UP Study Reveals Insights on the Probiotic and Antifungal Benefits of Bacteria in Burong Isda

UP Study Reveals Insights on the Probiotic and Antifungal Benefits of Bacteria in Burong Isda

Published: June 20, 2025
By: Harvey Sapigao

Limosilactobacillus fermentum colonies on agar, derived from burong isda. (Photo credit: Joshua Veluz)

Filipino fermented foods have long been known to contain bacteria that offer health benefits, also known as probiotics. Burong isda, a traditional fermented fish from Pampanga, contains a bacterium called Limosilactobacillus fermentum (L. fermentum), which is closely related to the well-known Lactobacillus probiotics.

 

Researchers from UP Diliman College of Science (UPD-CS) combined genomic and laboratory analyses to provide a comprehensive probiotic profile of two L. fermentum strains in burong isda. Their multidimensional approach also revealed the strains’ antifungal benefits against Aspergillus fumigatus (A. fumigatus), one of the most common fungi affecting immunodeficient individuals. Their study not only lays the groundwork for developing new probiotic products but is also possibly the first to report the antifungal effects of L. fermentum against A. fumigatus.

 

“Historically, probiotic research in the Philippines has relied heavily on culture-based methods and basic molecular techniques,”  said corresponding author Joshua Veluz from UPD-CS National Sciences Research Institute (NSRI). “This work underscores the value of combining genomics, metabolomics, and assays as a powerful and timely approach to uncovering the full probiotic potential of microbes found in Philippine fermented foods.”

 

Veluz, a Kapampangan, said that he has a keen interest in this research because he grew up eating burong isda. He became curious about its potential after learning that Filipino fermented foods also have health benefits aside from their cultural significance. This curiosity led him to begin working on the study in 2019. “This personal and academic connection made the study deeply meaningful to me,” he said.

 

Along with Veluz, the study authors are Paul Christian Gloria and Dr. Maria Auxilia Siringan of UPD-CS NSRI, along with Dr. Irineo Dogma Jr. of the University of Santo Tomas (UST).

 

A key characteristic of probiotics is their ability to survive the harsh conditions of the digestive system. They discovered that while these strains may struggle to grow in highly acidic environments like the stomach, they had no difficulty growing in less acidic conditions, as in most parts of the gastrointestinal tract.

 

Furthermore, the researchers discovered that the strains carry several genes known to help boost the host’s immune system, along with genes related to producing essential vitamins such as B1, B2, B6, and B9. The strains were also found to be non-pathogenic and have a very low potential to transfer antimicrobial resistance genes.

 

“Additionally, the strains produce compounds that inhibit the growth of certain fungi known to cause infections,” said Veluz. Previous studies have shown that L. fermentum possesses antifungal effects against different fungi, but this study may be the first to demonstrate its potential against A. fumigatus. This suggests that L. fermentum could serve as a broad antifungal product, including against A. fumigatus.

 

The researchers are now exploring additional probiotic properties of the strains and assessing their stability to ensure they can be safely used for future health applications. “We aim to further characterize their functional traits and contribute to the growing field of probiotic research in the Philippines, especially using OMICs,” concluded Veluz.

 

References:

Veluz, J. T., Gloria, P. C. T., Siringan, M. A. T., & Dogma, I. J. (2025). Beyond Buro: Probiotic and Antifungal Traits of Limosilactobacillus fermentum, from Philippine Burong Isda (Fermented Fish), Revealed by Genomics and Assays. The Microbe, 100334. https://doi.org/10.1016/j.microb.2025.100334

 

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UP Physicists Visualize Evolution of Global Values Over Four Decades

UP Physicists Visualize Evolution of Global Values Over Four Decades

Published: June 18, 2025
By: Eunice Jean C. Patron

Scientists from the University of the Philippines – Diliman College of Science’s National Institute of Physics (UPD-CS NIP) have generated culture maps using data from the Integrated Values Survey (IVS).

 

Scatter plots of individual respondents from four countries surveyed in Wave 7. (Photo credit: Euste et al., 2025)

Using a method called principal component analysis (PCA), physicists John Lawrence Euste, Hannah Christina Arjonillo, and Dr. Caesar Saloma derived time-resolved pairs of complementary maps from the IVS data collected over forty years from over 120 countries: one showing cultural differences between countries, and the other showing cultural variations within a specific country, based on survey respondents. A total of seven separate surveys were conducted from 1981 to 2022.

 

Measuring culture change

 

“From our perspective as applied physicists, we wanted to detect and measure how culture has evolved, which is usually only described anecdotally,” Dr. Saloma shared, explaining that their work falls under sociophysics, a branch of physics concerned with modeling and quantifying social phenomena using methods initially developed in statistical and instrumentation physics. “We tried to quantify how culture varies over time in geographically separated populations,” he added.

 

Countries are represented as points on the first map. By tracking their movement over time, the team found that countries have generally become more focused on self-expression values. In the second map, the points represent respondents within each country. The team measured cultural diversity using the standard deviational ellipse (SDE) area. Countries with smaller SDEs exhibited less cultural diversity and tended to uphold more traditional values, while those with larger SDEs showed more cultural diversity and leaned more toward self-expression values.

 

“I looked into the literature to see if we could actually measure culture, and I found that there are models of cultural dynamics and change,” Euste said, explaining how he became interested in quantifying cultural change. “But then I realized that there weren’t many models that actually examined real-world cultural dynamics—how cultural values have changed based on actual empirical data.”

 

Transforming data into cultural maps

 

The physicists first aggregated the survey data (more than 300,000 total respondents) by averaging responses per country. Next, they applied PCA to the country-aggregated responses. This approach generated a map where each country is represented as a single point, making it easier to analyze cultural differences between countries.

 

“But the country-level map only shows each country as a single point, which doesn’t reflect the cultural diversity within countries. For example, the Philippines isn’t culturally homogeneous; it doesn’t make sense to represent the whole country with just one cultural profile,” Euste noted. So they used the transformation matrix derived from the country-level PCA. This matrix helps map individual responses into coordinates on the same cultural map, ensuring consistency between the country-level and respondent-level representations.

