This week in PLOS Biology

In PLOS Biology this week you can read about a new protein used by the parasite Toxoplasma and how rhodopsin is recycled in the eye.



Image credit: doi: pbio.1001845

Lena Pernas, John C. Boothroyd & colleagues shed new light on the host-pathogen interactions of a globally prevalent and often chronic disease – toxoplasmosis, caused by the parasitic protozoan Toxoplasma gondii. The parasite lives in vacuoles within human cells, and recruits mitochondria to the membranes of the vacuole (the benefit to the parasite is presumed to be a metabolic one). Pernas and colleagues showed that a parasite protein ‘MAF1’ is needed to recruit the mitochondria. MAF1 is only present in two of the toxoplasma strains tested, suggesting that evolutionary niches exist where association with mitochondria is either advantageous or disadvantageous. Also read more in the accompanying synopsis.



Image credit: doi: pbio.1001847

Rhodopsin is a photoresponsive protein found in the cells of the retina which is vital for our perception of light. After it is activated by light it must then be degraded or recycled, but some aspects of the recycling pathway are unclear. In new research published this week, Shiuan Wang, Hugo Bellen & colleagues found that in flies, an evolutionarily conserved protein complex called the retromer is required for the recycling of rhodopsins. Interestingly, when retromer subunits were up-regulated, degeneration of photoreceptor cells could be alleviated in some contexts. This could have potential therapeutic uses if it also works in humans.


Category: Biology, Cell biology, Cell signalling, Disease, Infectious disease, Molecular biology, PLOS Biology, Research | Leave a comment

This week in PLOS Biology

In PLOS Biology this week you can read about a new General Ecosystem Model for predicting the effects of human activities, a global attempt to characterise a protein superfamily and new information about how a vital human transcription factor folds.



Image credit: doi:10.1371/journal.pbio.1001841.g007

Human activities (such as climate change) are causing degradation of ecosystems at an unprecedented rate worldwide. One approach now commonly taken by scientists trying to understand these impacts is to model them mathematically. This week in PLOS Biology, Michael Harfoot, Drew Purves and colleagues make what is really the first attempt at modelling whole ecosystems mechanistically on a global scale – using their ‘General Ecosystem Model’ (GEM). It covers organisms of all sizes and can be simulated at any spatial scale from local to global. By using fundamental ecological processes experienced by all species (e.g. reproducing or being eaten), encoding them mathematically and then simulating the impacts of future scenarios, this GEM has the potential to help us manage key environmental issues better. The model is being released as open source code to allow it to be used and improved upon.


New research by Susan Mashiyama, Patricia Babbitt and colleagues sets out to revolutionise our knowledge of one of the great protein superfamilies: the cytosolic glutathione S-transferases (cytGSTs), whose main role involves making lipophilic (‘fat loving’) toxins soluble, so they can be attacked by other enzymes in the body. The authors made a systematic survey of the current knowledge of more than 13,000 cytGSTs, and then attempted to fill in the gaps regarding their structure and function. The resulting picture is dizzyingly complex, but represents an important first step for the work that lies ahead. Read more in the accompanying synopsis.



Image credit: Kasembeli et al.

Stat3 is a transcription factor that is upregulated in some pathological conditions, including inflammatory diseases and cancer. Moses Kasembeli, David Tweardy and colleagues found that the folding and function of Stat3 are regulated by its interaction with TRiC – a type of protein called a chaperonin, which assist in the folding of other proteins. Manipulation of Stat3′s interaction with TRiC could be explored for therapeutic purposes.


Category: Bioinformatics, Biology, Cancer, Climate, Computational biology, Disease, Ecology, Environment, Evolution, Molecular biology, PLOS Biology, Resources | Leave a comment

This week in PLOS Biology

In PLOS Biology this week, you can read how two independent research teams have identified a new gene involved in circadian rhythms, and how we can improve the power of participatory medicine.



