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MICROBIOLOGY (208 journals)                  1 2 3     

Acta Microbiologica et Immunologica Hungarica     Full-text available via subscription   (Followers: 6)
Addiction Genetics     Open Access   (Followers: 3)
Advances in Applied Microbiology     Full-text available via subscription   (Followers: 12)
Advances in Microbiology     Open Access   (Followers: 13)
Advances in Molecular Imaging     Open Access   (Followers: 3)
African Journal of Clinical and Experimental Microbiology     Open Access   (Followers: 1)
African Journal of Microbiology Research     Open Access   (Followers: 1)
American Journal of Infectious Diseases and Microbiology     Open Access   (Followers: 10)
American Journal of Microbiological Research     Open Access  
American Journal of Microbiology     Open Access   (Followers: 13)
American Journal of Molecular Biology     Open Access   (Followers: 3)
American Journal of Stem Cell Research     Open Access   (Followers: 1)
Annals of Clinical Microbiology and Antimicrobials     Open Access   (Followers: 4)
Annals of Microbiology     Hybrid Journal   (Followers: 6)
Annual Review of Microbiology     Full-text available via subscription   (Followers: 21)
Antimicrobial Agents and Chemotherapy     Full-text available via subscription   (Followers: 11)
Applied and Environmental Microbiology     Full-text available via subscription   (Followers: 22)
Applied Biochemistry and Microbiology     Hybrid Journal   (Followers: 7)
Applied Microbiology and Biotechnology     Hybrid Journal   (Followers: 21)
Archives of Microbiology     Hybrid Journal   (Followers: 3)
Beneficial Microbes     Full-text available via subscription   (Followers: 2)
Bio-Research     Full-text available via subscription  
BioArchitecture     Full-text available via subscription  
Biocell     Open Access   (Followers: 1)
Biomaterials Science     Full-text available via subscription   (Followers: 3)
Biomedical Research     Open Access   (Followers: 3)
BioMolecular Concepts     Full-text available via subscription   (Followers: 2)
Biomolecules     Open Access   (Followers: 1)
BMC Microbiology     Open Access   (Followers: 5)
Brazilian Journal of Microbiology     Open Access   (Followers: 2)
Canadian Journal of Infectious Diseases & Medical Microbiology     Hybrid Journal   (Followers: 1)
Canadian Journal of Microbiology     Full-text available via subscription   (Followers: 3)
Cell Biology : Research & Therapy     Partially Free  
Cell Host & Microbe     Full-text available via subscription   (Followers: 5)
Cell Medicine     Open Access  
Cell Regeneration     Open Access  
Cell Stem Cell     Full-text available via subscription   (Followers: 15)
Cells     Open Access  
Cellular & Molecular Immunology     Hybrid Journal   (Followers: 8)
Cellular Microbiology     Hybrid Journal   (Followers: 4)
Cheese: Chemistry, Physics and Microbiology     Full-text available via subscription   (Followers: 2)
Chimerism     Full-text available via subscription  
Clinical Microbiology and Infection     Hybrid Journal   (Followers: 12)
Clinical Microbiology Newsletter     Hybrid Journal   (Followers: 2)
Clinical Microbiology Reviews     Full-text available via subscription   (Followers: 9)
Comparative Immunology, Microbiology and Infectious Diseases     Hybrid Journal   (Followers: 7)
Computational Molecular Bioscience     Open Access   (Followers: 1)
Continental Journal of Microbiology     Open Access   (Followers: 3)
Critical Reviews in Microbiology     Hybrid Journal   (Followers: 5)
Current Issues in Molecular Biology     Open Access  
Current Microbiology     Hybrid Journal   (Followers: 4)
Current Molecular Imaging     Hybrid Journal  
Current Opinion in Microbiology     Hybrid Journal   (Followers: 13)
Current Tissue Engineering     Hybrid Journal   (Followers: 1)
Current Topics in Microbiology and Immunology     Hybrid Journal   (Followers: 2)
Diagnostic Microbiology and Infectious Disease     Hybrid Journal   (Followers: 2)
Disease and Molecular Medicine     Open Access   (Followers: 1)
DNA Barcodes     Open Access  
Egyptian Journal of Biochemistry and Molecular Biology     Full-text available via subscription  
Emerging Microbes & Infections     Open Access   (Followers: 1)
Environmental Microbiology     Hybrid Journal   (Followers: 7)
Environmental Microbiology Reports     Hybrid Journal   (Followers: 3)
Enzyme and Microbial Technology     Hybrid Journal   (Followers: 5)
Epigenetics of Degenerative Diseases     Open Access  
European Journal of Clinical Microbiology & Infectious Diseases     Hybrid Journal   (Followers: 9)
European Journal of Microbiology and Immunology     Open Access   (Followers: 5)
Experimental and Molecular Pathology     Hybrid Journal  
Fems Immunology & Medical Microbiology     Hybrid Journal   (Followers: 6)
Fems Microbiology Ecology     Hybrid Journal   (Followers: 6)
Fems Microbiology Letters     Hybrid Journal   (Followers: 13)
Fems Microbiology Reviews     Hybrid Journal   (Followers: 15)
Folia Histochemica et Cytobiologica     Open Access  
Folia Microbiologica     Hybrid Journal   (Followers: 1)
Food Microbiology     Hybrid Journal   (Followers: 11)
Frontiers in Cell and Developmental Biology     Open Access   (Followers: 1)
Frontiers in Cellular and Infection Microbiology     Open Access   (Followers: 2)
Frontiers in Cellular Neuroscience     Open Access  
Frontiers in Microbiology     Open Access   (Followers: 4)
Frontiers in Molecular Neuroscience     Open Access  
Future Microbiology     Full-text available via subscription   (Followers: 1)
Future Virology     Full-text available via subscription   (Followers: 3)
Gene Expression     Full-text available via subscription  
Genetica si Biologie Moleculara     Open Access   (Followers: 1)
Genetics and Molecular Research     Open Access   (Followers: 2)
Geomicrobiology Journal     Hybrid Journal   (Followers: 1)
Gut Microbes     Full-text available via subscription   (Followers: 1)
Indian Journal of Microbiology     Hybrid Journal   (Followers: 1)
Indian Journal of Pathology and Microbiology     Open Access   (Followers: 1)
Infection Ecology & Epidemiology     Open Access   (Followers: 6)
International Arabic Journal of Antimicrobial Agents     Open Access   (Followers: 4)
International Journal of Antimicrobial Agents     Hybrid Journal  
International Journal of Bacteriology     Open Access  
International Journal of Bioassays     Open Access   (Followers: 5)
International Journal of Biotechnology and Molecular Biology Research     Open Access  
International Journal of Food Microbiology     Hybrid Journal   (Followers: 11)
International Journal of Infection and Microbiology     Open Access   (Followers: 1)
International Journal of Medical Microbiology     Hybrid Journal   (Followers: 4)
International Journal of Systematic and Evolutionary Microbiology     Full-text available via subscription   (Followers: 2)
International Microbiology     Open Access   (Followers: 2)
Invertebrate Immunity     Open Access  