 

“This method ensures that the outputs from both levels are consistent,” Arjonillo added. “The third approach helps align the two, allowing us to compare both the country means and the full respondent distributions over time.” 

At the country level, the physicists discovered that the Philippines is currently traditional—placing a high premium on religion, parent-child ties, deference to authority, and traditional family structures—but also leans toward self-expression through support for environmental protection, gender equality, and active participation in collective socio-economic life. From 1996 to 2019, the country has shown a slight decline in traditional values and a rise in self-expression.

 

Interestingly, the countries that are culturally closest to the Philippines are Latin American nations like Bolivia, Guatemala, Mexico, and Nicaragua—likely a reflection of the country’s history of over 300 years of Spanish colonization, rather than its geographic neighbors in East or Southeast Asia.

 

Real-world applications

 

The physicists believe that their findings and the approaches they used can serve as tools to support policymakers in decision-making. “The study can help people understand how cultural values change over time, guiding policymakers in tailoring policies that better align with a country’s cultural values,” Euste said. “This is useful for understanding broader cultural trends and how they evolve.”

 

Dr. Saloma explains that legislations, policies, and regulations are more effective if they are grounded on scientific evidence. “Policies work best when they rely on scientific data and findings; it’s why quantifying cultural evolution matters,” he added.

 

“[Our study] is still a work in progress,” Arjonillo concluded. “What’s important for us is to create tools for measurement—that’s the point of instrumentation. This is what we hope to evaluate and continue making progress on, not just in physics, but wherever we can find useful data.”

 

References:

Euste, J. L., Arjonillo, H. C., & Saloma, C. (2025). Time-resolved culture maps derived from the integrated values survey data (1981–2022). Physica A: Statistical Mechanics and its Applications, 659, 130317. https://doi.org/10.1016/j.physa.2024.130317

 

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Ang Nakaabang na Krisis: Kalidad ng Groundwater sa Pilipinas at Kung Bakit Ito Mahalaga

Ang Nakaabang na Krisis:
Kalidad ng Groundwater sa Pilipinas at Kung Bakit Ito Mahalaga

Published: June 11, 2025
By: John Kenneth R. Fraga
Translated by: Dr. Ian Kendrich C. Fontanilla

Sinusukat ng mga kawani ng PGHI Project ang kalidad ng tubig sa ilalim ng lupa gamit ang multimeter sa isa sa mga kagubatang lugar sa Ilocos Sur. (Photo credit: Jacquilyn L. Estrada)

Ang groundwater—tubig na nakatago sa ilalim ng lupa—ay isang likas-yamang hindi nakikita, ngunit tiyak na hindi nalalayo sa isipan ng mga Pilipino. Ang hindi tagong yamang ito ay mahalaga para sa pang-araw-araw na buhay, lalo na sa agrikultura, kung saan ito ang nagbibigay-buhay sa irigasyon. Gayunpaman, habang lumalaki ang ating pangangailangan sa pagkain at lumalalim pa ang naabot natin sa ilalim ng lupa gamit ang teknolohiya, nahaharap sa isang malubhang krisis ang estado ng groundwater dahil sa labis na paggamit nito at kontaminasyon na nangangailangan ng agarang pansin.

 

Sa Pilipinas, lalong pinalalala ang mga problemang ito ng mga natatanging hamon na dulot ng tag-ulan at tag-init panahon sa bansa. Sa matitinding panahon, ang mga run-off mula sa mga sakahan ay maaaring magdala ng mga nakapipinsalang kemikal sa ilalim ng lupa, na nagbabanta sa ecological services na ibinibigay nito, ang biodiversity sa lugar, at ang public health. Sa kasamaang palad, sa kabila ng mga pagsisikap na subaybayan ang water quality, ang buong lawak ng mga problemang ito ay hindi lubos na nauunawaan. Bunsod nito, hindi pa buo ang mga datos na nakakalap at hindi rin pare-pareho ang pagsusuring ginagawa sa buong bansa.

 

Isang pangkat ng mga mananaliksik na pinamumunuan ni Dr. Francis S. Magbanua ng University of the Philippines Diliman College of Science, Institute of Biology (UPD-CS IB), at partners sa proyekto mula sa Ilocos Sur, Benguet, Nueva Ecija, Cebu, at Davao del Norte ay masusing sinusuri ang sitwasyon. Ang kanilang pag-aaral ay nakatuon sa kung paano nag-iiba ang kalidad ng groundwater sa pagitan ng mga agrikultural at magugubat lugar sa nag-iibang panahon. Ang kanilang natuklasan ay kapwa nagbibigay-liwanag at nakababahala.

 

Ipinakita ng pananaliksik na ang paggamit ng lupa (gawing sakahan o panatilihin ang gubat) at ang panahon (tag-ulan o tag-init) ay may malaking epekto sa kalidad ng groundwater, ngunit sa magkaibang paraan. Ang paggamit ng lupain para sa agrikultura ay madalas nagdudulot ng groundwater na mas mainit at mas mayaman sa kemikal ngunit mas mababa rin ang kalidad. Tumataas din ang panganib ng kontaminasyon ng groundwater kapag talamak ang mga gawaing pang-agrikultura. Ang mga magugubat lugar, sa kabilang banda, ay tumutulong sa pagpapanatili ng groundwater na mas malamig, mas malinis, at mas mayaman sa oxygen. Gayunpaman, ang anyo ng lupa—tulad ng mga matatarik na slope—ay maaaring makaapekto sa dami ng organic matter na naiipon sa groundwater.

