Predicting landscape-genetic consequences of habitat loss, fragmentation and mobility for multiple species of woodland birds

Inference concerning the impact of habitat fragmentation on dispersal and gene flow is a key theme in landscape genetics. Recently, the ability of established approaches to identify reliably the differential effects of landscape structure (e.g. land-cover composition, remnant vegetation configuration and extent) on the mobility of organisms has been questioned. More explicit methods of predicting and testing for such effects must move beyond post hoc explanations for single landscapes and species. Here, we document a process for making a priori predictions, using existing spatial and ecological data and expert opinion, of the effects of landscape structure on genetic structure of multiple species across replicated landscape blocks. We compare the results of two common methods for estimating the influence of landscape structure on effective distance: least-cost path analysis and isolation-by-resistance. We present a series of alternative models of genetic connectivity in the study area, represented by different landscape resistance surfaces for calculating effective distance, and identify appropriate null models. The process is applied to ten species of sympatric woodland-dependant birds. For each species, we rank a priori the expectation of fit of genetic response to the models according to the expected response of birds to loss of structural connectivity and landscape-scale tree-cover. These rankings (our hypotheses) are presented for testing with empirical genetic data in a subsequent contribution. We propose that this replicated landscape, multi-species approach offers a robust method for identifying the likely effects of landscape fragmentation on dispersal.

State-related alterations of gene expression in bipolar disorder : a systematic review

Objective:  Alterations in gene expression in bipolar disorder have been found in numerous studies. It is unclear whether such alterations are related to specific mood states. As a biphasic disorder, mood state-related alterations in gene expression have the potential to point to markers of disease activity, and trait-related alterations might indicate vulnerability pathways. This review therefore evaluated the evidence for whether gene expression in bipolar disorder is state or trait related.

Methods:  A systematic review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline for reporting systematic reviews, based on comprehensive database searches for studies on gene expression in patients with bipolar disorder in specific mood states, was conducted. We searched Medline, Embase, PsycINFO, and The Cochrane Library, supplemented by manually searching reference lists from retrieved publications.

Results:  A total of 17 studies were included, comprising 565 patients and 418 control individuals. Six studies evaluated intraindividual alterations in gene expression across mood states. Two of five studies found evidence of intraindividual alterations in gene expression between a depressed state and a euthymic state. No studies evaluated intraindividual differences in gene expression between a manic state and a euthymic state, while only one case study evaluated differences between a manic state and a depressed state, finding altered expression in seven genes. No study investigated intraindividual variations in gene expression between a euthymic state and multiple states of various polarities (depressive, manic, hypomanic). Intraindividual alterations in expression of the same genes were not investigated across studies. Only one gene (the brain-derived neurotrophic factor gene; BDNF) was investigated across multiple studies, showing no alteration between bipolar disorder patients and control individuals.

Conclusions:  There is evidence of some genes exhibiting state-related alterations in expression in bipolar disorder; however, this finding is limited by the lack of replication across studies. Further prospective studies are warranted, measuring gene expression in various affective phases, allowing for assessment of intraindividual differences.

Consideration of multiple template switches is critical to the determination of the recombination rate on the HIV genome

Retroviral recombination drives viral diversity and facilitates the emergence of immune escape and drug resistant mutants that contribute to disease progression. Current estimates of retroviral recombination rates are based on indirect measurements that do not take into account the effects of multiple recombination events. In the presence of multiple template switches, any even number of template switches result in no observed recombination and any odd number is detected as a single recombination event. We demonstrate that ignoring multiple recombination events consistently underestimates the true recombination rate, especially over large genetic distances and high rates of recombination. Here, we present a novel approach to measure rates of recombination across different gene segments regardless of the effects of genetic distance and the overall rate of recombination. We apply these tools to a novel HIV-1 marker system, which mimics the recombination process between closely related genomes, analogous to those found within the quasispecies of an infected individual. We directly measure the recombination rate in gag, correcting for the effects of multiple template switches and background recombination. Furthermore, our analysis indicates that recombination rates are likely to vary across the viral genome. This system is applicable to other studies to accurately measure the recombination rate that is critical for the diversification of retroviruses.

Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease

Current single-locus-based analyses and candidate disease gene prediction methodologies used in genome-wide association studies (GWAS) do not capitalize on the wealth of the underlying genetic data, nor functional data available from molecular biology. Here, we analyzed GWAS data from the Wellcome Trust Case Control Consortium (WTCCC) on coronary artery disease (CAD). Gentrepid uses a multiple-locus-based approach, drawing on protein pathway- or domain-based data to make predictions. Known disease genes may be used as additional information (seeded method) or predictions can be based entirely on GWAS single nucleotide polymorphisms (SNPs) (ab initio method). We looked in detail at specific predictions made by Gentrepid for CAD and compared these with known genetic data and the scientific literature. Gentrepid was able to extract known disease genes from the candidate search space and predict plausible novel disease genes from both known and novel WTCCC-implicated loci. The disease gene candidates are consistent with known biological information. The results demonstrate that this computational approach is feasible and a valuable discovery tool for geneticists.

A five-gene hedgehog signature developed as a patient preselection tool for hedgehog inhibitor therapy in medulloblastoma

Purpose: 

IPA: Integrated predictive gene signature from gene expression based breast cancer patient samples

Background: Novel predictive markers are needed to accurately diagnose the breast cancer patients so they do not need to undergo any unnecessary aggressive therapies. Various gene expression studies based predictive gene signatureshave generated in the recent past to predict the binary estrogen-receptor subclass or to predict the therapy response subclass. However, the existing algorithms comes with many limitations, including low predictive performances over multiple cohorts of patients and non-significant or limited biological roles associated with thepredictive gene signatures. Therefore, the aim of this study is to develop novel predictive markers with improved performances.Methods: We propose a novel prediction algorithm called IPA to construct a predictive gene signature for performing multiple prediction tasks of predicting estrogen-receptor based binary subclass and predicting chemotherapy response (neoadjuvantly) based binary subclass. The constructed gene signature with considering multiple classification techniques was used to evaluate the algorithm performance on multiple cohorts of breast cancer patients.Results: The evaluation on multiple validation cohorts demonstrated that proposed algorithm achieved stable and high performance to perform prediction tasks, with consideration given to any classification techniques. We show that the predictive gene signature of our proposed algorithm reflects the mechanisms underlying the estrogen-receptors or response to therapy with significant greater biological interpretations, compared with the other existing algorithm.

An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

3T3-L1 adipocytes display phenotypic characteristics of multiple adipocyte lineages

Differentiated 3T3-L1 adipocytes are a widely used in vitro model of white adipocytes. In addition to classical white and brown adipocytes that are derived from different cell lineages, beige adipocytes have also been identified, which have characteristics of both white and brown adipocytes. Here we show that 3T3-L1 adipocytes display features of multiple adipocytes lineages. While the gene expression profile and basal bioenergetics of 3T3-L1 adipocytes was typical of white adipocytes, they responded acutely to catecholamines by increasing oxygen consumption in an UCP1-dependent manner, and by increasing the expression of genes enriched in brown but not beige adipocytes. Chronic exposure to catecholamines exacerbated this phenotype. However, a beige adipocyte differentiation procedure did not induce a beige adipocyte phenotype in 3T3-L1 fibroblasts. These multiple lineage features should be considered when interpreting data from experiments utilizing 3T3-L1 adipocytes.

Characterization of antibody V segment diversity in the Tasmanian devil (Sarcophilus harrisii)

The Tasmanian devil (Sarcophilus harrisii) immune system has recently been under scrutiny because of the emergence of a contagious cancer, which has decimated devil numbers. Here we provide a comprehensive description of the Tasmanian devil immunoglobulin variable regions. We show that heavy chain variable (VH) and light chain variable (VL) repertoires are similar to those described in other marsupial taxa: VL diversity is high, but VH diversity is restricted and belongs only to clan III. As in other mammals, one VH and one Vλ germline family and multiple incomplete Vκ germline sequences were identified in the genome. High Vκ variation was observed in transcripts and we predict that it may have arisen by gene conversion and/or somatic mutations, as it does not appear to have originated from germline variation. Phylogenetic analyses revealed that devil VL gene segments are highly complex and ancient, with some lineages predating the separation of marsupials and eutherians. These results indicate that although the evolutionary history of immune genes lead to the expansions and contractions of immune gene families between different mammalian lineages, some of the ancestral immune gene variants are still maintained in extant species. A high degree of similarity was found between devil and other marsupial VH segments, demonstrating that they originated from a common clade of closely related sequences. The VL families had a higher variation than VH both between and within species. We suggest that, similar to other studied marsupial species, the complex VL segment repertoire compensates for the limited VH diversity in Tasmanian devils.

