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 ( watanabe.kozo.mj@ehime-u.ac.jp ).

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.