Image Credit: Flickr user shirokazan

Circadian rhythms are biological processes which are self-perpetuating but also entrained to the local environment by external cues, and usually happen on a cycle of around 24 hours. These cycles are central to the lives of humans and other animals, for example in regulating sleeping and feeding patterns and processes such as hormone production and cell regeneration. Over the last few decades, scientists have identified a network of interconnected ‘clock genes’ involved in daily rhythms; however some critical components are still missing. This week in PLOS Biology two independent studies identify a new clock component; CHRONO. Ron Anafi, John Hogenesch and colleagues started their search by identifying candidates with five key features of known clock genes. Akihiro Goriki, Toru Takumi and co-authors performed a genome-wide analysis for genes that were the target of BMAL1, a known core component of the cellular clock mechanism. A link was found between CHRONO and the regulation of organism-wide stress responses, which will likely be a major future focus of future work, given the importance of this for human health. Also read more in the accompanying synopsis.


Also this week you can read a Perspective as part of our Public Engagement in Science Series. Author Barbara Prainsack discusses participatory medicine – for example web-based platforms such as CureTogether – where patients can pool information about their symptoms and treatments and compare with other similar patients. Prainsack argues that for true participatory medicine to work, public actors in the health domain should not dismiss these citizen-led initiatives and should get involved in order to help ensure they are run in a responsible and accountable manner.


Category: Bioinformatics, Biology, Cell biology, Computational biology, Disease, PLOS Biology, Research | Leave a comment

Deep Reads: Christine Weber reflects on lab life and becoming a scientist

The first in our series following on from the PLOS Genetics Deep Reads article “Recommendations from Jane Gitschier’s Bookshelf” comes from Christine Weber, a PhD student in Fiona Watt’s lab at King’s College London, UK. Besides her research project in cancer immunology she enjoys writing about various kinds of science topics and is a big fan of science outreach in general. 

Natural Obsessions, by Natalie Angier, is the book which perhaps inspired me most when it comes to science. The title might be slightly misleading, as the story is in fact about life in a science laboratory: portrayed in one of the most authentic and insightful ways I’ve come across. Indeed, the title already points towards one aspect of science which accounts for most of its excitement, infectiousness, and ability to persistently chain researchers to the bench: science can be an obsession. In this case, the obsession we’re talking about is The Search for the Oncogene.

The book tells the story of Robert (Bob) Weinberg‘s lab during the 1970s and 80s; incredibly productive decades from which half a dozen major findings resulted. For people fascinated by cancer or genetics, Weinberg doesn’t need any introduction. His research into oncogenes—genes with the potential to cause cancer—has made him famous. This book gives a detailed account of events right from the beginning, when his lab started their substantial contribution to the field, and was still far-off the spotlight.

A labeled DNA segment (a known oncogene) in a mouse oocyte. By unknown photographer [Public domain], via Wikimedia Commons

We get to know all the scientists involved, and we hear about the challenges they faced during the race to publication. The author recounts stories of hard work, clever thinking, and lots of serendipity. But there’s also the dark side of science: competition, sometimes even within the lab; frustration over time-consuming experiments or negative results; and not least scientists who lose their faith in research and decide to leave.

I’ve read Natural Obsessions twice: once when I was an undergrad and just contemplating the idea of a scientific career; the second time was about a year ago, in the third year of my PhD project, when a colleague recommended the book and reminded me of it. At the beginning of my studies, it was easy to fall for the enthusiasm portrayed in the book. The author skilfully unravels complex methods in molecular biology in a way that a lay person can easily follow while still getting a grasp of the excitement and drive behind the experiments. Even just the passionate report of her first encounter with purified DNA in a dish got me hooked.

I’ve had similar outbreaks of excitement when working at the bench during one of my practical classes and the idea of turning this into a profession appealed to me. The scientists portrayed in the book seemed to be the kind of passionate, driven people I wanted to surround myself with. The work they did sounded almost unreal – I definitely put them on a pedestal. I was certain I could never learn to work this kind of magic at the bench.

Image credit: Bock et al. (2006)

When I read the book again last year I noticed that my perspective had somewhat changed. After years of experimental work I was suddenly surprisingly familiar with key aspects of the book: the frustration and hard work, the power of surprise, and also the overwhelming excitement of positive results. But one thing I hadn’t noticed the first time now suddenly caught my eye: politics.

