MicrobiologyBytes

A growing number of RNA viruses are known to depend on virus-encoded ion channels for efficient production of infectious virions and, in some cases, for the subsequent infection of cells. Viroporins are small hydrophobic proteins, usually less than 100 amino acids in length, and typically contain one or two transmembrane domains; oligomerization is therefore necessary for the formation of ion channel complexes. By far the best characterized viroporin is the M₂ proton channel of influenza A virus, which is the target for the antiviral drugs amantadine and rimantadine. M₂ sets a precedent for viroporins as therapeutic targets that has driven research into the ion channels of other clinically important viruses. In the light of rapid RNA virus evolution generating drug resistance, new compounds targeting viroporins could be a valuable addition to future combinatorial antiviral strategies. Difficulties associated with working with membrane proteins in high-throughput systems lend support to a rational approach for drug development based on the availability of high-resolution molecular structures (Plugging the holes in hepatitis C virus antiviral therapy. PNAS USA 28 July 2009).

In a recent issue of PNAS, researchers describe the structure of a complete viroporin complex, the p7 ion channel of hepatitis C virus (HCV), at 16-Å resolution by using single-particle electron microscopy (The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy. 2009 PNAS USA 106: 12712–12716). The hexameric p7 complex (42 kDa) is one of the smallest objects to be visualized by these methods to date which, combined with the hydrophobic nature of p7, makes this work an impressive technical achievement. The study provides optimism that p7 inhibitors could one day become part of HCV therapy.

Related:

• Viroporins
• Hepatitis C Virus: a mountain to climb
• A breakthrough in understanding hepatitis C virus

In PNAS, Warren Olanowa and Stanley Prusiner ask, Is Parkinson’s disease a prion disorder?
Parkinson’s disease (PD) is an age-related, neurodegenerative disease that affects approximately one million people in the United States. Pathologically, the disease is characterized by a loss of dopamine neurons in the substantia nigra coupled with proteinaceous inclusions in nerve cells and terminals, known as Lewy bodies and Lewy neurites, respectively. PD pathology is also known to affect nondopamine neurons in the upper and lower brainstem, olfactory system, cerebral hemisphere, spinal cord, and autonomic nervous system. The cause of cell death in PD is not known, but proteolytic stress with the accumulation of misfolded proteins has been implicated.

In the current issue of PNAS, Desplats et al demonstrate that nerve cells which overexpress tagged alpha-synuclein can transmit the protein to neural stem cells in both in vitro and in vivo models (Inclusion formation and neuronal cell death through neuron-to-neuron transmission of alpha-synuclein. 2009 PNAS USA 106:13004–13005). This important study could explain the remarkable finding that human embryonic dopamine nerve cells implanted into the striatum of patients with PD develop PD pathology with loss of dopamine markers and classic Lewy bodies. It also provides insight into how alpha-synuclein pathology might sequentially spread throughout the nervous system in PD.

It is thus possible that PD is a prion disorder resulting from increased production and/or impaired clearance of proteins such as alpha-synuclein, leading to misfolding and the formation of toxic oligomers, aggregates, and cell death. Further, it is possible that alpha-synuclein is a prion protein that can self-aggregate and be transmitted to unaffected cells, thus extending the disease process. While genetic causes represent an obvious source of increased levels of aberrantly folded alpha-synuclein in familial PD cases, a combination of aging, oxidative stress, inflammation, environmental toxins, hereditary factors, and impaired clearance may all feature in varying ways in causing altered metabolism of alpha-synuclein, resulting in the pathogenesis of sporadic PD. This concept suggests that drugs directed toward reducing the formation and/or facilitating the clearance of misfolded alpha-synuclein, so as to arrest or reverse the self-propagation process, might represent a novel therapeutic interventions for the treatment of PD.