        1 2 3     

Journal Cover Trends in Microbiology
   [11 followers]  Follow    
   Full-text available via subscription Subscription journal
     ISSN (Print) 0966-842X
     Published by Elsevier Homepage  [2563 journals]   [SJR: 3.65]   [H-I: 122]
  • Chlamydia genomics: providing novel insights into chlamydial biology
    • Abstract: Publication date: Available online 31 May 2014
      Source:Trends in Microbiology
      Author(s): Nathan L. Bachmann , Adam Polkinghorne , Peter Timms
      Chlamydiaceae are obligate intracellular pathogens that have successfully evolved to colonize a diverse range of hosts. There are currently 11 described species of Chlamydia, most of which have a significant impact on the health of humans or animals. Expanding chlamydial genome sequence information has revolutionized our understanding of chlamydial biology, including aspects of their unique lifecycle, host–pathogen interactions, and genetic differences between Chlamydia strains associated with different host and tissue tropisms. This review summarizes the major highlights of chlamydial genomics and reflects on the considerable impact these have had on understanding the biology of chlamydial pathogens and the changing nature of genomics tools in the ‘post-genomics’ era.

      PubDate: 2014-06-03T14:28:49Z
  • The role of matrix in HIV-1 envelope glycoprotein incorporation
    • Abstract: Publication date: Available online 2 June 2014
      Source:Trends in Microbiology
      Author(s): Philip R. Tedbury , Eric O. Freed
      Incorporation of the viral envelope (Env) glycoprotein is a critical requirement for the production of infectious HIV-1 particles. It has long been appreciated that the matrix (MA) domain of the Gag polyprotein and the cytoplasmic tail of Env are central players in the process of Env incorporation, but the precise mechanisms have been elusive. Several recent developments have thrown light on the contributions of both proteins, prompting a re-evaluation of the role of MA during Env incorporation. The two domains appear to play distinct but complementary roles, with the cytoplasmic tail of Env responsible for directing Env to the site of assembly and the matrix domain accommodating the cytoplasmic tail of Env in the Gag lattice.

      PubDate: 2014-06-03T14:28:49Z
  • Contents and Editorial Board
    • Abstract: Publication date: June 2014
      Source:Trends in Microbiology, Volume 22, Issue 6

      PubDate: 2014-06-03T14:28:49Z
  • DNA methylation in Caulobacter and other Alphaproteobacteria during cell
           cycle progression
    • Abstract: Publication date: Available online 1 June 2014
      Source:Trends in Microbiology
      Author(s): Saswat S. Mohapatra , Antonella Fioravanti , Emanuele G. Biondi
      In Caulobacter crescentus, methylation of DNA by CcrM plays an important part in the regulation of cell cycle progression. Thanks to this methyltransferase, the activity of which is cell cycle regulated, the chromosome transitions between a hemimethylated state in the S-phase to a fully methylated condition in the G1 and G2 phases. Any perturbation in CcrM expression, such as depletion or constitutive expression, causes severe developmental defects. Several studies suggest that the role of CcrM is conserved across the Alphaproteobacteria. In the past few years, the importance of methylation on the expression of cell cycle regulated genes has emerged, suggesting that CcrM-dependent methylation can direct the binding of transcription factors to specific methylated sequences and affect the expression of genes depending on the methylation state of their promoters. CcrM activity has recently been linked to GcrA, a cell cycle master regulator that controls the expression of several genes during S-phase. Here, we review recent findings that establish the global role of methylation in cell cycle progression, and also explore the significance of a CcrM–GcrA epigenetic module that has co-evolved in Alphaproteobacteria, including Caulobacter, in controlling several genes involved in cell division, polarity, and motility.

      PubDate: 2014-06-03T14:28:49Z
  • Biofilms, flagella, and mechanosensing of surfaces by bacteria
    • Abstract: Publication date: Available online 1 June 2014
      Source:Trends in Microbiology
      Author(s): Robert Belas
      Formation of a bacterial biofilm is a developmental process that begins when a cell attaches to a surface, but how does a bacterial cell know it is on or near a surface in the first place' The phase of this ‘swim-or-stick’ switch is determined by a sensory transduction mechanism referred to as surface sensing, which involves the rotating bacterial flagellum. This review explores six bacterial species as models of flagellar mechanosensing of surfaces to understand the current state of our knowledge and the challenges that lie ahead. A common link between these bacteria is a requirement for the proper function of the flagellar motor stators that channel ions into the cell to drive flagellar rotation. Conditions that affect ion flow act as a signal that, ultimately, controls the master transcriptional regulatory circuits controlling the flagellar hierarchy and biofilm formation.