Early in your scientific career it is important to learn how to successfully deal—and negotiate—with different characters. The book is quite frank about that, both from the group leader’s perspective but also from that of his employees. While I was now familiar with the methodology and routine in a lab, I could still learn something from the ways in which the scientists communicated with each other in Weinberg’s lab (or sometimes in fact failed to do so).

In the meantime I also had the chance to meet Bob Weinberg personally at my research institute. He wasn’t at all what I had imagined him to be after reading the book; he looked and talked like all the other professors—ways I was very familiar with by then. It was rather his profound knowledge and experience, and the ability to connect various different fields with each other that impressed me now.

Incubator. Photo courtesy of Christine Weber.

Incubator. Photo courtesy of Christine Weber.

I had time to study the publications of his lab members, too. Their work was certainly elegantly done (considering the limitations of the available technology at the time), but it basically followed the same routine I had encountered in my own lab. The way Weinberg led his team during the 80s equally didn’t strike me as extraordinary anymore. It was a very productive lab that got a lot of attention and was under quite some pressure, but certainly no bunch of super-humans defining history. Rather, smart people who were good at their jobs, a boss with an excellent nose for projects that were worth investing time in, and an adequate portion of luck.

That’s when it hit me that at some point during the past few years—subtly—I must have become a scientist. Natural Obsessions is a wonderfully precise tale about everyday life in the lab; it’s a tale about a scientist’s job. It was nice to remind myself of the excitement I had felt when reading the book for the first time—one of the reasons why I got into science. A lot of this enthusiasm is still there and resonates with the book, because in addition to Weinberg’s thrilling story about cancer genes I now also have my own research experiences (not that grand, of course) that are brought to mind while reading. In my opinion Natural Obsessions is a must read for everyone who is thinking about a career in science and also provides plenty of thought-provoking material for established researchers.

The author has declared that no competing interests exist.

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This Week in PLOS Biology

In PLOS Biology this week, you can read how plant pathogens convert flowers to leaves, how gut bugs might suppress bowel inflammation, and how endocytosis pathways talk to each other.


Image credit - Andrew Davis

Image credit – Andrew Davis

Parasites are often able to modify the behaviour of their host to benefit their own lifecycle. A new study by Allyson MacLean, Saskia Hogenhout and co-workers set out to discover how the bacterial plant parasite phytoplasma does just this. Phytoplasma relies on leafhoppers to spread and propagate it. They identified a protein, SAP54, which is produced by the bugs and manipulates the floral transcription programme, transforming flowers into leaves and resulting in a sterile plant which is a perfect nursery for leafhoppers to lay their eggs.



Image Credit: 10.1371/journal.pbio.1001639

We know that the bacteria living in our gut affect health and disease, but many of the mechanisms still elude us. These are particularly pertinent questions for sufferers of conditions such as inflammatory bowel disease (IBD), which are associated with gut microbial imbalance. Guillaume Sarrabayrouse, Francine Jotereau and colleagues found that a newly identified class of regulatory T cells of the human immune system can be activated by a bacterium commonly found in the gut. These regulatory T cells can then tone down inflammation reactions, which are prevalent in conditions such as IBD. Interestingly patients with IBD are known to have fewer of these bacteria and these findings could have therapeutic implications. Read more in the accompanying synopsis.


Endocytosis is the process by which substances (such as proteins), or sections of the cell membrane are imported into the cell. The substance is ‘engulfed’ into the cell through several alternative pathways which involve invagination of the membrane to form spherical protein-encapsulated vesicles. Most commonly, a molecule called clathrin is involved, but recently more has been understood about clathrin-independent pathways. In a research article this week, Natasha Chaudhary, Robert Parton and colleagues discover substantial cross-talk between two of these non-clathrin pathways; the caveolar pathway and the CLIC/GEEC pathway.


