THE 5-th DNA METABARCODING SPRING SCHOOL @ BIAŁOWIEŻA (POLAND)

DNA metabarcoding is a rapidly evolving method for assessing biodiversity from environmental DNA. It has a wide range of applications including biodiversity monitoring, animal diet assessment, or reconstruction of paleo communities among many others. This approach integrates several scientific areas and requires a broad range of skills beyond the classical ecological knowledge. It relies on molecular techniques such as PCR and next generation sequencing (NGS) and requires competence in bioinformatics and biostatistics to analyze sequencing data.

The DNA Metabarcoding Spring School is now in its 5-th edition and this year it is co-organized by the metabarcoding.org team and the Mammal Research Institute, Polish Academy of Sciences in Białowieża, Poland. The DNA Metabarcoding Spring School will be held 1 – 5 June 2015. Participants can register for the school (24 places) by sending an email to the following address : bialowieza2015@metabarcoding.org

The email must contain a brief curriculum vitae and a letter of motivation indicating how your research relates to DNA metabarcoding and what you are hoping to gain from the school. As part of the course program, each participant is required to give a 5 min-talk on his/her research and how it relates to DNA metabarcoding.

Registration deadline is 15 April 2015. There is no registration fee for the workshop. Participants will have to pay for accommodation, meals and travel. The cost for accommodation and meals for 6 days is estimated @ 1500 PLN ( 360€).

More detailed information, including tentative schedule, activities, and speakers can be found @ http://metabarcoding.org/spip.php?article70

Methods in Ecological Genomics Analysis workshops (MEGA 2015)

Ecological genomics is the new and extremely powerful way to address old-standing ecological and evolutionary questions. We endeavor to teach the methods that we have developed specifically for working with non-model organisms to students with limited or no genomics or bioinformatics experience. Two back-to-back workshops will take place at the Mote Tropical Research Laboratory, using reef-building corals as subjects for specific research projects. The projects are designed to yield novel publishable results, and we encourage students to continue collaborating on these projects after the course has ended. Students making significant contributions to data analysis and manuscript preparation will be offered authorship (see previous publications stemming from our workshops at Mote).

Click on these links to see syllabi and costs (costs include accommodation but not board):

Instructor-in-chief: Mikhail V. Matz (google scholar page)

Applications now open for the summer 2015 “Bioinformatics & Biodiversity” Undergraduate Workshop

Following on from a highly successful event last year, we’re very excited to announce the second annual “Bioinformatics & Biodiversity” Undergraduate Workshop at the University of New Hampshire, scheduled for July 27-30, 2015 in Durham, NH. Click here to download a PDF flyer – we encourage you to post and share this opportunity!

2015_workshop_flyer

Microscopic eukaryotes (meiofauna e.g. nematode worms, copepods, protists, fungi, etc.) are some of the most abundant animals on Earth, but species within these groups are often overlooked by the general public and even many biologists. This NSF-sponsored workshop will explore the field of environmental DNA sequencing, including collection and analysis of data. Students will learn how high-throughput approaches (rRNA gene surveys, metagenomics) are being used to investigate the biodiversity of microbial eukaryotes and deepen our knowledge of ecosystem function. The workshop program will be a combination of lectures and practical exercises, where students will learn about traditional taxonomic approaches and also gain experience using the command line and bioinformatics tools to analyze environmental DNA datasets.

We welcome applications from undergraduates currently enrolled in any higher-educational institution in the USA.  All applicants are expected to have taken, at minimum, an introductory college-level course in Biology. Successful applicants will receive a stipend to cover all costs including travel.

To apply, e-mail the following materials to eukhits@gmail.com by Monday April 13, 2015:

  • Curriculum Vitae (including contact details for references)
  • Statement of interest (indicating biology courses taken and how attending the workshop would benefit your long-term career goals; maximum length 1 page)
  • Reference letters are recommended but not required

Frequently Asked Questions

Q. Can international/overseas students apply for this workshop? 

A.  No, unfortunately workshop application is restricted to students currently enrolled at US-based institutes (which includes international students attending US colleges). For future workshops we may extend the application process to students enrolled at overseas institutes (this will depend on the conditions of our funding). Thanks for your interest, and keep an eye on on the RCN website for future opportunities.