 

Sa panahon ng tag-ulan, ang pagtaas ng pag-ulan ay tumutulong na palamigin ang groundwater at mapabuti ang antas ng oxygen nito. Pinapataas din nito ang pH habang dinadala ng tubig-ulan ang mga mineral at organic matter sa ilalim ng lupa. Baliktad nito, ang tag-init ay nagdudulot naman ng mas mainit na temperatura ng tubig sa lupa. Bagaman maaaring tumaas antas ng oxygen dahil bumabagal ang daloy ng tubig, ang pangkalahatang kalidad ng groundwater ay maaaring bumaba rin. Ang mas mababang antas naman ng groundwater ay maaaring magdulot ng mas mataas na konsentrasyon ng dissolved ions at iba pang suliranin ukol sa kalidad ng tubig. Sa kabilang banda, natuklasan ng pag-aaral na walang pinagsamang epekto ang paggamit ng lupa at panahon, na nangangahulugang habang ang bawat factor ay may kanya-kanyang epekto sa groundwater, hindi nila pinapaigting ang epekto ng bawat isa.

 

Ngunit kahit tila hindi nakatali sa isa’t isa ang mga epektong ito, malinaw ang mensahe: parehong mahalaga ang paggamit ng lupa at mga pagbabago sa panahon upang maunawaan ang kalagayan ng mga pinagkukunan natin ng groundwater. Halimbawa, ang pagkakaroon ng dissolved organic compounds (DOC) ay maaaring pahiwatig ng mga aktibidad ng tao malapit sa groundwater, ngunit batay sa pag-aaral, nakikita rin ang DOC sa mga magugubat na lugar, na maaaring maging indikasyon ng disturbances dulot ng paggamit ng lupa ng tao.

 

Paghahambing ng mga na-transpormang halaga ng temperatura ng groundwater, pH, DO, EC, at DOC batay sa mga panahon (tagtuyot vs tag-ulan) at gamit ng lupa (pang-agrikultura vs kagubatan) (Photo credit: Velasco et al., 2025)

“Isang limitadong yaman ang groundwater, at ang kalidad nito ay patuloy na bumababa,” babala ng mga mananaliksik. “Ang paglaki ng ating populasyon, pag-unlad ng ekonomiya, at mga pagbabago sa kapaligiran ay lahat nag-aambag sa pressure sa mahalagang yamang ito.” Binibigyang-diin ng pag-aaral na patuloy na lalala ang mga panganib sa public health at biodiversity kung walang isasagawaang komprehensibong pambansang paraan ng pamamahala at pagbabantay ng kalidad ng groundwater.


Ang pag-aaral na ito ay bahagi lamang ng mas malawak na pananaliksik na tinaguriang Philippine Groundwater Health Index (PGHI) Project, na naglalayong mas maunawaan at maprotektahan ang groundwater sa bansa. Pinondohan ng Department of Science and Technology (DOST) at minomonitor ng DOST-Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (PCAARRD), layunin ng proyekto na magbigay ng siyentipikong kaalaman para makabuo ng mga epektibong polisiya upang mapangalagaan ang mahalagang yamang ito. Ang mga mananaliksik ay nangolekta ng tubig mula sa mga balon at bukal sa mga agrikultural at magugubat na lugar sa limang lalawigan: Ilocos Sur, Benguet, Nueva Ecija, Cebu, at Davao del Norte.


Sa huli, binibigyang-diin ng pag-aaral ang isang simple ngunit mahalagang katotohanan: ang malinis at ligtas na groundwater ay kritikal para sa kinabukasan ng Pilipinas. Sa pamamagitan ng pagkilala sa factors na nakakaapekto sa kalidad ng groundwater at paggawa ng mga hakbang upang protektahan ito, maaari nating matiyak na ang mga susunod na henerasyon ay magkakaroon ng access sa malinis na tubig na kakailanganin tungo sa pag-unlad.


References:

Velasco, A. B., Magbanua, F. S., del Rosario, J. S., Estrada, J. L., Fraga, J. K. R., Mondejar, J. P., Sapitan, J. F. J. F., Geroza, I. P., Tenoc. G. L., & Husana, D. E. M. 2024. Groundwater Quality Variations during Wet and Dry Seasons in Agricultural and Forested Areas in the Philippines. Water Resources, 51(2), 293–305. DOI: 10.1134/S0097807824604849

 

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UP Researchers Predict Antimicrobial Resistance Using AI Models

UP Researchers Predict Antimicrobial Resistance Using AI Models

Published: June 13, 2025
By: Eunice Jean C. Patron

Escherichia coli (E. coli) is a common bacterium that lives in the intestines of animals and humans, and it is often used to identify fecal contamination within the environment. E. coli can also easily develop resistance to antibiotics, making it an ideal organism for testing antimicrobial resistance—especially in certain agricultural environments where fecal material is used as manure or wastewater is reused.

 

Traditional laboratory methods for analyzing antimicrobial resistance are often time-consuming and labor-intensive, making them impractical for large-scale monitoring. As a result, researchers are exploring faster approaches using whole-genome sequencing (WGS) and predictive modeling.

 

Marco Christopher Lopez and Dr. Pierangeli Vital of the University of the Philippines – Diliman College of Science’s Natural Sciences Research Institute (UPD-CS NSRI), along with Dr. Joseph Ryan Lansangan of the UPD School of Statistics, tested various artificial intelligence (AI) prediction models to determine the antimicrobial resistance of E. coli using genetic data and laboratory test results from the National Center for Biotechnology Information (NCBI) database.

Disk Diffusion Assay plate. (Photo credit: Dr. Pierangeli Vital)

“We selected the models based on their strengths in handling biological and imbalanced data,” Dr. Vital explained. “These models were chosen to compare performance across different learning strategies and to identify which is most suitable for predicting antibiotic resistance.”

 

The AI models used were Random Forest (RF), which is well-suited for high-dimensional data; Support Vector Machine (SVM), which excels in classification tasks, particularly when dealing with complex decision boundaries; and two ensemble methods—Adaptive Boosting (AB) and Extreme Gradient Boosting (XGB)—which enhance accuracy by focusing on hard-to-classify samples.