Category: Biology, Cell biology, Cell signalling, Developmental biology, Disease, Immunology, Microbiology, Molecular biology, Plant biology, PLOS Biology, Research | Leave a comment

Wearable science: The 2014 PLOS Comp Biol T-shirt competition

What do you want to see on the front of this year’s PLOS Comp Biol t-shirt? Enter our fifth annual t-shirt competition by sending us an eye-catching, innovative design that highlights a recent development in computational biology, and your entry could be featured on the t-shirts we’ll be handing out at July’s ISMB 2014 conference in Boston, USA!

To enter the competition, email your design to ploscompbiol[at] by Friday 9th May 2014.

Image credit: Chris Lauber and Katrin Sameith

The winning design for 2013. Image credit: Chris Lauber and Katrin Sameith

We’re looking for designs that:

  • are visually striking;
  • capture a recent advance or innovation in the field;
  • appeal to the computational biology community.

If you’re the lucky winner, not only will you get a free t-shirt, you’ll also see your design and research featured here on PLOS Biologue. Read our write-up of last year’s winning design.

Please review the following design requirements carefully before beginning your entry:

  • Style: Keep your design simple, readable and visible–type at 12pt or larger; lines at 4pt or larger
  • Logo: Do not include the PLOS Computational Biology logo or name in your design; this would be added later
  • Colours: Solid colours only (max. of 4 colours), with no shading
  • No Photographs or complex dimensional images
  • Maximum size: 12” x 12” (30cm x 30cm)
  • Resolution: 150 ppi minimum (pixels per inch); must be sharp (fuzzy images will not be accepted)
  • No Background: Do not include any background (white or colour) behind your image
  • Acceptable File Types: Original layered files .psd, .eps, .ai, or .pdf (hi-resolution)
  • Your design does not have to originate from a PLOS article. But if it does, then please include a URL to the PLOS article and a brief explanation of your design.
  • Please do not submit images that have been published by another publisher.
  • PLOS will place your design on a t-shirt made specifically for PLOS Computational Biology.  PLOS will determine the overall design of the t-shirt with the winning image placed to fit while following the organization’s style guide requirements.

Get creative and showcase your research at the same time! Send in your entries, or any queries, to ploscompbiol[at] We want to hear from you!

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The dynamical relationship of brain structure and function, environmental factors affecting autism and a budgie’s flight path: the PLOS Comp Biol March issue

Here is our selection of highlights published in PLOS Computational Biology for March.

Using mathematical models to design better anti-arrhythmic drugs. Image Credit: Megan Cummins, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

Using mathematical models to design better anti-arrhythmic drugs.
Image Credit: Megan Cummins, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai

The relationship between brain structure and function is a central endeavour for neuroscience research, but the mechanisms that shape this relationship are highly debated. Authors Arnaud Messé et al. addressed this issue by systematically comparing functional connectivity taken from imaging data with simulations from increasingly complex computational models. The study demonstrates the existence of a dynamical regime in the brain that appears to be largely induced and shaped by the underlying anatomy. It also revealed that the critical importance of specific anatomical connections in shaping the global anatomo-functional structure of this dynamical regime, notably connections between hemispheres.

One paper from our March issue was featured in the news. The first looked at the environmental factors affecting autism by analysing the spatial incidence patterns of autism and intellectual disability drawn from insurance claims for nearly one third of the total US population. Authors Andrey Rzhetsky et al. found strong statistical evidence that environmental factors drive the apparent spatial heterogeneity of both phenotypes. Read the New Scientist article about it here.

Another of this month’s papers investigated the means by which birds choose routes while flying in cluttered environments. Budgerigars were trained to fly through a tunnel that gave them a choice of two routes. When one of the passages was substantially wider than the other, the birds tended to fly through the wider passage, regardless of whether this passage was on the right or the left. Bhagavatula et al. developed a mathematical model of the interaction between the birds’ individual biases with their tendency to prefer the wider passage. The model reveals that this interplay is beneficial for expediting the passage of a flock of birds through a complex environment. A video of one of the experiments can be found here.

Category: Bioinformatics, Biology, Computational biology, PLOS Computational Biology | Leave a comment

An Invitation to Contribute to the Second Life of the Synthetic Biology Collection


Synthetic Biologist Dr. Jean Peccoud introduces a major rejuvenation of the PLOS Synthetic Biology Collection and calls on the community to lead the direction of the next update.

