MicrobiologyBytes

Herpes simplex virus (HSV) is an important pathogenic agent that causes recurrent oral and genital lesions, blindness and encephalitis. It is a member of the family Herpesviridae, which contains three subfamilies (alpha- beta- and gammaherpesvirinae) whose members infect humans to cause a variety of ailments, from benign rashes to nasopharyngeal carcinoma. Although this review focuses on HSV, the assembly steps that occur in the nucleus and the proteins involved are highly conserved among all family members, which suggests that antiviral agents that block these steps might be effective against many different herpesviruses and their associated diseases. Despite this potential, a broadly effective compound has yet to be realized, in part because many of the processes are only poorly understood in sufficient molecular detail. This review outlines these intranuclear assembly steps and illustrate potential and existing antiviral strategies that exploit them.

Herpes simplex virus capsid assembly and DNA packaging: a present and future antiviral drug target. (2011) Trends Microbiol. 19(12) :606-613

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Recent evidence shows that the quadrivalent HPV vaccine prevents several HPV-related diseases in men. However, despite the licensure of the vaccine in the USA for men 9 through 26 years of age, rates of male vaccination are very low. Research on acceptability, in general, indicates strong interest in vaccination among men, parents, and healthcare providers, though female vaccination is typically seen as a higher priority. Cost-effectiveness studies indicate that in the context of modest female vaccination rates and with the specification of a broad range of disease outcomes (e.g. genital warts, anogenital cancers, and oropharyngeal cancers), male vaccination can be quite cost-effective.

This review describes the indications for vaccinating men with the quadrivalent human papillomavirus (HPV) vaccine, reports on the U.S. rates of male vaccination, and reviews the recent research on acceptability of vaccinating men and research on the cost-effectiveness of adding men to existing female HPV immunization programs.

Summary: Men are at high risk for HPV infection and can benefit from vaccination, but vaccination rates among men remain extremely low. More research needs to be done on the predictors of uptake of HPV vaccine among men and on the development of interventions to increase male vaccination.

Human papillomavirus vaccine and men: what are the obstacles and challenges? (2012) Curr Opin Infect Dis. 25(1): 86-91

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By convention, the human adenovirus replication cycle is divided into two phases, an early and a late phase, which are separated by the onset of viral DNA replication. Based on temporal changes of the gene expression pattern as revealed by DNA microarray analysis, adenovirus type 2 (Ad2) infection in human primary lung fibroblasts can be divided into four periods. The first period is from 0 to 12 h after infection before or shortly after adenoviral gene expression has commenced. During this time, changes in cellular gene expression are likely to be triggered by the virus entry process, such as attachment of virus to cell surface receptors, and its intracellular transport along microtubules.

The second period covers the time from 12 to 24 h after infection and follows activation of the immediate early E1A gene. During this period, there is an increase in the number of differentially expressed cellular genes. About 50% of these genes are involved in cell cycle regulation, cell proliferation and antiviral response. The third period extends from 24 to 42 h after infection. By this time, the virus has gained control of the cellular metabolic machinery, resulting in an efficient replication of the viral genome. Additional changes in cellular gene expression are modest during this phase. During the fourth and last period, when the cytopathic effect becomes apparent, the number of down-regulated genes increases dramatically including many genes involved in intra- and extracellular structure.

The most intensive battle between the adenovirus and its host takes place during the second period after adenovirus genes expression has started. The major functions of the early gene products are to force the host cell to enter the S phase in order to provide optimal conditions for viral DNA replication and to suppress the host antiviral response. Adenoviruses encode several regulatory proteins within the early regions E1A, E1B, E3, and E4. The immediate-early E1A gene encodes two regulators of viral and cellular gene expression, the E1A-243R and E1A-289R proteins. The E1A proteins act as promiscuous transcriptional activators or repressors of cellular genes. E1A proteins are essential for promoting the host cell to enter the S phase. This is achieved by the binding of the E1A proteins to members of the retinoblastoma tumor suppressor (pRB) family, thereby releasing the E2F transcription factors, which are activators of genes required in the S-phase.

The transcriptome of the adenovirus infected cell. Virology. 9 Jan 2012
Alternations of cellular gene expression following an adenovirus type 2 infection of human primary cells were studied by using superior sensitive cDNA sequencing. In total, 3791 cellular genes were identified as differentially expressed more than 2-fold. Genes involved in DNA replication, RNA transcription and cell cycle regulation were very abundant among the up-regulated genes. On the other hand, genes involved in various signaling pathways including TGF-β, Rho, G-protein, Map kinase, STAT and NF-κB stood out among the down-regulated genes. Binding sites for E2F, ATF/CREB and AP2 were prevalent in the up-regulated genes, whereas binding sites for SRF and NF-κB were dominant among the down-regulated genes. It is evident that the adenovirus has gained a control of the host cell cycle, growth, immune response and apoptosis at 24h after infection. However, efforts from host cell to block the cell cycle progression and activate an antiviral response were also observed.

