Launching the PLOS Genetics Research Prize 2015

2014-11-05 15_03_13-Greenshot

September 2007 Issue Image. Electronic rolled fingerprint. Image Credit: Sarah E. Medland

What did you do when you turned 10? Throw a party? Have a sleepover? Eat chocolate cake? We would love to do all these things with our readers, authors and editors (especially the chocolate cake), but after much deliberation, we decided on a more research-oriented birthday treat.

We’re awarding a US$5000 prize for the best PLOS Genetics Research Article published in 2014. We’re very excited about this opportunity to recognize the outstanding work we publish and, at the same time, involve the genetics community in the selection process for this!

We’re taking nominations from the public until Wednesday September 16 2015 10:59 AM UTC, and our senior editorial team will select the final winner based on those nominations. To reflect the journal’s aims of publishing high quality research and fostering community engagement, the winning Research Article will be chosen based upon scientific excellence and community impact.

Brithday Cake US

Birthday Cake. Image from Flickr. CC0 US Government work.

Please join us in the celebrations and nominate your favorite paper! For more information on the Prize, please see the Program Page and Program Rules. Questions regarding the Prize can also be sent to plosgenetics@plos.org.

Category: Genetics, Uncategorized | Tagged , | 1 Comment

Understanding Images: Plants Limit Crossovers

Authors: Javier Varas and Mónica Pradillo from Universidad Complutense de Madrid, Madrid, Spain.

Competing interests: Javier Varas and Mónica Pradillo are authors of the work discussed in this blog.

In the July issue of PLOS Genetics, the regulation of meiotic crossover in plants was investigated by Varas et al.

Meiosis is a key event in the life of all sexually reproductive organisms, with major implications on the transmission of genetic information and on genome evolution. This process requires specialized features to generate haploid gametes from diploid cells. Meiosis consists of two divisions without an intervening S phase. During the first meiotic division, the formation of chiasmata between homologous chromosomes holds them together to promote their accurate segregation. These connections prevent uneven distribution of chromosomes that could lead to aneuploidy, as in Down syndrome. Chiasmata are the cytological manifestations of reciprocal interchanges of DNA (crossovers) and homologous recombination is the molecular process underlying the formation of crossovers.

Arabidopsis thaliana. Image credit: Varas et al, 2015.

Arabidopsis thaliana. Image credit: Varas et al, 2015.

Meiotic crossovers result from the repair of double-strand DNA breaks induced by SPO11. These double-strand breaks can be processed by multiple recombination pathways with specific intermediates to generate either non-reciprocal interchanges, non-crossovers, or reciprocal interchanges, crossovers. Crossover distribution is non-random and is tightly regulated by several mechanisms. All chromosomes receive at least one crossover (an obligate crossover), and formation of a crossover at a given site generally reduces crossover formation at adjacent regions – a phenomenon known as positive interference. In addition, crossover homeostasis ensures a stable number of crossovers despite variability in the number of double-strand breaks.

Meiotic Recombination in Plants

In plants, most of our knowledge about meiotic recombination has come through studies of the model species Arabidopsis thaliana. We have selected this species to demonstrate that in plants, as in yeast and mouse, increased double-strand break formation is not accompanied by increased crossover formation. Our study describes the meiotic phenotype of the Atfas1-4 mutant, defective for the large subunit of the histone chaperone CAF-1. This mutant shows developmental abnormalities; their stems, roots, siliques (seed pods) and flowers are reduced in size and the leaves are serrated. It also has reduced heterochromatin content and increased frequency of somatic homologous recombination.