Swine influenza virus PA and neuraminidase gene reassortment into human H1N1iInfluenza Virus is associated with an altered pathogenic phenotype linked to increased MIP-2 expression

Swine are susceptible to infection by both avian and human influenza viruses, and this feature is thought to contribute to novel reassortant influenza viruses. In this study, the influenza virus reassortment rate in swine and human cells was determined. Coinfection of swine cells with 2009 pandemic H1N1 virus (huH1N1) and an endemic swine H1N2 (A/swine/Illinois/02860/09) virus (swH1N2) resulted in a 23% reassortment rate that was independent of α2,3- or α2,6-sialic acid distribution on the cells. The reassortants had altered pathogenic phenotypes linked to introduction of the swine virus PA and neuraminidase (NA) into huH1N1. In mice, the huH1N1 PA and NA mediated increased MIP-2 expression early postinfection, resulting in substantial pulmonary neutrophilia with enhanced lung pathology and disease. The findings support the notion that swine are a mixing vessel for influenza virus reassortants independent of sialic acid distribution. These results show the potential for continued reassortment of the 2009 pandemic H1N1 virus with endemic swine viruses and for reassortants to have increased pathogenicity linked to the swine virus NA and PA genes which are associated with increased pulmonary neutrophil trafficking that is related to MIP-2 expression. IMPORTANCE: Influenza A viruses can change rapidly via reassortment to create a novel virus, and reassortment can result in possible pandemics. Reassortments among subtypes from avian and human viruses led to the 1957 (H2N2 subtype) and 1968 (H3N2 subtype) human influenza pandemics. Recent analyses of circulating isolates have shown that multiple genes can be recombined from human, avian, and swine influenza viruses, leading to triple reassortants. Understanding the factors that can affect influenza A virus reassortment is needed for the establishment of disease intervention strategies that may reduce or preclude pandemics. The findings from this study show that swine cells provide a mixing vessel for influenza virus reassortment independent of differential sialic acid distribution. The findings also establish that circulating neuraminidase (NA) and PA genes could alter the pathogenic phenotype of the pandemic H1N1 virus, resulting in enhanced disease. The identification of such factors provides a framework for pandemic modeling and surveillance.

Pan-serotype diagnostic for foot-and-mouth disease using the consensus antigen of nonstructural protein 3B

An amino acid consensus sequence for the seven serotypes of foot-and-mouth disease virus (FMDV) nonstructural protein 3B, including all three contiguous repeats, and its use in the development of a pan-serotype diagnostic test for all seven FMDV serotypes are described. The amino acid consensus sequence of the 3B protein was determined from a multiple-sequence alignment of 125 sequences of 3B. The consensus 3B (c3B) protein was expressed as a soluble recombinant fusion protein with maltose-binding protein (MBP) using a bacterial expression system and was affinity purified using amylose resin. The MBP-c3B protein was used as the antigen in the development of a competition enzyme-linked immunosorbent assay (cELISA) for detection of anti-3B antibodies in bovine sera. The comparative diagnostic sensitivity and specificity at 47% inhibition were estimated to be 87.22% and 93.15%, respectively. Reactivity of c3B with bovine sera representing the seven FMDV serotypes demonstrated the pan-serotype diagnostic capability of this bioreagent. The consensus antigen and competition ELISA are described here as candidates for a pan-serotype diagnostic test for FMDV infection.

Maternal mental well-being during pregnancy and glucocorticoid receptor gene promoter methylation in the neonate

Maternal mental health during pregnancy has been linked to health outcomes in progeny. Mounting evidence implicates fetal “programming” in this process, possibly via epigenetic disruption. Maternal mental health has been associated with glucocorticoid receptor methylation (nuclear receptor subfamily 3, group C, member 1 [NR3C1]) in the neonate; however, most studies have been small (n < 100) and have failed to control for multiple testing in the statistical analysis. The Barwon Infant Study is a population-derived birth cohort with antenatal recruitment. Maternal depression and anxiety were assessed using the Edinburgh Postnatal Depression Scale and psychological distress using the Perceived Stress Scale. NR3C1 cord blood methylation levels were determined using Sequenom MassArray for 481 participants. Maternal psychological distress and anxiety were associated with a small increase in neonate NR3C1 methylation at specific CpG sites, thus replicating some previous findings. However, associations were only nominally significant and did not remain after correction for the number of CpG sites and exposures investigated. As the largest study to explore the relationship between maternal well-being and offspring NR3C1 cord blood methylation, our results highlight the need for caution when interpreting previous findings in this area. Future studies must ensure they are adequately powered to detect the likely small effect sizes while controlling for multiple testing.

Multiple dispersal vectors drive range expansion in an invasive marine species

The establishment and subsequent spread of invasive species is widely recognised as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, eDNA plankton sampling and hydrodynamic modelling we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow; a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.