​Dr. Shinji Takahashi from Tohoku University, together with the Molecular Ecology and Health Laboratory members Mr. Arthien Pelingen (Researcher), Mr. Karim Clivaz (M2), and Mr. Tsubasa Moriya (B4), collected environmental DNA (eDNA) and macroinvertebrates from Tenryu River, Shizuoka Prefecture on November 9-11, 2022.

​This recently concluded field work also serves as a follow-up of the August collection trip this year (Read here: collaborative-fieldwork-of-three-universities-in-kizu-and-tenryu-rivers.html). Accordingly, we focused on (1) identifying Ayu (Plecoglossus altivelis altivelis) spawning sites and on (2) observing macroinvertebrate distribution in relation to the riverine spatial habitat diversity. 

​On this three-day activity, we have successfully confirmed spawning of Ayu this season and positively identified different habitat types as we recorded various environmental parameters such as water temperature, pH, turbidity, etc. to be correlated in several macroinvertebrate studies.

Ehime University-Center for Marine Environmental Studies (EU-CMES) represented by the head of the Molecular Ecology and Health (MEcoH) Laboratory, Dr. Kozo Watanabe and JSPS Postdoctoral Fellow Dr. Khristina Judan Cruz visited the Central Luzon State University, Science City of Munoz, Nueva Ecija, Philippines last October 12-13, 2022 for initial talks on the establishment of an EU satellite office in CLSU as well as the possibility of a cross-appointment of CLSU faculty members to EU. Dr. Watanabe and Dr. Judan Cruz discussed future EU-CLSU activities with CLSU President Dr. Edgar A. Orden, Vice President for Academic Affairs Dr. Renato G. Reyes, Dean of the College of Science Dr. Evaristo A. Abella, Dean of the College of Fisheries Dr. Ravelina R. Velasco and Director for Freshwater Aquaculture Center-CLSU Dr. Karl Marx A. Quiazon. A Memorandum of Understanding between the two universities was signed last January 22, 2022 to establish and strengthen International Collaboration for academic and research activities.
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​​Dr. Watanabe also visited several research projects and facilities in CLSU such as the CLSU Nanotechnology Facility and the Freshwater Aquaculture Center. The visit coincided with the CLSU Research Innovation and Development (RIDe) Festival that highlighted quality outputs of the university’s research and development  projects.

​Current research collaboration between MEcoH and CLSU includes the genome-wide scan of genetically-improved tilapia particularly the FaST strain developed by CLSU, and integrating nanotechnology with bioactive compounds for anti-quorum sensing and anticancer evaluations.

​Dr. Kozo Watanabe, head of the Molecular Ecology and Health (MEcoH) Laboratory, Ehime University (EU), together with Dr. Yasutsugu Suzuki (Project Associate Professor) and Ms. Irish Coleen Asin (PhD candidate) from the same laboratory visited the National Institute of Molecular Biology and Biotechnology (NIMBB), University of the Philippines Diliman (UP Diliman), Quezon City, Philippines last October 10, 2022. 

​The representatives from Ehime University as well as Dr. Thaddeus Carvajal, Associate Professor at De La Salle University, met with Dr. Ma. Anita Bautista, Professor and Principal Investigator of the Functional Genomics Laboratory (FGL) of NIMBB-UP Diliman, for a talk on possible future collaboration between Ehime University and NIMBB. Also present in the meeting were Ms. Adria Lao (PhD candidate), Ms. Coleen Pangilinan (MSc candidate), and Mr. Aldwin Adiong (BSc candidate) of FGL-NIMBB who have presented their past and current research works on mosquito viral metagenomics and metatranscriptomics. Overall, this kick-off meeting provided an opportunity to build good rapport from both sides, and to set out and discuss various areas for collaborative work on mosquito research projects.

​Dr. Watanabe, Dr. Suzuki, and Ms. Asin have also been a given a tour of the facilities of NIMBB as well as the University of the Philippines System – Philippine Genome Center during this fruitful visit.

Representatives from Ehime University (EU) and De La Salle University (DLSU) celebrated the official opening of the EU-DLSU International Collaborative Research Laboratory (ICRL) located at the George S.K. Ty Advanced Instrumentation Bldg, DLSU Laguna Campus on Tuesday morning, 11 October 2022. The ribbon-cutting ceremony was led by Dr. Kozo Watanabe, Professor of Molecular Ecology and Health (MEcoH) Laboratory at the Center for Marine Environmental Studies (CMES), EU, and Dr. Jonathan Dungca, Vice President for Laguna Campus and Dean of the College. Also present were Dr. Divina Amalin, Director of the Center for Natural Sciences and Environmental Research (CENSER), Drs. Ma. Luisa Enriquez, Mary Jane Flores, Thaddeus Carvajal, faculty members at the Department of Biology, DLSU, and members of the Biological Control Research Unit, CENSER. Also present are Dr. Yasutsugu Suzuki, Associate Professor of EU-CMES, and Ms. Irish Coleen Asin, PhD candidate from UE-CMES.

