MicrobiologyBytes

“More researchers should engage with the blogosphere”

The blogosphere differs from mass media and specialized media in many respects, but the same considerations apply in disseminating new scientific results there. Authors of papers in press have the right to correct misrepresentations and to point to results that will appear in a paper. But a full discussion should await the paper’s publication.
Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.
Moreover, there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

Nature 457, 1058 (26 February 2009)

HIV is evolving rapidly to escape the human immune system. Researchers have shown HIV is able to adapt rapidly to counter human genes controlling immune system molecules that can target it for destruction. Progression to AIDS is tied to genes which control production of key immune system molecules called human leucocyte antigens (HLAs). Humans differ in the HLA genes they have, and even small differences can have a big impact on how quickly AIDS develops. Researchers found mutations that enabled HIV effectively to neutralise the effect of a particular HLA gene were more frequent in populations with a high prevalence of that specific gene.

BBC News

Adaptation of HIV-1 to human leukocyte antigen class I. Nature, 25 February 2009
The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic provides a rare opportunity to witness host–pathogen co-evolution involving humans. A focal point is the interaction between genes encoding human leukocyte antigen (HLA) and those encoding HIV proteins. HLA molecules present fragments (epitopes) of HIV proteins on the surface of infected cells to enable immune recognition and killing by CD8+ T cells; particular HLA molecules, such as HLA-B*57, HLA-B*27 and HLA-B*51, are more likely to mediate successful control of HIV infection1. Mutation within these epitopes can allow viral escape from CD8+ T-cell recognition. Here we analysed viral sequences and HLA alleles from >2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents. Initial analysis of the HLA-B*51-restricted epitope, TAFTIPSI (reverse transcriptase residues 128–135), showed a strong correlation between the frequency of the escape mutation I135X and HLA-B*51 prevalence in the 9 study cohorts (P = 0.0001). Extending these analyses to incorporate other well-defined CD8+ T-cell epitopes, including those restricted by HLA-B*57 and HLA-B*27, showed that the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P < 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level. This process of viral adaptation may dismantle the well-established HLA associations with control of HIV infection that are linked to the availability of key epitopes, and highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV.

Related:

• Why is HIV a pathogen?
• How does HIV cause AIDS?
• Immune exhaustion in HIV infection
• HIV-2 – a kinder AIDS virus?

Genome recombination is important for its role in unlinking deleterious mutations from those that may be neutral or beneficial, allowing populations at least partial escape from the negative fitness effects of accumulating deleterious mutations. Similarly, recombination allows otherwise asexual organisms such as viruses and bacteria to avoid the evolution-retarding effects of “clonal interference”, which results from competition among distinct beneficial mutations that reside concurrently in multiple genomes – eventually one dominates within the population at the expense of the rest.

In viruses, where genetic exchange between different species or even unrelated taxa is possible, recombination is also capable of generating spectacular genetic diversity. While natural recombination between distantly related genomes has only rarely been shown to occur in double-stranded DNA and RNA viruses, it is apparently quite common amongst most reverse-transcribing, positive-sense single-stranded RNA and single-stranded DNA viruses.

Maize streak virus (MSV), the type strain of the genus Mastrevirus in the family Geminiviridae, has a simple genome consisting of virion sense movement protein (mp) and coat protein (CP) (cp) genes, and a complementary sense replication-associated protein (rep) gene that is expressed in two alternatively spliced isoforms. Separating the complementary and virion sense genes are a long intergenic region (LIR), containing the v-ori and transcriptional promoter elements, and a short intergenic region (SIR), containing the complementary sense ori and transcription termination elements. A recent paper describes a conceptually simple but powerful new experimental system to demonstrate how recombination in geminiviruses such as MSV can be a remarkably efficient mechanism capable of rapidly generating progeny genomes with increased fitness.

Rapid host adaptation by extensive recombination. 2009 J Gen Virol 90: 734-746
Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.

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Antibiotics aren’t just for fighting infections. As Julian Davies describes in this article in Microbiology Today, they play a part in the bacterial signalling network:

Microbial products with antibiotic activity exhibit many other types of bioactivity; the word antibiotic describes a specific function, but the compounds are multifunctional. The fact that a particular product has inhibitory activity in the laboratory does not mean that it plays such a role in nature. Antibiotics have a number of effects on bacterial physiology; for example they may affect the ability to swarm or form biofilms, or act as mutagens and induce bacterial lysogens to produce phage. Less well appreciated is the fact that they also affect the function of plant cells and those of human hosts, and may cause undesirable side reactions; these secondary effects often occur at sub-inhibitory concentrations.

