Overlapping motifs (PTAP and PPEY) within the Ebola virus VP40 protein function independently as late budding domains: involvement of host proteins TSG101 and VPS-4

The VP40 protein of Ebola virus can bud from mammalian cells in the form of lipid-bound, virus-like particles (VLPs), and late budding domains (L-domains) are conserved motifs (PTAP, PPxY, or YxxL; where "x" is any amino acid) that facilitate the budding of VP40-containing VLPs. VP40 is unique in that potential overlapping L-domains with the sequences PTAP and PPEY are present at amino acids 7 to 13 of VP40 (PTAPPEY). L-domains are thought to function by interacting with specific cellular proteins, such as the ubiquitin ligase Nedd4, and a component of the vacuolar protein sorting (vps) pathway, tsg101. Mutational analysis of the PTAPPEY sequence of VP40 was performed to understand further the contribution of each individual motif in promoting VP40 budding. In addition, the contribution of tsg101 and a second member of the vps pathway, vps4, in facilitating budding was addressed. Our results indicate that (i) both the PTAP and PPEY motifs contribute to efficient budding of VP40-containing VLPs; (ii) PTAP and PPEY can function as L-domains when separated and moved from the N terminus (amino acid position 7) to the C terminus (amino acid position 316) of full-length VP40; (iii) A VP40-PTAP/tsg101 interaction recruits tsg101 into budding VLPs; (iv) a VP40-PTAP/tsg101 interaction recruits VP40 into lipid raft microdomains; and (v) a dominant-negative mutant of vps4 (E228Q), but not wild-type vps4, significantly inhibited the budding of Ebola virus (Zaire). These results provide important insights into the complex interplay between viral and host proteins during the late stages of Ebola virus budding.     

Fat Oxidation,Fitness and Skeletal Muscle Expression of Oxidative/Lipid Metabolism Genes in South Asians: Implications for Insulin Resistance?

Background

South Asians are more insulin resistant than Europeans, which cannot be fully explained by differences in adiposity. We investigated whether differences in oxidative capacity and capacity for fatty acid utilisation in South Asians might contribute, using a range of whole-body and skeletal muscle measures.

Methodology/Principal Findings

Twenty men of South Asian ethnic origin and 20 age and BMI-matched men of white European descent underwent exercise and metabolic testing and provided a muscle biopsy to determine expression of oxidative and lipid metabolism genes and of insulin signalling proteins. In analyses adjusted for age, BMI, fat mass and physical activity, South Asians, compared to Europeans, exhibited; reduced insulin sensitivity by 26% (p = 0.010); lower VO_2max (40.6±6.6 vs 52.4±5.7 ml.kg⁻¹.min⁻¹, p = 0.001); and reduced fat oxidation during submaximal exercise at the same relative (3.77±2.02 vs 6.55±2.60 mg.kg⁻¹.min⁻¹ at 55% VO_2max, p = 0.013), and absolute (3.46±2.20 vs 6.00±1.93 mg.kg⁻¹.min⁻¹ at 25 ml O₂.kg⁻¹.min⁻¹, p = 0.021), exercise intensities. South Asians exhibited significantly higher skeletal muscle gene expression of CPT1A and FASN and significantly lower skeletal muscle protein expression of PI3K and PKB Ser473 phosphorylation. Fat oxidation during submaximal exercise and VO_2max both correlated significantly with insulin sensitivity index and PKB Ser473 phosphorylation, with VO_2max or fat oxidation during exercise explaining 10–13% of the variance in insulin sensitivity index, independent of age, body composition and physical activity.

Conclusions/Significance

These data indicate that reduced oxidative capacity and capacity for fatty acid utilisation at the whole body level are key features of the insulin resistant phenotype observed in South Asians, but that this is not the consequence of reduced skeletal muscle expression of oxidative and lipid metabolism genes.     

Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.     

The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.     

Host T cells are the main producers of IL-17 within the central nervous system during initiation of experimental autoimmune encephalomyelitis induced by adoptive transfer of Th1 cell lines

Experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis, has long been thought to be mediated by Th1 CD4(+) T cells. Using adoptive transfer techniques, transfer of CNS specific Th1 T cells was sufficient to induce EAE in naive mice. However, recent studies found a vital role for IL-17 in induction of EAE. These studies suggested that a fraction of IL-17-producing T cells that contaminate Th1 polarized cell lines are largely responsible for initiation of EAE. In this study, we tracked the appearance and cytokine production capacity of adoptively transferred cells within the CNS of mice throughout EAE disease. IL-17-producing, adoptively transferred cells were not enriched over the low percentages present in vitro. Thus, there was no selective recruitment and/or preferential proliferation of adoptively transferred IL-17-producing cells during the induction of EAE. Instead a large number of CNS infiltrating host T cells in mice with EAE were capable of producing IL-17 following ex vivo stimulation. The IL-17-producing T cells contained both alphabeta and gammadelta TCR(+) T cells with a CD4(+)CD8(-) or CD4(-)CD8(-) phenotype. These cells concentrated within the CNS within 3 days of adoptive transfer, and appeared to play a role in EAE induction as adoptive transfer of Th1 lines derived from wild-type mice into IL-17-deficient mice induced reduced EAE clinical outcomes. This study demonstrates that an encephalitogenic Th1 cell line induces recruitment of host IL-17-producing T cells to the CNS during the initiation of EAE and that these cells contribute to the incidence and severity of disease.     

