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

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

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

 

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

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

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

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

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

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

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

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).


For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Biologists Investigate Multidrug-resistant Salmonella in Chicken

UP Biologists Investigate Multidrug-resistant Salmonella in Chicken

Published: April 25, 2025
By: Eunice Jean C. Patron

Biologists from the University of the Philippines Diliman – College of Science, Institute of Biology (UPD-CS IB) call for further and more in-depth surveillance of foodborne pathogens like the bacterium Salmonella in poultry products. Infections caused by Salmonella typically result in symptoms such as fever, abdominal pain, diarrhea, nausea, and sometimes vomiting, which usually appear 6 to 72 hours after ingestion of Salmonella, and can last 2-7 days.

 

There is a need for the Philippines to uncover circulating antimicrobial resistance genes (ARGs) that pose risks to food safety and public health. (Photo credit: Nagpala et al., 2025)

The rapid rise of multidrug-resistant (MDR) bacteria makes treating bacterial infections increasingly difficult, and the widespread use of antibiotics in agricultural, clinical, and residential environments leave few immediate solutions. MDR Salmonella is widely acknowledged as a major global public health issue, with scientists reporting the bacteria as one of the leading causes of diarrhea and outbreaks worldwide annually, including in the Philippines. As a large producer and consumer of meat, the Philippines faces a pressing need to monitor these potential threats, and explore the genome of MDR Salmonella to identify the most common types of Salmonella, assess their disease-causing abilities, and uncover circulating antimicrobial resistance genes (ARGs) that pose risks to food safety and public health.

 

Using whole genome sequencing (WGS) and phenotypic antimicrobial resistance (AMR) testing, Michael Joseph Nagpala, Jonah Feliza Mora, Rance Derrick Pavon, and Dr. Windell Rivera from the Pathogen-Host-Environment Interactions Research Laboratory (PHEIRL) of the UPD-CS IB examined the genetic makeup and AMR of Salmonella collected from chicken meat, the second most consumed meat in the country, sold in retail wet markets across Metro Manila.

 

The most predominant type of Salmonella was Infantis, followed by Brancaster, Anatum, London, Uganda, and Derby, all of which possessed diverse virulence and resistance genes. High levels (>45%) of multidrug resistance were observed when tested against antimicrobial panels, with a total of 50 ARGs detected, conferring resistance to 12 different drug classes. Numerous plasmids — small, circular DNA pieces that play a vital role in spreading resistance — were also identified in some types of Salmonella.

 

“Our study suggests a need for proper surveillance of contaminating bacteria as well as regulations on antimicrobial use at the farm level, as infections from MDR Salmonella, especially among vulnerable populations and from highly virulent serovars (types of Salmonella), can lead to life-threatening, systemic, and untreatable manifestations,” the team said.

 

The biologists further emphasized that there is a clear and significant risk of MDR Salmonella variants spreading within wet markets and food animal value chains, as well as the potential for cross-contamination and undetected transmission in kitchens and homes.

 

“Mitigating this concern requires multi-sectoral policies, regulations, and standards—especially regarding proper antibiotic use, increased awareness of AMR and MDR at the farm, clinical, and community levels, and support for research and development of antimicrobial alternatives, and surveillance of foodborne pathogens and resistance,” the team concluded.

 

The study was supported by the Department of Agriculture-Biotechnology Program Office.

 

 

References:

Mora, J. F., Meclat, V. Y., Calayag, A. M., Campino, S., Hafalla, J. C., Hibberd, M. L., Phelan, J. E., Clark, T. G., & Rivera, W. L. (2024). Genomic analysis of Salmonella enterica from metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes. Frontiers in Microbiology, 14. https://doi.org/10.3389/fmicb.2023.1304283

 

Nagpala, M. J., Mora, J. F., Pavon, R. D., & Rivera, W. L. (2025). Genomic characterization of antimicrobial-resistant Salmonella enterica in chicken meat from wet markets in Metro Manila, Philippines. Frontiers in Microbiology, 16. https://doi.org/10.3389/fmicb.2025.1496685

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Scientists Analyze Thin Films Deposited with Femtosecond Pulsed Laser

UP Scientists Analyze Thin Films Deposited with Femtosecond Pulsed Laser

Published: April 23, 2025
By: Eunice Jean C. Patron

Traditional pulsed laser deposition (PLD) methods typically use high-energy lasers with nanosecond-long pulses. Inspired by this, scientists from the University of the Philippines – Diliman College of Science (UPD-CS) challenged the conventional approach by using a lower-energy femtosecond laser with nanojoule pulse energy.

