Archive for the ‘Science’ Category

Human papillomavirus and the cell cycle

Wednesday, May 20th, 2009

Human Papillomavirus Human papillomaviruses (HPVs) are DNA viruses associated with major human cancers. As such there is a strong interest in developing new means, such as vaccines and microbicides, to prevent HPV infections. Developing the latter requires a better understanding of the infectious life cycle of HPVs. The HPV infectious cycle is closely linked to the differentiation state of the stratified epithelium it infects, with progeny virus only made in the terminally differentiating suprabasal compartment. It has long been recognized that HPV must first establish its infection within the basal layer of stratified epithelium, but why this is the case has not been understood. In part this restriction might reflect specificity of expression of entry receptors. However, this hypothesis could not fully explain the differentiation restriction of HPV infection, since many cell types can be infected with HPVs in monolayer cell culture.

Chemical biology approaches have been used to reveal that cell cycle progression through mitosis is critical for HPV infection. Using infectious HPV16 particles containing the intact viral genome, G1-synchronized human keratinocytes as hosts, and early viral gene expression as a readout for infection, researchers learned that the recipient cell must enter M phase (mitosis) for HPV infection to take place. Late M phase inhibitors had no effect on infection, whereas G1, S, G2, and early M phase cell cycle inhibitors efficiently prevented infection. They concluded that host cells need to pass through early prophase for successful onset of transcription of the HPV encapsidated genes. These findings provide one reason why HPVs initially establish infections in the basal compartment of stratified epithelia. Only this compartment of the epithelium contains cells progressing through the cell cycle, and therefore it is only in these cells that HPVs can establish their infection. By defining a major condition for cell susceptibility to HPV infection, these results also have potentially important implications for HPV control.

Establishment of Human Papillomavirus Infection Requires Cell Cycle Progression. 2009 PLoS Pathog 5(2): e1000318
Human papillomaviruses (HPV), which comprise more than 100 genotypes, are the most prevalent sexually transmitted infection and are associated with multiple human cancers including all cervical cancers, many other anogenital cancers, and 25% of head and neck cancers. The HPV life cycle is closely linked to epithelial differentiation of skin keratinocytes, with initial infection occurring only in the undifferentiated proliferating basal compartment of the epithelium and progeny virus production only in the terminally differentiated suprabasal compartment. So far, little is known about how host cells restrict the HPV life cycle to specific stages of skin cell development. Here, by identifying small molecule inhibitors of HPV infection, we discovered that cell cycle progression through mitosis is critical for the establishment of HPV infection. In addition, our further chemical genetic dissection of this process showed that early steps of mitosis are required for HPV infection and early gene expression. Our findings provide one reason why HPV only infects undifferentiated proliferating cells and provide new leads for the development of preventive and therapeutic strategies against HPV infection.

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Nature Collections – Malaria

Friday, April 3rd, 2009

Nature Collections Malaria There’s a great collection of freely available resources On the Nature website under Nature Collections – Malaria (maybe NPG is finally getting the message about open access – hey Nature, it’s good to share :-)

The world is on the verge of making major inroads against malaria – a deadly disease that still claims the lives of more than 1 million people annually, mostly children less than 5 years of age. Over the past decade, scientists, large pharmaceutical companies and small biotechnology firms, governments and philanthropic organizations have come together to mount a full frontal attack on malaria, and there is now even talk of the ‘E word’ – that is, eradication. This collection highlights advances in the deployment of existing tools, and in the basic science of malaria – particularly those flowing from sequencing of the malaria parasite genomes – that will underpin the next generation of malaria-control tools, which will be needed if the scourge of malaria is to be eradicated.

