Monthly Archives: January 2014

Accommodation required for new postdoc Michael Stocks

Michael will be joining Terry’s team as a postdoc working on the ruff project.

He will be needing some accommodation.

If you are looking for a flat mate, please contact him: <>

Lab meeting, Tue 4th Feb 10am B52

Hello everyone,

Our next molecular ecology meeting will be on Tuesday 4th Feb at 10am in B52.
Lillian Lieber: It’s Slime Time! Microsatellite marker development to elucidate basking shark connectivity in the Northeast Atlantic
Ben Wielstra: The genomic architecture of a moving hybrid zone
Current available dates for giving talks are:
  • April 1st
  • May 6th
  • June 3rd
  • August 5th
  • September 2nd
Please let me know ( if new members of your group need to be added to the lab mailing list.
Mauricio Montaño-Rendón

Congratulations to Alain and Lisette on the birth of there son.Newborn

Postdoc in marine genomics/bioinformatics in Sweden

Post–?doctoral position in Marine Genomics/Bioinformatics at the Department of Chemistry and Molecular Biology and the Centre for Marine Evolutionary Biology (CeMEB)

The department Research and graduate education at the Department of Chemistry and Molecular biology comprise a wide scientific field from the atomic and molecular levels all the way through cells to intact organisms. Much of the phenomena studied here impact on our natural environment and living systems. We participate in undergraduate programs in chemistry, molecular biology, medicinal chemistry, biology, marine sciences, pharmacy, genomics, bioinformatics and systems biology. For more information about the department see: The research group The research group where this post–?doc position is placed is engaged in various marine projects with emphasis on functional genomics of osmoregulation and signalling in unicellular eukaryotes like the yeasts Saccharomyces cerevisiae and the marine yeast Debaryomyces hansenii, the diatom Skeletonema marinoi, and the barnacle Balanus improvisus. In this barnacle cloning and functional characterization of genes encoding octopamine receptors, pheromones, aquaporins and Na/K–?ATPases have been conducted. The group is also in charge of genome sequencing projects of eight marine organisms. This is part of an activity within CEMEB that is called IMAGO that aims at building an infrastructure based on novel marine model organisms that are well adapted to explore essential questions in ecology and evolution. For more information about the involved research group see the home page of Anders Blomberg:–?anders.

The centre for marine evolutionary biology – CeMEB The post–?doc employed will be part of highly active research consortium at the Univerisity of Gothenburg (CeMEB). The Linnaeus Centre for Marine Evolutionary Biology, CeMEB, brings together a broad expertise in biology. The main focus is on evolutionary processes and mechanisms in marine species and populations. The goal is to increase our understanding of how marine organisms adapt to new environmental conditions, for example changing seawater pH, temperature and salinity. CeMEB started in July 2008, when the consortium was selected for a ten year Linnaeus grant that was awarded by the Swedish Research Councils. For more information about CeMEB:

Job assignments The project is part of the CeMEB ambitions to establish eight marine organisms as potent marine genetic model system as part of the Infrastructure for Marine Model Organisms (IMAGO;–?marine–?genome–?projects). An essential step in this process is to finalize the genome sequence of these eight organisms. We currently have in the order of one tera–?base of sequence information in total, mainly based on next generation sequencing platform Illumina, providing a rich source of sequence information based on short reads. We are currently in the process of complementing this source by alternative NGS technologies, e.g. PacBio, and other means to improve the assembly process. In several of the genome projects various novel approaches for genome assembly are currently being tested and optimised, and for some genomes we are now approaching a phase of finalizing and publishing. This two–?years post–?doc position (with an option of one additional year) aims at supporting annotation and publication, both in scientific journals as well as in local and central databases, of these marine genomes. The work will also include analysis of RAD–?sequencing and RNA–?seq data. One important aspect of the position is to work closely with the responsible researchers for the various organisms in order to explore the genome sequences for interesting and novel genes and features.