      PubDate: 2014-06-03T14:28:49Z
  • Getting Wrinkly Spreaders to demonstrate evolution in schools
    • Abstract: Publication date: June 2014
      Source:Trends in Microbiology, Volume 22, Issue 6
      Author(s): Andrew J. Spiers
      Understanding evolution is crucial to modern biology, but most teachers would assume that practical demonstrations of evolution in school laboratories are unfeasible. However, perhaps they have not heard of ‘evolution in a test tube’ and how Wrinkly Spreaders can form the basis for both practical demonstrations of bacterial evolution and further work.

      PubDate: 2014-06-03T14:28:49Z
  • Putting together a scientific team: collaborative science
    • Abstract: Publication date: Available online 1 June 2014
      Source:Trends in Microbiology
      Author(s): L. Garry Adams
      One of the most enjoyable parts of a science career is collaborative team experiences and developing life-long social networks. When the hypothesis being tested requires innovative efforts greater than any single laboratory, collaboration becomes an essential component for success – everyone is a stakeholder and trust is the driving force.

      PubDate: 2014-06-03T14:28:49Z
  • Through the looking glass: witnessing host–virus interplay in
    • Abstract: Publication date: Available online 25 May 2014
      Source:Trends in Microbiology
      Author(s): Jean-Pierre Levraud , Nuno Palha , Christelle Langevin , Pierre Boudinot
      Host–pathogen interactions can be very complex at all scales; understanding organ- or organism-level events require in vivo approaches. Besides traditional host models such as mice, the zebrafish offers an attractive cocktail of optical accessibility and genetic tractability, blended with a vertebrate-type immunity, where innate responses can easily be separated from adaptive ones. Applied to viral infections, this model has revealed unexpected idiosyncrasies among organs, which we believe may apply to the human situation. We also argue that the dynamic analysis of virus spread and immune response in zebrafish make this model particularly well suited to the exploration of the concept of infection tolerance and resistance in relation to viral diseases.

      PubDate: 2014-05-27T10:19:13Z
  • Methylocella: a gourmand among methanotrophs
    • Abstract: Publication date: Available online 26 May 2014
      Source:Trends in Microbiology
      Author(s): Peter F. Dunfield , Svetlana N. Dedysh
      A recent article in Nature describes the ability of Methylocella silvestris to grow simultaneously on methane and longer chain alkanes, something never before observed in the microbial world. It adds to a growing list of unique metabolic traits that distinguish Methylocella from any other bacterium.

      PubDate: 2014-05-27T10:19:13Z
  • Reconstructing the evolutionary origins and phylogeography of hantaviruses
    • Abstract: Publication date: Available online 19 May 2014
      Source:Trends in Microbiology
      Author(s): Shannon N. Bennett , Se Hun Gu , Hae Ji Kang , Satoru Arai , Richard Yanagihara
      Rodents have long been recognized as the principal reservoirs of hantaviruses. However, with the discovery of genetically distinct and phylogenetically divergent lineages of hantaviruses in multiple species of shrews, moles, and insectivorous bats from widely separated geographic regions, a far more complex landscape of hantavirus host distribution, evolution, and phylogeography is emerging. Detailed phylogenetic analyses, based on partial and full-length genomes of previously described rodent-borne hantaviruses and newly detected non-rodent-borne hantaviruses, indicate an Asian origin and support the emerging concept that ancestral non-rodent mammals may have served as the hosts of primordial hantaviruses.

      PubDate: 2014-05-22T09:51:22Z
  • Fluoroquinolone resistan mechanisms, impact on bacteria, and role in
           evolutionary success
    • Abstract: Publication date: Available online 16 May 2014
      Source:Trends in Microbiology
      Author(s): Liam S. Redgrave , Sam B. Sutton , Mark A. Webber , Laura J.V. Piddock
      Quinolone and fluoroquinolone antibiotics are potent, broad-spectrum agents commonly used to treat a range of infections. Resistance to these agents is multifactorial and can be via one or a combination of target-site gene mutations, increased production of multidrug-resistance (MDR) efflux pumps, modifying enzymes, and/or target-protection proteins. Fluoroquinolone-resistant clinical isolates of bacteria have emerged readily and recent data have shown that resistance to this class of antibiotics can have diverse, species-dependent impacts on host-strain fitness. Here we outline the impacts of quinolone-resistance mutations in relation to the fitness and evolutionary success of mutant strains.

      PubDate: 2014-05-22T09:51:22Z
  • The target cell genus does not matter
    • Abstract: Publication date: Available online 14 May 2014
      Source:Trends in Microbiology
      Author(s): Sophie Bleves , Thibault G. Sana , Romé Voulhoux
      Two type VI secreted phospholipases D of Pseudomonas aeruginosa were identified as trans-kingdom virulence effectors, targeting both prokaryotic and eukaryotic host cells. Each of them triggers killing bacterial competitors and internalization into non-phagocytic cells. These type VI lipolytic enzymes are widely distributed among pathogens and may constitute a conserved strategy.

      PubDate: 2014-05-16T09:14:58Z
  • The gut microbiome, probiotics, bile acids axis, and human health
    • Abstract: Publication date: Available online 14 May 2014
      Source:Trends in Microbiology
      Author(s): Mitchell Lawrence Jones , Catherine Tomaro-Duchesneau , Satya Prakash
      The human gut microbiome produces potent ligands to bile acid receptors, and probiotics could act as therapeutics of bile acid dysmetabolism. A recent study in Cell Reports demonstrates that probiotic VSL#3 affects bile acid deconjugation and excretion, as well as the gut–liver FXR–FGF15 axis.