Contents:

  • Malaria: The end of the beginning – After decades of work, a pioneering malaria vaccine may soon reach the final phase of clinical trials. A vaccine that is far from perfect – but which may provide new direction and save thousands of lives.
  • Malaria vaccine gets shot in the arm from tests – Promising results pave the way for a vaccine candidate to undergo full-blown trials across Africa.
  • Malaria: The big push – Zambia, with help from partners around the world, is stepping up its battle against malaria.
  • The billion-dollar malaria moment – For years the global malaria effort has been asking for more resources. Now the field needs to figure out a systematic strategy for spending the money effectively.
  • Review: Malaria research in the post-genomic era

Articles:

  • Comparative genomics of the neglected human malaria parasite Plasmodium vivax
  • Genome sequence of the human malaria parasite Plasmodium falciparum
  • Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
  • The genome of the simian and human malaria parasite Plasmodium knowlesi

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Biotransformation of arsenic by algae

Thursday, March 26th, 2009

Laguna Verde Arsenic is the most common toxic substance in the environment, ranking first on the US Superfund list of hazardous substances. It is introduced to the environment primarily from geologic sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are well known for their elevated arsenic content and thus provide an excellent setting in which to study microbe–arsenic interactions. So far, studies aimed at identifying the organisms participating in these and other arsenic transformations have focused almost entirely on microorganisms belonging to the domains Archaea and Bacteria. In contrast, comparatively little attention has been paid to the Eukarya that inhabit these extreme environments, much less their potential contribution to biogeochemical cycles in these extreme habitats. Now it would appear that algae play a significant role in arsenic cycling in the geothermal environment as also found in a range of marine and freshwater environments. These observations indicate that arsenic methylation forms an important component of the global arsenic biogeocycle.

Biotransformation of arsenic by a Yellowstone thermoacidophilic eukaryotic alga. PNAS USA March 10, 2009
Arsenic is the most common toxic substance in the environment, ranking first on the Superfund list of hazardous substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. Geothermal environments are known for their elevated arsenic content and thus provide an excellent setting in which to study microbial redox transformations of arsenic. To date, most studies of microbial communities in geothermal environments have focused on Bacteria and Archaea, with little attention to eukaryotic microorganisms. Here, we show the potential of an extremophilic eukaryotic alga of the order Cyanidiales to influence arsenic cycling at elevated temperatures. Cyanidioschyzon sp. isolate 5508 oxidized arsenite [As(III)] to arsenate [As(V)], reduced As(V) to As(III), and methylated As(III) to form trimethylarsine oxide (TMAO) and dimethylarsenate [DMAs(V)]. Two arsenic methyltransferase genes, CmarsM7 and CmarsM8, were cloned from this organism and demonstrated to confer resistance to As(III) in an arsenite hypersensitive strain of Escherichia coli. The two recombinant CmArsMs were purified and shown to transform As(III) into monomethylarsenite, DMAs(V), TMAO, and trimethylarsine gas, with a Topt of 60–70°C. These studies illustrate the importance of eukaryotic microorganisms to the biogeochemical cycling of arsenic in geothermal systems, offer a molecular explanation for how these algae tolerate arsenic in their environment, and provide the characterization of algal methyltransferases.

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Are viruses alive?

Wednesday, March 25th, 2009

Robot One of my sons asked me this question a few days ago. I said no, but I’m happy that others agree with me:

Ten reasons to exclude viruses from the tree of life. 2009 Nature Reviews Microbiology 7: 306-311
When viruses were discovered, they were accepted as missing links between the inert world and living organisms. However, this idea was soon abandoned as information about their molecular parasitic nature accumulated. Recently, the notion that viruses are living organisms that have had a role in the evolution of some essential features of cells has experienced a renaissance owing to the discovery of unusually large and complex viruses that possess typical cellular genes. Here, we contend that there is strong evidence against the notion that viruses are alive and represent ancient lineages of the tree of life.

Viruses do not reproduce by division, but are replicated by the self-assembly of preformed components. This, not size, differentiates them from cellular living organisms such as bacteria. A virus-infected cell is more like a car factory than a womb.
Also, unlike living organisms, no virus has the means of generating its own energy – they are all energy pirates.

