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101.
Anthony T Papenfuss Zhi-Ping Feng Katina Krasnec Janine E Deakin Michelle L Baker Robert D Miller 《BMC genomics》2015,16(1)
Background
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 family was present in the ancestral mammal and is found in extant marsupials and monotremes, but has been lost from the eutherian lineage. The function of this family is as yet unknown, however, their predicted structure may be consistent with presentation of antigens to T-cells.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1745-4) contains supplementary material, which is available to authorized users. 相似文献102.
103.
The monoclonal antibody B13-DE1 binds fluorescein, several fluorescein derivatives, and three peptide mimotopes. Our results revealed that this antibody also catalyzed the redox reaction of resazurin to resorufin, which are both structurally related to fluorescein. By using sodium sulfite as a reducing agent, the antibody B13-DE1 lowered the activation energy of this reaction. The Michaelis-Menten constant and turnover number of the catalyzed reaction were determined as 4.2 μmol/l and 0.0056 s(-1) , respectively. Because the results showed that fluorescein inhibited the catalytic activity of the antibody, we assume that the antigen-binding site and the catalytic active site are identical. 相似文献
104.
Rahman LN Bamm VV Voyer JA Smith GS Chen L Yaish MW Moffatt BA Dutcher JR Harauz G 《Amino acids》2011,40(5):1485-1502
Dehydrins are intrinsically unstructured proteins that are expressed in plants experiencing extreme environmental conditions
such as drought or low temperature. Although their role is not completely understood, it has been suggested that they stabilize
proteins and membrane structures during environmental stress and also sequester metals such as zinc. Here, we investigate
two dehydrins (denoted as TsDHN-1 and TsDHN-2) from Thellungiella salsuginea. This plant is a crucifer that thrives in the Canadian sub-Arctic (Yukon Territory) where it grows on saline-rich soils and
experiences periods of both extreme cold and drought. We show using circular dichroism and attenuated total reflection-Fourier
transform infrared spectroscopy that ordered secondary structure is induced and stabilized in these proteins, both in free
and vesicle-bound form, by association with zinc. In membrane-associated form, both proteins have an increased proportion
of β-strand conformation induced by the cation, in addition to the amphipathic α-helices formed by their constituent K-segments.
These results support the hypothesis that dehydrins stabilize plant plasma and organellar membranes in conditions of stress,
and further that zinc may be an important co-factor in stabilization. Whereas dehydrins in the cytosol of a plant cell undergoing
dehydration or temperature stress form bulk hydrogels and remain primarily disordered, dehydrins with specific membrane- or
protein-associations will have induced ordered secondary structures. 相似文献
105.
Michèle?F.?PfabEmail author Janine?E.?Victor Adrian?J.?Armstrong 《Biodiversity and Conservation》2011,20(5):1001-1012
Biodiversity targets, or estimates of the quantities of biodiversity features that should be conserved in a region, are fundamental
to systematic conservation planning. We propose that targets for species should be based on the quantitative thresholds developed
for the Vulnerable category of the IUCN Red List system, thereby avoiding future listings of species in an IUCN Red List threat
category or an increase in the extinction risk, or ultimate extinction, of species already listed as threatened. Examples
of this approach are presented for case studies from South Africa, including threatened taxa listed under the IUCN Red List
criteria of A to D, a species listed as Near Threatened, a species of conservation concern due to its rarity, and one species
in need of recovery. The method gives rise to multiple representation targets, an improvement on the often used single representation
targets that are inadequate for long term maintenance of biodiversity or the arbitrary multiple representation and percentage
targets that are sometimes adopted. Through the implementation of the resulting conservation plan, these targets will ensure
that the conservation status of threatened species do not worsen over time by qualifying for higher categories of threat and
may actually improve their conservation status by eliminating the threat of habitat loss and stabilizing population declines.
The positive attributes ascribed to the IUCN Red List system, and therefore to the species targets arising from this approach,
are important when justifying decisions that limit land uses known to be detrimental to biodiversity. 相似文献
106.
