IPA Recipients for July 2019

Michelle T. Cirunay
National Institute of Physics
College of Science
UP Diliman

Statistical signatures of the spatial imprints of road network growth. International Journal of Modern Physics C 29(10), 1850099 (2018). DOI:10.1142/S0129183118500997

Qualitatively, when you look at the road network of Metro Manila from a map, you will find irregular curves and blocks. Moreover, visually the component cities would have different road network layouts. In this work, we try to measure the roads and areas enclosed by the roads in all the Metro Manila cities. Here, although the component cities appear to be physically different, statistically it is found that they similar to each other. In particular they obey distributions having power-law tails. This implies that they share a governing process of city formation called self-organization or the process of unsupervised growth over time due to multiple local contributors on the ground. These findings are supported by simulations whose underlying assumptions are based on the fact that we want roads to be direct connections between locations but locally, they tend to curve due to geographical constraints. This work can be used as a basis for conducting more quantitative studies on Metro Manila in the hope of finding solutions to the burgeoning problems of the metropolis.

The work is one of the first quantitative analyses of the road network cover of the Metropolitan Manila conurbation. As in any other systems in the natural and social domain, the very first step towards understanding is to describe it. In this case, apart from the simple fractal analyses, the roads and enclosed areas are characterized according to their lengths and degree of sinuousity and their shapefactors. To go beyond simple physical and statistical description of the system, we aim to replicate the observed complex behaviors via simple modelling rules. These steps i.e. description and modelling, serve as foundation for more rigorous approaches geared towards finding solutions to the problems of urban spaces and the societies that live in them. Additionally, to our knowledge, this is one of the first works of this kind that deal with the Metro Manila conurbation.

Link to the article: http://dx.doi.org/10.1142/S0129183118500997
Impact factor (2017/2018): 0.919

Oliver John V. Belleza1, Jortan O. Tun
2, Gisela P. Concepcion2 and Aaron Joseph L. Villaraza
1Institute of Chemistry
2Marine Science Institute
College of Science
UP Diliman

On the inhibition of capsaicin response in dorsal root ganglion neurons by nobilamide B and analogues: a structure-activity relationship study. Medicinal Chemistry Communications. 2018, 9, 1673-1678

Nobilamide B is a neuroactive peptide previously isolated from bacteria associated with mollusks Chicoreus nobilis and Conus tribblei found in the Philippines. This peptide, consisting of seven amino acids, was found to be a long-acting antagonist of the transient receptor potential vanilloid-1 (TRPV1) channel, making it an attractive lead compound for the development of an anti-pain drug. Alanine-substituted analogues of nobilamide B were chemically synthesized and tested for neuroactivity in a primary culture of dorsal root ganglion neurons extracted from mice. Three analogues ([Ala7]-nobilamide B, [Ala5]-nobilamide B, and [Ala3]-nobilamide B) were found to inhibit capsaicin response in these neurons with activity comparable to that of the native peptide. Three other analogues ([Ala4]-nobilamide B, [Ala2]-nobilamide B, and [Ala1]-nobilamide B) displayed only minimal blocking. Our results indicate the importance of D amino acids to the peptide’s structure and activity. This information provides a better understanding of its mechanism of action, and thus useful in the discovery of synthetic analogues with improved inhibitory activity on the TRPV1 channel towards the development of a novel anti-pain drug.

Synthetic analogues of nobilamide B were made to aid in the investigation of the peptide’s activity on the TRPV1 channel. Three analogues were found to exhibit inhibitory activity that is comparable to the natural product. Our results also created a better understanding of the native peptide’s mechanism of action. This information is useful in the discovery and development of a novel anti-pain drug which targets TRPV1.

Links to the article: https://pubs.rsc.org/en/content/articlelanding/2018/md/c8md00304a
Impact factor: (2017/2018) 2.342

Christine Aubrey C. Justo and Windell L. Rivera
Institute of Biology
College of Science
UP Diliman

Aptamer Selection against a Trichomonas vaginalis Adhesion Protein for Diagnostic Applications. ACS Infectious Diseases, 4: 1306-1315. DOI: 10.1021/acsinfecdis.8b00065

Trichomonas vaginalis is a sexually transmitted agent that may infect men, women, and infants from infected mothers. It is the world’s most prevalent non-viral sexually transmitted agent but remains underreported with no established surveillance method. Diagnostic kits for T. vaginalis are available in the market but only a few have access to these kits. With the collaboration of UPD and URV, an aptamer or single-stranded DNA specific for T. vaginalis surface protein AP65 has been developed using a plate-based selection method. The aptamer can be used as an alternative to antibody for the detection of T. vaginalis. With its DNA nature, it can be used in the development of more robust and even point-of-care diagnostic assays/kits for T. vaginalis. The selected AP65_1 was found to be specific to T. vaginalis. Current efforts now focus on the use of the selected aptamers for the development of specific, sensitive, robust, and point-of-care assay for T. vaginalis.

