Hot off the presses! Apr 01 Nature Reviews Microbiology

The Apr 01 issue of the Nature Reviews Microbiology is now up on Pubget (About Nature Reviews Microbiology): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(4):243 (2010)
  Resistance to antimicrobials has become a worldwide problem. In the United States alone, methicillin-resistant Staphylococcus aureus has claimed over 18,000 lives to date.
• Editorial: A step in the right direction
  - Nature Reviews Microbiology 8(4):244 (2010)
  The recent announcement by GlaxoSmithKline (GSK) that it will make the structures of over 13,500 compounds from its antimalarial screening programme publicly available is another welcome example of a pharmaceutical company's support for research on diseases that affect developing nations. Under its 'Open Lab' structure, GSK will allow any interested party to develop these compounds further as antimalarials.
• Innate immunity: Detailed detection
  - Nature Reviews Microbiology 8(4):245 (2010)
  Two recent papers have revealed further details of how RNA viruses such as West Nile virus (WNV) and influenza virus engage the host innate immune system.Recognition of RNA virus infection by pattern recognition receptors (PRRs) triggers an antiviral signalling cascade that culminates in the induction of type I interferons (IFNs) and a proinflammatory response.
• Archaea: A road to eukaryotes?
  - Nature Reviews Microbiology 8(4):246 (2010)
  Even though Archaea and Eukarya share a common ancestor, they are dissimilar in their cellular architecture. In a recent issue of the Proceedings of the National Academy of Sciences USA, Küper and colleagues report on the unusual outer membrane of the archaeon Ignicoccus hospitalis and show that this organism has a cellular architecture that is similar to that of eukaryotes.
• Bacterial physiology: Circadian 'gating' of cell division
  - Nature Reviews Microbiology 8(4):246 (2010)
  The physiology of most organisms is regulated by the circadian clock, which shows a periodicity of ~ 24 hours and can be changed by environmental cues. In the cyanobacterium Synechococcus elongatus the clock regulates the cell cycle, but how the two are linked was unclear.
• Parasitology: Multiple signals for apical secretion
  - Nature Reviews Microbiology 8(4):246 (2010)
  Invasion of host erythrocytes by Plasmodium falciparum merozoites requires attachment to the erythrocyte surface and the coordinated release of the contents of the apical organelles (micronemes and rhoptries) into the host cell. Publishing in PLoS Pathogens, Singh et al.
• In brief: Viral immune evasion, Biofilms, Bacterial physiology
  - Nature Reviews Microbiology 8(4):247 (2010)
  Retroviral infection in vivo requires an immune escape virulence factor encrypted in the envelope protein of oncoretroviruses Schlecht-Louf , G.et al. Proc. Natl Acad. Sci. USA 107, 3782–3787 (2010)
• Environmental microbiology: Electricity blankets the seabed
  - Nature Reviews Microbiology 8(4):248 (2010)
  Our understanding of how certain types of bacteria generate electrical currents in microbial fuel cells has progressed rapidly in recent years. These so-called exoelectrogenic bacteria are thought to use outer-membrane cytochromes, soluble electron shuttles and conductive nanowires to mediate the extracellular transport of electrons to facilitate cell-to-cell communication and energy transfer.
• Antimicrobials: Reactive resistance
  - Nature Reviews Microbiology 8(4):248 (2010)
  Treatment of bacteria with low concentrations of bactericidal antibiotics can generate multidrug resistance through an increase in the mutation rate that is driven by the formation of reactive oxygen species (ROS), according to a report from Mike Kohanski, Mark DePristo and Jim Collins in a recent issue of Molecular Cell.Previous work from Kohanski, Collins and co-workers had shown that all major classes of bactericidal antibiotics kill cells by inducing the formation of highly toxic hydroxyl radicals, which can damage DNA, proteins and lipids.
• Cooking with GAS
  - Nature Reviews Microbiology 8(4):249 (2010)
  This month's Genome Watch discusses another fascinating example of the latest application of second-generation sequencing techniques to the study of bacterial populations.
• In the News
  - Nature Reviews Microbiology 8(4):250 (2010)
  There are two broad-spectrum antivirals available (ribavirin and interferon-α), but both can have severe side effects.
• Call of the wild: antibiotic resistance genes in natural environments
  Allen HK Donato J Wang HH Cloud-Hansen KA Davies J Handelsman J - Nature Reviews Microbiology 8(4):251 (2010)
  Antibiotic-resistant pathogens are profoundly important to human health, but the environmental reservoirs of resistance determinants are poorly understood. The origins of antibiotic resistance in the environment is relevant to human health because of the increasing importance of zoonotic diseases as well as the need for predicting emerging resistant pathogens. This Review explores the presence and spread of antibiotic resistance in non-agricultural, non-clinical environments and demonstrates the need for more intensive investigation on this subject.
• Antibiotic resistance and its cost: is it possible to reverse resistance?
  Andersson DI Hughes D - Nature Reviews Microbiology 8(4):260 (2010)
  Most antibiotic resistance mechanisms are associated with a fitness cost that is typically observed as a reduced bacterial growth rate. The magnitude of this cost is the main biological parameter that influences the rate of development of resistance, the stability of the resistance and the rate at which the resistance might decrease if antibiotic use were reduced. These findings suggest that the fitness costs of resistance will allow susceptible bacteria to outcompete resistant bacteria if the selective pressure from antibiotics is reduced. Unfortunately, the available data suggest that the rate of reversibility will be slow at the community level. Here, we review the factors that influence the fitness costs of antibiotic resistance, the ways by which bacteria can reduce these costs and the possibility of exploiting them.