Regulation of Crossover Formation in Arabidopsis                  

Image credit: Varas et al, 2015

Image credit: Varas et al, 2015

Arabidopsis has approximately 15 times more double-strand breaks than crossovers. To estimate the number of double-strand breaks in Atfas1-4, we counted foci corresponding to phosphorylated histone H2AX (γH2AX), a sensitive marker that can be used to examine the DNA damage produced and the subsequent repair of the DNA lesion, and the recombinases AtRAD51 and AtDMC1 which are involved in DNA strand invasion during the beginning of the homologous recombination process. In our issue image, the cell on the right corresponds to a dual immuno-localization of the axial element protein AtASY1 (shown in green in the above image) and AtRAD51 (shown in red). We concluded that the number of double-strand breaks is increased by more than 50% in Atfas1-4.

These extra double-strand breaks could be processed by the different pathways which participate in normal conditions; nevertheless, we did not detect an increase in crossovers. We tested whether non-crossover gene conversion frequencies change in Atfas1-4 relative to wild-type plants. To estimate the gene conversion frequencies we used lines with fluorescent pollen grains. Pollen tetrads from plants heterozygous for fluorescent and non-fluorescent alleles present two fluorescent pollen grains and two non-fluorescent pollen grains (top left tetrad in the figure). If gene conversion occurs, a non-Mendelian 3:1 ratio is observed (bottom left tetrad). In the mutant the frequency of these tetrads was increased compared to the wild-type. Therefore, in Atfas1-4 the excess of double-strand breaks produces an increase in the frequency of gene conversion events.

Implications of Findings

Image credit: Varas et al, 2015.

Image credit: Varas et al, 2015.

Our findings show that the number of crossovers can be constrained in plant species even when the number of double-strand breaks increases during meiosis. The extra double strand breaks produced in Atfas1-4 are processed to non-crossovers in order to keep the same crossover frequency as the wild type, resulting in an increase in gene conversion frequency. These results highlight the complex regulation of crossover formation during Arabidopsis meiosis. Our results demonstrate that despite considerable divergence in molecular components that drive meiosis, there is conservation of the homeostatic mechanism which regulates recombination from fungi to plants to animals.

Original Article

Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4  PLoS Genet 11(7): e1005301. doi:10.1371/journal.pgen.1005301

Category: Uncategorized | 1 Comment

The Trouble with Transparency

Last week we posted an article by two journalists, Paul D. Thacker and Charles Seife, who argued that the integrity of the scientific and medical literature depends on protecting tools that ensure greater transparency about financial ties to industry that could potentially bias research results. We have heard from many groups who were deeply offended by the article. Our intention was not to cause offense and we wish to express our apologies to any members of the scientific community who felt the post misrepresented their situation. A desire for transparency is in line with the competing interests policies of PLOS, but we appreciate that the realities of implementation may pose challenges. We have since offered to others, including Dr. Kevin Folta, one of the cases mentioned in the post, the opportunity to contribute their views to the debate, under similar conditions, on this blog.

The tools in question in the original piece by Thacker and Seife include public records and Freedom of Information Act requests. These tools, the authors argue, give reporters, and members of the public, access to documents with the potential to uncover undeclared conflicts of interest, dubious research practices, fraud and scientific misconduct. Without these tools, the authors go on to say, the integrity of the scientific and medical literature could be in jeopardy.

We felt the message—that if researchers disclose any and all ties, financial or otherwise, to industries that benefit from research that they engage in, it helps build public confidence in that research by virtue of showing there is nothing to hide—is one that is well worth debating.

That financial conflicts of interest can influence research results is well-documented in the scientific and medical literature. Against a backdrop where research output doubles nearly every decade and concerns over fraud, misconduct and research reliability are on the rise, we at PLOS Biology believe that efforts to boost scientific integrity, literacy and transparency are sorely needed. That’s why when two journalists with a track record for exposing corruption in science came to us with an article outlining the reasons to protect tools to ensure transparency – even though many scientists see the tools as invasive and disruptive — we offered to consider their piece for our blog.

Nonetheless, we appreciate that some of the parties mentioned in the article took grave offense at the authors’ characterization of their situation. In particular, Dr. Kevin Folta, one of several cases mentioned in the article, has publicly stated some of his issues with the article and the authors’ interpretation. Unfortunately, our processes went wrong and we failed to respond as quickly as we should have to Dr. Folta’s initial message to us. We are reviewing our processes to ensure that a similar failure will not be repeated.