      PubDate: 2014-05-16T09:14:58Z
  • Clostridium difficile spore biology: sporulation, germination, and spore
           structural proteins
    • Abstract: Publication date: Available online 7 May 2014
      Source:Trends in Microbiology
      Author(s): Daniel Paredes-Sabja , Aimee Shen , Joseph A. Sorg
      Clostridium difficile is a Gram-positive, spore-forming obligate anaerobe and a major nosocomial pathogen of worldwide concern. Owing to its strict anaerobic requirements, the infectious and transmissible morphotype is the dormant spore. In susceptible patients, C. difficile spores germinate in the colon to form the vegetative cells that initiate Clostridium difficile infections (CDI). During CDI, C. difficile induces a sporulation pathway that produces more spores; these spores are responsible for the persistence of C. difficile in patients and horizontal transmission between hospitalized patients. Although important to the C. difficile lifecycle, the C. difficile spore proteome is poorly conserved when compared to members of the Bacillus genus. Further, recent studies have revealed significant differences between C. difficile and Bacillus subtilis at the level of sporulation, germination, and spore coat and exosporium morphogenesis. In this review, the regulation of the sporulation and germination pathways and the morphogenesis of the spore coat and exosporium will be discussed.

      PubDate: 2014-05-11T08:32:33Z
  • Diversity of diversity: conceptual and methodological differences in
           biodiversity estimates of eukaryotic microbes as compared to bacteria
    • Abstract: Publication date: Available online 8 May 2014
      Source:Trends in Microbiology
      Author(s): Jean-David Grattepanche , Luciana F. Santoferrara , George B. McManus , Laura A. Katz
      Recent advances such as high-throughput sequencing (HTS) have changed conceptions about the magnitude of diversity on Earth. This is especially true for microbial lineages, which have seen the discovery of great numbers of rare forms in places such as the human gut as well as diverse environments (e.g., freshwater, marine, and soil). Given the differences in perceptions of diversity for bacterial and eukaryotic microbes, including divergent species concepts, HTS tools used to eliminate errors and population-level variation in bacteria may not be appropriate for microbial eukaryotes and may eliminate valid species from the data. We discuss here how the nature of biodiversity varies among microbial groups and the extent to which HTS tools designed for bacteria are useful for eukaryotes.

      PubDate: 2014-05-11T08:32:33Z
  • Selective packaging of the influenza A genome and consequences for genetic
    • Abstract: Publication date: Available online 2 May 2014
      Source:Trends in Microbiology
      Author(s): Marie Gerber , Catherine Isel , Vincent Moules , Roland Marquet
      Influenza A viruses package their segmented RNA genome in a selective manner. Electron tomography, biochemical assays, and replication assays of viruses produced by reverse genetics recently unveiled molecular details of this mechanism, whereby different influenza viral strains form different and unique networks of direct intermolecular RNA–RNA interactions. Together with detailed views of the three-dimensional structure of the viral ribonucleoparticles, these recent advances help us understand the rules that govern genome packaging. They also have deep implications for the genetic reassortment processes, which are responsible for devastating pandemics.

      PubDate: 2014-05-06T08:04:37Z
  • Starting small: using microbiology to foster scientific literacy
    • Abstract: Publication date: Available online 5 May 2014
      Source:Trends in Microbiology
      Author(s): Amy F. Savage , Brooke A. Jude
      In order to achieve scientific literacy for all students, Bard College recently implemented Citizen Science, a common January course for all first-year students. Structured around the question ‘how do we reduce the global burden of disease'’, this course uses microbiological tools to develop an understanding of potential answers.

      PubDate: 2014-05-06T08:04:37Z
  • Contents and Editorial Board
    • Abstract: Publication date: May 2014
      Source:Trends in Microbiology, Volume 22, Issue 5

      PubDate: 2014-05-02T07:36:43Z
  • Virus discovery: are we scientists or genome collectors'
    • Abstract: Publication date: May 2014
      Source:Trends in Microbiology, Volume 22, Issue 5
      Author(s): Marta Canuti , Lia van der Hoek
      Some scientists now proclaim that future pandemics can be successfully forecasted, allowing the planning of useful intervention strategies for pandemic preparedness. We underline the fundamental importance of performing dedicated investigations when viruses are discovered, to guarantee public health authorities the availability of nonerroneous information about potential upcoming threats.

      PubDate: 2014-05-02T07:36:43Z
  • Chemosensory signaling systems that control bacterial survival
    • Abstract: Publication date: Available online 1 May 2014
      Source:Trends in Microbiology
      Author(s): Kuang He , Carl E. Bauer
      Recent studies have revealed that several Gram-negative species utilize variations of the well-known chemotaxis signaling cascade to switch lifestyles in order to survive environmental stress. The two survival strategies covered in this review are the development of dormant cyst cells and biofilm formation. Each of these structures involves exopolysaccharide-mediated cell–cell interactions, which result in multicellular communities that confer resistance to stress conditions such as desiccation and antibiotics. This review is centered on recent advances in the understanding of phosphate flow and novel output signals in chemosensory signaling pathways that are involved in cyst formation and biofilms.