Binding site for Robo receptors revealed by dissection of the leucine-rich repeat region of Slit

Recognition of the large secreted protein Slit by receptors of the Robo family provides fundamental signals in axon guidance and other developmental processes. In Drosophila, Slit-Robo signalling regulates midline crossing and the lateral position of longitudinal axon tracts. We report the functional dissection of Drosophila Slit, using structure analysis, site-directed mutagenesis and in vitro assays. The N-terminal region of Slit consists of a tandem array of four independently folded leucine-rich repeat (LRR) domains, connected by disulphide-tethered linkers. All three Drosophila Robos were found to compete for a single highly conserved site on the concave face of the second LRR domain of Slit. We also found that this domain is sufficient for biological activity in a chemotaxis assay. Other Slit activities may require Slit dimerisation mediated by the fourth LRR domain. Our results show that a small portion of Slit is able to induce Robo signalling and indicate that the distinct functions of Drosophila Robos are encoded in their divergent cytosolic domains.     

Technique for chestband contour shape-mapping in lateral impact

The chestband transducer permits noninvasive measurement of transverse plane biomechanical response during blunt thorax impact. Although experiments may reveal complex two-dimensional (2D) deformation response to boundary conditions, biomechanical studies have heretofore employed only uniaxial chestband contour quantifying measurements. The present study described and evaluated an algorithm by which source subject-specific contour data may be systematically mapped to a target generalized anthropometry for computational studies of biomechanical response or anthropomorphic test dummy development. Algorithm performance was evaluated using chestband contour datasets from two rigid lateral impact boundary conditions: Flat wall and anterior-oblique wall. Comparing source and target anthropometry contours, peak deflections and deformation-time traces deviated by less than 4%. These results suggest that the algorithm is appropriate for 2D deformation response to lateral impact boundary conditions.     

Lysophosphatidic acid,human osteoblast formation,maturation and the role of 1α,25-Dihydroxyvitamin D3 (calcitriol)

The simplest signalling lipid Lysophosphatidic acid (LPA) elicits pleiotropic actions upon most mammalian cell types. Although LPA has an established role in many biological processes, particularly wound healing and cancer, the function of LPA for human osteoblast (hOB) biology is still unravelling. Early studies, identified in this review, gave a reliable indication that LPA, via binding to one of several transmembrane receptors, stimulated multiple intracellular signalling networks coupled to changes in cell growth, fibronectin binding, maturation and survival. The majority of studies exploring the actions of LPA on hOB responses have done so using the lipid in isolation. Our own research has focussed on the co-operation of LPA with the active vitamin D3 metabolite, 1α25,dihydroxycholecalciferol (calcitriol), in light of a serendipitous discovery that calcitriol, in a serum-free culture setting, was unable to promote hOB maturation. We subsequently learnt that the serum-borne factor co-operating with calcitriol to enhance hOB differentiation was LPA bound to the albumin fraction of whole serum. Recent studies from our laboratory have identified that LPA and calcitriol are a potent pairing for securing hOB formation from their stem cell progeny. Greater understanding of the ability of LPA to influence, for example, hOB growth, maturation and survival could be advantageous in developing novel strategies aimed at improving skeletal tissue repair and regeneration. Herein this review provides an insight into the diversity of studies exploring the actions of a small lipid on a major cell type key to bone tissue health and homeostasis. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.     

A framework for the practical science necessary to restore sustainable,resilient, and biodiverse ecosystems

Demand for restoration of resilient, self‐sustaining, and biodiverse natural ecosystems as a conservation measure is increasing globally; however, restoration efforts frequently fail to meet standards appropriate for this objective. Achieving these standards requires management underpinned by input from diverse scientific disciplines including ecology, biotechnology, engineering, soil science, ecophysiology, and genetics. Despite increasing restoration research activity, a gap between the immediate needs of restoration practitioners and the outputs of restoration science often limits the effectiveness of restoration programs. Regrettably, studies often fail to identify the practical issues most critical for restoration success. We propose that part of this oversight may result from the absence of a considered statement of the necessary practical restoration science questions. Here we develop a comprehensive framework of the research required to bridge this gap and guide effective restoration. We structure questions in five themes: (1) setting targets and planning for success, (2) sourcing biological material, (3) optimizing establishment, (4) facilitating growth and survival, and (5) restoring resilience, sustainability, and landscape integration. This framework will assist restoration practitioners and scientists to identify knowledge gaps and develop strategic research focused on applied outcomes. The breadth of questions highlights the importance of cross‐discipline collaboration among restoration scientists, and while the program is broad, successful restoration projects have typically invested in many or most of these themes. Achieving restoration ecology's goal of averting biodiversity losses is a vast challenge: investment in appropriate science is urgently needed for ecological restoration to fulfill its potential and meet demand as a conservation tool.     

Scaled marginal models for multiple continuous outcomes

In studies that involve multivariate outcomes it is often of interest to test for a common exposure effect. For example, our research is motivated by a study of neurocognitive performance in a cohort of HIV-infected women. The goal is to determine whether highly active antiretroviral therapy affects different aspects of neurocognitive functioning to the same degree and if so, to test for the treatment effect using a more powerful one-degree-of-freedom global test. Since multivariate continuous outcomes are likely to be measured on different scales, such a common exposure effect has not been well defined. We propose the use of a scaled marginal model for testing and estimating this global effect when the outcomes are all continuous. A key feature of the model is that the effect of exposure is represented by a common effect size and hence has a well-understood, practical interpretation. Estimating equations are proposed to estimate the regression coefficients and the outcome-specific scale parameters, where the correct specification of the within-subject correlation is not required. These estimating equations can be solved by repeatedly calling standard generalized estimating equations software such as SAS PROC GENMOD. To test whether the assumption of a common exposure effect is reasonable, we propose the use of an estimating-equation-based score-type test. We study the asymptotic efficiency loss of the proposed estimators, and show that they generally have high efficiency compared to the maximum likelihood estimators. The proposed method is applied to the HIV data.