We continue to believe that this is an important, if highly charged, issue that merits discussion. On Monday we offered Dr. Folta the opportunity to provide his views on conflicts of interest on PLOS Biologue. We invite your comments and are currently approaching others to showcase and present a variety of views and experiences relating to the FOIA, COI disclosures and transparency in scientific research and publishing.

 

Category: Debate, Editorial policy, Funding, Publishing, Research | 5 Comments

Post Removed by PLOS – The Fight Over Transparency: Round Two

 

Statement from PLOS:

PLOS Blogs is, and will continue to be, a forum that allows scientists to debate controversial topics. However, given additional information for further inquiry and analysis, PLOS has determined that the Biologue post that had occupied this page, “The Fight over Transparency: Round Two,” was not consistent with at least the spirit and intent of our community guidelines. PLOS has therefore decided to remove the post, while leaving the comments on it intact. We believe that this topic is important and that it should continue to be discussed and debated, including on PLOS blogs and in PLOS research articles.

We sincerely apologize for any distress that the content of this post caused any individual. Comments and questions can be sent to blogs@plos.org

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Microbiome Evolution, Molecular Recognition and Interaction Webs: the PLOS Comp Biol July Issue

Here are our highlights from July’s PLOS Computational Biology

 

Neutral Models of Microbiome Evolution

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes) and how they correlate with host health, disease, phenotype, physiology and ecology. However, few studies have focused on how these microbiomes may have evolved. Qinglong Zeng and colleagues develop an agent-based framework to study the dynamics of microbiome evolution. Their framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled.

 

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein

July Issue Image: Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA. Credit: Pomès et al.

July Issue Image: Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA. Credit: Pomès et al.

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. Xuhui Huang and colleagues propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Their results hold the potential to be widely applied in the studies of other molecular recognition systems.

 

What Can Interaction Webs Tell Us About Species Roles?

Matrix structure of complete Tatoosh network, organized by groups. Credit: Sander et al.

Matrix structure of complete Tatoosh network, organized by groups. Credit: Sander et al.

Ecological interactions are highly diverse, even when considering a single species: the species might feed on a first, disperse the seeds of a second, and pollinate a third. Elizabeth L. Sander and colleagues extend the group model – a method for identifying broad patterns of interaction across a food web – to networks which contain multiple types of interactions. Using this new method, the authors test whether combining different interaction types leads to a better definition of the roles species play in ecological communities.

Category: Biology, Cell biology, Ecology, Microbiology, PLOS Computational Biology, Uncategorized | Tagged , , , , | 1 Comment

Understanding Images: A Genetic Framework in Legumes Controls Infection of Nodules

 

In a piece reflecting on June’s PLOS Genetics issue image, authors Simon Kelly and Simona Radutoiu discuss the science behind their image.

Authors: Simon Kelly and Simona Radutoiu, Aarhus University, and Carbohydrate Recognition and Signalling Centre in Denmark.

Competing interests: Simon Kelly and Simona Radutoiu are authors of the paper discussed in this blog.

Confocal laser scanning microscopy image of a nodule section illustrating the internal infection pattern of the endophyte Rhizobium mesosinicum, strain KAW12 (red) and of the incompatible symbiont Mesorhizobium loti, strain exoU (green). Image Credit: Rafal Zgadzaj

Confocal laser scanning microscopy image of a nodule section illustrating the internal infection pattern of the endophyte Rhizobium mesosinicum, strain KAW12 (red) and of the incompatible symbiont Mesorhizobium loti, strain exoU (green). Image Credit: Rafal Zgadzaj

The soil environment harbors a diverse range of bacteria, many of which could potentially be detrimental if they are able to gain entry to plant tissues. We are interested in determining how the host plant selects which bacteria are able to colonize its tissues and to identify important endophyte factors that allow them to be accommodated by the host plant. In this issue of PLOS Genetics we investigate the genetic components and molecular signals that allow the endophyte Rhizobium mesosinicum strain KAW12 (KAW12) to colonize symbiotically induced nodules on the model legume Lotus japonicus. We have used different symbiotic and endophytic strains and performed mixed inoculations of wild-type or symbiotic L. japonicus mutants in order to identify the respective contributions of the different interacting partners – legume host, symbiont and endophyte.

