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991.
Amrute-Nayak M Antognozzi M Scholz T Kojima H Brenner B 《The Journal of biological chemistry》2008,283(7):3773-3781
In muscle inorganic phosphate strongly decreases force generation in the presence of millimolar MgATP, whereas phosphate slows shortening velocity only at micromolar MgATP concentrations. It is still controversial whether reduction in shortening velocity by phosphate results from phosphate binding to the nucleotide-free myosin head or from binding of phosphate to an actomyosin-ADP state as postulated for the inhibition of force generation by phosphate. Because most single-molecule studies are performed at micromolar concentrations of MgATP where phosphate effects on movement are rather prominent, clarification of the mechanisms of phosphate inhibition is essential for interpretation of data in which phosphate is used in single molecule studies to probe molecular events of force generation and movement. In in vitro assays we found that inhibition of filament gliding by inorganic phosphate was associated with increased fragmentation of actin filaments. In addition, phosphate did not extend dwell times of Cy3-EDA-ATP (2'(3')-O-[[2-[[6-[2-[3-(1-ethyl-1,3-dihydro-3,3-dimethyl-5-sulfo-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-5-sulfo-3H-indolio]-1-oxohexyl]amino]ethyl]carbamoyl]ATP) but reduced the number of Cy3-signals per field of view, approaching 50% at phosphate concentrations of 1-2 mM. Apparently, inhibition of movement does not result from binding of phosphate to an actomyosin-ADP intermediate as proposed by Hooft and coworkers (Hooft, A. M., Maki, E. J., Cox, K. K., and Baker, J. E. (2007) Biochemistry 46, 3513-3520) but, rather, from forming a strong-binding actomyosin-phosphate intermediate. 相似文献
992.
F. Domingo A.J. Brenner L. Gutiérrez S.C. Clark L.D. Incoll C. Aguilera 《Biologia Plantarum》2003,46(2):257-262
The water relations and stomatal conductances of three perennial plant species, Stipa tenacissima L., Anthyllis cytisoides L., and Retama sphaerocarpa (L.) Boiss., dominant on the upper slopes, mid-slopes and floor of a valley, respectively, in semi-arid south-east Spain,
were investigated to test the hypothesis that differences in plant-soil water relations could account for the different distributions
of each species in the catena. Diurnal measurements of water potential (Ψw), relative water content (RWC) and stomatal conductance (gs) of leaves were made over one year. Leaf temperature, air humidity, wind-speed and incident quantum flux density were measured
concurrently. Soil water content was determined gravimetrically at 0 – 5 cm and 15 – 20 cm depths. Measurements of Ψw, RWC and gs were analysed according to meteorological conditions, based on the maxima for daily air temperature and atmospheric saturation
water vapour deficit and on soil moisture content. The hypothesis that plant-soil water relations can explain the distribution
of the three species along the catena from valley side to valley floor was rejected for Anthyllis and Stipa but confirmed for Retama.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
993.
994.
Jose Eduardo de la Torre-Bárcena Sergios-Orestis Kolokotronis Ernest K. Lee Dennis Wm. Stevenson Eric D. Brenner Manpreet S. Katari Gloria M. Coruzzi Rob DeSalle 《PloS one》2009,4(6)
Background
Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group.Methodology
We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations.Conclusions
We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized. 相似文献995.
