119 research outputs found

    RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus

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    <p>Abstract</p> <p>Background</p> <p>In all jawed vertebrates, highly polymorphic genes of the major histocompatibility complex (MHC) encode antigen presenting molecules that play a key role in the adaptive immune response. Their polymorphism is composed of multiple copies of recently duplicated genes, each possessing many alleles within populations, as well as high nucleotide divergence between alleles of the same species. Experimental evidence is accumulating that MHC polymorphism is a result of balancing selection by parasites and pathogens. In order to describe MHC diversity and analyse the underlying mechanisms that maintain it, a reliable genotyping technique is required that is suitable for such highly variable genes.</p> <p>Results</p> <p>We present a genotyping protocol that uses Reference Strand-mediated Conformation Analysis (RSCA), optimised for recently duplicated MHC class IIB genes that are typical for many fish and bird species, including the three-spined stickleback, <it>Gasterosteus aculeatus</it>. In addition we use a comprehensive plasmid library of MHC class IIB alleles to determine the nucleotide sequence of alleles represented by RSCA allele peaks. Verification of the RSCA typing by cloning and sequencing demonstrates high congruency between both methods and provides new insight into the polymorphism of classical stickleback MHC genes. Analysis of the plasmid library additionally reveals the high resolution and reproducibility of the RSCA technique.</p> <p>Conclusion</p> <p>This new RSCA genotyping protocol offers a fast, but sensitive and reliable way to determine the MHC allele repertoire of three-spined sticklebacks. It therefore provides a valuable tool to employ this highly polymorphic and adaptive marker in future high-throughput studies of host-parasite co-evolution and ecological speciation in this emerging model organism.</p

    Thermo-Elastic Topology Optimization For High Temperatures Gradients Using Load Separation

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    Designing components for thermo-mechanical loads is a challenging process. While mechanical loads like forces or pressure demand a stiff and thick-walled design, thermal loads create temperature gradients, resulting in thermo-mechanical stress from the structure's temperature proportional and, therefore, uneven expansion. In contrast to a pure mechanical load case, an initial design before optimization can already include stress levels beyond the limit of the material. Therefore, common optimization approaches for a preliminary design use exemplary systems with low-temperature gradients, so thermal stresses do not exceed the limit. From there, energy density is used to calculate the topology optimizations sensitivity and therefore decide which elements to remove and which to keep. This paper describes a novel approach for reducing thermo-mechanical stress by following the stress corresponding temperature gradients from the heat source to the sink to calculate a new sensitivity that helps to grow cooling channels. The optimization is exemplarily shown on a piston for internal combustion engines. While handling delta temperatures of 600K, results show a reduction in thermo-mechanical stress while reducing the component's mass. Because the approach reduces critical stress in a component, it allows the initial design (before the topology optimization) to have stress levels way above yield strength

    Scoping carbon dioxide removal options for Germany–What is their potential contribution to Net-Zero CO2_{2}?

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    In its latest assessment report the IPCC stresses the need for carbon dioxide removal (CDR) to counterbalance residual emissions to achieve net zero carbon dioxide or greenhouse gas emissions. There are currently a wide variety of CDR measures available. Their potential and feasibility, however, depends on context specific conditions, as among others biophysical site characteristics, or availability of infrastructure and resources. In our study, we selected 13 CDR concepts which we present in the form of exemplary CDR units described in dedicated fact sheets. They cover technical CO2 removal (two concepts of direct air carbon capture), hybrid solutions (six bioenergy with carbon capture technologies) and five options for natural sink enhancement. Our estimates for their CO2 removal potentials in 2050 range from 0.06 to 30 million tons of CO2, depending on the option. Ten of the 13 CDR concepts provide technical removal potentials higher than 1 million tons of CO2 per year. To better understand the potential contribution of analyzed CDR options to reaching net-zero CO2 emissions, we compare our results with the current CO2 emissions and potential residual CO2 emissions in 2050 in Germany. To complement the necessary information on technology-based and hybrid options, we also provide an overview on possible solutions for CO2 storage for Germany. Taking biophysical conditions and infrastructure into account, northern Germany seems a preferable area for deployment of many concepts. However, for their successful implementation further socio-economic analysis, clear regulations, and policy incentives are necessary

    Extensive Copy-Number Variation of Young Genes across Stickleback Populations

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    MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

    The Effect of Climate Fluctuation on Chimpanzee Birth Sex Ratio

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    Climate and weather conditions, such as the North Atlantic Oscillation, precipitation and temperature influence the birth sex ratio (BSR) of various higher latitude species, including deer, elephant seals or northern human populations. Although, tropical regions show only little variation in temperature, climate and weather conditions can fluctuate with consequences for phenology and food resource availability. Here, we evaluate, whether the BSR of chimpanzees, inhabiting African tropical forests, is affected by climate fluctuations as well. Additionally, we evaluate, if variation in consumption of a key food resource with high nutritional value, Coula edulis nuts, is linked to both climate fluctuations and variation in BSR. We use long-term data from two study groups located in Taï National Park, Côte d'Ivoire to assess the influence of local weather conditions and the global climate driver El Niño Southern Oscillation (ENSO) on offspring sex. Côte d'Ivoire has experienced considerable climate variation over the last decades, with increasing temperature and declining precipitation. For both groups we find very similar time windows around the month of conception, in which offspring sex is well predicted by ENSO, with more males following low ENSO values, corresponding to periods of high rainfall. Furthermore, we find that the time spent cracking and feeding on Coula nuts is strongly influenced by climate conditions. Although, some of our analysis suggest that a higher proportion of males is born after periods with higher nut consumption frequency, we cannot conclude decisively at this point that nut consumption may influence shifts in BSR. All results combined suggest that also chimpanzees may experience climate related shifts in offspring sex ratios as response to climate fluctuation

    Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes

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    Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments

    Observation of Cosmic Ray Anisotropy with Nine Years of IceCube Data

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