Colonisation of Lotus japonicus Nodules by Endophytic Bacteria

 Section of an M. loti nodZ-induced nodule presenting KAW12 (*) and M. loti nodZ (arrow) infection. Image credit: Zgadzaj et al.

Section of an M. loti nodZ-induced nodule presenting KAW12 (*) and M. loti nodZ (arrow) infection. Image credit: Zgadzaj et al.

The legume root nodule is a unique environmental niche induced by symbiotic bacteria, where multiple symbiotic and endophytic bacterial species can co-exist. Several endophytes were tested for their ability to colonize L. japonicus nodules that were induced by its usual symbiotic rhizobia (Mesorhizobium loti) in co-inoculation experiments. Our study identified KAW12 as an endophyte that uses the symbiotically induced infection threads to co-colonize L. japonicus nodules without inducing nodule necrosis, providing us with a system to study host and endophyte genetic features that are important for such interactions.

Root hair infection threads (arrows) colonised by M. loti exoU (green) and KAW12 (red). Image credit: Zgadzaj et al.

Root hair infection threads (arrows) colonised by M. loti exoU (green) and KAW12 (red). Image credit: Zgadzaj et al.

Initiation of the symbiotic process requires Nod-factor signaling. Nod factors are signal molecules produced by symbiotic rhizobia and recognized by the plant through Nod-factor receptors. This perception triggers the initiation of the infection pathway, through which rhizobia enter the plant, as well as initiation of nodule organogenesis. Using symbiotic strains that produce different types of Nod factors as co-inoculating partners, we determined that intact Nod-factor signaling provided by the symbiont is required for nodule colonization by the endophytic KAW12 bacteria.

 

Exopolysaccharides are Key for Chronic Infection

Exopolysaccharide (EPS) production is important during symbiosis5. The M. loti exoU strain utilized in this study is affected in EPS biosynthesis and is thus impaired in symbiosis due to an inability to form infection threads. To further investigate this we isolated an EPS-deficient strain of KAW12 and performed co-inoculation experiments with M. loti exoU. Strikingly, nodule colonization by the KAW12 EPS mutant was absent, indicating that EPS is a key molecule required by the endophyte to allow for nodule colonization.

Endophyte Nodule Occupancy is Host-Controlled

To study the role of the legume host in mixed inoculations we took advantage of the large collection of L. japonicus mutants available to identify host genetic components required for nodule colonization by the endophyte. Our results revealed that the mutation of genes required for infection thread formation prevented nodule colonization by the KAW12 endophyte. In contrast, KAW12 colonization of nodules formed on plant mutants in genes required for supporting nitrogen-fixation within nodules was not impaired.

L. japonicus. Image credit: Kazuhiro Tsugita, Flickr.

L. japonicus. Image credit: Kazuhiro Tsugita, Flickr.

The presence of endophytes within legume nodules may restrict the occupancy of effective nitrogen-fixing symbionts and therefore represents a major challenge that contributes to limiting legume cultivation. Our study shows that the well-established genetic resources available for the model legume L. japonicus can be utilised in co-inoculation studies to identify genetic and molecular factors important for determining compatibility with soil bacteria, providing further avenues to address this issue.

 

References and Further Reading

1          Broghammer, A. et al. Legume receptors perceive the rhizobial lipochitin oligosaccharide signal molecules by direct binding. Proc Natl Acad Sci U S A 109, 13859-13864, doi:10.1073/pnas.1205171109 (2012).

