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991.
Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean 总被引:1,自引:0,他引:1
Archaea have been detected throughout the oceanic water column and are quantitatively important members of picoplankton in the deep ocean. Two common groups, group I Crenarchaeota and group II Euryarchaeota, are consistently detected in warm hydrothermal fluid and are assumed to have been drawn into the subseafloor, mixed with hydrothermal fluid and then expelled. However, because they remain resistant to cultivation, very little is known about their physiology. Here we show that cold deep-seawater from the axial valley of Endeavour Segment on the Juan de Fuca Ridge contains not only groups I and II archaea as expected, but also unique potentially archaeal nitrogenase (nifH) genes, which are required for nitrogen fixation. These nifH genes are phylogenetically distinct and have dissimilar G+C content compared with those of hydrothermal vent archaea, suggesting that they belong to non-thermophilic deep-sea archaea. Furthermore, this sample did not contain mcrA genes, which are present in methanogens, the only known archaeal nitrogen fixers. These nifH genes were not detected in upper water column samples, or in a deep-seawater sample 100 km away from the spreading axis of the Juan de Fuca Ridge. We propose that these unique nifH genes may be localized to archaea that circulate through the nitrogen-poor subseafloor at the mid-ocean ridge as part of their life cycle. 相似文献
992.
Turinsky AL Ah-Seng AC Gordon PM Stromer JN Taschuk ML Xu EW Sensen CW 《In silico biology》2005,5(2):187-198
We have created a new Java-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs; an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet; and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a local stand-alone application, with or without connection to the Internet. It is available free of charge and as open source via http://bluejay.ucalgary.ca. 相似文献
993.
Julie?L?MorrisonEmail author Rainer?Breitling Desmond?J?Higham David?R?Gilbert 《BMC bioinformatics》2005,6(1):233
Background
Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method – based on the PageRank algorithm employed by the popular search engine Google – that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information. 相似文献994.
Richard?Ewan Julie?Huxley-Jones A?Paul?Mould Martin?J?Humphries David?L?Robertson Raymond?P?Boot-HandfordEmail author 《BMC evolutionary biology》2005,5(1):31
Background
Integrins are a functionally significant family of metazoan cell surface adhesion receptors. The receptors are dimers composed of an alpha and a beta chain. Vertebrate genomes encode an expanded set of integrin alpha and beta chains in comparison with protostomes such as drosophila or the nematode worm. The publication of the genome of a basal chordate, Ciona intestinalis, provides a unique opportunity to gain further insight into how and when the expanded integrin supergene family found in vertebrates evolved. 相似文献995.
Bahnson A Athanassiou C Koebler D Qian L Shun T Shields D Yu H Wang H Goff J Cheng T Houck R Cowsert L 《BMC cell biology》2005,6(1):19-27
Background
Time-lapse microscopic imaging provides a powerful approach for following changes in cell phenotype over time. Visible responses of whole cells can yield insight into functional changes that underlie physiological processes in health and disease. For example, features of cell motility accompany molecular changes that are central to the immune response, to carcinogenesis and metastasis, to wound healing and tissue regeneration, and to the myriad developmental processes that generate an organism. Previously reported image processing methods for motility analysis required custom viewing devices and manual interactions that may introduce bias, that slow throughput, and that constrain the scope of experiments in terms of the number of treatment variables, time period of observation, replication and statistical options. Here we describe a fully automated system in which images are acquired 24/7 from 384 well plates and are automatically processed to yield high-content motility and morphological data.Results
We have applied this technology to study the effects of different extracellular matrix compounds on human osteoblast-like cell lines to explore functional changes that may underlie processes involved in bone formation and maintenance. We show dose-response and kinetic data for induction of increased motility by laminin and collagen type I without significant effects on growth rate. Differential motility response was evident within 4 hours of plating cells; long-term responses differed depending upon cell type and surface coating. Average velocities were increased approximately 0.1 um/min by ten-fold increases in laminin coating concentration in some cases. Comparison with manual tracking demonstrated the accuracy of the automated method and highlighted the comparative imprecision of human tracking for analysis of cell motility data. Quality statistics are reported that associate with stage noise, interference by non-cell objects, and uncertainty in the outlining and positioning of cells by automated image analysis. Exponential growth, as monitored by total cell area, did not linearly correlate with absolute cell number, but proved valuable for selection of reliable tracking data and for disclosing between-experiment variations in cell growth.Conclusion
These results demonstrate the applicability of a system that uses fully automated image acquisition and analysis to study cell motility and growth. Cellular motility response is determined in an unbiased and comparatively high throughput manner. Abundant ancillary data provide opportunities for uniform filtering according to criteria that select for biological relevance and for providing insight into features of system performance. Data quality measures have been developed that can serve as a basis for the design and quality control of experiments that are facilitated by automation and the 384 well plate format. This system is applicable to large-scale studies such as drug screening and research into effects of complex combinations of factors and matrices on cell phenotype. 相似文献996.