• Artemisinin resistance: current status and scenarios for containment
  Dondorp AM Yeung S White L Nguon C Day NP Socheat D von Seidlein L - Nature Reviews Microbiology 8(4):272 (2010)
  Artemisinin combination therapies are the first-line treatments for uncomplicated Plasmodium falciparum malaria in most malaria-endemic countries. Recently, partial artemisinin-resistant P. falciparum malaria has emerged on the Cambodia–Thailand border. Exposure of the parasite population to artemisinin monotherapies in subtherapeutic doses for over 30 years, and the availability of substandard artemisinins, have probably been the main driving force in the selection of the resistant phenotype in the region. A multifaceted containment programme has recently been launched, including early diagnosis and appropriate treatment, decreasing drug pressure, optimising vector control, targeting the mobile population, strengthening management and surveillance systems, and operational research. Mathematical modelling can be a useful tool to evaluate possible strategies for containment.
• Resistance to and synthesis of the antibiotic mupirocin
  Thomas CM Hothersall J Willis CL Simpson TJ - Nature Reviews Microbiology 8(4):281 (2010)
  Mupirocin, a polyketide antibiotic produced by Pseudomonas fluorescens, is used to control the carriage of methicillin-resistant Staphylococcus aureus on skin and in nasal passages as well as for various skin infections. Low-level resistance to the antibiotic arises by mutation of the mupirocin target, isoleucyl-tRNA synthetase, whereas high-level resistance is due to the presence of an isoleucyl-tRNA synthetase with many similarities to eukaryotic enzymes. Mupirocin biosynthesis is carried out by a combination of type I multifunctional polyketide synthases and tailoring enzymes encoded in a 75 kb gene cluster. Chemical synthesis has also been achieved. This knowledge should allow the synthesis of new and modified antibiotics for the future.
• Ethanolamine utilization in bacterial pathogens: roles and regulation
  - Nature Reviews Microbiology 8(4):290 (2010)
  Ethanolamine is a compound that can be readily derived from cell membranes and that some bacteria can use as a source of carbon and/or nitrogen. The complex biology and chemistry of this process has been under investigation since the 1970s, primarily in one or two species. However, recent investigations into ethanolamine utilization have revealed important and intriguing differences in gene content and regulatory mechanisms among the bacteria that harbour this catabolic ability. In addition, many reports have connected this process to bacterial pathogenesis. In this Progress article, I discuss the latest research on the phylogeny and regulation of ethanolamine utilization and its possible roles in bacterial pathogenesis.
• Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors
  - Nature Reviews Microbiology 8(4):296 (2010)
  Mycobacterium tuberculosis survives in antigen-presenting cells (APCs) such as macrophages and dendritic cells. APCs present antigens in association with major histocompatibility complex (MHC) class II molecules to stimulate CD4+ T cells, and this process is essential to contain M. tuberculosis infection. Immune evasion allows M. tuberculosis to establish persistent or latent infection in macrophages and results in Toll-like receptor 2 (TLR2)-dependent inhibition of MHC class II transactivator expression, MHC class II molecule expression and antigen presentation. This reduction of antigen presentation might reflect a general mechanism of negative-feedback regulation that prevents excessive T cell-mediated inflammation and that M. tuberculosis has subverted to create a niche for survival in infected macrophages and evasion of recognition by CD4+ T cells.

Hot off the presses! Jun 01 Nature Reviews Microbiology

The Jun 01 issue of the Nature Reviews Microbiology is now up on Pubget (About Nature Reviews Microbiology): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(6):383 (2010)
  All organisms must acquire carbon from their environment for the generation of energy and the production of macromolecules such as proteins and lipids. Archaea use several different carbon fixation mechanisms, depending on the environment in which they are found.
• Editorial: Biodiversity 2010: the tip of the iceberg
  - Nature Reviews Microbiology 8(6):384 (2010)
  This year is the United Nations' International Year of Biodiversity, which provides us with an opportunity to take stock of efforts to assess the impact of human activities on global species diversity. In some of the more remote parts of the world, efforts to limit our impact seem to be having a positive effect.
• Virology: Cleaving the tether
  - Nature Reviews Microbiology 8(6):385 (2010)
  Tetherin (also known as BST2) restricts enveloped viruses by preventing their release from the surface of infected cells. However, several viruses have developed strategies to circumvent this restriction.
• Bacterial pathogenesis: Targeting SUMO
  - Nature Reviews Microbiology 8(6):386 (2010)
  One of the mechanisms by which intracellular bacteria, such as Listeria monocytogenes, subvert host cell functions is to interfere with host protein post-translational modifications such as ubiquitylation, which alter protein function and stability. Cossart and colleagues now show that L. monocytogenes
• In brief: Marine microbiology, Bacterial physiology, Innate immunity
  - Nature Reviews Microbiology 8(6):386 (2010)
  Proteorhodopsin phototrophy promotes survival of marine bactera during starvation Gómez-Consarnau, L.et al. PLoS Biol. 8, e100358 (2010)
• Environmental microbiology: You are what you eat
  - Nature Reviews Microbiology 8(6):387 (2010)
  The bacteria in the human gut provide their host with energy by degrading dietary polysaccharides. Writing in Nature, Hehemann et al.