Related:

• Stanley Prusiner at the SGM: Prion Biology and Diseases
• What the heck are prions for?
• Drugs for treatment of prion infections
• Alzheimer’s Disease and Prions

With football managers blaming the state of the pitch for the failure of their teams to win big matches, anything that improves the condition of turf can only be welcome. In this article in Microbiology Today (pdf) Alan Gange describes how mould diseases can devastate the sward and some work being done to exploit the power of beneficial microbes to act as “biostimulants” and improve the health of turf grasses:

April 2009: both Manchester United and Arsenal lose their FA Cup semi final matches at Wembley Stadium. Afterwards, both managers, Sir Alex Ferguson and Arsène Wenger, blamed the state of the Wembley pitch, Ferguson describing it as “spongy and dead”. A few days later, the head groundsman was sacked and the pitch re-laid at a cost approaching £100,000. This is the sixth time that the pitch has been replaced since it was first laid in 2006. Whether the pitch or the groundsman were in any way to blame for the fact that Everton scored more times in the penalty shoot-out than did United is, of course, debatable. However, these facts illustrate how important the quality of the playing surface is in sport and the vast sums of money that are spent to construct and maintain these surfaces. The highest quality turf surfaces are to be found on golf courses. There are over 2,500 golf courses in the UK and nearly 32,000 worldwide. The quality of the tees, fairways and greens is of the utmost importance and are always to blame when one’s approach shot hits the rough or that critical putt is missed! Sports turf is an unusual plant community, composed of just a few grass species. In British fairways and football pitches, the predominant grass is Lolium perenne (perennial rye). In our golf tees and greens, the desirable grasses are species of bents (Agrostis) and fescues (Festuca), with many cultivars of each species available. However, all turf systems become invaded by the weed grass Poa annua (annual meadow grass). Poa is undesirable, because it is nutrient and water hungry, susceptible to disease and provides an inferior quality playing surface. The control of Poa is the key to successful sports turf management.

Read more

Related:

• Toxins for microbial attack and plant defence
• Biological pest control of bark beetles

Retroviruses, such as HIV, that are already within cells are more easily transmitted when they spread through direct contact between cells than if they are floating free in the bloodstream. Researchers have recorded video of virus activity within cells that helps explains why cell-to-cell transmission is so efficient and may in turn provide insights into potential targets for a new generation of antiretroviral drugs.

Cell-to-cell transmission of retroviruses is a thousand times more efficient than extracellular infection, and because retroviruses spread through the tight cell-cell interface, they are out of reach of the immune system. Using imaging technology that can track individual virus particles in real time, the research team discovered that retrovirus-infected cells can specifically assemble daughter viruses at the point of contact between cells. Ten times more of these particles are found at these cellular connection points than elsewhere at the surface of cells. The ability of infected cells to specifically produce viruses only at cell interfaces offers an explanation of how viruses spread so efficiently. The team identified a clue to how virus assembly is targeted to these points of contact: it involves a retrovirus protein called Env that docks with uninfected cells and then attracts the viral particles to these sites. If this adhesion molecule lacked a cytoplasmic tail, then the virus particles did not assemble at the patches of contact between cells.

Somewhere down the road it is possible that we may be able to develop completely new antiviral strategies based on targeting cell-to-cell transmission.

Assembly of the Murine Leukemia Virus Is Directed towards Sites of Cell–Cell Contact. 2009 PLoS Biol 7(7): e1000163 doi:10.1371/journal.pbio.1000163
We have investigated the underlying mechanism by which direct cell–cell contact enhances the efficiency of cell-to-cell transmission of retroviruses. Applying 4D imaging to a model retrovirus, the murine leukemia virus, we directly monitor and quantify sequential assembly, release, and transmission events for individual viral particles as they happen in living cells. We demonstrate that de novo assembly is highly polarized towards zones of cell–cell contact. Viruses assembled approximately 10-fold more frequently at zones of cell contact with no change in assembly kinetics. Gag proteins were drawn to adhesive zones formed by viral Env glycoprotein and its cognate receptor to promote virus assembly at cell–cell contact. This process was dependent on the cytoplasmic tail of viral Env. Env lacking the cytoplasmic tail while still allowing for contact formation, failed to direct virus assembly towards contact sites. Our data describe a novel role for the viral Env glycoprotein in establishing cell–cell adhesion and polarization of assembly prior to becoming a fusion protein to allow virus entry into cells.