2          Radutoiu, S. et al. Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases. Nature 425, 585-592 (2003).

3         Oldroyd, G. E. D., Murray, J. D., Poole, P. S. & Downie, J. A. The rules of engagement in the legume-rhizobial symbiosis. Annu. Rev. Genet. 45, 119-144, doi:10.1146/annurev-genet-110410-132549 (2011).

4          Kawaharada, Y. et al. Receptor-mediated exopolysaccharide perception controls bacterial infection. Nature 523, 308-12 (2015).

5          Kelly, S. J. et al. Conditional requirement for exopolysaccharide in the Mesorhizobium-Lotus symbiosis. Mol Plant Microbe Interact 26, 319-329, doi:10.1094/mpmi-09-12-0227-r (2013).

 

 

 

Category: Biology, Blog, Cell biology, Cell signalling, Genetics, Image, Microbiology, Molecular biology, Open access, PLOS Genetics, Research | Tagged , | 1 Comment

PLOS Genetics’ Tenth Anniversary

2015 marks the tenth anniversary of publishing cutting-edge research at PLOS Genetics. Since the inaugural issue on the 25th of July 2005, PLOS Genetics has been dedicated to supporting the scientists that make up the genetics community with ethical rigour, thorough peer reviewing and lively scientific discussion. As the years have gone by we have seen a wealth of expertise rotate through our Editorial Board, and we are delighted to have worked so closely with much of our community.

Image credit: Flickr vpisteve CC BY

Image Credit: Flickr vpisteve CC BY

On the occasion of our tenth anniversary we are highlighting and celebrating many aspects of PLOS Genetics. In order to recognise the outstanding work published in PLOS Genetics, the Editors are awarding a prize for the best Research Article of 2014. Articles will be nominated by the wider community and our Editors-in-Chief and Section Editors will select a winner from the nominated works. To reflect the journal’s aims of publishing high quality research and fostering community engagement, the winner will be chosen based upon scientific excellence and community impact. Nominations will open in a few weeks, so keep a lookout for updates! In the meantime, why not refresh your memory and browse through our 2014 volume?

As well as celebrating recent publications we want to acknowledge the richness of research that we have published over the years. We are launching a collection of the ten most downloaded articles in PLOS Genetics’ history to form a PLOS Genetics Tenth Anniversary Collection. Each article in the collection will be accompanied by a commentary, written by an expert in the field, and the collection will include a reflective editorial from our Editors-in-Chief, looking back upon the past decade.

The first ever cover image for PLOS Genetics from July 2005. Image Credit: Photograph by Erwin and Peggy Bauer, USFWS; line graphic by Felice Macera.

The first ever cover image for PLOS Genetics from July 2005. Image Credit: Photograph by Erwin and Peggy Bauer, USFWS; line graphic by Felice Macera.

PLOS Genetics owes much of its success to our outstanding Editorial Board. These individuals work tirelessly to encourage, assess and improve our submissions, whilst being vital members of the genetics community and making outstanding scientific contributions in their respective fields.  To celebrate ten years of hard work, research, and immense dedication from our Editorial Board, we are inviting our editors to contribute to PLOS Biologue. In these posts, our editors reflect on how their areas of research have developed and changed over the last ten years, and explain what their hopes are for future research. The first post in this series is from Beth Sullivan on the last ten years of chromosome biology, which provides an exciting insight into the challenges and achievements this field has seen over the decade. The second post has been written by John Greally, and focuses on the future of epigenetics research. He suggests that isolated EWAS needs to be replaced with a new approach, involving the concurrent testing of the epigenome, transcriptome and genome.

To keep the discussion going, John Greally will be hosting a tweetchat on July 29 at 11-12 EDT. Members of the genetics community will be on Twitter discussing the future of epigenetics research and how to support progress. Be part of the conversation at #epig20.