Q. For the CV (including references), exactly how many and what kind of references are preferred? 

A. One letter of recommendation can accompany the application (written by a professor or research supervisor) – this is optional, but may significantly increase the strength of your application. On your CV you can also list contact information for any additional professional references (up to three references); for example, you may want to list references relating to any relevant work experience or research projects.

 

NSF Dimensions of Biodiversity Funding Opportunity

[reposting an email from the American Society for Microbiology]

The National Science Foundation (NSF) has requested that ASM bring to the attention of interested members the following funding opportunity:

Dimensions of Biodiversity FY 2015
URL: http://www.nsf.gov/pubs/2015/nsf15533/nsf15533.htm 
Full Proposal Deadline: April 9, 2015 (due by 5 p.m. proposer’s local time)

Synopsis of Program:

Despite centuries of discovery, most of our planet’s biodiversity remains unknown. The scale of the unknown diversity on Earth is especially troubling given the rapid and permanent loss of biodiversity across the globe. The goal of the Dimensions of Biodiversity campaign is to transform, by 2020, how we describe and understand the scope and role of life on Earth.

This campaign promotes novel integrative approaches to fill the most substantial gaps in our understanding of the diversity of life on Earth. It takes a broad view of biodiversity, and focuses on the intersection of genetic, phylogenetic, and functional dimensions of biodiversity. Successful proposals must integrate these three dimensions to understand interactions and feedbacks among them. While this focus complements several core programs in BIO and GEO, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, in novel ways, to understand their synergistic roles in critical ecological and evolutionary processes.

Award Information:      

  • Anticipated Type of Award: Standard Grant or Continuing Grant
  • Estimated Number of Awards: 8 to 12
  • Anticipated Funding Amount: $16,000,000 to $22,000,000

More Information:  

Matthew D. Kane, BIO/DEB: (703) 292-7186, Dimensions@nsf.gov

Sincerely,
Ronald M. Atlas, Ph.D.
Chair, Public and Scientific Affairs Board

Joint Genome Institute – Metagenomics workshop & 10th Annual Meeting

Announcement from the Joint Genome Institute Mailing list:

February 9 – 13, 2015

The U.S. Department of Energy Joint Genome Institute is offering a five-day workshop on Microbial Genomics and Metagenomics (MGM). The MGM Workshop include seminars and extensive hands-on tutorials on how to use the IMG family of systems for comparative analysis of isolate genomes and metagenomes. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. For more information and to register, click here. Attendance is limited, so act now!

March 24 – 26, 2015

The DOE Joint Genome Institute’s 10th Annual Genomics of Energy & Environment Meeting registration is open.  See the current roster of speakers and register now for the March 24-26, 2015 event. Check out and register for the workshops too.

Once you’ve registered, please submit poster abstracts (from which short talks will be selected). Guidance for abstracts and posters can be found here.

Wrap-up post – “Ecometagenomics” Symposium at BES/SFE meeting

Thanks to everyone who attended our Symposium at the Joint British/French Ecological Society Meeting last week in Lille, France –  “Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA”. A collection of Tweets from this session is now available here on Storify.

We had a great turnout for the meeting session, followed by a hugely successful wine & cheese social sponsored in conjunction with the BES Plants, Soils, and Ecosystems Special Interest Group. And of course we managed to find plenty of holiday cheer walking around the streets of Lille!

2014-12-10 19.45.00

Simon, Dorota, Holly and Serita (left to right), on their way to the wine & cheese social!

 

Moore Foundation EOI call – Marine Microeukaryotes as Experimental Model Systems

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:

  1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
  2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.
    MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

  1. The lead researcher’s name, institution, and expertise.
  2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for
    transformability (category 2 above).
  3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened.
  4. A methodological or technical challenge that is hindering the development of a genetically
    manipulable marine microeukaryotic system that is ripe for solving and how you would address this
    challenge (3-5 sentences).
  5. The research team that would tackle this challenge, and why each team member’s expertise is relevant
    (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at samantha.forde@moore.org.