Read more

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• Streptomyces
• Antibiotics, your gut, and you
• Towards The Next 80 Years of Penicillin Production

Prion diseases are a closely related group of fatal neurodegenerative disorders affecting the central nervous system of humans and animals. They include Creutzfeldt-Jakob disease (CJD), Gerstmann-Straussler-Scheinker disease (GSS), fatal familial insomnia (FFI), and kuru in humans; bovine spongiform encephalopathy (BSE) in cattle; and scrapie in sheep. The identification of variant CJD (vCJD) in the U.K. in 1996 and the subsequent experimental confirmation that BSE in cattle and vCJD in humans are caused by the same prion strain has led to a variety of concerns relating to public health. Iatrogenic transmission of classical (sporadic) CJD by a contaminated neurosurgical instrument has been reported, and epidemiological evidence suggests a fraction of apparently sporadic CJD may be caused by unrecognized iatrogenic infection during general surgery. The unknown but potentially substantial prevalence of clinically silent infection with vCJD prions in populations exposed to dietary BSE prions, together with the much wider tissue distribution of infectivity in vCJD, highlights the concerns of risk of infection through contact with surgical instruments. Secondary vCJD arising from blood transfusion has now been documented, indicating significant prionemia in asymptomatic donors during the incubation period. This wide distribution of infectivity makes common surgical and endoscopic procedures, in addition to neurosurgery and eye surgery, a potential risk factor for iatrogenic transmission of vCJD. Further, it is established that tissue prions withstand many forms of sterilization techniques and that the metal-adsorbed agent is even more resistant to both thermal and chemical treatments.

Highly sensitive, quantitative cell-based assay for prions adsorbed to solid surfaces. PNAS USA February 9, 2009
Prions are comprised principally of aggregates of a misfolded host protein and cause fatal transmissible neurodegenerative disorders of humans and animals, such as variant Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. Prions pose significant public health concerns, including contamination of blood products and surgical instruments; require laborious and often insensitive animal bioassay to detect; and resist conventional hospital sterilization methods. A major experimental advance was the cell culture-based scrapie cell assay, allowing prion titres to be estimated more precisely and an order of magnitude faster than by animal bioassays. Here we describe a bioassay method that exploits the marked binding affinity of prions to steel surfaces. Using steel wires as a concentrating and sensitization tool and combining with an adapted scrapie cell endpoint assay we can achieve, for mouse prions, a sensitivity 100X higher than that achieved in standard mouse bioassays. The rapidity and sensitivity of this assay offers a major advance over small animal bioassay in many aspects of prion research. In addition, its specific application in assay of metal-bound prions allows evaluation of novel prion decontamination methods.

Related:

• What the heck are prions for?
• Prion infectivity found in fat tissues of mice
• Prions in Milk
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Measles virus (MV) is one of the most contagious human pathogens. It is transmitted by aerosols, infecting a new host via the upper respiratory tract. Eventually, infection can spread to many organs of the body. The host cell receptors for MV are well defined: CD46, a member of the human complement regulatory proteins and a ubiquitous cellular receptor found on all nucleated cells, and CD150 or SLAM (signalling lymphocyte activation molecule), a membrane glycoprotein present on activated B cells, T cells and monocytes. It is generally believed that laboratory and vaccine strains of MV use both CD150 and CD46 as their cellular receptors, but wild-type MV strains mainly use CD150.

Oncolytic viruses have been selected or engineered to replicate in tumour cells. Approaches towards targeting cancer cells frequently exploit antigens that are unique to or are over expressed on the surface of tumour cells. As cell surface recognition and virus entry is the key first step for specific targeting, engineering oncolytic viruses in order to recognize exclusively the tumour cell-surface is important. Therefore, retargeting of oncolytic viruses a promising approach to exploit the potential of virotherapy.

In a recently published paper (Genetically engineered attenuated measles virus specifically infects and kills primary multiple myeloma cells. J Gen Virol. 2009 90: 693-701), researchers describe use of a mouse monoclonal antibody Wue-1, which is specific for B cells and their malignant counterparts, to retarget a CD46- and CD150-blinded recombinant MV towards Wue-1+ cells. This engineered virus with altered receptors specifically and efficiently infected primary multiple myeloma cells and induced apoptosis.

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Although virotherapy of hard-to-treat tumours with engineered viruses is a tantalizing prospect, this approach is still limited to laboratory studies at present. In order to develop a practical oncolytic treatments, successful tests in vitro using susceptible cells must lead to evaluation of the efficacy of tumour reduction in vivo in animal models with objective measurable parameters of safety and efficacy. Only then will we be ready to begin consideration of human trials of these potent new weapons in the fight against cancer.

Related:

• How Measles Virus Infects Cells
• Measles vaccination and SSPE
• Measles and Mumps in the USA
• Measles virus: cellular receptors, tropism and pathogenesis. J Gen Virol. 2006 87: 2767-2779

Researchers have identified two molecules that enable Escherichia coli (E. coli), the bacterium that causes many urinary tract infections (UTIs), to survive and reproduce, thereby providing possible new targets for antibiotic therapy. These molecules, siderophores, are iron-chelating compounds secreted by microorganisms. The new siderophores, yersiniabactin and salmochelin, were shown to allow disease-producing bacteria strains to steal iron from their hosts, making it easier for these bacteria to survive and reproduce. Their identification also presents a potential way to selectively eradicate the pathogenic E. coli strains without adversely affecting those strains that normally populate the gut.