      PubDate: 2014-05-02T07:36:43Z
  • Post-exposure therapy of filovirus infections
    • Abstract: Publication date: Available online 30 April 2014
      Source:Trends in Microbiology
      Author(s): Gary Wong , Xiangguo Qiu , Gene G. Olinger , Gary P. Kobinger
      Filovirus infections cause fatal hemorrhagic fever characterized by the initial onset of general symptoms before rapid progression to severe disease; the most virulent species can cause death to susceptible hosts within 10 days after the appearance of symptoms. Before the advent of monoclonal antibody (mAb) therapy, infection of nonhuman primates (NHPs) with the most virulent filovirus species was fatal if interventions were not administered within minutes. A novel nucleoside analogue, BCX4430, has since been shown to also demonstrate protective efficacy with a delayed treatment start. This review summarizes and evaluates the potential of current experimental candidates for treating filovirus disease with regard to their feasibility and use in the clinic, and assesses the most promising strategies towards the future development of a pan-filovirus medical countermeasure.

      PubDate: 2014-05-02T07:36:43Z
  • Bacterial persisters: formation, eradication, and experimental systems
    • Abstract: Publication date: Available online 23 April 2014
      Source:Trends in Microbiology
      Author(s): Sophie Helaine , Elisabeth Kugelberg
      Persisters are multidrug-tolerant bacteria that could account for the relapse of infections. For a long time, persisters have been assumed to be nonreplicating dormant bacteria, but the growth status of these recalcitrant cells is still debated. Toxin–antitoxin (TA) modules have an important role in the formation of persisters and several studies show that they can form in response to different triggers. These findings, together with the invention of new tools to study persisters, could have important implications for the development of novel therapeutics to eradicate persisting subpopulations.

      PubDate: 2014-04-27T11:06:30Z
  • PIP2: choreographer of actin-adaptor proteins in the HIV-1 dance
    • Abstract: Publication date: Available online 23 April 2014
      Source:Trends in Microbiology
      Author(s): Vera Rocha-Perugini , Mónica Gordon-Alonso , Francisco Sánchez-Madrid
      The actin cytoskeleton plays a key role during the replication cycle of human immunodeficiency virus-1 (HIV-1). HIV-1 infection is affected by cellular proteins that influence the clustering of viral receptors or the subcortical actin cytoskeleton. Several of these actin-adaptor proteins are controlled by the second messenger phosphatidylinositol 4,5-biphosphate (PIP2), an important regulator of actin organization. PIP2 production is induced by HIV-1 attachment and facilitates viral infection. However, the importance of PIP2 in regulating cytoskeletal proteins and thus HIV-1 infection has been overlooked. This review examines recent reports describing the roles played by actin-adaptor proteins during HIV-1 infection of CD4+ T cells, highlighting the influence of the signaling lipid PIP2 in this process.

      PubDate: 2014-04-27T11:06:30Z
  • Exploring bacterial epigenomics in the next-generation sequencing era: a
           new approach for an emerging frontier
    • Abstract: Publication date: Available online 8 April 2014
      Source:Trends in Microbiology
      Author(s): Poyin Chen , Richard Jeannotte , Bart C. Weimer
      Epigenetics has an important role for the success of foodborne pathogen persistence in diverse host niches. Substantial challenges exist in determining DNA methylation to situation-specific phenotypic traits. DNA modification, mediated by restriction-modification systems, functions as an immune response against antagonistic external DNA, and bacteriophage-acquired methyltransferases (MTase) and orphan MTases – those lacking the cognate restriction endonuclease – facilitate evolution of new phenotypes via gene expression modulation via DNA and RNA modifications, including methylation and phosphorothioation. Recent establishment of large-scale genome sequencing projects will result in a significant increase in genome availability that will lead to new demands for data analysis including new predictive bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing technologies that detect modification coupled with mass spectrometry to discover new adducts is a powerful tactic to study bacterial epigenetics, which is poised to make novel and far-reaching discoveries that link biological significance and the bacterial epigenome.

      PubDate: 2014-04-12T16:04:27Z
  • Marine metaproteomics: deciphering the microbial metabolic food web
    • Abstract: Publication date: Available online 11 April 2014
      Source:Trends in Microbiology
      Author(s): Timothy J. Williams , Ricardo Cavicchioli
      Metaproteomics can be applied to marine systems to discover metabolic processes in the ocean. This review describes current breakthroughs regarding marine microbes in the areas of microbial procurement of nutrients, important and previously unrecognized metabolic processes, functional roles for proteins with previously unknown functions, and intricate networks of metabolic interactions between symbiotic microbes and their hosts. By recognizing that metaproteomics empowers our understanding of the roles that marine microbes play in global biogeochemical cycles, the achievements to date from this advancing field highlight the enormous potential that the future holds.

      PubDate: 2014-04-12T16:04:27Z
  • Harnessing the power of omics in microbiology
    • Abstract: Publication date: Available online 3 April 2014
      Source:Trends in Microbiology
      Author(s): Gail Teitzel

      PubDate: 2014-04-07T16:18:01Z
  • Overcoming the current deadlock in antibiotic research
    • Abstract: Publication date: April 2014
      Source:Trends in Microbiology, Volume 22, Issue 4
      Author(s): Till F. Schäberle , Ingrid M. Hack
      Antibiotic-resistant bacteria are on the rise, making it harder to treat bacterial infections. The situation is aggravated by the shrinking of the antibiotic development pipeline. To finance urgently needed incentives for antibiotic research, creative financing solutions are needed. Public–private partnerships (PPPs) are a successful model for moving forward.

      PubDate: 2014-04-02T06:03:40Z
  • Phylogeny, culturing, and metagenomics of the human gut microbiota
    • Abstract: Publication date: Available online 31 March 2014
      Source:Trends in Microbiology
      Author(s): Alan W. Walker , Sylvia H. Duncan , Petra Louis , Harry J. Flint
      The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.