Related:

• Retroviruses
• Retrovirus infection of resting cells
• HIV infection is due to the sins of the fathers

Viral hepatitis is mostly caused by five distinct viruses named hepatitis A–E. Despite their names, the five viruses are unrelated, with totally different genome structures and replication mechanisms. Hepatitis E virus (HEV) is responsible for endemic hepatitis as well as sporadic epidemics of acute, enterically transmitted hepatitis in the developing world. HEV accounts for more than 50% of acute viral hepatitis in young adults in these regions, with a case fatality of 1–2% in regular patients and up to 20% in pregnant women. Because there is no robust cell culture system for this virus, and because it is not closely related to any other well-characterized virus, little is known about the molecular biology of HEV or its strategy for replication.

HEV is a small, non-enveloped, icosahedral virus with a positive-sense RNA genome of 7.2 kb. Its genomic RNA is polyadenylated and contains three open reading frames (ORFs). HEV was originally classified in the Caliciviridae family because of its structural similarity to other caliciviruses. However, it is now regarded as the sole member of the Hepevirus genus. The genomic RNA of HEV exhibits several distinct features compared to the genomic RNA of caliciviruses, including a methylated cap at the 5′-end and an ORF1 with functional domains arranged in a different order.

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A recent paper in PNAS describes the crystal structure of HEV at 3.5-Å resolution (Structure of the hepatitis E virus-like particle suggests mechanisms for virus assembly and receptor binding. PNAS USA July 21, 2009). The capsid protein of this virus contains three linear domains that form distinct structural elements:

• S, the continuous capsid
• P1, three-fold protrusions
• P2, two-fold spikes

Each domain possesses a potential polysaccharide-binding site that may function in receptor binding. Receptor binding to P1 at the capsid protein interface may lead to capsid disassembly and cell entry. These findings significantly advance the understanding of HEV and are useful for the development of vaccines and antiviral medications.

A ProMED-mail post
Date: Wed 22 Jul 2009
Source: Emax Health [edited]
http://www.emaxhealth.com/2/39/32382/east-london-crow-tests-positive-west-nile-virus.html

The Middlesex-London Health Unit announced that a dead crow found in London’s east end has tested positive for West Nile virus and is the 1st in Middlesex-London to test positive for the disease this year [2009].

“What this tells us is that West Nile virus is still present in our community and that we need to be vigilant in protecting ourselves from mosquito bites and reducing the places where they breed,” says Andrew Powell, Vector-Borne Disease Coordinator with the Middlesex-London Health. “The community has always been a great partner in our surveillance and control programs, whether by letting us know when they find dead birds or by eliminating standing water found on their properties.”

To protect yourself and your family against West Nile virus [infection], the Health Unit recommends:

• Wearing light coloured clothing with long-sleeves, pants and socks in areas where mosquitoes are present, especially at dusk and dawn when they are most active.
• Using an insect repellent with DEET. Follow directions for use, especially for children.
• Fixing holes in screens, windows and doors.
• Regularly emptying standing water from garbage cans, wheelbarrows, toys, flowerpots and saucers, pool covers, tires, and other items around your home and yard.
• Cleaning clogged eaves troughs.
• Cleaning and changing water in bird baths every other day.
• Keeping pool pumps circulating.
• Aerating ponds or stocking them with fish.
• Covering openings in rain barrels.

