Collection Overview: Ten Years of Wonderful Open Access Science

To mark our tenth Anniversary at PLOS Biology, we are launching a special, celebratory Tenth Anniversary PLOS Biology Collection which showcases 10 specially selected PLOS Biology research articles drawn from a decade of publishing excellent science. It also features newly commissioned articles, including thought-provoking pieces on the Open Access movement (past and present), on article-level metrics, and on the history of the Public Library of Science. Each research article highlighted in the collection is also accompanied by a PLOS Biologue blog post to extend the impact of these remarkable studies to the widest possible audience.As we celebrate 10 years of PLOS Biology, 10 years of the Public Library of Science, and 10 years of strong advocacy and trail-blazing for the Open Access movement, we mustn''t forget the real star of the show – the fantastic science that we''ve published.It''s hard to cast one''s mind back 10 years and recall the scepticism with which open access publishing was initially received. A key concern at the time was that the model would be tainted with the stigma of “vanity publishing,” and that this model, in which the author pays to publish, is incompatible with integrity, editorial rigour, and scientific excellence. As also discussed in the accompanying editorial [1], the sheer quality of the science that has appeared in PLOS Biology has been vital for dispelling this myth.Our tenth anniversary provides us with a great opportunity to celebrate all of the 1800 or so research articles published in PLOS Biology since our launch in 2003. Unable to showcase each one in turn, we turned to our Editorial Board to help us pick the top 10 research articles to feature in a special Tenth Anniversary PLOS Biology Collection (www.ploscollections.org/Biology10thAnniversary). During the month of October, we will also publish a PLOS Biologue blog post (http://blogs.plos.org/biologue/) for each of these selected research articles, trying to capture and convey what it is about them that the staff editors, the editorial board, and the authors feel is special.By now, you''re probably wondering which papers we selected. The selection is detailed in Box 1, with links to each article. If you haven''t read these articles before, we urge you to read them now and to judge for yourself. As Editorial Board Member Steve O''Rahilly put it, “I think a common theme in many of the best PLOS Biology papers is that they are rich in data that is analysed very carefully and self-critically and presented without hype. However the conclusions are important for the biological community and their insights are likely to stand the test of time.”As well as publishing research articles, PLOS Biology has a thriving Magazine section that has hosted scientific and policy debates, aired polemical and provocative views, celebrated scientific lives in obituaries, reviewed interesting books, and explored unsolved mysteries. One example of how this section has triggered productive community debate is Rosie Redfield''s Perspective on how genetics should be taught to undergraduates [2]. Yet we don''t seek just to provoke debate, but also to enlighten; take a moment to read Georgina Mace''s editorial on the current issues and debates in the sustainability sciences [3]. We also try to break down barriers between fields [4] and to promote public engagement with science [5],[6].We feel strongly that our role doesn''t end with publishing the research article itself. Instead, we aim to unpackage the fascinating discoveries published in PLOS Biology by commissioning articles that explain the significance and impact of the research we publish to audiences of varying expertise. These companion articles range from Primers, which are written by experts who contextualise research articles for those in the field; to Synopses, which are written by science writers who digest an article for our wider readership of biologists; and finally, to PLOS Biologue blog posts, which distil research discoveries for a more general scientifically engaged public. We also use social media to bring these findings to the attention of a global online audience.Of course, the continued success of PLOS Biology doesn''t rest solely on the amazing research we''ve already published; it also hinges on the ground-breaking science we strive to publish in the future. Maintaining the high quality of the biology that we publish is of vital importance to us, not least because, as Editorial Board Member Robert Insall reflects, “What I like about PLOS Biology is that it avoids other journals'' fixation on fashion and the biggest names. This means the papers PLOS Biology is publishing now will last longer and mean more in a generation''s time.”

