the cellulose yield and to manipulate the material properties. The native BNC surface allowed for cell adhesion and cell proliferation in vitro but triggered an inflammatory response during prolonged implantation in an animal host system. Modification of the material is recommended to improve its biocompatibility in vivo.

In this paper, we described and characterized two nanocellulose-producing bacteria isolated from local nata starter cultures. The nanocellulose produced by the two bacterial isolates were compared to determine if differences between material properties and in vitro biocompatibility were species-dependent. The two bacteria (Komagataeibacter hansenii and Gluconoacetobacter sp.) used in this study were isolated and produced significant bacterial nanocellulose (BNC) yield which will be useful in the future studies. The macroscopic appearance and chemical nature of BNCs produced by the two isolates were generally similar regardless of the isolate and/or substrate used in this study. The differences in the BNC yield and fiber microstructure were related to the variation of organism-substrate combination. Therefore, these factors must be optimized to maximize the cellulose yield and to manipulate the material properties. The native BNC surface allowed for cell adhesion and cell proliferation in vitro but triggered an inflammatory response during prolonged implantation in an animal host system. Modification of the material is recommended to improve its biocompatibility in vivo.

Link to the article: doi: 10.1177/0885328219852728
Impact factor: (2018/2019) 1.313

Paul Lloydson J. Alvarez1, Florinia E. Merca1 and Lilia M. Fernando2
1Institute of Chemistry, College of Arts and Sciences (UP Los Baños)
2Institute of Crop Science, College of Agriculture and Food Science (UP Los Baños)

Indole-3-Acetic Acid Synthesis by Plant Growth Promoting Klebsiella sp. (PGPB1) via Indole-3-Pyruvic Acid Pathway and its Uptake in Plants, Philippine Journal of Crop Science, 44(3): 1-9, December 2019

TLC analysis of EAF1 and EAF2 along with the standard compounds (IAA and IAAld). IAA spots appeared as reddish pink spots after color development with van Ehmann’s reagent and heating to 90°C.

Rice seedlings incubated in distilled water (control) and with IAA treatment after 7 days (A) and 14 days (B).

15N-labeled tryptophan was used to trace the synthesis of indole-3-acetic acid (IAA) by Klebsiella sp. (PGPB1). Thin layer chromatography (TLC) and high performance liquid chromatography (HPLC) showed the presence of IAA in the crude extracts. In addition, indole-3-pyruvic acid (IPyA) was also detected by HPLC in the crude extracts. The crude extract, IAA and IPyA fractions were found to be enriched with 15N. The presence of IPyA in the extract indicates that PGPB1 is using the IPyA pathway in synthesizing IAA. Application of the 15N-labeled IAA improved the growth of rice seedlings in terms of fresh weight, root length and shoot length. Rice seedlings were also found to be enriched in 15N, a proof that they were able to absorb the applied 15N-labeled IAA.

Indole-3-acetic acid (IAA) plays a major role in plant growth and development. There is an increasing interest in studying the bacterial synthesis of IAA in view of its possible role in plant-bacteria interactions. Klebsiella sp. (PGPB1) is utilized by UPLB-BIOTECH in their biofertilizers. Experiments showed that the addition of tryptophan to culture media resulted in higher production of IAA. This study will determine the pathway used by PGPB1 in synthesizing IAA using tryptophan as a precursor. The results of the study will provide information about the intermediates in IAA synthesis that are formed from tryptophan once introduced to a specific culture of bacteria, and hoe the efficiency of IAA production using bacterial cultures can be increased.

Link to the article: https://www.cabdirect.org/cabdirect/abstract/20203113778
Impact factor: (2018/2019) 0.135

Alexandra B. Santos-Putungan
Institute of Mathematical Sciences and Physics
College of Arts and Sciences
UP Los Baños

Selective Capture of CO2 over N2 and CH4: B Clusters and their Size Effects, Materials Today Communications, 22: 100712, 2020

Carbon dioxide in the atmosphere poses a major problem. Different efforts have been made to reduce CO2 in the atmosphere to lessen the effect of global warming. Thus, it is essential to separate CO2 for other gas mixtures such as N2 and CH4. These three gas molecules are often found in post combustion processes and in natural gas sweetening. In this work, using Density Functional Theory, we were able to find that using the prototype B8 and B12 clusters, we were able to separate the abovementioned gas molecules at room temperature. We found that separation of CO2 with N2 is possible only for B12, and not on B8, while the separation of CO2 with CH4 can be observed on both clusters. We were able to establish a selectivity trend on the CO2 adsorption over N2 and CH4 with B planar-cluster size, and significantly above.

