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201.
Differential expression analysis for sequence count data 总被引:22,自引:0,他引:22
High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form
of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability
throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution,
with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package. 相似文献
202.
Corti A 《Cellular and molecular neurobiology》2010,30(8):1163-1170
Chromogranin A (CgA) is an acidic glycoprotein belonging to a family of regulated secretory proteins stored in the dense core
granules of the adrenal medulla and of many other neuroendocrine cells and neurons. This protein is frequently used as a diagnostic
and prognostic serum marker for a range of neuroendocrine tumors. Circulating CgA is also increased in patients with other
diseases, including subpopulations of patients with non-neuroendocrine tumors, with important prognostic implications. A growing
body of evidence suggests that CgA is more than a diagnostic/prognostic marker for cancer patients. Indeed, results of in
vitro experiments and in vivo studies in animal models suggest that this protein and its fragments can affect several elements
of the tumor microenvironment, including fibroblasts and endothelial cells. In this article, recent findings implicating CgA
as a modulator of the tumor microenvironment and suggesting that abnormal secretion of CgA could play important roles in tumor
progression and response to therapy in cancer patients are reviewed and discussed. 相似文献
203.
Jang do S Lee HJ Lee B Hong BH Cha HJ Yoon J Lim K Yoon YJ Kim J Ree M Lee HC Choi KY 《FEBS letters》2006,580(17):4166-4171
Failure to detect the intermediate in spite of its existence often leads to the conclusion that two-state transition in the unfolding process of the protein can be justified. In contrast to the previous equilibrium unfolding experiment fitted to a two-state model by circular dichroism and fluorescence spectroscopies, an equilibrium unfolding intermediate of a dimeric ketosteroid isomerase (KSI) could be detected by small angle X-ray scattering (SAXS) and analytical ultracentrifugation. The sizes of KSI were determined to be 18.7A in 0M urea, 17.3A in 5.2M urea, and 25.1A in 7M urea by SAXS. The size of KSI in 5.2M urea was significantly decreased compared with those in 0M and 7M urea, suggesting the existence of a compact intermediate. Sedimentation velocity as obtained by ultracentrifugation confirmed that KSI in 5.2M urea is distinctly different from native and fully-unfolded forms. The sizes measured by pulse field gradient nuclear magnetic resonance (NMR) spectroscopy were consistent with those obtained by SAXS. Discrepancy of equilibrium unfolding studies between size measurement methods and optical spectroscopies might be due to the failure in detecting the intermediate by optical spectroscopic methods. Further characterization of the intermediate using (1)H NMR spectroscopy and Kratky plot supported the existence of a partially-folded form of KSI which is distinct from those of native and fully-unfolded KSIs. Taken together, our results suggest that the formation of a compact intermediate should precede the association of monomers prior to the dimerization process during the folding of KSI. 相似文献
204.
Rhamnolipids, produced by Pseudomonas aeruginosa, represent an important group of biosurfactants having various industrial, environmental, and medical applications. Current
methods for rhamnolipid quantification involve the use of strong hazardous acids/chemicals, indirect measurement of the concentration
of sugar moiety, or require the availability of expensive equipment (HPLC-MS). A safer, easier method that measures the whole
rhamnolipid molecules would significantly enhance strain selection, metabolic engineering, and process development for economical
rhamnolipid production. A semi-quantitative method was reported earlier to differentiate between the rhamnolipid-producing
and non-producing strains using agar plates containing methylene blue and cetyl trimethylammonium bromide (CTAB). In this
study, a rapid and simple method for rhamnolipid analysis was developed by systematically investigating the complexation of
rhamnolipids and methylene blue, with and without the presence of CTAB. The method relies on measuring the absorbance (at
638 nm) of the rhamnolipid−methylene blue complex that partitions into the chloroform phase. With P. aeruginosa fermentation samples, the applicability of this method was verified by comparison of the analysis results with those obtained
from the commonly used anthrone reaction technique. 相似文献
205.
206.
207.