• Innate immunity: The stress connection
  - Nature Reviews Microbiology 8(6):387 (2010)
  Smoking and prolonged stress have been linked to increased susceptibility to bacterial infection. New research in Cell Host and Microbe now shows that this may be caused by a decrease in antimicrobial peptide (AMP) activity as a result of increased stimulation of a neuroendocrine signalling pathway.
• Fungal ecology: Chaos reigns at low temperatures
  - Nature Reviews Microbiology 8(6):388 (2010)
  Environmental factors such as temperature and pressure alter the structure and function of macromolecules in the cell and so define the physiochemical window for microbial growth. For example, growth is limited at low temperatures owing to an increase in non-covalent interactions among macromolecules that results in the molecules and cellular membranes becoming more rigid.
• Quorum sensing: Setting the threshold
  - Nature Reviews Microbiology 8(6):388 (2010)
  A negative regulator that controls the activation threshold for quorum sensing in Pseudomonas aeruginosa has been identified, according to a new report from Richard Siehnel, Pradeep Singh and colleagues.Quorum sensing allows bacteria to communicate with each other through the production and perception of small extracellular signal molecules such as acyl homoserine lactones (HSLs).
• Bacterial pathogenesis: Opening the gates of type III secretion
  - Nature Reviews Microbiology 8(6):389 (2010)
  Bacterial pathogens subvert host cell pathways by using type III secretion systems (T3SSs) to deliver bacterial effectors through a translocon pore into the host cytosol. Three studies, each investigating a different organism, now show that type III secretion is controlled by changes in the oxygen level and by the pH in the host cell.
• Attack of the clones
  - Nature Reviews Microbiology 8(6):390 (2010)
  This month's Genome Watch discusses two recent examples of the use of next-generation sequencing techniques in public health settings.
• In the news
  - Nature Reviews Microbiology 8(6):391 (2010)
  Many experts think that the 2012 target for the eradiction of polio is likely to be missed, but hope has been renewed following the remarkable success of anti-polio programmes in Nigeria and India, two global hotspots for polio infection. In Nigeria, improved funding and management of public health programmes coupled with better ties between such programmes and local Muslim leaders, who had previously obstructed efforts to combat polio, have resulted in only 2 children becoming paralyzed with polio so far this year compared with 123 during the same period last year.
• Molecular mechanisms of complement evasion: learning from staphylococci and meningococci
  - Nature Reviews Microbiology 8(6):393 (2010)
  The complement system is a crucial component of the innate immune response in humans. Recent studies in Staphylococcus aureus and Neisseria meningitidis have revealed how these bacteria escape complement-mediated killing. In addition, new structural data have provided detailed insights into the molecular mechanisms of host defence mediated by the complement system and how bacterial proteins interfere with this process. This information is fundamental to our understanding of bacterial pathogenesis and may facilitate the design of better vaccines.
• Carbon metabolism of intracellular bacterial pathogens and possible links to virulence
  - Nature Reviews Microbiology 8(6):401 (2010)
  New technologies such as high-throughput methods and 13C-isotopologue-profiling analysis are beginning to provide us with insight into the in vivo metabolism of microorganisms, especially in the host cell compartments that are colonized by intracellular bacterial pathogens. In this Review, we discuss the recent progress made in determining the major carbon sources and metabolic pathways used by model intracellular bacterial pathogens that replicate either in the cytosol or in vacuoles of infected host cells. Furthermore, we highlight the possible links between intracellular carbon metabolism and the expression of virulence genes.
• Behind the smile: cell biology and disease mechanisms of Giardia species
  - Nature Reviews Microbiology 8(6):413 (2010)
  The eukaryotic intestinal parasite Giardia intestinalis was first described in 1681, when Antonie van Leeuwenhoek undertook a microscopic examination of his own diarrhoeal stool. Nowadays, although G. intestinalis is recognized as a major worldwide contributor to diarrhoeal disease in humans and other mammals, the disease mechanisms are still poorly understood. Owing to its reduced complexity and proposed early evolutionary divergence, G. intestinalis is used as a model eukaryotic system for studying many basic cellular processes. In this Review we discuss recent discoveries in the molecular cell biology and pathogenesis of G. intestinalis.
• How antibiotics kill bacteria: from targets to networks
  Kohanski MA Dwyer DJ Collins JJ - Nature Reviews Microbiology 8(6):423 (2010)
  Antibiotic drug–target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug–target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.
• Building Fe–S proteins: bacterial strategies
  - Nature Reviews Microbiology 8(6):436 (2010)
  The broad range of cellular activities carried out by Fe–S proteins means that they have a central role in the life of most organisms. At the interface between biology and chemistry, studies of bacterial Fe–S protein biogenesis have taken advantage of the specific approaches of each field and have begun to reveal the molecular mechanisms involved. The multiprotein systems that are required to build Fe–S proteins have been identified, but the in vivo roles of some of the components remain to be clarified. The way in which cellular Fe–S cluster trafficking pathways are organized remains a key issue for future studies.
• Autotrophic carbon fixation in archaea
  - Nature Reviews Microbiology 8(6):447 (2010)
  The acquisition of cellular carbon from inorganic carbon is a prerequisite for life and marked the transition from the inorganic to the organic world. Recent theories of the origins of life assume that chemoevolution took place in a hot volcanic flow setting through a transition metal-catalysed, autocatalytic carbon fixation cycle. Many archaea live in volcanic habitats under such constraints, in high temperatures with only inorganic substances and often under anoxic conditions. In this Review, we describe the diverse carbon fixation mechanisms that are found in archaea. These reactions differ fundamentally from those of the well-known Calvin cycle, and their distribution mirrors the phylogenetic positions of the archaeal lineages and the needs of the ecological niches that they occupy.