 

These AI prediction models most accurately predicted resistance to streptomycin and tetracycline, showing high accuracy and reliably distinguishing resistant strains from susceptible ones. On the other hand, ciprofloxacin was the most challenging to predict due to the limited number of resistant samples in the data (only 4%), which led to difficulty in identifying resistance and poor sensitivity. Among the models, AB and XGB consistently delivered good results, even when tested on imbalanced antimicrobial resistance data.

 

“We think that this strategy has great potential for real-time monitoring of antimicrobial resistance, particularly in agriculture.” Dr. Vital said, emphasizing the potential use of AI prediction models in the sector. “As DNA sequencing becomes faster and cheaper, prediction models such as ours can pick up resistant bacteria early—before they lead to outbreaks. This can facilitate better decision-making in food safety, agriculture, and public health programs.”

 

The researchers recommend including more diverse sample types and data sources—such as metagenomic data, which is DNA from all microbes in a sample—to better understand and predict how bacteria develop resistance.

 

Dr. Vital also highlighted the value of collaboration between fields—like how microbiologists and statisticians worked together in this study. “More so, the integration of (micro)biological concepts to statistics and predictive modelling to have an impactful result/outcome to the community, in this instance, agricultural food safety.” she said.

 

The study, titled “Prediction models for antimicrobial resistance of Escherichia coli in an agricultural setting around Metro Manila, Philippines,” was published in the Malaysian Journal of Microbiology, an open-access, peer-reviewed journal that serves as a platform for scientific communication among researchers and academics working with microbes and microbial products. It was also funded by NSRI and the Department of Science and Technology’s Grant to Outstanding Achievements in Science and Technology through the National Academy of Science and Technology.

 

References:

Lopez, M. C. D. P., Lansangan, J. R. G., & Vital, P. G. (2025). Prediction models for antimicrobial resistance of Escherichia coli in an agricultural setting around Metro Manila, Philippines. Malaysian Journal of Microbiology. https://doi.org/10.21161/mjm.240650

 

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The Hidden Crisis: Groundwater Quality in the Philippines and Why It Matters

The Hidden Crisis: Groundwater Quality in the Philippines and Why It Matters

Published: June 11, 2025
By: John Kenneth R. Fraga

PGHI Project staff measuring onsite groundwater quality using a multimeter in one of the forested sites in Ilocos Sur. (Photo credit: Jacquilyn L. Estrada)

Groundwater—water trapped beneath the Earth’s surface—is a resource that may be out of sight, but it is certainly not out of mind for many Filipinos. This invisible resource is vital for everyday life, especially in agriculture, where it provides the lifeblood for irrigation. However, as our demand for food grows and technology allows us to tap deeper into the Earth, groundwater faces an urgent crisis of over-extraction and contamination that demands immediate attention.

 

In the Philippines, these problems are further complicated by the unique challenges posed by the country’s wet and dry seasons. During extreme weather events, runoff from farmlands can carry harmful chemicals into the groundwater, threatening the ecological services it provides, its biodiversity, and the general public’s health. Unfortunately, despite efforts to monitor water quality, the full extent of these problems remains poorly understood. Consequently, this produces patchy data and inconsistent assessments nationwide.

 

A team of researchers headed by Dr. Francis S. Magbanua of the University of the Philippines Diliman College of Science, Institute of Biology (UPD-CS IB), and project partners from Ilocos Sur, Benguet, Nueva Ecija, Cebu, and Davao del Norte have taken a closer look at the situation. Their study focused on how groundwater quality varies between agricultural and forested areas across seasons. The findings were both enlightening and concerning.

 

The research showed that land use (agricultural or forested) and the season (wet or dry) significantly impact groundwater quality, but in different ways. Agricultural land use generally leads to warmer, more chemically rich but poorer groundwater quality. It also increases the risk of groundwater contamination due to farming activities. Forested areas, on the other hand, help maintain cooler, cleaner, and more oxygen-rich groundwater. However, their terrain—such as steep slopes—can influence the amount of organic matter present in the groundwater.

 

During the wet season, increased rainfall helps cool groundwater and improves its oxygen levels. It also raises pH as rainwater carries minerals and organic material into the groundwater. Quite the opposite, the dry season brings warmer groundwater temperatures. Although oxygen levels may sometimes rise due to reduced water movement, overall groundwater quality tends to decline. Lower groundwater levels can lead to more concentrated dissolved ions and potential water quality concerns. Interestingly, the study found no combined effect of land use and season, meaning that while each factor influences groundwater quality independently, they do not amplify each other’s impact.

 

But even though the effects may be independent, the message is clear: both land use and seasonal changes are crucial to understanding the state of groundwater resources. For example, the presence of dissolved organic compounds (DOC) is indicative of human activities but was also observed in the forested sites of this study, suggesting potential disturbance across different land use types.

 

 

Comparison of transformed values of groundwater temperature, pH, DO, EC, and DOC between seasons (dry vs wet) and land uses (agricultural vs forested). (Photo credit: Velasco et al., 2025)

“Groundwater is a limited resource, and its quality is steadily declining,” the researchers warn. “Human population growth, economic development, and environmental changes all contribute to the pressure on this vital resource.” The study emphasizes that the risks to public health and biodiversity will continue to grow without a comprehensive, nationwide approach to managing and monitoring groundwater quality.

 

This research is part of a larger effort called the Philippine Groundwater Health Index (PGHI) Project, which seeks to better understand and protect the country’s groundwater. Funded by the Department of Science and Technology (DOST) and monitored by the DOST-Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (PCAARRD), the project aims to provide the scientific backing needed for effective policies to safeguard this essential resource. The team collected water from wells and springs in agricultural and forested areas in five provinces: Ilocos Sur, Benguet, Nueva Ecija, Cebu, and Davao del Norte.

 

In the end, the study underscores a simple but vital truth: clean, safe groundwater is critical for the future of the Philippines. By recognizing the factors that affect groundwater quality and taking action to protect it, we can ensure that future generations have access to the clean water they need to thrive.

