eDNA
WORKSHOP
The First International Environmental DNA (eDNA) Workshop in Hong Kong
The University of Hong Kong
16 - 27 October 2023
Registration
Registration is closed
Description
Environmental DNA (eDNA) is a new and rapidly growing field of science focused on the development and application of eDNA across a wide range of research disciplines including conservation biology, ecology, and environmental sciences. eDNA is DNA extracted indirectly from environmental samples (e.g. water or soil) and can be used to survey all levels of biological diversity (i.e. fish, birds, insects, protist, virus) from individual samples. This powerful approach has led to a global revolution in how environmental data are collected and subsequently analysed, including implementation of eDNA for government applications and policies, and serving as the basis for multi-million-dollar companies. Hong Kong, along with the neighbouring region has seen an uptick in eDNA interest in recent years, however the current progress of application of eDNA is far behind global achievements. To facilitate Hong Kong’s eDNA progress, increased coordinated efforts to educate and direct research efforts are needed.
The First International Workshop on Environmental DNA (eDNA) brings participant face-to-face with leading international eDNA experts at The University of Hong Kong to provide a broad overview of the approaches used in eDNA studies. Information will be disseminated to participants through a series of subject lectures, field and laboratory demonstrations. No previous experience with eDNA, genetics or molecular biology is required for participation.
Outcome
At the end of the workshop, you’ll be able to:
Design your own eDNA study
Understand the fundamentals of
Conducting eDNA research
Metabarcoding for eDNA applications
Bioinformatics pipeline for processing high throughput sequence data
Conduct field and laboratory procedures for single and multi-species studies
Synthesize and publish eDNA generated data and findings.
Target audience
Postgraduate students (MPhil, PhD students), early career researchers (e.g. post-docs) and senior researchers with a desire to integrate eDNA methodologies into their research.
Agenda
Week 1
Introduction to eDNA and current state of the field
Providing an initial overview of eDNA terminology and associated fields, applications and common pitfalls researchers face.
Field trip for hands on eDNA sampling
Including necessary precautions for preventing contamination, use of field blanks in sampling design and sampling of different eDNA sources.
Introduction metabarcoding for eDNA based research
Providing an overview of the molecular method, i.e., how to design species specific primers, following international standards for reporting primer specifications, and applications for eDNA research. Understanding the pitfalls and obtacles.
Metabarcoding laboratory session
Hands on library prepration practice. Overview of the 2-step library preparation procedure.
Group Dinner and networking event with the broader committee
Week 2
Introduction to bioinformatics and initial data exploration
Coding basics, quality checking of raw sequence data, preliminary data assessment procedures
Taxonomic assignments of sequencing reads
Reference database overview, pitfalls and obstacles, taxonomic assignment procedures, introduction to biostatistics and data analyses
Data visualization using R
Introduction to R and ggplot2 package for visualizing eDNA metabarcoding data
Data analysis and manuscript drafting
Week two will include incorporation of data from a recent eDNA study that will be jointly analyzed and prepared for publication by the participating members
Instructors
Dr. Micaela Hellstrom
MIX Research,
Sweden
www.mixresearch.se micaela@mixresearch.se
Dr. Matthieu Leray
Smithsonian Institute,
Panama
Dr Micaela Hellström is a senior scientist, CEO, advisor, and founder at MIX Research Sweden AB. She holds a PhD in applied genetics and ecotoxicology with over 30 years’ experience in DNA and eDNA method development and research coordincation. MIX Research provides senior project leadership within consultancy and academia on applied genetics, eDNA and conservation projects, and and adivisory between government, industry, and citizen science groups.
Dr Hellström is actively engaged internationally, including serving as a member of the EU COST Action project DNAquaNet, and having established genetics’ labs in Sweden, Belgium, Vietnam, Thailand and Indonesia. She has also fine tuned and developed several eDNA field and laboratory protocols and developed eDNA extraction methods and the first CEN eDNA field-sampling standard as a member of the steering group for the Swedish eDNA standards SIS. She has supervised more than 50 university students and authored more than 60 reports for the Swedish government, 20+ peer reviewed scientific publications (1050 citations) and 50+ conference abstracts.
Dr. Matthieu Leray is an early career staff scientist at the Smithsonian Tropical Research Institute (STRI) in Panama. Using both broad-scale environmental sampling and experimental manipulations of small-scale model systems, he focuses in particular on the following three questions: What are the nature and causes of biodiversity patterns in the ocean? How do these biodiversity patterns influence ecosystem function? How do ecological interactions (i.e., trophic and symbiotic) evolve and promote the stability and resilience of marine communities? In the past three years he has led a multidisciplinary and highly collaborative research program funded by the Gordon and Betty Moore foundation that investigates the evolution and functional roles of bacteria, archaea, viruses and other microbes associated with marine animals of plants separated by the isthmus of Panama ~3 million years ago.