Hot off the presses! Jan 01

The Jan 01 issue of the is now up on Pubget (About ): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(1):1 (2010)
  Although bacteria are single-celled organisms, many photosynthetic Cyanobacteria can effectively become multicellular, growing as filaments in which some cells differentiate to carry out specific functions. On page 39, Flores and Herrero review the differentiation of vegetative cyanobacterial cells into heterocysts, which are metabolically specialized cells that provide the cyanobacterial filament with a micro-oxic environment in which to fix nitrogen, even under oxygenic conditions.
• Editorial: Eradicating infectious diseases in 2010
  - Nature Reviews Microbiology 8(1):2 (2010)
  December 2009 marked the thirtieth anniversary of the certification of smallpox eradication. This triumph encouraged thinking about the eradication of other diseases, not only those of humans but also those of livestock, which can be of great economic importance.
• Innate immunity: Bacteria ensure injury is only skin deep
  - Nature Reviews Microbiology 8(1):3 (2010)
  Immune defences in the skin must maintain a balance between restricting excessive inflammation following injury and preserving the ability to rapidly respond to microbial infections. This problem is compounded by the presence of a diverse range of commensal organisms, some of which can become opportunistic pathogens if the skin barrier is breached.
• Bacterial pathogenesis: Position effect of effectors
  - Nature Reviews Microbiology 8(1):4 (2010)
  Many pathogens survive inside the host by injecting effector proteins into host cells. Secreted effectors can have various functions that facilitate bacterial survival, including prevention of phagocytosis.
• Bacterial physiology: Bacillus does the two-step
  - Nature Reviews Microbiology 8(1):4 (2010)
  Bacteria can begin to divide before chromosome segregation has been completed, and therefore bacterial cell division and chromosome partitioning must be tightly controlled. Two detailed analyses in a recent issue of Molecular Microbiology now report that Bacillus subtilis ensures that chromosome segregation and cell division are accurately coupled by using two DNA translocases that have different but complementary roles at different points in the division cycle.
• Immune evasion: Staying undetected
  - Nature Reviews Microbiology 8(1):4 (2010)
  Downregulation of major histocompatibility complex (MHC) molecules is a well-recognized immune evasion mechanism used by several viruses. Cowpox virus (CPXV), for example, encodes the immune evasion protein CPXV203, which inhibits MHC class I trafficking by sequestering it in the endoplasmic reticulum (ER).
• In brief: Environmental microbiology, Bacterial pathogenesis, Cellular microbiology
  - Nature Reviews Microbiology 8(1):5 (2010)
  Conversion and conservation of light energy in a photosynthetic microbial mat ecosystem Al-Najjar, M., de Beer, D., Jørgensen, B. B., Kühl, M. & Polerecky, L.ISME J.12 Nov 2009 (doi:10.1038/ismej.2009.121)
• Environmental microbiology: Viral lipid in bloom
  - Nature Reviews Microbiology 8(1):6 (2010)
  Every year, the unicellular coccolithophore Emiliania huxleyi forms massive blooms in the North Atlantic Ocean, making it a key player in global carbon cycling. E. huxleyi
• Bacterial secretion: Respiratory remnants
  - Nature Reviews Microbiology 8(1):6 (2010)
  Some non-exported bacterial redox enzymes contain remnant twin-arginine signal peptides that can be reactivated into functional twin-arginine transport (Tat) export signals, according to a report in the latest issue of Microbiology.The Tat pathway is a general secretory pathway that transports fully folded proteins across the cytoplasmic membrane of prokaryotes and the thylakoid membrane of chloroplasts.
• In the news
  - Nature Reviews Microbiology 8(1):7 (2010)
  The World AIDS Day campaign is now in its twenty-first year. The overall theme for the 2009 Word AIDS Day, which was held on 1 December, was universal access and human rights, and this theme was interpreted in different ways by individual nations.
• The molecular basis of the host response to lipopolysaccharide
  Bryant CE Spring DR Gangloff M Gay NJ - Nature Reviews Microbiology 8(1):8 (2010)
  Lipopolysaccharide (LPS), which is produced by Gram-negative bacteria, is a powerful activator of innate immune responses. LPS binds to the proteins Toll-like receptor 4 (TLR4) and MD2 to activate pro-inflammatory signalling pathways. The TLR4–MD2 receptor complex is crucial for the host recognition of Gram-negative bacterial infection, and pathogens have devised many strategies to evade or manipulate TLR4–MD2 activity. The TLR4–MD2 signalling pathway is therefore potentially an important therapeutic target. This Progress article focuses on recent exciting data that have revealed the structural basis of TLR4–MD2 recognition of LPS.
• Bacterial competition: surviving and thriving in the microbial jungle
  Hibbing ME Fuqua C Parsek MR Peterson SB - Nature Reviews Microbiology 8(1):15 (2010)
  Most natural environments harbour a stunningly diverse collection of microbial species. In these communities, bacteria compete with their neighbours for space and resources. Laboratory experiments with pure and mixed cultures have revealed many active mechanisms by which bacteria can impair or kill other microorganisms. In addition, a growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature. The next challenge is to integrate the findings of these laboratory and theoretical studies and to evaluate the predictions that they generate in more natural settings.
