Archive for August, 2009

MicrobiologyBytes Podcasts

Monday, August 31st, 2009

MicrobiologyBytes 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:

WHO launches new Hendra virus website

Saturday, August 29th, 2009

WHO Hendra virus website

Guinea Worm: Countdown to Zero

Friday, August 28th, 2009

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Influenza virus M1 protein blocks the classical complement pathway

Thursday, August 27th, 2009

The genome of the influenza A virus is composed of eight segments of single stranded RNA, which exist as vRNP with nucleocapsid protein (NP) and RNA dependent RNA polymerase. vRNP is surrounded by matrix protein 1 (M1), which is the most abundant protein in influenza virus particles. It is widely accepted that M1 plays significant roles in many aspects of virus life cycle. M1 interacts with RNA and ribonucleoproteins, virus envelope protein, and is involved in transcription inhibition, RNP nuclear import/export, and budding process. M1 expressed on the infected cell surface is responsible for cross reactive recognition by cytotoxic T lymphocytes. Studies suggest that some M1 mutations affect virus particle morphology and are involved in virus-host protein interaction. Several host proteins have been found to associate with M1. These interactions implicate a broad range of biological significances, such as vRNP export and viral morphogenesis. The interactions between M1 and host proteins are critical for viral propagation but it is unknown if M1 protein has any effects on host immune responses.

Complement

This paper demonstrates that M1 protein is able to interact with complement C1qA and plays an important inhibitory function in the classical complement pathway. The N terminal domain of M1 protein is required for its binding to the globular region of C1qA. As a consequence, M1 blocks the interaction between C1qA and heat aggregated IgG in vitro and inhibits hemolysis. M1 protein prevents the complement mediated neutralization of influenza virus in vitro. In addition, studies on mice indicate that the administration of M1 can promote a higher virus propagation rate in lung and shortened survival of mice infected with the virus. Taken together, these results strongly suggest that M1 protein plays a critical role in protecting the influenza virus from host innate immune system.

Influenza A virus M1 blocks the classical complement pathway through interacting with C1qA. J Gen Virol. Aug 5 2009

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Picorna-like viruses associated with colony collapse disorder of bees

Wednesday, August 26th, 2009

Bee As the premier managed pollinator, the western honey bee, Apis mellifera, contributes more than $14 billion to USA agriculture annually. Beginning in 2006, the American apiculture industry experienced catastrophic losses of unknown origin. The phenomenon, called colony collapse disorder (CCD), was identified by a set of distinctive characteristics, including the absence of dead bees in or near the colony and the presence of abundant brood, honey, and pollen despite vastly reduced numbers of adult workers.

To differentiate among possible explanations for CCD, a new study used whole-genome microarray analysis, comparing gut gene expression in adult worker bees from healthy and CCD colonies. Researchers assayed the gut because it is the principal site of pesticide detoxification and an integral component in the immune defense against pathogens in A. mellifera. Samples from colonies varying in CCD severity were collected on the U.S. east and west coasts in the winter of 2006–2007 and compared with healthy “historical” controls collected in 2004 and 2005.

No simple explanations for the cause of CCD emerge from the microarray analysis. Although gene transcript analysis did not clearly identify a specific cause for CCD, this study documents several patterns possibly suggestive of a causal mechanism. The reduced protein synthetic capabilities that would accompany ribosomal hijacking by multiple picorna-like viruses would leave bees unable to respond to additional stresses from pesticides, nutrition, or pathogens. Although any interpretation of the presence of these rRNA fragments is speculative, the reported interaction between bee picorna-like viruses and rRNA is suggestive of a possible root cause of CCD.

Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera). PNAS USA August 24 2009 doi: 10.1073/pnas.0906970106
Colony collapse disorder (CCD) is a mysterious disappearance of honey bees that has beset beekeepers in the United States since late 2006. Pathogens and other environmental stresses, including pesticides, have been linked to CCD, but a causal relationship has not yet been demonstrated. Because the gut acts as a primary interface between the honey bee and its environment as a site of entry for pathogens and toxins, we used whole-genome microarrays to compare gene expression between guts of bees from CCD colonies originating on both the east and west coasts of the United States and guts of bees from healthy colonies sampled before the emergence of CCD. Considerable variation in gene expression was associated with the geographical origin of bees, but a consensus list of 65 transcripts was identified as potential markers for CCD status. Overall, elevated expression of pesticide response genes was not observed. Genes involved in immune response showed no clear trend in expression pattern despite the increased prevalence of viruses and other pathogens in CCD colonies. Microarray analysis revealed unusual ribosomal RNA fragments that were conspicuously more abundant in the guts of CCD bees. The presence of these fragments may be a possible consequence of picorna-like viral infection, including deformed wing virus and Israeli acute paralysis virus, and may be related to arrested translation. Ribosomal fragment abundance and presence of multiple viruses may prove to be useful diagnostic markers for colonies afflicted with CCD.

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Mineral weathering by bacteria

Tuesday, August 25th, 2009

Soil Exposure of minerals to rainwater, temperature changes and oxidative conditions results in weathering. All these events have driven the formation of sediments, soils and landscapes, determining soil fertility and water quality. Plants and microbes are also involved in formation and destruction of minerals. For example, microorganisms contribute to precipitation of new minerals and to carbonate production. Whereas carbonate precipitation strongly impacts global carbon cycling – mineral weathering – plays a fundamental role in the environment by influencing the bioavailability of chemical elements that can be either beneficial or toxic to living organisms. Microbial mineral weathering is a widespread key process, not only because of its ecological significance but also because it affects human health, as well as architectural and artistic patrimony. Moreover, bacterial mineral weathering is used by industries to recover scarce metals from ore, and fungi might be useful for bioremediation of asbestos-rich soils. Another exciting possibility is the future use of efficient mineral-weathering bacteria to replace chemical fertilization; these microbes are able to promote the growth of plants by releasing trapped mineral nutrients. This biofertilization might result in a reduction of both economical cost and environmental impact of crop production.