      PubDate: 2014-04-02T06:03:40Z
  • Anthrax lethal and edema toxins in anthrax pathogenesis
    • Abstract: Publication date: Available online 27 March 2014
      Source:Trends in Microbiology
      Author(s): Shihui Liu , Mahtab Moayeri , Stephen H. Leppla
      The pathophysiological effects resulting from many bacterial diseases are caused by exotoxins released by the bacteria. Bacillus anthracis, a spore-forming bacterium, is such a pathogen, causing anthrax through a combination of bacterial infection and toxemia. B. anthracis causes natural infection in humans and animals and has been a top bioterrorism concern since the 2001 anthrax attacks in the USA. The exotoxins secreted by B. anthracis use capillary morphogenesis protein 2 (CMG2) as the major toxin receptor and play essential roles in pathogenesis during the entire course of the disease. This review focuses on the activities of anthrax toxins and their roles in initial and late stages of anthrax infection.

      PubDate: 2014-04-02T06:03:40Z
  • Contents and Editorial Board
    • Abstract: Publication date: April 2014
      Source:Trends in Microbiology, Volume 22, Issue 4

      PubDate: 2014-04-02T06:03:40Z
  • Ménage à trois: an evolutionary interplay between human
           papillomavirus, a tumor, and a woman
    • Abstract: Publication date: Available online 24 March 2014
      Source:Trends in Microbiology
      Author(s): Natalia Shulzhenko , Heidi Lyng , Gerdine F. Sanson , Andrey Morgun
      Cervical cancer is the third most common cancer in women with human papillomavirus (HPV) being a key etiologic factor of this devastating disease. In this article, we describe modern advances in the genomics and transcriptomics of cervical cancer that led to uncovering the key gene drivers. We also introduce, herein, a model of cervical carcinogenesis that explains how the interplay between virus, tumor, and woman results in the selection of clones that simultaneously harbor genomic amplifications for genes that drive cell cycle, antiviral response, and inhibit cell differentiation. The new model may help researchers understand the controversies in antiviral therapy and immunogenetics of this cancer and may provide a basis for future research directions in early diagnostics and personalization of therapy.

      PubDate: 2014-03-27T15:42:34Z
  • Will omics help to cure the flu'
    • Abstract: Publication date: Available online 26 March 2014
      Source:Trends in Microbiology
      Author(s): Stephan Ludwig
      Influenza virus infections are still a major burden to mankind and our antiviral arsenal against these pathogens is limited. The cellular responses to infection might provide novel targets for intervention strategies. Josset et al. combined comparative transcriptome analysis with literature-based prediction tools for in silico identification of novel host-directed drugs.

      PubDate: 2014-03-27T15:42:34Z
  • Single cell genomics of deep ocean bacteria
    • Abstract: Publication date: Available online 27 March 2014
      Source:Trends in Microbiology
      Author(s): Weizhou Zhao , Siv G.E. Andersson
      SAR11 is one of the most abundant bacterioplanktons in the upper surface waters of the oceans. In a recent issue of The ISME Journal, Thrash and colleagues present the genomes of four single SAR11 cells isolated from the deep oceans that are enriched in genes for membrane biosynthetic functions.

      PubDate: 2014-03-27T15:42:34Z
  • Supersize me: how whole-genome sequencing and big data are transforming
    • Abstract: Publication date: Available online 22 March 2014
      Source:Trends in Microbiology
      Author(s): Rowland R. Kao , Daniel T. Haydon , Samantha J. Lycett , Pablo R. Murcia
      In epidemiology, the identification of ‘who infected whom’ allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control.

      PubDate: 2014-03-22T15:25:46Z
  • Archaeal viruses and bacteriophages: comparisons and contrasts
    • Abstract: Publication date: Available online 16 March 2014
      Source:Trends in Microbiology
      Author(s): Maija K. Pietilä , Tatiana A. Demina , Nina S. Atanasova , Hanna M. Oksanen , Dennis H. Bamford
      Isolated archaeal viruses comprise only a few percent of all known prokaryotic viruses. Thus, the study of viruses infecting archaea is still in its early stages. Here we summarize the most recent discoveries of archaeal viruses utilizing a virion-centered view. We describe the known archaeal virion morphotypes and compare them to the bacterial counterparts, if such exist. Viruses infecting archaea are morphologically diverse and present some unique morphotypes. Although limited in isolate number, archaeal viruses reveal new insights into the viral world, such as deep evolutionary relationships between viruses that infect hosts from all three domains of life.

      PubDate: 2014-03-17T15:04:01Z
  • Loop de loop: viral RNA evades IFIT1 targeting
    • Abstract: Publication date: Available online 13 March 2014
      Source:Trends in Microbiology
      Author(s): Justin A. Roby , Brian D. Clarke , Alexander A. Khromykh
      In a landmark finding published in Science, Hyde et al. have demonstrated that a hairpin RNA structure adjacent to the 5′ cap of alphavirus genomic RNA confers the ability of these viruses to evade restriction by the interferon-induced host protein IFIT1.

      PubDate: 2014-03-17T15:04:01Z
  • Ordering microbial diversity into ecologically and genetically cohesive
    • Abstract: Publication date: Available online 13 March 2014
      Source:Trends in Microbiology
      Author(s): B. Jesse Shapiro , Martin F. Polz
      We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a ‘reverse ecology’ approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.

      PubDate: 2014-03-17T15:04:01Z
  • Long-lived reservoirs of HIV-1
    • Abstract: Publication date: Available online 15 March 2014
      Source:Trends in Microbiology
      Author(s): Thomas D. Zaikos , Kathleen L. Collins
      HIV-1 persistence in long-lived cellular reservoirs remains a major barrier to a cure. In a recent Nature Medicine paper, Buzon et al. identify memory T cells with stem cell-like properties (TSCM) that harbor infectious provirus and that likely contribute to HIV-1 persistence.