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When a virus infects a cell, it hijacks resources of the cell to manufacture and release a new generation of progeny virus particles. Yet despite its central importance, methods to precisely quantify virus production at the cellular level are lacking. Most approaches measure the production of virus by sampling from a population of infected cells, providing average values that mask the potentially wide-ranging and significant behaviors of individual cells.

Within a laboratory culture of virus-infected cells, or within a tissue of an infected host, individual cells can diverge in behavior from the average or majority of infected cells. However, these rare cells may nevertheless contribute importantly to the long-term behavior of the infection, well beyond their initial encounter with the virus. Because these rare cell behaviors are generally obscured during average-cell measures of infection, they highlight the need for single-cell measures of behavior that can be readily performed on many individual cells to reveal the extent of cell heterogeneity. This paper demonstrates a method to measure the kinetics of virus production from individual cells, without confounding effects from secondary infections. The method combines a series of simple steps that can be performed in any cell biology or virology facility, without reliance on specialized equipment.

Kinetics of virus production from single cells. Virology. 03 Jan 2012
The production of virus by infected cells is an essential process for the spread and persistence of viral diseases, the effectiveness of live-viral vaccines, and the manufacture of viruses for diverse applications. Yet despite its importance, methods to precisely measure virus production from cells are lacking. Most methods test infected-cell populations, masking how individual cells behave. Here we measured the kinetics of virus production from single cells. We combined simple steps of liquid-phase infection, serial dilution, centrifugation, and harvesting, without specialized equipment, to track the production of virus particles from BHK cells infected with vesicular stomatitis virus. Remarkably, cell-to-cell differences in latent times to virus release were within a factor of two, while production rates and virus yield spanned over 300-fold, highlighting an extreme diversity in virus production for cells from the same population. These findings have fundamental and technological implications for health and disease.

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What would happen if all the leaves fell off the trees and did not rot? We’d be buried under them and all plants would run out of nutrients and die, then we would starve. So the seemingly non-sexy buisness of rotting is rather important when it comes to element and nutrient cycles.

In ecological studies, leaf litter degradation is often estimated by measuring parameters such as soil respiration, litter mass loss or the activities of specific microbial enzymes in soil extracts. In microbiology, the degradation of plant-derived compounds such as lignocellulose has been studied using a few microbial model species and has recently led to the sequencing of the genomes of different saprotrophic fungal species which use different strategies to degrade plant material, thus revealing the full enzymatic machinery implicated in this process. Under natural conditions, litter degradation is generally carried out by consortia of species that either act simultaneously or replace one another on a common piece of plant debris in a sometimes predictable manner and not by a single microbial species. It can therefore be anticipated that the molecular machinery deployed to completely mineralize litter in the field is far more complex and diverse than the machinery observed in a single microbial genome. In addition, it is likely that the diversity of this machinery is partly controlled by litter chemistry and complexity and therefore by plant community composition.

By allowing access to the genome contents of the different microorganisms present in a common environment (metagenomics) or to the set of genes they express (metatranscriptomics), environmental genomics offers a novel opportunity to decipher at the molecular level, complex ecological processes such as plant organic matter degradation, thus bridging the gap between global field measurements and targeted genomic approaches.

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils. (2012) PLoS ONE 7(1): e28967. doi:10.1371/journal.pone.0028967
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)–0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.

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Iron is a highly abundant metal on earth and is vital for virtually all organisms. Despite its abundance, iron deficiency is the most prevalent nutrition disorder worldwide. It mostly affects infants, young children and women in developing countries. Iron deficiency has major health consequences such as infection, poor pregnancy outcome, and impaired physical and cognitive development. Several trials have shown that iron deficiency can be effectively controlled by both iron supplementation and fortification programmes. However, safety of iron supplementation has been questioned and there is evidence suggesting that untargeted oral iron supplementation in regions with high prevalence of malaria transmission and infectious diseases can cause an increase in infections, hospital admission and mortality in young children. This might be at least partly ascribed to iron also being an essential requirement for the growth of most bacterial species. Importantly, iron availability is frequently involved in the expression of virulence-associated properties in pathogenic bacteria:

