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  • bacteria
  • Duke University biomedical engineers have harvested genes for ion channels from bacteria that, with a few tweaks, can create and enhance electrical signaling in human cells, making the cells more electrically excitable. (innovations-report.com)
  • While bacterial genes encoding sodium channels are different than their human counterparts, evolution has conserved many similarities of ion channel design since multi-celled animals diverged from bacteria hundreds of millions of years ago. (innovations-report.com)
  • The team set out to sequence the genomes of 112 B. dolosa isolates taken from 14 of the infected patients, mapping genetic changes over time to reveal both the route of the infection's spread and which genes faced the greatest selective pressure - in other words, how the bacteria evolved when challenged by human defenses and medical treatment. (innovations-report.com)
  • Microarray analysis was used to identify genes that were differentially expressed when pneumococci replicated in the vitreous of rabbit eyes as compared with bacteria grown in vitro in Todd Hewitt medium. (nih.gov)
  • Researchers have developed a way to use firefly luciferase - which is much brighter than bacterial luciferase - as a chemiluminescent reporter in bacteria. (photonics.com)
  • A lab manual was published, which emphasized how genetics can be used to study pathogenic bacteria, a growing field with a dramatic need for researchers trained in bacterial genetics. (asmscience.org)
  • By using the sacB gene onto the suicide plasmid will convert sucrose to levans which are toxic to the gram-ve bacteria. (protocol-online.org)
  • Herein, we review engineered light-sensor systems with potential for in vivo regulation of gene expression in bacteria, and highlight different means of extending the range of available light input and transcriptional output signals. (diva-portal.org)
  • Genes that encode for ion channels in bacteria can be utilized and altered in simple ways to provide human cells with the creation or enhancement of electrical signaling, an essential part of life's most fundamental processes. (labroots.com)
  • Wiersinga and the Laboratory for Experimental Internal Medicine discovered which gene-protein combination renders the lethal bacteria B. pseudomallei harmless. (infectioncontroltoday.com)
  • To demonstrate the effectiveness of RNAlater at preserving RNA in intact bacteria, samples from five bacterial species, Escherichia coli, Pseudomonas aeruginosa, Campylobacter fetus, Bacillus subtilis and Staphylococcus aureus, were suspended in RNAlater and incubated at 25°C or 4°C for up to one week. (thermofisher.com)
  • To determine if storage of bacteria in RNAlater affects gene expression patterns, we compared the expression profile obtained with RNA isolated from B. subtilis that had been stored overnight in RNAlater at 25°C (Figure 2A) with the profile from RNA prepared from freshly harvested B. subtilis (Figure 2B). (thermofisher.com)
  • A comparison of these replicate arrays demonstrates that RNAlater is extremely effective at preserving gene expression profiles in bacteria. (thermofisher.com)
  • Seemingly simple organisms, such as bacteria and amoebas, have a much higher gene density than humans. (wikipedia.org)
  • They took a gene from a bacterium that provided resistance to the antibiotic kanamycin, inserted it into a plasmid and then induced another bacteria to uptake the plasmid. (wikipedia.org)
  • Boyer and Cohen expressed other genes in bacteria. (wikipedia.org)
  • Because mannanase is not commonly found in similar beetles, and the characteristic of the gene is bacterial, the gene is thought to have originated from bacteria in the beetle's gut, and transposed to the beetle's genome through horizontal gene transfer (HGT). (wikipedia.org)
  • Although horizontal gene transfer from bacteria to eukaryotes have been known to occur, albeit rarely, the HhMAN1 is the first to have a known and beneficial function to the recipient. (wikipedia.org)
  • These unique features and other features gave significance of the T-even phages, this includes transduction which is responsible for transfer of drug resistant features, lysogenic conversion is responsible for acquisition of new characteristics such as the formation of new enzymes, random insertion into bacterial chromosome can induce insertional mutation, epidemiological typing of bacteria (phage typing), phages are used extensively in genetic engineering where they serve as cloning vectors. (wikipedia.org)
  • Equipped with this gene, the former II-R strain bacteria were now protected from the host's immune system and could kill the host. (wikipedia.org)
  • It serves as a riboswitch that binds directly to thiamine pyrophosphate (TPP) to regulate gene expression through a variety of mechanisms in archaea, bacteria and eukaryotes. (wikipedia.org)
  • genomes
  • The genomic contexts are determined with a multiple center star clustering topology on the basis of a user-provided protein sequence and all (or a set of) chromosomes from the publicly available archaeal and bacterial genomes. (nih.gov)
  • Genetics: Analysis of Genes and Genomes, 6th edition. (wikipedia.org)
  • GLIMMER 3.0 also improves the generated training set data by comparing the long-ORF with universal amino acid distribution of widely disparate bacterial genomes. (wikipedia.org)
