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121.
122.
Brinkman CC Sheasley-O'Neill SL Ferguson AR Engelhard VH 《Journal of immunology (Baltimore, Md. : 1950)》2008,181(3):1814-1824
Exogenous dendritic cells display restricted trafficking when injected in vivo and stimulate CD8 T cell responses that are localized to a small number of lymphoid compartments. By examining these responses in the presence and absence of FTY720, a drug that causes sequestration of T cells in lymph nodes, we demonstrate that a significant fraction of divided CD8 T cells redistribute into Ag-free lymph nodes within 3 days of activation. Despite variation in the level of expression of CD62L, redistribution of these cells is CD62L-dependent. Redistributed CD8 T cells exhibit characteristics of differentiated effectors. However, when re-isolated from Ag-free lymph nodes 3 days after activation and transferred into naive mice, they persist for at least 3 wk and expand upon Ag challenge. Thus, CD8 T cells that redistribute to Ag-free lymph nodes 3 days after immunization contain memory precursors. We suggest that this redistribution process represents an important mechanism for establishment of lymph node resident central memory, and that redistribution to Ag-free nodes is an additional characteristic to be added to those that distinguish memory precursors from terminal effectors. 相似文献
123.
Shannan J. Ho Sui Amber Fedynak William W. L. Hsiao Morgan G. I. Langille Fiona S. L. Brinkman 《PloS one》2009,4(12)
Background
It has been noted that many bacterial virulence factor genes are located within genomic islands (GIs; clusters of genes in a prokaryotic genome of probable horizontal origin). However, such studies have been limited to single genera or isolated observations. We have performed the first large-scale analysis of multiple diverse pathogens to examine this association. We additionally identified genes found predominantly in pathogens, but not non-pathogens, across multiple genera using 631 complete bacterial genomes, and we identified common trends in virulence for genes in GIs. Furthermore, we examined the relationship between GIs and clustered regularly interspaced palindromic repeats (CRISPRs) proposed to confer resistance to phage.Methodology/Principal Findings
We show quantitatively that GIs disproportionately contain more virulence factors than the rest of a given genome (p<1E-40 using three GI datasets) and that CRISPRs are also over-represented in GIs. Virulence factors in GIs and pathogen-associated virulence factors are enriched for proteins having more “offensive” functions, e.g. active invasion of the host, and are disproportionately components of type III/IV secretion systems or toxins. Numerous hypothetical pathogen-associated genes were identified, meriting further study.Conclusions/Significance
This is the first systematic analysis across diverse genera indicating that virulence factors are disproportionately associated with GIs. “Offensive” virulence factors, as opposed to host-interaction factors, may more often be a recently acquired trait (on an evolutionary time scale detected by GI analysis). Newly identified pathogen-associated genes warrant further study. We discuss the implications of these results, which cement the significant role of GIs in the evolution of many pathogens. 相似文献124.
We evaluated PCR primer sets to determine the most effective technique for identifying sex of northern ungulates. We sought
markers that required only a single pair of primers to amplify both X- and Y-linked alleles; that amplified X- and Y-linked
products that were easily distinguishable using agarose gel electrophoresis; and that produced short amplicons amenable to
amplification using DNA of poor quality and low quantity, as is often found in non-invasively collected samples such as feces.
Primer pairs KY1/KY2 and SE47/SE48, which amplify X- and Y-specific alleles of the amelogenin gene, met our criteria and were
tested for moose (Alces alces), mountain goat (Oreamnos americanus), Sitka black-tailed deer (Odocoileus hemionus sitkensis), and caribou (Rangifer tarandus). KY primers amplified shorter PCR products than did SE primers; moreover, SE primers inconsistently amplified certain Y-chromosome
products, creating potential for misidentification of sex. DNA fragments amplified using KY primers were sequenced for each
species, allowing us to characterize a 45-bp deletion for Y-linked alleles (136-bp product) relative to X-linked alleles (181-bp
product) in all species and a 9-bp deletion in the X-linked allele of moose relative to other species. This is the first sex-determination
technique using PCR reported for several ungulate species of Alaska. Although other protocols exist for cervids and bovids,
this is the first report of markers meeting the aforementioned criteria for Odocoileus, the most abundant and intensively managed genus of large mammals in North America. 相似文献
125.
Winsor GL Khaira B Van Rossum T Lo R Whiteside MD Brinkman FS 《Bioinformatics (Oxford, England)》2008,24(23):2803-2804
As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community. AVAILABILITY: http://www.burkholderia.com. Source code: GNU GPL. 相似文献
126.
A habitat suitability analysis for littoral mussel beds in the Dutch Wadden Sea was carried out. The analysis was based on
the presence of mussel beds in the years 1960–1970, and a number of environmental characteristics: wave action, flow velocity,
median grain size, emersion times and distance to a gully border. The habitat model describes mussel bed appearance quantitatively.
It predicts the distribution of mussel beds quite well, as well as the distribution of spatfall in the years 1994 and 1996.
From the analysis we found that wave action (maximum orbital velocity) was the main structuring factor. A low orbital velocity
was preferred. Neither very low, nor maximum flow velocities were favourable for mussel beds. Very coarse sands or silty environments
were not preferred. Sites close to the low water line showed lower mussel bed appearance; when emersion time was above 50%
, hardly any mussel beds could be found. The habitat suitability analysis and the construction of a habitat suitability map
was performed in the framework of the discussions on a further or reduced exploitation of the tidal flats in the Dutch Wadden
Sea by cockle and mussel fishery activities.
Electronic Publication 相似文献
127.
Vivona S Gardy JL Ramachandran S Brinkman FS Raghava GP Flower DR Filippini F 《Trends in biotechnology》2008,26(4):190-200
Genome sequences from many organisms, including humans, have been completed, and high-throughput analyses have produced burgeoning volumes of 'omics' data. Bioinformatics is crucial for the management and analysis of such data and is increasingly used to accelerate progress in a wide variety of large-scale and object-specific functional analyses. Refined algorithms enable biotechnologists to follow 'computer-aided strategies' based on experiments driven by high-confidence predictions. In order to address compound problems, current efforts in immuno-informatics and reverse vaccinology are aimed at developing and tuning integrative approaches and user-friendly, automated bioinformatics environments. This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations. 相似文献
128.
129.
Chalker AF Minehart HW Hughes NJ Koretke KK Lonetto MA Brinkman KK Warren PV Lupas A Stanhope MJ Brown JR Hoffman PS 《Journal of bacteriology》2001,183(4):1259-1268
A comparative genomic approach was used to identify Helicobacter pylori 26695 open reading frames (ORFs) which are conserved in H. pylori J99 but highly diverged in other eubacteria. A survey of selected pathways of central intermediary metabolism was also carried out, and genes with a potentially selective role in H. pylori were identified. Forty-five ORFs identified in these two analyses were screened using a rapid vector-free allelic replacement mutagenesis technique, and 33 were shown to be essential in vitro. Notably, 13 ORFs gave essentiality results which are unexpected in view of their known or proposed functions, and phylogenetic analysis was used to investigate the annotation of 7 such ORFs which are highly diverged. We propose that the products of a number of these H. pylori-specific essential genes may be suitable targets for novel anti-H. pylori therapies. 相似文献
130.