Box 1. Research Articles Featured in the Tenth Anniversary PLOS Biology Collection

Our Editorial Board Members helped us select 10 articles from the great science published during PLOS Biology''s first decade to feature in our Tenth Anniversary Collection. Please access these articles from the list below and from our Collection page. To read the PLOS Biologue blog posts that accompany them, please go to http://blogs.plos.org/biologue/ for more information.Carmena J et al. (2003) Learning to Control a BrainMachine Interface for Reaching and Grasping by Primates  Primer: Current Approaches to the Study of Movement Control  Synopsis: Retraining the Brain to Recover Movement Brennecke J et al. (2004) Principles of MicroRNA–Target Recognition  Synopsis: Seeds of Destruction: Predicting How microRNAs Choose Their Target Voight BF et al. (2005) A Map of Recent Positive Selection in the Human Genome  Synopsis: Clues to Our Past: Mining the Human Genome for Signs of Recent Selection Palmer C et al. (2007) Development of the Human Infant Intestinal Microbiota  Synopsis: Microbes Colonize a Baby''s Gut with Distinction Levy S et al. (2007) The Diploid Genome Sequence of an Individual Human  Synopsis: A New Human Genome Sequence Paves the Way for Individualized Genomics Illingworth R et al. (2008) A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci Silva J et al. (2008) Promotion of Reprogramming to Ground State Pluripotency by Signal Inhibition  Synopsis: A Shortcut to Immortality: Rapid Reprogramming with Tissue Cells Coppé J-P et al. (2008) Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor Shu X et al. (2011) A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms Bonds MH et al. (2012) Disease Ecology, Biodiversity, and the Latitudinal Gradient in Income  Synopsis: Which Came First: Burden of Infectious Disease or Poverty?     

HPID: the Human Protein Interaction Database

The Human Protein Interaction Database (http://www.hpid.org) was designed (1) to provide human protein interaction information pre-computed from existing structural and experimental data, (2) to predict potential interactions between proteins submitted by users and (3) to provide a depository for new human protein interaction data from users. Two types of interaction are available from the pre-computed data: (1) interactions at the protein superfamily level and (2) those transferred from the interactions of yeast proteins. Interactions at the superfamily level were obtained by locating known structural interactions of the PDB in the SCOP domains and identifying homologs of the domains in the human proteins. Interactions transferred from yeast proteins were obtained by identifying homologs of the yeast proteins in the human proteins. For each human protein in the database and each query submitted by users, the protein superfamilies and yeast proteins assigned to the protein are shown, along with their interacting partners. We have also developed a set of web-based programs so that users can visualize and analyze protein interaction networks in order to explore the networks further. AVAILABILITY: http://www.hpid.org.     

DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile

Dividing protein structures into domains is proven useful for more accurate structural and functional characterization of proteins. Here, we develop a method, called DDOMAIN, that divides structure into DOMAINs using a normalized contact-based domain-domain interaction profile. Results of DDOMAIN are compared to AUTHORS annotations (domain definitions are given by the authors who solved protein structures), as well as to popular SCOP and CATH annotations by human experts and automatic programs. DDOMAIN's automatic annotations are most consistent with the AUTHORS annotations (90% agreement in number of domains and 88% agreement in both number of domains and at least 85% overlap in domain assignment of residues) if its three adjustable parameters are trained by the AUTHORS annotations. By comparison, the agreement is 83% (81% with at least 85% overlap criterion) between SCOP-trained DDOMAIN and SCOP annotations and 77% (73%) between CATH-trained DDOMAIN and CATH annotations. The agreement between DDOMAIN and AUTHORS annotations goes beyond single-domain proteins (97%, 82%, and 56% for single-, two-, and three-domain proteins, respectively). For an "easy" data set of proteins whose CATH and SCOP annotations agree with each other in number of domains, the agreement is 90% (89%) between "easy-set"-trained DDOMAIN and CATH/SCOP annotations. The consistency between SCOP-trained DDOMAIN and SCOP annotations is superior to two other recently developed, SCOP-trained, automatic methods PDP (protein domain parser), and DomainParser 2. We also tested a simple consensus method made of PDP, DomainParser 2, and DDOMAIN and a different version of DDOMAIN based on a more sophisticated statistical energy function. The DDOMAIN server and its executable are available in the services section on http://sparks.informatics.iupui.edu.     

Prion-like proteins and their computational identification in proteomes

Introduction: The aberrant or misfolded forms of the prion protein have been described as the causative agents of rare transmissible spongiform encephalopathies. In addition, proteins associated with frequently occurring neurodegenerative disorders, such as Alzheimer’s and Parkinson’s, are shown to share prion-like properties and to spread the disease in the brain.