997.
998.
Leonid Heifets Julie Simon Van Pham 《Annals of clinical microbiology and antimicrobials》2005,4(1):1-7
Background
Eradication of Helicobacter pylori is an important objective in overcoming gastric diseases. Many regimens are currently available but none of them could achieve 100% success in eradication. Eugenol and cinnamaldehyde that are commonly used in various food preparations are known to possess antimicrobial activity against a wide spectrum of bacteria.Aim
The present study was performed to assess the in vitro effects of eugenol and cinnamaldehyde against indigenous and standard H. pylori strains, their minimum inhibitory concentrations (MICs) and time course lethal effects at various pH.Methods
A total of 31 strains (29 indigenous and one standard strain of H. pylori ATCC 26695, one strain of E. coli NCIM 2089) were screened. Agar dilution method was used for the determination of drug sensitivity patterns of isolates to the commonly used antibiotics and broth dilution method for the test compounds.Results
Eugenol and cinnamaldehyde inhibited the growth of all the 30 H. pylori strains tested, at a concentration of 2 μg/ml, in the 9th and 12th hours of incubation respectively. At acidic pH, increased activity was observed for both the compounds. Furthermore, the organism did not develop any resistance towards these compounds even after 10 passages grown at sub-inhibitory concentrations.Conclusion
These results indicate that the two bioactive compounds we tested may prevent H. pylori growth in vitro, without acquiring any resistance. 相似文献999.
Pelletier JP Boileau C Boily M Brunet J Mineau F Geng C Reboul P Laufer S Lajeunesse D Martel-Pelletier J 《Arthritis research & therapy》2005,7(5):R1091-R1102
This study sought to evaluate the levels of mRNA expression and protein synthesis of MMP-13, cathepsin K, aggrecanase-1 (ADAMTS-4),
aggrecanase-2 (ADAMTS-5) and 5-lipoxygenase (5-LOX) in cartilage in the experimental anterior cruciate ligament (ACL) dog
model of osteoarthritis (OA), and to examine the effects of treatment with licofelone, a 5-lipoxygenase (LOX)/cyclooxygenase
(COX) inhibitor, on the levels of these catabolic factors. Sectioning of the ACL of the right knee was performed in three
experimental groups: group 1 received no active treatment (placebo group); and groups 2 and 3 received therapeutic concentrations
of licofelone (2.5 or 5.0 mg/kg/day orally, respectively) for 8 weeks, beginning the day following surgery. A fourth group
consisted of untreated dogs that were used as normal controls. Specimens of cartilage were selected from lesional areas of
OA femoral condyles and tibial plateaus, and were processed for real-time quantitative PCR and immunohistochemical analyses.
The levels of MMP-13, cathepsin K, ADAMTS-4, ADAMTS-5 and 5-LOX were found to be significantly increased in OA cartilage.
Licofelone treatment decreased the levels of both mRNA expression and protein synthesis of the factors studied. Of note was
the marked reduction in the level of 5-LOX gene expression. The effects of the drug were about the same at both tested dosages.
In vivo treatment with therapeutic dosages of licofelone has been found to reduce the degradation of OA cartilage in experimental
OA. This, coupled with the results of the present study, indicates that the effects of licofelone are mediated by the inhibition
of the major cartilage catabolic pathways involved in the destruction of cartilage matrix macromolecules. Moreover, our findings
also indicate the possible auto-regulation of 5-LOX gene expression by licofelone in OA cartilage. 相似文献
1000.