 

References:

Velasco, A. B., Magbanua, F. S., del Rosario, J. S., Estrada, J. L., Fraga, J. K. R., Mondejar, J. P., Sapitan, J. F. J. F., Geroza, I. P., Tenoc. G. L., & Husana, D. E. M. 2024. Groundwater Quality Variations during Wet and Dry Seasons in Agricultural and Forested Areas in the Philippines. Water Resources, 51(2), 293–305. DOI: 10.1134/S0097807824604849

 

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Towards Safer Philippine Alcohol: UP Chemists Identify Promising Methods for Detecting Methanol in Lambanog

Towards Safer Philippine Alcohol: UP Chemists Identify Promising Methods for Detecting Methanol in Lambanog

Published: June 05, 2025
By: Eunice Jean C. Patron

The study reviews existing scientific methods for detecting methanol in lambanog, a traditional Filipino alcoholic beverage. (Photo credit: Ralff Nestor Nacor)

Scientists from the University of the Philippines – Diliman College of Science’s Institute of Chemistry (UPD-CS IC) have published a comprehensive analysis of existing techniques for detecting methanol—an industrial chemical highly toxic to humans—in lambanog, a popular traditional alcoholic beverage in the Philippines.

 

Emphasizing that methanol can be dangerous—even fatal—at high concentrations, Kristine Anne Ladines and Dr. Cynthia Grace Gregorio aimed to identify detection techniques that are effective, affordable, and simple enough for small producers, such as micro, small, and medium enterprises (MSMEs), to use—potentially through portable or paper-based testing kits.

 

“Lambanog holds cultural and economic significance in the Philippines, but repeated methanol poisoning incidents have harmed its reputation and endangered lives. Many cases of death and hospitalization have been linked to unsafe, unregulated production,” Ladines said. “Given these serious public health risks, we were driven to help find solutions that empower small producers to test and ensure the safety of their products.”

 

By identifying affordable and practical detection methods, the review can help inform national agencies such as the Food and Drug Administration about which technologies are best suited for widespread use among small producers.

 

“It can guide regulatory policies to mandate methanol testing using appropriate tools, helping ensure consumer safety while supporting industry compliance,” Ladines added.

 

Ladines believes that government and academic institutions can support MSMEs in adopting safer production and testing methods in several ways—including training and education on safe fermentation and distillation practices, providing subsidies or grants for acquiring basic detection equipment or kits, and developing accessible technologies such as low-cost paper-based sensors tailored for field use.

 

The paper, titled “Finding MeOH: A literature review on methods for the determination of methanol in Lambanog and alcoholic beverages,” is published in JSFA reports, a food science journal publishing papers on food science and agriculture, with particular emphasis on the agriculture/food interface

 

References:

Ladines, K. A., & Gregorio, C. G. (2025). Finding MeOH: A literature review on methods for the determination of methanol in Lambanog and alcoholic beverages. JSFA reports. https://doi.org/10.1002/jsf2.229

 

 

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UP-Developed Model Maaaring Makatuklas ng Maagang Senyales ng Metastasis sa mga Pasyente ng Breast Cancer

UP-Developed Model Maaaring Makatuklas ng Maagang Senyales ng Metastasis sa mga Pasyente ng Breast Cancer

Published: June 02, 2025
By: Harvey Sapigao
Translated by: Dr. Ian Kendrich C. Fontanilla and Regina Joyce E. Ferrer

Si Regina Joyce Ferrer ng UPD-CS na sinusuri ang breast cancer organoids. (Kuha ni: Dr. Michael Velarde)

Sa Pilipinas, ang breast cancer ang pangunahing uri ng kanser sa kababaihan, na may mahigit 33,000 bagong kaso na naiulat noong 2022. Sa taon ding iyon, kumitil ito ng mahigit 11,000 buhay, kaya’t pumapangalawa sa lung cancer ang breast cancer sa sanhi ng pagkamatay sa bansa na may kinalaman sa cancer.

 

Kapag agresibo, ang breast cancer ay maaaring kumalat sa ibang bahagi ng katawan sa pamamagitan ng isang proseso na tinatawag na metastasis. Gayunpaman, bago ito mangyari, kinakailangan munang pasukin ng cancer cells ang mga ugat tulad ng lymphatic at blood vessels upang makarating sila sa iba’t ibang bahagi ng katawan. Ang kondisyong ito, na kilala bilang lymphovascular invasion (LVI), ay nagsisilbing maagang indikasyon ng metastasis para sa mga duktor. Sa kasalukuyan, ang LVI ay maaari lamang matukoy kapag tinanggal ang tumor sa isang operasyon at sinuri ang tissue na nakapalibot dito.

 

Pero ngayon, may mga biologist mula sa University of the Philippines (UP) ang nakabuo ng isang mathematical model na kayang tukuyin ang LVI sa mga pasyente ng breast cancer bago pa man sila sumalang sa isang operasyon. Ipinakita rin ng kanilang pag-aaral ang ugnayan ng LVI at drug resistance, na maaaring magpaliwanag kung bakit ang mga pasyente ng breast cancer na may LVI ay hindi gaanong gumagaling gamit ang anti-cancer drugs.

 

“If we can detect LVI earlier, doctors could personalize patient treatment and improve their outcomes. This could help avoid ineffective treatments and focus on strategies that work better for aggressive breast cancer,” ayon kay Dr. Michael Velarde, ang pangunahing mananalisksik ng grupo mula sa UP Diliman College of Science Institute of Biology (UPD-CS IB). [“Kung mas maaga nating matutukoy ang LVI, mabibigyan natin ang mga pasyente ng kaukulang paggamot para sa kanilang ikagagaling. Makakatulong ito upang maiwasan ang mga hindi epektibong paggamot at sa halip ay tumuon sa mga strategy na mas mabisa laban sa agresibong uri ng breast cancer.”]

 

Bukod kay Dr. Velarde, kasama sa pag-aaral sina Allen Joy Corachea, Regina Joyce Ferrer, Lance Patrick Ty, at Madeleine Morta ng UPD-CS IB, at mga mananaliksik mula sa Philippine Genome Center at UP Manila.