Areas covered: Interest in the prion phenomenon has crystallized in a series of computational methods aimed at uncovering prion-like proteins at the proteome level. These programs rely on the identification of sequence signatures similar to those of yeast prions, whose structural conversion is driven by specific domains enriched in glutamine/asparagine residues. A myriad of prion-like candidates, similar to those in yeast, are predicted to exist in organisms across all kingdoms of life. We review here the role of prions, prionoids and prion-like proteins in health and disease, with a special focus on the algorithms and databases developed for their prediction and classification.

Expert commentary: Computational approaches provide novel insights into prion-like protein functions, their regulation and their role in disease.     

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH‐like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH‐like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.      

CBS domains: structure, function, and pathology in human proteins

The cystathionine--synthase (CBS) domain is an evolutionarily conserved protein domain that is present in the proteome of archaebacteria, prokaryotes, and eukaryotes. CBS domains usually come in tandem repeats and are found in cytosolic and membrane proteins performing different functions (metabolic enzymes, kinases, and channels). Crystallographic studies of bacterial CBS domains have shown that two CBS domains form an intramolecular dimeric structure (CBS pair). Several human hereditary diseases (homocystinuria, retinitis pigmentosa, hypertrophic cardiomyopathy, myotonia congenital, etc.) can be caused by mutations in CBS domains of, respectively, cystathionine--synthase, inosine 5'-monophosphate dehydrogenase, AMP kinase, and chloride channels. Despite their clinical relevance, it remains to be established what the precise function of CBS domains is and how they affect the structural and/or functional properties of an enzyme, kinase, or channel. Depending on the protein in which they occur, CBS domains have been proposed to affect multimerization and sorting of proteins, channel gating, and ligand binding. However, recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites. chloride channel; cystathionine -synthase; AMP-activated protein kinase     

Gene note. Characterization of a tomato karyopherin {alpha} that interacts with the Tomato Yellow Leaf Curl Virus (TYLCV) capsid protein

A karyopherin (LeKAP1) cDNA was isolated from tomato plants. The deduced LeKAP1 protein sequence of 527 amino acids showed similarity to other plant karyopherin proteins. When LeKAP1 was expressed in a yeast two-hybrid system together with the gene coding for the capsid protein (CP) of the tomato yellow curl leaf virus (TYLCV), it interacted directly with CP. Thus, LeKAP1 may be involved in the nuclear import of TYLCV CP and, potentially, the TYLCV genomes during viral infection of the host tomato cells.     

SCOPExplorer: a tool for browsing and analyzing structural classification of proteins (SCOP) data

We have developed a tool, named "SCOPExplorer", for browsing and analyzing SCOP information. SCOPExplorer 1) contains a tree-style viewer to display an overview of protein structure data, 2) is able to employ a variety of options to analyze SCOP data statistically, and 3) provides a function to link protein domains to protein data bank (PDB) resources. SCOPExplorer uses an XML-based structural document format, named "SCOPML", derived from the SCOP data. To evaluate SCOPExplorer, proteins containing more than 20 domains were analyzed. The Skp1-Skp2 protein complex and the Fab fragment of IgG2 contain the largest numbers of domains in the current eukaryotic SCOP database. These proteins are known to either bind to various proteins or generate diversity. This suggests that the more domains a protein has, the more interactions or more variability it will be capable of. (SCOPExplorer is available for download at http://scopexplorer.ulsan.ac.kr).     

Are changes in breeding habitat responsible for recent population changes of long-distance migrant birds?

Capsule: The direction and magnitude of changes in structure of UK woodlands since the 1980s, are inconsistent with them playing a causative role in the declines of four migrant bird species in upland oak woods.

Aims: To investigate whether changes in woodland structure were a possible cause of population changes of four Afro-Palearctic migrants (Wood Warbler Phylloscopus sibilatrix, Tree Pipit Anthus trivialis, Pied Flycatcher Ficedula hypoleuca and Common Redstart Phoenicurus phoenicurus) in the upland oakwoods of western and northern Britain.