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Comprehensive map of global malaria

Tuesday, March 24th, 2009

Malaria is one of the most common infectious diseases in the world and one of the greatest global public health problems. The Plasmodium falciparum parasite causes approximately 500 million cases each year and over one million deaths in sub-Saharan Africa. More than 40% of the world’s population is at risk of malaria. The parasite is transmitted to people through the bites of infected mosquitoes. These insects inject a life stage of the parasite called sporozoites, which invade human liver cells where they reproduce briefly. The liver cells then release merozoites (another life stage of the parasite), which invade red blood cells. Here, they multiply again before bursting out and infecting more red blood cells, causing fever and damaging vital organs. The infected red blood cells also release gametocytes, which infect mosquitoes when they take a blood meal. In the mosquito, the gametocytes multiply and develop into sporozoites, thus completing the parasite’s life cycle. Malaria can be prevented by controlling the mosquitoes that spread the parasite and by avoiding mosquito bites by sleeping under insecticide-treated bed nets. Effective treatment with antimalarial drugs also helps to decrease malaria transmission.

Malaria map

In 1998, the World Health Organization and several other international agencies launched Roll Back Malaria, a global partnership that aims to reduce the human and socioeconomic costs of malaria. Targets have been continually raised since this time and have culminated in the Roll Back Malaria Global Malaria Action Plan of 2008, where universal coverage of locally appropriate interventions is called for by 2010 and the long-term goal of malaria eradication again tabled for the international community. For malaria control and elimination initiatives to be effective, financial resources must be concentrated in regions where they will have the most impact, so it is essential to have up-to-date and accurate maps to guide effort and expenditure. In 2008, researchers of the Malaria Atlas Project constructed a map that stratified the world into three levels of malaria risk: no risk, unstable transmission risk (occasional focal outbreaks), and stable transmission risk (endemic areas where the disease is always present). Now, researchers extend this work by describing a new evidence-based method for generating continuous maps of P. falciparum endemicity within the area of stable malaria risk over the entire world’s surface. They then use this method to produce a P. falciparum endemicity map for 2007. Endemicity is important as it is a guide to the level of morbidity and mortality a population will suffer, as well as the intensity of the interventions that that will be required to bring the disease under control or additionally to interrupt transmission.

The researchers identified nearly 8,000 surveys of P. falciparum parasite rates (Pf PR; the percentage of a population with parasites detectable in their blood) completed since 1985 that met predefined criteria for inclusion into a global database of PfPR data. They then used ‘‘model-based geostatistics’’ to build a world map of P. falciparum endemicity for 2007 that took into account where and, importantly, when and all these surveys were done. Predictions were comprehensive (for every area of stable transmission globally) and continuous (predicted as a endemicity value between 0% and 100%). The population at risk of three levels of malaria endemicity were identified to help summarize these findings: low endemicity, where PfPR is below 5% and where it should be technically feasible to eliminate malaria; intermediate endemicity where PfPR is between 5% and 40% and it should be theoretically possible to interrupt transmission with the universal coverage of bed nets; high endemicity is where PfPR is above 40% and suites of locally appropriate intervention will be needed to bring malaria under control. The global level of malaria endemicity is much reduced when compared with historical maps. Nevertheless, the resulting map indicates that in 2007 almost 60% of the 2.4 billion people at malaria risk were living in areas with a stable risk of P. falciparum transmission – 0.69 billion people in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africaþ), and 0.04 billion in the Americas. The people of the Americas were all in the low endemicity class. Although most people exposed to stable risk in CSE Asia were also in the low endemicity class (88%), 11% were in the intermediate class, and 1% were in the high endemicity class. By contrast, high endemicity was most common and widespread in the Africaþ region (53%), but with significant numbers in the intermediate (30%), and low (17%) endemicity classes.

The accuracy of this new world map of P. falciparum endemicity depends on the assumptions made in its construction and critically on the accuracy of the data fed into it, but because of the statistical methods used to construct this map, it is possible to quantify the uncertainty in the results for all users. Thus, this map (which, together with the data used in its construction, will be freely available) represents an important new resource that clearly indicates areas where malaria control can be improved (for example, Africa) and other areas where malaria elimination may be technically possible. In addition, planned annual updates of the global P. falciparum endemicity map and the PfPR database by the Malaria Atlas Project will help public health experts to monitor the progress of the malaria control community towards international control and elimination targets.

