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61.
Haas BJ Volfovsky N Town CD Troukhan M Alexandrov N Feldmann KA Flavell RB White O Salzberg SL 《Genome biology》2002,3(6):research0029.1-research002912
62.
The organization of filamentous actin (F-actin) in living cells of the oomycete Phytophthora cinnamomi was determined during zoosporogenesis and zoospore encystment by microinjecting sporangia with fluorescently labeled phalloidin and observing resultant fluorescence by confocal microscopy. In multinucleate sporangia prior to the induction of cleavage, phalloidin labeling took the form of plaques which occurred mainly in the periphery of the sporangia. After induction of cleavage, phalloidin labeling showed that the plaques disappeared and that F-actin began to accumulate along the developing cleavage planes and around nuclei and water expulsion vacuoles. F-actin labeling was also observed near the plasma membrane in zoospores and young cysts but reverted to the plaque form in older cysts. Localization of F-actin close to the developing cleavage planes is consistent with the idea that actin microfilaments function in the positioning and expansion of the cleavage membranes. Observations of plaques of actin in living sporangia provide evidence that plaques are not aldehyde-induced fixation artifacts. Copyright 1998 Academic Press. 相似文献
63.
Serglycin is the major proteoglycan in most hematopoietic cells, including
monocytes and macrophages. The monoblastic cell line U937-1 was used to
study the expression of serglycin during proliferation and differentiation.
In unstimulated proliferating U937-1 cells serglycin mRNA is
nonconstitutively expressed. The level of serglycin mRNA was found to
correlate with the synthesis of chondroitin sulfate proteoglycan (CSPG).
The U937-1 cells were induced to differentiate into different types of
macrophage-like cells by exposing the cells to PMA, RA, or VitD3. These
inducers of differentiation affected the expression of serglycin mRNA in
three different ways. The initial upregulation seen in the normally
proliferating cells was not observed in PMA treated cells. In contrast, RA
increased the initial upregulation, giving a reproducible six times
increase in serglycin mRNA level from 4 to 24 h of incubation, compared to
a four times increase in the control cells. VitD3 had no effect on the
expression of serglycin mRNA. The incorporation of (35S)sulfate into CSPG
decreased approximately 50% in all three differentiated cell types.
Further, the (35S)CSPGs expressed were of larger size in PMA treated cells
than controls, but smaller after RA treatment. This was due to the
expression of CSPGs, with CS-chains of 25 and 5 kDa in PMA and RA treated
cells, respectively, compared to 11 kDa in the controls. VitD3 had no
significant effect on the size of CSPG produced. PMA treated cells secreted
75% of the (35S)PGs expressed, but the major portion was retained in cells
treated with VitD3 or RA. The differences seen in serglycin mRNA levels,
the macromolecular properties of serglycin and in the PG secretion
patterns, suggest that serglycin may have different functions in different
types of macrophages.
相似文献
64.
65.
Third-generation sequencing technologies can generate very long reads with relatively high error rates. The lengths of the reads, which sometimes exceed one million bases, make them invaluable for resolving complex repeats that cannot be assembled using shorter reads. Many high-quality genome assemblies have already been produced, curated, and annotated using the previous generation of sequencing data, and full re-assembly of these genomes with long reads is not always practical or cost-effective. One strategy to upgrade existing assemblies is to generate additional coverage using long-read data, and add that to the previously assembled contigs. SAMBA is a tool that is designed to scaffold and gap-fill existing genome assemblies with additional long-read data, resulting in substantially greater contiguity. SAMBA is the only tool of its kind that also computes and fills in the sequence for all spanned gaps in the scaffolds, yielding much longer contigs. Here we compare SAMBA to several similar tools capable of re-scaffolding assemblies using long-read data, and we show that SAMBA yields better contiguity and introduces fewer errors than competing methods. SAMBA is open-source software that is distributed at https://github.com/alekseyzimin/masurca. 相似文献
66.
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses 总被引:3,自引:0,他引:3 下载免费PDF全文
Holmes EC Ghedin E Miller N Taylor J Bao Y St George K Grenfell BT Salzberg SL Fraser CM Lipman DJ Taubenberger JK 《PLoS biology》2005,3(9):e300
Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002–2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003–2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance. 相似文献
67.