Vanessa B. Fortes Júlio César Bicca-Marques 《International journal of primatology》2008,29(3):717-722
We located 4 brown howlers (1 adult male, 2 adult females, and 1 juvenile male) showing abnormally lighter pelage in 3 social
groups comprising 5, 6, and 9 individuals in a 20 ha-forest fragment in the State of Rio Grande do Sul, Brazil. Two additional
groups composed only of normally colored individuals also live in the fragment, which is isolated from nearby fragments by
267–1009 m. They were the only brown howlers with abnormal pelage color out of a total of 386 individuals belonging to 67
groups in 21 fragments in the 5876-ha study area. The isolation of the forest fragment, its high howler density (2.2 individuals⁄ha),
and large group size (8.8 ± 2.4 individuals) may decrease the likelihood of successful immigration into the population, leading
to an increased probability of inbreeding that may facilitate the expression of rare alleles. 相似文献
208.
Random network models have been a popular tool for investigating cortical network dynamics. On the scale of roughly a cubic millimeter of cortex, containing about 100,000 neurons, cortical anatomy suggests a more realistic architecture. In this locally connected random network, the connection probability decreases in a Gaussian fashion with the distance between neurons. Here we present three main results from a simulation study of the activity dynamics in such networks. First, for a broad range of parameters these dynamics exhibit a stationary state of asynchronous network activity with irregular single-neuron spiking. This state can be used as a realistic model of ongoing network activity. Parametric dependence of this state and the nature of the network dynamics in other regimes are described. Second, a synchronous excitatory stimulus to a fraction of the neurons results in a strong activity response that easily dominates the network dynamics. And third, due to that activity response an embedding of a divergent-convergent feed-forward subnetwork (as in synfire chains) does not naturally lead to a stable propagation of synchronous activity in the subnetwork; this is in contrast to our earlier findings in isolated subnetworks of that type. Possible mechanisms for stabilizing the interplay of volleys of synchronous spikes and network dynamics by specific learning rules or generalizations of the subnetworks are discussed. 相似文献
209.
A significant macrophage and T-cell infiltrate commonly occurs in inflammatory joint conditions such as rheumatoid arthritis
that have significant bone destruction. Cytokines produced by activated macrophages and T cells are implicated in arthritis
pathogenesis and are involved in osteoclast-mediated bone resorption. The scope of the present review is to analyze current
knowledge and to provide a better understanding of how macrophage-derived factors promote the differentiation of a novel T-helper
subset (Th17) that promotes osteoclast formation and activation. 相似文献
210.
Lucas Spohn Christiane Fichter Martin Werner Silke Lassmann 《Journal of cell communication and signaling》2016,10(1):41-47
Background: The EGF receptor is a therapeutic target in cancer cells, whereby mutations of EGFR and/or signalling members act as predictive markers. EGFR however also exhibits dynamic changes of subcellular localization, leading to STAT5 complex formation, nuclear translocation and induction of Aurora-A expression in squamous cancer cells. We previously described high EGFR and Aurora-A expression in esophageal cancer cells. Here, we investigated subcellular localization of EGFR and STAT5 in esophageal cancer cells. Results: Quantitative immunofluorescence analyses of four esophageal cancer cell lines reflecting esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinomas (EAC) revealed that the subcellular localization of EGFR was shifted from a membranous to cytoplasmic localization upon EGF-stimulation in OE21 (ESCC) cells. Thereby, EGFR in part co-localized with E-Cadherin. In parallel, phosphorylated STAT5-Tyr694 appeared to increase in the nucleus and to decrease at the cell membrane. In three additional cell lines, EGFR was only marginally (Kyse-410/ESCC; OE19/EAC) and weakly (OE33, EAC) detectable at the cell membrane. Partial co-localization of EGFR and E-Cadherin occurred in OE33 cells. Post EGF-stimulation, EGFR was detected in the cytoplasm, resembling endosomal compartments. Furthermore, OE19 and OE33 exhibited nuclear STAT5-Tyr694 phosphorylation upon EGF-stimulation. None of the four cell lines showed nuclear EGFR expression and localization. Conclusion: In contrast to other (squamous) cancer cells, activation of EGFR in esophageal squamous cancer cells does not result in nuclear translocation of EGFR. Still, the subcellular localization of EGFR may influence STAT5-associated signaling pathways in esophageal cancer cells and hence possibly also the responses to ErbB, respective EGFR-targeted therapies. 相似文献