Hot off the presses! Sep 01 Nat Rev Microbiol

The Sep 01 issue of the Nat Rev Microbiol is now up on Pubget (About Nat Rev Microbiol): 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:

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  - Nat Rev Microbiol 9(9):627 (2011)
  
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  - Nat Rev Microbiol 9(9):628 (2011)
  
• Symbiosis: Establishing the roots of a relationship | PDF (437 KB)
  - Nat Rev Microbiol 9(9):629 (2011)
  Pathogens and symbionts both interact closely with their host, but with vastly different outcomes. For a fungus to establish a mycorrhiza, a symbiotic interaction with plants in which the fungus penetrates the root tissue, it must overcome the immune defences of the plant and induce remodelling of the roots.
• Bacterial pathogenesis: The importance of first impressions | PDF (188 KB)
  - Nat Rev Microbiol 9(9):630 (2011)
  Pathogenic bacteria use adhesion factors, or adhesins, to facilitate their interaction with the host. However, most known adhesins are species specific and do not participate in the initial contact with the host cell, as their expression is induced during infection.
• Evolution: Timeline of the ancient mariners | PDF (173 KB)
  - Nat Rev Microbiol 9(9):630 (2011)
  Changes in the composition of ancient planktonic communities can be studied by microscopic and chemical analyses of sediments and are usually explained by changes in environmental conditions. However, the viral populations that are associated with these communities, and their roles during these changes, are poorly understood.
• Immunology | Pathogenesis | Transcription | PDF (87 KB)
  - Nat Rev Microbiol 9(9):630 (2011)
  A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins Corti, D.et al. Science28 Jul 2011 (10.1126/science.1205669)
• Industrial microbiology: Turning up the heat on biomass degradation | PDF (344 KB)
  - Nat Rev Microbiol 9(9):631 (2011)
  Cellulosic biomass can be used as a feedstock for biofuel production, but before it can be enzymatically or chemically hydrolyzed, it must undergo a pretreatment process involving high temperature coupled with extreme pH or steam explosion. Writing in Nature Communications, Graham et al.
• Microbial ecology: Bacterial volatiles give the game away | PDF (218 KB)
  - Nat Rev Microbiol 9(9):632 (2011)
  Aphids are a major crop pest, but chemical pesticides lead to the emergence of resistant organisms, and biological control can be hampered by the natural dispersal of many aphid predators. When aphids feed on plant phloem sap they excrete honeydew, a complex mixture of sugars, amino acids, lipids and organic acids that can serve as a growth medium for bacteria.
• Bacterial secretion: Contact killing by Pseudomonas | PDF (165 KB)
  - Nat Rev Microbiol 9(9):632 (2011)
  The type VI secretion system (T6SS) is a recently discovered export system that is used by Gram-negative bacteria to deliver effector proteins to other cells in a cell contact-dependent manner. The mechanism of the T6SS and the functions of the secreted effectors are not well understood.
• Real-time sequencing | PDF (187 KB)
  - Nat Rev Microbiol 9(9):633 (2011)
  This month's Genome Watch describes the impact of next-generation sequencing on the 'real-time' analysis of pathogen genomes during outbreaks.
• In the news | PDF (194 KB)
  - Nat Rev Microbiol 9(9):634 (2011)
  Tracking public health via Twitter Several studies have used messages ('tweets') posted on Twitter, a social networking and microblogging service, to track the spread of a single disease such as the flu. During the International Conference on Weblogs and Social Media, held in Barcelona, Spain, on 18 July 2011, Paul and Dredze reported a broad analysis of 1.5 million health-related tweets (filtered out of 2 billion public tweets) to obtain insight into how Twitter users view allergies, flu, insomnia, cancer, obesity, depression, pain and other ailments. As geographical information was publicly available in many of the tweets, the researchers identified certain health trends across the United States, such as when and where the allergy and flu seasons peaked. However, the authors acknowledged that there are limitations to what can be discovered about health issues via Twitter, as there is a limit to what most people are willing to share on social media. BBC/Johns Hopkins University Call for TB blood test ban The WHO says that the commercial tests which are designed to detect active tuberculosis (TB) in the blood give incorrect results in around 50% of cases, and it is urging countries to ban these tests and instead rely on other, accurate microbiological or molecular tests. The recommendation is the result of an evaluation of 94 published and unpublished studies, including 67 on pulmonary TB and 27 on extrapulmonary TB. According to the WHO, the TB blood tests put the patients' lives in danger and may contribute to the spread of the disease because of the inconsistency of the test results. Most of the commercial blood tests are produced in Europe and North America but are sold mainly in the developing world, where regulations that call for extensive evidence of accuracy are lacking. The ban recommendation applies only to blood tests for active TB. Blood tests for inactive, or latent, TB are currently under review. BBC/Stop TB Redesigning the toilet The Bill & Melinda Gates Foundation will invest US$42 million in grants to create and test new approaches to improving sanitation in poor countries. About 40% of people in the world have no access to safe, sanitary toilets, and 1 billion people practise open defecation, which causes diseases that lead to about 1.5 million child deaths per year. The new grants aim to develop affordable latrines, promote sanitation in communities and find new ways to capture and store waste, processing it into energy, fertilizer and even fresh water. Sanitation is the least attractive part of world development but, in terms of changing people's lives, it is fundamental. Before the end of the year, the Bill & Melinda Gates Foundation hopes to have 50–60 groups working on ideas for the next generation of toilets, which should run without water or electricity and not be attached to a sewer system. The Guardian/Seattle Times/Associated Press Oral health and fertility Around 10% of the population is believed to have severe periodontal disease, which is linked with poor sperm quality in men, heart disease, type 2 diabetes and miscarriage. A new study of 3,500 women in Australia has found that, in addition, gum disease affects fertility in women by increasing the average length of time that it takes to conceive from 5 months to 7 months. The authors suggest that the underlying cause is