Genomics and computational molecular biology.


:There has been a dramatic increase in the number of completely sequenced bacterial genomes during the past two years as a result of the efforts both of public genome agencies and the pharmaceutical industry. The availability of completely sequenced genomes permits more systematic analyses of genes, evolution and genome function than was otherwise possible. Using computational methods - which are used to identify genes and their functions including statistics, sequence similarity, motifs, profiles, protein folds and probabilistic models - it is possible to develop characteristic genome signatures, assign functions to genes, identify pathogenic genes, identify metabolic pathways, develop diagnostic probes and discover potential drug-binding sites. All of these directions are critical to understanding bacterial growth, pathogenicity and host-pathogen interactions.


Curr Opin Microbiol


Brutlag DL




Has Abstract


1998-06-01 00:00:00














  • When protons attack: microbial strategies of acid adaptation.

    abstract::Inducible tolerance to acidic and alkaline environments is recognized as an important survival strategy for many prokaryotic and eukaryotic microorganisms. Recent developments in understanding this phenomenon include the identification of regulatory genes, specific tolerance mechanisms and genes associated with tolera...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Foster JW

    更新日期:1999-04-01 00:00:00

  • Inter-kingdom signaling: chemical language between bacteria and host.

    abstract::Chemical communication between cells ensures coordination of behavior. In prokaryotes, this chemical communication is usually referred to as quorum sensing, while eukaryotic cells signal through hormones. In the past years, a growing number of reports have shown that bacterial quorum sensing signals, called autoinduce...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Pacheco AR,Sperandio V

    更新日期:2009-04-01 00:00:00

  • Eco-Aging: stem cells and microbes are controlled by aging antagonist FoxO.

    abstract::The review highlights the dual role that the conserved master regulator FoxO has in aging by coordinating both stem cell proliferation and antimicrobial peptides, effector molecules of the innate immune system. As observed in non-senescent Hydra, continuously high activity of the transcription factor FoxO contributes ...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Mortzfeld BM,Bosch TC

    更新日期:2017-08-01 00:00:00

  • Genomics of clostridial pathogens: implication of extrachromosomal elements in pathogenicity.

    abstract::The recently decoded genomes of the major clostridial toxin-producing pathogens Clostridium perfringens, Clostridium tetani, Clostridium botulinum and Clostridium difficile have provided a huge amount of new sequence data. Recent studies have focused on the identification and investigation of pathogenic determinants a...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Brüggemann H

    更新日期:2005-10-01 00:00:00

  • Chemotaxis and cell differentiation in Dictyostelium.

    abstract::Dictyostelium genome sequencing predicts an unexpectedly large number of genes. Many are absent from yeast but present in animals and presumably support cellular abilities not found in yeast. Prominent amongst these abilities is chemotaxis, where great strides are being made in understanding how cells orient in a grad...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Kay RR

    更新日期:2002-12-01 00:00:00

  • Modulation of natural killer cell activity by viruses.

    abstract::Since their discovery, our understanding of NK cells has evolved from branding them marginal innate immunity cells to key players in anti-viral and anti-tumor immunity. Importance of NK cells in control of various viral infections is perhaps best illustrated by the existence of plethora of viral mechanisms aimed to mo...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Lisnić VJ,Krmpotić A,Jonjić S

    更新日期:2010-08-01 00:00:00

  • Taking the pseudo out of pseudogenes.

    abstract::Pseudogenes are defined as fragments of once-functional genes that have been silenced by one or more nonsense, frameshift or missense mutations. Despite continuing increases in the speed of sequencing and annotating bacterial genomes, the identification and categorisation of pseudogenes remains problematic. Even when ...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Goodhead I,Darby AC

    更新日期:2015-02-01 00:00:00

  • Epichloë endophytes: fungal symbionts of grasses.

    abstract::Recent developments have increased our understanding of the evolution of mutualistic associations between Epichloë endophytes and their grass hosts. Most of the asexual species appear to be interspecific hybrids. Although endophytes form compatible associations with their natural hosts, transfers to other hosts elicit...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Scott B

    更新日期:2001-08-01 00:00:00

  • Two-component signal transduction as potential drug targets in pathogenic bacteria.

    abstract::Gene clusters contributing to processes such as cell growth and pathogenicity are often controlled by two-component signal transduction systems (TCSs). Specific inhibitors against TCS systems work differently from conventional antibiotics, and developing them into new drugs that are effective against various drug-resi...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Gotoh Y,Eguchi Y,Watanabe T,Okamoto S,Doi A,Utsumi R