Qualifications/eligibility We are looking for a highly motivated person with a doctoral degree in bioinformatics or in another relevant area where the research has been focused on sequenced–?based analysis. Earlier experience of working with large amounts of NGS sequence data is a necessary requirement.

Criteria/assessment The qualified candidate shall have experience with the major techniques in Bioinformatics. In addition, you must have used Linux/Unix systems as well as programming in script–?based language, such as Perl and/or Python. It is furthermore a merit if you have used or created databases for handling and analyses of sequence data, or if you have earlier experience of analysis of data on population genomics. Understanding of biological evolution and evolutionary processes, extracted from sequence data, is also a merit. The work will to a large extend mean various ways of interacting with researchers outside your own field of expertise, and therefore it is necessary that you have good communication skills. Earlier experience with genome projects is an asset.

For further information please contact

Professor Anders Blomberg, e–?post:

Professor Kerstin Johanesson, e–?post:

Head of Department Per Sunnerhagen, e–?

The application and how to apply The application shall include: –? Cover letter with an explanation of why you apply for the position –? CV including scientific publications –? Copy of exam certificate –? Two referees (name, telephone no, relation)

For more information and how to apply online see:–?in–?the–?job–? application–? portal/?languageId=0&disableRedirect=true&id=19144&Dnr=592082&Type=E

Application with reference number: PER 2014/14 The application must be received no later than 4th of February

worries about Primer3

Please note the new version of primer3 doesnt not give the same primer Tm’s as the earlier version which we know works well. The primer Tms in the new version can be 2-3 degrees higher or lower per primer creating a difference of 5 or so degrees between the forward and reverse (when the standard we use is 0.5C). This will affect how well your PCR product amplifies and what PCR annealing temperature should be used.

Avoid using the new version (Primer3web version 4.0.0) – the top webpage with a google of “primer3″ -

Use the old version = primer3 version 0.4.0 (use this – it is known to work well)
It was on this website

but if that webpage is not active (or you havent got it bookmarked) -
the same (good) version is provided here =

or here (again this is the good version, but do check)

Please come and chat if this isnt clear.
Id recommend recording which Primer3 version you use (and the webpage) and also state this in papers.


Terry’s group meeting tomorrow 24/1 12pm B52

rhubarb popping

Dear all,

I was intrigued to learn you can hear rhubarb popping, have a listen on the following real time recording:

Association for the Study for Animal Behaviour (ASAB) Conference, Sheffield, 7-9th April 2014

The Department of Animal and Plant Sciences is hosting the ASAB Easter Conference in Sheffield on Monday 7th, Tuesday 8th and Wednesday 9th April 2014.

Registration has now just opened and all information is available on:

Any question, please ask.


Room required for visitor to Beckerman lab

Andrew Beckerman has a PhD student from Chile visiting his group. They will come in Feb, for around 3 months, and are looking for accommodation. If anyone can help, please drop Andrew a line (
Many thanks

Come to NZ!

Hi everyone!

I am missing you all and very keen to keep up collaborations with the Mol Ecol Lab. So, if you are thinking about your next step please consider collaborating with me in Auckland, perhaps by
-applying for a fellowship e.g. Marie Curie (we can make a good case for e.g. NZ offering excellent learning opportunities in quantitative genetics)
-applying for some money for a short term visit (e.g.,, or from UK institutions such as the Royal Society
-stopping by after a conference “nearby”
-thinking about PhD studies abroad (e.g. Commonwealth scholarships are likely to be offered to UK citizens wanting to come to NZ, see, Auckland offers PhD scholarships open to international students:

I am currently developing projects working with some wonderful NZ species including hihi and Stewart Island robin – in particular, I am very interested in the genetic basis of quantitative traits in these populations and how this might constrain the adaptive response of the species e.g. in response to climate change.

Please pass on my contact details to any postdocs or students who might be interested in collaborating and we can investigate funding opportunities together.

Anna Santure

P.S. It goes without saying that social visits are welcome any time!