The MLHU Vector-Borne Disease Surveillance Team has made more than 2104 monitoring visits to approximately 220 sites this summer [2009], treating over 8 hectares of surface water; this is in addition to the treatment of more than 100 000 roadside catch basins in London and Middlesex County. Although the Health Unit is reporting its 1st West Nile Virus-positive bird, none of the mosquitoes trapped so far this summer have tested positive for the disease [virus]. [Byline: Ruzik Tuzik]

[This report provides additional evidence of the presence of West Nile virus (WNV) in the UK. Previous reports in 2006 indicated that sentinel chickens developed antibodies to WNV or a closely related flavivirus, and a 2003 publication reported detection of WNV neutralizing antibody and small WNV-related RNA fragments in migratory and resident wild birds (Journal of General Virology for October 2003. Buckley A, Dawson A, Moss SR, Hinsley SA, Bellamy PE, Gould EA. Serological evidence of West Nile virus, Usutu virus and Sindbis virus infection of birds in the UK <http://www.sgm.ac.uk/JGVDirect/19341/19341a.htm>). The question of whether WNV is endemic in the UK or periodically reintroduced by wild birds remains unresolved, but repeated detection of the virus or specific WNV antibodies would add weight for endemicity. - Mod.TY]

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To control mosquito-borne diseases like dengue fever, researchers need to look at the behavior of people, not just the insect that transmits the disease. Vector-borne diseases constitute a largely neglected and enormous burden on public health in many resource-challenged environments, demanding efficient control strategies that could be developed through improved understanding of pathogen transmission. Human movement – which determines exposure to vectors – is a key behavioral component of vector-borne disease epidemiology that is poorly understood.

A new paper attempts to develop a conceptual framework to organize past studies by the scale of movement and then examine movements at fine-scale – i.e. people going through their regular, daily routine – that determine exposure to insect vectors for their role in the dynamics of pathogen transmission. The authors develop a model to quantify risk of vector contact across locations people visit, with emphasis on mosquito-borne dengue virus in the Amazonian city of Iquitos, Peru.

An example scenario illustrates how movement generates variation in exposure risk across individuals, how transmission rates within sites can be increased, and that risk within sites is not solely determined by vector density, as is commonly assumed. This analysis illustrates the importance of human movement for pathogen transmission, yet little is known – especially for populations most at risk to vector-borne diseases (e.g. dengue, leishmaniasis, etc.). The authors outline several important considerations for designing epidemiological studies to encourage investigation of individual human movement, based on this experience studying dengue.

The incidence of dengue fever in Iquitos has varied from around five percent to over 30 percent after new virus serotype introductions. There is no vaccine and no cure for dengue, which is transmitted by the tiger-striped, day-biting mosquito, Aedes aegypti. To track individual human movement, the research team used satellite-based global positioning system (GPS) and culturally-sensitive interviews that were developed by the team. The researchers developed a conceptual model showing that the relevance of human movement at a particular scale depends on vector behavior. Focusing on Aedes aegypti, they illustrated how vector-biting behavior combined with fine-scale movements of individual humans engaged in daily routines can influence transmission. They also outlined several considerations for designing epidemiological studies to encourage studies of individual human movement. They hope to arrive at a better notion of the spatial scale on which dengue transmission occurs and from an operational standpoint, at what scale to focus interventions. Another aim is to encourage researchers of other mosquito-borne diseases, such as malaria, to perform more incisive examination of individual movements.