This work reports the plate-based selection of aptamers or single-stranded DNA that can serve as recognition molecule for T. vaginalis AP65. The aptamer can be used as an alternative to antibody for the detection of the sexually transmitted agent T. vaginalis. The aptamer can be used for the development of low cost, robust, sensitive, and specific diagnostic assay for T. vaginalis.

Link to the article: http://pubs.acs.org/doi/10.1021/acsinfecdis.8b00065
Impact factor: (2017/2018) 4.325

Michael Y. Roleda
Marine Science Institute
College of Science
UP Diliman

Carbonic anhydrase activity in seaweeds: overview and recommendations for measuring activity with an electrometric method, using Macrocystis pyrifera as a model species. Marine Biology 165 (5): 88

Carbonic anhydrase (CA) is essential for photosynthesis in algae as it accelerates the interconversion of carbon dioxide (CO2) and bicarbonate (HCO3−) to supply and maintain the organism’s internal inorganic carbon (Ci) pool and supply CO2 to RuBisCO to drive the photosynthetic process. Our literature review showed that the commonly used Wilbur–Anderson method has been widely modified since its introduction in 1948, mostly without being optimized for the species tested. Based on the review, an optimized protocol for measuring CA in Macrocystis pyrifera was developed, which showed that the assay conditions could strongly affect CA activity. Using the optimized assay, CAexteral and CAinternal activities were readily measured in Macrocystis with higher precision compared to the non-optimized method. The CAinternal activity was twice as high than CAexternal, which was attributed to the Ci uptake mechanisms of Macrocystis. This study suggests that the CA assay needs to be optimized for each species prior to experimental work to obtain accurate and precise results.

Our study showed the importance of assay optimization. Using an optimized method to measure carbonic anhydrase, a zinc metalloenzyme that catalyzes the interconversion of carbon dioxide (CO2) and bicarbonate (HCO3−) − in many living organisms, a higher data accuracy and precision were measured compared to non-optimized method.

Links to the article: https://doi.org/10.1007/s00227-018-3348-5
Impact factor: (2017/2018) 2.215

Milany Anne M. Luay1, Mary France R. Gonzaga2, Sharmaine Kae D. Po1 and Erna C. Arollado2
1Department of Pharmacy 
2Institute of Pharmaceutical Science
College of Pharmacy
UP Manila

Determination of Antiangiogenic Activity of Telescopium Telescopium (Horn snail) Extract using in ovo Chorioallantoic Membrane (CAM) Assay. Acta Medica Philippina 52(4):366-373

One mechanism of growth and spread of cancer cells is through angiogenesis. Angiogenesis is the formation of blood vessels from pre-existing ones. These blood vessels supplies oxygen and nutrients for the growth of cancer cells. By preventing this process to occur, cancer cells are starved and do not grow and spread. Therefore, the use of anti-angiogenic agents has been an advantageous therapy for cancer. This study evaluated the potential antiangiogenic activity of Telescopium telescopium or locally known as Bagongon. It is highly abundant in the country and consumed as food by the locals.

Antiangiogenic activity was tested using a partially opened fertilized duck egg where the growth of the blood vessels was easily observed. Blood vessel’s growth parameters (Diameter and length) were measured before and after the treatment with Telescopium telescopium extracts. These parameters determine the extent of growth of blood vessels indicating their corresponding capacity to block angiogenesis. Based on the results, after treatment with a certain concentration of Telescopium telescopium extract, blood vessel size and length were reduced at a significant level. Growth of new blood vessels was inhibited, thus also inhibiting angiogenesis.

This study sought to further study marine invertebrates, specifically Telescopium telescopium, for cancer biology as aside from mollusks emerging as one of the most important sources in developing novel chemotherapeutic agents against tumor cells, this widely distributed species of strong potential remains unexplored until today.

