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71.
AGenDA: homology-based gene prediction 总被引:2,自引:0,他引:2
Taher L Rinner O Garg S Sczyrba A Brudno M Batzoglou S Morgenstern B 《Bioinformatics (Oxford, England)》2003,19(12):1575-1577
We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment. 相似文献
72.
73.
Frederique Zindy Youngsoo Lee Daisuke Kawauchi Olivier Ayrault Leila Ben Merzoug Yang Li Peter J. McKinnon Martine F. Roussel 《PloS one》2015,10(6)
Dicer, a ribonuclease III enzyme, is required for the maturation of microRNAs. To assess its role in cerebellar and medulloblastoma development, we genetically deleted Dicer in Nestin-positive neural progenitors and in mice lacking one copy for the Sonic Hedgehog receptor, Patched 1. We found that conditional loss of Dicer in mouse neural progenitors induced massive Trp53-independent apoptosis in all proliferative zones of the brain and decreased proliferation of cerebellar granule progenitors at embryonic day 15.5 leading to abnormal cerebellar development and perinatal lethality. Loss of one copy of Dicer significantly accelerated the formation of mouse medulloblastoma of the Sonic Hedgehog subgroup in Patched1-heterozygous mice. We conclude that Dicer is required for proper cerebellar development, and to restrain medulloblastoma formation. 相似文献
74.
The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed. 相似文献
75.
Fernanda A. H. Batista Leandro S. Goto Wanius Garcia Derminda I. de Moraes Mario de Oliveira Neto Igor Polikarpov Marcia R. Cominetti Heloísa S. Selistre-de-Araújo Leila M. Beltramini Ana Paula Ulian Araújo 《European biophysics journal : EBJ》2010,39(8):1193-1205
Lectins have been classified into a structurally diverse group of proteins that bind carbohydrates and glycoconjugates with
high specificity. They are extremely useful molecules in the characterization of saccharides, as drug delivery mediators,
and even as cellular surface makers. In this study, we present camptosemin, a new lectin from Camptosema ellipticum. It was characterized as an N-acetyl-d-galactosamine-binding homo-tetrameric lectin, with a molecular weight around 26 kDa/monomers. The monomers were stable over
a wide range of pH values and exhibited pH-dependent oligomerization. Camptosemin promoted adhesion of breast cancer cells
and hemagglutination, and both activities were inhibited by its binding of sugar. The stability and unfolding/folding behavior
of this lectin was characterized using fluorescence and far-UV circular dichroism spectroscopies. The results indicate that
chemical unfolding of camptosemin proceeds as a two-state monomer-tetramer process. In addition, small-angle X-ray scattering
shows that camptosemin behaves as a soluble and stable homo-tetramer molecule in solution. 相似文献
76.
In this paper, partitioning behaviors of typical neutral (Alanine), acidic (Glutamic acid) and basic (Lysine) amino acids
into imidazolium-based ionic liquids [C4mim][PF6], [C6mim][PF6], [C8mim][PF6], [C6mim][BF4] and [C8mim][BF4] as extracting solvents were examined. [C6mim][BF4] showed the best efficiency for partitioning of amino acids. The partition coefficients of amino acids in ionic liquids were
found to depend strongly on pH of the aqueous solution, amino acid and ionic liquid chemical structures. Different chemical
forms of amino acids in aqueous solutions were pH dependent, so the pH value of the aqueous phase was a determining factor
for extraction of amino acids into ionic liquid phase. Both water content of ionic liquids and charge densities of their anionic
and cationic parts were important factors for partitioning of cationic and anionic forms of amino acids into ionic liquid
phase. Extracted amino acids were back extracted into phosphate buffer solutions adjusted on appropriate pH values. The results
showed that ionic liquids could be used as suitable modifiers on the stationary phase of an HPLC column for efficient separation
of acidic, basic, and neutral amino acids. 相似文献
77.
Mohamed Ben Sghaier Jihed Boubaker Aicha Neffati Ilef Limem Ines Skandrani Wissem Bhouri Ines Bouhlel Soumaya Kilani Leila Chekir‐Ghedira Kamel Ghedira 《化学与生物多样性》2010,7(7):1754-1763
The mutagenic and antimutagenic effects of the essential oil extracted from the aerial parts of Teucrium ramosissimum were evaluated by the bacterial reverse mutation assay in Salmonella typhimurium TA98, TA100, and TA1535, with and without exogenous metabolic activation (S9 fraction). The T. ramosissimum essential oil showed no mutagenic effect. In contrast, our results established that it possessed antimutagenic effects against sodium azide (SA), aflatoxin B1 (AFB1), benzo[a]pyrene (B[a]P), and 4‐nitro‐o‐phenylenediamine (NOPD). The antioxidant capacity of the tested essential oil was evaluated using enzymatic, i.e., the xanthine/xanthine oxidase (X/XOD) assay, and nonenzymatic systems, i.e., the nitro‐blue tetrazolium (NBT)/riboflavin and the DPPH assays. A moderate free radical‐scavenging activity was observed towards DPPH. and O$\rm{{_{2}^{{^\cdot} -}}}$ . In contrast, T. ramosissimum essential oil showed no effect for all the tested concentrations in the X/XOD assay. 相似文献
78.