  • Since cereals that absorbed extra nitrogen would typically lodge, or fall over before harvest, semi-dwarfing genes were bred into their genomes. (wikipedia.org)
  • Genome
  • What if the genome-wide dN/dS ratio was a red herring, when what they really wanted to know was what was happening to specific genes? (innovations-report.com)
  • In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in terms of a million base pairs, or megabase (Mb). (wikipedia.org)
  • The human genome has a gene density of 12-15 genes/Mb, while the genome of the C. elegans roundworm is estimated to have 200. (wikipedia.org)
  • HhMAN1 is a gene in the genome of Hypothenemus hampei, a.k.a. (wikipedia.org)
  • The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White. (wikipedia.org)
  • GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome. (wikipedia.org)
  • However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome. (wikipedia.org)
  • Genetic
  • On the other hand, the advanced search tool enables a user to search genetic information by categories, custom query, wild-card search and field-specific search, which uses the gene name, the description, the cluster of orthologous groups (COGs) id, the GO term, the KEGG enzyme commission (EC) number, etc. as key words. (wikipedia.org)
  • Genetic modification involves the mutation, insertion, or deletion of genes. (wikipedia.org)
  • Other methods exploit natural forms of gene transfer, such as the ability of Agrobacterium to transfer genetic material to plants, or the ability of lentiviruses to transfer genes to animal cells. (wikipedia.org)
  • The process of selective breeding, in which organisms with desired traits (and thus with the desired genes) are used to breed the next generation and organisms lacking the trait are not bred, is a precursor to the modern concept of genetic modification. (wikipedia.org)
  • Yet, T-even phages are in fact among the largest and highest complexity virus, in which these phages genetic information is made up of around 160 genes. (wikipedia.org)
  • Prokaryotes, whose initial cell has additional or transformed genetic material, reproduce through asexual reproduction but may, in lateral gene transfer, display processes such as bacterial conjugation, transformation and transduction, which are similar to sexual reproduction although they do not lead to reproduction. (wikipedia.org)
  • organisms
  • Because of evolutionary conservation, when organisms along the evolutionary tree share common features that are important, there are many similarities between the human and bacterial sodium ion channels. (labroots.com)
  • Advances followed that allowed scientists to manipulate and add genes to a variety of different organisms and induce a range of different effects. (wikipedia.org)
  • Containing about 160 genes, these virulent viruses are among the largest, most complex viruses that are known and one of the best studied model organisms. (wikipedia.org)
  • Model organisms are usually required to be simple with as few as five genes. (wikipedia.org)
  • The THI element is an extension of a previously detected thiamin-regulatory element, the thi box, there is considerable variability in the predicted length and structures of the additional and facultative stem loops represented in dark blue in the secondary structure diagram Analysis of operon structures has identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms. (wikipedia.org)
  • expression
  • Differential bacterial gene expression during experimental pneumococcal endophthalmitis. (nih.gov)
  • 112 genes demonstrated increased expression during growth in the eye whereas 22 were downregulated. (nih.gov)
  • S. pneumoniae enhances and represses the expression of a variety of genes during endophthalmitis. (nih.gov)
  • Transcription of representative genes (x axis) displaying differential expression was analyzed by qRT-PCR of pooled bacterial RNA isolated independently from samples used for array experiments. (nih.gov)
  • Because gene expression within a cell population fluctuates randomly, investigators must monitor individual cells if they want to follow the activity as genes switch on and off. (photonics.com)
  • Along with graduate student Yun Zhang and professor of veterinary medicine Gregory J. Phillips, Yeung used the chemiluminescence technique to perform quantitative studies of gene expression in two bacterial lines. (photonics.com)
  • Light of different wavelengths can serve as a transient, noninvasive means of regulating gene expression for biotechnological purposes. (diva-portal.org)
  • Fully genetically encoded light sensors take advantage of the favorable characteristics of light, do not need the supplementation of any chemical inducers or co-factors, and have been demonstrated to control gene expression in Escherichia coli. (diva-portal.org)
  • Furthermore, we discuss advances in multiplexing different light sensors for achieving multichromatic control of gene expression and indicate developments that could facilitate the construction of efficient systems for light-regulated, multistate control of gene expression. (diva-portal.org)
  • Parts for controlling gene expression are of special importance in living systems, and specifically promoters are needed for enabling and simplifying rational design. (diva-portal.org)