      PubDate: 2014-03-17T15:04:01Z
  • How yeast can be used as a genetic platform to explore virus–host
           interactions: from ‘omics’ to functional studies
    • Abstract: Publication date: Available online 16 March 2014
      Source:Trends in Microbiology
      Author(s): Peter D. Nagy , Judit Pogany , Jing-Yi Lin
      The yeast Saccharomyces cerevisiae is an advanced model organism that has emerged as an effective host to gain insights into the intricate interactions of viruses with host cells. RNA viruses have limited coding potential and need to coopt numerous host cellular factors to facilitate their replication. To identify the host factors subverted by viruses, high-throughput genomics and global proteomics approaches have been performed with plant viruses such as brome mosaic virus (BMV) and tomato bushy stunt virus (TBSV). Accordingly, several hundred susceptibility and restriction factors for BMV and TBSV have been identified using yeast as a model host. Amazingly, host factors affecting viral genetic recombination and evolution have also been identified in genome-wide screens in yeast. The roles of many yeast host factors involved in various steps of the viral replication process have been validated by exploiting the orthologous genes in plant hosts. This Opinion summarizes the advantages of using simple viruses and yeast model host to advance our general understanding of virus–host interactions. The knowledge gained on host factors could lead to novel specific or broad-range resistance and antiviral tools against viruses.

      PubDate: 2014-03-17T15:04:01Z
  • Different paths to pathogenesis
    • Abstract: Publication date: Available online 12 March 2014
      Source:Trends in Microbiology
      Author(s): Jonathan P. Allen , Egon A. Ozer , Alan R. Hauser
      In a recent issue of Cell Host & Microbe, Elsen and colleagues identify a novel hemolysin in a highly virulent Pseudomonas aeruginosa strain that lacks a type III secretion system. Their analysis provides another example of how individual strains of P. aeruginosa utilize different virulence mechanisms to cause severe infections.

      PubDate: 2014-03-12T14:41:27Z
  • Spectinamides: a challenge, a proof, and a suggestion
    • Abstract: Publication date: Available online 11 March 2014
      Source:Trends in Microbiology
      Author(s): Miguel Viveiros , Marco Pieroni
      New drugs and shorter regimens are needed to fight resistant forms of tuberculosis. Screening of chemical libraries for mining hit compounds is the common approach to find new antituberculars. A new medicinal chemistry and biology directed research rational has recently been successfully described by Lee and coworkers in Nature Medicine.

      PubDate: 2014-03-12T14:41:27Z
  • Comparative analysis of the molecular mechanisms of recombination in
           hepatitis C virus
    • Abstract: Publication date: Available online 11 March 2014
      Source:Trends in Microbiology
      Author(s): Andrea Galli , Jens Bukh
      Genetic recombination is an important evolutionary mechanism for RNA viruses. The significance of this phenomenon for hepatitis C virus (HCV) has recently become evident, with the identification of circulating recombinant forms in HCV-infected individuals and by novel data from studies permitted by advances in HCV cell culture systems and genotyping protocols. HCV is readily able to produce viable recombinants, using replicative and non-replicative molecular mechanisms. However, our knowledge of the required molecular mechanisms remains limited. Understanding how HCV recombines might be instrumental for a better monitoring of global epidemiology, to clarify the virus evolution, and evaluate the impact of recombinant forms on the efficacy of oncoming combination drug therapies. For the latter, frequency and location of recombination events could affect the efficacy of multidrug regimens. This review will focus on current data available on HCV recombination, also in relation to more detailed data from other RNA viruses.

      PubDate: 2014-03-12T14:41:27Z
  • New insights into the crosstalk between Shigella and T lymphocytes
    • Abstract: Publication date: Available online 6 March 2014
      Source:Trends in Microbiology
      Author(s): Wilmara Salgado-Pabón , Christoph Konradt , Philippe J. Sansonetti , Armelle Phalipon
      Subversion of host immune responses is the key infection strategy employed by most, if not all, human pathogens. Modulation of the host innate response by pathogens has been vastly documented. Yet, especially for bacterial infections, it was only recently that cells of the adaptive immune response were recognized as targets of bacterial weapons such as the type III secretion system (T3SS) and its effector proteins. In this review, we focus on the recent advances made in the understanding of how the enteroinvasive bacterium Shigella flexneri interferes with the host adaptive response by targeting T lymphocytes, especially their migration capacities.

      PubDate: 2014-03-07T14:34:18Z
  • Functional and phylogenetic assembly of microbial communities in the human
    • Abstract: Publication date: Available online 5 March 2014
      Source:Trends in Microbiology
      Author(s): Afrah Shafquat , Regina Joice , Sheri L. Simmons , Curtis Huttenhower
      Microbial communities associated with the human body, that is, the human microbiome, are complex ecologies critical for normal development and health. The taxonomic and phylogenetic composition of these communities tends to significantly differ among individuals, precluding the definition of a simple, shared set of ‘core’ microbes. Here, we review recent evidence and ecological theory supporting the assembly of host-associated microbial communities in terms of functional traits rather than specific organisms. That is, distinct microbial species may be responsible for specific host-associated functions and phenotypes in distinct hosts. We discuss how ecological processes (selective and stochastic forces) governing the assembly of metazoan communities can be adapted to describe microbial ecologies in host-associated environments, resulting in both niche-specific and ‘core’ metabolic and other pathways maintained throughout the human microbiome. The extent to which phylogeny and functional traits are linked in host-associated microbes, as opposed to unlinked by mechanisms, such as lateral transfer, remains to be determined. However, the definition of these functional assembly rules within microbial communities using controlled model systems and integrative ‘omics’ represents a fruitful opportunity for molecular systems ecology.