Methods: Bird population estimates and measures of woodland structure were recorded in two time periods 1982–85 and 2003–04 across six regions of the UK. We modelled the effect of habitat change and initial habitat state on population changes between the two time periods. The predicted effects of habitat change on populations were then compared with observed population changes across the different regions.

Results: All four species underwent population declines; there were also significant increases in ground cover and understorey cover. The number of birds in 2003–04 was influenced by habitat structure at this time in addition to showing regional differences. Change in bird numbers varied between regions and was affected by both the initial habitat state and change in habitat structure, with regional variation in the effect of habitat change. There was however no relationship between the predicted effect of change in habitat structure on population size and observed regional population changes.

Conclusions: Changes in woodland structure are unlikely to be the main driver of population change in these four migrant bird species, and large-scale factors affecting demographics in other parts of their breeding range or in their wintering areas are likely reasons for local population declines.     

Open Labware: 3-D Printing Your Own Lab Equipment

The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before.Applications of 3-D printing technologies (Fig. 1A, Box 1) have become as diverse as the types of materials that can be used for printing. Replacement parts at the International Space Station may be printed in orbit from durable plastics or metals, while back on Earth the food industry is starting to explore the same basic technology to fold strings of chocolate into custom-shaped confectionary. Also, consumer-oriented laser-cutting technology makes it very easy to cut raw materials such as sheets of plywood, acrylic, or aluminum into complex shapes within seconds. The range of possibilities comes to light when those mechanical parts are combined with off-the-shelf electronics, low-cost microcontrollers like Arduino boards [1], and single-board computers such as a Beagleboard [2] or a Raspberry Pi [3]. After an initial investment of typically less than a thousand dollars (e.g., to set-up a 3-D printer), the only other materials needed to build virtually anything include a few hundred grams of plastic (approximately US$30/kg), cables, and basic electronic components [4,5].Open in a separate windowFig 1Examples of open 3-D printed laboratory tools. A ₁, Components for laboratory tools, such as the base for a micromanipulator [18] shown here, can be rapidly prototyped using 3-D printing. A _2, The printed parts can be easily combined with an off-the-shelf continuous rotation servo-motor (bottom) to motorize the main axis. B ₁, A 3-D printable micropipette [8], designed in OpenSCAD [19], shown in full (left) and cross-section (right). B ₂, The pipette consists of the printed parts (blue), two biro fillings with the spring, an off-the-shelf piece of tubing to fit the tip, and one screw used as a spacer. B ₃, Assembly is complete with a laboratory glove or balloon spanned between the two main printed parts and sealed with tape to create an airtight bottom chamber continuous with the pipette tip. Accuracy is ±2–10 μl depending on printer precision, and total capacity of the system is easily adjusted using two variables listed in the source code, or accessed via the “Customizer” plugin on the thingiverse link [8]. See also the first table.

Box 1. Glossary

Open source

A collective license that defines terms of free availability and redistribution of published source material. Terms include free and unrestricted distribution, as well as full access to source code/blueprints/circuit board designs and derived works. For details, see http://opensource.org.

Maker movement

Technology-oriented extension of the traditional “Do-it-Yourself (DIY)” movement, typically denoting specific pursuits in electronics, CNC (computer numerical control) tools such as mills and laser cutters, as well as 3-D printing and related technologies.

3-D printing

Technology to generate three-dimensional objects from raw materials based on computer models. Most consumer-oriented 3-D printers print in plastic by locally melting a strand of raw material at the tip (“hot-end”) and “drawing” a 3-D object in layers. Plastic materials include Acrylnitrile butadiene styrene (ABS) and Polylactic acid (PLA). Many variations of 3-D printers exist, including those based on laser-polymerization or fusion of resins or powdered raw materials (e.g., metal or ceramic printers).

Arduino boards

Inexpensive and consumer-oriented microcontroller boards built around simple processors. These boards offer a variety of interfaces (serial ports, I2C and CAN bus, etc.), μs-timers, and multiple general-purpose input-output (GPIO) pins suitable for running simple, time-precise programs to control custom-built electronics.