Based on the results of our previous work regarding the strong chemisorption of CO2 molecule on B10-B13 clusters, we considered the prototype B8 and B12 planar-type clusters and perform a comparative study of the adsorption of the three molecules (CO2, N2 and CH4) on these clusters. We find that, at room temperature, a selective adsorption of CO2 over N2 can be observed on B12 cluster, but not on B8. Moreover, selective adsorption of CO2 over CH4 at room temperature is possible for both clusters.

Link to the article: https://www.sciencedirect.com/science/article/pii/S2352492819305719
Impact factor: (2018/2019) 1.859

Editha C. Jose1 and Ivy Carol B. Lomerio1
1Institute of Mathematical Sciences and Physics, College of Arts and Sciences (UP Los Baños)

Control Problem on a Rough Circular Domain and Homogenization, Asymptotic Analysis, 115: 19-46, 2019

A circular oscillating domain

Homogenization theory started in the late 19th century when physicists like Poisson, Maxwell, and Einstein solved specific problems involving two-phase conductors and viscosity of suspensions. In the early 1960’s, homogenization theory became a well-established discipline in mathematics. Its wide applications attracted scientists especially in physics, engineering and other natural sciences.

Homogenization theory has been introduced in order to describe the behavior of composite materials, those that are made up of two or more finely mixed constituents, which are widely used in the industry. At present, the theory is not anymore limited to the study of composite materials. A number of works consider domains with oscillating boundaries and study some physical parameters such as conductivity and elasticity on these types of boundaries. The focus of homogenization is to describe the macroscopic characteristic of the whole material or domain.

In our study, we considered a circular domain with inner oscillating boundary. We pose an optimal control problem on the oscillating part of this domain and we want to find the “best” solution to this problem that gets close to a desired prescribed state. We call this solution as the optimal control.

This work is a significant addition to researches in optimal control and homogenization theory. In this article, we consider a rapidly oscillating circular domain which models domains from applications such as fans in jet engines and heat radiator. Turbulence can occur during rotation of such materials and thus comes the importance of studying control problems associated with fluid flow in varying oscillating domains. This research and similar works on control theory and homogenization show the crucial role of theoretical mathematics to other sciences, specifically physics, engineering and materials science.

Link to the article: https://content.iospress.com/articles/asymptotic-analysis/asy191526
Impact factor: (2018/2019) 0.808

Nacita B. Lantican1, Andrew B. Montecillo1 , Mark Dondi M. Arboleda2 , Hildie Maria E. Nacorda2 and Saul M. Rojas1
1Institute of Biological Sciences, College of Arts and Sciences (UP Los Baños)
2School of Environmental Science and Management (UP Los Baños)

Draft Genome Sequences of Six Bacteria Isolated from the Benham Bank, Philippine Rise, Philippines, Microbiology Resource Announcements, . doi: 10.1128/MRA.00777-19, 2019

The Benham Bank Seamount is the shallowest part of the Philippine Rise located in the east of mainland Luzon, which interacts with the Pacific Ocean. It was previously shown to host a diverse community of corals with associated reef fishes, benthic invertebrates, and Halimeda algae, in which microorganisms thrive and coevolve. This unique offshore environment was thought to harbor bacteria that may be involved in the production of novel bioactive compounds that can be used as antimicrobial and anticancer drugs, fungicides, herbicides or pesticides. In this paper, the authors reported the draft whole-genome sequences of six bacterial isolates obtained from the near-bottom waters and surface sediments of the Benham Bank.

Genomic DNA of the isolates were extracted and sent to the Molecular Biology Service Unit, University of Alberta for genome sequencing using Illumina MiSeq reagent kit v2 (2×250-bp cycles). The raw reads were trimmed using Trimmomatic tool and De novo assembly was performed using Unicycler v0.4.6.0 implemented online in Galaxy (https://usegalaxy.org/). The draft genome sequences were annotated using the Rapid Annotation using Subsystems Technology (RAST) version and then the taxonomic classification of the isolates was established using the Microbial Genome Atlast (MiGA) analysis. Production of secondary metabolites was predicted using antiSMASH v4.

MiGA analysis revealed that three of the isolates belong to novel species of the following genera: Dermacoccus, Idiomarina and Flavobacterium while three other species indicated novel strains of Bacillus infantis and Vibrio alginolyticus and Vibrio owensii. A total of 26 gene clusters for putative biosynthetic secondary metabolites were predicted using antiSMASH from all of the genomes combined, which may hold potential as antibiotics.

The study reports the draft genome sequence assemblies of six bacteria Isolated from the Benham Bank Seamount, Philippine Rise Philippines. The draft genome sequences of these isolates are valuable resources for the discovery of novel marine bioactive natural products such as pigments and antibiotics.

Link to the article: https://mra.asm.org/content/8/29/e00777-19
Impact factor: Not Applicable