Our twitter followers have been active in our anniversary celebrations by tweeting their favourite papers and images. The public has voted to select the Anniversary Image which will grace all our celebration activities. The winning image was announced earlier today, and you can read more about it here. This image will take pride of place on our homepage, and we will also be featuring articles from the PLOS Genetics archive over the anniversary period.

We appreciate the hard work and dedication shown by all of our contributors, and it was a delight to be able to thank our reviewers at the close of last year. The readers, authors, reviewers and editors of PLOS Genetics have come together to create and nourish this journal over the past ten years, and these celebrations are as much about you as about the journal.  As 2015 continues we will take the opportunity to reflect, plan for the future, and celebrate with the genetics community. Watch this space!

Category: Announcement, Community, Genetics, News, PLOS Genetics, Publishing | 3 Comments

Winner of the PLOS Genetics issue image campaign

 

E-cadherin

Claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse (October 2014). Image Credit: Tia DiTommaso

Earlier this month we launched a campaign to solicit people’s favourite PLOS Genetics issue images, published over the last ten years, from a selection of five. The winning image depicts claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse and was featured as PLOS Genetics’ October 2014 issue image. Submitted by Tia DiTommaso et al, in their paper entitled ‘Keratin 76 Is Required for Tight Junction Function and Maintenance of the Skin Barrier’, this image depicts claudin 1 in green, E-cadherin in red and keratin 14 in blue, and the work highlights the role of Keratin 76 in wound repair and barrier activity in the skin. Find out more about the research behind the image in this post from the authors, published as part of our ‘Understanding Images’ series. The image will be featured on the journal’s Twitter account and homepage during PLOS Genetics’ tenth anniversary week.

Thank you to all who voted!

 

Author: Jessica Miller, Publications Assistant, PLOS Genetics

Category: Announcement, Genetics, PLOS Genetics | Tagged , | Leave a comment

What’s your favourite PLOS Genetics issue image?

PLOS Genetics is celebrating its ten year anniversary in July. Over the last decade, we have seen some eye-catching issue images and we would like to know which one is your favourite. The winning image will then be featured on the PLOS Genetics’  homepage and Twitter account during the journal’s tenth anniversary week.

Take a look at the five images below, and let us know which is your favourite (or tell us about one you like which isn’t included) by taking the following survey: https://www.surveymonkey.com/r/2X6R2XZ

Journal issue images are chosen by the Editors-in-Chief each month, and this selection was picked by the journal staff here in Cambridge, UK.

The last day of the survey is Friday 24th July, so vote soon!

 

Early sensory development in the inner ear

Early sensory development in the inner ear (January 2006). Image Credit: Amy Kiernan

Rolled thumb print

Rolled thumb print (September 2007). Image Credit: Sarah E. Medland

 

 

 

 

 

 

 

 

C albicans

Candida albicans colony morphology (December 2009). Image Credit: Oliver Homann and Jeanselle Dea

Drosophila testis

Reporter construct expression in Drosophila testis and male genital tract (June 2013). Image Credit: Helen White-Cooper

 

 

 

 

 

 

 

 

Claudin 1

Claudin 1, E-cadherin and keratin 14 in the tail skin of a mouse (October 2014). Image Credit: Tia DiTommaso

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J. Andrew Bangham (1947 – 2014): Enterprising scientist who broke new ground in computational biology and image analysis

Andrew teaching in Italy

Andrew Bangham, former Professor in Computer Science at the University of East Anglia, Norwich, was a pioneering researcher with the rare ability to integrate diverse disciplines: from computer science and electrophysiology to plant development and visual art. He is best known for developing the theory of ‘sieves’, which find frequent application in modern computer vision including artistic rendering of images, and for interdisciplinary approaches to modelling plant growth and development. He was also an inspirational teacher who cultivated and encouraged talent during the birth and flowering of computer science.

