Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

GPCRTree: online hierarchical classification of GPCR function

Background: G protein-coupled receptors (GPCRs) play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings: Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion: A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree

Semen quality and reproductive hormones in Faroese men: a cross-sectional population-based study of 481 men

Objectives To determine semen quality and reproductive hormone levels in young Faroese men. Design Descriptive cross-sectional study of Faroese men compared with Danish men. Setting Faroese one-centre study. Participants 481 men born from 1981 to 1987 and investigated from 2007 to 2010. Outcome measures Sperm concentration, semen volume, total sperm count, sperm motility, sperm morphology and reproductive hormone levels. Results Sperm concentrations for the Faroese men were lower than for the Danish men (crude median 40 vs 48 mill/ml, p<0.0005). Semen volume was higher, and thus the total sperm counts did not differ (159 vs 151 mill, p=0.2). Motility and morphology did not differ between the Faroese and Danes. The inhibin B/follicle-stimulating hormone ratios for the Faroese men were lower than for the Danes (64 vs 76, p=0.001). Similarly, lower total testosterone/luteinising hormone (LH) ratio (4.6 vs 6.0, p<0.0005) and lower calculated free-testosterone/LH ratio (94 vs 134, p<0.0005) were detected for the Faroese men. Conclusions Semen quality among the Faroese men is at the same low level as reported for Danish men, and the reproductive hormone levels furthermore indicated a lower Leydig cell capacity for testosterone production. The influence of environmental exposure and genetic factors on semen quality has to be studied further

Different environmental variables predict distribution and cover of the introduced red seaweed Eucheuma denticulatum in two geographical locations

In this study we examined abiotic and biotic factors that could potentially influence the presence of a non-indigenous seaweed, Eucheuma denticulatum, in two locations, one outside (Kane'ohe Bay, Hawai'i, USA) and one within (Mafia Island, Tanzania) its natural geographical range. We hypothesized that the availability of hard substrate and the amount of wave exposure would explain distribution patterns, and that higher abundance of herbivorous fishes in Tanzania would exert stronger top-down control than in Hawai'i. To address these hypotheses, we surveyed E. denticulatum in sites subjected to different environmental conditions and used generalized linear mixed models (GLMM) to identify predictors of E. denticulatum presence. We also estimated grazing intensity on E. denticulatum by surveying the type and the amount of grazing scars. Finally, we used molecular tools to distinguish between indigenous and non-indigenous strains of E. denticulatum on Mafia Island. In Kane'ohe Bay, the likelihood of finding E. denticulatum increased with wave exposure, whereas on Mafia Island, the likelihood increased with cover of coral rubble, and decreased with distance from areas of introduction (AOI), but this decrease was less pronounced in the presence of coral rubble. Grazing intensity was higher in Kane'ohe Bay than on Mafia Island. However, we still suggest that efforts to reduce non-indigenous E. denticulatum should include protection of important herbivores in both sites because of the high levels of grazing close to AOI. Moreover, we recommend that areas with hard substrate and high structural complexity should be avoided when farming non-indigenous strains of E. denticulatum

Identification of Long stress-induced non-coding transcripts that have altered expression in cancer

AbstractIt has recently become clear that the transcriptional output of the human genome is far more abundant than previously anticipated, with the vast majority of transcripts not coding for protein. Utilizing whole-genome tiling arrays, we analyzed the transcription across the entire genome in both normal human bronchial epithelial cells (NHBE) and NHBE cells exposed to the tobacco carcinogen NNK. Our efforts focused on the characterization of non-coding transcripts that were greater than 300 nucleotides in length and whose expression was increased in response to NNK. We identified 12 Long Stress-Induced Non-coding Transcripts that we term LSINCTs. Northern blot analysis revealed that these transcripts were larger than predicted from the tiling array data. Quantitative real-time RT-PCR performed across a panel of normal cell lines indicates that these transcripts are more abundantly expressed in rapidly growing tissues or in tissues that are more prone to cellular stress. These transcripts that have increased expression after exposure to NNK also had increased expression in a number of lung cancer cell lines and also in many breast cancer cell lines. Collectively, our results identified a new class of long stress responsive non-coding transcripts, LSINCTs, which have increased expression in response to DNA damage induced by NNK. LSINCTs interestingly also have increased expression in a number of cancer-derived cell lines, indicating that the expression is increased in both, correlating cellular stress and cancer