Janine M LaSalle 《Epigenetics》2011,6(7):862-869
The etiologic paradigm of complex human disorders such as autism is that genetic and environmental risk factors are independent and additive, but the interactive effects at the epigenetic interface are largely ignored. Genomic technologies have radically changed perspective on the human genome and how the epigenetic interface may impact complex human disorders. Here, I review recent genomic, environmental and epigenetic findings that suggest a new paradigm of “integrative genomics” in which genetic variation in genomic size may be impacted by dietary and environmental factors that influence the genomic saturation of DNA methylation. Human genomes are highly repetitive, but the interface of large-scale genomic differences with environmental factors that alter the DNA methylome such as dietary folate is under-explored. In addition to obvious direct effects of some environmental toxins on the genome by causing chromosomal breaks, non-mutagenic toxin exposures correlate with DNA hypomethylation that can lead to rearrangements between repeats or increased retrotransposition. Since human neurodevelopment appears to be particularly sensitive to alterations in epigenetic pathways, a further focus will be on how developing neurons may be particularly impacted by even subtle alterations to DNA methylation and proposing new directions towards understanding the quixotic etiology of autism by integrative genomic approaches.Key words: DNA methylation, copy number variation, autism, neurodevelopment, genomics, epigenomics, epigenetics, folate, folic acid, environmental exposures, Alu, MeCP2, LINE-1 相似文献
107.
108.
Nalls MA Couper DJ Tanaka T van Rooij FJ Chen MH Smith AV Toniolo D Zakai NA Yang Q Greinacher A Wood AR Garcia M Gasparini P Liu Y Lumley T Folsom AR Reiner AP Gieger C Lagou V Felix JF Völzke H Gouskova NA Biffi A Döring A Völker U Chong S Wiggins KL Rendon A Dehghan A Moore M Taylor K Wilson JG Lettre G Hofman A Bis JC Pirastu N Fox CS Meisinger C Sambrook J Arepalli S Nauck M Prokisch H Stephens J Glazer NL Cupples LA Okada Y Takahashi A Kamatani Y Matsuda K Tsunoda T Tanaka T Kubo M 《PLoS genetics》2011,7(6):e1002113
White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse ancestral backgrounds. 相似文献
109.
110.
Scott D. Tiegs Peter S. Levi Janine Rüegg Dominic T. Chaloner Jennifer L. Tank Gary A. Lamberti 《Ecosystems》2011,14(4):598-614
We tested the hypothesis that the carcasses of anadromous Pacific salmon (Oncorhynchus spp.) constitute a significant source of nutrients in the nutrient-poor freshwaters where these fish migrate, spawn, senesce,
and die. In a 110 m-long stream reach in Southeast Alaska, we retained nearly 3000 salmon carcasses and compared streamwater
nitrogen (N), phosphorus (P), and the biomass of benthic biofilm in this reach with an upstream reference reach. The study
spanned 5 months, bracketed the entire salmon run, and encompassed significant seasonal variation in abiotic stream conditions.
Concentrations of dissolved and particulate N and P followed distinctly unimodal patterns through time, which tracked the
abundance of live salmon, and we observed strong predictive relationships between live-salmon abundance and streamwater-nutrient
concentrations. In contrast, we did not observe clear relationships between salmon carcasses and streamwater nutrients. Biofilm
biomass within our study reaches seemed to more closely track the abundance of live salmon than the abundance of carcasses.
The experimental retention of carcasses had a minor or undetectable influence on nutrient concentrations and biofilm within
the study reach as compared to the reference reach. We conclude that physical factors such as temperature, discharge, nutrient
limitation, and irradiance vary seasonally in ways that maximize the influence of nutrients provisioned by live salmon and
minimize the influence of carcass-derived nutrients on the aspects of stream ecosystems that we examined. Overall, our results
promote a new perspective on the ecological role of salmon in freshwaters, and contribute to a more mechanistic understanding
of how migratory fishes can influence aquatic ecosystems. 相似文献