My thoughts on Brexit

Prelude: If you want to vote Brexit, I’m fine with that. I happen to not agree with you, but you are entitled to your opinion and I hope you still read this. I think the quality of the debate in this referendum has been terrible – a race to the bottom of ludicrous statements from both sides. So, as a scientist, a humanist and an optimist, here are my thoughts:

My biggest fear for the EU referendum is not that the UK economy will suffer, or that science will suffer, or that we’ll be worse off as a result of an exit. Those are storms that can be weathered. My biggest fear is that this has become a debate about immigration (particularly in the Labour heartlands). Britain has never been a country that sought to blame others for its ills. On the event of an exit, when the promised prosperity fails to materialise, when there are still no more hospital beds, or school places, or teachers; when we are signed up to an undiluted TTIP because we need to fast-track the illusion that we can trade with the world; when fracking is commonplace because we have lost our European allies who are currently leading the charge on preventing it; my biggest fear is this: Who will we blame next?

The start of the 20th Century in Europe was a tinderbox of feelings of helplessness and persecution by outside powers. Political ambition tapped into those feelings and ultimately it cost a generation in bloodshed. Afterwards, the EU was created to produce stability and peace through cooperation.

There is little doubt that the EU isn’t perfect and needs to move back towards its initial beginnings and away from the promotion of corporate interests above others, but is being held responsible for an awful lot of failings that are the result of poor policy decisions by governments we elected. These are the same governments that are promising to ring in the new Utopia once we are free of EU shackles. Sure, we can vote them out of power if they don’t deliver, but what replaces them? Political disenfranchisement is at an all-time high because the last 20 years would suggest it would be more of the same.

We are entering a time of great uncertainty: My child will likely grow up in a world where antibiotic resistance means that surgery is once again risky and now-treatable diseases are once again killers; where drought induced by climate change causes mass migration of desperate people on a scale that makes current levels look benign. I don’t want to be part of a world where we pull up the drawbridge and try to figure out how to protect ourselves at the expense of others. I want to be part of a world where we pull together as a species and through cooperation solve the global problems that we currently face. That is what we have always done as a nation. It is why our grandparents walked into the abyss at Normandy or Ypres or Jutland. It is why I am proud to be British.

More job opportunities for phage research

Li Deng currently has two open positions (one bioinformatics postdoc, one PhD) in her lab in Munich.

To apply for either position, please send your electronic application (in English) in a single PDF file – including CV and a complete list of publications, statement of research interests, and at least two reference letters – to Dr. Li Deng, email: li.deng@helmholtz-muenchen.de. Institute of Groundwater Ecology, Helmholtz Zentrum Munich, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany. Informal enquiries can also be addressed to the same email address.

Postdoctoral Position in Bioinformatics, Microbial Metagenomics

A newly founded DFG Emmy Noether research lab is seeking a highly motivated post-doctoral bioinformatician to work on computational analysis of metagenomics data, with a particular emphasis on bacteriophage communities. The successful applicant will be involved in the development and the use of new methods and tools for handling, analyzing and interpreting metagenomic sequencing data, as well as further development and/or application of multivariate analysis methods for comparative metagenomics.

Required Qualifications:

  • Recent PhD in Computational Biology, Bioinformatics, (environmental) genomics, or a related field.
  • Experience in any of the following areas: viral genomics, metagenomics, microbial ecology.
  • Strong experience in scripting tools (e.g. Perl or Python) in order to mine data files.
  • Good experience with processing and analysis of genomic/metagenomic data using compute clusters / high-performance computing.
  • Good experience with using standard bioinformatics tools and databases programming (e.g. SQL).
  • Good experience with using analytic tools (e.g. R or Matlab).
  • Fluency in English both spoken and written.
  • Knowledge Biology/Biochemistry and understanding of key and complex biological concepts (genes, pathways, microbial phylogeny and microbial ecology.).
  • Ability to independently carry out creative research with tenacity and of the highest quality standards.
  • At least one first author paper in an international peer reviewed journal.

Our Offer:

  • Working in an innovative, well- equipped and scientifically stimulating surrounding.
  • Working as part of a young and motivated team.
  • Further training opportunities.
  • The possibility to work with first-hand state-of-the-art datasets.

The position starts as soon as possible with a standard public service salary (TVöD EG 13). Duration: 2 years; option of further extension to 5 years.


PhD in Environmental Microbiology

A newly founded DFG Emmy Noether research lab is seeking a highly motivated PhD student to work on metagenomic analysis of polluted microbial and viral communities.

Required Qualifications:

  • Master in microbiology, molecular biology, (environmental) genomics, or a related field.
  • Experience in any of the following areas: viral genomics, metagenomics, microbial ecology.
  • Fluency in English both spoken and written.
  • Experience with flow cytometers is advantageous.

Our Offer:

  • Working in an innovative, well- equipped and scientifically stimulating surrounding.
  • Working as part of a young and motivated team.
  • Further training opportunities.

The position starts as soon as possible with a standard public service salary (TVöD EG 13). Duration: 3 years; option of further extension.