A world malaria map: Plasmodium falciparum endemicity in 2007. 2009 PLoS Med 6(3): e1000048
Efficient allocation of resources to intervene against malaria requires a detailed understanding of the contemporary spatial distribution of malaria risk. It is exactly 40 y since the last global map of malaria endemicity was published. This paper describes the generation of a new world map of Plasmodium falciparum malaria endemicity for the year 2007. A total of 8,938 P. falciparum parasite rate (PfPR) surveys were identified using a variety of exhaustive search strategies. Of these, 7,953 passed strict data fidelity tests for inclusion into a global database of PfPR data, age-standardized to 2–10 y for endemicity mapping. A model based geostatistical procedure was used to create a continuous surface of malaria endemicity within previously defined stable spatial limits of P. falciparum transmission. These procedures were implemented within a Bayesian statistical framework so that the uncertainty of these predictions could be evaluated robustly. The uncertainty was expressed as the probability of predicting correctly one of three endemicity classes; previously stratified to be an informative guide for malaria control. Population at risk estimates, adjusted for the transmission modifying effects of urbanization in Africa, were then derived with reference to human population surfaces in 2007. Of the 1.38 billion people at risk of stable P. falciparum malaria, 0.69 billion were found in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africaþ), and 0.04 billion in the Americas. All those exposed to stable risk in the Americas were in the lowest endemicity class. The vast majority (88%) of those living under stable risk in CSE Asia were also in this low endemicity class; a small remainder(11%) were in the intermediate endemicity class; and the remaining fraction (1%) in high endemicity areas. High endemicity was widespread in the Africaþ region, where 0.35 billion people are at this level of risk. Most of the rest live at intermediate risk (0.20 billion), with a smaller number (0.11 billion) at low stable risk. High levels of P. falciparum malaria endemicity are common in Africa. Uniformly low endemic levels are found in the Americas. Low endemicity is also widespread in CSE Asia, but pockets of intermediate and very rarely high transmission remain. There are therefore significant opportunities for malaria control in Africa and for malaria elimination elsewhere. This 2007 global P. falciparum malaria endemicity map is the first of a series with which it will be possible to monitor and evaluate the progress of this intervention process.

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It’s good to talk

Monday, March 23rd, 2009

Telephone We all live in an information rich, highly interconnected world, and the success of evolution can be measured in terms of how living organisms make sense of and respond to information. Past posts on quorum sensing are some of the most popular out of all the subjects I have covered on MicrobiologyBytes. Quorum sensing is the use of small molecules by bacteria to coordinate behavior by groups of individual cells and carry out decision-making processes.

Bacteria have evolved a number of communication systems which can be broadly described as contact-independent and contact-dependent signaling mechanisms. Quorum sensing is a contact-independent process since it involves transfer of secreted molecules called autoinducers. As autoinducer levels increase throughout a growing bacterial population, changes in gene transcription are triggered resulting in altered growth rates and group dynamics. There is an energy cost in producing these compounds and throwing them out of the cell, and in some conditions, the secretion of autoinducers may attract unwanted attention from competitors (Bacterial landlines: contact-dependent signaling in bacterial populations. Curr Opin Microbiol. Feb 24 2009). Contact-dependent signaling methods allow bacteria to carry out more direct, and possibly less costly, communication between cells – it’s the landline alternative to expensive cellphone bills.

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Known methods of contact-dependent signaling include C-signaling in Myxococcus xanthus which allows groups of cells to coordinate motile behavior. The process is mediated by a non-diffusable 17 kDa surface protein encoded by the csgA gene. Contact between neighboring myxobacteria initiates a p17-dependent signaling cascade resulting in expression of genes required for control of motility or for sporulation.