Leila M. Luheshi Wolfgang Hoyer Teresa Pereira de Barros Iris van Dijk H?rd Ann-Christin Brorsson Bertil Macao Cecilia Persson Damian C. Crowther David A. Lomas Stefan St?hl Christopher M. Dobson Torleif H?rd 《PLoS biology》2010,8(3)
Protein aggregation, arising from the failure of the cell to regulate the synthesis or degradation of aggregation-prone proteins, underlies many neurodegenerative disorders. However, the balance between the synthesis, clearance, and assembly of misfolded proteins into neurotoxic aggregates remains poorly understood. Here we study the effects of modulating this balance for the amyloid-beta (Aβ) peptide by using a small engineered binding protein (ZAβ3) that binds with nanomolar affinity to Aβ, completely sequestering the aggregation-prone regions of the peptide and preventing its aggregation. Co-expression of ZAβ3 in the brains of Drosophila melanogaster expressing either Aβ42 or the aggressive familial associated E22G variant of Aβ42 abolishes their neurotoxic effects. Biochemical analysis indicates that monomer Aβ binding results in degradation of the peptide in vivo. Complementary biophysical studies emphasize the dynamic nature of Aβ aggregation and reveal that ZAβ3 not only inhibits the initial association of Aβ monomers into oligomers or fibrils, but also dissociates pre-formed oligomeric aggregates and, although very slowly, amyloid fibrils. Toxic effects of peptide aggregation in vivo can therefore be eliminated by sequestration of hydrophobic regions in monomeric peptides, even when these are extremely aggregation prone. Our studies also underline how a combination of in vivo and in vitro experiments provide mechanistic insight with regard to the relationship between protein aggregation and clearance and show that engineered binding proteins may provide powerful tools with which to address the physiological and pathological consequences of protein aggregation. 相似文献
79.
Nalin Gupta Edwardine Nodzenski Nikolai N. Khodarev Jianqing Yu Leila Khorasani Michael A. Beckett Donald W. Kufe Ralph R. Weichselbaum 《EMBO reports》2001,2(6):536-540
Angiostatin is a cleavage product of plasminogen that has anti-angiogenic properties. We investigated whether the effects of angiostatin on endothelial cells are mediated by ceramide, a lipid implicated in endothelial cell signaling. Our results demonstrate that angiostatin produces a transient increase in ceramide that correlates with actin stress fiber reorganization, detachment and death. DNA array expression analysis performed on ceramide-treated human endothelial cells demonstrated induction of certain genes involved in cytoskeleton organization. Specifically, we report that treatment with angiostatin or ceramide results in the activation of RhoA, an important effector of cytoskeletal structure. We also show that treatment of endothelial cells with the antioxidant N-acetylcysteine abrogates morphological changes and cytotoxic effects of treatment with angiostatin or ceramide. These findings support a model in which angiostatin induces a transient rise in ceramide, RhoA activation and free radical production. 相似文献
80.
Efficient embryogenesis and regeneration in freshly isolated and cultured wheat (Triticum aestivum L.) microspores without stress pretreatment 总被引:1,自引:0,他引:1
Shariatpanahi ME Belogradova K Hessamvaziri L Heberle-Bors E Touraev A 《Plant cell reports》2006,25(12):1294-1299
The major advantage of doubled haploids in plant breeding is the immediate achievement of complete homozygosity. Desired genotypes are thus fixed in one generation, reducing time and cost for cultivar or inbred development. Among the different technologies to produce doubled haploids, microspore embryogenesis is by far the most common. It usually requires reprogramming of microspores by stress such as cold, heat, and starvation, followed by embryo development under stress-free conditions. We report here the development of a simple and efficient isolated microspore culture system for producing doubled haploid wheat plants in a wide spectrum of genotypes, in which embryogenic microspores and embryos are formed without any apparent stress treatment. Microspores were isolated from fresh spikes in a nutrient-free medium by stirring and cultured in medium A2 in the dark at 25°C. Once embryogenic microspores were formed, ovaries and phytohormones were added directly to the cultures without changing the medium. The cultures were incubated in the dark at 25–27°C until the formation of embryos and then the embryos were transferred to regeneration medium. The regeneration frequency and percentage of green plants increased significantly using this protocol compared to the shed microspore culture method.Communicated by W. Harwood 相似文献