Calling all marine virus-loving postdocs

IMG_0892There is currently a great fellowship opportunity for any non-UK citizens to come over to the UK and spend a couple of years working with me at the university in the beautiful city of Exeter. Funded by The Royal Society, the Newton International Fellowship is open to early career researchers with fewer than 7 years postdoctoral experience.

My research looks at host-viral interactions in marine heterotrophs, with a focus on the pelagiphages – the most abundant (but woefully understudied) viruses in the world and how such interactions shape marine biogeochemistry. Our approach combines bioinformatic analyses of metagenomic and single cell genomic data with experimental work on cultured isolates to better understand the extent and impact of viral metabolic reprogramming within microbial communities. Current funding already includes scheduled cruises to sample within both the Bermuda Atlantic Time Series (as part of the BIOS-SCOPE project) and the Western Channel Observatory.

If you’re interested in writing a joint proposal (deadline is the 9th of March) and meet the requirements of the fellowship, then send your CV and a brief outline of the kinds of research you’d be interested in to b.temperton@exeter.ac.uk.

Network Fluidity – A case for reproducible science

I’ve been working on some transcriptional network analysis of SAR11 over the last few months, hoping to compare it to other papers to see how genome streamlining affects network modularity. Turns out this is almost impossible to do because:

  1.  Network topology is frighteningly sensitive to parameter choice (see figure)
  2. I am yet to find a paper where the details of WGCNA network construction are sufficiently documented for me to see how the network was constructed, or indeed, why certain parameter choices were made.

Effects.of.params.on.network

Hopefully, when this analysis is completed, the R markdown supp docs describing how the network was constructed will provide pain relief for the next person who attempts this kind of comparison…

A Fantastic Opportunity to work with one of the best

Featured imageMy old postdoc supervisor, mentor and all-round-good-egg Steve Giovannoni is looking for a 3-4 year postdoc as part of a NASA-led aerosols program to look into microbial plankton community dynamics.

Here’s some reasons why this post is awesome:

  1. You’ll have ‘NASA’ on your CV
  2. Steve is one of the nicest, most knowledgeable and insightful scientists you could care to meet
  3. Oregon is beautiful
  4. You’ll be unlocking the secrets of what happens to critical biogeochemical systems as oceans warm.
  5. I said NASA, right?

Here are some details:

Announcement:  NASA’s  Earth Venture suborbital investigations program has awarded 30 million in funding to a team led by Mike Behrenfeld for a project, titled “North Atlantic Aerosols and Marine Ecosystems Study”.  It was one of 5 selected by NASA for funding from 33 proposals that were submitted.  Professor Giovannoni’s laboratory will be measuring phytoplankton bloom dynamics at the species and subspecies level over the course of the field campaign, which includes four cruises in the North Atlantic, the first scheduled for November, 2015.  More information about the award can be found at: http://www.spaceref.com/news/viewpr.html?pid=44514.

Position Adverstisement: A post-doctoral scholar position is available immediately in Stephen Giovannoni’s laboratory in the Department of Microbiology, Oregon State University to study microbial plankton community dynamics. This is a three-to-four year position on a large, integrated scientific team that has been funded by NASA to study the North Atlantic spring bloom and its and its influences on aerosol production.  We are seeking scientists with experience and a record of publications in molecular microbial ecology, particularly large-scale rRNA sequencing studies of microbial diversity. Applicants must make a three-year commitment and be willing to go to sea for 3-4 week research cruises each year.  Send CV and three letters of reference to: Dr. Stephen Giovannoni, Dept. of Microbiology, 220 Nash Hall, Oregon State University, Corvallis, OR 97331. OSU is an AA/EOE.

Science on Tour: Thoughts from an Early Career Marine Microbiologist Working in KAUST (King Abdullah University of Science and Technology), Saudi Arabia

For the past few weeks, my volunteer and all-round-good-egg Jo Warwick has been in KAUST on secondment to share her knowledge of algal culturing techniques. She has been kind enough to write a guest blog post to document her travels and experiences:


KAUST is extra pretty at duskKAUST is a very young and totally individual university located on the entirely tourist-free Saudi Arabian Red Sea coast. Currently one month into a four-month post, and as a relatively recent marine biology graduate with research experience in scale-up culture of marine phytoplankton, my role here at KAUST is somewhere between an intern and a researcher. My team is part of the Computational Bioscience Research Centre, currently specialising in the isolation and characterisation of local Red Sea cyanobacteria, for which, it is anticipated, certain industrial applications will be determined.

Harbour at dusk_2

Having opened its doors a mere five years ago, in a country that few western scientists would previously have been able to visit, KAUST makes for a very unique environment in which to undertake research. First impressions of the university grounds and facilities inspire awe. Built adjacent to the turquoise blue of the Red Sea, the humidity and scorching sunshine outdoors are successfully mitigated by plentiful shade and continuous breezes, courtesy of the clever, grand-scale architecture and verdant landscaping. Indoors the heat is totally banished by mega-scale air con. The overall feeling is of space, calm, comfort, and a total lack of budgetary constraints. These impressions are only magnified within the laboratories. If KAUST has an unofficial motto, it might be something along the lines of: “Why buy one piece of state of the art equipment, when you can use a half-dozen?” Thus one is shown the ‘corridor’ of electron microscopes; the hanger of ten (count them!) NMR systems.

