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51.
Background
The number of genes declared differentially expressed is a random variable and its variability can be assessed by resampling techniques. Another important stability indicator is the frequency with which a given gene is selected across subsamples. We have conducted studies to assess stability and some other properties of several gene selection procedures with biological and simulated data. 相似文献52.
Moisy D Avilov SV Jacob Y Laoide BM Ge X Baudin F Naffakh N Jestin JL 《Journal of virology》2012,86(17):9122-9133
Influenza virus has evolved replication strategies that hijack host cell pathways. To uncover interactions between viral macromolecules and host proteins, we applied a phage display strategy. A library of human cDNA expression products displayed on filamentous phages was submitted to affinity selection for influenza viral ribonucleoproteins (vRNPs). High-mobility-group box (HMGB) proteins were found to bind to the nucleoprotein (NP) component of vRNPs. HMGB1 and HMGB2 bind directly to the purified NP in the absence of viral RNA, and the HMG box A domain is sufficient to bind the NP. We show that HMGB1 associates with the viral NP in the nuclei of infected cells, promotes viral growth, and enhances the activity of the viral polymerase. The presence of a functional HMGB1 DNA-binding site is required to enhance influenza virus replication. Glycyrrhizin, which reduces HMGB1 binding to DNA, inhibits influenza virus polymerase activity. Our data show that the HMGB1 protein can play a significant role in intranuclear replication of influenza viruses, thus extending previous findings on the bornavirus and on a number of DNA viruses. 相似文献
53.
Amino acid selective isotope labeling is a useful approach to simplification of nuclear magnetic resonance (NMR) spectra of large proteins. Cell-free protein synthesis offers essentially unlimited flexibility of labeling patterns but is labor-intensive and expensive. In vivo labeling is simple in principle but generally requires auxotrophic strains, inhibitors of amino acid synthesis, or complex media formulations. We describe a simple procedure for amino acid selective labeling of proteins expressed in prototrophic Escherichia coli strains. Excellent labeling selectivity was achieved for histidine, lysine, methionine, and alanine. Simplicity and robustness of this protocol make it a useful tool for protein NMR. 相似文献
54.
55.
Yakovlev AA Gorokhovatsky AY Onufriev MV Beletsky IP Gulyaeva NV 《Biochemistry. Biokhimii?a》2008,73(3):332-336
We show that an enzyme exists in rat brain capable of cleaving the caspase-3 specific peptide substrate Ac-DEVD-AMC at low
pH. The enzyme shows properties of a cysteine protease and is localized, predominantly, in lysosomes. We have purified this
enzyme from rat brain and identified it by MALDI-TOF MS. The enzyme possessing “acidic” DEVDase activity in rat brain appears
to be cathepsin B. It remains obscure, whether cathepsin B participates in cleavage of caspase-3 substrates in vivo. We suggest that under certain conditions (e.g. in hypoxia) cathepsin B participates in cleavage of caspase-3 substrates
in brain cells.
Published in Russian in Biokhimiya, 2008, Vol. 73, No. 3, pp. 408–413. 相似文献
56.
57.
Alteration of apoptotic protease-activating factor-1 (APAF-1)-dependent apoptotic pathway during development of rat brain and liver. 总被引:5,自引:0,他引:5
Katsuya Ota Alexander G Yakovlev Asako Itaya Masanori Kameoka Yasuharu Tanaka Koichiro Yoshihara 《Journal of biochemistry》2002,131(1):131-135
Brain and liver extracts of rats at different stages after birth were examined for cytochrome c/dATP-dependent caspase (DEVDase)-activation (mitochondria pathway) in vitro. The caspase-activating activity in the brain extracts rapidly decreased after birth, reaching approximately 50 and 5%, at 1 and 2 weeks, respectively, of that in a 3-days- newborn sample, and essentially no caspase-activation was detected in the adult rat brain extracts. Such a dramatic change was not detected in the liver samples, suggesting that the observed abrogation of the cytochrome c-dependent mitochondria pathway after birth is a brain-specific event. In order to determine the factor(s) lacking in adult brain, we separately measured Apaf-1, procaspase 9, and pro-DEVDase activities using a supplementation assay. In adult brain, Apaf-1 activity was scarcely detected, while the tissue retained low but significant amounts of procaspase 9 (16% of that in the fetal tissue) and a pro-DEVDase (3.4%). In contrast, adult liver extracts retained relatively high levels of all of these factors. Immunoblot analyses clearly indicated that the expression of Apaf-1 and procaspase 3 is markedly suppressed within 4 weeks after birth in brain tissue while they are even expressed in adult liver. Considering these results together, we propose that, in the brain, the cytochrome c-dependent mitochondria pathway, which is essential for the programmed cell death during normal morphogenesis, is abrogated within 2-4 weeks after birth, whereas the pathway is still active in other adult tissues such as liver. 相似文献
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59.
The accuracy of global Smith-Waterman alignments and Pareto-optimal alignments depending on the degree of sequence similarity
(percent of coincidence, %id, and the number of removed fragments NGap) has been examined. An algorithm for constructing a set of three to six alignments has been developed of which the best alignment
on the average exceeds in accuracy the best alignment that can be constructed using the Smith-Waterman algorithm. For weakly
homologous sequences (%id 15, NGap 20), the increase in accuracy is on the average about 8%, with the average accuracy of the global Smith-Waterman alignments
being about 38% (the accuracy was estimated on model test sets). 相似文献
60.
D. O. Gimranov V. G. Kotov M. M. Rumyantsev V. I. Silaev A. G. Yakovlev T. I. Yakovleva N. V. Zelenkov M. V. Sotnikova M. M. Devyashin N. A. Plasteeva N. E. Zaretskaya I. M. Nurmukhametov N. G. Smirnov P. A. Kosintsev 《Doklady biological sciences》2018,482(1):191-193
The vertebrate fauna from the cave deposits in Imanai Cave in the Southern Urals (53°02′ N, 56°26′E) has been studied. It contains 715 bones that belonged to at least 11 individuals of fossil lion (Panthera (Leo) ex gr. fossilis-spelaea). It has been established that this is one of the largest Eurasian burial sites of fossil lions. The bones were accumulated due to the natural death of animals inside the cave. The age and sex estimations have shown that at least six adult males and five adult females died there. According to the accompanying fauna, radiocarbon, geochemical, and mineralogical analyses and archaeological finds, the interval of the lion bone accumulation is determined as the first half to middle of Late Pleistocene (OIS 5–3). 相似文献