Link to the article: https://www.actamedicaphilippina.org/article/5142-determination-of-the-antiangiogenic-activity-of-telescopium-telescopium-horn-snail-extract-using-in-ovo-chorioallantoic-membrane-cam-assay
Impact factor: Not yet available

Roland Dominic G. Jamora1, Joshua Emmanuel E. Abejero1 and Joseph P. Anlacan2
1Department of Neurosciences
2Department of Psychiatry and Behavioral Medicine
College of Medicine
UP Manila

Long term outcomes of pallidal deep brain stimulation in X-linked dystonia parkinsonism (XDP): Up to 84 months follow up and review of literature. Parkinsonism Relat Disord. 2018 Sep 21. pii: S1353-8020(18)30418-8

The authors reviewed eleven XDP patients who underwent bilateral pallidal neurostimualtion (globus pallidus interna deep brain stimulation) from October 2009 to September 2018. XDP is a movement disorder endemic in Panay Island, Philippines.

The Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS) and Unified Parkinson’s Disease Rating Scale (UPDRS)-III scores were reviewed from baseline up to the longest follow-up together with the demographic and clinical data. The 10 published case reports on DBS in XDP were also reviewed.

The mean age was 39 + 9.2 years with a mean disease duration of 3 years (range 1-9 years). An immediate response for dystonia post-DBS (1 month) was seen in all cases, with a mean BFMDRS score of 23.3 + 12.12 [from a mean baseline of 36.3 + 12.1] and a small change in the mean UPDRS-III score of 20 + 10.39 [from a mean baseline of 24.04 + 8.74]. At 12 months (n=10), the mean BFMDRS score was 13.7+ 10.63 and the mean UPDRS-III score was 19 + 13.19. There was improvement in the clinical and functional stage of the patients, with majority in Stage 1 (n=3) and Stage 2 (n=5) at their last follow-up.

Bilateral pallidal stimulation (GPi-DBS) should be considered as a treatment option for XDP. It is effective in the first 12 months in controlling dystonia with variable response in controlling parkinsonism. It may be effective in up to 72-84 months, as seen in two patients.

The article provides additional evidence on the utility of bilateral pallidal stimulation in alleviating the symptoms of X-linked dystonia parkinsonism (XDP). This article also report on 2 patients with the longest documented follow up in literature, at 72 and 84 months after surgery. As XDP has no cure yet, pallidal neurostimulation offers relief of symptoms (dystonia and parkinsonism).

Link to the article: doi: 10.1016/j.parkreldis.2018.09.022
Impact factor: (2017/2018) 4.721

Renerico P. Gentalan Jr., Nestor C. Altoveros, Teresita H. Borromeo, Leah E. Endonela, Antonio G. Lalusin and Consorcia E. Reaño
Institute of Crop Science
College of Agriculture and Food Science
UP Los Baños

Systematic establishment of colour descriptor states through image-base phenotyping. Plant Genetic Resources-Characterization and Utilization. 1-4. DOI: 10.1017/S1479262118000291

The morphological characterization and the subsequent diversity assessment of plant genetic resources rely on the accuracy and precision of descriptor lists. Particularly for color, psychophysical subjective assessment is used to discriminate the various descriptor states of the crop. With the advent of novel image-based phenotyping techniques, objective methods of characterizing color may be developed. The study proposes a systematic method for determining color descriptor states through image analysis, using pili (Canarium ovatum) as a model. Kernel images of 52 pili accessions from the core collection of the Institute of Crop Science and National Plant Genetic Resources Laboratory, University of the Philippines Los Baños were captured using a calibrated VideometerLab 3 setup. Color descriptor states were derived from the average International Commission on Illumination lightness (L*), green–red (a*) and blue–yellow (b*) color component values. values. Cluster analysis and subsequent color-parameter averaging per cluster were performed to produce representative color values of descriptor states. The protocol described can be applied to elucidating color descriptor states of all parts of the plant of all crop species.

Often linked to subjectivity, the work specifically gives importance to objectively creating color descriptor states. The method described by the author will facilitate the systematic creation of a descriptor list and the subsequent thorough characterization of plant color. 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/S1479262118000291
Impact factor: (2017/2018) 0.712

Eldrin DLR. Arguelles
National Institute of Molecular Biology and Biotechnology
UP Los Baños

Descriptive Study of Some Epiphytic Algae Growing on Hydrilla verticillata (L.f ) Royle (Hydrocharitaceae) found in the Shallow Freshwater Lake Laguna de Bay (Philippines). Egyptian Journal of Aquatic Biology and Fisheries, 23(2): 15-28

