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  • organisms
  • In the 1980's Carl Woese suggested that the deoxyribonucleic acid (DNA) sequences of certain common genes could be used to measure relatedness among radically different organisms. (openwetware.org)
  • Using homology inference approach and expert analyses, we identified the translation apparatus proteins for 39 of these organisms. (plos.org)
  • When prokaryotic organisms transcribe DNA into RNA it involves in many cases the binding of a sigma factor upstream of the transcription start site. (dtu.dk)
  • Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. (wikipedia.org)
  • La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol III. (wikipedia.org)
  • Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring. (wikipedia.org)
  • Most thinking in genetics has focused upon vertical transfer, but horizontal gene transfer is important, and among single-celled organisms is perhaps the dominant form of genetic transfer. (wikipedia.org)
  • Studies in the 1960's used DNA hybridization and protein cross-reactivity techniques to measure similarity between known orthologous proteins, such as hemoglobin and Cytochrome C. In 1965, Émile Zuckerkandl and Linus Pauling introduced the concept of the molecular clock, proposing that steady rates of mutation could be used to estimate the time since two organisms diverged. (wikipedia.org)
  • Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms. (wikipedia.org)
  • Soon after that, Healy reported the metagenomic isolation of functional genes from "zoolibraries" constructed from a complex culture of environmental organisms grown in the laboratory on dried grasses in 1995. (wikipedia.org)
  • plasmid
  • In this communication, we demonstrate that ChvG is involved in the regulation of acid-inducible genes, including aopB and katA , residing on the circular and linear chromosomes, respectively, and the tumor-inducing (Ti)-plasmid-harbored vir genes, virB and virE . (pnas.org)
  • The T-DNA and the vir genes required for T-DNA transfer are located on a large plasmid called the tumor-inducing (Ti) plasmid. (pnas.org)
  • Improved vectors and methods for regulating the expression in bacteria of a eucaryotic anti-viral protein, such as mature human immune interferon, the gene for which has been cloned onto a bacterial plasmid, is disclosed. (freepatentsonline.com)
  • Bacterial conjugation, a process that involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact. (wikipedia.org)
  • A transposable element (TE) (also called a transposon or jumping gene) is a mobile segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome, thereby inducing horizontal gene transfer of antibiotic resistance. (wikipedia.org)
  • Functional
  • 5. The improved expression vector of claim 4 wherein the temperature sensitive repressor protein is functional from about 30° C. to about 36° C. (freepatentsonline.com)
  • The primers developed in this study are thus advantageous for functional characterization of foreign 16S rRNA in E. coli with no artifacts. (frontiersin.org)
  • The lowest identity of functional 16S rRNA gene to that of E. coli was as low as 80%, implying that hundreds of simultaneous nucleotide changes are permitted in the maintenance of ribosome function. (frontiersin.org)
  • This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches. (plos.org)
  • Also, the topographical and physical proximity between 5S rRNA and 23S rRNA, which forms the peptidyl transferase and GTPase-associating center, suggests that 5S rRNA acts as a mediator between the two functional centers of the ribosome by forming, together with 5S rRNA-binding proteins and other components of the central protuberance, intersubunit bridges and tRNA-binding sites. (wikipedia.org)
  • molecules
  • In order for the bacteria to use quorum sensing constitutively, they must possess three characteristics: to secrete a signaling molecule, an autoinducer, to detect the change in concentration of signaling molecules, and to regulate gene transcription as a response. (wikipedia.org)
  • At high cell density, the local concentration of signaling molecules may exceed its threshold level, and trigger changes in gene expressions. (wikipedia.org)
  • genome
  • The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. (biomedcentral.com)
  • Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. (plos.org)
  • The genome also contains a CRISPR region, which is functionally linked to lateral gene transfer, host cell defense, replication, and regulation. (wikipedia.org)
  • The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome. (wikipedia.org)
  • In 2004, Gene Tyson, Jill Banfield, and colleagues at the University of California, Berkeley and the Joint Genome Institute sequenced DNA extracted from an acid mine drainage system. (wikipedia.org)
  • phylum
  • The Chlamydiae are bacterial phylum and class whose members are a group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from pathogens of humans and animals to symbionts of ubiquitous protozoa. (wikipedia.org)
  • molecular
  • Recent advances in molecular tools for gene sequencing and in other types of microorganism identification dramatically expanded our knowledge of the contribution of microbes in their (and our) environment. (openwetware.org)
  • Your goal in this semester long project, is to use both culture and molecular methods of bacterial identification to investigate the diversity of bacteria in soil from a Wellesley greenhouse habitat and to explore the specific role of some of the bacteria in that community. (openwetware.org)