    更新日期:2010-04-01 00:00:00

  • Microbial diversity of hypersaline environments: a metagenomic approach.

    abstract::Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadra...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Ventosa A,de la Haba RR,Sánchez-Porro C,Papke RT

    更新日期:2015-06-01 00:00:00

  • The mystery of aging and rejuvenation - a budding topic.

    abstract::In the process of yeast budding, an aged and deteriorated mother cell gives rise to a youthful and pristine daughter cell. This remarkable event offers a tractable model system for identifying factors affecting life expectancy and it has been established that multiple aging factors operate in parallel. Herein, we will...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Nyström T,Liu B

    更新日期:2014-04-01 00:00:00

  • Toxins from anaerobic bacteria: specificity and molecular mechanisms of action.

    abstract::Major advances have been made in the past five years in the identification of cellular targets of toxins produced by anaerobic bacteria. These targets include the vesicular membrane docking and fusion apparatus, the actin cytoskeleton, the signal transduction machinery and the cell membrane. The recent discovery that ...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Boquet P,Munro P,Fiorentini C,Just I

    更新日期:1998-02-01 00:00:00

  • Single-cell reporters for pathogen responses to antimicrobial host attacks.

    abstract::Host-pathogen interactions are often heterogeneous involving individual encounters between host and pathogen cells with diverse molecular mechanisms, response networks, and diverging outcomes. Single-cell reporters can identify the various types of interactions and participating pathogen subsets, help to unravel under...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Roche B,Bumann D

    更新日期:2021-02-01 00:00:00

  • Spirochetal motility and chemotaxis in the natural enzootic cycle and development of Lyme disease.

    abstract::Two-thirds of all bacterial genomes sequenced to-date possess an organelle for locomotion, referred to as flagella, periplasmic flagella or type IV pili. These genomes may also contain a chemotaxis-signaling system which governs flagellar rotation, thus leading a coordinated function for motility. Motility and chemota...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Motaleb MA,Liu J,Wooten RM

    更新日期:2015-12-01 00:00:00

  • Cell division is dispensable but not irrelevant in Streptomyces.

    abstract::In part, members of the genus Streptomyces have been studied because they produce many important secondary metabolites with antibiotic activity and for the interest in their relatively elaborate life cycle. These sporulating filamentous bacteria are remarkably synchronous for division and genome segregation in special...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: McCormick JR

    更新日期:2009-12-01 00:00:00

  • Two's company: studying interspecies relationships with dual RNA-seq.

    abstract::Organisms do not exist isolated from each other, but constantly interact. Cells can sense the presence of interaction partners by a range of receptors and, via complex regulatory networks, specifically react by changing the expression of many of their genes. Technological advances in next-generation sequencing over th...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Wolf T,Kämmer P,Brunke S,Linde J

    更新日期:2018-04-01 00:00:00

  • Bioengineering novel in vitro metabolic pathways using synthetic biology.

    abstract::Huge numbers of enzymes have evolved in nature to function in aqueous environments at moderate temperatures and neutral pH. This gives us, in principle, the unique opportunity to construct multistep reaction systems of considerable catalytic complexity in vitro. However, this opportunity is rarely exploited beyond res...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Meyer A,Pellaux R,Panke S

    更新日期:2007-06-01 00:00:00

  • Roles of adaptor proteins in regulation of bacterial proteolysis.

    abstract::Elimination of non-functional or unwanted proteins is critical for cell growth and regulation. In bacteria, ATP-dependent proteases target cytoplasmic proteins for degradation, contributing to both protein quality control and regulation of specific proteins, thus playing roles parallel to that of the proteasome in euk...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Battesti A,Gottesman S

    更新日期:2013-04-01 00:00:00

  • Quantitative bacterial transcriptomics with RNA-seq.

    abstract::RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features (promoters...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Creecy JP,Conway T

    更新日期:2015-02-01 00:00:00

  • Bacterial chemotaxis to pollutants and plant-derived aromatic molecules.

    abstract::There is accumulating evidence that motile bacteria are chemotactically attracted to environmental pollutants that they can degrade. Chemotaxis, the ability of motile bacteria to detect and respond to specific chemicals in the environment, can increase an organism's chances of locating useful sources of carbon, nitrog...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Parales RE,Harwood CS