Microscopic examination of submerged roots and leaf fragments Hydrilla verticillata (L.f) Royle showed a diverse collection of algal epiphytes. In this study, the species composition and distribution of epiphytic algae living on the submerged plant tissues of aquatic macrophyte Hydrilla verticillata (L.f) Royle found at the largest freshwater shallow lake “Laguna de Bay” in the Philippines was studied, and documented with a detailed description for each species. A total of 15 algal species belonging to 12 genera of three algal phyla were observed including, 7 Cyanophyceae, 3 Bacillariophyceae 3 Trebouxiophyceae, and 2 Chlorophyceae. Of these taxa, the occurrence of a rare microalga Franceia amphitricha (Lagerheim) Hegewald is reported for the first time in the Philippines. These taxonomic records will serve as a preliminary study on the taxonomic account of epiphytic algae inhabiting the aquatic macrophyte, water thyme (Hydrilla verticillata L. f. Royle) found in Laguna de Bay contributing important information on the algal biodiversity as part of the living resources of the Philippines.

Most of the phycological studies in the Philippines mainly focused on seasonal variations of phytoplankton in different lentic and lotic systems, with a little concern on epiphytic algal and cyanobacterial communities associated to aquatic macrophytes. In this study, the species composition and distribution of epiphytic algae living on the submerged plant tissues of aquatic macrophyte Hydrilla verticillata (L.f) Royle found at the largest freshwater shallow lake “Laguna de Bay” in the Philippines was studied, and documented with a detailed description for each species. A total of 15 algal species belonging to 12 genera of three algal phyla were observed including, 7 Cyanophyceae, 3 Bacillariophyceae 3 Trebouxiophyceae, and 2 Chlorophyceae. Of these taxa, the occurrence of a rare microalga Franceia amphitricha (Lagerheim) Hegewald is reported for the first time in the Philippines. These taxonomic records will add to the pool of data useful for understanding the epiphytic algal flora composition of aquatic macrophytes found in Philippine freshwater habitats.

Link to the article: http://ejabf.journals.ekb.eg/article_29300_88c7342dfde5dcba7b0e8c80fb81d160.pdf
Impact factor: Not yet available

Laurence E. Robles1, Patrick C. Cabaitan1 and Maria Eleanor B. Aurellado2
1Marine Science Institute, College of Science, UP Diliman
2Institute of Biological Sciences, College of Arts and Sciences, UP Los Baños

Effects of competition on the territorial behaviour of a farmer damselfish, Plectroglyphidodon lacrymatus (Perciformes: Pomacentridae). Journal of Fish Biology 93:1197–1206. https://doi.org/10.1111/jfb.13841

The jewel damselfish is a coral reef fish that cultivates algal farms and aggressively defends it from other competitors. It is also one of the most common farming damselfish observed in many degraded Philippine coral reefs. However, there are other species of farmers co-occurring in coral reefs that are less aggressive than the jewel damselfish. We examined how aggressive interactions between the jewel damselfish and other farmer individuals affected its territory size and habitat composition within its territory in the Bolinao-Anda Reef Complex, Pangasinan. We found that the territories of jewel damselfish with neighboring individuals from the same species were nearly 50% smaller than those with neighboring individuals from different, but less aggressive species. Correspondingly, we observed that the jewel damselfish was more aggressive towards members of the same species than towards individuals belonging to other species. Despite these differences in the territoriality towards different neighboring competitors, we found no differences in algal cover inside the territories of jewel damselfish. However, juvenile coral occurrence was much lower inside jewel damselfish territories, irrespective of whether the fish had a neighboring competitor or not. This study suggests that the competitive abilities of a competitor can limit the spatial extent of a farmer’s territory and might explain why the jewel damselfish usually dominates the coral reef flats. The lower abundance of juvenile corals inside the jewel damselfish territories also suggests that the dominance of the jewel damselfish could slow down the recovery of coral reefs.

Territorial farming damselfishes, such as the jewel damselfish, are often common in many Philippine coral reefs. By cultivating algae, farming damselfishes can influence the benthic community and affect coral recruitment, but the magnitude of their effects might be affected by their interactions with other competitor farmers. We examined the aggressive interaction between the jewel damselfish and other species of competitor farmers to gain insights on the possible effects on the territory size and benthic assemblages of jewel damselfish territories. Such information is important in understanding the spatial distribution of these farmers and their effects on the coral reef benthos, which might affect coral reef resilience.

Link to the article: https://doi.org/10.1111/jfb.13841
Impact factor: (2017/2018) 1.702