 

UPD-CS scientists examined how thin films of the high-temperature superconductor BSCCO (bismuth strontium calcium copper oxide) are formed using a low-energy femtosecond pulsed laser. (Photo credit: Joy Kristelle De Mata)

Joy Kristelle De Mata and Dr. Lean Dasallas of the UPD-CS Materials Science and Engineering Program (MSEP), along with Dr. Roland Sarmago and Dr. Wilson Garcia of the UPD-CS National Institute of Physics (NIP), examined how thin films of the high-temperature superconductor BSCCO (bismuth strontium calcium copper oxide)—commonly used in power cables, generators, and magnets—are formed using a low-energy femtosecond pulsed laser.

 

Key Challenges and Expectations

“A key challenge in this process is maintaining the stoichiometric ratio of elements in the film, as deviations can significantly impact material properties,” De Mata explained in an interview. To understand the process better, their team studied how varying the type and pressure levels of the background gas affect the thin film’s composition and how evenly the material spreads.

 

The scientists discovered that using low-energy femtosecond PLD (fs-PLD) at high gas pressure does not fully replicate the composition of the original material. Existing computational models commonly used in PLD, which predict how materials spread during deposition, did not accurately explain these differences. This suggests that the fs-PLD process is more complex than expected, highlighting the need for improved models to enhance thin film production for real-world applications.

 

“Our results demonstrate that the background gas type and pressure significantly influence film composition,” De Mata added. “While fs-PLD offers advantages over nanosecond-PLD, achieving correct stoichiometry in thin films remains challenging, necessitating further optimization of deposition conditions.”

 

Industrial applications of fs-PLD

De Mata emphasized that while the fs-PLD process shows promise, it is not yet fully scalable for industrial applications, such as electronics, due to several limitations. The mismatch between the elements in the deposited thin film and the original material can lead to inconsistencies in mass production. Additionally, because fs-PLD uses low energy, the deposition process is slower, making large-scale manufacturing more costly.

 

“Despite these challenges, fs-PLD remains a valuable technique for high-quality thin film fabrication in research and specialized applications,” she said. Moving forward, the team plans to study other factors, such as substrate heating, to see how temperature affects the thin film. “The current models used do not fully account for the observed deviations in film composition. We aim to refine these models for greater applicability to fs-PLD.”

 

References:

De Mata, J. K., Sarmago, R., Garcia, W., & Dasallas, L. (2025). Spatial variation of the elemental components of thin films from BiSrCaCuO target deposited using low energy femtosecond pulsed laser deposition in high background gas pressure. Journal of Vacuum Science & Technology B, 43(2). https://doi.org/10.1116/6.0004082

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Scientists Develop Advanced Impact-Based Flood Forecasting System

UP Scientists Develop Advanced Impact-Based Flood Forecasting System

Published: April 14, 2025
By: Eunice Jean C. Patron

The massive floods that tropical cyclones bring now demand urgent and science-based decision-making.

 

The Impact-Based Flood Forecasting System determines specific areas in the Philippines that are most likely to be affected by severe flooding. (Photo credit: Dr. Alfredo Mahar Lagmay)

Considered one of the most devastating natural hazards globally, floods pose critical threats to both human life and economic stability. The Philippines is no stranger to flooding, as approximately 20 tropical cyclones enter the Philippine Area of Responsibility (PAR) each year. According to the 2023 World Risk Index Report, the country also ranks first among those most affected by extreme weather events.

 

Dr. Alfredo Mahar Lagmay, a professor at the University of the Philippines – Diliman College of Science’s National Institute of Geological Sciences (UPD-CS NIGS) and executive director of the UP Resilience Institute (UPRI), together with scientists from the UPRI Nationwide Operational Assessment of Hazards (NOAH) Center and Dr. Gerry Bagtasa of the UPD-CS Institute of Environmental Science and Meteorology (IESM), with assistance from Dr. Bernard Alan Racoma of IESM and in partnership with the Academic Alliance for Anticipatory Action (4As), developed an impact-based flood forecasting system capable of predicting flooding in the entire Philippines. The system was funded by the United States Agency for International Development’s Bureau for Humanitarian Assistance (USAID-BHA).

 

“This system can determine whether a neighborhood is likely to be affected by a major flood event 24 hours in advance,” Dr. Lagmay explained, noting that the system was able to forecast the flooding in Davao, Palawan, and Borongan this year. “When accessed on the NOAH website, areas prone to flooding due to severe weather are shown in map view or tabular format, with the number of potentially affected people listed down to barangay level.”

 

The tool can forecast flooding in specific areas based on accumulated rainfall forecasts (predicted total rainfall) and 100-year rain return flood hazard maps, which are maps showing areas prone to severe flooding based on historical data. By adjusting global weather models to match the country’s specific geography and weather patterns, the system releases predictions that are more accurate.

 

The Impact-Based Flood Forecasting System was released in 2024 and has been available for public use since then. The system empowers Filipino citizens by enabling them to validate the data it provides. “The public can contribute information through the LyfSaver app, allowing FIlipinos to report floods in their area.” Dr. Lagmay added.