• Molecular mechanisms of Escherichia coli pathogenicity
  Croxen MA Finlay BB - Nature Reviews Microbiology 8(1):26 (2010)
  Escherichia coli is a remarkable and diverse organism. This normally harmless commensal needs only to acquire a combination of mobile genetic elements to become a highly adapted pathogen capable of causing a range of diseases, from gastroenteritis to extraintestinal infections of the urinary tract, bloodstream and central nervous system. The worldwide burden of these diseases is staggering, with hundreds of millions of people affected annually. Eight E. coli pathovars have been well characterized, and each uses a large arsenal of virulence factors to subvert host cellular functions to potentiate its virulence. In this Review, we focus on the recent advances in our understanding of the different pathogenic mechanisms that are used by various E. coli pathovars and how they cause disease in humans.
• Compartmentalized function through cell differentiation in filamentous cyanobacteria
  Flores E Herrero A - Nature Reviews Microbiology 8(1):39 (2010)
  Within the wide biodiversity that is found in the bacterial world, Cyanobacteria represents a unique phylogenetic group that is responsible for a key metabolic process in the biosphere — oxygenic photosynthesis — and that includes representatives exhibiting complex morphologies. Many cyanobacteria are multicellular, growing as filaments of cells in which some cells can differentiate to carry out specialized functions. These differentiated cells include resistance and dispersal forms as well as a metabolically specialized form that is devoted to N2 fixation, known as the heterocyst. In this Review we address cyanobacterial intercellular communication, the supracellular structure of the cyanobacterial filament and the basic principles that govern the process of heterocyst differentiation.
• The cell biology of rabies virus: using stealth to reach the brain
  Schnell MJ McGettigan JP Wirblich C Papaneri A - Nature Reviews Microbiology 8(1):51 (2010)
  Rabies virus, the prototypical neurotropic virus, causes one of the most lethal zoonotic diseases. According to official estimates, over 55,000 people die of the disease annually, but this is probably a severe underestimation. A combination of virulence factors enables the virus to enter neurons at peripheral sites and travel through the spinal cord to the brain of the infected host, where it often induces aggression that facilitates the transfer of the virus to a new host. This Review summarizes the current knowledge of the replication cycle of rabies virus and virus– host cell interactions, both of which are fundamental elements in our quest to understand the life cycle of rabies virus and the pathogenesis of rabies.
• Viruses as vaccine vectors for infectious diseases and cancer
  Draper SJ Heeney JL - Nature Reviews Microbiology 8(1):62 (2010)
  Recent developments in the use of viruses as vaccine vectors have been facilitated by a better understanding of viral biology. Advances occur as we gain greater insight into the interrelationship of viruses and the immune system. Viral-vector vaccines remain the best means to induce cellular immunity and are now showing promise for the induction of strong humoral responses. The potential benefits for global health that are offered by this field reflect the scope and utility of viruses as vaccine vectors for human and veterinary applications, with targets ranging from certain types of cancer to a vast array of infectious diseases.
• Mass spectrometry tools for the classification and identification of bacteria
  - Nature Reviews Microbiology 8(1):74 (2010)
  Mass spectrometry has become an important analytical tool in biology in the past two decades. In principle, mass spectrometry offers high-throughput, sensitive and specific analysis for many applications in microbiology, including clinical diagnostics and environmental research. Recently, several mass spectrometry methods for the classification and identification of bacteria and other microorganisms, as well as new software analysis tools, have been developed. In this Review we discuss the application range of these mass spectrometry procedures and their potential for successful transfer into microbiology laboratories.
• Correspondence: Are correctional facilities amplifying the epidemic of community-acquired methicillin-resistant Staphylococcus aureus?
  - Nature Reviews Microbiology 8(1):83 (2010)
  In their recent Review (Waves of resistance: Staphylococcus aureus in the antibiotic era. Nature Rev. Microbiol. 7, 629–641 (2009)

Hot off the presses! Mar 01

The Mar 01 issue of the is now up on Pubget (About ): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(3):155 (2010)
  The study of the molecular biology of bacteria goes back nearly a century, but some fundamental processes, such as DNA replication and compaction, remain poorly understood. On page 163, Katayama and colleagues describe recent progress in our understanding of the initiation of DNA replication, focusing on the control of the regulatory protein DnaA and the replication origin.
• Editorial: A birthday gift for GAVI
  - Nature Reviews Microbiology 8(3):156 (2010)
  The GAVI Alliance was established in 2000 in response to the need to dramatically increase vaccine coverage for children in developing countries. Initially called the Global Alliance for Vaccination and Immunization, it is a coalition of partners, including national governments, international organizations, bilateral donors (donors that deal directly with one government), the vaccine production industry and non-governmental organizations.
• Symbiosis: Breaking the rhizobial barrier
  - Nature Reviews Microbiology 8(3):157 (2010)
  Rhizobial bacteria form mutualistic endosymbioses with legumes, in which they induce the formation of root nodules and fix nitrogen. The rhizobia constitute a phylogenetically diverse range of soil bacteria, and it is thought that repeated and independent horizontal gene transfer events led to the spread of symbiotic capabilities to previously non-symbiotic bacteria.
• Viral infection: miRNAs help KSHV lay low
  - Nature Reviews Microbiology 8(3):158 (2010)
  Kaposi's sarcoma-associated herpesvirus (KSHV) establishes a long-term, latent infection in its target cells, during which a limited repertoire of viral genes is expressed. Among these are 17 microRNAs (miRNAs), which have an unclear role in the viral life cycle.
