Abstract：
:The identification and quantification of the proteins that a whole organism expresses under certain conditions is a main focus of high-throughput proteomics. Advanced proteomics approaches generate new biologically relevant data and potent hypotheses. A practical report of what proteome studies can and cannot accomplish in common laboratory settings is presented here. The review discusses the most popular tandem mass-spectrometry-based methods and focuses on how to produce reliable results. A step-by-step description of proteome experiments is given, including sample preparation, digestion, labeling, liquid chromatography, data processing, database searching and statistical analysis. The difficulties and bottlenecks of proteome analysis are addressed and the requirements for further improvements are discussed. Several diverse high-throughput proteomics-based studies of microorganisms are described.
journal_name
Trends Microbioljournal_title
Trends in microbiologyauthors
Kolker E,Higdon R,Hogan JMdoi
10.1016/j.tim.2006.03.005subject
Has Abstractpub_date
2006-05-01 00:00:00pages
229-35issue
5eissn
0966-842Xissn
1878-4380pii
S0966-842X(06)00076-Xjournal_volume
14pub_type
杂志文章,评审abstract：:The evolution of virulence in Salmonella is driven by horizontal gene transfer. This has given rise to highly flexible pathogens that are able to colonize new niches and extend their host range. Tracing the record of horizontal gene transfer can provide clues to the virulence factors that contribute to the formation o...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S0966-842X(97)01082-2
更新日期：1997-08-01 00:00:00
abstract：:Bacterial motility relies chiefly on the rotation of a molecular propeller, the flagellar filament, which is constructed from the protein flagellin. Here, flagellin sequence conservation and diversity is examined in the light of the recently determined flagellar filament structure. As expected, the surface-exposed dom...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2006.02.008
更新日期：2006-04-01 00:00:00
abstract：:The existence of peptidoglycan (PG) in chlamydiae has long been debated. Genome sequencing of members of the Chlamydiaceae family and Protochlamydia amoebophila has uncovered a nearly complete pathway for PG synthesis in these organisms. The recent use of microarray and proteomic analysis methods has revealed that PG ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2005.12.004
更新日期：2006-02-01 00:00:00
abstract：:To enhance infection, enveloped viruses exploit adhesion molecules expressed on the surface of host cells. Specifically, phosphatidylserine (PS) receptors - including members of the human T cell immunoglobulin and mucin domain (TIM)-family - have gained attention for their ability to mediate the entry of many envelope...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2019.10.004
更新日期：2020-03-01 00:00:00
abstract：:Cancer progression begins when malignant cells colonize adjacent sites, and it is characterized by increasing tumor heterogeneity, invasion and dissemination of cancer cells. Clinically, progression is the most relevant stage in the natural history of cancers. A given virus is usually regarded as oncogenic because of ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2016.03.008
更新日期：2016-08-01 00:00:00
abstract：:Pathogenic Yersinia express a complex array of iron-regulated functions and possess mechanisms for inorganic iron and hemin acquisition. These include a unique temperature-regulated hemin storage system, high-affinity transport processes for hemin and inorganic iron, and an iron-responsive regulatory system controllin...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/0966-842x(93)90129-f
更新日期：1993-07-01 00:00:00
abstract：:The Archaea include microorganisms growing in some of the most extreme environments on earth. Consequently, their cellular components are remarkably stable entities and have considerable potential in the biotechnology industry. Here, we review the structure of archaeal enzymes in the context of their ability to functi...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s0966-842x(98)01316-x
更新日期：1998-08-01 00:00:00
abstract：:A holistic approach to understanding the mechanisms by which stress influences the pathogenesis of infectious disease has resulted in the development of the field of microbial endocrinology. This transdisciplinary field represents the intersection of microbiology with mammalian endocrinology and neurophysiology, and i...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2007.11.005
更新日期：2008-02-01 00:00:00
abstract：:Transcriptional regulation enables adaptation in bacteria. Typically, only a few transcriptional events are well understood, leaving many others unidentified. The recent genome-wide identification of transcription factor binding sites in Mycobacterium tuberculosis has changed this by deciphering a molecular road-map o...
