• genomes
  • Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13- (deepdyve.com)
  • Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. (biomedcentral.com)
  • It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • rRNAs
  • In eukaryotes, the LSU contains 5S, 5.8S, and 28S rRNAs and even more proteins. (wikipedia.org)
  • Therefore, we mutationally investigated the role of the base pair using several 16S rRNAs from gamma- and betaproteobacteria. (frontiersin.org)
  • We found that both the native base pairs (gammaproteobacterial 19A-916U and betaproteobacterial 19C-916G) and the non-native 19A-916G pair retained function, whereas the non-native 19C-916U was defective 16S rRNAs. (frontiersin.org)
  • Subsequent functional screening identified various 16S rRNAs from proteobacteria, all of which contained native 19A-916U or 19C-916G base pairs. (frontiersin.org)
  • The 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers. (wikipedia.org)
  • organisms
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • phylogenetic
  • 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)
  • These genes are frequently used in microbial phylogenetic analyses, so well-established techniques exist for their study. (wikipedia.org)
  • chromosome
  • The prepilin peptidase (called PibD in crenarchaeota and FlaK in euryarchaeota) is essential for the maturation of the archaellins and is generally encoded elsewhere on the chromosome. (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)
  • It was found to consist of 1,743,135 base pairs arranged in a circular chromosome with an estimated 1,864 protein coding genes and 22 pseudogenes. (wikipedia.org)
  • The genome of Methylobacillus flagellatus is a circular chromosome that is approximately 3Mbp long, and it encodes about 2,766 proteins. (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)
  • soil
  • 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)
  • where resistance genes are obtained either from the indigenous human microbiota or from environmental microorganisms to which an individual is exposed (e.g., via food, water or soil). (frontiersin.org)
  • plasmid
  • 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)
  • Whereas
  • 90% amino acid identity with known gene products, whereas on 13 inserts no resistance gene could be identified with high confidence, in which case we predicted resistance to be mainly mediated by antibiotic efflux. (frontiersin.org)
  • strains
  • Using Web Services, we shall construct a workflow to investigate how this promoter structure is conserved throughout different bacterial strains. (dtu.dk)
  • enzymes
  • 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)
  • antibiotic resistance
  • 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)
  • obligate
  • In addition, it is an obligate chemolithoautotroph, and so genes commonly used in carbon fixation were present. (wikipedia.org)
  • 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)
  • 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)
  • archaeal
  • This led microbiologists to believe that the archaeal motility structure is not only functionally, but also structurally reminiscent of bacterial flagella. (wikipedia.org)
  • horizontal gene tra
  • 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)
  • 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)
  • Taken together, our results show that sponge microbiota host diverse and novel resistance genes that may be harnessed by phylogenetically distinct bacteria. (frontiersin.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)
  • strain
  • Strain B. safensis JPL-MERTA-8-2 is (so far) the only bacterial strain shown to grow noticeably faster in micro-gravity environments than on the Earth surface. (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)
  • 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)
  • 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)
  • 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)
  • lateral gene tra
  • It has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer. (wikipedia.org)
  • The genome also contains a CRISPR region, which is functionally linked to lateral gene transfer, host cell defense, replication, and regulation. (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)
  • present
  • The genes coding for the signaling components such as flaC, flaD, flaE are only present in Euryarchaeota and interact with Chemotaxis proteins (e.g. (wikipedia.org)
  • Here, we present a study where manipulation of cultural growth conditions and in planta experiments have been used to validate the expression stability of reference gene candidates for the plant pathogen Pectobacterium atrosepticum , belonging to the family Enterobacteriaceae . (biomedcentral.com)
  • rRNA is one of only a few gene products present in all cells. (wikipedia.org)
  • Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present. (wikipedia.org)
  • temperate
  • 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)
  • important
  • Several important proteins which interact with 5S rRNA are listed below. (wikipedia.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)
  • 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)
  • Ribosomal RNA characteristics are important in evolution, thus taxonomy, and medicine. (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)
  • different
  • Of twelve reference gene candidates tested, four proved to be stably expressed both in six different cultural growth conditions and in planta . (biomedcentral.com)
  • 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)
  • genetic
  • Most proteins that make up the archaellum are encoded within one genetic locus. (wikipedia.org)
  • This genetic locus contains 7-13 genes which encode proteins involved in either assembly or function of the archaellum. (wikipedia.org)
  • The genetic markers that contribute to detecting and monitoring the susceptibility of P. falciparum to doxycycline, the pfmdt and pftetQ genes, have recently been identified. (biomedcentral.com)
  • The objective of this study was to estimate the genetic parameters for milk β-hydroxybutyrate (BHBA), acetone (Ac), fat protein ratio (FPR) and energy balance (EB) using milk test day records and investigate the effect of early lactation FPR and EB on milk ketone body concentrations. (readbyqxmd.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)
  • host
  • 6. A bacterial host transformed with the expression vector according to any of the claims 1 or 2. (freepatentsonline.com)
  • 9. The method of claim 8 wherein immediately prior to lysing the temperature of the bacterial host organism is raised to a point at which the temperature sensitive repressor protein is inactivated. (freepatentsonline.com)
  • 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)
  • concentration
  • Additionally, it was demonstrated that the rotation of the archaellum is dependent on ATP concentration in the cell rather than PMF (proton motive force) as in the bacterial flagellum. (wikipedia.org)