• In brief: Virology, Systems biology, Bacterial physiology
  - Nature Reviews Microbiology 8(3):158 (2010)
  Repulsion of superinfecting virions: a mechanism for rapid virus spread Doceul, V.et al. Science21 Jan 2010 (doi:10.1126/science.1183173)
• Industrial microbiology: Fuelling the renewable revolution
  - Nature Reviews Microbiology 8(3):158 (2010)
  The production of fuels and other high-value chemicals through microbial fermentation has the potential to provide a sustainable alternative to petrochemicals. Publishing in Nature, Jay Keasling and colleagues now describe the engineering of Escherichia coli to produce structurally tailored fatty acids and their derivatives from simple sugars and plant-derived biomass.
• In brief: Bacterial pathogenicity, Environmental microbiology, Innate immunity
  - Nature Reviews Microbiology 8(3):159 (2010)
  A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria Hood, R. D.et al. Cell Host Microbe 7, 25–37 (2010)
• Archaea: Singled out from the crowd
  - Nature Reviews Microbiology 8(3):160 (2010)
  Ubiquitin is a small eukaryotic protein with a characteristic β-grasp fold that can be conjugated to other proteins. In many cases, the conjugated protein is then targeted for degradation by the proteasome, and ubiquitin is recycled for further rounds of conjugation.
• Parasitology: Epigenetic regulation of VSG expression
  - Nature Reviews Microbiology 8(3):160 (2010)
  The controversial issue of the chromatin structure at VSG expression site loci in African trypanosomes seems to have been resolved with the publication of two papers in Eukaryotic Cell showing that nucleosomes are depleted at active VSG expression sites.In the bloodstream of the mammalian host, Trypanosoma brucei avoids immune detection by periodically switching its variant surface glycoprotein (VSG) 'coat' by a process known as antigenic variation.
• Taming the next-gen beast
  - Nature Reviews Microbiology 8(3):161 (2010)
  This month's Genome Watch discusses how alternative approaches to using second-generation sequencing technologies are powerful tools for the analysis of common pathogenic bacteria.
• In the news
  - Nature Reviews Microbiology 8(3):162 (2010)
  Experts warn that a patient's weight should be taken into account when prescribing antibiotics, as body weight can affect the distribution and metabolism of a drug. With obesity levels rising in many parts of the world, Matthew Falagas and Drosos Karageorgopoulos, in an article published in The Lancet, advise doctors to tailor antibiotic doses to a patient's weight and body composition to achieve maximal benefit from treatment.
• Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC
  - Nature Reviews Microbiology 8(3):163 (2010)
  Chromosomal replication must be limited to once and only once per cell cycle. This is accomplished by multiple regulatory pathways that govern initiator proteins and replication origins. A principal feature of DNA replication is the coupling of the replication reaction to negative-feedback regulation. Some of the factors that are important in this process have been discovered, including the clamp (DNA polymerase III subunit-β (DnaN)), the datA locus, SeqA, DnaA homologue protein (Hda) and YabA, as well as factors that are involved at other stages of the regulatory mechanism, such as DnaA initiator-associating protein (DiaA), the DnaA-reactivating sequence (DARS) loci and Soj. Here, we describe the regulation of DnaA, one of the central proteins involved in bacterial DNA replication, by these factors in Escherichia coli, Bacillus subtilis and Caulobacter crescentus.
• Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens
  - Nature Reviews Microbiology 8(3):171 (2010)
  How can probiotic bacteria transduce their health benefits to the host? Bacterial cell surface macromolecules are key factors in this beneficial microorganism–host crosstalk, as they can interact with host pattern recognition receptors (PRRs) of the gastrointestinal mucosa. In this Review, we highlight the documented signalling interactions of the surface molecules of probiotic bacteria (such as long surface appendages, polysaccharides and lipoteichoic acids) with PRRs. Research on host–probiotic interactions can benefit from well-documented host–microorganism studies that span the spectrum from pathogenicity to mutualism. Distinctions and parallels are therefore drawn with the interactions of similar molecules that are presented by gastrointestinal commensals and pathogens.
• Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
  Dillon SC Dorman CJ - Nature Reviews Microbiology 8(3):185 (2010)
  Emerging models of the bacterial nucleoid show that nucleoid-associated proteins (NAPs) and transcription contribute in combination to the dynamic nature of nucleoid structure. NAPs and other DNA-binding proteins that display gene-silencing and anti-silencing activities are emerging as key antagonistic regulators of nucleoid structure. Furthermore, it is becoming clear that the boundary between NAPs and conventional transcriptional regulators is quite blurred and that NAPs facilitate the evolution of novel gene regulatory circuits. Here, NAP biology is considered from the standpoints of both gene regulation and nucleoid structure.
• The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
  Srikhanta YN Fox KL Jennings MP - Nature Reviews Microbiology 8(3):196 (2010)
  In several host-adapted pathogens, phase variation has been found to occur in genes that encode methyltransferases associated with type III restriction–modification systems. It was recently shown that in the human pathogens Haemophilus influenzae, Neisseria gonorrhoeae and Neisseria meningitidis phase variation of a type III DNA methyltransferase, encoded by members of the mod gene family, regulates the expression of multiple genes. This novel genetic system has been termed the 'phasevarion' (phase-variable regulon). The wide distribution of phase-variable mod family genes indicates that this may be a common strategy used by host-adapted bacterial pathogens to randomly switch between distinct cell types.
