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41.
A model of globin evolution 总被引:1,自引:0,他引:1
Vinogradov SN Hoogewijs D Bailly X Mizuguchi K Dewilde S Moens L Vanfleteren JR 《Gene》2007,398(1-2):132-142
Putative globins have been identified in 426 bacterial, 32 Archaeal and 67 eukaryote genomes. Among these sequences are the hitherto unsuspected presence of single domain sensor globins within Bacteria, Fungi, and a Euryarchaeote. Bayesian phylogenetic trees suggest that their occurrence in the latter two groups could be the result of lateral gene transfer from Bacteria. Iterated psiblast searches based on groups of globin sequences indicate that bacterial flavohemoglobins are closer to metazoan globins than to the other two lineages, the 2-over-2 globins and the globin-coupled sensors. Since Bacteria is the only kingdom to have all the subgroups of the three globin lineages, we propose a working model of globin evolution based on the assumption that all three lineages originated and evolved only in Bacteria. Although the 2-over-2 globins and the globin-coupled sensors recognize flavohemoglobins, there is little recognition between them. Thus, in the first stage of globin evolution, we favor a flavohemoglobin-like single domain protein as the ancestral globin. The next stage comprised the splitting off to single domain 2-over-2 and sensor-like globins, followed by the covalent addition of C-terminal domains resulting in the chimeric flavohemoglobins and globin-coupled sensors. The last stage encompassed the lateral gene transfers of some members of the three globin lineages to specific groups of Archaea and Eukaryotes. 相似文献
42.
Temporal and spatial trends in nitrogen and phosphorus inputs to the watershed of the Altamaha River,Georgia, USA 总被引:4,自引:0,他引:4
The watershed of the Altamaha River, Georgia, is one of the largest in the southeastern U.S., draining 36,718 km2 (including parts of metro Atlanta). We calculated both nitrogen (fertilizer, net food and feed import, atmospheric deposition,
and biological N fixation in agricultural and forest lands) and phosphorus (fertilizer and net food and feed import) inputs
to the watershed for 6 time points between 1954 and 2002. Total nitrogen inputs rose from 1,952 kg N km−2 yr−1 in 1954 to a peak of 3,593 kg N km−2 yr−1 in 1982 and then declined to 2,582 kg N km−2 yr−1 by 2002. Phosphorus inputs rose from 409 kg P km−2 yr−1 in 1954 to 532 kg P km−2 yr−1 in 1974 before declining to 412 kg P km−2 yr−1 in 2002. Fertilizer tended to be the most important input of both N and P to the watershed, although net food and feed import
increased in importance over time and was the dominant source of N input by 2002. When considered on an individual basis,
fertilizer input tended to be highest in the middle portions of the watershed (Little and Lower Ocmulgee and Lower Oconee
sub-watersheds) whereas net food and feed imports were highest in the upper reaches (Upper Oconee and Upper Ocmulgee sub-watersheds).
Although the overall trend in recent years has been towards decreases in both N and P inputs, these trends may be offset due
to continuing increases in animal and human populations. 相似文献
43.
Christian Weirich Douglas R Keene Katja Kirsch Matthias Heil Elena Neumann Robert Dinser 《Matrix biology》2007,26(4):314-323
OBJECTIVE: Pseudoachondroplasia (PSACH) is a dominantly inherited chondrodysplasia associated with mutations of cartilage oligomeric matrix protein (COMP), characterized clinically by disproportionate dwarfism and laxity of joints and ligaments. Studies in chondrocytes and cartilage biopsies suggest that the cartilage disease is caused by retention of mutant COMP in the endoplasmic reticulum of chondrocytes and by disruption of the collagen network of the extracellular matrix. The pathogenesis of the tendon disease remains unclear in the absence of a cell culture model, with available tendon biopsies leading to conflicting results with respect to the intracellular retention of mutant COMP. METHODS: We established a cell culture model using adenoviral gene transfer in tendon fibroblast cultures. We compared the effect of expression of three PSACH-associated COMP mutants and the wildtype protein on COMP secretion, matrix composition and cellular viability. RESULTS: Our results show that mutants D475N and D469Delta are retained within the endoplasmic reticulum of tendon cells similar to what is known from chondrocytes, whereas mutant H587R is secreted like wildtype COMP. In spite of this difference, the collagen I matrix formed in culture appears disturbed for all three mutants. All COMP-mutants induce apoptotic cell death irrespective of their differing secretion patterns. CONCLUSION: Pathogenic pathways leading to tendon disease in humans appear to be heterogeneous between different COMP mutants. 相似文献
44.
