• amino acids
  • It has just 700 genes and is the first bacterial strain identified that cannot make its own amino acids - the building blocks for the proteins essential to life - but depends instead on a supply from its host. (newscientist.com)
  • Nitrogen is the most important nutrient in plants because it is required for chlorophyll production and other cellular compounds (proteins, nucleic acids, and amino acids) [ 1 ]. (hindawi.com)
  • Site-directed mutagenesis defined two highly conserved amino acids, cysteine-265 and aspartate-234, as being essential for the phosphatase activity of the AtPTP1 protein, suggesting a common catalytic mechanism for PTPases from all eukaryotic systems. (plantcell.org)
  • The large CSI of about 150-180 amino acids within a conserved region of Gyrase B (between amino acids 529-751), is commonly shared between various Proteobacteria, Chlamydiales, Planctomycetes and Aquificales species. (wikipedia.org)
  • Similarly a large CSI of about 100 amino acids in RpoB homologs (between amino acids 919-1058) is present in various species belonging to Proteobacteria, Bacteroidetes-Chlorobi, Chlamydiales, Planctomycetes and Aquificales. (wikipedia.org)
  • bacteria
  • Deadly bacteria may be evolving antibiotic resistance by mimicking human proteins, according to a new study by the Translational Genomics Research Institute (TGen). (phys.org)
  • Similar methyltransferase proteins are found in other highly infectious bacteria , including the pathogen Mycobacterium tuberculosis that causes Tuberculosis, a disease that results in more than 1 million deaths annually. (phys.org)
  • When the researchers viewed this species under the microscope, they found that the cells were covered with much smaller bacteria - the first species ever discovered to parasitise another bacterium. (newscientist.com)
  • They also sequenced the genes from four selected bacterial species and screened them for the production of plant-growth promoting enzymes, hormones, and other metabolic factors that might help explain how the bacteria improve plant growth. (webwire.com)
  • The presence of the endophytic bacteria was confirmed by searching for the glowing protein. (webwire.com)
  • Due to the ubiquity of many of the species within this group, their clinical significance has traditionally been dismissed, and when isolated from clinical specimens, the bacteria have merely been regarded as contaminants [ 12 ]. (intechopen.com)
  • This is not present in any other bacteria species and could be used to characterize members of the phylum Thermotogae from all other bacteria. (wikipedia.org)
  • The discovery of Pup indicates that like eukaryotes, bacteria may use a small-protein modifier to control protein stability. (wikipedia.org)
  • UBact is a homolog of Pup, and is found in several phyla of gram-negative bacteria (Pup is found predominantly in the gram-positive bacterial phylum Actinobacteria). (wikipedia.org)
  • pathogens
  • This process of "molecular mimicry" may help explain why bacterial human pathogens , many of which were at one time easily treatable with antibiotics, have re-emerged in recent years as highly infectious public health threats, according to the study published May 26 in the journal Public Library of Science (PLoS) One . (phys.org)
  • Using genomic sequencing, the spelling out of billions of genetic instructions stored in DNA, the study identified several methyltransferase protein families that are very similar in otherwise very distantly related human bacterial pathogens. (phys.org)
  • In general, these bacterial pathogens are considered "highly clonal," meaning that the overall gene content of each species is very similar. (phys.org)
  • Upon infection, bacterial pathogens dump more than 200 proteins into human macrophage cells called 'effector proteins. (phys.org)
  • Pathogens have evolved arsenals of suppressive molecules in order to counteract MAMP-induced defences, such as type III secreted protein effectors, toxins acting as hormone mimics and extracellular polysaccharides (EPS). (bath.ac.uk)
  • Other than protection from UV, desiccation and antimicrobials, we revealed that chelation of calcium ions by EPS of diverse bacterial pathogens, prevents calcium influx in plants to the cytosol from the apoplast. (bath.ac.uk)
  • in a higher eukaryote, but it has since been detected in xylem of resistant lines of some other species such as tomato, tobacco and cotton infected with vascular pathogens. (bath.ac.uk)
  • The emergence of livestock-associated methicillin-resistant Staphylococcus aureus and the description of a novel methicillin-resistant gene, mecC, have renewed concerns regarding the role of animals as reservoirs and a source for the evolution of novel, virulent zoonotic pathogens. (intechopen.com)