  • Similar results were obtained when arrays were probed with RNA prepared from B. subtilis cells that were stored in RNAlater for one week at 4°C. RNAlater is thus an ideal solution for maintaining the expression profile of bacterial mRNA when immediate RNA isolation is not possible or practical. (thermofisher.com)
  • Gene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. (embopress.org)
  • Simultaneous specific and global regulation thus constitutes an additional-but often neglected-layer of complexity in gene expression. (embopress.org)
  • An experimental‐computational approach is applied to dissect the contribution of specific transcription factor‐mediated versus global growth‐dependent regulation to bacterial gene expression, and obtain a quantitative understanding of dynamic adaptations in arginine biosynthesis of E. coli . (embopress.org)
  • We present a model‐based approach to quantitatively dissect simultaneous contributions from specific transcription factors and the global growth status to bacterial gene expression, based on parameter inference from GFP‐based promoter activity measurements. (embopress.org)
  • We show that growth rate can be used to predict the unregulated expression baseline of a gene, since growth rate dependence of global regulation occurs both in steady state and during transient changes in growth rate. (embopress.org)
  • We obtain a quantitative understanding of both specific and global regulation in arginine biosynthesis, as demonstrated by accurate model‐based predictions of complex transient geneexpression responses to simultaneous perturbation in growth rate and arginine availability. (embopress.org)
  • The researchers are seeking to develop a system for monitoring bacterial gene expression in response to signals from the natural environment using a blend of membrane diffusion cell, genomics and optical detection technologies. (stanford.edu)
  • Other unique features of the T-even virus is its regulated gene expression. (wikipedia.org)
  • The expression platform is what regulates gene expression. (wikipedia.org)
  • Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. (wikipedia.org)
  • A TPP riboswitch in Neurospora crassa (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes A TPP riboswitch in plants modifies splicing and alternative 3'-end processing A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript. (wikipedia.org)
  • A riboswitch in Listeria monocytogenes regulates the expression of its downstream gene. (wikipedia.org)
  • regulation
  • We thereby uncover two principles of joint regulation: (i) specific regulation by repression dominates the transcriptional response during metabolic steady states, largely repressing the biosynthesis genes even when biosynthesis is required and (ii) global regulation sets the maximum promoter activity that is exploited during the transition between steady states. (embopress.org)
  • In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation. (wikipedia.org)
  • For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box (now the SAM-I riboswitch), the THI-box (a region within the TPP riboswitch), the RFN element (now the FMN riboswitch) and the B12-box (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. (wikipedia.org)
  • In this regulation, the riboswitch interferes with transcription of the gene. (wikipedia.org)
  • metabolic
  • While some of these genes reflect changes in metabolic requirements, some appear to play a role in immune evasion and pathogenesis in the eye. (nih.gov)
  • Prior to the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. (wikipedia.org)
  • microorganisms
  • I know that counterselectable markers are often instrumental for the construction of mutants when under appropriate growth conditions, a counterselectable gene promotes the death of the microorganisms harboring it. (protocol-online.org)
  • The developed technology should enable monitoring of genes of many microorganisms of environmental significance and will form the foundation of a novel environmental sensing technology for accurate measurements of classes of contaminants and environmental conditions. (stanford.edu)
  • infection
  • Researchers at Harvard Medical School and Children's Hospital Boston have retraced the evolution of an unusual bacterial infection as it spread among cystic fibrosis patients by sequencing scores of samples collected during the outbreak, since contained. (innovations-report.com)
  • Cystic fibrosis (CF) is a hereditary disease that renders the lungs susceptible to bacterial infection. (innovations-report.com)
  • The group where the gene for Toll2 was switched off, survived the bacterial infection," says Wiersinga. (infectioncontroltoday.com)
  • knockout
  • I am trying to knockout a gene which is essential for growth of the pathogen Pseudomonas aeruginosa PAO1 (has no sacB gene in it). (protocol-online.org)
  • I check for the gene knockout in 'centrimide+kan+amp' plate with PAO1 using the gene inserted suicide vector pFS100 and get no growth (showing the gene is essential) whereas the control plate without antibiotic markers show growth. (protocol-online.org)
  • Mice with genes knocked out (knockout mouse) were created in 1989. (wikipedia.org)
  • researchers
  • Publishing their results in Nature Communications, the researchers maneuvered around that barrier by engineering ion channels from bacterial genes, which are smaller. (labroots.com)