Diana Stralberg D. Richard Cameron Mark D. Reynolds Catherine M. Hickey Kirk Klausmeyer Sylvia M. Busby Lynne E. Stenzel W. David Shuford Gary W. Page 《Biodiversity and Conservation》2011,20(1):19-40
Conservation of migratory shorebirds and waterfowl presents unique challenges due to extensive historic loss of wetland habitats, and current reliance on managed landscapes for wintering and migratory passage. We developed a spatially-explicit approach to estimate potential shorebird and waterfowl densities in California by integrating mapped habitat layers and statewide bird survey data with expert-based habitat rankings. Using these density estimates as inputs, we used the Marxan site-selection program to identify priority shorebird and waterfowl areas at the ecoregional level. We identified 3.7 million ha of habitat for shorebirds and waterfowl, of which 1.4 million ha would be required to conserve 50% of wintering populations. To achieve a conservation goal of 75%, more than twice as much habitat (3.1 million ha) would be necessary. Agricultural habitats comprised a substantial portion of priority areas, especially at the 75% level, suggesting that under current management conditions, large areas of agricultural land, much of it formerly wetland, are needed to provide the habitat availability and landscape connectivity required by shorebird and waterfowl populations. These habitats were found to be largely lacking recognized conservation status in California (96% un-conserved), with only slightly higher levels of conservation for priority shorebird and waterfowl areas. Freshwater habitats, including wetlands and ponds, were also found to have low levels of conservation (67% un-conserved), although priority shorebird and waterfowl areas had somewhat higher levels of conservation than the state as a whole. Conserving migratory waterfowl and shorebirds will require a diversity of conservation strategies executed at a variety of scales. Our modeled results are complementary with other approaches and can help prioritize areas for protection, restoration and other actions. Traditional habitat protection strategies such as conservation easements and fee acquisitions may be of limited utility for protecting and managing significant areas of agricultural lands. Instead, conservation strategies focused on incentive-based programs to support wildlife friendly management practices in agricultural settings may have greater utility and conservation effectiveness. 相似文献
45.
Ching-Yi Lin Hsin-Mei Ku Wen-Shi Tsai Sylvia K. Green Fuh-Jyh Jan 《Transgenic research》2011,20(2):261-270
Tomato leaf curl Taiwan virus (ToLCTWV) and Tomato spotted wilt virus (TSWV) are two major tomato viruses that cause serious economic losses. In this study, a partial C2 gene from ToLCTWV and
the middle half of the N gene of TSWV were fused as a chimeric transgene to develop multiple virus resistance in transgenic
plants. This construct was introduced into Nicotiana benthamiana and tomato by Agrobacterium-mediated transformation. Several transgenic lines showed no symptom post agro-inoculation with ToLCTWV and displayed high
resistance to TSWV. The detection of siRNAs indicated that the resistance was via RNA silencing. This study demonstrated that
linkage of gene segments from two viruses with distinct genomic organization, one DNA and the other RNA, can confer multiple
virus resistance in transgenic plants via gene silencing. 相似文献
46.