  • genomic
  • But now, as two papers and a commentary in the current issue of the journal Science suggest, the powerful techniques of genomic research are providing new ways to investigate the lives of these bacterial cells. (nytimes.com)
  • strains
  • McLean and his colleagues discovered the organisms by searching for bacterial strains in human saliva samples. (newscientist.com)
  • Individual strains were then supplemented with a gene for a protein that glows under ultraviolet light, and inoculated into the roots of fresh poplar cuttings that had been developing new roots in water. (webwire.com)
  • mimics
  • Because these proteins are so similar to the human proteins, it mimics them and enables them to interfere with the body's immunity response, thereby protecting the pathogen,'' Dr. Champion said. (phys.org)
  • Molecular
  • Altogether, evidence suggests a role of the Francisella tularensis protein in a mechanism of molecular mimicry. (phys.org)
  • Identifying small differences between the pathogen and human proteins through Next Generation genome-wide datasets could help develop molecular targets in the development of new drug treatments, she said. (phys.org)
  • In molecular biology, the Aar small RNA is a small RNA (sRNA) produced by species of Acinetobacter. (wikipedia.org)
  • taxa
  • The signs are also observed alongside significant reductions in vaginal lactobacilli, which are replaced by an outgrowth of diverse, strict and facultative anaerobic bacterial taxa that commonly includes Gardnerella vaginalis, Dialister spp. (frontiersin.org)
  • These CSIs were most likely introduced in an ancestor of the group of species before the members of the taxa diverged. (wikipedia.org)
  • Figure 2 shows an example of 5aa CSI found in a conserved region that is commonly present in the species belonging to phyla X, Y and Z, but it is absent in other phyla (A, B and C). This signature indicates a specific relationship of taxa X, Y and Z and also A, B and C. Based upon the presence or absence of such an indel, in out-group species (viz. (wikipedia.org)
  • subgroups
  • Group specific CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla and subgroups within it. (wikipedia.org)
  • genus
  • Staphylococcus aureus is the most significant species within this genus by virtue of its versatility as a pathogen in humans and animals [ 4 , 5 ]. (intechopen.com)
  • Promoters
  • The oxidized form of this factor specifically binds to the promoters of constituent genes of OxyR regulon, including katG (hydroperoxidase-catalase HPІ), gorA (glutathione reductase), grxA (glutaredoxin 1), trxC(thioredoxin 2), ahpCF (alkyl hydroperoxide reductase), dps (nonspecific DNA binding protein) and oxyS (a small regulatory RNA). (wikipedia.org)
  • Genomics
  • Nicole Lockhart, Ph.D., program director, and Lawrence Brody, Ph.D., division director, both in NHGRI's Division of Genomics and Society, were there to tackle some of the ethics questions related to gene editing. (genome.gov)
  • For example, I'm working with a team at UC Berkeley and UCSF through the Innovative Genomics Institute to develop procedures for clinical use of gene editing in adults that will ultimately provide affordable options for patients with genetic disease. (genome.gov)
  • humans
  • These proteins also were found in hosts such as humans, mouse and rat. (phys.org)
  • Possible work-arounds for CRISPR clinical trials would include using Cas9 proteins from different bacterial species, which humans bodies have never seen. (genome.gov)
  • Other Staphylococcus species, collectively termed coagulase-negative staphylococci (CNS), are responsible for a variety of opportunistic infections in humans and animals [ 11 ]. (intechopen.com)
  • By sequencing the genome, Dr. Gordon and his colleagues found many genes devoted to processing carbohydrates that humans cannot digest. (nytimes.com)
  • enzymes
  • a third ORF (pmsE) encoded a protein with strong similarity with enzymes involved in the biosynthesis of siderophores in other bacterial species. (csic.es)
  • The genes include many genes coding for metabolic enzymes and antioxidant enzymes demonstrating the role of these enzymes in reorganization of metabolism under stress conditions. (wikipedia.org)
  • different
  • Although the overall sequence of the orthologs is highly similar, the study identifies a protein domain carrying distinct amino acid variations present in the different organisms. (phys.org)