Andrew was born just after the war into a scientific and artistic family. He was the eldest son of medical doctors Rosalind and Alec Bangham, and grew up outside Cambridge where Alec (later FRS) was a researcher at the Babraham Institute of Animal Physiology. Andrew’s village upbringing was filled with sailing, photography and painting; his uncle Patrick Heron had a strong influence on Andrew’s later interest in the perception of colour.

Andrew found his vocation soon after finishing high school. Unsure whether he would have the sufficient grades to study medicine, his father arranged for him to spend six months in the US, working with eminent physiologist Dan Tosteson at Duke University in North Carolina. He took to experimental research like a duck to water. Fired up by his experiences at Duke, and by the publication of his first paper, Andrew arrived at University College London (UCL) to study physiology.

The late 1960s and early 1970s were a tremendously exciting time for electrophysiology and UCL had multiple Nobel prize-winning physiologists working there. After his undergraduate degree—during which he met his future wife Kate, a medical student—he stayed on at UCL to complete a PhD in the Biophysics Department, where he worked on the electrophysiology of mitochondria. Further developing the lipid film techniques first acquired in the Tosteson lab, Andrew shared his work with colleagues at Cambridge and at the University of East Anglia (UEA).This led to an invitation to join the UEA Biology Department in 1973, in order to continue studying the electrical properties of cells and tissues.

Computational methods were still in their infancy, and Andrew became one of the first to use computers to address physiological questions. He wrote computer programmes to interpret the very noisy electrical traces produced by his experiments, inventing new filtering techniques to pick out signals in the noise. In the 1970s, the challenges of using computing in research were not purely technical, but also financial. Andrew established new ways of raising research money, setting up contracts to do modelling for local commercial companies on the University’s mainframe computers.

Through this work he was eventually able to buy a state-of-the-art Sun computer, which offered enough computing power for work on a new class of information filters, which he would later call ‘sieves’. By analogy with physical sieves, which pass objects depending on their size, computational sieves filter signals using medians—in contrast to the more conventional mean-based filters. Andrew realized that the potential for sieves was in the growing field of computer vision.

Eventually he decided to devote himself full-time to computational problems, moving in mid-1980s from UEA’s Biology Department to its School of Information Systems. Undaunted by the need to master a whole new field of mathematics known as mathematical morphology, Andrew formulated a new theoretical treatment for computer vision. He extended his funding approach to his new department by setting up contacts between numerous research groups and local and national companies, such as the local Norwich shoe company Start-rite, Britain’s Post Office, and the Independent Television Commission.

Andrew also realised that his median sieves allowed him to extract striking colour patterns from photographs, reminiscent of the paintings by Heron. Andrew became deeply interested in the relationship between median sieves and the ways in which human brains interpret visual signals. He developed software—later known as PhotoArtmaster—that offered tools for the digital alteration and analysis of photographs, and which he sold through his company Fo2Pix.

Patterns of growth in the Snapdragon model. Image Credit: Bangham et al.

Patterns of growth in the Snapdragon model. Image Credit: Bangham et al.

Throughout this period of entrepreneurship and programming, Andrew retained a strong interest in biology. In the mid-1990s he began collaborating with Professor Enrico Coen at the John Innes Centre, who shared Andrew’s passion for understanding pattern and form. They tackled the problem of how the petals of the garden snapdragon grow using a combination of computational and experimental approaches. Inspired by these experiences, Andrew established UEA’s D’Arcy Thompson Centre for Computational Biology.

A passionate sailor, and devoted to his family, Andrew had a broad network of friends, colleagues and students in Norwich and beyond. At a celebration of his scientific work at the John Innes Centre, speaker after speaker talked of Andrew’s influential role in their work, of his enthusiasm, and of his ability to articulate the links between individual problems and whole scientific fields. Colleagues described him as the unusual combination of unconventional thinker, wonderful host, inspiring teacher and supportive colleague.

Andrew, Enrico and colleagues published their work on the genetic control of tissue growth in PLOS Computational Biology and PLOS Biology:

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002071

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000537

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