  • resistance
  • The problem is i am using a suicide vector pFS100 a derivative of pGP704 carrying a 'pir' dependent origin of replication from plasmid R6K and gene encoding resistance to ampicillin and kanamycin but no sacB gene marker in it. (protocol-online.org)
  • Since then important traits including dwarfing genes and rust resistance have been introduced. (wikipedia.org)
  • cells
  • Too large, unfortunately, to be readily delivered to cells through a virus -- standard procedure in modern gene therapy techniques. (innovations-report.com)
  • To skirt this size issue, the Duke team delivered smaller ion channels engineered from bacterial genes to primary human cells in a laboratory setting. (innovations-report.com)
  • Our technique, however, uses much smaller bacterial ion channels that proved successful in human cells in the laboratory. (innovations-report.com)
  • You could imagine using this to alter electrically dead cardiac scar tissue after a heart attack to bridge gaps between healthy cells," said Nguyen, who also points out that all three genes are small enough to be delivered simultaneously by a single virus. (innovations-report.com)
  • Select genes potentially playing a role in virulence during endophthalmitis were deleted, and mutants were tested for reduced eye pathogenesis and altered adhesion to host cells. (nih.gov)
  • Bacterial adhesion to ARPE-19 cells. (nih.gov)
  • Their size impedes their direct delivery into cells via virus, a standard procedure used in many current gene therapy techniques. (labroots.com)
  • At right, the speed that is gained by treating the cells with a trio of bacterial genes can be seen. (labroots.com)
  • You could imagine using this to alter electrically dead cardiac scar tissue after a heart attack to bridge gaps between healthy cells,' commented Nguyen, who noted that the three genes are all small enough for simultaneously delivery by one virus. (labroots.com)
  • sequences
  • The results consist in a dynamic web page where a consistent color-coding permits a rapid visual evaluation of the relative positioning of genes with similar sequences within the synteny. (nih.gov)
  • In the gene list view, the links "G O D H S T B..." lead the user to a locus information tool, where detailed information such as operon & regulon, domains & families, sequences, annotations, etc. are shown. (wikipedia.org)
  • plasmid
  • About 50% of these clones will have replaced the original wild type gene with a mutated one and at the same time got rid of the suicide plasmid backbone from the chromosme. (protocol-online.org)
  • Under such conditions, certain bacterial genes are turned on leading to the transfer of its tDNA from its root-inducing plasmid (Ri plasmid) into the plant through the wound. (wikipedia.org)
  • small
  • The pores in bacterial cell walls are too small for the charged luciferin molecules to fit through. (photonics.com)
  • firing small particles from a gene gun. (wikipedia.org)
  • These data included conserved RNA secondary structures often found in the untranslated regions (UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. (wikipedia.org)
  • Genetic
  • On the other hand, the advanced search tool enables a user to search genetic information by categories, custom query, wild-card search and field-specific search, which uses the gene name, the description, the cluster of orthologous groups (COGs) id, the GO term, the KEGG enzyme commission (EC) number, etc. as key words. (wikipedia.org)
  • Genetic modification involves the mutation, insertion, or deletion of genes. (wikipedia.org)
  • Yet, T-even phages are in fact among the largest and highest complexity virus, in which these phages genetic information is made up of around 160 genes. (wikipedia.org)
  • found
  • GLIMMER algorithm found 1680 genes out of 1717 annotated genes in Haemophilus influenzae where fifth order Markov model found 1574 genes. (wikipedia.org)
  • GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order Markov model found 104 genes. (wikipedia.org)
  • These data included conserved RNA secondary structures often found in the untranslated regions (UTRs) of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers. (wikipedia.org)
  • order
  • Bacterial DNA has a gene density on the order of 500-1000 genes/Mb. (wikipedia.org)
  • In order for the T-even phage to infect its host and begin its life cycle it must enter the first process of infection, adsorption of the phage to the bacterial cell. (wikipedia.org)
  • There was a comparison made between interpolated Markov model used by GLIMMER and fifth order Markov model in the paper Microbial gene identification using interpolated Markov models. (wikipedia.org)
  • helps
  • Reverse scanning helps in identifying the coding portion of the gene more accurately which is contained in the context window of IMM. (wikipedia.org)
  • responsible
  • The parasite Trypanosoma brucei, responsible for causing African sleeping sickness is being identified by GLIMMER 2.0" Third version of GLIMMER, "GLIMMER 3.0" was released in 2007 and it was published in the paper Identifying bacterial genes and endosymbiont DNA with Glimmer. (wikipedia.org)
  • identification
  • GLIMMER 1.0" was released in 1998 and it was published in the paper Microbial gene identification using interpolated Markov model. (wikipedia.org)