Iron Availability Increases the Pathogenic Potential of Salmonella Typhimurium and Other Enteric Pathogens at the Intestinal Epithelial Interface. (2012) PLoS ONE 7(1): e29968. doi:10.1371/journal.pone.0029968
Recent trials have questioned the safety of untargeted oral iron supplementation in developing regions. Excess of luminal iron could select for enteric pathogens at the expense of beneficial commensals in the human gut microflora, thereby increasing the incidence of infectious diseases. The objective of the current study was to determine the effect of high iron availability on virulence traits of prevalent enteric pathogens at the host-microbe interface. A panel of enteric bacteria was cultured under iron-limiting conditions and in the presence of increasing concentrations of ferric citrate to assess the effect on bacterial growth, epithelial adhesion, invasion, translocation and epithelial damage in vitro. Translocation and epithelial integrity experiments were performed using a transwell system in which Caco-2 cells were allowed to differentiate to a tight epithelial monolayer mimicking the intestinal epithelial barrier. Growth of Salmonella typhimurium and other enteric pathogens was increased in response to iron. Adhesion of S. typhimurium to epithelial cells markedly increased when these bacteria were pre-incubated with increasing iron concentration), whereas this was not the case for the non-pathogenic Lactobacillus plantarum. Cellular invasion and epithelial translocation of S. typhimurium followed the trend of increased adhesion. Epithelial damage was increased upon incubation with S. typhimurium or Citrobacter freundii that were pre-incubated under iron-rich conditions. In conclusion, our data fit with the consensus that oral iron supplementation is not without risk as iron could, in addition to inducing pathogenic overgrowth, also increase the virulence of prevalent enteric pathogens.

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First it was foot and mouth virus.
Then it was bluetongue virus.
Now it is Schmallenberg virus.
So here’s 10 things you didn’t know about Schmallenberg virus:

1. Schmallenberg virus was first isolated in Schmallenberg, Germany, in November 2011.
2. Schmallenberg virus is a Bunyavirus, one of a large group of of negative-stranded RNA viruses.
3. Why should I care? In cows, Schmallenberg virus causes fever and a drastic reduction in milk production. In sheep it causes congenital malformations and stillborn lambs (also stillborn calves in cows).
4. Schmallenberg virus was first identifed in the UK on 23rd January 2012.
5. Like Bluetongue, Schmallenberg virus is transmitted by midges (Culicoides spp.), which means we will be unlikely to be able to eradicate it – vaccination of anaimals is the only likely effective response.
6. Where did Schmallenberg virus come from? The virus genome is most closely related to sequences of a different Orthobunyavirus called Shamonda virus which belongs to the so-called Simbu serogroup known to infect ruminants and be transmitted by midges. In other words, it has form. But whether it is newly evolved (unlikely) or just newly discovered we don’t yet know.
7. How did Schmallenberg virus reach the UK? We don’t know. It could have been due to animal movements, but since it was first identifed in eastern England, it’s possible that it arrived in midges travelling under their own steam.
8. Is Schmallenberg virus going to spread to other parts of the UK and other countries? Yes, you can bet on that (just like bluetongue did).
9. Can I catch Schmallenberg virus? Honest answer: We don’t know. Possibly, but there have been no reports of human illness from areas where the virus is known to exist, so I wouldn’t worry too much.
10. Where can I find the latest news about Schmallenberg virus? Right here.
11. OK, one last time, why should I care? Because Schmallenberg virus is going to cost European and probably worldwide ecomonies millions of pounds. And that will affect you.

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Staphylococcus aureus is responsible for the vast majority of bacterial skin infections in humans. The propensity for S. aureus to infect skin involves a balance between cutaneous immune defense mechanisms and virulence factors of the pathogen. The tissue architecture of the skin is different from other epithelia especially since it possesses a corneal layer, which is an important barrier that protects against the pathogenic microorganisms in the environment. The skin surface, epidermis, and dermis all contribute to host defense against S. aureus. Conversely, S. aureus utilizes various mechanisms to evade these host defenses to promote colonization and infection of the skin.

This review focuses on host-pathogen interactions at the skin interface during the pathogenesis of S. aureus colonization and infection.

Host-pathogen interactions between the skin and Staphylococcus aureus. Curr Opin Microbiol. 01 Dec 2011

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Regulons are the basic units of cellular response systems in bacterial cells, and represent a most basic concept in bacterial studies. A bacterial regulon is a group of operons that are transcriptionally co-regulated by the same regulatory machinery, consisting of trans regulators (transcription factors or simply TFs) and cis regulatory binding elements in the promoters of the operons they regulate. Operationally, a regulon contains operons regulated by one same transcription factor. Since the term regulon was first proposed in 1964, 173 regulons have been fully or partially identified in E. coli K12 and many more in other bacteria e.g. B. subtilis.

Loosely speaking, regulons can be categorized into two classes: local and global regulons, with the former corresponding to regulons consisting of only a few component operons and the latter having a relatively large number of operons. While the functionalities of the known regulons have been well studied, very little is known about how regulons are organized in a bacterial genome.

This paper examines the organizational principles of regulons in bacterial genomes, looking at E. coli K12 and Bacillus subtilis. The key findings are (1) operons of each regulon tend to form a few closely located clusters along with genome; (2) TFs are under stronger evolutionary constraints than their TGs; and (3) the global arrangement of the component operons of all the (known) regulons in a genome tend to minimize a simple scoring function.

Genomic Arrangement of Regulons in Bacterial Genomes. (2012) PLoS ONE 7(1): e29496. doi:10.1371/journal.pone.0029496
Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF’s genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles. Tweet