共查询到20条相似文献,搜索用时 31 毫秒
1.
MOTIVATION: COMPARE is a multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species. The COMPARE interface provides access to a wide array of information including genomic structure, expression data, annotations, pathways and literature links for human and three widely studied animal models (zebrafish, Drosophila and mouse). A consensus ortholog-finding pipeline combining several ortholog prediction methods allows accurate comparisons of data across species and has been utilized to transfer information from well studied organisms to more poorly annotated ones. AVAILABILITY: http://compare.ibdml.univ-mrs.fr. 相似文献
2.
Briones C Manrubia SC Lázaro E Lazcano A Amils R 《Molecular phylogenetics and evolution》2005,34(2):371-381
The last two decades have witnessed an unsurpassed effort aimed at reconstructing the history of life from the genetic information contained in extant organisms. The availability of many sequenced genomes has allowed the reconstruction of phylogenies from gene families and its comparison with traditional single-gene trees. However, the appearance of major discrepancies between both approaches questions whether horizontal gene transfer (HGT) has played a prominent role in shaping the topology of the Tree of Life. Recent attempts at solving this controversy and reaching a consensus tree combine molecular data with additional phylogenetic markers. Translation is a universal cellular function that involves a meaningful, highly conserved set of genes: both rRNA and r-protein operons have an undisputed phylogenetic value and rarely undergo HGT. Ribosomal function reflects the concerted expression of that genetic network and consequently yields information about the evolutionary paths followed by the organisms. Here we report on tree reconstruction using a measure of the performance of the ribosome: antibiotic sensitivity of protein synthesis. A large database has been used where 33 ribosomal systems belonging to the three major cellular lineages were probed against 38 protein synthesis inhibitors. Different definitions of distance between pairs of organisms have been explored, and the classical algorithm of bootstrap evaluation has been adapted to quantify the reliability of the reconstructions obtained. Our analysis returns a consistent phylogeny, where archaea are systematically affiliated to eukarya, in agreement with recent reconstructions which used information-processing systems. The integration of the information derived from relevant functional markers into current phylogenetic reconstructions might facilitate achieving a consensus Tree of Life. 相似文献
3.
The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material
among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related
species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance
genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities
reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies
in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known
sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary
model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic
distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource
use and ecosystem resilience. 相似文献
4.
Horizontal gene transfer and bacterial diversity 总被引:7,自引:0,他引:7
Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into
or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits
from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character
of bacterial species and thereby promotes microbial diversification and speciation. This review discusses how the recent influx
of complete chromosomal sequences of various microorganisms has allowed for a quantitative assessment of the scope, rate and
impact of horizontally transmitted information on microbial evolution. 相似文献
5.
转基因植物检测体系在环境污染物突变性评价中的应用The 总被引:1,自引:1,他引:0
很多环境污染物都能对生物体产生诱变性,可利用多种测试材料与方法对其基因毒性进行检测。转基因植物检测体系不仅能对环境污染的诱变性大小进行评价,而且还可以进一步分析其突变的分子机理。本文介绍了转基因植株检测体系的应用前景。
Abstract: Environmental contaminants are powerful mutagenic factors for organisms. Several testing materials and methods have been used to assess the genotoxicity of environmental factors. Transgenic plants testing system can not only evaluate the level of genotoxicity, but also provide information on the genetic effects at molecular level. We introduce the use of transgenic plants in biomonitoring environmental factors. 相似文献
6.
7.
Recent advances in the genetics of the clostridia 总被引:27,自引:0,他引:27
Several laboratories around the world have started work on genetic analysis of clostridia. Interest in this diverse group of anaerobic organisms has grown with increasing awareness of the benefits that may accrue from their biotechnological exploitation. Research to date has focussed on construction of shuttle vectors containing replicons from clostridial and streptococcal plasmids, development of methods for transferring genes, and molecular cloning of genes--especially those involved in toxigenicity, fermentative metabolism and polysaccharide utilization. In selected species gene transfer by protoplast transformation, electroporation and conjugation has been accomplished and transposable elements have been introduced. It can be anticipated that our understanding of the molecular biology of these interesting organisms will grow rapidly in the future, bringing with it improved prospects for rational biotechnological exploitation. 相似文献
8.
Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.The discovery of the existence of prokaryotic microbes dates back more than 300 years. Since then, our picture of our distant microscopic relatives has undergone several revolutions: from being the living “proofs” of the existence of spontaneous generation, they became later the “archaic” representatives of our distant ancestors, to finally be legitimately recognized as exceptionally diverse organisms, keystone to any ecosystem, including the most familiar and the most hostile environments on Earth. Similarly, although they were first seen as elementary and unbreakable bricks of life, they are now seen as genetically composite bodies, heavyweight champions of “gene robbery.” The most recent of these revolutions has indeed been the realization of their unparalleled ability to integrate genetic material coming from more or less evolutionarily distant organisms. This mechanism is called “horizontal gene transfer” as opposed to vertical transmission from mother to daughter cell. 相似文献
9.
Zoran Minic 《Symbiosis (Philadelphia, Pa.)》2009,47(3):121-132
It has been postulated that life originated in a similar environment to those of deep sea hydrothermal vents. These environments
are located along volcanic ridges and are characterized by extreme conditions such as unique physical properties (temperature,
pressure), chemical toxicity, and absence of photosynthesis. However, numerous living organisms have been discovered in these
hostile environments, including a variety of microorganisms and many animal species which live in intimate and complex symbioses
with sulfo-oxidizing and methanotrophic bacteria. Recent proteomic analyses of the endosymbiont ofRiftia pachyptila and genome sequences of some free living and symbiotic bacteria have provided complementary information about the potential
metabolic and genomic capacities of these organisms. The evolution of these adaptive strategies is connected with different
mechanisms of genetic adaptation including horizontal gene transfer and . various structural and functional mutations. Therefore,
the organisms in this environment are good models for studying the evolution of prokaryotes and eukaryotes as well as different
aspects of the biology of adaptation. This review describes some current research concerning metabolic and plausible genetic
adaptations of organisms in a deep sea environment, usingRiftia pachyptila as model. 相似文献
10.
Abstract Several laboratories around the world have started work on genetic analysis of clostridia. Interest in this diverse group of anaerobic organisms has grown with increasing awareness of the benefits that may accrue from their biotechnological exploitation. Research to date has focussed on construction of shuttle vectors containing replicons from clostridial and streptococcal plasmids, development of methods for transferring genes, and molecular cloning of genes—especially those involved in toxigenicity, fermentative metabolism and polysaccharide utilization. In selected species gene transfer by protoplast transformation, electroporation and conjugation has been accomplished and transposable elements have been introduced. It can be anticipated that our understanding of the molecular biology of these interesting organisms will grow rapidly in the future, bringing with it improved prospects for rational biotechnological exploitation. 相似文献
11.
12.
PAUL J. FRITZ E. LUCILE WHITE ELLIOT S. VESELL KENNETH M. PRUITT 《Nature: New biology》1971,230(12):119-122
13.
The transfer of genetic information by transformation, conjugation and transduction in bacteria occurs frequently in nature. These diverse gene transfer mechanisms in bacteria are the result of evolution and are not linked to reproduction as in eukaryotic organisms. In this review, gene transfer in bacteria will be considered from an evolutionary perspective. 相似文献
14.
Model organisms have proved to be highly informative for many types of genetic studies involving ‘conventional’ genes. The results have often been successfully generalized to other closely related organisms and also, perhaps surprisingly frequently, to more distantly related organisms. Because of the wealth of previous knowledge and their availability and convenience, model organisms were often the species of choice for many of the earlier studies of transposable elements. The question arises whether the results of genetic studies of transposable elements in model organisms can be extrapolated in the same ways as those of conventional genes? A number of observations suggest that special care needs to be taken in generalizing the results from model organisms to other species. A hallmark of many transposable elements is their ability to amplify rapidly in species genomes. Rapid spread of a newly invaded element throughout a species range has also been demonstrated. The types and genomic copy numbers of transposable elements have been shown to differ greatly between some closely related species. Horizontal transfer of transposable elements appears to be more frequent than for nonmobile genes. Furthermore, the population structure of some model organisms has been subject to drastic recent changes that may have some bearing on their transposable element genomic complements. In order to initiate discussion of this question, several case studies of transposable elements in well-studied Drosophila species are presented. 相似文献
15.