 

Bago ang operasyon, ang mga pasyente ng breast cancer ay binibigyan ng mga anti-cancer drug tulad ng doxorubicin at anthracyclines upang paliitin muna ang mga tumor. Kung minsan, nagiging mabisa ang droga at napapaliit ang tumor hanggang sa tuluyang mawala, kaya di na nangangailangang sumalang sa operasyon. Subalit maaari ring lumiit lang ang tumor pero di nawawala, kaya’t mangangailangan pa rin ng surgical removal. Dito lang malalaman ng mga duktor kung may LVI ang mga pasyente.

 

Mula sa clinical data na hinango sa 625 pasyente ng breast cancer sa Philippine General Hospital at maging sa pampublikong datos, napansin ng grupo ni Dr. Velarde na karamihan sa mga pasyenteng may LVI ay hindi rin gaanong gumagaling sa anti-cancer drugs.

 

Pinatunayan pa nila ang koneksyon sa pagitan ng LVI at drug resistance sa pamamagitan ng pagkuha ng mga tumor sample at pagpapatubo ng mga ito sa laboratoryo upang maging organoids – maliliit na tila organ na gumagaya sa tunay na mga organ. Ipinakita ng kanilang tests na ang mga organoid na positibo sa LVI ay hindi gaanong tumutugon sa mga anti-cancer drug kung ikukumpara sa mga negatibo sa LVI.

 

Natuklasan nila na may ilang enzymes pala ang sangkot sa paglusaw ng mga anti-cancer drug, gaya ng UGT1 at CYP enzymes, na nakitang mas marami sa mga pasyenteng may LVI. Kapag ang mga enzymes na ito ay mas marami, mas mabilis na nalulusaw ang mga anti-cancer drug, na nagpapababa sa kanilang bisa. Dahil dito, kapag mataas ang UGT1 at CYP enzymes sa mga pasyenteng ito, tataas din ang posibilidad na makaliligtas ang kanilang tumor at maaari pang kumalat sa ibang parte ng katawan.

 

Gamit ang mga kaalamang ito, nakabuo sila ng regression model na nagsusuri sa pag-express ng UGT1 at CYP genes sa mga biopsy ng pasyente bago sumalang sa operasyon. Tumugma naman sa 92% ang prediksyon ng kanilang modelo kapag ikinumpara sa resulta ng pagsusuri ng tissue mula sa surgery.

 

“Importantly, our approach can be implemented in the Philippines using locally available genomic technologies, making earlier detection and tailored treatment more accessible to Filipino patients,” dagdag pa ni Dr. Velarde. [“Ang mahalaga, maaaring ipatupad sa Pilipinas ang aming pamamaraan gamit ang locally available genomic technologies, upang mas mapabilis ang access at mapaaga ang paglapat ng personalized treatment sa mga pasyenteng Pilipino.”].

 

Gayunpaman, binanggit ni Dr. Velarde na nasa early stages of development pa ang kanilang model at hindi pa maaaring ipampalit sa nakagawiang paraan sa pagtuklas ng LVI. “More validation studies are needed before this can be used in clinics.” [“Mas marami pang pag-aaral ang kakailanganin bago ito tuluyang magamit sa mga klinika.”]

 

Plano rin ng grupo na i-validate ang kanilang mga resulta sa pamamagitan ng pagsubok sa mga gene signature sa mas maraming pasyenteng Pilipino na may breast cancer. Balak din nilang imbestigahan kung paano nauugnay ang UGT1 at CYP genes sa LVI upang matukoy ang mga kombinasyon ng gamot na mas epektibo para sa mga pasyenteng LVI-positive. “Our goal is to develop a practical test that can be used in Philippine hospitals to guide doctors in choosing the best treatment for each patient,” pagtatapos ni Dr. Velarde. [“Ang aming layunin ay makabuo ng isang praktikal na pagsusuri na maaaring gamitin sa mga ospital sa Pilipinas upang gabayan ang mga doktor sa pagpili ng pinakamahusay na paggamot para sa bawat pasyente.”

 

References:

Corachea, A. J. M., Ferrer, R. J. E., Ty, L. P. B., Aquino, L. A., Morta, M. T., Macalindong, S. S., Uy, G. L. B., Odoño, E. G., Llames, J. S., Tablizo, F. A., Paz, E. M. C. C., Dofitas, R. B., & Velarde, M. C. (2025). Lymphovascular invasion is associated with doxorubicin resistance in breast cancer. Laboratory Investigation, 104115. https://doi.org/10.1016/j.labinv.2025.104115

 

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UP-Developed Model Shows Promise in Detecting Early Signs of Metastasis In Breast Cancer Patients

UP-Developed Model Shows Promise in Detecting Early Signs of Metastasis In Breast Cancer Patients

Published: May 26, 2025
By: Harvey Sapigao

UPD-CS Biologist Regina Joyce Ferrer analyzing breast cancer organoids. (Photo credit: Dr. Michael Velarde)

In the Philippines, breast cancer is the most common type of cancer among women, with over 33,000 new cases reported in 2022. That year, it claimed more than 11,000 lives, making it the second leading cause of cancer-related mortality in the country, following lung cancer.

 

Aggressive breast cancers can spread to other organs, a process called metastasis. Before it does, however, the cancer cells must first invade the lymphatic and blood vessels, which enables them to travel to different parts of the body. This condition, known as lymphovascular invasion (LVI), serves as an early indicator of metastasis for doctors. Currently, LVI can only be detected by examining tissue surrounding the tumor that has been surgically removed.

 

Now, biologists from the University of the Philippines (UP) have developed a mathematical model that can detect LVI in breast cancer patients even before surgical treatment. Their study also revealed links between LVI and drug resistance, helping explain why breast cancer patients with LVI respond poorly to anticancer drugs.