Single board computers

Inexpensive single-board computers capable of running a mature operating system with graphical-user interface, such as Linux. Like microcontroller boards, they offer a variety of hardware interfaces and GPIO pins to control custom-built electronics.It therefore comes as no surprise that these technologies are also routinely used by research scientists and, especially, educators aiming to customize existing lab equipment or even build sophisticated lab equipment from scratch for a mere fraction of what commercial alternatives cost [6]. Designs for such “Open Labware” include simple mechanical adaptors [7], micropipettes (Fig. 1B) [8], and an egg-whisk–based centrifuge [9] as well as more sophisticated equipment such as an extracellular amplifier for neurophysiological experiments [10], a thermocycler for PCR [11], or a two-photon microscope [12]. At the same time, conceptually related approaches are also being pursued in chemistry [13–15] and material sciences [16,17]. See also

Laminin-alpha1 globular domains 3 and 4 induce heterotrimeric G protein binding to alpha-syntrophin's PDZ domain and alter intracellular Ca2+ in muscle

-Syntrophin is a component of the dystrophin glycoprotein complex (DGC). It is firmly attached to the dystrophin cytoskeleton via a unique COOH-terminal domain and is associated indirectly with -dystroglycan, which binds to extracellular matrix laminin. Syntrophin contains two pleckstrin homology (PH) domains and one PDZ domain. Because PH domains of other proteins are known to bind the -subunits of the heterotrimeric G proteins, whether this is also a property of syntrophin was investigated. Isolated syntrophin from rabbit skeletal muscle binds bovine brain G-subunits in gel blot overlay experiments. Laminin-1-Sepharose or specific antibodies against syntrophin, - and -dystroglycan, or dystrophin precipitate a complex with G from crude skeletal muscle microsomes. Bacterially expressed syntrophin fusion proteins and truncation mutants allowed mapping of G binding to syntrophin's PDZ domain; this is a novel function for PDZ domains. When laminin-1 is bound, maximal binding of G_s and G occurs and active G_s, measured as GTP-³⁵S bound, decreases. Because intracellular Ca²⁺ is elevated in Duchenne muscular dystrophy and G_s is known to activate the dihydropyridine receptor Ca²⁺ channel, whether laminin also altered intracellular Ca²⁺ was investigated. Laminin-1 decreases active (GTP-S-bound) G_s, and the Ca²⁺ channel is inhibited by laminin-1. The laminin ₁-chain globular domains 4 and 5 region, the region bound by DGC -dystroglycan, is sufficient to cause an effect, and an antibody that specifically blocks laminin binding to -dystroglycan inhibits G binding by syntrophin in C₂C₁₂ myotubes. These observations suggest that DGC is a matrix laminin, G protein-coupled receptor. Duchenne muscular dystrophy; protein G -subunit; pleckstrin homology domain     

Comparative genetic analysis of PP2A-Cdc55 regulators in budding yeast

Cdc55, a regulatory B subunit of the protein phosphatase 2A (PP2A) complex, plays various functions during mitosis. Sequestration of Cdc55 from the nucleus by Zds1 and Zds2 is important for robust activation of mitotic Cdk1 and mitotic progression in budding yeast. However, Zds1-family proteins are found only in fungi but not in higher eukaryotes. In animal cells, highly conserved ENSA/ARPP-19 family proteins bind and inhibit PP2A–B55 activity for mitotic entry.

In this study, we compared the relative contribution of Zds1/Zds2 and ENSA-family proteins Igo1/Igo2 on Cdc55 functions in budding yeast mitosis. We confirmed that Igo1/Igo2 can inhibit Cdc55 in early mitosis, but their contribution to Cdc55 regulation is relatively minor compared with the role of Zds1/Zds2. In contrast to Zds1, which primarily localized to the sites of cell polarity and in the cytoplasm, Igo1 is localized in the nucleus, suggesting that Igo1/Igo2 inhibit Cdc55 in a manner distinct from Zds1/Zds2.

Our analysis confirmed an evolutionarily conserved function of ENSA-family proteins in inhibiting PP2A-Cdc55, and we propose that Zds1-dependent sequestration of PP2A-Cdc55 from the nucleus is uniquely evolved to facilitate closed mitosis in fungal species.     

Climate and land use change impacts on Mediterranean high-mountain vegetation in the Apennines since the 1950s

Background: High-mountain ecosystems are centres of plant diversity that are particularly sensitive to land-use and climate change.