    更新日期:2002-06-01 00:00:00

  • Emerging views on integrin signaling via Rac1 during invasin-promoted bacterial uptake.

    abstract::Enteropathogenic Yersinia species encode invasin, which promotes uptake into host cells by binding beta1 integrins. Invasin may cluster integrin heterodimers extracellularly and cause the integrin alpha and beta chains to splay apart in the cytoplasm. Cdc42 signaling is not essential for Yersinia uptake, whereas invas...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Wong KW,Isberg RR

    更新日期:2005-02-01 00:00:00

  • Bioprospecting in the developing world.

    abstract::During the past ten years, species-rich nations in the developing world have sought to capitalize on their 'biological patrimony' through a variety of business relationships with multinational corporations as a means of underwriting their conservation efforts. Initially lauded, these relationships have generated more ...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Garrity GM,Hunter-Cevera J

    更新日期:1999-06-01 00:00:00

  • Control of transcription by nucleoid proteins.

    abstract::Nucleoid proteins are a group of abundant DNA binding proteins that modulate the structure of the bacterial chromosome. They have been recruited as specific negative and positive regulators of gene transcription and their fluctuating patterns of expression are often exploited to impart an additional level of control w...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章


    authors: McLeod SM,Johnson RC

    更新日期:2001-04-01 00:00:00

  • Collaborative signaling by bacterial chemoreceptors.

    abstract::Motile bacteria seek optimal living habitats by following gradients of attractant and repellent chemicals in their environment. The signaling machinery for these chemotactic behaviors, although assembled from just a few protein components, has extraordinary information-processing capabilities. Escherichia coli, the be...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Parkinson JS,Ames P,Studdert CA

    更新日期:2005-04-01 00:00:00

  • Sustained sensing as an emerging principle in second messenger signaling systems.

    abstract::Bacteria utilize a diverse set of nucleotide second messengers to regulate cellular responses by binding macromolecular receptors (RNAs and proteins). Recent studies on cyclic di-GMP (c-di-GMP) have shown that this signaling molecule binds multiple receptors to regulate different steps in the same biological process. ...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Orr MW,Galperin MY,Lee VT

    更新日期:2016-12-01 00:00:00

  • Molecular basis of pathogenicity in Blastomyces dermatitidis: the importance of adhesion.

    abstract::An understanding of the molecular bases of pathogenicity in Blastomyces dermatitidis and related systemic dimorphic fungi has been limited until recent years. Yeast cells of B. dermatitidis display an adhesion promoting protein termed WI-1. Recent studies entailing homologous gene targeting and mutation of WI-1 have p...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Klein BS

    更新日期:2000-08-01 00:00:00

  • Genomic analysis using conditional phenotypes generated by antisense RNA.

    abstract::Antisense technology has been widely used to regulate gene expression. A tetracycline (tet)-regulated antisense-RNA-expressing system has been developed and used to downregulate chromosomally derived genes expressed in Staphylococcus aureus. This downregulation subsequently provides an evaluation of the virulence fact...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Yin D,Ji Y

    更新日期:2002-06-01 00:00:00

  • Flexible genomic islands as drivers of genome evolution.

    abstract::Natural prokaryotic populations are composed of multiple clonal lineages that are different in their core genomes in a range that varies typically between 95 and 100% nucleotide identity. Each clonal lineage also carries a complement of not shared flexible genes that can be very large. The compounded flexible genome p...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Rodriguez-Valera F,Martin-Cuadrado AB,López-Pérez M

    更新日期:2016-06-01 00:00:00

  • Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids.

    abstract::Kinetoplastea such as trypanosomatid parasites contain specialized peroxisomes that uniquely contain enzymes of the glycolytic pathway and other parts of intermediary metabolism and hence are called glycosomes. Their specific enzyme content can vary strongly, quantitatively and qualitatively, between different species...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Szöör B,Haanstra JR,Gualdrón-López M,Michels PA

    更新日期:2014-12-01 00:00:00

  • Gene expression in Kinetoplastids.

    abstract::Kinetoplastid parasites adapt to different environments with wide-reaching control of gene expression, but transcription of nuclear protein-coding genes is polycistronic: there is no individual control of transcription initiation. Mature mRNAs are made by co-transcriptional trans splicing and polyadenylation, and comp...

    journal_title:Current opinion in microbiology

    pub_type: 杂志文章,评审


    authors: Clayton CE

    更新日期:2016-08-01 00:00:00