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, terminators, operons, among others) to be pinpointed on any bacterial transcriptome. Once the transcriptome is mapped, the activity of transcriptional features can be quantified. Here we highlight how quantitative transcriptome analysis can reveal biological insights and briefly discuss some of the challenges to be faced by the field of bacterial transcriptomics in the near future.
journal_name
Curr Opin Microbioljournal_title
Current opinion in microbiologyauthors
Creecy JP,Conway Tdoi
10.1016/j.mib.2014.11.011subject
Has Abstractpub_date
2015-02-01 00:00:00pages
133-40eissn
1369-5274issn
1879-0364pii
S1369-5274(14)00178-7journal_volume
23pub_type
杂志文章,评审abstract：:Macrophages protect their host by engulfing foreign bodies within phagosomes that rapidly develop into microbicidal organelles. Numerous pathogens, such as species of Toxoplasma, Leishmania, Mycobacterium, Salmonella and Legionella, thrive in human macrophages, sometimes with disastrous effects. Defining the survival ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(02)00286-2
更新日期：2002-02-01 00:00:00
abstract：:Single microbial cells can now be sequenced using DNA amplified by the Multiple Displacement Amplification (MDA) reaction. The few femtograms of DNA in a bacterium are amplified into micrograms of high molecular weight DNA suitable for DNA library construction and Sanger sequencing. The MDA-generated DNA also performs...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2011.12.002
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abstract：:Environmental pathogenic fungi present a paradox in that they are virulent in animals without requiring animal hosts for replication or survival, a phenomenon we call 'ready-made' virulence. In the human pathogenic fungus Cryptococcus neoformans, the capacity for virulence in animals may originate from environmental s...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(03)00082-1
更新日期：2003-08-01 00:00:00
abstract：:All organisms must secure essential trace nutrients, including iron, zinc, manganese and copper for survival and proliferation. However, these very nutrients are also highly toxic if present at elevated levels. Mammalian immunity has harnessed both the essentiality and toxicity of micronutrients to defend against micr...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2016.05.013
更新日期：2016-08-01 00:00:00
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
doi：10.1016/j.mib.2004.12.009
更新日期：2005-02-01 00:00:00
abstract：:Appreciation for the prevalence and diversity of noncoding, small RNAs (sRNAs) has grown enormously in the past decade. A major role for sRNAs in all organisms is to regulate gene expression, often at the level of mRNA translation or stability. However, a few sRNAs have been shown to function by regulating transcripti...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2007.03.008
更新日期：2007-04-01 00:00:00
abstract：:Some RNA virus genomes bear 5'-triphosphates, which can be recognized in the cytoplasm of infected cells by host proteins that mediate anti-viral immunity. Both the innate sensor RIG-I and the interferon-induced IFIT proteins bind to 5'-triphosphate viral RNAs. RIG-I signals for induction of interferons during RNA vir...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.04.009
更新日期：2013-08-01 00:00:00
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2004.08.011
更新日期：2004-10-01 00:00:00
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2009.12.008
更新日期：2010-02-01 00:00:00
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2014.02.003
更新日期：2014-04-01 00:00:00
abstract：:For many Gram-negative bacteria, like Brucella, the type IV secretion system (T4SS) has a critical role in bacterial virulence. In Brucella, the VirB T4SS permits the injection of bacterial effectors inside host cells, leading to subversion of signaling pathways and favoring bacterial growth and pathogenesis. The virB...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2012.11.005
更新日期：2013-02-01 00:00:00
abstract：:The opportunistic fungal pathogen Aspergillus fumigatus adapts to iron limitation by upregulation of iron uptake mechanisms including siderophore biosynthesis and downregulation of iron-consuming pathways to spare iron. These metabolic changes depend mainly on the transcription factor HapX. Consistent with the crucial...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2011.06.002
更新日期：2011-08-01 00:00:00
abstract：:Molecular phylogenetic studies reveal that many endosymbioses between bacteria and invertebrate hosts result from ancient infections followed by strict vertical transmission within host lineages. Endosymbionts display a distinctive constellation of genetic properties including AT-biased base composition, accelerated s...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(00)00088-6
更新日期：2000-06-01 00:00:00
abstract：:Leishmania parasites are able to delay the onset of cell-mediated immunity by selectively impairing the ability of infected macrophages to produce interleukin (IL)-12. Leishmania infection arrests the JAK/STAT-mediated signal transduction involved in activation of the IL-12 p40 promoter; the phosphorylation defects ma...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S1369-5274(99)80077-0
更新日期：1999-08-01 00:00:00