UTIs are among the most common bacterial infections worldwide. Half of all women will experience a UTI at some point in their lives, and in 20 to 40% of these patients, the infection recurs. 90% of all UTIs are caused by E. coli, which may come from the human gut, where several strains of the bacteria reside. Some of those strains help their human hosts by aiding digestion and blocking other infectious organisms.

To study how friendly and infection-causing E. coli strains differ, researchers used a new approach called metabolomics. Instead of examining genes, metabolomics analyzes all the chemicals produced by a cell, which includes bacterial growth signals, toxins, and waste products. This allowed them to look at the end products of many genes working together. Bacteria studied in the experiment came from patients with recurrent UTIs. The researchers cultured E. coli from both stool and urine samples and found that the strains from urine made more yersiniabactin and salmochelin. Iron is an important nutrient typically kept under tight control by the host, and there is evidence that competition for iron has been raging for millennia between disease-causing microbes and the hosts they exploit. There may, however, be multiple ways to take advantage of the infectious bacterial strains’ reliance on siderophores. Researchers will try to block or disrupt the activity of the proteins that make siderophores, but they also may use a “Trojan horse” strategy. To steal iron, siderophores have to be sent out from the cell, bind to the iron, and then be taken back into the cell. If we can design an antibiotic that looks like a siderophore, we might be able to trick only disease-causing bacteria into taking up the drug while leaving other bacteria alone.

Quantitative Metabolomics Reveals an Epigenetic Blueprint for Iron Acquisition in Uropathogenic Escherichia coli. 2009 PLoS Pathog 5(2): e1000305
Bacterial pathogens are frequently distinguished by the presence of acquired genes associated with iron acquisition. The presence of specific siderophore receptor genes, however, does not reliably predict activity of the complex protein assemblies involved in synthesis and transport of these secondary metabolites. Here, we have developed a novel quantitative metabolomic approach based on stable isotope dilution to compare the complement of siderophores produced by Escherichia coli strains associated with intestinal colonization or urinary tract disease. Because uropathogenic E. coli are believed to reside in the gut microbiome prior to infection, we compared siderophore production between urinary and rectal isolates within individual patients with recurrent UTI. While all strains produced enterobactin, strong preferential expression of the siderophores yersiniabactin and salmochelin was observed among urinary strains. Conventional PCR genotyping of siderophore receptors was often insensitive to these differences. A linearized enterobactin siderophore was also identified as a product of strains with an active salmochelin gene cluster. These findings argue that qualitative and quantitative epi-genetic optimization occurs in the E. coli secondary metabolome among human uropathogens. Because the virulence-associated biosynthetic pathways are distinct from those associated with rectal colonization, these results suggest strategies for virulence-targeted therapies.

Related:

• Iron Uptake and Virulence
• Spread of Pathogenicity Islands in Escherichia coli
• The continuing evolution of E. coli O157:H7

The pathogenesis of HIV begins with a profound depletion of CD4+ T cells in the gut followed by a long period of clinically silent but dynamic virus replication and diversification with high host cell turnover before the onset of AIDS. The AIDS-defining opportunistic infections and tumors mark the end-point of a long balancing act between virus and host that occurs when CD4+ T cell numbers fall below a level that can sustain immunity. Comparative studies of lentivirus infections in other species show that AIDS is not an inevitable outcome of infection because simian immunodeficiency virus in natural hosts seldom causes disease. What distinguishes pathogenic from ‘passenger’ infection is a systemic activation of immune responses followed by destruction of the integrity of lymphoid follicles. Macrophage and dendritic cell infection also contribute to pathogenesis. Maedi-Visna virus infection in sheep, which targets these cells but not T lymphocytes, also leads to progressive disease and death that resembles the wasting and brain diseases of HIV without the T cell immunodeficiency. Thus, lessons from pathogenic and nonpathogenic lentivirus infections provide insight into the complex syndrome called AIDS.

Why is HIV a pathogen? Trends Microbiol. 2008 16(12):555-60

Related:

• How does HIV cause AIDS?
• Immune exhaustion in HIV infection
• HIV “can never be cured”
• HIV-2 – a kinder AIDS virus?

In 1928, by chance, Alexander Fleming discovered penicillin, which was subsequently developed and saved millions from death by infectious disease. In this article in Microbiology Today, Kevin Brown recounts the story of this amazing antibiotic and tells something of the man who found it:

In many ways Fleming could have only discovered the original wonder drug in his musty, dusty, overcrowded, cluttered laboratory at St Mary’s Hospital. After all, if there was no possibility of contamination there could have been no penicillin. Some might argue that without Fleming, there would have been none either. Certainly, the chance contamination of culture plates was common, but Fleming’s genius was to notice something unusual and act upon it. As a scientist, he was very much in the tradition of the 19th-century lone researcher interested in unusual phenomena. This approach was to pay dividends when in September 1928 he returned from a 6-week holiday to find not only that a plate of staphylococci, he had been working on before his holiday had become contaminated by a fungus, but that there was the now classic zone of inhibition around the mould. Ever the master of understatement, Fleming’s response was typical of the man: “That’s funny!”

Read more

Related:

• Towards The Next 80 Years of Penicillin Production
• Penicillin: Triumph and Tragedy
• Antibiotics will not get rid of your cold