• The population genetics of commensal Escherichia coli
  - Nature Reviews Microbiology 8(3):207 (2010)
  The primary habitat of Escherichia coli is the vertebrate gut, where it is the predominant aerobic organism, living in symbiosis with its host. Despite the occurrence of recombination events, the population structure is predominantly clonal, allowing the delineation of major phylogenetic groups. The genetic structure of commensal E. coli is shaped by multiple host and environmental factors, and the determinants involved in the virulence of the bacteria may in fact reflect adaptation to commensal habitats. A better characterization of the commensal niche is necessary to understand how a useful commensal can become a harmful pathogen. In this Review we describe the population structure of commensal E. coli, the factors involved in the spread of different strains, how the bacteria can adapt to different niches and how a commensal lifestyle can evolve into a pathogenic one.
• A complex journey: transmission of microbial symbionts
  - Nature Reviews Microbiology 8(3):218 (2010)
  The perpetuation of symbioses through host generations relies on symbiont transmission. Horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. Mixed modes also exist. In this Review we describe the journey of symbionts from the initial contact to their final residence. We provide an overview of the molecular mechanisms that mediate symbiont attraction and accumulation, interpartner recognition and selection, as well as symbiont confrontation with the host immune system. We also discuss how the two main transmission modes shape the evolution of the symbiotic partners.
• Viral shape-shifting: norovirus evasion of the human immune system
  - Nature Reviews Microbiology 8(3):231 (2010)
  Noroviruses are the most common cause of food-borne gastroenteritis worldwide, and explosive outbreaks frequently occur in community settings, where the virus can immobilize large numbers of infected individuals for 24–48 hours, making the development of effective vaccines and antiviral therapies a priority. However, several challenges have hampered therapeutic design, including: the limitations of cell culture and small-animal model systems; the complex effects of host pre-exposure histories; differential host susceptibility, which is correlated with blood group and secretor status; and the evolution of novel immune escape variants. In this Review, we discuss the molecular and structural mechanisms that facilitate the persistence of noroviruses in human populations.
• Correspondence: Spectrum of latent tuberculosis — existing tests cannot resolve the underlying phenotypes
  - Nature Reviews Microbiology 8(3):242 (2010)
  In their recent Review (The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Rev. Microbiol. 7, 845–855 (2009)
• Author Reply: Spectrum of latent tuberculosis — existing tests cannot resolve the underlying phenotypes: author's reply
  - Nature Reviews Microbiology 8(3):242 (2010)
  We agree with the comments in response to our Review (The spectrum of latent tuberculosis: rethinking the biology and intervention strategies. Nature Rev. Microbiol. 7, 845–855 (2009)

Hot off the presses! May 01

The May 01 issue of the is now up on Pubget (About ): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• In this issue
  - Nature Reviews Microbiology 8(5):309 (2010)
  The phrase 'good fences make good neighbours' suggests that keeping a little distance between ourselves and our immediate neighbours can be important to maintain good community relations. This phrase could equally be applied to the microbial world, in which the communities can comprise a range of different microorganisms that are often competing for limited resources.
• Editorial: China: a life sciences giant
  - Nature Reviews Microbiology 8(5):310 (2010)
  A recent press release from Nature China showed that the number of articles published by Chinese researchers in five top research journals (Cell, Science, Nature, The Lancet and The New England Journal of Medicine) nearly doubled between 2008 and 2009, providing a clear indication of the growth of life science research in China. Since 2007, China has ranked second only to the United States in terms of the number of scientific publications produced, and the indication is that the trends of increasing quantity and, importantly, quality will continue for the foreseeable future.
• Fungal genetics: Expanding horizons through chromosome exchange
  - Nature Reviews Microbiology 8(5):311 (2010)
  Members of the ascomycete fungi genus Fusarium range from plant pathogens to soil dwellers. The publication of a genomic comparison of several Fusarium species sheds light on the differences between these species and shows that horizontal transfer of entire chromosomes between species has important consequences for the lifestyle and host range of these pathogens.
• Bacterial virulence: Modifying virulent behaviour
  - Nature Reviews Microbiology 8(5):312 (2010)
  Post-translational modification of cell surface factors is known to be important for the virulence of many bacterial pathogens, including Campylobacter jejuni, a major worldwide cause of bacterial diarrhoea. Now, Cullen and Trent describe the identification of a phosphoethanolamine transferase that modifies components of the flagella and lipo-oligosaccharide in the C. jejuni
• Techniques and applications: Real-time view of AMP-mediated killing
  - Nature Reviews Microbiology 8(5):312 (2010)
  Atomic force microscopy (AFM) has provided microbiologists with powerful images of bacterial cells and cell surface structures at the nanometre scale. However, image acquisition times of several minutes per frame have limited the use of AFM for studying highly dynamic cellular processes.
• Plant immunity: Helping plants to fight back
  - Nature Reviews Microbiology 8(5):312 (2010)
  A new report in Nature Biotechnology shows that a pattern recognition receptor (PRR) can be transferred between two plant families, conferring broad-spectrum bacterial resistance.Plants, like humans, can detect pathogen-associated molecular patterns (PAMPs) using cell surface PRRs.
