I am Maria Angenica F. Regilme, or Nica for short, I am currently a PhD student in the MECOH laboratory. I joined the laboratory as a Research student in September 2016 as a Japanese government scholar and started my PhD program from 2018 April until present.
My PhD dissertation’s main goal is to use a wholistic approach of studying the relationship between the vector, host, microbiome including the pathogen and the environment to create a substantial information for an effective vector borne disease (VBDs) control. For my dissertation, I focused on the top VBDs: mosquito-borne diseases focusing on dengue mosquitoes, Aedes aegypti and Aedes albopictus and tick-borne diseases vectors, Ixodes ovatus and Haemaphysalis flava.
The overall objective of my dissertation is to know the gene flow pattern among arthropod vector (e.g. mosquitoes and ticks) populations can be influenced by environmental factors (e.g.roads and altitude) and the hosts affecting the pathogen transmission. The presentation is for 45 minutes followed by question and answer portion from the audience for 15 minutes and a close meeting with the thesis panelist: Kozo sensei, Kitamura sensei and Miyake sensei.
Finally, after more than 3 years I was able to present my thesis dissertation last 18 August, it was a hybrid style of thesis presentation wherein the thesis panelist are online via zoom while I present my thesis with my labmates in the seminar room. Before my presentation, I was nervous but I told myself to do my best because this is my only chance to get a PhD degree and to share the importance of my research to controlling vector-borne diseases. After the presentation and the question and answer portion, tears of joy fell into my eyes, I could only thank God, my family and friends, MECOH lab members (former and present), co-authors, collaborators, funding agencies and everyone who helped me in this PhD journey and most especially Kozo sensei for the support and guidance, without it, I will not be able to present my dissertation. I still don’t know the results of my thesis dissertation if I can be able to get the PhD degree. I can only hope that through God’s will I can get the degree and still continue doing research after PhD that can have an impact on improving the lives of people for example, research about tropical diseases.
My heart is full of gratitude to everyone who have helped me, almost 6 years of PhD journey is one of the most memorable moments in my life that shaped me to become a future scientist and taught me many learnings in my life. Again, thank you!
The AMR team (Prof. Kozo Watanabe, Prof. Satoru Suzuki, Yuichiro Shimada, Ryota Ueda, Ngure Kagia, and Kenneth Bongulto) went for another sample collection from wastewater treatment plants, river, and coastal area in Matsuyama, Ehime. The sample collection aimed to collect water samples and isolate environmental bacteria and test for antimicrobial resistance genes (ARGs).
Two different wastewater treatment plants were visited for the sampling. Water samples were collected from the wastewater influent and effluent. Environmental parameters were gathered per sampling site.
Water samples were also collected from the coastal area and river where the wastewater effluent flows out.
The AMR team (Prof. Kozo Watanabe, Yuichiro Shimada, Ryota Ueda, Ngure Kagia, and Kenneth Bongulto) collected wastewater samples from a pig farm last July 14, 2022. The aim of the sample collection is to isolate environmental bacteria and test for antimicrobial resistance genes (ARGs).
Wastewater samples were collected from three different sections (influent, sequencing batch reactor, and effluent basin) of the wastewater treatment system. Environmental parameters were also gathered per sampling site.
Environmental DNA (eDNA) sampling was performed again in Satsunai river, Hokkaido, Japan last July 6 to 10. Water samples for eDNA detection were collected from river and hyporheic zone. Macroinvertebrates both from benthic and hyporheic zones were also collected for morphological identification and DNA metabarcoding analysis.
Professor Negishi from Hokkaido University performs water sampling from the hyporheic zone of Satsunai river for eDNA detection of macroinvertebrates.
Water sample collected from the hyporheic zone were aseptically transferred to a sterile container for transport.
Dan a Research student from MECOH lab performs water collection from the Satsunai river for eDNA detection.
Dan together with the graduate students from Hokkaido University.
Dr. Levente-Péter Kolcsár (JSPS postdoctoral fellow) went on a field collection trip in the Japanese Alps, between 12-18 June. The aim of the trip was to collect crane flies (Diptera: Tipuloidea) along mountain rivers and streams for morphological and molecular studies. The main targeted group was a poorly known hairy-eyed crane fly genus (Tricyphona), in which several new species are suspected.
Dr. Daichi Kato from Echigo-Matsunoyama Museum of Natural Science, Matsunoyama, Niigata Pref. also joined the field collection between 14-16 June.
During the trip over 1200 specimens belonging to 150-160 species were collected.
Mr. Dan Joseph Logronio, a research student from the MECOH Lab performed eDNA collection in Satsunai river, Hokkaido, Japan last June 19 to assess macroinvertebrate communities both in benthic and hyporheic zones. DNA metabarcoding will be used for the identification of taxa present in the sample. This is a collaborative project with the Laboratory of Watershed Conservation and Management, Graduate School of Environmental Science, Hokkaido University headed by Dr. Junjiro Negishi.
