Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage

Major histocompatibility complex (MHC) class I genes are found in the genomes of all jawed vertebrates. The evolution of this gene family is closely tied to the evolution of the vertebrate genome. Family members are frequently found in four paralogous regions, which were formed in two rounds of genome duplication in the early vertebrates, but in some species class Is have been subject to additional duplication or translocation, creating additional clusters. The gene family is traditionally grouped into two subtypes: classical MHC class I genes that are usually MHC-linked, highly polymorphic, expressed in a broad range of tissues and present endogenously-derived peptides to cytotoxic T-cells; and non-classical MHC class I genes generally have lower polymorphism, may have tissue-specific expression and have evolved to perform immune-related or non-immune functions. As immune genes can evolve rapidly and are subject to different selection pressure, we hypothesised that there may be divergent, as yet unannotated or uncharacterised class I genes. Results: Application of a novel method of sensitive genome searching of available vertebrate genome sequences revealed a new, extensive sub-family of divergent MHC class I genes, denoted as UT, which has not previously been characterized. These class I genes are found in both American and Australian marsupials, and in monotremes, at an evolutionary chromosomal breakpoint, but are not present in non-mammalian genomes and have been lost from the eutherian lineage. We show that UT family members are expressed in the thymus of the gray short-tailed opossum and in other immune tissues of several Australian marsupials. Structural homology modelling shows that the proteins encoded by this family are predicted to have an open, though short, antigen-binding groove. Conclusions: We have identified a novel sub-family of putatively non-classical MHC class I genes that are specific to marsupials and monotremes. This

TFG Promotes Organization of Transitional ER and Efficient Collagen Secretion

Collagen is the most abundant protein in the animal kingdom. It is of fundamental importance during development for cell differentiation and tissue morphogenesis as well as in pathological processes such as fibrosis and cancer cell migration. However, our understanding of the mechanisms of procollagen secretion remains limited. Here, we show that TFG organizes transitional ER (tER) and ER exit sites (ERESs) into larger structures. Depletion of TFG results in dispersion of tER elements that remain associated with individual ER-Golgi intermediate compartments (ERGICs) as largely functional ERESs. We show that TFG is not required for the transport and packaging of small soluble cargoes but is necessary for the export of procollagen from the ER. Our work therefore suggests a key relationship between the structure and function of ERESs and a central role for TFG in optimizing COPII assembly for procollagen export.Medical Research Council UK/MR/J000604/1Medical Research Council UK/MR/K018019/1Medical Research Council UK/MR/G080184

Comparing distribution of harbour porpoise using Generalized Additive Models and hierarchical Bayesian models with Integrated Nested Laplace Approximation

Open Access via Elsevier agreement Acknowledgments We thank colleagues at the University of Aberdeen, Moray First Marine, NERI, Hi-Def Aerial Surveying Ltd and Ravenair for essential support in the field, particularly Tim Barton, Bill Ruck, Rasmus Nielson and Dave Rutter. L.D.W. was supported by the Marine Alliance for Science and Technology for Scotland (MASTS), the University of Aberdeen and Marine Scotland Science. Collaboration between the University of Aberdeen and Marine Scotland was supported by the Marine Collaboration Research Forum (MarCRF). Digital aerial surveys in 2010 were funded by Moray Offshore Renewables Ltd and 2014 by Marine Scotland. Additional funding for analysis of the combined datasets was provided by Marine Scotland. Collaboration between the University of Aberdeen and Marine Scotland was supported by MarCRF.Peer reviewedPublisher PD

Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha)

Variation at 13 microsatellite loci was previously surveyed in approximately 7400 chinook salmon (Oncorhynchus tshawytscha) sampled from 50 localities in the Fraser River drainage in southern British Columbia. Evaluation of the utility of the microsatellite variation for population-specific stock identification applications indicated that the accuracy of the stock composition estimates generally improved with an increasing number of loci used in the estimation procedure, but an increase in accuracy was generally marginal after eight loci were used. With 10–14 populations in a simulated fishery sample, the mean error in population-specific estimated stock composition with a 50-popula-tion baseline was <1.4%. Identification of individuals to specific populations was highest for lower Fraser River and lower and North Thompson River populations; an average of 70% of the individual fish were correctly assigned to specific populations. The average error of the estimated percentage for the seven populations present in a coded-wire tag sample was 2% per population. Estimation of stock composition in the lower river commercial net fishery prior to June is of key local fishery management interest. Chinook salmon from the Chilcotin River and Nicola River drainages were important contributors to the early commercial fishery in the lower river because they comprised approximately 50% of the samples from the net fishery prior to mid April