inflammation, as women with gum disease have raised blood levels of inflammation markers. BBC GMOs to fight HIV Advances on the use of two genetically modified organisms (GMOs) for the development of anti-HIV microbicides were recently reported. The first GMO is a bacterium, Lactobacillus jensenii (which is commonly found in the reproductive tract of healthy women), that was engineered to express cyanovirin-N, a cyanobacterial protein that inhibits HIV-1 entry into host cells. The bioengineered bacterium, when introduced into the vagina of macaques, reduced the transmission of a chimeric simian HIV by 63%. Furthermore, a sixfold reduction in viral loads was seen in infected macaques that received the modified L. jensenii. The second GMO is an engineered tobacco plant that produces a monoclonal antibody, P2G12, that binds proteins on the HIV surface to block infection. The purified antibody is being tested on a small number of women in the United Kingdom to establish its safety. Much bigger trials in women who are at risk of contracting HIV would be necessary to test whether the antibody could prevent infection. If successful, the investigators envisage that P2G12 would be used in combination with other HIV-neutralizing antibodies, also produced in plants, to create a broadly protective vaginal microbicide. Both lines of research could lead to cheaper microbicides to reduce HIV transmission in women. Mucosal Immunol./PRNewswire/The Guardian/Nature News Outbreak news Escherichia coli. The Robert Koch Institute, the federal disease control agency in Germany, declared on 26 July 2011 that the outbreak of enterohaemorrhagic Escherichia coli O104:H4 was over, as no cases had been reported in the previous 3 weeks. In total, 46 deaths and 3,910 infections, including 782 with a serious kidney complication (haemolytic uremic syndrome), were reported to the European Centre for Disease Prevention and Control (ECDC). A single batch of contaminated fenugreek seeds imported from Egypt was believed to be the most probable source of the outbreak. However, the ECDC warned that sporadic cases and new infection clusters would probably continue to occur, as there may be some contaminated seeds that are unaccounted for, and asymptomatic human carriers can transmit the pathogen during food handling. Reuters/CIDRAP In the News was compiled with the assistance of David Ojcius, University of California, Merced, USA. David's links to infectious disease news stories can be accessed on his Twitter page (@Ojcius).
• Manipulation of host membranes by bacterial effectors
  - Nat Rev Microbiol 9(9):635 (2011)
  Bacterial pathogens interact with host membranes to trigger a wide range of cellular processes during the course of infection. These processes include alterations to the dynamics between the plasma membrane and the actin cytoskeleton, and subversion of the membrane-associated pathways involved in vesicle trafficking. Such changes facilitate the entry and replication of the pathogen, and prevent its phagocytosis and degradation. In this Review, we describe the manipulation of host membranes by numerous bacterial effectors that target phosphoinositide metabolism, GTPase signalling and autophagy.
• The DNA-packaging nanomotor of tailed bacteriophages
  - Nat Rev Microbiol 9(9):647 (2011)
  Tailed bacteriophages use nanomotors, or molecular machines that convert chemical energy into physical movement of molecules, to insert their double-stranded DNA genomes into virus particles. These viral nanomotors are powered by ATP hydrolysis and pump the DNA into a preformed protein container called a procapsid. As a result, the virions contain very highly compacted chromosomes. Here, I review recent progress in obtaining structural information for virions, procapsids and the individual motor protein components, and discuss single-molecule in vitro packaging reactions, which have yielded important new information about the mechanism by which these powerful molecular machines translocate DNA.
• Bacterial transcriptomics: what is beyond the RNA horiz-ome?
  - Nat Rev Microbiol 9(9):658 (2011)
  Over the past 3 years, bacterial transcriptomics has undergone a massive revolution. Increased sequencing capacity and novel tools have made it possible to explore the bacterial transcriptome to an unprecedented depth, which has revealed that the transcriptome is more complex and dynamic than expected. Alternative transcripts within operons challenge the classic operon definition, and many small RNAs involved in the regulation of transcription, translation and pathogenesis have been discovered. Furthermore, mRNAs may localize to specific areas in the cell, and the spatial organization and dynamics of the chromosome have been shown to be important for transcription. Epigenetic modifications of DNA also affect transcription, and RNA processing affects translation. Therefore, transcription in bacteria resembles that in eukaryotes in terms of complexity more closely than was previously thought. Here we will discuss the contribution of 'omics' approaches to these discoverie! s as well as the possible impact that they are expected to have in the future.
• Streptolysin S-like virulence factors: the continuing sagA
  - Nat Rev Microbiol 9(9):670 (2011)
  Streptolysin S (SLS) is a potent cytolytic toxin and virulence factor that is produced by nearly all Streptococcus pyogenes strains. Despite a 100-year history of research on this toxin, it has only recently been established that SLS is just one of an extended family of post-translationally modified virulence factors (the SLS-like peptides) that are produced by some streptococci and other Gram-positive pathogens, such as Listeria monocytogenes and Clostridium botulinum. In this Review, we describe the identification, genetics, biochemistry and various functions of SLS. We also discuss the shared features of the virulence-associated SLS-like peptides, as well as their place within the rapidly expanding family of thiazole/oxazole-modified microcins (TOMMs).
• Imaging mass spectrometry in microbiology
  - Nat Rev Microbiol 9(9):683 (2011)
  Imaging mass spectrometry tools allow the two-dimensional visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies, and are becoming increasingly useful for microbiology applications. These tools, comprising different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by enabling the generation of chemical hypotheses based on the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this Innovation article, we explore the wide range of imaging mass spectrometry techniques that is available to microbiologists and describe the unique applications of these tools to microbiology with respect to the types of samples to be investigated.