Dr. Lagmay and his team also collaborated with other organizations, such as the FYT PH Media’s crowdsourcing platform, YesPinoy’s disaster response training program, and the Quezon City Disaster Risk Reduction and Management Office, as well as the Public Affairs and Information Services Department, to integrate the automated system’s features into other components of disaster risk reduction and management.

 

The team won best innovation pitch among 64 entries nationwide in the Preparedness and Response Excellence in the Philippines (PREP) Innovation Challenge. (Photo credit: Dr. Alfredo Mahar Lagmay)

In the paper where they talked about the system, published in the Asian Journal of Agriculture and Development (AJAD), the scientists acknowledged that the system has achieved some level of success, it is just the beginning of a larger process. They emphasized that further development of the tool’s functions, collaborations among citizens and stakeholders, and good governance are essential for improving disaster risk reduction and management in the country.

 

“After winning the best innovation pitch among 64 entries nationwide in the Preparedness and Response Excellence in the Philippines (PREP) Innovation Challenge, we will add more hazards such as rain-triggered landslides and possibly storm surge hazards to the forecasting system,” Dr. Lagmay shared. The PREP challenge was organized by the United Nations World Food Programme (WFP) and the USAID, which seeks to identify and scale innovative and cost-effective solutions to enhance disaster preparedness and food security for vulnerable populations in the Philippines.

 

Citizens can donate to support this effort through this link

 

References:

Lagmay, A. , Bagtasa, G. , Andal, D. , Andal, F. , Aldea, J. , Bencito, D. , and K. Liporada. 2024. An Impact-Based Flood Forecasting System for Citizen Empowerment. Asian Journal of Agriculture and Development (AJAD) 21(20th Anniversary Issue):p. 129–148.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Physicist Among Winners of Prestigious Breakthrough Prize in Fundamental Physics

UP Physicist Among Winners of Prestigious Breakthrough Prize in Fundamental Physics

Published: April 10, 2025
By: The ATLAS Collaboration

Dr. Marvin Flores, Assistant Professor of the University of the Philippines – Diliman College of Science National Institute of Physics (UPD-CS NIP) and the Team Leader of the ATLAS group based in the Philippines, is among the thousands of researchers worldwide honored with the 2025 Breakthrough Prize in Fundamental Physics, awarded to the A Toroidal LHC ApparatuS (ATLAS) Collaboration at the Conseil Européen pour la Recherche Nucléaire (CERN)’s Large Hadron Collider (LHC) alongside its sister experiments A Large Ion Collider Experiment (ALICE), Compact Muon Solenoid (CMS), and Large Hadron Collider beauty (LHCb).

 

Dr. Flores at the LHC Detector. (Photo credit: Dr. Marvin Flores)

ATLAS is one of the largest and most complex scientific instruments ever built. As a general-purpose particle detector measuring over 40 metres in length and around 25 metres in height, it was designed to investigate the fundamental building blocks of matter and the forces governing our universe. Its cutting-edge systems track particles produced in particle collisions at unprecedented energies, enabling discoveries like the Higgs boson and searches for new physics beyond the Standard Model.

 

The Breakthrough Prize specifically highlights the ATLAS Collaboration’s significant contributions to particle physics, including detailed measurements of Higgs boson properties, studies of rare processes and matter-antimatter asymmetry, and the exploration of nature under the most extreme conditions.

 

“The Breakthrough Prize is a testament to the dedication and ingenuity of the ATLAS Collaboration and our colleagues across the LHC experiments,” said ATLAS Spokesperson Stephane Willocq. “This prize recognises the collective vision and monumental effort of thousands of ATLAS collaborators worldwide.” 

 

UPD-CS NIP has been at the forefront of ATLAS research since 2021, contributing to the search for new physics beyond the Standard Model (BSM).

 

“Our team’s work on BSM modelling and simulation exemplifies the innovation driving ATLAS forward,” said Dr. Flores. “This recognition affirms the impact of our contributions and inspires us to continue exploring the universe’s most fundamental questions.”


“The successes of Run 2 showcase the ingenuity of the ATLAS Collaboration — not only in collecting data with a detector of outstanding precision, but also in our relentless drive to improve our understanding of it,” said Andreas Hoecker, former ATLAS Spokesperson.

 

While the ATLAS Collaboration celebrates the recognition of the Breakthrough Prize, its focus remains firmly on the future. The third operation period of the LHC is currently underway and preparations for the High-Luminosity LHC upgrade are advancing rapidly. NIP’s High Energy Physics & Phenomenology (HEP-PH) team of 15 physicists and students is deeply involved in preparing ATLAS for its next chapter. Although their current contributions are currently in the theoretical and phenomenological side, the team is ramping up their experimental involvement through concrete steps like the formation of the ATLAS Philippine Cluster involving other Philippine universities.

 

“We are now preparing the ATLAS detectors of the future — designed to harness this unprecedented data and further push our understanding of the universe’s fundamental building blocks,” concludes Willocq.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.