Since we launched the Synthetic Biology Collection in 2012, PLOS journals have seen a steady submission of new papers in the field. Today, we are pleased to announce a major reorganization of the collection and would like to request your participation to shape the collection further.

Ivan Morozov (Virginia Bioinformatics Institute)

Ivan Morozov (Virginia Bioinformatics Institute)

The idea of developing a Synthetic Biology Collection was first discussed with PLOS and in particular, PLOS ONE, while Synthetic Biology was evolving fast as a discipline. With its editorial policy precluding editors from making decisions on papers based on anticipated significance and it’s facilitation to serving interdisciplinary fields, PLOS ONE served this emerging community well. Since the launch of the initial collection there have been over 60 articles curated.

Second Life of the Collection

Today, we announce a major update to the Synthetic Biology Collection. As the number of articles included in the collection has grown, it has become necessary to divide the collection into eight sections corresponding to different areas of synthetic biology, namely:

In addition to the Collection Overview, we are also including two pieces of commentary published in PLOS Biology. The inclusion of two articles published in a PLOS journal other than PLOS ONE is a sign of upcoming changes to the Synthetic Biology Collection. As Synthetic Biology becomes an integral part of the life sciences, it is time to reflect this evolution by including articles published across the suite of PLOS journals in the Synthetic Biology Collection.

Identifying all of the synthetic biology papers published across the PLOS journals is a rather ambitious – and somewhat overwhelming – project. As editors, we are always afraid of not doing justice to some important work that we may have overlooked.  In other cases, we have struggled to decide if a particular paper belonged in the Collection.


Community-Driven Editing – Your Suggestions Wanted

So, as we move forward, we would like to conduct an experiment in crowd-editing.  We would like to have your input. Tell us what papers you think should be included in the Synthetic Biology Collection. You can send us references to papers published in any PLOS journal, all we ask is that you don’t make the selection based on your perception of the article’s significance.

We’d like to continue to be consistent with the editorial policies that allowed Synthetic Biology to flourish at PLOS and see the collection as a way to quickly identify synthetic biology papers published in the PLOS journals irrespective of their perceived significance. In other words, we want to be as inclusive as possible. In particular, if you spot a synthetic biology paper published in PLOS ONE that has not been included in the collection please do bring it to our attention.

We can’t promise that we will include every suggested reference but we will consider each and every one.  This community-driven approach to the development of this collection will enable us to make it more comprehensive and useful to all of us.

So, pitch in. Send us your picks. Get involved. We want to hear from you.

To submit a suggestion for the Synthetic Biology Collection:


  • Tweet your suggestion with the hashtag #CurateSynBio and a URL to the paper
  • Leave a comment on this blog with a URL to your proposed suggestion


PLOS will be attending the SynBioBeta 2014 Conference at Imperial College London on Thursday April 3rd. Please do pop by and meet members of the PLOS journal teams!


Jean PeccoudDr. Jean Peccoud, is a Associate Professor at Virginia Bioinformatics Institute, specializing in computational synthetic biology. He is also a PLOS ONE Academic Editor and, alongside Dr. Mark Isalan, is Curator of the PLOS Synthetic Biology Collection.

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This week in PLOS Biology

In PLOS Biology this week you can read about animals’ adaptability to climate change, generation of antibody diversity, age-related sleep problems, economic models of poverty and a new form of the yeast Candida albicans.



Image credit: Gilles Bourgoin

As the climate continues to change, to what extent will species be able to keep pace with altered temperatures and shifted seasons? In a research article this week Floriane Plard, Jean-Michel Gaillard, Christophe Bonenfant, and colleagues attempt to address this question using a long-term dataset on roe deer of France’s Champagne region. They found that although spring now arrives in the region two weeks earlier than it did in 1985, roe deer have failed to keep their reproductive cycle in sync with the flush of fresh green leaves needed by the mothers to make nutritious milk. The result is a general reduction in the survival of the foals, and a decline of the deer population growth as a whole. We can draw a sombre warning from these findings: not all species should be expected to adapt to changing climates. Read more in the accompanying synopsis.