Gharib M Marcantonio M Lehmann SG Courcelles M Meloche S Verreault A Thibault P 《Molecular & cellular proteomics : MCP》2009,8(3):506-518
Sulfation and phosphorylation are post-translational modifications imparting an isobaric 80-Da addition on the side chain of serine, threonine, or tyrosine residues. These two post-translational modifications are often difficult to distinguish because of their similar MS fragmentation patterns. Targeted MS identification of these modifications in specific proteins commonly relies on their prior separation using gel electrophoresis and silver staining. In the present investigation, we report a potential pitfall in the interpretation of these modifications from silver-stained gels due to artifactual sulfation of serine, threonine, and tyrosine residues by sodium thiosulfate, a commonly used reagent that catalyzes the formation of metallic silver deposits onto proteins. Detailed MS analyses of gel-separated protein standards and Escherichia coli cell extracts indicated that several serine, threonine, and tyrosine residues were sulfated using silver staining protocols but not following Coomassie Blue staining. Sodium thiosulfate was identified as the reagent leading to this unexpected side reaction, and the degree of sulfation was correlated with increasing concentrations of thiosulfate up to 0.02%, which is typically used for silver staining. The significance of this artifact is discussed in the broader context of sulfation and phosphorylation site identification from in vivo and in vitro experiments. 相似文献
47.
Hamdan FF Gauthier J Araki Y Lin DT Yoshizawa Y Higashi K Park AR Spiegelman D Dobrzeniecka S Piton A Tomitori H Daoud H Massicotte C Henrion E Diallo O;SD Group Shekarabi M Marineau C Shevell M Maranda B Mitchell G Nadeau A D'Anjou G Vanasse M Srour M Lafrenière RG Drapeau P Lacaille JC Kim E Lee JR Igarashi K Huganir RL Rouleau GA Michaud JL 《American journal of human genetics》2011,(3):1427-316
Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder. 相似文献
48.
Two Routes of Metabolic Cross-Feeding between Bifidobacterium adolescentis and Butyrate-Producing Anaerobes from the Human Gut 总被引:3,自引:0,他引:3 下载免费PDF全文
Alvaro Belenguer Sylvia H. Duncan A. Graham Calder Grietje Holtrop Petra Louis Gerald E. Lobley Harry J. Flint 《Applied microbiology》2006,72(5):3593-3599
Dietary carbohydrates have the potential to influence diverse functional groups of bacteria within the human large intestine. Of 12 Bifidobacterium strains of human gut origin from seven species tested, four grew in pure culture on starch and nine on fructo-oligosaccharides. The potential for metabolic cross-feeding between Bifidobacterium adolescentis and lactate-utilizing, butyrate-producing Firmicute bacteria related to Eubacterium hallii and Anaerostipes caccae was investigated in vitro. E. hallii L2-7 and A. caccae L1-92 failed to grow on starch in pure culture, but in coculture with B. adolescentis L2-32 butyrate was formed, indicating cross-feeding of metabolites to the lactate utilizers. Studies with [13C]lactate confirmed carbon flow from lactate, via acetyl coenzyme A, to butyrate both in pure cultures of E. hallii and in cocultures with B. adolescentis. Similar results were obtained in cocultures involving B. adolescentis DSM 20083 with fructo-oligosaccharides as the substrate. Butyrate formation was also stimulated, however, in cocultures of B. adolescentis L2-32 grown on starch or fructo-oligosaccharides with Roseburia sp. strain A2-183, which produces butyrate but does not utilize lactate. This is probably a consequence of the release by B. adolescentis of oligosaccharides that are available to Roseburia sp. strain A2-183. We conclude that two distinct mechanisms of metabolic cross-feeding between B. adolescentis and butyrate-forming bacteria may operate in gut ecosystems, one due to consumption of fermentation end products (lactate and acetate) and the other due to cross-feeding of partial breakdown products from complex substrates. 相似文献
49.
50.
Schneider MR Dahlhoff M Horst D Hirschi B Trülzsch K Müller-Höcker J Vogelmann R Allgäuer M Gerhard M Steininger S Wolf E Kolligs FT 《PloS one》2010,5(12):e14325