Despite these impressions, at present one must allow that there is perhaps space alongside the remarkable facilities. The KAUST community is incredibly friendly. All the students and nearly all the staff live on-site, giving it the feel of the world’s most international (and cooperative) village. To my mind, the scientific community of KAUST is under construction. Everyday conversations that we take for granted: the sharing of practical experience in protocols; the hints and tips for overcoming particular quirks in equipment or model organisms, are less easy to come by at present. The academic community of KAUST will need time, and continued personnel investment, to achieve the internal density for collaboration so important to any scientific institution.

Jo goes divingThe dichotomous nature of KAUST runs throughout the experience of living and working here: The promise of novel research in an understudied environment, using top of the line equipment, verses the frustration in obtaining everyday consumables or training from a long logistical pipeline; The safety of living in a ‘gated community’ where everyone is looked after, against the restrictions in terms of geographical and personal freedom inherent in living in such a place. Of course, it really is very early days for KAUST. It is an incredible achievement that such a place exists at all, and the intrinsic potential of the university is palpable. Over time it is hoped that those aspects of KAUST most likely to cause frustration, will at least in the most part, be resolved. The key to living and working in KAUST appears to be patience (and it probably doesn’t hurt to get into a locally popular hobby such as SCUBA diving, golf, or badminton, either).

A New Single Cell Genomics Capability at PML

Lion

Lion

We have just heard that our NERC Capital bid to fund the equipment for an environmental Single Cell Genomics (eSCG) facility at Plymouth Marine Laboratory has been funded. This is a huge addition to the capability for molecular microbiology in the South West and beyond, particularly when coupled to the long-term time series of marine microbial communities that is an integral component of the Western Channel Observatory (WCO).

In the past decade, metagenomics and community profiling has been used to try and understand the biogeochemical role of marine microbial communities, to predict what ecological services they provide and how robust these are to predicted environmental changes. Indeed, studies at the WCO have been integral to understanding the seasonality of microbial communities and the waxing and waning of certain species as environmental conditions change. These community profiling studies have been complemented by metagenomics, which attempts to identify the functional capacity of the identified members of the community.

Metagenomics, however, is not without its issues. Metagenomic studies involve concentrating microbes onto a filter, then extracting all of the DNA of that community at once, smashing it up, sequencing it and then trying to piece together the world’s hardest jigsaw to gain understanding of what biological processes are being encoded by the community. Imagine trying to understand the role of lions in a savannah ecosystem. The research involves dragging a net across a savannah, capturing anything in its path – lions, wildebeest, plants, rocks, insects, etc. We then blend them all together into a nice meaty-with-green-bits soup, extract the DNA and sequence it. Out of the billions of DNA reads, we try and identify those that came from lions and piece those together into meaningful pathways. Because the re-assembly of DNA is so complex, most of the putative proteins we identify have no known function. It’s like aliens coming to earth and seeing a lion’s whisker for the very first time, lying on the floor. There would be no hope of identifying their sensory function without seeing how they are arranged on a lion’s face. The second biggest problem is that some constructs look very lion-like, but some constructs look like lion-wildebeest mash-ups. Scientists have to make a call on whether the DNA sequence is an artefactual construct, or whether they have discovered a new species of lion that has dagger-like teeth but moos and eats grass.

Single-cell genomics allows us to understand lions by sequencing lions. Flow cytometric sorting of microbial cells acts like a gate on our savannah net, manned by a gatekeeper who has two jobs. If the net captures a lion, it is directed into its own individual cage. If it isn’t a lion, it gets redirected out of the net. Because we are now assembling DNA from an individual organism, we can be relatively certain that any discovery of novel function is genuine and not due to cutting and pasting DNA from different organisms together. The assembly is also less complex and thus provides longer sequences of DNA. This means that the putative function of novel genes can be predicted based on the function of known neighbouring genes (in bacteria, at least).

Perhaps most importantly, we can start to understand just how different one lion is from another lion. Even microbial organisms that are thought be identical by community profiling techniques (16S or 18S rRNA analyses) can contain vastly different gene suites that allow them to access different resources, become pathogenic, defend themselves against viruses etc. etc. These functions are inserted and lost within genomes from similar and sometimes distantly related organisms. What the single-cell genomics facility at PML will allow us to do is identify for the first time how the functional capacity of microbial populations in the WEC shifts with changing conditions throughout the seasons. Which functions are universal? Which functions are transient? What functions are associated with the rare, but persistent species that form hubs in community metabolic networks? How are other organisms exploiting communal resources from these organisms? How do the viral defenses of these organisms alter over time and between organisms? How are the viruses adapting to overcome these defenses?

Quite simply, single cell genomics will increase the resolution with which we can understand marine microbial communities in the WEC to an unprecedented level.