Dr. Gert-Jan Jeunen
University of Otago,
New-Zealand
Dr. Vasco Elbrecht
Leibniz Institute,
Germany
Dr Gert-Jan Jeunen is a Research Fellow at the University of Otago. His research is funded through the Royal Society of New Zealand and focuses on environmental and ancient DNA applications in Antarctica and the Southern Ocean. Dr Jeunen is currently working on a variety of projects, including (i) investigating ecosystem shifts in the Southern Ocean through historical eDNA obtained from marine sponge specimens stored in scientific collections, (ii) examining dietary changes of Antarctic apex predators induced by alterations in the food web through a metabarcoding approach, and (iii) developing software applications on curated reference database creation and primer design to facilitate metabarcoding analysis.
Dr. Vasco Elbrecht is passionate about development of molecular methods. He contributes to the research on biodiversity detection from bulk samples to environmental DNA by combining his hands on laboratory experience with his bioinformatics programming skills. After completing his PhD at the University of Duisburg Essen (DE), he spend 2 years as a Postdoc at the Biodiversity Institute of Ontario in Guelph (CA) continuing his work on method validation. He then started his own Jr. research group at the Museum König in Bonn (DE) to develop Nanopore sequencing based eDNA methods. By processing and sequencing samples at the point of collection, the need for specialised laboratory infrastructure is reduced, thus democratising the detection of biodiversity. For many years Dr. Elbrecht was also involved with industry as a consultant or Startup co founder, and decided recently to peruse this more applied avenue full time. As an application specialist he now helps to scale Next Generation Sequencing protocols by bringing them onto Hamilton liquid handling systems.
Dr. Mathew Seymour
The University of Hong Kong,
Hong Kong
Dr. Isis Guibert
The University of Hong Kong,
Hong Kong
About eDNA
Non-invasive & Cost effective
Environmental DNA (eDNA) is DNA isolated from environmental samples without directly sampling whole, multicellular, organisms. eDNA sampling has drastically increased the application of eDNA analysis as a non-invasive and cost effective assessment tool. It is a non-invasive, rapid and cost-effective alternative to traditional biodiversity sampling
Impact on environmental sciences, medicine, agriculture, forensics, evolution and molecular ecology
The discovery of environmental DNA (eDNA), is drastically altering scientific thought leading to many major advancements and creation of interdisciplinary research within the fields of environmental sciences, medicine, agriculture, forensics, evolution and molecular ecology.
Applicable to all levels of biological diversity (i.e. fish, birds, insects, protist, virus)
eDNA is DNA extracted indirectly from environmental samples (e.g. water or soil) and can be used to survey all levels of biological diversity (i.e. fish, birds, insects, protist, virus) from individual samples. This powerful approach has led to a global revolution in how environmental data are collected and subsequently analyzed, including implementation of eDNA for government applications and policies, and serving as the basis for multi-million-dollar companies.
eDNA based research philosophy, study design and execution with emphasis on metabarcoding utilization
Given the extensive, and growing, range of eDNA research applications, analyses and methodologies, it can be quite intimidating to even begin an eDNA based project. This workshop will therefore introduce eDNA based research philosophy, study design and execution with emphasis on metabarcoding utilization.
Sponsors & supporters
Croucher Foundation
eDNA & eEcology Lab
The eDNA collaborative
Committee
Dr. Mathew Seymour – School of Biological Sciences – The University of Hong Kong
Dr. Isis Guibert - Swire Institute of Marine Science - The University of Hong Kong
Dr. David M. Baker - Swire Institute of Marine Science - The University of Hong Kong
Dr. Shelby McIlroy - Swire Institute of Marine Science - The University of Hong Kong
Prof. Kenneth Leung – State Key Laboratory of Marine Pollution – City University of Hong Kong
Dr. Meng Yan – State Key Laboratory of Marine Pollution – City University of Hong Kong
Prof. Jianwen Qiu – Department of Biology – Hong Kong Baptist University
Dr. Jerome Hui – School of Life Sciences – The Chinese University of Hong Kong
Dr. Jonathan J. Fong – Science Unit - Lingnan University
Dr. Anthony Lau – Science Unit – Lingnan University
Dr. Chi Chiu Cheang – Department of Science and Environmental Studies – EdUHK
Dr. Matthieu Leray - Smithsonian Tropical Research Institute, Panama
Dr. Micaela Hellström - CEO of MIX Research Sweden AB, Sweden
Dr. Gert-Jan Jeunen - University of Otago, New Zealand
Dr. Vasco Elbrecht – Leibniz Institute, Germany
Visiting Information
Hotel/accommodation
HKU is located in the Island side of Hong Kong. We recommend our participants to choose the accommodation near HKU or in the island side for easier travel and saving time. The CEDARS of HKU has prepared a list of hostels and hotel near HKU for guests’ consideration, please find: List of hostel and hotel near HKU. We have selected a few to show below so you can have a preview of hotels in Hong Kong.