journal_title：Trends in microbiology
pub_type： 评论,杂志文章
doi：10.1016/j.tim.2015.02.002
更新日期：2015-03-01 00:00:00
abstract：:Insect endogenous retroviruses (IERVs) are present in the genome of several species. Previous studies have shown a relationship between the envelope glycoproteins (Envs) and fusion proteins (FPs) of several baculoviruses. We used this sequence similarity to predict fusion domains in the Envs of IERVs. We suggest that ...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/s0966-842x(03)00119-7
更新日期：2003-06-01 00:00:00
abstract：:The term 'type III secretion' has seen widespread use. However, problems persist in nomenclature. We propose that the standard abbreviation for this kind of secretion should be 'T3S' and that 'type III secretion system' should be abbreviated to 'T3SS'. There is also a need for a new terminology to distinguish flagella...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2006.02.009
更新日期：2006-04-01 00:00:00
abstract：:Cryptococcosis remains a significant cause of morbidity and mortality world-wide, particularly among AIDS patients. Yet, to date, there are no licensed vaccines clinically available to treat or prevent cryptococcosis. In this review, we provide a rationale to support continued investment in Cryptococcus vaccine resear...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2017.10.002
更新日期：2018-05-01 00:00:00
abstract：:The role of Bacillus anthracis virulence factors in its pathogenesis has been subjected to intense investigation with the aim of finding novel preventive and therapeutic protocols. Toxins that are endocytosed and act in the cytosol of host cells have a central role in B. anthracis infection. Understanding of anthrax t...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2007.10.003
更新日期：2007-11-01 00:00:00
abstract：:Fungal growth, development and pathogenicity require hyphal tip growth, which is supported by polar exocytosis at the expanding growth region. It is assumed that molecular motors transport growth supplies along the fibrous elements of the cytoskeleton, such as microtubules, to the hyphal apex. Recent advances in live-...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2006.11.007
更新日期：2007-01-01 00:00:00
abstract：:Evolution, climate change, and vaccination: in these cases and more, scientists, policymakers, and educators are confronted by organized campaigns to spread doubt, denial, and rejection of the scientific community's consensus on central scientific principles. To overcome these threats, scientists not only need to spre...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2012.10.002
更新日期：2012-12-01 00:00:00
abstract：:No curative drug against HIV has yet been found, despite enormous efforts aimed at reverse transcriptase and a variety of other targets. The long terminal repeat (LTR) of HIV-1 has recently become a promising site for antiviral action. This article briefly summarizes information on the nature of this target and potent...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/0966-842x(94)90666-1
更新日期：1994-05-01 00:00:00
abstract：:A recent paper by Castilla et al. reported the detection of prions in the blood of scrapie-infected hamsters using a biochemical amplification method that is conceptually analogous to the polymerase chain reaction. This technological advance raises the possibility that prion diseases in humans and livestock could soon...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2006.02.001
更新日期：2006-04-01 00:00:00
abstract：:Rolling circle DNA replication is inherently continuous and unregulated. This 'go-for-broke' strategy works well for lytic phages but is suicidal for plasmids that must coexist with their host. Plasmids have consequently evolved elaborate copy number control systems that operate at the transcriptional, translational a...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S0966-842X(97)01143-8
更新日期：1997-11-01 00:00:00
abstract：:DNA damage that blocks the transcription of genes is prioritized for repair by transcription-coupled DNA repair pathways. RNA polymerases stalled at DNA lesions obstruct repair enzymes, but this situation is turned to the advantage of the cell by transcription-repair coupling factors that remove the stalled RNA polyme...
journal_title：Trends in microbiology
pub_type： 杂志文章
doi：10.1016/j.tim.2007.05.005
更新日期：2007-07-01 00:00:00
abstract：:The rumen of sheep and cattle represents a mobile, self-sustaining fermentation system for plant material. Analysis of the rumen flora continues to provide fundamental knowledge of anaerobic microbiology and is now yielding microbial genes that have potential in biotechnology. Recent research has provided fascinating ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S0966-842X(97)01159-1
更新日期：1997-12-01 00:00:00
abstract：:Genome analyses of double strand DNA tailed bacteriophages argue that they evolve by recombinational reassortment of genes and by the acquisition of novel genes as simple genetic elements termed morons. These processes suggest a model for early virus evolution, wherein viruses can be regarded less as having derived fr...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/s0966-842x(00)01863-1
更新日期：2000-11-01 00:00:00
abstract：:Over the past two decades infections due to antibiotic-resistant bacteria have escalated world-wide, affecting patient morbidity, mortality, and health care costs. Among these bacteria, Enterococcus faecium and Enterococcus faecalis represent opportunistic nosocomial pathogens that cause difficult-to-treat infections ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2017.01.004
更新日期：2017-06-01 00:00:00
abstract：:Strictly lytic phages have been consensually preferred for phage therapy purposes. In contrast, temperate phages have been avoided due to an inherent capacity to mediate transfer of genes between bacteria by specialized transduction - an event that may increase bacterial virulence, for example, by promoting antibiotic...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2018.10.008
更新日期：2019-04-01 00:00:00
abstract：:Recently, a new group of multicellular microorganisms was discovered, called 'cable bacteria', which are capable of generating and mediating electrical currents across centimetre-scale distances. By transporting electrons from cell to cell, cable bacteria can harvest electron donors and electron acceptors that are wid...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2017.10.011
更新日期：2018-05-01 00:00:00
abstract：:Bacteria must segregate their DNA and position a septum to grow and divide. In many bacteria, MinD is involved in spatial regulation of the cytokinetic Z ring, and ParAs are involved in chromosome and plasmid segregation. The use of the MinD/ParA family to provide positional information for spatial organization contin...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2012.05.002
更新日期：2012-09-01 00:00:00
abstract：:Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patte...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2019.04.005
更新日期：2019-09-01 00:00:00
abstract：:Activation of innate immune signaling pathways through cytosolic RIG-I-like receptors (RLR) is a crucial response that is antagonized by many viruses. A variety of RNA-related pathogen-associated molecular patterns (PAMPS) have been identified and their role in RLR activation has been examined. Recent studies suggest ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2011.12.005
更新日期：2012-03-01 00:00:00
abstract：:Many reports have documented that Staphylococcus aureus can invade host cells and persist intracellularly for various periods of time in cell culture models. However, it is not clear whether intracellular persistence of S. aureus also occurs in the course of infections in whole organisms. This is a subject of intense ...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2008.11.005
更新日期：2009-02-01 00:00:00
abstract：:Recent American successes against poliomyelitis and measles have been attributed to repeated 'pulse' vaccination campaigns. Whilst logistic and economic constraints will be crucial, a deeper epidemiological understanding of the mechanism, strengths and weaknesses of pulse vaccination will optimize the chances of succe...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/S0966-842X(97)81769-6
更新日期：1997-01-01 00:00:00
abstract：:Most cases of candidiasis have been attributed to Candida albicans, but Candida glabrata, Candida parapsilosis and Candida tropicalis, designated as non-C. albicans Candida (NCAC), have been identified as frequent human pathogens. Moreover, Candida biofilms are an escalating clinical problem associated with significan...
journal_title：Trends in microbiology
pub_type： 杂志文章,评审
doi：10.1016/j.tim.2016.09.004
更新日期：2017-01-01 00:00:00