Dr. Levente-Péter Kolcsár (JSPS postdoctoral fellow) went on a field collection trip to Okinawa Island, Japan between 24-31 May, 2022. The aim of the trip was to collect crane flies (Diptera: Tipuloidea) along different aquatic and wet habitats. The crane fly fauna of the island is poorly investigated, and many species new to science or new to Japan are suspected from Okinawa and surrounding areas.
During the trip around 550-600 specimens belonging to 52 species were collected, from which 14 suspected to be new to science.
Ngure Kagia from Kenya and Irish Coleen Asin from the Philippines joined the MECOH laboratory as new PhD candidates.
Ngure finished his MSc. in Bioinformatics at the University of Leicester- Leicester UK. He has previously worked in the wet and dry laboratory on antimicrobial resistance (AMR) projects in Kilifi, Kenya and Cambridge, UK. Ngure has also worked on measles virus isolation in Nairobi, Kenya. His future interest in the MECOH laboratory revolve around the dynamics of antimicrobial resistant bacteria (ARB) in our environment.
From the Philippines is Coleen who has obtained her Master of Science degree in Molecular Biology and Biotechnology at the University of the Philippines Diliman. She has worked on various research projects, one of which was surveillance of mosquito viruses thru mosquito viral metagenomics at UP Diliman. She has also worked on SARS-CoV-2 whole genome sequencing as a member of the Philippine Genome Center’s COVID-19 biosurveillance team. Going forward, she intends to focus and continue her research on mosquitoes and insect-specific viruses in the MECOH laboratory.
Khristina Judan Cruz (Karen) joins the MEcoH Lab as a postdoctoral fellow to do research work on the genome-wide signatures in genetically improved tilapia. She obtained her PhD in Biology at De La Salle University - Manila where she worked on the genetic characterization and gene expression analyses on Philippine genetically enhanced farmed tilapia. She plans to include comparative transcriptomics in her future projects. She is an Associate Professor at the Central Luzon State University, Science City of Munoz, Nueva Ecija, Philippines. Her research experience also includes integrating nanotechnology and bioactive compounds (nanobioapproach) for biomedical applications such as quorum sensing inhibition and anti-cancer action.
Kenneth and Dan are both new PhD candidates from the Philippines that recently joined the MECOH laboratory.
Kenneth obtained his MSc in Biology at the De La Salle University - Manila, where he worked on nontuberculous mycobacteria isolated from patients with multidrug-resistant pulmonary tuberculosis (MDR TB). He has been part of research projects which revolved around tuberculosis, HIV, and dengue. For his future research projects, he plans to explore on the acquisition and mechanism of antimicrobial resistance genes (ARGs) in both clinical and environmental bacterial strains.
Dan finished his Master`s degree in Genetics minor in Molecular Biology and Biotechnology at the University of the Philippines - Los Baños (UPLB). He worked as Research Assistant and Associate Researcher at Southeast Asian Fisheries Development Center / Aquaculture Department (SEAFDEC/AQD) in the Philippines for 7 years. His research experiences include aquaculture, fish health and fish genetics. For his future research projects, he plans to explore the applications of DNA metabarcoding, population genomics and transcriptomics for the conservation and management of aquatic resources.
Last March 7, the Molecular Ecology and Health Laboratory (MECOH) has moved to the General Research Bldg. 2, where the Division of Ecosystem Health Sciences of the Center for Marine Environmental Studies (CMES) is located. Although it was only a 150-meter away from its old home, we all worked hard together and managed to accomplish the mission. Now MECOH is part of CMES, both in name and in reality. The space is more than three times larger than before. It is very helpful because the number of people and lab equipment is increasing.
MECOH family is growing! Here are some photos of the new MECOH laboratories and its members.
Ph.D position is available for international student in the integrated research area of wastewater-based epidemiology and bioinformatics at Molecular Ecology and Health (MECOH) Lab of Ehime University, Japan (Application deadline: 30th April 2022)
Description of the position
The selected PhD candidate will work on wastewater-based epidemiology mainly targeting pathogenic viruses. WET Lab (e.g., DNA/RNA isolation and purification from wastewater, q-PCR) and DRY Lab research (e.g., Phylogenetic analysis, Next-generation Sequencing (NGS)-data processing) will be integrated; their weight balance will be determined based on the expertise and research interest of the candidate. Previous experiences with high-throughput data analysis (e.g., NGS bioinformatics), molecular laboratory analysis (DNA and RNA), and/or wastewater-based epidemiology (e.g., viral detection/quantification) is an advantage.
Examples of research topics include but not limited to:
Application deadline and start date of the position
Application and selection processes
Applicants are encouraged to send the files below to Prof. Kozo Watanabe by email ( firstname.lastname@example.org ).
If you have any questions regarding the said position, please contact the email address above.