• In brief: Fungal physiology, Viral immune evasion, Metagenomics
  - Nature Reviews Microbiology 8(5):313 (2010)
  N-acetylglucosamine induces white to opaque switching, a mating prerequisite in Candida albicans Huang , G.et al. PLoS Pathog. 6, e1000806 (2010) (doi: 10.1371/journal.ppat.1000806)
• HIV: Second hideout for HIV-1
  - Nature Reviews Microbiology 8(5):314 (2010)
  Immature multipotent haematopoietic progenitor cells (HPCs) are a second reservoir of latent HIV-1 infection, according to a new report in Nature Medicine.Although highly active antiretroviral therapy (HAART) has greatly reduced mortality from HIV-1 infection, it cannot completely eradicate the virus owing to viral persistence as a provirus in latently infected cells.
• Bacterial secretion: The two faces of MycP1
  - Nature Reviews Microbiology 8(5):314 (2010)
  Mycobacterium tuberculosis uses ESX1, a type VII secretion system, to deliver virulence factors into host cells. Because some of the proteins secreted by ESX1, such as ESAT6 (also known as EsxA), are important for virulence and also highly immunogenic, the system is transcriptionally regulated to maintain a balance between virulence and immunogenicity.
• A glut from the gut: metagenomics takes a giant step foward
  - Nature Reviews Microbiology 8(5):315 (2010)
  Interest in the bacteria that inhabit the human gut has increased greatly in recent years, as technological advancements have allowed new discoveries. This month's Genome Watch reviews a recent study of the microorganisms in the human gut that sets a new marker for the field of metagenomics.
• In the News
  - Nature Reviews Microbiology 8(5):316 (2010)
  A new class of drug that could be used to treat tuberculosis has been identified.
• Bacteriophage resistance mechanisms
  Labrie SJ Samson JE Moineau S - Nature Reviews Microbiology 8(5):317 (2010)
  Phages are now acknowledged as the most abundant microorganisms on the planet and are also possibly the most diversified. This diversity is mostly driven by their dynamic adaptation when facing selective pressure such as phage resistance mechanisms, which are widespread in bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. In this Review, we highlight the most important antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these systems.
• Anaplasma phagocytophilum and Ehrlichia chaffeensis: subversive manipulators of host cells
  Rikihisa Y - Nature Reviews Microbiology 8(5):328 (2010)
  Anaplasma spp. and Ehrlichia spp. cause several emerging human infectious diseases. Anaplasma phagocytophilum and Ehrlichia chaffeensis are transmitted between mammals by blood-sucking ticks and replicate inside mammalian white blood cells and tick salivary-gland and midgut cells. Adaptation to a life in eukaryotic cells and transmission between hosts has been assisted by the deletion of many genes that are present in the genomes of free-living bacteria (including genes required for the biosynthesis of lipopolysaccharide and peptidoglycan), by the acquisition of a cholesterol uptake pathway and by the expansion of the repertoire of genes encoding the outer-membrane porins and type IV secretion system. Here, I review the specialized properties and other adaptations of these intracellular bacteria.
• Medically important bacterial–fungal interactions
  Peleg AY Hogan DA Mylonakis E - Nature Reviews Microbiology 8(5):340 (2010)
  Whether it is in the setting of disease or in a healthy state, the human body contains a diverse range of microorganisms, including bacteria and fungi. The interactions between these taxonomically diverse microorganisms are highly dynamic and dependent on a multitude of microorganism and host factors. Human disease can develop from an imbalance between commensal bacteria and fungi or from invasion of particular host niches by opportunistic bacterial and fungal pathogens. This Review describes the clinical and molecular characteristics of bacterial–fungal interactions that are relevant to human disease.
• A look behind closed doors: interaction of persistent viruses with dendritic cells
  Lambotin M Raghuraman S Stoll-Keller F Baumert TF Barth H - Nature Reviews Microbiology 8(5):350 (2010)
  Persistent infections with HIV, hepatitis B virus and hepatitis C virus are major causes of morbidity and mortality worldwide. As sentinels of the immune system, dendritic cells (DCs) are crucial for the generation of protective antiviral immunity. Recent advances in our understanding of the role of DCs during infection with these viruses provide insights into the mechanisms used by these viruses to exploit DC function and evade innate and adaptive immunity. In this Review we highlight the current knowledge about the interaction between DCs and these viruses and the underlying mechanisms that might influence the outcome of viral infections.
• The arrival, establishment and spread of exotic diseases: patterns and predictions
  Randolph SE Rogers DJ - Nature Reviews Microbiology 8(5):361 (2010)
  The impact of human activities on the principles and processes governing the arrival, establishment and spread of exotic pathogens is illustrated by vector-borne diseases such as malaria, dengue, chikungunya, West Nile, bluetongue and Crimean–Congo haemorrhagic fevers. Competent vectors, which are commonly already present in the areas, provide opportunities for infection by exotic pathogens that are introduced by travel and trade. At the same time, the correct combination of environmental conditions (both abiotic and biotic) makes many far-flung parts of the world latently and predictably, but differentially, permissive to persistent transmission cycles. Socioeconomic factors and nutritional status determine human exposure to disease and resistance to infection, respectively, so that disease incidence can vary independently of biological cycles.
• Detecting genomic islands using bioinformatics approaches
  - Nature Reviews Microbiology 8(5):373 (2010)
  Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of medical and environmental interest, and they have had a substantial impact on bacterial evolution. Therefore, there is growing interest in efficiently identifying GIs in newly sequenced bacterial genomes. Several computational methods for detecting GIs have been developed recently, presenting researchers with a myriad of choices. Here, we discuss the limitations and benefits of the main approaches that are available and present guidelines to aid researchers in effectively identifying these important genomic regions.