The Role of Human Movement in the Transmission of Vector-Borne Pathogens. PLoS Negl Trop Dis 3(7): e481 doi:10.1371/journal.pntd.0000481
Human movement is a key behavioral factor in many vector-borne disease systems because it influences exposure to vectors and thus the transmission of pathogens. Human movement transcends spatial and temporal scales with different influences on disease dynamics. Here we develop a conceptual model to evaluate the importance of variation in exposure due to individual human movements for pathogen transmission, focusing on mosquito-borne dengue virus. We develop a model showing that the relevance of human movement at a particular scale depends on vector behavior. Focusing on the day-biting Aedes aegypti, we illustrate how vector biting behavior combined with fine-scale movements of individual humans engaged in their regular daily routine can influence transmission. Using a simple example, we estimate a transmission rate (R0) of 1.3 when exposure is assumed to occur only in the home versus 3.75 when exposure at multiple locations – e.g. market, friends – due to movement is considered. Movement also influences for which sites and individuals risk is greatest. For the example considered, intriguingly, our model predicts little correspondence between vector abundance in a site and estimated R0 for that site when movement is considered. This illustrates the importance of human movement for understanding and predicting the dynamics of a disease like dengue. To encourage investigation of human movement and disease, we review methods currently available to study human movement and, based on our experience studying dengue in Peru, discuss several important questions to address when designing a study. Human movement is a critical, understudied behavioral component underlying the transmission dynamics of many vector-borne pathogens. Understanding movement will facilitate identification of key individuals and sites in the transmission of pathogens such as dengue, which then may provide targets for surveillance, intervention, and improved disease prevention.

Related:

• Dengue Virus
• Pathogenic Flaviviruses
• Changing patterns of chikungunya virus

This summer on MicrobiologyBytes we’ll be revisiting a few old favourites – some of the most popular posts on this site. Today’s post is:

In an effort to combat climate change, aid energy independence and counteract diminishing supplies of fossil fuels, there has been a resurgence of research on renewable and carbon-neutral energy sources. Biofuel production captures the energy of the sun as chemical energy in the bonds of biologically produced materials. All routes to biofuels hence start with photosynthesis, and it is at that point where they diverge. There are basically three routes to convert renewable resources into energy-rich, fuel-like molecules or fuel precursors:

• Direct production by photosynthetic organisms such as plants and algae
• Fermentative or nonfermentative production by heterotrophic microorganisms such as bacteria, yeast or fungi
• Chemical conversion of biomass to fuels

On the first route, production of fuels directly from CO₂ using photosynthetic metabolism appears desirable as it is carbon-neutral in the strictest sense and does not rely on expensive feedstocks. However, this approach faces several major hurdles, most importantly scalability and land use issues. This revies focusses on the fermentative and nonfermentative metabolism of heterotrophic microorganisms and the different fuels they can supply. The emphasis is on the pathways leading to the new generation of microbial fuels, in particular on the key biocatalysts that convert metabolic intermediates into fuel-like molecules, and on the parameters that govern their cost-effective production. Because much of this research has been carried out in biotechnology companies and is unpublished, the citation of some recent patent literature is included.

The exploitation of diverse metabolic pathways leading to energy-rich, fuel-like hydrocarbons opens up a path to develop renewable fuels that go far beyond the restrictions of bioethanol and plant-derived biodiesel. As novel biocatalysts leading to a greater variety of hydrocarbon products are being discovered, microbiologists will have an even more expansive tool box at their disposal to design better fuel to fit the need of different engines. The metabolic efficiency of a particular pathway has a profound impact on the economics of fuel production in a microbial host. Furthermore, microbial fuels that are easy to recover and do not require additional chemical conversion have the best chances to be developed in cost-effective and unsubsidized commercial processes.

New microbial fuels: a biotech perspective. Curr Opin Microbiol. 2009 12(3): 274-81
Bioethanol and plant oil-derived biodiesel are generally considered first generation biofuels. Recognizing their apparent disadvantages, scientists and engineers are developing more sustainable and economically feasible second generation biofuels. The new microbial fuels summarized here have great potential to become viable replacements or at least supplements of petroleum-derived liquid transportation fuels. Yields and efficiencies of the four metabolic pathways leading to these microbial fuels - mostly designed and optimized in Escherichia coli and Saccharomyces cerevisiae using modern tools of metabolic engineering and synthetic biology - and the robustness of the biocatalysts that convert the metabolic intermediates to, in some cases, finished and engine-ready fuels, will determine if they can be commercially successful and contribute to alleviating our dependence on fossil fuels.

Related:

• Microdiesel: microbiology can reduce your carbon footprint
• Termites: wood-munching fuel factories