  • The review presents a list of promoter and reporter genes that could be used to develop different kind of sensors, and a perspective of sensors to measure quantitatively the nitrogen is presented. (hindawi.com)
  • Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. (genecards.org)
  • Multiple transcript variants encoding different protein isoforms were identified through sequence analysis. (genecards.org)
  • Other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect the interpretation of a CSI. (wikipedia.org)
  • Therefore, based upon their presence or absence, it should be possible to identify both known and even previously unknown species belonging to these groups in different environments. (wikipedia.org)
  • A key issue in bacterial phylogeny is to understand how different bacterial species are related to each other and their branching order from a common ancestor. (wikipedia.org)
  • coli
  • The pmsB gene induced low levels of SA production in E. coli when expressed under control of the lacZ promoter. (csic.es)
  • Such differences in 3'TAIL lead to species-specific SDs (designated SDEc for E. coli and SDBs for B. subtilis) that can form strong and well-positioned SD/aSD pairing in one species but not in the other. (uottawa.ca)
  • Selection mediated by the species-specific 3'TAIL is expected to favour SDBs against SDEc in B. subtilis but favour SDEc against SDBs in E. coli. (uottawa.ca)
  • Studies of E. coli response to H2O2 have shown that exposure to H2O2 elevated mRNA levels of 140 genes, of which 30 genes are members of the OxyR regulon. (wikipedia.org)
  • In E.coli, negative autoregulation of SoxS protein serves as a dampening mechanism for the soxRS redox stress response. (wikipedia.org)
  • The stress response regulation activities of RpoE are modulated by the Hfq protein in E. coli. (wikipedia.org)
  • lysine
  • Background: Disrupting the balance of histone lysine methylation alters the expression of genes involved in tumorigenesis including proto-oncogenes and cell cycle regulators. (utexas.edu)
  • HUMAN
  • The methyltransferase protein also was found to have an ortholog, or similar counterpart, in human DNA. (phys.org)
  • A successful trip could answer some of Daly's lingering questions about the species itself and, more broadly, may provide clues on how human activities affect this unique, seemingly removed ecosystem. (bio-medicine.org)
  • We might find that these species have an important role in human diseases. (newscientist.com)
  • These transgenes are capable of producing proteins in the plants that have never been in the human diet over the course of human evolution, stretching back thousands, even millions of years. (beforeitsnews.com)
  • or, they claim that these proteins are inconsequential and do not represent a threat to human health, or the health of the biosphere as whole because they say so - a plea to their own self-appointed, baseless authority. (beforeitsnews.com)
  • The recent finding of human immune responses to CRISPR-Cas9 proteins in human cells is an important finding. (genome.gov)
  • They also discovered genes devoted to processing some materials produced by the human cells like mucin. (nytimes.com)
  • this figure was based on estimates that the human microbiome includes around 100 trillion bacterial cells and an adult human typically has around 10 trillion human cells. (wikipedia.org)
  • Arabidopsis
  • For in depth analysis of mechanisms we use model species such as Arabidopsis and tomato, but I also research more applied aspects, such as epidemiology, detection and resistance screening of certain tropical crop species of world importance. (bath.ac.uk)
  • In this study, we isolated a cDNA encoding a putative protein tyrosine phosphatase (PTPase) from Arabidopsis (referred to as AtPTP1 ). (plantcell.org)
  • cells
  • Single-protein counting experiments in vivo reveal that isogenic cells under seemingly identical experimental conditions display considerable diversity in expression [ 6 ]. (royalsocietypublishing.org)
  • Several microfluidic devices have been reported to substantially increase experimental throughput by harnessing the reproduction of bacterial cells to continuously regenerate the sample and also allowing imaging of many replicate colonies in parallel [ 7 , 8 ]. (royalsocietypublishing.org)
  • The bacterial cells are much smaller, which is why we do not look like an overgrown petri dish. (nytimes.com)
  • structural
  • Oxidized SoxR then induces the expression of SoxS protein, which in turn activates the transcription of structural genes of the SoxRS regulon. (wikipedia.org)
  • The structural genes under this regulon include sodA (Mn-superoxide dismutase(SOD)), zwf (glucose-6-phosphate dehydrogenase(G6PDH)), acnA (aconitase A), nfsA (nitrate reductase A), fumC (fumarase C) and nfo (endonuclease IV) among others. (wikipedia.org)