Soil microbes play an essential role in the environment by contributing to the release of key nutrients from primary minerals that are required not only for their own nutrition but also for that of plants. Although the role of fungi in mineral weathering is beginning to be elucidated, the relative impact of bacteria in this process and the molecular mechanisms involved remain poorly understood. This ppaer discusses the ecological relevance of bacterial weathering, mainly in the soil and especially in acidic forest ecosystems, which strongly depend on mineral weathering for their sustainability; molecular mechanisms and genetic determinants involved in the dissolution of complex minerals under aerobic conditions; the potential applications of genomic resources to the study of bacterial weathering.

Mineral weathering by bacteria: ecology, actors and mechanisms. Trends Microbiol. Aug 4 2009

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Pathogenesis and treatment of dengue fever

Monday, August 24th, 2009

Dengue virus Platelet-activating factor (PAF) is a potent and versatile mediator of inflammation that is produced by numerous cell types and tissues, and particularly by leukocytes. PAF acts on a single receptor (PAFR) that may be expressed on the plasma membrane or the outer leaflet of the nucleus of various cell types, but especially leukocytes, platelets, and endothelial cells. The endogenous release of PAF may account for several of the manifestations of acute inflammation. The administration of PAF to rodents or humans reproduces many features of the systemic inflammatory response syndrome, including hypotension, increased vascular permeability, hemoconcentration, cytokine release, and shock.

Dengue fever and dengue shock or hemorrhagic syndromes (DSS) are mosquito-borne diseases caused by 1 of 4 serotypes of Dengue virus (DEN 1–4). There are an estimated 50–100 million cases of dengue fever and 20,000 deaths annually mostly in tropical and subtropical regions of the world. The large number of infected individuals, the lack of clinical or laboratory markers that indicate which patients will develop severe disease, and the lack of specific treatment place an enormous burden on health systems of low-income countries. Treatment of dengue fever and of the severe forms of dengue infection is supportive only.

DSS is defined as fever with hemorrhage manifestations, thrombocytopenia, and hemoconcentration or other signs of plasma leakage. Severe dengue infection is characterized by increased vascular permeability, altered number of leucocytes, increased hematocrit, thrombocytopenia, and varying degree of hemorrhage. The extensive plasma leakage in various serous cavities of the body may result in profound and intractable shock. Hemorrhage, when it occurs, may contribute to hypotension. These features remarkably resemble the pathophysiological changes observed after the systemic activation of PAFR in experimental animals.

This data provide strong evidence of the involvement of PAFR in the pathogenesis of experimental dengue infection in mice. It also suggest that therapeutic use of PAFR antagonists may be feasible in humans, as this class of compounds prevents the manifestations and lethality of dengue infection even when given days after the onset of disease. The PAFR antagonist UK-74,505 used in this study has a good safety profile and has been shown to effectively block the PAFR in humans when given orally. It is possible that therapeutic use of PAFR antagonists in humans may ameliorate manifestations of dengue and prevent evolution to severe disease.

Essential role of platelet-activating factor receptor in the pathogenesis of Dengue virus infection. PNAS USA July 30, 2009. doi: 10.1073/pnas.0906467106
Severe dengue infection in humans causes a disease characterized by thrombocytopenia, increased levels of cytokines, increased vascular permeability, hemorrhage, and shock. Treatment is supportive. Activation of platelet-activating factor (PAF) receptor (PAFR) on endothelial cells and leukocytes induces increase in vascular permeability, hypotension, and production of cytokines. We hypothesized that activation of PAFR could account for the major systemic manifestations of dengue infection. Inoculation of adult mice with an adapted strain of Dengue virus caused a systemic disease, with several features of the infection in humans. In PAFR−/− mice, there was decreased thrombocytopenia, hemoconcentration, decreased systemic levels of cytokines, and delay of lethality, when compared with WT infected mice. Treatment with UK-74,505, an orally active PAFR antagonist, prevented the above-mentioned manifestations, as well as hypotension and increased vascular permeability, and decreased lethality, even when started 5 days after virus inoculation. Similar results were obtained with a distinct PAFR antagonist, PCA-4246. Despite decreased disease manifestation, viral loads were similar (PAFR−/−) or lower (PAFR antagonist) than in WT mice. Thus, activation of PAFR plays a major role in the pathogenesis of experimental dengue infection, and its blockade prevents more severe disease manifestation after infection with no increase in systemic viral titers, suggesting that there is no interference in the ability of the murine host to deal with the infection. PAFR antagonists are disease-modifying agents in experimental dengue infection.

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Science Online London (Solo09)

Saturday, August 22nd, 2009

Science Online London Today I’m going to be at Science Online London (programme). I wasn’t able to attend in person last year, but I followed the live streams online and gained a lot from it. You can follow @soloconf on Twitter, hashtag #solo09, but judging from last year, most of the action will be in the Solo09 FriendFeed Room:

The Web is rapidly changing the communication, practice and culture of science. Science online London 2009 will explore the latest trends in science online. How is the Web affecting the work of researchers, science communicators, journalists, librarians, educators, students? What can you do to make the best use of the growing number of online tools? This is the follow-up conference to last year’s Science Blogging 2008: Londonconference. The name of the event was changed to reflect the variety of science-related activities happening online today. Topics include blogging and microblogging, online communities, open access and open data, new teaching and research tools, author identifiers and measuring the impact of research.

See you there, or see you online.

An introduction to T cells

Friday, August 21st, 2009

Nice introduction on YouTube:

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