  • Your goal in this semester long project is to use both culture-based and culture-independent molecular methods of bacterial identification to investigate the diversity of bacteria in soil from a Wellesley greenhouse habitat and to explore the specific role of some of the bacteria in that community. (openwetware.org)
  • While initial phylogenies closely matched the fossil record, observations that some genes appeared to evolve at different rates led to the development of theories of molecular evolution. (wikipedia.org)
  • Molecular signatures in the form of conserved indels (CSIs) and proteins (CSPs) have been found to be uniquely shared by each separate order, providing a means of distinguishing each clade from the other and supporting the view of shared ancestry of the families within each order. (wikipedia.org)
  • microbial
  • Moreover, it is well recognized that the excessive use of broad-spectrum antibiotics can affect the relative proportions of gut microbial populations and foster bacterial resistance . (deepdyve.com)
  • These genes are frequently used in microbial phylogenetic analyses, so well-established techniques exist for their study. (wikipedia.org)
  • Escherichia
  • Most of the 260 known proteins involved in translation have been identified and studied in the bacteria Escherichia coli and Bacillus subtilis , two common cellular models in biology. (plos.org)
  • populations
  • The genetic determinants of these enzymes are often located on mobile elements facilitating the rapid dissemination of the genes in various bacterial populations [ 8 ]. (hindawi.com)
  • Resistance patterns and prevalence of the aminoglycoside modifying enzymes in clinical isolates showing multidrug-resistant patterns have also been reported from various parts of India and it has been shown that high level aminoglycoside resistance genes are widely disseminated among Indian populations [ 11 , 12 ]. (hindawi.com)
  • However, they have a receptor that detects AHLs from other bacteria and change their gene expression in accordance with the presence of other "quorate" populations of Gram-negative bacteria. (wikipedia.org)
  • amino
  • It should also be noted that H. thermophilus lacks the typical PSP (phosphoserine phosphatase) genes involved in amino acid metabolism. (wikipedia.org)
  • Now the P site contains the beginning of the peptide chain of the protein to be encoded and the A site has the next amino acid to be added to the peptide chain. (wikipedia.org)
  • This difference in rate reflects, in part, the difference between polymerizing four types of nucleotides to make nucleic acids and polymerizing 20 types of amino acids to make proteins. (wikipedia.org)
  • Conserved proteins undergo fewer amino amino acid replacements, or are more likely to substitute amino acids with similar biochemical properties. (wikipedia.org)
  • These compounds can range from heterologous proteins and amino-acids to vitamins. (wikipedia.org)
  • after cleavage, the mature protein is only 38 amino acids in length. (wikipedia.org)
  • Surprisingly, the N-terminal 11 amino acid region of the mature protein triggers symptom development in Nicotiana benthamiana plants. (wikipedia.org)
  • strains
  • Using Web Services, we shall construct a workflow to investigate how this promoter structure is conserved throughout different bacterial strains. (dtu.dk)
  • coli
  • The results point towards the novel mechanism of drug resistance in E. coli from UTI patients in India as they confirm the presence of genes encoding enzymes that cause resistance to aminoglycoside drugs. (hindawi.com)
  • obligate
  • In addition, it is an obligate chemolithoautotroph, and so genes commonly used in carbon fixation were present. (wikipedia.org)
  • Phytoplasmas are obligate bacterial parasites of plant phloem tissue and of the insect vectors that are involved in their plant-to-plant transmission. (wikipedia.org)
  • microbiome
  • In mammals, herbivores such as cattle depend on their rumen microbiome to convert cellulose into proteins, short chain fatty acids, and gases. (wikipedia.org)
  • These methods are now largely being replaced by high throughput sequencing, such as targeted microbiome analysis (e.g., 16s rRNA sequencing) and metagenomics. (wikipedia.org)
  • organism's
  • Consensus exists among evolutionary biologists that one should not separate an organism's genes from the context of its resident microbes. (wikipedia.org)
  • Despite
  • Archaellum versus Bacterial flagellum Despite the limited amount of details presently available regarding the structure and assembly of archaellum, it has become increasingly evident from multiple studies that archaella play important roles in a variety of cellular processes in archaea. (wikipedia.org)
  • different
  • Because ChvG regulates unlinked acid-inducible genes encoding different functions in different ways, we hypothesize that ChvG is a global sensor protein that can directly or indirectly sense extracellular acidity. (pnas.org)
  • Of twelve reference gene candidates tested, four proved to be stably expressed both in six different cultural growth conditions and in planta . (biomedcentral.com)
  • Sigma factors also have important regulatory functions and many different factors acts to ensure differential regulation of different classes of genes under different conditions. (dtu.dk)
  • In other words, the rRNA genes are needed constantly by the cell, however required at different amounts depending on the growth rate of the cell. (dtu.dk)
  • In general, it is assumed that each different gene variant represents a different type of microbe. (wikipedia.org)
