Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open (anyone can join with a Mendeley account), and I’m trying to keep them regularly updated with new articles (Mendeley members can also add articles, which I strongly encourage!):

  • Eukaryotic HTP Studies – Publications relevant to high-throughput environmental sequencing approaches focused on microbial eukaryotes. Articles will include any type of -Omic methods (marker gene amplicons, metagenomics, metatranscriptomics, etc.), eukaryote-focused tools/pipelines, and review/opinion pieces.
  • rRNA in Eukaryotes – Literature related to the ribosomal repeat array in eukaryotic genomes – variation in rRNA gene copy number, intragenomic polymorphisms, concerted evolution, transposable elements and their evolutionary and ecological implications.
  • Environmental PCRs – primer sets and bias – Literature related to primer set usage and bias across all taxonomic groups (bacteria, archaea, fungi and microbial eukaryotes) – includes primer sets and methods focused on 16S, 18S, ITS, other rRNA, COI, and other marker genes used for environmental sequencing.
  • eDNA in aquatic ecosystems – This group focuses on environmental DNA (eDNA) applications in aquatic ecosystems, include use of eDNA in bioassessment and environmental monitoring. Literature collection covers methods, analytical tools, and empirical studies (both basic and applied science).

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).