abstract：:The ability to control uptake across the mucosa and to protect the gut from harmful substances present in the lumen is defined as intestinal barrier function. Two routes are usually distinguished for transepithelial transport. The paracellular route allows the passage of ions and small molecules and is mainly regulate...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.12.003
更新日期：2014-02-01 00:00:00
abstract：:Gram-positive pathogens are a major cause of community-acquired and hospital-acquired infections, and exhibit a remarkable ability to develop antibiotic resistance. Methicillin-resistant Staphylococcus aureus (MRSA), glycopeptide-resistant enterococci (GRE) and multidrug-resistant pneumococci are currently the major r...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.08.006
更新日期：2010-10-01 00:00:00
abstract：:High throughput, deep sequencing assays are powerful tools for gaining insights into virus-host interactions. Sequencing assays can discover novel viruses and describe the genomes of novel and known viruses. Genomic information can predict viral proteins that can be characterized, describe important genes in the host ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.04.006
更新日期：2013-08-01 00:00:00
abstract：:Recent work has shown that Immunoglobulin-like (Ig-like) domains occur frequently on the surface of tailed dsDNA bacteriophages. Several of these Ig-like domains are added to bacteriophage structural proteins via programmed ribosomal frameshifts, and their evolutionary patterns suggest that they can be exchanged by ho...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2007.05.018
更新日期：2007-08-01 00:00:00
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journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.04.006
更新日期：2010-06-01 00:00:00
abstract：:Stan Falkow looked at the world with his eyes peering from the outer membrane of a gram-negative bacterium. It was a great vantage point from which to dream about the possible superpowers these organisms might have. He mused about these dreams with his trainees who sometimes found through rigorous scientific explorati...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2020.01.004
更新日期：2020-04-01 00:00:00
abstract：:Single cell genomics (SCG) uncovers hereditary information at the most basic level of biological organization. It is emerging as a powerful complement to cultivation-based and microbial community-focused research approaches. SCG has been instrumental in identifying metabolic features, evolutionary histories and inter-...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2012.09.001
更新日期：2012-10-01 00:00:00
abstract：:Selective autophagy is an important effector mechanism of cell autonomous immunity, in particular against invasive bacterial species. Anti-bacterial autophagy is activated by rupture of bacteria-containing vacuoles and exposure of bacteria to the cytosol. The autophagy cargo receptors p62, NDP52 and Optineurin detect ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2013.03.010
更新日期：2013-06-01 00:00:00
abstract：:Much of what we know about cytokinesis in bacteria has come from studies with Escherichia coli, and efforts to comprehensively understand this fundamental process in this organism continue to intensify. Major recent advances include in vitro assembly of a membrane-tethered version of FtsZ into contractile rings in lip...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2010.09.015
更新日期：2010-12-01 00:00:00
abstract：:Quorum sensing, or the control of gene expression in response to cell density, is used by both gram-negative and gram-positive bacteria to regulate a variety of physiological functions. In all cases, quorum sensing involves the production and detection of extracellular signalling molecules called autoinducers. While u...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s1369-5274(99)00025-9
更新日期：1999-12-01 00:00:00
abstract：:Proteomic studies are designed to yield either qualitative information on proteins (identification, distribution, posttranslational modifications, interactions, structure and function) or quantitative information (abundance, distribution within different localizations, temporal changes in abundance due to synthesis an...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2012.02.005
更新日期：2012-06-01 00:00:00
abstract：:Barring bioavailability and nutritional limitations, virtually all organic anthropogenic chemicals can be naturally biodegraded. It is to this phenomenon we owe thanks to the long established 'tritrophic trinity' of microbe-plant-insect interactions. Over hundreds of millennia these organisms have coevolved, producing...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2004.04.007
更新日期：2004-06-01 00:00:00
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
doi：10.1016/S1369-5274(99)80030-7
更新日期：1999-04-01 00:00:00
abstract：:The family Arenaviridae consists of a unique genus (Arenavirus) that currently comprises 22 viral species, as recognized by the International Committee for Taxonomy of Viruses. Seven newly discovered represent putative new species. Here, our aims were to provide the most comprehensive phylogenetic analysis of members ...
journal_title：Current opinion in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.mib.2008.06.001
更新日期：2008-08-01 00:00:00