 

“If we can detect LVI earlier, doctors could personalize patient treatment and improve their outcomes. This could help avoid ineffective treatments and focus on strategies that work better for aggressive breast cancer,” said corresponding author Dr. Michael Velarde of the UP Diliman College of Science Institute of Biology (UPD-CS IB).

 

Along with Dr. Velarde, the study’s authors are Allen Joy Corachea, Regina Joyce Ferrer, Lance Patrick Ty, and Madeleine Morta of UPD-CS IB, and researchers from the Philippine Genome Center and UP Manila.

 

Before surgery, breast cancer patients are given anticancer drugs such as doxorubicin and anthracyclines to shrink the tumors first. In some cases, the treatment is so effective that the tumors disappear completely, eliminating the need for surgery. In other cases, however, the tumors only shrink, requiring surgical removal. It is only after this procedure that doctors can determine if the patients have LVI.

 

From the clinical data of 625 breast cancer patients at the Philippine General Hospital, along with publicly available data, Dr. Velarde and his co-authors observed that the majority of patients with LVI also responded poorly to the anticancer drugs.

 

They further confirmed the link between LVI and drug resistance by collecting tumor samples and growing them in a lab into organoids – small, organ-like structures that mimic real organs. Their tests revealed that LVI-positive organoids were indeed less receptive to anticancer drugs compared to LVI-negative ones.

 

They discovered that certain genes involved in breaking down anticancer drugs, called the UGT1 and CYP genes, are more abundant in patients with LVI. When these genes are more abundant, the drugs are broken down more quickly, reducing their effectiveness. As a result, patients with high activity of UGT1 and CYP genes are more likely to have tumors that survive chemotherapy and eventually metastasize.

 

Using these insights, they developed a regression model that analyzed the expression patterns of UGT1 and CYP genes. Their model correctly predicted LVI status at the time of biopsy and before surgery 92% of the time.

 

“Importantly, our approach can be implemented in the Philippines using locally available genomic technologies, making earlier detection and tailored treatment more accessible to Filipino patients,” added Dr. Velarde.

 

However promising, Dr. Velarde noted that the model is still in its early stages of development and is not yet ready to replace current methods for diagnosing LVI. “More validation studies are needed before this can be used in clinics.”

 

The authors also plan to validate their results by testing the gene signatures of larger groups of Filipino breast cancer patients. They plan to further investigate how UGT1 and CYP genes are related to LVI to identify drug combinations that work better for LVI-positive patients. “Our goal is to develop a practical test that can be used in Philippine hospitals to guide doctors in choosing the best treatment for each patient,” concluded Dr. Velarde.

 

References:

Corachea, A. J. M., Ferrer, R. J. E., Ty, L. P. B., Aquino, L. A., Morta, M. T., Macalindong, S. S., Uy, G. L. B., Odoño, E. G., Llames, J. S., Tablizo, F. A., Paz, E. M. C. C., Dofitas, R. B., & Velarde, M. C. (2025). Lymphovascular invasion is associated with doxorubicin resistance in breast cancer. Laboratory Investigation, 104115. https://doi.org/10.1016/j.labinv.2025.104115

 

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UP Scientists Explore Marine Microbial Genomes from Mabini, Batangas

UP Scientists Explore Marine Microbial Genomes from Mabini, Batangas

Published: May 15, 2025
By: Eunice Jean C. Patron

Submarine groundwater discharge (SGD) is a process in which groundwater from land seeps into the ocean, transporting freshwater, nutrients, metals, and even pollutants into marine ecosystems. The diverse microbial communities in these SGD sites make them hotspots for biological and chemical activity, playing a crucial role in maintaining ecosystem balance. Studying these microorganisms helps scientists not only understand their impact on marine ecosystems, but also explore their potential applications in medicine and biotechnology.

While studies have primarily focused on its geological and physico-chemical aspects, scientists from the University of the Philippines – Diliman College of Science (UPD-CS) conducted the first detailed microbial genomic study of an SGD site in the country, uncovering the diversity and potential roles of microbial communities in Mabini, Batangas.

 

Collection of microbial mats for total DNA extraction to be followed by metagenomic sequencing and analysis. Photo credit: SGD Project 2: Marine Benthic Geochemistry and Ecosystems Associated with Submarine Groundwater Discharge (SGD)

Joshua Veluz, Paul Christian Gloria, Laurence Anthony Mallari, and Dr. Maria Auxilia Siringan of the Microbiological Research and Services Laboratory (MRSL) at the UPD-CS Natural Sciences Research Institute (NSRI), along with Ann Elizabeth Enova of the UPD-CS Marine Science Institute (MSI), reconstructed 17 metagenome-assembled genomes (MAGs) from microbial mats collected in Acacia, Mabini, Batangas. MAGs are genomes assembled from environmental samples without the need for cultivation and isolation.

 

“Our findings reveal diverse bacterial genomes with functional genes related to nutrient cycling, potentially supporting marine ecosystem health,” the researchers explained in an interview. Additionally, they identified biosynthetic gene clusters (BGCs) associated with the production of bioactive compounds. These BGCs enable microbes to produce antibiotics, anticancer agents, and other bioactive metabolites.

 

Their study underscores the vital role of microbial ecosystems in SGD sites, particularly in sustaining marine biodiversity and driving biogeochemical cycles. It also emphasizes the potential of these microbes to address the global demand for new antimicrobial agents.

 

“The baseline information and insights generated through our study are essential references in developing and establishing policies and regulations on environmental protection of our marine resources, such as those found in SGD-influenced sites in Mabini, Batangas,” the researchers said. They added that they also presented their findings and project outcomes to an audience of over 50 people at the Mabini Tourism Office, emphasizing the biodiversity in SGD-associated sites and providing recommendations. The meeting attendees included Mabini’s local government officials, tourism industry representatives, divers, and Bantay-Dagat members.

