*  Identification of Genes Coding Aminoglycoside Modifying Enzymes in E. coli of UTI Patients in India
... act primarily by impairing bacterial protein synthesis through binding to prokaryotic ribosomes via 16S ribosomal RNA (16S rRNA ... Identification of Genes Encoding Aminoglycoside Enzymes. Detection of aminoglycoside resistance genes rrs (rrs1 and rrs2), ... aphA3 gene in 13 (34.2%), and aacC-aphD gene in 7 (18.42%). No amplification of genes could be seen for seven isolates (Figures ... sixteen isolates containing two genes, five isolates containing no genes, and other isolates containing a single gene. None of ...
  https://www.hindawi.com/journals/tswj/2016/1875865/
*  Microbiota - Wikipedia
"16S rDNA", the sequence of DNA which encodes the ribosomal RNA molecule).[48] Since ribosomes are present in all living ... RNA and protein-based approaches[edit]. Metatranscriptomics studies have been performed to study the gene expression of ... A common marker for human microbiome studies is the gene for bacterial 16S rRNA (i.e. " ... The metabolic pathways that these genes are involved in can then be predicted with tools such as MG-RAST,[60] CAMERA[61] and ...
  https://en.wikipedia.org/wiki/Microbiota
*  Resources and tools for the high-throughput, multi-omic study of intestinal microbiota, Briefings in Bioinformatics | 10.1093...
Many gut metagenomics studies still perform 16S ribosomal RNA (rRNA) sequencing, and pipelines used correspond to QIIME or ... the Ribosomal Database Project classifiers may help in the assignment of rRNA gene sequences into bacterial taxonomy [135]. ... or translated protein database searches [30]. That is, the assignment may be based on full protein-coding genes (CDSs) by means ... BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides . ...
  https://www.deepdyve.com/lp/ou_press/resources-and-tools-for-the-high-throughput-multi-omic-study-of-QU4byFWU0i
*  Novel vectors and method for controlling interferon expression - Hoffmann-La Roche Inc.
... the gene for which has been cloned onto a bacterial p ... the expression in bacteria of a eucaryotic anti-viral protein, ... The SD sequence is a sequence of 3 to 9 bses which are complementary to bases at the 3'-end of 16s ribosomal RNA known as the ... In a preferred embodiment of this invention, the gene which encodes for the above-mentioned protein is inserted into the DNA of ... The prior art has uncovered varous obstacles to expressing eucaryotic proteins whose genes have been cloned onto bacterial ...
  http://www.freepatentsonline.com/4582800.html
*  Archaellum - Wikipedia
Fox based on the differences in the sequence of ribosomal RNA (16S rRNA) genes. This domain possesses numerous fundamental ... Most proteins that make up the archaellum are encoded within one genetic locus. This genetic locus contains 7-13 genes which ... Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. Microbiology 149, 3051-72 (2003 ... Trends Microbiol 20, 307-12 (2012). Patenge, N., Berendes, A., Engelhardt, H., Schuster, S.C. & Oesterhelt, D. The fla gene ...
  https://en.wikipedia.org/wiki/Archaellum
*  BISC209:Project1 - OpenWetWare
He picked the genes that encode ribosomal RNA (rRNA). Ribosomes, the protein-RNA complexes that are the scaffold on which ... Comparing sequences of the gene (16S DNA) that encodes 16S rRNA in different bacteria can be used to identify them. We can also ... Analyze Diversity of Soil Bacterial Community & Relationships Strategy for Identification of Culturable Bacteria in a Soil ... Clone 16S rDNA PCR products into a plasmid vector and transform E. coli with plasmid ⇓ Pick transformed E.coli colonies and ...
  https://openwetware.org/wiki/?title=BISC209:Project1&oldid=379490
*  5S ribosomal RNA - Wikipedia
16S and 23S) rRNA genes. Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central ... and their bacterial relatives share many features but also display marked differences. Organelle genomes encode SSU and LSU ... Maraia, RJ; Intine, RV (2002). "La protein and its associated small nuclear and nucleolar precursor RNAs". Gene expression. 10 ... Page for 5S ribosomal RNA at Rfam 5SData 5S Ribosomal RNA at the US National Library of Medicine Medical Subject Headings (MeSH ...
  https://en.wikipedia.org/wiki/5S_ribosomal_RNA
*  Frontiers | PCR Primer Design for 16S rRNAs for Experimental Horizontal Gene Transfer Test in Escherichia coli | Bioengineering...