For official visitors of the university, current staff or students, our halls also provide guest rooms for temporary accommodation. The charge is around $400hkd/night. The numbers of guest room are limited, and bookings are on first come first serve basis. Please contact the hall office directly for reservation and other arrangements:
Hall Email Address Telephone Number
Lee Hysan Hall lhhall@hku.hk (852) 2986 5109
R. C. Lee Hall rclhall@hku.hk (852) 2986 5202
Simon K. Y. Lee Hall skyhall@hku.hk (852) 3917 0300
St. John’s College stjohns@hku.hk (852) 2817 7102
Starr Hall starr@hku.hk (852) 3910 2127
Swire Hall swwarden@hku.hk (852) 3917 0320
Wei Lun Hall weilun@hku.hk (852) 2986 5889
Other hotel options
Nina Hotel – Island South
55 Wong Chuk Hang Road, Aberdeen, Hong Kong
+852 3968 8888
Email: info.is@ninahotelgroup.com
Website: https://www.ninahotelgroup.com/en/nina-hotel-island-south
Price: ~$1365hkd/night
South Nest
47 Shek Pai Wan Road, Aberdeen, Hong Kong
+852 2122 9222 (Enquires)
+852 6641 9328 (WhatsApp)
Email: info@southnesthk.com
Website: https://southnesthk.com/
Price: ~$750hkd/night
Regal Oriental Hotel
30, 38 Sa Po Rd, Kowloon City
+852 2718 0333
Email: booking@regalhotel.com
Price: ~$500hkd/night
Restaurants
There are 23 catering outlets within HKU campus. Please find more information in the following link: HKU Catering Outlets . Outside of the campus, there are plenty of choices within walking distance to HKU. You can check it out through the following link: Restaurants in this district . Or you can also use a popular online map system in Hong Kong called CentaMap.com (http://www.centamap.com ). For vegetarian option, here are some recommendations:
BIJAS Vegetarian
(G/F Run Run Shaw Tower, Central Podium, Centennial Campus)
https://www.cedars.hku.hk/campuslife/catering/CCOutletD
Big Dill
(G/F, 123-125 Third Street, Western District)
https://www.openrice.com/en/hongkong/r-big-dill-western-district-international-meatless-menu-r670229
LN COFFEE
(G/F, Altro, 118 Second Street, Sai Ying Pun, Western District)
https://www.openrice.com/en/hongkong/r-ln-coffee-western-district-western-vegetarian-r485637
Po Lin Yuen Vegetarian Food
(G/F, 308 Queen's Road West, Sai Ying Pun, Western District)
Attraction
If you want to sightsee in Hong Kong, here are some tourist spots suggested by Hong Kong Tourism Board.
The Peak
-A place where you can see the spectacular view of HK
https://www.discoverhongkong.com/in/explore/attractions/best-vantage-points-on-peak.html
Hong Kong’s Star Ferry
-A sailing between the Victoria’s Harbours
https://www.discoverhongkong.com/in/explore/attractions/sailing-icon-hong-kong-s-star-ferry.html
Central Market
-A market for souvenirs and food
https://www.discoverhongkong.com/in/explore/attractions/central-market-for-our-time.html
Tai O
-A fishing settlement of stilt houses
Transportation
If you need to get from airport to HKU, you can either take the MTR from Airport Station to HKU Station or A10 bus (get off at Shek Tong Tsui Municipal Services Building station and walk 12 minutes). To travel between the city and HKU, the most efficient way is MTR. But you can also take the bus. If you want to take the bus, you could check the details in the link of several bus companies in HK, and CentaMap.com (http://www.centamap.com ).
MTR
MTR Station Location Maps
http://www.mtr.com.hk/en/customer/services/system_map.html
Citybus (mainly serve in Hong Kong Island)
https://www.citybus.com.hk/home/default.aspx?intLangID=2
Kowloon Motor Bus (mainly serve in Kowloon, New Territories and Hong Kong Island)
New Lantao Bus (mainly serve in Lantau Island)
HKU Campus Map