The Gram-positive soil bacterium Bacillus subtilis also undergoes a contact-dependent differentiation process as a means to produce dormant spores when faced with starvation. Under nutrient poor conditions, vegetative B. subtilis cells divide asymmetrically, forming a large mother cell and a smaller daughter cell called a forespore. Despite their intimate association, the mother cell and the forespore remain separated by two membranes and maintain distinct gene expression profiles. Endospore formation is an energy intensive process that is coordinated by multiple signaling pathways. Contact-dependent signaling plays an important role in allowing the cells to coordinate this process.

Contact-dependent inhibition also occurs in E. coli, where a single E. coli cell in the logarithmic phase of growth can use a CDI system to inhibit the growth of hundreds of susceptible target cells in mixed cultures, forcing them to enter a viable but non-replicating state. However, one of the first recognized instances of contact-dependent communication between bacteria was, arguably, conjugation mediated by sex (F) pili. Bacteria encode a large variety of other pilus types and adhesive molecules, many of which have been studied primarily with respect to their abilities to modulate bacteria–host cell interactions. However, it is feasible that some of these organelles also function in inter-bacterial communication. For example, recent studies indicate that several types of soil bacteria can express complex networks of electrically conductive pili known as nanowires.

Although quorum sensing has been getting all the attention recently, we have known about contact-dependent communication mechanisms in bacteria for far longer. Perhaps only now are we realizing how these complimentary systems might fit together and how they could shed light on the development of true multicellularity during evolution.

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Badgers to be given anti-TB jabs

Sunday, March 22nd, 2009

Badgers in the wild will be vaccinated against bovine tuberculosis for the first time next year
BBC News

Maggots or MRSA?

Saturday, March 21st, 2009

BBC News
BBC News

Larval therapy for leg ulcers (VenUS II): randomised controlled trial. BMJ 2009;338:b773
Objective: To compare the clinical effectiveness of larval therapy with a standard debridement technique (hydrogel) for sloughy or necrotic leg ulcers.
Design: Pragmatic, three armed randomised controlled trial.
Setting: Community nurse led services, hospital wards, and hospital outpatient leg ulcer clinics in urban and rural settings, United Kingdom.
Participants: 267 patients with at least one venous or mixed venous and arterial ulcer with at least 25% coverage of slough or necrotic tissue, and an ankle brachial pressure index of 0.6 or more.
Interventions: Loose larvae, bagged larvae, and hydrogel.
Main outcome measures: The primary outcome was time to healing of the largest eligible ulcer. Secondary outcomes were time to debridement, health related quality of life (SF-12), bacterial load, presence of meticillin resistant Staphylococcus aureus, adverse events, and ulcer related pain (visual analogue scale, from 0 mm for no pain to 150 mm for worst pain imaginable).
Results: Time to healing was not significantly different between the loose or bagged larvae group and the hydrogel group (hazard ratio for healing using larvae v hydrogel 1.13, 95% confidence interval 0.76 to 1.68; P=0.54). Larval therapy significantly reduced the time to debridement (2.31, 1.65 to 3.2; P<0.001). Health related quality of life and change in bacterial load over time were not significantly different between the groups. 6.7% of participants had MRSA at baseline. No difference was found between larval therapy and hydrogel in their ability to eradicate MRSA by the end of the debridement phase (75% (9/12) v 50% (3/6); P=0.34), although this comparison was underpowered. Mean ulcer related pain scores were higher in either larvae group compared with hydrogel (mean difference in pain score: loose larvae v hydrogel 46.74 (95% confidence interval 32.44 to 61.04), P<0.001; bagged larvae v hydrogel 38.58 (23.46 to 53.70), P<0.001).
Conclusions: Larval therapy did not improve the rate of healing of sloughy or necrotic leg ulcers or reduce bacterial load compared with hydrogel but did significantly reduce the time to debridement and increase ulcer pain.