George J. Cerniglia Nabendu Pore Jeff H. Tsai Susan Schultz Rosemarie Mick Regine Choe Xiaoman Xing Turgut Durduran Arjun G. Yodh Sydney M. Evans Cameron J. Koch Stephen M. Hahn Harry Quon Chandra M. Sehgal William M. F. Lee Amit Maity 《PloS one》2009,4(8)
Background
Epidermal growth factor receptor (EGFR) inhibitors have shown only modest clinical activity when used as single agents to treat cancers. They decrease tumor cell expression of hypoxia-inducible factor 1-α (HIF-1α) and vascular endothelial growth factor (VEGF). Hypothesizing that this might normalize tumor vasculature, we examined the effects of the EGFR inhibitor erlotinib on tumor vascular function, tumor microenvironment (TME) and chemotherapy and radiotherapy sensitivity.Methodology/Principal Findings
Erlotinib treatment of human tumor cells in vitro and mice bearing xenografts in vivo led to decreased HIF-1α and VEGF expression. Treatment altered xenograft vessel morphology assessed by confocal microscopy (following tomato lectin injection) and decreased vessel permeability (measured by Evan''s blue extravasation), suggesting vascular normalization. Erlotinib increased tumor blood flow measured by Power Doppler ultrasound and decreased hypoxia measured by EF5 immunohistochemistry and tumor O2 saturation measured by optical spectroscopy. Predicting that these changes would improve drug delivery and increase response to chemotherapy and radiation, we performed tumor regrowth studies in nude mice with xenografts treated with erlotinib and either radiotherapy or the chemotherapeutic agent cisplatin. Erlotinib therapy followed by cisplatin led to synergistic inhibition of tumor growth compared with either treatment by itself (p<0.001). Treatment with erlotinib before cisplatin led to greater tumor growth inhibition than did treatment with cisplatin before erlotinib (p = 0.006). Erlotinib followed by radiation inhibited tumor regrowth to a greater degree than did radiation alone, although the interaction between erlotinib and radiation was not synergistic.Conclusions/Significance
EGFR inhibitors have shown clinical benefit when used in combination with conventional cytotoxic therapy. Our studies show that targeting tumor cells with EGFR inhibitors may modulate the TME via vascular normalization to increase response to chemotherapy and radiotherapy. These studies suggest ways to assess the response of tumors to EGFR inhibition using non-invasive imaging of the TME. 相似文献996.
Kasper Daniel Hansen Liana F. Lareau Marco Blanchette Richard E. Green Qi Meng Jan Rehwinkel Fabian L. Gallusser Elisa Izaurralde Donald C. Rio Sandrine Dudoit Steven E. Brenner 《PLoS genetics》2009,5(6)
Alternative mRNA splicing adds a layer of regulation to the expression of thousands of genes in Drosophila melanogaster. Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are degraded by the nonsense-mediated mRNA decay (NMD) pathway. This coupling of alternative splicing and NMD provides a mechanism for gene regulation that is highly conserved in mammals. NMD is also active in Drosophila, but its effect on the repertoire of alternative splice forms has been unknown, as has the mechanism by which it recognizes targets. Here, we have employed a custom splicing-sensitive microarray to globally measure the effect of alternative mRNA processing and NMD on Drosophila gene expression. We have developed a new algorithm to infer the expression change of each mRNA isoform of a gene based on the microarray measurements. This method is of general utility for interpreting splicing-sensitive microarrays and high-throughput sequence data. Using this approach, we have identified a high-confidence set of 45 genes where NMD has a differential effect on distinct alternative isoforms, including numerous RNA–binding and ribosomal proteins. Coupled alternative splicing and NMD decrease expression of these genes, which may in turn have a downstream effect on expression of other genes. The NMD–affected genes are enriched for roles in translation and mitosis, perhaps underlying the previously observed role of NMD factors in cell cycle progression. Our results have general implications for understanding the NMD mechanism in fly. Most notably, we found that the NMD–target mRNAs had significantly longer 3′ untranslated regions (UTRs) than the nontarget isoforms of the same genes, supporting a role for 3′ UTR length in the recognition of NMD targets in fly. 相似文献
997.