Six simple guidelines for introducing new genera of fungi

We formulate five guidelines for introducing new genera, plus one recommendation how to publish the results of scientific research. We recommend that reviewers and editors adhere to these guidelines. We propose that the underlying research is solid, and that the results and the final solutions are properly discussed. The six criteria are: (1) all genera that are recognized should be monophyletic; (2) the coverage of the phylogenetic tree should be wide in number of species, geographic coverage, and type species of the genera under study; (3) the branching of the phylogenetic trees has to have sufficient statistical support; (4) different options for the translation of the phylogenetic tree into a formal classification should be discussed and the final decision justified; (5) the phylogenetic evidence should be based on more than one gene; and (6) all supporting evidence and background information should be included in the publication in which the new taxa are proposed, and this publication should be peer-reviewed

Avidin related protein 2 shows unique structural and functional features among the avidin protein family

BACKGROUND: The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin. RESULTS: In the present study, we have employed multiple biochemical methods to better understand the structure-function relationship of AVR proteins focusing on AVR2. Firstly, we have solved the high-resolution crystal structure of AVR2 in complex with a bound ligand, D-biotin. The AVR2 structure reveals an overall fold similar to the previously determined structures of avidin and AVR4. Major differences are seen, especially at the 1–3 subunit interface, which is stabilized mainly by polar interactions in the case of AVR2 but by hydrophobic interactions in the case of AVR4 and avidin, and in the vicinity of the biotin binding pocket. Secondly, mutagenesis, competitive dissociation analysis and differential scanning calorimetry were used to compare and study the biotin-binding properties as well as the thermal stability of AVRs and avidin. These analyses pinpointed the importance of residue 109 for biotin binding and stability of AVRs. The I109K mutation increased the biotin-binding affinity of AVR2, whereas the K109I mutation decreased the biotin-binding affinity of AVR4. Furthermore, the thermal stability of AVR2(I109K) increased in comparison to the wild-type protein and the K109I mutation led to a decrease in the thermal stability of AVR4. CONCLUSION: Altogether, this study broadens our understanding of the structural features determining the ligand-binding affinities and stability as well as the molecular evolution within the protein family. This novel information can be applied to further develop and improve the tools already widely used in avidin-biotin technology

Humanized NOG Mice for Intravaginal HIV Exposure and Treatment of HIV Infection

Humanized mice provide a sophisticated platform to study human immunodeficiency virus (HIV) virology and to test antiviral drugs. This protocol describes the establishment of a human immune system in adult NOG mice. Here, we explain all the practical steps from isolation of umbilical cord blood derived human CD34+ cells and their subsequent intravenous transplantation into the mice, to the manipulation of the model through HIV infection, combination antiretroviral therapy (cART), and blood sampling. Approximately 75,000 hCD34+ cells are injected intravenously into the mice and the level of human chimerism, also known as humanization, in the peripheral blood is estimated longitudinally for months by flow cytometry. A total of 75,000 hCD34+ cells yields 20%–50% human CD45+ cells in the peripheral blood. The mice are susceptible to intravaginal infection with HIV and blood can be sampled once weekly for analysis, and twice monthly for extended periods. This protocol describes an assay for quantification of plasma viral load using droplet digital PCR (ddPCR). We show how the mice can be effectively treated with a standard-of- care cART regimen in the diet. The delivery of cART in the form of regular mouse chow is a significant refinement of the experimental model. This model can be used for preclinical analysis of both systemic and topical pre-exposure prophylaxis compounds as well as for testing of novel treatments and HIV cure strategies