For more than three years (since April 2006) I’ve been experimenting with podcasts covering all aspects of microbiology. I decided to have a break over the last month, and during that time I have been thinking about the future. On balance, I feel that the audio format of the podcasts does not add much value to the content beyond what could be achieved with text and images in the style of standard posts on this site. In some circumstances though, a video can add significant value, so I have decided not to post any more audio podcasts for the foreseeable future and to invest the time in producing occasional videos which you will be able to view on this site. All of the old podcast files will remain available here.
Thanks for listening, and here’s the first of the new videos:
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.
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.
Cells arrange their components – proteins, lipids, and nucleic acids – in organized and reproducible ways to optimize their activities and to improve cell efficiency and survival. Eukaryotic cells have a complex arrangement of subcellular structures such as membrane-bound organelles and cytoskeletal transport systems. However, subcellular organization is also important in prokaryotic cells, including rod-shaped bacteria such as E. coli, most of which lack such well-developed systems of organelles and motor proteins for transporting cellular cargoes. In fact, it has remained somewhat mysterious how bacteria are able to organize and spatially segregate their interiors.
The E. coli chemotaxis network, a system important for the bacterial response to environmental cues, is one of the best-understood biological signal transduction pathways and serves as a useful model for studying bacterial spatial organization because its components display a nonrandom, periodic distribution in mature cells. Chemotaxis receptors aggregate and cluster into large sensory complexes that localize to the poles of bacteria. To understand how these clusters form and what controls their size and density, a recent study used ultrahigh-resolution light microscopy, called photoactivated localization microscopy, to visualize individual chemoreceptors in single E. coli cells. From these high-resolution images, the authors were able to determine that receptors are not actively distributed or attached to specific locations in cells. Instead, it appears that random receptor diffusion and receptor–receptor interactions are sufficient to generate the observed complex, ordered pattern. This simple mechanism, termed stochastic self-assembly, may prove to be widespread in both prokaryotic and eukaryotic cells.
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Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. 2009 PLoS Biol 7(6): e1000137 doi:10.1371/journal.pbio.1000137
The Escherichia coli chemotaxis network is a model system for biological signal processing. In E. coli, transmembrane receptors responsible for signal transduction assemble into large clusters containing several thousand proteins. These sensory clusters have been observed at cell poles and future division sites. Despite extensive study, it remains unclear how chemotaxis clusters form, what controls cluster size and density, and how the cellular location of clusters is robustly maintained in growing and dividing cells. Here, we use photoactivated localization microscopy (PALM) to map the cellular locations of three proteins central to bacterial chemotaxis (the Tar receptor, CheY, and CheW) with a precision of 15 nm. We find that cluster sizes are approximately exponentially distributed, with no characteristic cluster size. One-third of Tar receptors are part of smaller lateral clusters and not of the large polar clusters. Analysis of the relative cellular locations of 1.1 million individual proteins (from 326 cells) suggests that clusters form via stochastic self-assembly. The super-resolution PALM maps of E. coli receptors support the notion that stochastic self-assembly can create and maintain approximately periodic structures in biological membranes, without direct cytoskeletal involvement or active transport.
Kaposi’s sarcoma (KS) is a multifocal tumour only found in a few groups of people, including elderly Mediterranean men, individuals in Africa and patients with immune disorders. The tumours arise from the formation of new blood or lymphatic vessels (angiogenesis or lymphangiogenesis) due to the proliferation of endothelial cells. In 1994 Chang and Moore identified a new virus, Kaposi’s sarcoma-associated herpesvirus (KSHV) as the cause of these tumours.
Unlike other herpesviruses, the seroprevalence of KSHV is not ubiquitous, perhaps only 5% in those countries with low KSHV rates such as the USA and Northern Europe). Like all herpesviruses, KSHV infection persists for the life of the host and can enter either of two states: latency or lytic reactivation. In latency, the minimum number of viral genes is expressed to maintain the virus genome in dividing cells, evading immune detection. Lytic reactivation occurs when the virus re-enters productive replication to generate new progeny, lysing the host cell in the process. And like all herpesviruses KSHV likes to mess with the immune system of its host. The KSHV genome contains 86 genes, almost a quarter of which encode proteins with immunoregulatory activities such as T- and B-cell function, complement activation, the innate antiviral interferon response and natural killer cell activity. Many of these gene are homologues of cellular proteins.
The KSHV proteins MIR1 and MIR2 ubiquitinate the cytoplasmic tail of MHC-I which triggers endocytosis and proteasomal degradation. This protects KSHV-infected cells from NK-mediated lysis. MIR2 can also down-regulate other components of the immune synapse, ICAM (CD54) and PECAM (CD31) by the same mechanism.