... we used the common universal primers Bac8f and UN1541r to obtain a nearly full-length gene. However, we noticed that these ... we used the common universal primers Bac8f and UN1541r to obtain a nearly full-length gene. However, we noticed that these ... We recently demonstrated that the Escherichia coli ribosome is robust enough to accommodate foreign 16S rRNAs from diverse ... We recently demonstrated that the Escherichia coli ribosome is robust enough to accommodate foreign 16S rRNAs from diverse ...
  https://www.frontiersin.org/articles/10.3389/fbioe.2017.00014/full
*  Absence of association between Plasmodium falciparum small sub-unit ribosomal RNA gene mutations and in vitro decreased...
... the pfmdt and pftetQ genes, have recently been identified. However, these markers are not sufficient to explain in vitro ... In this paper, the association between polymorphism of the small sub-unit ribosomal RNA apicoplastic gene pfssrRNA (PFC10_ ... The pfssrRNA gene is not associated with in vitro decreased susceptibility of P. falciparum to doxycycline. Identifying new in ... been associated with efflux or ribosomal protection proteins but rather attributed to mutations in the 16S rRNA-encoding genes ...
  https://malariajournal.biomedcentral.com/articles/10.1186/s12936-015-0878-x
*  Evaluation of reference genes for real-time RT-PCR expression studies in the plant pathogen Pectobacterium atrosepticum | BMC...
Two of these genes (recA and ffh), encoding recombinase A and signal recognition particle protein, respectively, proved to be ... Of twelve reference gene candidates tested, four proved to be stably expressed both in six different cultural growth conditions ... In addition, genes proC and gyrA, encoding pyrroline-5-carboxylate reductase and DNA gyrase, respectively, also displayed ... Thus, the identification of reference genes whose expression does not change during the course of the experiment is of ...
  https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-7-50
*  Stockton University NAMS Research Symposium Abstracts - Spring 2013 [Not This Year's Abstracts] | The Evolving Paleontologist
Preliminary identification of microbes using the 16S ribosomal RNA gene sequence identified seven bacteria isolates as being ... This study describes further characterization of those bacteria using the single copy protein encoding gene lepA and focuses on ... Background Bacterial infections can be controlled by (a) inhibiting bacterial growth, (b) being bactericidal, or (c) inhibiting ... Currently, the identified genes are being tested individually to identify suppressors.. 9. Role of Sample Preparation in In ...
  https://matthewbonnan.wordpress.com/ospreysci/abstracts/
*  MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes | BMC Bioinformatics | Full Text
It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate ... This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open ... a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among ... Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-97
*  Exercise 2
σ70 promters of rRNA genes. The ribosomal RNA (rRNA) genes encode essential products for the translation machinery of the ... The rRNA genes are regulated by two σ70 promoters, P1 and P2 upstream of the 16S rRNA (which is the first gene of the operon) ... DNA»RNA»protein. When prokaryotic organisms transcribe DNA into RNA it involves in many cases the binding of a sigma factor ... characters long!) Set element 'kingdom'='bac' (using bacterial models) and set 'mol'='ssu' (predict only 16S, Small Submit Unit ...
  http://www.cbs.dtu.dk/courses/embrace/2008-02-06/doc/exercise2.php
*  Ribosomal RNA - Wikipedia
... the 5S and 23S ribosomal RNAs). Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a ... rRNA is one of only a few gene products present in all cells. For this reason, genes that encode the rRNA (rDNA) are sequenced ... Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, and is essential for protein synthesis in all living ... "Homo sapiens 5S ribosomal RNA". "Homo sapiens 5.8S ribosomal RNA". "Homo sapiens 28S ribosomal RNA". "Homo sapiens 18S ...
  https://en.wikipedia.org/wiki/Ribosomal_RNA
*  BISC209:Project1 - OpenWetWare
He picked the genes that encode ribosomal RNA (rRNA). Ribosomes, the protein-RNA complexes that are the scaffold on which ... Comparing sequences of the gene (16S DNA) that encodes 16S rRNA in different bacteria can be used to identify them. We can also ... PCR Amplify rRNA gene sequences from Genomic DNA from "Universal" Bacterial Primers ... create glycerol stocks in 96 well plates to freeze and send away for 16s rRNA gene sequencing. ⇓ Analyze Diversity of Soil ...