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Genomic fossils in lemurs shed light on HIV

Friday, March 20th, 2009

Microcebus murinus Lentiviruses are mammalian retroviruses known to infect cattle, cats, horses, sheep, and primates. They are the focus of intense study due to their causative association with AIDS in human. Although our knowledge on the origin and early evolution of HIV has grown exponentially over the past few years, much remains unresolved about the deeper relationships between primate and non-primate lentiviruses, the origin of lentiviruses, and their mode of structural evolution over long periods of evolutionary time. This is because these viruses evolve extremely rapidly, in a conflicting relationship with their hosts, and while their high mutation rate provides a wealth of information documenting their recent history, it also quickly erases evidence of their deeper ancestry. The lifecycle of retroviruses is atypical compared to other viruses in that after appropriate receptor recognition and entry in a specific cell type, their RNA genome is reverse transcribed into double-stranded DNA and integrated into the host genome as a provirus. Occasionally this process can take place in the host germline, and the integrated copy, also called endogenous retrovirus (ERV), may be transmitted vertically from parent to offspring and reach fixation in the host population. As such, ERVs constitute a fossil record of past viral infections that potentially provide an alternative way of gaining insights into the deep evolutionary history of present day exogenous retroviruses.

Although many ERVs have been characterized in mammals (e.g. 8% of the human genome), apparently very few derive from lentiviruses. Two reasons have traditionally been put forward to explain their absence in mammalian genomes: (i) they are of relatively recent evolutionary origin and endogenization has not yet commonly occurred, and/or (ii) they were not able to enter germ cells because of a very specific cell tropism. Recently however, an endogenous lentivirus called RELIK has been identified in the genome of rabbits and hares, whose germline integration was dated at least 12 millions years old. This discovery not only showed that lentiviruses were able to infiltrate mammalian germlines, but also demonstrated that this group of viruses is probably much older than what could previously be inferred based on sequence comparison of extant exogenous lentiviruses. New research now shows that a retrovirus related to HIV became stably integrated into the genomes of lemurs around 4.2 million years ago. The discovery of prosimian immunodeficiency virus (pSIV) offers new insights into the evolution of lentiviruses.

Based on “fossil” sequences collected from different lemur species, the researchers computationally reconstructed an apparently intact and complete DNA sequence for the ancestral prosimian lentivirus. The discovery that two different species of lemurs endemic to Madagascar suffered, independently and quasi-simultaneously, multiple germline infections of pSIV provides evidence that lentiviruses have repeatedly infiltrated the germline of prosimian species. These findings should allow future functional analysis of the extinct virus and advance our understanding of the biology of lentiviruses, including HIV. In addition, the characterization of this ancient lentivirus in lemurs raises the possibility that HIV-like retroviruses are still circulating today in the mammalian fauna of Madagascar.

Parallel Germline Infiltration of a Lentivirus in Two Malagasy Lemurs. 2009 PLoS Genet 5(3): e1000425
Retroviruses normally infect the somatic cells of their host and are transmitted horizontally, i.e., in an exogenous way. Occasionally, however, some retroviruses can also infect and integrate into the genome of germ cells, which may allow for their vertical inheritance and fixation in a given species; a process known as endogenization. Lentiviruses, a group of mammalian retroviruses that includes HIV, are known to infect primates, ruminants, horses, and cats. Unlike many other retroviruses, these viruses have not been demonstrably successful at germline infiltration. Here, we report on the discovery of endogenous lentiviral insertions in seven species of Malagasy lemurs from two different genera – Cheirogaleus and Microcebus. Combining molecular clock analyses and cross-species screening of orthologous insertions, we show that the presence of this endogenous lentivirus in six species of Microcebus is the result of one endogenization event that occurred about 4.2 million years ago. In addition, we demonstrate that this lentivirus independently infiltrated the germline of Cheirogaleus and that the two endogenization events occurred quasi-simultaneously. Using multiple proviral copies, we derive and characterize an apparently full length and intact consensus for this lentivirus. These results provide evidence that lentiviruses have repeatedly infiltrated the germline of prosimian species and that primates have been exposed to lentiviruses for a much longer time than what can be inferred based on sequence comparison of circulating lentiviruses. The study sets the stage for an unprecedented opportunity to reconstruct an ancestral primate lentivirus and thereby advance our knowledge of host–virus interactions.

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