​The ceremony was followed by a tour of the facilities at the ICRL. The laboratory is equipped with advanced research infrastructure in line with its vision to “be the leading research unit dedicated to advancing, applying and facilitating high standards of research practice for Philippine and Japanese students, faculty and staff of both universities.” Under the mentorship of recognized scientists from EU and DLSU, the ICRL will provide a hub in conducting high-quality collaborative research between Filipino and Japanese students, faculty, and staff.

​A seminar session was also conducted wherein Dr. Kozo Watanabe first discussed the functions and roles of the EU-DLSU ICRL. Dr. Thaddeus Carvajal and Dr. Yasutsugu Suzuki also delivered their talks on “The Importance of Studying Vector Biology & Ecology of Mosquito-borne Diseases for Designing Appropriate Vector Control Strategies” and “Understanding Mosquito-virus Interactions Toward Vector Control”, respectively. The seminar was livestreamed and was attended by participants online.

​The ICRL is a product of a long standing cooperation between the two universities that started in 2016. In October 21, 2021, the Memorandum of Agreement was signed by Dr. Nishina Hiroshige, President of EU, and Br. Bernard Oca, President of DLSU, to start the establishment of ICRL (then known as the Ehime University Satellite Office Philippines). Currently, the ICRL implements several privately and publicly funded research projects, and houses the Center for Vector of Diseases of Public Health Importance in the Philippines for Region IV, a niche center under the DOST Science for Change Program.

​On 17th - 22nd September 2022, Professor Kozo Watanabe visited two universities in Bangladesh -Dhaka University, at Dhaka city and Mawlana Bhashani Science and Technology University (MBSTU), at Tangail city. Professor Watanabe attended in several meetings and seminars organized by both universities and discussed about the possible way of future collaborations. 

Mohamad Mosleh Uddin, a PhD student of MECoH lab went Bangladesh (22nd August -28th September, 2022) for his sampling purpose. He collected mosquito samples from the Dhaka City area.

Along these large rivers, different habitat types were identified, inspected, and compared with one another. Despite the scorching heat, the fieldwork was successful as samples for several projects were collected including macroinvertebrates and eDNA.

​At the start of August 2022, Art from the Philippines joined the MEcoH Lab as the newest PhD student. Emerging from a rigorous taxonomic training of Philippine macroinvertebrates during his Master’s in the Ateneo de Manila University (AdMU), Art will explore combined ecological and genomic approaches in studying the stream macroinvertebrates i.e. how the abiotic factors and genetic similarities and/or differences play into their roles in the river dynamics. With these in sight, he envisions to contribute into an interdisciplinary understanding of addressing the changes in current environmental patterns using macroinvertebrates as models.

Some poorly known species collected during the field trip.

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).

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. 

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​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.
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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.

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.

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Dan

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. 

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:

• Develop machine-learning based techniques to detect viruses suspected to be highly infectious to humans or other vectors from genome sequences of known and unknown exhaustive viruses collected from sewage or river water in Japan and developing countries in Asia.
• Establish a surveillance system for DNA/RNA sequences of exhaustive viruses collected from wastewater and to enrich epidemiological information on diverse pathogenic and potentially pathogenic viruses in in Japan and developing countries in Asia.

 
Application deadline and start date of the position

• Application deadline: the 30th April, 2022.
• Start date of the position: Between June 2022 – October 2022 (flexible and late start also negotiable)

 
Eligibility

1. Only non-Japanese nationals are eligible to apply for this position (Japanese nationals are not eligible).
2. There is no age limit.
3. Master's degree in related fields (e.g., molecular biology, environmental science, bioinformatics, microbiology, virology) is required before the start date of the said position (not by the time of application).

 
Contract details

• Duration of contract: Maximum of 4 years and 6 months.

• Full financial support (stipend, tuition, and round-trip ticket) is guaranteed by MECOH’s research projects, and can also be complemented by additional support from scholarships from private foundations in Japan.
• The candidate should be able to work independently, with very good or excellent English communication skills, and can work harmoniously with a team of multi-disciplinary field.
• The successful PhD candidate will also have the chance to study outside of Japan (e.g., Germany, Switzerland, and the USA) for a short period of time (1-2 months) with an additional financial support from the MECOH Lab, under the international collaborative framework of the lab.

 
Application and selection processes
Applicants are encouraged to send the files below to Prof. Kozo Watanabe by email ( [email protected] ).

1. CV (any format)
2. Application letter within 3 pages that explains the applicant’s past research activities and motivation to study in the MECOH lab (any format)
3. PDF of the published paper/s if the applicants have any reviewed Journal publication/s.

 

• Applicants will receive an acknowledgement email from Prof. Watanabe within one week from the application date (not immediate response). If the applicants don't receive any reply, please contact Prof. Watanabe again for your confirmation.
• Shortlisted applicants will be requested for online interview (PPT based presentation and QA). Details will be provided via email.
• Unsuccessful candidates will be notified by Prof Watanabe via email.

 
If you have any questions regarding the said position, please contact the email address above.