Aims: We investigated the ecological trends associated with land use and climate change since the 1950s in different vegetation types in high-mountain habitats in the central Apennines.

Methods: We analysed temporal changes in: Pinus mugo scrub, calcareous subalpine grasslands and alpine scree vegetation, comparing historical and recent vegetation records from vegetation plots from two periods (1955–1980 and 1990–2014) for their ecological indicator values (Landolt temperature and nutrient indicators) and structural traits (growth forms) over time using generalised linear models (GLMs).

Results: We observed significant temporal differences in the ecology and structure of the analysed habitats. In the Pinus mugo scrub we detected a reduction of subalpine and herbaceous species and in calcareous alpine screes we observed an increment of the lower montane, montane and subalpine species and of dwarf shrubs. Conversely, subalpine grasslands were stable over time.

Conclusions: Ecological changes that have occurred in the Central Apennines, following changes in type and intensity of land use and recent warming are consistent with those observed in other European mountains, for which climate and land-use changes are claimed as the main driving forces.     

Control of Na+-K+-ATPase beta 1-subunit expression: role of 3'-untranslated region

Using in vitro translation and cell transfection assays, we previously demonstrated that the Na⁺-K⁺-ATPase ₁ mRNA species containing its longest 3'-untranslated region (UTR) exhibited the lowest translational efficiency. Here, employing deletions and in vivo expression assays, using direct injection of plasmids into rat ventricular myocardium, we identified a 143-nt segment located in the distal 3'-UTR of ₁ mRNA that was associated with decreased luciferase expression; interestingly, this segment contains three AUUUA motifs. Using RNA-protein binding assays and UV cross-linking of cRNA with cytosolic proteins of rat heart, we identified an 38-kDa protein that specifically bound to the cRNA encoding the 143-nt segment of ₁ mRNA 3'-UTR. Mutation of three nucleotides located in the middle region of the 143-nt segment, which was predicted to greatly disrupt a putative stem-loop structure of the cRNA in this region, was associated with reduced binding of the mutated cRNA to the protein migrating at 38 kDa. The cRNA encoding a segment of cyclooxygenase-2 mRNA 3'-UTR containing six AUUUA sequences did not bind the protein migrating at 38 kDa and did not compete with the binding of the wild-type 143-nt ₁ cRNA to the protein. The above results suggest that the 143-nt segment in the distal segment of the 3'-UTR of ₁ mRNA may play an important role in the control of ₁-subunit expression. RNA-protein binding; AUUUA sequence; plasmid expression in heart; direct myocardial injection; cardiac expression     

Do bridge construction activities influence birds using the River Mersey,in northwest England?

Capsule: Bridge construction works over a major river did not adversely impact the overall wintering and breeding bird assemblage, although contrasting species-specific trends in breeding number were noted.

Aims: To determine whether the wintering water-bird and breeding bird assemblage using the River Mersey, in northwest England, was influenced by bridge construction works.

Methods: Common bird census and wintering bird surveys were carried out before and during construction of the Mersey Gateway bridge. The species abundance and richness of wintering water-birds, assigned to a group (‘Waterfowl’, ‘Wader’, ‘Wetland species’ and ‘Gull’) and breeding birds, assigned to a group (‘Salt marsh species’, ‘Waterfowl species’, ‘Wader species’, ‘Warbler species’ and ‘Other passerine species’), were separately compared before and during the works.

Results: We found little evidence that the bridge construction displaced wintering water-birds and instead found that for most bird groups, their assemblages were higher during the construction works, compared to before. Similarly, we found no evidence that the bridge construction reduced breeding density of any bird group. Contrasting species-specific trends were, however, noted, with some species only recorded breeding during the construction works, and other species recorded in higher breeding densities before the works.

Conclusion: The inadvertent increase in the mud-flats around the bridge structure since the works resulted in more mud-flat being exposed for a greater amount of time, and thus increased the foraging opportunities for many birds. This may at least partly explain why overall wintering bird abundance and richness increased since the works began. Although most breeding birds either increased or remained stable, in number since the works, a small number reduced. This may have been a consequence of the removal of suitable nesting habitat. This study provides a preliminary assessment of the influence of bridge construction on birds.     