  • characterization
  • ARSDA includes functions to take advantage of HTS data in the new sequence format for downstream data analysis such as gene expression characterization. (uottawa.ca)
  • Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for non-linear clustering of transcriptomic data, comprehensive sequence alignment and phylogenetic functions. (uottawa.ca)
  • Important components of the HMP were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e. of individual bacterial species). (wikipedia.org)
  • recombinant
  • A recombinant cosmid clone (pMB374-07) of a WCS374 gene library harboring loci necessary for the biosynthesis of salicylic acid (SA) and this second siderophore pseudomonine was isolated. (csic.es)
  • The recombinant AtPTP1 protein specifically hydrolyzed phosphotyrosine, but not phosphoserine/threonine, in protein substrates. (plantcell.org)
  • model species
  • A number of HTS files for model species are in the process of being processed and deposited at http://coevol.rdc.uottawa.ca to demonstrate that this approach not only saves a huge amount of storage space and transmission bandwidth, but also dramatically reduces time in downstream data analysis. (uottawa.ca)
  • scientists
  • The scientists identified 78 bacterial endophytes from poplar and willow. (webwire.com)
  • I think we need to work with scientists and stakeholders across the fields of medicine, agriculture and synthetic biology to ensure responsible progress with gene editing. (genome.gov)
  • Transcription
  • Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Innate Immune System . (genecards.org)
  • Altered defence gene transcription was revealed by cDNA-AFLP techniques. (bath.ac.uk)
  • Regulation of the soxRS regulon occurs by a two-stage process: the SoxR protein is first converted to an oxidized form that enhances soxS transcription, and the increased level of SoxS protein in turn activates the expression of the regulon. (wikipedia.org)
  • expression
  • We determined by reverse transcriptase-mediated PCR that the pmsCEAB genes are cotranscribed and that expression is iron regulated. (csic.es)
  • I contrasted gene expression results between ARSDA and Cufflinks so readers can better appreciate the strength of ARSDA. (uottawa.ca)
  • The method makes it possible to analyse the rate of gene expression at the level of single proteins over the bacterial cell cycle. (royalsocietypublishing.org)
  • An increase in the expression of LacI is observed at the beginning of the cell cycle, possibly because some gene copies are de-repressed as a result of partitioning inequalities at cell division. (royalsocietypublishing.org)
  • For this reason, methods for counting expression events for cytoplasmic proteins are limited. (royalsocietypublishing.org)
  • sigma
  • At least three known genes including xthA and katE are regulated by a sigma factor, KatF(RpoS), whose synthesis is turned on during the stationary phase. (wikipedia.org)
  • In some bacterial species, such as Clostridium botulinum, this sigma factor may be necessary for sporulation. (wikipedia.org)
  • important
  • An important paralog of this gene is SPACA3 . (genecards.org)
  • The analysis of genes and metabolically important gene products from endophytes resulted in the identification of many possible mechanisms that could help these microbes thrive within a plant environment, and potentially affect the growth and development of their plant host. (webwire.com)
  • This perception is, however, changing as many species have emerged as important causes of nosocomial infections, particularly in relation to foreign-device-related infections and infections in immunocompromised patients [ 1 , 13 ]. (intechopen.com)
  • XthA (exonuclease III, a DNA repair enzyme) and KatE (catalase) are known to play important roles in the defense against oxidative stress but interestingly KatF regulon genes are not induced by oxidative stress. (wikipedia.org)
  • found
  • Researchers cruising for creatures that live in the deepest parts of the Pacific Ocean found a new species of sea anemone living in the unlikeliest of habitats ?the carcass of a dead whale. (bio-medicine.org)
  • Most CSIs that have been identified have been found to exhibit high predictive value and they generally retain the specificity for the originally identified clades of species. (wikipedia.org)
  • Figure 1 shows an example of 5aa CSI found in all species belonging to the taxon X. This is a distinctive characteristic of this taxon as it is not found in any other species. (wikipedia.org)