Mosquito larvae crude extract have been found to alter the mitotic rate of several mouse epithelial cell populations such as enterocytes and tongue keratinocytes. Also, the dialysed fraction inhibits hepatocyte proliferation in hepatectomized males. These experiments suggested an inhibitory effect on the G1/S interphase. Consequently, we suggested the presence of some molecule or molecules related to the TGF-beta superfamily. In the present paper, we have assayed the crude extract on human mononuclear cells and the dialysed fraction of the extract on tongue keratinocyte proliferation. Furthermore, different protein fractions obtained using a molecular exclusion chromatographic column were assayed on hepatocyte proliferation of hepatectomized mice. Three groups of proteins have been isolated. Results show a dose-dependent effect of crude extract on mononuclear cell proliferation and the dialysed extract caused an inhibitory effect on tongue keratinocyte proliferation. With regard to the hepatocyte mitotic rate, an inhibitory effect appeared only in animals receiving the fraction with lower molecular weight. These results suggest the presence in mosquito larvae of some peptidic molecule or molecules resembling the activity of members of the TGF-beta superfamily. 相似文献
998.
Long‐term continental changes in wing length,but not bill length,of a long‐distance migratory shorebird
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David B. Lank Cailin Xu Brian A. Harrington Richard I. Guy Morrison Cheri L. Gratto‐Trevor Peter W. Hicklin Brett K. Sandercock Paul Allen Smith Eunbi Kwon Jennie Rausch Lisa D. Pirie Dominix Diana J. Hamilton Julie Paquet Sydney E. Bliss Sarah G. Neima Christian Friis Scott A. Flemming Alexandra M. Anderson Ronald C. Ydenberg 《Ecology and evolution》2017,7(9):3243-3256
We compiled a >50‐year record of morphometrics for semipalmated sandpipers (Calidris pusilla), a shorebird species with a Nearctic breeding distribution and intercontinental migration to South America. Our data included >57,000 individuals captured 1972–2015 at five breeding locations and three major stopover sites, plus 139 museum specimens collected in earlier decades. Wing length increased by ca. 1.5 mm (>1%) prior to 1980, followed by a decrease of 3.85 mm (nearly 4%) over the subsequent 35 years. This can account for previously reported changes in metrics at a migratory stopover site from 1985 to 2006. Wing length decreased at a rate of 1,098 darwins, or 0.176 haldanes, within the ranges of other field studies of phenotypic change. Bill length, in contrast, showed no consistent change over the full period of our study. Decreased body size as a universal response of animal populations to climate warming, and several other potential mechanisms, are unable to account for the increasing and decreasing wing length pattern observed. We propose that the post‐WWII near‐extirpation of falcon populations and their post‐1973 recovery driven by the widespread use and subsequent limitation on DDT in North America selected initially for greater flight efficiency and latterly for greater agility. This predation danger hypothesis accounts for many features of the morphometric data and deserves further investigation in this and other species. 相似文献
999.
Michelle A. Duennes Chris Petranek Esteban Pineda Diez de Bonilla Jorge Mérida-Rivas Oscar Martinez-López Philippe Sagot Rémy Vandame Sydney A. Cameron 《Conservation Genetics》2017,18(3):553-572
Mexico and Central America are among the most biodiverse regions on Earth, harboring many species with high levels of interpopulation morphological and genetic diversity. The mountainous topography of this region contains isolated sky island habitats that have the potential to promote speciation. This has been studied in vertebrates, yet few studies have examined the phylogeographic and genetic structure of insect species encompassing this region. Here we investigate geographic patterns of genetic and morphological divergence and speciation among widespread populations of the highly polymorphic bumble bee Bombus ephippiatus and its closest relative B. wilmattae. We used DNA sequences from a fragment of cytochrome oxidase I (COI), genotypes for twelve microsatellite markers, and morphometric data from wings to construct a well-supported inference of the divergences among these taxa. We have found complex patterns of genetic isolation and morphological divergence within B. ephippiatus across its geographic range and present evidence that B. ephippiatus comprises multiple independent evolutionary lineages. The pattern of their diversification corresponds to geographic and environmental isolating mechanisms, including the Mexican highlands, the lowlands of the Isthmus of Tehuantepec in southern Mexico, the Nicaraguan Depression, the patchily distributed volcanic ranges in Nuclear Central America and Pleistocene glacial cycles. These results have important implications for the development and distribution of B. ephippiatus as a commercial pollinator in Mexico and Central America. 相似文献
1000.