Short communication. First record of larval Brama brama (Pisces: Bramidae) and Corphaena hippurus (Pisces: Coryphaenidae) in the Adriatic Sea

The occurrence of early larval stages of Brama brama and Coryphaena hippurus is reported for the first time in Adriatic waters. Two larvae of B.brama between 4.36 and 5.00 mm, and two larvae of C.hippurus between 4.75 and 4.95 mm standard length, were found in ichthyoplankton collections taken off the River Neretva estuary (43010N, 17°250E) and station Stoncica, island Vis (43°000N, 16°20E) (eastern middle Adriatic), respectively. The capture of both species (B.brama) in August 1998; C.hippurus in May 1998) is in agreement with their proposed seasonal life cycle in the Adriatic Sea.      

An approach to systematic detection of protein structural motifs

A procedure to detect similar local structures of proteins fromC coordinates is presented. First, the conformations of seven-residuepeptide segments are approximated by a limited number of representatives,each of which is assigned a symbol. Thus, the overall conformationof a protein is represented by a symbol string. The comparisonof these symbol strings using a sequence alignment techniquethen gives pairs of similar local structures. These pairs areconsidered candidates of structural motifs. The applicationof the procedure to the analysis of 93 proteins gave 858 pairsof similar local structures, which included several well-knownstructural motifs such as the nucleotide-binding ßß-unitand the calcium-binding EF hand. The characterization of aminoacid patterns of similar local structures given by the procedureshould be useful for the development of protein structure predictionbased on the acquisition of empirical rules from a large-scaledatabase.     

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

I introduce an open-source R package ‘dcGOR’ to provide the bioinformatics community with the ease to analyse ontologies and protein domain annotations, particularly those in the dcGO database. The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies including Gene Ontology. Although increasing in popularity, this database needs statistical and graphical support to meet its full potential. Moreover, there are no bioinformatics tools specifically designed for domain ontology analysis. As an add-on package built in the R software environment, dcGOR offers a basic infrastructure with great flexibility and functionality. It implements new data structure to represent domains, ontologies, annotations, and all analytical outputs as well. For each ontology, it provides various mining facilities, including: (i) domain-based enrichment analysis and visualisation; (ii) construction of a domain (semantic similarity) network according to ontology annotations; and (iii) significance analysis for estimating a contact (statistical significance) network. To reduce runtime, most analyses support high-performance parallel computing. Taking as inputs a list of protein domains of interest, the package is able to easily carry out in-depth analyses in terms of functional, phenotypic and diseased relevance, and network-level understanding. More importantly, dcGOR is designed to allow users to import and analyse their own ontologies and annotations on domains (taken from SCOP, Pfam and InterPro) and RNAs (from Rfam) as well. The package is freely available at CRAN for easy installation, and also at GitHub for version control. The dedicated website with reproducible demos can be found at http://supfam.org/dcGOR.

This is a PLOS Computational Biology Software Article

     

Habitat preference of female Corncrakes Crex crex: implications for the conservation of breeding sites in a secretive species

Capsule: Forb-rich and diverse, annually mown vegetation is the preferred Corncrake Crex crex breeding habitat in floodplains.

Aims: To identify habitat preferences of female Corncrakes and characteristics of breeding sites in floodplain habitats and derive recommendations for management.

Methods: We tracked six female Corncrakes and compared vegetation characteristics at 78 male calling sites with regard to breeding records and diurnal call activity of males, because we expect the latter to indicate female occurrence. Additionally, we analysed how practice and timing of land use in the preceding year affected vegetation structure.

Results: Females preferred areas with high cover of forbs and a distinct relief heterogeneity, which was associated with overall vegetation diversity. All calling sites with breeding records and diurnal call incidence of males showed high forb and low sedge cover, low litter heights and a close location to ditches. Favourable conditions were best provided by mowing in the preceding year.

Conclusion: In eutrophic habitats, female Corncrakes preferred a vegetation structure created by annual mowing. Because nests and unfledged chicks are threatened by mowing operations, we recommend an alternating management regime based on the identification of breeding sites using male diurnal calling activity.