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 总被引:15,自引:0,他引:15 下载免费PDF全文
Read TD Brunham RC Shen C Gill SR Heidelberg JF White O Hickey EK Peterson J Utterback T Berry K Bass S Linher K Weidman J Khouri H Craven B Bowman C Dodson R Gwinn M Nelson W DeBoy R Kolonay J McClarty G Salzberg SL Eisen J Fraser CM 《Nucleic acids research》2000,28(6):1397-1406
The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and Chlamydia pneumoniae strain AR39 (1 229 853 nt) were determined using a random shotgun strategy. The MoPn genome exhibited a general conservation of gene order and content with the previously sequenced C.trachomatis serovar D. Differences between C.trachomatis strains were focused on an ~50 kb ‘plasticity zone’ near the termination origins. In this region MoPn contained three copies of a novel gene encoding a >3000 amino acid toxin homologous to a predicted toxin from Escherichia coli 0157:H7 but had apparently lost the tryptophan biosyntheis genes found in serovar D in this region. The C.pneumoniae AR39 chromosome was >99.9% identical to the previously sequenced C.pneumoniae CWL029 genome, however, comparative analysis identified an invertible DNA segment upstream of the uridine kinase gene which was in different orientations in the two genomes. AR39 also contained a novel 4524 nt circular single-stranded (ss)DNA bacteriophage, the first time a virus has been reported infecting C.pneumoniae. Although the chlamydial genomes were highly conserved, there were intriguing differences in key nucleotide salvage pathways: C.pneumoniae has a uridine kinase gene for dUTP production, MoPn has a uracil phosphororibosyl transferase, while C.trachomatis serovar D contains neither gene. Chromosomal comparison revealed that there had been multiple large inversion events since the species divergence of C.trachomatis and C.pneumoniae, apparently oriented around the axis of the origin of replication and the termination region. The striking synteny of the Chlamydia genomes and prevalence of tandemly duplicated genes are evidence of minimal chromosome rearrangement and foreign gene uptake, presumably owing to the ecological isolation of the obligate intracellular parasites. In the absence of genetic analysis, comparative genomics will continue to provide insight into the virulence mechanisms of these important human pathogens. 相似文献
68.
MOTIVATION: Computational gene finding systems play an important role in finding new human genes, although no systems are yet accurate enough to predict all or even most protein-coding regions perfectly. Ab initio programs can be augmented by evidence such as expression data or protein sequence homology, which improves their performance. The amount of such evidence continues to grow, but computational methods continue to have difficulty predicting genes when the evidence is conflicting or incomplete. Genome annotation pipelines collect a variety of types of evidence about gene structure and synthesize the results, which can then be refined further through manual, expert curation of gene models. RESULTS: JIGSAW is a new gene finding system designed to automate the process of predicting gene structure from multiple sources of evidence, with results that often match the performance of human curators. JIGSAW computes the relative weight of different lines of evidence using statistics generated from a training set, and then combines the evidence using dynamic programming. Our results show that JIGSAW's performance is superior to ab initio gene finding methods and to other pipelines such as Ensembl. Even without evidence from alignment to known genes, JIGSAW can substantially improve gene prediction accuracy as compared with existing methods. AVAILABILITY: JIGSAW is available as an open source software package at http://cbcb.umd.edu/software/jigsaw. 相似文献
69.
William H Majoros Mihaela Pertea Arthur L Delcher Steven L Salzberg 《BMC bioinformatics》2005,6(1):1-13
Background
The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity.Results
As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN.Conclusions
In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques. 相似文献70.
Clunes MT Lindsay SL Roussa E Quinton PM Bovell DL 《Journal of molecular histology》2004,35(4):339-345
The localisation of the vacuolar proton pump (V-H+ -ATPase) and the enzyme carbonic anhydrase II (CAII) was investigated in the human eccrine sweat gland employing standard immunohistochemical techniques after antigen retrieval using microwave heat treatment and high pressure. The high-pressure antigen retrieval unmasked the presence of V-H+ -ATPase in the clear cells of the secretory coil, with a distribution similar to that previously observed for CAII. However, the dark cells were unreactive to both antibodies. In addition, heat and high-pressure antigen retrieval demonstrated the presence of CAII in the apical zone of luminal cells of the reabsorptive duct, a location not previously reported. The localisation of V-H+ -ATPase and CAII in the secretory coil clear cells suggests that the formation of HCO3- and H+ by carbonic anhydrase II and the transport of H+ by V-H+ -ATPase may play an role in sweat fluid secretion. Their presence at the apex of the duct cells indicates involvement in ductal ion reabsorption. 相似文献