The KSHV vOX2 protein causes the cellular CD200 receptor to deliver an inhibitory signal to granulocytes, although the mechanism by which this acts is not yet well defined.
The KCP protein is present on the surface of KSHV virions and infected cells and protects them from complement attack by accelerating the decay of the classical pathway C3 convertase enzyme complex.
The K15 protein activates MAP kinases and this affects immune function.
KSHV encodes a family of 12 miRNAs. These regulate both B- and T-cell function.
The K1 protein reduces the presence of B cell receptors on the surface of B cells and interferes with the production of cytokines, and inhibits apoptosis.
The MIR2 protein down-regulates tetherin, which is involved in normal B-cell differentiation.
Three KSHV chemokine homologues (vCCL1–3) have affinity for chemokine receptors (CCRs) and this affects T-cell responses.
KSHV proteins inhibit interferon pathways.
Since KSHV infection results in lifelong persistence of the virus, these immunomodulation activities are clearly successful in preventing its elimination by the immune system. Many questions about KSHV infection remain unanswered, but we have learned valuable lessons about the normal function of the immune system through studying this virus.
When fish school, birds flock, insects and bacteria swarm, a population of similar individuals cruises along similar, sometimes cyclic, paths. How do the members of a swarm anticipate the movement of others to coordinate movement with them? And how do members, when each is moving rapidly near to others, avoid impeding their neighbor’s motion? These general issues, which have yet to be resolved for any schooling, flocking, or swarming organism, can be investigated in swarming bacteria. Such investigation might have practical value because swarming enables pathogens like Proteus, for example, to invade the urinary tract and to spread along the surface of catheters placed in the urethra. The behavior of swarming individuals might also suggest ways to speed high density automobile or pedestrian traffic and ways to avoid traffic jams. Bacterial sensory systems and behaviors are more amenable to analysis than those of animals. Because they are relatively small; several thousand bacteria can be followed in a time lapse movie of a swarm. Among bacteria that swarm are the hyperflagellated bacteria, all of the Myxobacteria, which lack flagella, and the Bacteriodetes that include Cytophaga, Flavobacteria, and Bacteriodes. Millions of Myxococcus xanthus cells are found to swarm outward for more than a week at a steady rate of approximately 0.1 mm/hr, a rate close to half the speed of individual cell movement. Swarming gives them a significant growth advantage: Whereas cells in the swarmcenter are competing with each other for nutrient and oxygen, cells at the swarm edge have practically unfettered access to both.
Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm spread efficiently while being able to perceive and interfere minimally with the motion of others. To this end, we investigate swarms of the myxobacterium, Myxococcus xanthus. Individual M. xanthus cells are elongated; they always move in the direction of their long axis; and they are in constant motion, repeatedly touching each other. Remarkably, they regularly reverse their gliding directions. We have constructed a detailed cell- and behavior-based computational model of M. xanthus swarming that allows the organization of cells to be computed. By using the model, we are able to show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. Cells at the swarm edge gain maximum exposure to nutrient and oxygen. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal M. xanthus cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Finally, we observe that, with time, reversals increase the cell alignment, and generate clusters of parallel cells.
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It’s been another busy year at MicrobiologyBytes, with more than 300 posts this year, and over half a million page views, so here’s a whistle-stop tour of just some of the topics we’ve looked at during the last year:
The 14th October 2008 was the first ever Open Access Day. Open Access is a fundamental component of a new system for exchanging scholarly research results which aims to:
transform health
maximize research outputs
enable faster scientific discoveries
inspire young people
transcend the wealth of the institution
realize cost savings
ensure medical research is conducted for the public good and made available to everyone who needs it
For more than three years (since April 2006) I’ve been experimenting with podcasts covering all aspects of microbiology. I decided to have a break over the last month, and during that time I have been thinking about the future. On balance, I feel that the audio format of the podcasts does not add much value to the content beyond what could be achieved with text and images in the style of standard posts on this site. In some circumstances though, a video can add significant value, so I have decided not to post any more audio podcasts for the foreseeable future and to invest the time in producing occasional videos which you will be able to view on this site. All of the old podcast files will remain available here.
Kaposi’s sarcoma (KS) is a multifocal tumour only found in a few groups of people, including elderly Mediterranean men, individuals in Africa and patients with immune disorders. The tumours arise from the formation of new blood or lymphatic vessels (angiogenesis or lymphangiogenesis) due to the proliferation of endothelial cells. In 1994 Chang and Moore identified a new virus, Kaposi’s sarcoma-associated herpesvirus (KSHV) as the cause of these tumours.