      PubDate: 2014-03-07T14:34:18Z
  • GSK3β and the control of infectious bacterial diseases
    • Abstract: Publication date: Available online 4 March 2014
      Source:Trends in Microbiology
      Author(s): Huizhi Wang , Akhilesh Kumar , Richard J. Lamont , David A. Scott
      Glycogen synthase kinase 3β (GSK3β) has been shown to be a crucial mediator of the intensity and direction of the innate immune system response to bacterial stimuli. This review focuses on: (i) the central role of GSK3β in the regulation of pathogen-induced inflammatory responses through the regulation of pro- and anti-inflammatory cytokine production, (ii) the extensive ongoing efforts to exploit GSK3β for its therapeutic potential in the control of infectious diseases, and (iii) the increasing evidence that specific pathogens target GSK3β-related pathways for immune evasion. A better understanding of complex bacteria–GSK3β interactions is likely to lead to more effective anti-inflammatory interventions and novel targets to circumvent pathogen colonization and survival.

      PubDate: 2014-03-07T14:34:18Z
  • Bat-derived influenza-like viruses H17N10 and H18N11
    • Abstract: Publication date: Available online 26 February 2014
      Source:Trends in Microbiology
      Author(s): Ying Wu , Yan Wu , Boris Tefsen , Yi Shi , George F. Gao
      Shorebirds and waterfowls are believed to be the reservoir hosts for influenza viruses, whereas swine putatively act as mixing vessels. The recent identification of two influenza-like virus genomes (designated H17N10 and H18N11) from bats has challenged this notion. A crucial question concerns the role bats might play in influenza virus ecology. Structural and functional studies of the two major surface envelope proteins, hemagglutinin (HA) and neuraminidase (NA), demonstrate that neither has canonical HA or NA functions found in influenza viruses. However, putative functional modules and domains in other encoded proteins are conserved, and the N-terminal domain of the H17N10 polymerase subunit PA has a classical structure and function. Therefore, potential genomic reassortments of such influenza-like viruses with canonical influenza viruses cannot be excluded at this point and should be assessed.

      PubDate: 2014-03-02T14:07:15Z
  • Molecular mechanisms of antimicrobial tolerance and resistance in
           bacterial and fungal biofilms
    • Abstract: Publication date: Available online 2 March 2014
      Source:Trends in Microbiology
      Author(s): Heleen Van Acker , Patrick Van Dijck , Tom Coenye
      The formation of microbial biofilms is an important reason for failure of antimicrobial therapy. However, the molecular mechanisms underlying the survival of biofilm cells are still not completely understood. In this review we discuss three mechanisms that play an important role in biofilm survival: (i) biofilm-specific protection against oxidative stress; (ii) biofilm-specific expression of efflux pumps; and (iii) protection provided by matrix polysaccharides. We demonstrate that these mechanisms are found both in bacterial and fungal biofilms and are often surprisingly similar between distantly related organisms. In addition, we give an overview of the data that suggests that these mechanisms may not be independent.

      PubDate: 2014-03-02T14:07:15Z
  • Omics approaches in food safety: fulfilling the promise'
    • Abstract: Publication date: Available online 23 February 2014
      Source:Trends in Microbiology
      Author(s): Teresa M. Bergholz , Andrea I. Moreno Switt , Martin Wiedmann
      Genomics, transcriptomics, and proteomics are rapidly transforming our approaches to the detection, prevention, and treatment of foodborne pathogens. Microbial genome sequencing in particular has evolved from a research tool into an approach that can be used to characterize foodborne pathogen isolates as part of routine surveillance systems. Genome sequencing efforts will not only improve outbreak detection and source tracking, but will also create large amounts of foodborne pathogen genome sequence data, which will be available for data-mining efforts that could facilitate better source attribution and provide new insights into foodborne pathogen biology and transmission. Although practical uses and application of metagenomics, transcriptomics, and proteomics data and associated tools are less prominent, these tools are also starting to yield practical food safety solutions.

      PubDate: 2014-02-25T13:48:09Z
  • A novel membrane fusion protein family in Flaviviridae'
    • Abstract: Publication date: Available online 23 February 2014
      Source:Trends in Microbiology
      Author(s): Yue Li , Yorgo Modis
      Enveloped viruses must fuse their lipid membrane to a cellular membrane to deliver their genome into the cytoplasm for replication. Viral envelope proteins catalyze this critical membrane fusion event. They fall into three distinct structural classes. In 2013, envelope proteins from a pestivirus and hepatitis C virus were found to have two distinct novel folds. This was unexpected because these viruses are in the same family as flaviviruses, which have class II fusion proteins. We propose that the membrane fusion machinery of the closely related pestiviruses and hepatitis C virus defines a new structural class. This and other recently identified structural relationships between viral fusion proteins shift the paradigm for how these proteins evolved.

      PubDate: 2014-02-25T13:48:09Z
  • Programmed necrosis in microbial pathogenesis
    • Abstract: Publication date: Available online 21 February 2014
      Source:Trends in Microbiology
      Author(s): Haripriya Sridharan , Jason W. Upton
      Programmed cell death is an important facet of hostpathogen interactions. Although apoptosis has long been implicated as the major form of programmed cell death in host defense, the past decade has seen the emergence of other forms of regulated death, including programmed necrosis. While the molecular mechanisms of programmed necrosis continue to be unveiled, an increasing number of viral and bacterial pathogens induce this form of death in host cells, with important consequences for infection, control, and pathogenesis. Moreover, pathogen strategies to manipulate or utilize this pathway are now being discovered. In this review, we focus on a variety of viral and bacterial pathogens where a role for programmed necrosis is starting to be appreciated. In particular, we focus on the mechanistic details of how the host or the pathogen might appropriate this pathway for its own benefit.

      PubDate: 2014-02-25T13:48:09Z
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