Background
Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp. 相似文献16.
Aminoglycoside has been known as a clinically important antibiotic for a long time, but genetic information for the biosynthesis of aminoglycoside is still insufficient. In this study, we tried to clone aminoglycoside-biosynthetic genes from soil DNA for accumulation of genetic information. We chose the genes encoding L-glutamine:(2-deoxy-)scyllo-inosose aminotransferase as the target, because it is specific for all types of aminoglycoside biosynthesis. By degenerate PCR, we obtained 33 individual clones that were homologous with aminotransferase genes in aminoglycoside biosynthesis. Phylogenetic analysis and alignment of these genes showed that horizontal gene transfer has occurred in the soil. Among these, several quite interesting genes were obtained. Some genes probably originated from non-actinomycetes, and some were far from the known homologs. These genes can be useful markers for the isolation of entire gene clusters and originating organisms. 相似文献
17.
Stacia R Engel Edith D Wong Robert S Nash Suzi Aleksander Micheal Alexander Eric Douglass Kalpana Karra Stuart R Miyasato Matt Simison Marek S Skrzypek Shuai Weng J Michael Cherry 《Genetics》2022,220(4)
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease. 相似文献
18.
A new IncQ plasmid R89S has been analysed by molecular-genetic methods. A restriction map of this plasmid has been constructed and regions of homology with the plasmid RSF1010 have been identified. A genetic map of the plasmid R89S has been prepared based on the deletion and insertion plasmid derivatives. The phenotypic analysis of the derivatives has identified the location of genes coding for replication, incompatibility, mobilization for genetic transfer and resistance to streptomycin in the genome of R89S. 相似文献
19.
A Thomas PJ Lee JE Dalton KJ Nomie L Stoica M Costa-Mattioli P Chang S Nuzhdin MN Arbeitman HA Dierick 《PloS one》2012,7(7):e40276
In Drosophila melanogaster few methods exist to perform rapid cell-type or tissue-specific expression profiling. A translating ribosome affinity purification (TRAP) method to profile actively translated mRNAs has been developed for use in a number of multicellular organisms although it has only been implemented to examine limited sets of cell- or tissue-types in these organisms. We have adapted the TRAP method for use in the versatile GAL4/UAS system of Drosophila allowing profiling of almost any tissue/cell-type with a single genetic cross. We created transgenic strains expressing a GFP-tagged ribosomal protein, RpL10A, under the control of the UAS promoter to perform cell-type specific translatome profiling. The GFP::RpL10A fusion protein incorporates efficiently into ribosomes and polysomes. Polysome affinity purification strongly enriches mRNAs from expected genes in the targeted tissues with sufficient sensitivity to analyze expression in small cell populations. This method can be used to determine the unique translatome profiles in different cell-types under varied physiological, pharmacological and pathological conditions. 相似文献
20.
With the number of organisms whose genomes have been sequenced, a vast amount of information concerning the genetic structure of an organism's genome has been collected. However, effective experiment means to study how this information is accessed have only recently been developed. In this review, three basic methods for identifying regions of protein-DNA interaction will be introduced. The first two, chromatin immunoprecipitation (ChIP)-chip and ChIP-PET (for paired-end ditag), rely on the enrichment provided by chromosomal immunoprecipitation to interrogate the genomic sequence for the interaction sites of a protein of interest. In contrast, protein microarrays allow the identification of DNA binding protein that interacts with a DNA sequence of interest. These complementary methods of exploring protein-DNA interactions will increase our fundamental knowledge of how the information contained within the genome sequence is accessed and processed. 相似文献