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*  A global pH sensor: Agrobacterium sensor protein ChvG regulates acid-inducible genes on its two chromosomes and Ti plasmid |...
This strain contains an rrn:gfp fusion with the mini-Tn5 transposon inserted onto an rrn gene encoding 16S ribosomal RNA. This ... Indeed, ChvG is required for the expression of aopB, which encodes an outer membrane protein exposed on the bacterial cell ... This included a 16S ribosomal RNA gene (Table 2) and the virulence-associated gene, chvH (Table 3). In addition, ChvG was not ... 3), suggesting that the 16S ribosomal RNA gene is not acid-inducible and not affected by ChvG. This finding suggests that the ...
  http://www.pnas.org/content/99/19/12369
*  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/
*  Ribosomal RNA - New World Encyclopedia
The bacterial 16S, 23S, and 5S rRNA genes are typically organized as a co-transcribed operon. There may be one or more copies ... ribosomal RNA is considered the most conserved (least variable) gene in all cells (Smit et al. 2007). (The proteins in ... 1989).) For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate ... The protein manufacturing unit of all living cells, the ribosome, is composed of ribosomal RNA and protein. It is at the site ...
  http://www.newworldencyclopedia.org/entry/Ribosomal_RNA
*  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
*  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
*  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
*  The rice white green leaf 2 gene causes defects in chloroplast development and affects the plastid ribosomal protein S9 |...
... play important roles in the translation of key proteins involved in chloroplast development and photosynthesis. PRPs have been ... The small subunit consists of the 16S rRNA and 24 PRPs, including 12 proteins encoded by plastid genes and 12 encoded by ... Transcription of chloroplast genes depends on the nucleus-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase ( ... Interestingly, some ribosomal proteins are not essential for the bacterial ribosome, but are essential for chloroplasts (Tiller ...
  https://rd.springer.com/article/10.1186%2Fs12284-018-0233-2
*  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
*  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
*  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
*  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
*  Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes
Most of the 260 known proteins involved in translation have been identified and studied in the bacteria Escherichia coli and ... in Mollicutes and define the translation apparatus that would be required in a cellular chassis mimicking a minimal bacterial ... However, comparative genomics has shown that the translation protein set can be much smaller. This is true for bacteria ... Using homology inference approach and expert analyses, we identified the translation apparatus proteins for 39 of these ...
  https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004363
*  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
*  Assessment of Molecular Markers for Classification of Bacterial Phyla using Topological Dissimilarity of Phylogenetic Trees
... genes are important molecular markers for placement of a new bacterial species into phyla. However, accuracy and c.. ... Single-copy conserved proteins and ribosomal RNA (rRNA) ... Single-copy conserved proteins and ribosomal RNA (rRNA) genes ... Except for 16S rRNA gene, 23S rRNA gene and some essential r-proteins, most of the known proteins probably were not qualified ... However, whether the proteins encoded by these conserved genes perform similarly compared to 16S rRNAs as molecular markers in ...
  https://www.omicsonline.org/open-access/assessment-of-molecular-markers-for-classification-of-bacterial-phyla-using-topological-dissimilarity-of-phylogenetic-trees-2329-9002-1000204-103924.html
*  Microbiology Society Journals | Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that...
The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, ... bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations ... 2011; ). rRNASelector: a computer program for selecting ribosomal RNA encoding sequences from metagenomic and ... 1991; ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115--175. Edited by Stackebrandt E ...
  https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.038075-0
*  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
*  CNS Whipple Disease: Background, Pathophysiology, Epidemiology
They used a gene that encodes for 16S ribosomal RNA (rRNA) in bacteria to characterize the nucleotide sequence of the bacillus ... T whippelii genome encodes for around 800 protein coding genes. It lacks key biosynthetic pathways and has a reduced capacity ... Relman used polymerase chain reaction (PCR) to amplify this unique bacterial 1321-base sequence of the 16S rRNA gene obtained ... The following findings confirmed that the isolates passaged were T whippelii: the amplified sequences of the 16S rRNA gene of ...
  https://emedicine.medscape.com/article/1166639-overview
*  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
*  Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study | PNAS
... proteins: S2, S3, and S4. Because of the complexity of ribosomal structure, which involves many protein-protein and protein-RNA ... A common ancestral gene gave rise to these gene families in the bacterial and archaeal lineages (35). Early in the history of ... Furthermore, the nif genes encoding the core proteins required for NIF are generally closely linked on prokaryotic chromosomes ... Although there is coevolution between ribosomal proteins and 16S rRNA, some phylogenies based on the two types of molecules are ...
  https://www.pnas.org/content/103/25/9584.full