  https://openwetware.org/wiki/BISC209:Project1
*  ATCC 35980 Strain Passport - StrainInfo
Campylobacter sputorum biovar sputorum strain ATCC 35980 16S ribosomal RNA gene, partial sequence. ATCC 35980 T ... Identification of Campylobacter jejuni on the basis of a species-specific gene that encodes a membrane protein ... Presence of internal transcribed spacers in the 16S and 23S ribosomal RNA genes of Campylobacter ... Approved Lists of Bacterial Names. Int J Syst Bacteriol 30, 225-420, 1980 ...
  http://www.straininfo.net/strains/6540
*  BISC209/S11:Project1 - OpenWetWare
He picked the genes that encode ribosomal RNA (rRNA). Ribosomes, the protein-RNA complexes that are the scaffold on which ... Comparing sequences of the gene (16S DNA) that encodes 16S rRNA in different bacteria can be used to identify them with much ... Amplify 16s ,span class=SpellE,rRNA,/span, genes in bacterial isolates by ,span class=SpellE,pcr,/span, for identification by,o ... PCR Amplify rRNA gene sequences from Genomic DNA from "Universal" Bacterial Primers ...
  https://openwetware.org/wiki/?title=BISC209/S11:Project1&oldid=420680
*  Most recent papers in the journal Asian-Australasian Journal of Animal Sciences | Read by QxMD
To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing. Results: After ... encoding these proteins and detected their mRNA distribution in different tissues. We also determined the role of AdipoQ in the ... in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of ... fiber levels on cecal microbiota composition in geese at day 70 according to pyrosequencing of the 16S ribosomal RNA gene. ...
  https://www.readbyqxmd.com/journal/48397
*  Complete genome sequence of Citrobacter werkmanii strain BF-6 isolated from industrial putrefaction | BMC Genomics | Full Text
C. werkmanii BF-6 and C. werkmanii NRBC 105721 exhibited the closest evolutionary relationships based on 16S ribosomal RNA and ... of the protein coding genes could be assigned to GO Ontology, KEGG Pathway, and COG (Clusters of Orthologous Groups) categories ... Furthermore, C. werkmanii BF-6 exhibits typical bacterial biofilm formation and development. In the RT-PCR experiments, we ... 84 tRNA genes, 25 rRNA operons, 3 microsatellite sequences and 34 minisatellite sequences. A previously unknown circular ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4157-9
*  Frontiers | Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes | Microbiology
Fifteen of 37 inserts harboured resistance genes that shared ,90% amino acid identity with known gene products, whereas on 13 ... Taken together, our results show that sponge microbiota host diverse and novel resistance genes that may be harnessed by ... Here, we applied functional metagenomics to study the presence and diversity of functional resistance genes in the sponges ... Fifteen of 37 inserts harboured resistance genes that shared ... inserts no resistance gene could be identified with high ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2016.01848/full
*  ASMscience | Detection and Characteri
... reasons to use genetic tests to identify antimicrobial resistance genes or mutations associated with resistance in bacterial ... All PCR assays for antimicrobial resistance genes, whether sold commercially or developed in-house, must be validated before ... DNA sequence analysis has been particularly helpful for identifying point mutations in genes associated with extended-spectrum- ... This chapter focuses specifically on genotypic methods for detecting and characterizing antimicrobial-resistant bacterial ...
  http://www.asmscience.org/content/book/10.1128/9781555816728.chap74
*  Frontiers | Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with...
The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and ... one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% ... The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and ... The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2013.00341/full
*  Frontiers | Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the...
... which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends ... Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States ... Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States ... 2008). Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2017.01974/full
*  Phylogenomic Analysis of Marine Roseobacters
In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC ... The ribosomal RNA gene is not sufficiently informative to give a highly resolved and well-supported phylogeny for these taxa, ... The tree using a concatenation of the best conserved ribosomal protein genes in the living world, constructed with each method ... By contrast, the 16S rRNA tree has the fewest number of genes supporting it (only 141 based on SH tests and 80 based on AU ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2904699/
*  Molecular characterization of a mosaic locus in the genome of 'Candidatus Liberibacter asiaticus'
Sequence analyses of conserve genomic loci such as 16S rRNA gene and 16S/23S intergenic spacer regions have been used to define ... Deng X, Chen J, Li H. Sequestering from host and characterization of sequence of a ribosomal RNA operon (rrn) from 'Candidatus ... genomic loci with variable TRN or prophage genes are also known to be valuable descriptors of bacterial genetic diversity [13- ... L. asiaticus' Strain Psy 62 is now available [9]. The annotated genome has 1,109 protein and 53 RNA coding loci and is readily ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC3296602/