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage

A school-based intervention to promote physical activity among adolescent girls: Rationale, design, and baseline data from the Girls in Sport group randomised controlled trial

Background: Physical activity levels decline markedly among girls during adolescence. School-based interventions that are multi-component in nature, simultaneously targeting curricular, school environment and policy, and community links, are a promising approach for promoting physical activity. This report describes the rationale, design and baseline data from the Girls in Sport group randomised trial, which aims to prevent the decline in moderate-to-vigorous intensity physical activity (MVPA) among adolescent girls. Methods/design: A community-based participatory research approach and action learning framework are used with measurements at baseline and 18-month follow-up. Within each intervention school, a committee develops an action plan aimed at meeting the primary objective (preventing the decline in accelerometer-derived MVPA). Academic partners and the State Department of Education and Training act as critical friends. Control schools continue with their usual school programming. 24 schools were matched then randomized into intervention (n = 12) and control (n = 12) groups. A total of 1518 girls (771 intervention and 747 control) completed baseline assessments (86% response rate). Useable accelerometer data (≥ 10 hrs/day on at least 3 days) were obtained from 79% of this sample (n = 1199). Randomisation resulted in no differences between intervention and control groups on any of the outcomes. The mean age (SE) of the sample was 13.6 (± 0.02) years and they spent less than 5% of their waking hours in MVPA (4.85 ± 0.06). Discussion: Girls in Sport will test the effectiveness of schools working towards the same goal, but developing individual, targeted interventions that bring about changes in curriculum, school environment and policy, and community links. By using community-based participatory research and an action learning framework in a secondary school setting, it aims to add to the body of literature on effective school-based interventions through promoting and sustaining increased physical activity participation among adolescent girls

Targeting the LOX/hypoxia axis reverses many of the features that make pancreatic cancer deadly: inhibition of LOX abrogates metastasis and enhances drug efficacy

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer‐related mortality. Despite significant advances made in the treatment of other cancers, current chemotherapies offer little survival benefit in this disease. Pancreaticoduodenectomy offers patients the possibility of a cure, but most will die of recurrent or metastatic disease. Hence, preventing metastatic disease in these patients would be of significant benefit. Using principal component analysis (PCA), we identified a LOX/hypoxia signature associated with poor patient survival in resectable patients. We found that LOX expression is upregulated in metastatic tumors from Pdx1‐Cre KrasG12D/+ Trp53R172H/+ (KPC) mice and that inhibition of LOX in these mice suppressed metastasis. Mechanistically, LOX inhibition suppressed both migration and invasion of KPC cells. LOX inhibition also synergized with gemcitabine to kill tumors and significantly prolonged tumor‐free survival in KPC mice with early‐stage tumors. This was associated with stromal alterations, including increased vasculature and decreased fibrillar collagen, and increased infiltration of macrophages and neutrophils into tumors. Therefore, LOX inhibition is able to reverse many of the features that make PDAC inherently refractory to conventional therapies and targeting LOX could improve outcome in surgically resectable disease

Considering sex as a biological variable in preclinical research

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154390/1/fsb2fj201600781r.pd

Selecting control genes for RT-QPCR using public microarray data

Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/ Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable

Individual Exposure to NO2 in Relation to Spatial and Temporal Exposure Indices in Stockholm, Sweden: The INDEX Study

Epidemiology studies of health effects from air pollution, as well as impact assessments, typically rely on ambient monitoring data or modelled residential levels. The relationship between these and personal exposure is not clear. To investigate personal exposure to NO2 and its relationship with other exposure metrics and time-activity patterns in a randomly selected sample of healthy working adults (20–59 years) living and working in Stockholm. Personal exposure to NO2 was measured with diffusive samplers in sample of 247 individuals. The 7-day average personal exposure was 14.3 µg/m3 and 12.5 µg/m3 for the study population and the inhabitants of Stockholm County, respectively. The personal exposure was significantly lower than the urban background level (20.3 µg/m3). In the univariate analyses the most influential determinants of individual exposure were long-term high-resolution dispersion-modelled levels of NO2 outdoors at home and work, and concurrent NO2 levels measured at a rural location, difference between those measured at an urban background and rural location and difference between those measured in busy street and at an urban background location, explaining 20, 16, 1, 2 and 4% (R2) of the 7-day personal NO2 variation, respectively. A regression model including these variables explained 38% of the variation in personal NO2 exposure. We found a small improvement by adding time-activity variables to the latter model (R2 = 0.44). The results adds credibility primarily to long-term epidemiology studies that utilise long-term indices of NO2 exposure at home or work, but also indicates that such studies may still suffer from exposure misclassification and dilution of any true effects. In contrast, urban background levels of NO2 are poorly related to individual exposure