  • Depending on what information is desired, different genes may be targeted. (wikipedia.org)
  • The underlying assumption is that each microbe in the sample will have a different sequence on the target gene, so a restriction enzyme will cut each microbe's DNA in a different place. (wikipedia.org)
  • horizontal gene tra
  • Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. (wikipedia.org)
  • Artificial horizontal gene transfer is a form of genetic engineering. (wikipedia.org)
  • Some Lepidoptera (e.g. monarch butterflies and silkworms) have been genetically modified by horizontal gene transfer from the wasp bracovirus. (wikipedia.org)
  • There are several mechanisms for horizontal gene transfer: Transformation, the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material (DNA or RNA). (wikipedia.org)
  • differences
  • Reference genes are also used to correct for differences between samples, such as variation in the total quantity of RNA and variation in RT-PCR efficiency. (biomedcentral.com)
  • bacteriophage
  • 4. The improved expression vector of claim 1 wherein said vector further comprises a mutant cI repressor gene derived from λ bacteriophage which mutant gene codes for a temperature sensitive repressor protein. (freepatentsonline.com)
  • Transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus (a bacteriophage, or phage). (wikipedia.org)
  • microbes
  • An important issue is that a high copy number of 16S rRNA genes in a certain group of microbes may over-estimate their proportion in the community [ 1 ]. (omicsonline.org)
  • For example, it is difficult for the DGGE method to detect microbes that comprise less than 0.5%-1% of a bacterial community. (wikipedia.org)
  • lateral gene tra
  • In the mid-1980s, Syvanen predicted that lateral gene transfer existed, had biological significance, and was involved in shaping evolutionary history from the beginning of life on Earth. (wikipedia.org)
  • It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer. (wikipedia.org)
  • important
  • A sensor protein ChvG is part of a chromosomally encoded two-component regulatory system ChvG/ChvI that is important for the virulence of Agrobacterium tumefaciens . (pnas.org)
  • Therefore, normalisation of the data against reference genes (i.e., genes whose expression do not change under the various experimental conditions) is an important step in the quantification of gene expression. (biomedcentral.com)
  • Pectobacterium atrosepticum (formerly known as Erwinia carotovora subspecies atroseptica [ 10 , 11 ]) is an important bacterial pathogen of potato in temperate regions, where it causes blackleg of plants and soft rot of tubers by the utilization of a huge machinery of plant cell wall degrading exoenzymes mainly encompassing pectinases, cellulases and proteases. (biomedcentral.com)
  • Ribosomal RNA characteristics are important in evolution, thus taxonomy, and medicine. (wikipedia.org)
  • Several important proteins which interact with 5S rRNA are listed below. (wikipedia.org)
  • 2005) observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution. (wikipedia.org)
  • As with proteins, nucleic acids that are important for the structure and function of non-coding RNA (ncRNA) can also be conserved. (wikipedia.org)
  • evolutionary
  • The Chlamydiae form a unique bacterial evolutionary group that separated from other bacteria about a billion years ago, and can be distinguished by the presence of several CSIs and CSPs. (wikipedia.org)
  • transcription
  • The kinase phosphorylates a transcription factor, which regulated gene transcription. (wikipedia.org)
  • Usually AHLs do not need additional processing, and bind directly to transcription factors to regulate gene expression. (wikipedia.org)
  • resistance
  • With the passage of time, the burden of bacterial infections is showing an ascending trend and this is largely due to the generation of resistance mechanisms by bacteria [ 2 , 3 ]. (hindawi.com)
  • Among the various patterns of resistance, reports across the globe continue to emerge on the resistance to aminoglycoside antibiotics which otherwise have been reported as highly potent drugs against life threatening Gram-negative bacterial infections [ 4 , 5 ]. (hindawi.com)
  • found
  • Inhibition of one major protein found in the inflammasome, Caspase-1, has been found to block the activation of IL-1beta thereby blocking the acute inflammation initiated by appliance tightening. (wordpress.com)
  • Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales. (wikipedia.org)
  • metabolic
  • Various metabolic processes were examined on a 1.5% Bacto-Agar with various organic compounds, incubated at 50-70 degrees C. 16S rRNA gene sequencing places the family of H. thermophilus, Aquificaceae, in close phylogenetic relationship to the family Aquifex based on 88.5% to 88.9% sequence similarity. (wikipedia.org)
  • Other genes of interest might be those that are key in various metabolic processes. (wikipedia.org)
  • However
  • However, it is not clear what genes ChvG regulates or what signal(s) it senses. (pnas.org)
  • However, it was responsible only for the responsiveness of katA and, to a limited extent, the vir genes to acidic pH. (pnas.org)
  • However, the study of pathogen gene expression inside infected host tissue poses some problems, as there is no straightforward way of measuring the total pathogen RNA concentration. (biomedcentral.com)
  • However, comparative genomics has shown that the translation protein set can be much smaller. (plos.org)