Antibodies are proteins that play an essential part in our immune response: they recognise foreign objects (such as bacteria and viruses), bind to them and either destroy them directly or flag them for the attention of another part of the immune system. But different pathogens require different antibodies, and to help maximise diversity the B lymphocyte cells that make antibodies are able to direct mutations to their antibody genes and thereby produce millions of different variations. But how exactly do they do this? New research by Jean-Marie Buerstedde, David Schatz and co-authors found that enhancer elements – DNA sequences that drive transcription of the antibody genes – are responsible for recruiting the mutagenic machinery to the correct targets. Interestingly this mechanism is shared broadly between species (mouse, human and chicken), and is therefore relatively ancient and evolutionarily conserved.



Image Credit: John Tann

The older we get, the more difficult it is to initiate and maintain a good night’s sleep. Sleep disorders affect about half of the population over the age of 65 and are associated with reduced quality of life and poor health. In research published this week, Athanasios Metaxakis, Linda Partridge and colleagues investigated the mechanisms by which ageing impairs sleep, using the fruit fly as a model organism (like us, flies are active during the day and sleep at night, and they also experience age-related sleep disruption). They found that reduced insulin signalling improves sleep quality in flies and protects against age-related sleep deterioration. This could have applications for potential therapeutic targets to improve sleep quality in humans.


An Essay by Calistus Ngonghala, Matthew Bonds and colleagues explores how coupled models of ecology and economic growth can provide key insights into factors driving the formation and persistence of poverty traps. Understanding why poverty persists in some human populations remains a significant challenge. Economists have developed various models to explain persistent poverty (for example neoclassical growth theory and more micro-orientated models) but Ngonghala and colleagues demonstrated the utility of coupling this information with ecological data, for example a model of infectious diseases.


Candida albicans is a fungus which can cause various infections in humans, including hospital-acquired infections which have become a source of major health concerns. This yeast is known to have the capacity to grow in several distinct forms, a shape-shifting skill that is critical for its ability to thrive in its human host. Li Tao, Guanghua Huang and colleagues report a new form of C. albicans – the ‘gray’ type, which along with the previously discovered ‘white’ and ‘opaque’ cell types forms a three-way switching system.


Category: Biology, Cell biology, Climate, Disease, Ecology, Environment, Immunology, Microbiology, Molecular biology, PLOS Biology, Research | Leave a comment

The Pick of RECOMB 2014

Image courtesy of Leslie Gaffney of The Broad Institute.

Image courtesy of Leslie Gaffney of The Broad Institute.

Keen bioinformaticians will soon be on their way to the RECOMB 2014 conference, this year held in Pittsburgh, USA, April 2nd -5th. At PLOS Computational Biology we are delighted to have published five research articles in association with the conference, which is a key gathering of those focused on computational, mathematical and biological sciences.

The five articles appearing in PLOS Computational Biology are:

RECOMB Program Chair Roded Sharan explains that, “The five papers were published in full in a special RECOMB 2014 section of PLOS Computational Biology. All other papers that were accepted to RECOMB 2014 were invited for submission of an edited journal version to a special issue of the Journal of Computational Biology.“

Among these five articles are two that present new methods and are included in our Methods section.  “HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data” introduces a new and efficient statistical method for analysing the phrasing of polyploid genomes.  The other paper presenting a new method is “MRFalign: Protein Homology Detection through Alignment of Markov Random Fields” which presents the advantages of MRF-MRF comparison over HMM-HMM comparison when detecting sequence-based protein homology.

This endeavour has been overseen by PLOS Computational Biology’s Thomas Lengauer. We would like to join Roded Sharan in thanking Thomas, Methods Deputy Editor, “for the countless hours he has spent on coordinating the review process and ensuring the success of this partnership”.


Category: Announcement, Bioinformatics, Computational biology, Conference, PLOS Computational Biology, Uncategorized | Tagged , , , , , | Leave a comment