 

Submarine groundwater discharge observed at one of the Mabini sites. Photo credit: SGD Project 2: Marine Benthic Geochemistry and Ecosystems Associated with Submarine Groundwater Discharge (SGD)

“We are currently working on publishing the metagenomic data from other sampling sites, which will allow for broader comparisons across different SGD environments,” they shared. “We also aim to publish metabarcode data from these sites, which will provide a more comprehensive picture of bacterial diversity in SGD-influenced habitats.”

 

The paper, titled “MAGnificent microbes: metagenome-assembled genomes of marine microorganisms in mats from a Submarine Groundwater Discharge Site in Mabini, Batangas, Philippines,” was published in Frontiers in Marine Science, which features research on marine species, ecosystems, and processes as well as human interactions with, and impacts on, ocean environments.

 

This research is also one of the major outputs of MRSL’s three-year project, Probing Microbial Diversity in Submarine Groundwater Discharge (SGD) Areas, under the program, “Biodiversity and Resilience of Coral Reefs and Associated Ecosystems in Submarine Groundwater Discharges Areas (BioRe CoARE SGD)”, funded by the Philippine Council for Agriculture, Aquatic and Natural Resources (PCAARRD) of the Department of Science and Technology (DOST).

 

References:

Veluz, J. T., Gloria, P. C., Mallari, L. A., Enova, A. E., & Siringan, M. A. (2025). MAGnificent microbes: Metagenome-assembled genomes of marine microorganisms in mats from a submarine groundwater discharge site in Mabini, Batangas, Philippines. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1500350

 

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UP Study Identifies Potential Biomarkers for Early Lung Cancer Detection

UP Study Identifies Potential Biomarkers for Early Lung Cancer Detection

Published: April 28, 2025
By: Eunice Jean C. Patron

Graphical abstract of the study. (Photo credit: Dimayacyac-Esleta et al., 2025)

According to the International Agency for Research on Cancer, lung cancer is the leading cause of cancer-related deaths worldwide, with nearly 2 million deaths. In the Philippines in 2022, it recorded 23,728 new cases—making it the second most common cancer after breast cancer—and caused 20,953 deaths, the highest among all cancer types. Non-small cell lung carcinoma (NSCLC) is the most common type of lung cancer, accounting for more than 80% of cases. Experts say that late diagnosis and challenges in treating late-stage cases are the main factors affecting the cancer mortality rate, including NSCLC.


Biomarkers, which are essential measurable indicators in lung cancer management, help identify lung cancer subtypes, guide treatment options, and predict outcomes. The lack of biomarkers that can be used to detect NSCLC, and lung cancer as a whole, prompted scientists from the University of the Philippines – Diliman College of Science (UPD-CS) to identify potential biomarkers for lung cancer, specifically NSCLC lung adenocarcinoma (LUAD).


To address this challenge, Dr. Baby Rorielyn Dimayacyac-Esleta, Ferdinand Mira, Lara Beatrice Suñga, Venus Pondevida from the UPD-CS Institute of Chemistry (IC); Lorenzo Zarate, Ben Joshua Porras, Dave Laurence Juntilla, and Dr. Eloise Prieto of the UPD-CS National Institute of Molecular Biology and Biotechnology (NIMBB); and Dr. Sullian Naval, Dr. Treah May Sayo, and Dr. Herdee Gloriane Luna of the Lung Center of the Philippines (LCP) conducted a quantitative proteomics analysis to examine total protein levels in tumor and adjacent normal tissue specimens from early-stage Filipino NSCLC LUAD patients, identifying 4,403 proteins with irregular expression in tumors.


The identified proteins are linked to cancer and play an important role in protein translation, carbohydrate metabolism, and the hexosamine biosynthesis pathway. According to the research, disrupting these functions may drive NSCLC progression.

A total of 33 proteins were identified as potential diagnostic biomarkers. “These proteins have aberrant expression in both gene and protein levels, and their gene levels are correlated with poor 5-year survival rate of NSCLC patients,” Dr. Esleta explained, noting that these proteins were previously detected in tissues and/or in the blood plasma of NSCLC patients, highlighting their potential for clinical use.


The proteins that the team identified can now be prioritized for qualification, verification, and validation in the biomarker development pipeline. During the qualification phase, a large collection of specimens will be analyzed using a targeted proteomics technique. “These proteins can be tested for possible application in the diagnosis of NSCLC to complement existing diagnostic methods such chest radiography, low dose computed tomography (LDCT) scan, and bronchoscopic examination, and significantly enhance the accuracy and sensitivity of detection,” Dr. Esleta added.


Dr. Esleta and her team are currently working on the establishment of the targeted proteomics pipeline in IC’s Clinical Proteomics Laboratory to have the capacity of continuing the goal of providing diagnostic protein biomarkers in the clinic.


Their research paper, titled “Discovery of Key Candidate Protein Biomarkers in Early-Stage Non-small Cell Lung Carcinoma through Quantitative Proteomics,” is now included in the Journal of Proteome Research, a publication which reports on global protein analysis and function, including genomics, spatio-temporal proteomics, metabonomics and metabolomics, and clinical proteomics. Their work was supported by the Department of Science and Technology (DOST) and the Philippine Council for Health Research and Development (PCHRD).


References:

Dimayacyac-Esleta, B. R., Mira, F. D., Zarate, L. M., Porras, B. J., Juntilla, D. L., Suñga, L. B., Pondevida, V. B., Naval, S. S., Sayo, T. M., Luna, H. G., & Prieto, E. I. (2025). Discovery of key candidate protein biomarkers in early-stage Nonsmall cell lung carcinoma through quantitative Proteomics. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00764


Ferlay, J., Ervik, M., Lam, F., Laversanne, M., Colombet, M., Mery, L., Piñeros, M., Znaor, A., Soerjomataram, I., & Bray, F. (2024). Global Cancer Observatory: Cancer Today. Lyon, France: International Agency for Research on Cancer. Retrieved from https://gco.iarc.who.int/today

Majeed, U., Manochakian, R., Zhao, Y., & Lou, Y. (2021). Targeted therapy in advanced non-small cell lung cancer: Current advances and future trends. Journal of Hematology & Oncology, 14(1).


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