Archive for May, 2009

The Good, the Bad, and the Deadly

Saturday, May 30th, 2009

Ah, the tasty fruiting bodies of Basidiomycetes! (mushrooms to you ;-) The snag is that some are poisonous. Which ones? Well, that’s the risky bit. Taylor Lockwood is a biologist and photographer whose new DVD, The Good, the Bad, and the Deadly tries to teach you the basics about toxic mushrooms and their edible look-alikes.

Although they are beautiful, there is no simple way of knowing which fungi are safe to eat and which poisonous. Do not experiment with edible fungi, and get expert advice if you are in any doubt. Do not trust visual identification alone, whether from books or websites, as fungi vary tremendously in size, shape, colour and sometimes even in growing habitat.

Why not grow your own?

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New malaria agent found in chimpanzees

Friday, May 29th, 2009

Malaria in Africa In 2002, the publication of the genome of Plasmodium falciparum, the most malignant agent of malaria, generated hope in the fight against this deadly disease by the opportunities it offered to discover new drug targets. Since then results have not lived up to the expectations. The development of comparative genomics to further understanding of P. falciparum has indeed been hindered by a lack of knowledge of closely related species’ genomes. Only one species, P. reichenowi, infecting chimpanzees, was previously known as a sister lineage of P. falciparum.

Researchers based in Gabon and France have now reported the discovery of a new malaria agent infecting chimpanzees in Central Africa. To investigate the diversity of Plasmodium parasites circulating in chimpanzees in Africa, the team collected blood from 19 wild-borne animals kept as pets by villagers in Gabon. Two were found infected by a Plasmodium parasite. This new species, named Plasmodium gaboni, is a close relative of the most virulent human malaria agent, P. falciparum. Based on its whole mitochondrial genome, they demonstrate that this new species is a close relative of P. falciparum and P. reichenowi. The analysis of its genome should thus offer the opportunity to explore P. falciparum specific adaptations to humans. These results suggest that malaria may have been present in early hominoids and may have experienced a radiation along with that of its hosts. This discovery highlights the paucity of our knowledge on the richness of Plasmodium species infecting primates and suggests more research in this area is urgently needed.

A New Malaria Agent in African Hominids. 2009 PLoS Pathog 5(5): e1000446
Plasmodium falciparum is the major human malaria agent responsible for 200 to 300 million infections and one to three million deaths annually, mainly among African infants. The origin and evolution of this pathogen within the human lineage is still unresolved. A single species, P. reichenowi, which infects chimpanzees, is known to be a close sister lineage of P. falciparum. Here we report the discovery of a new Plasmodium species infecting Hominids. This new species has been isolated in two chimpanzees (Pan troglodytes) kept as pets by villagers in Gabon (Africa). Analysis of its complete mitochondrial genome (5529 nucleotides including Cyt b, Cox I and Cox III genes) reveals an older divergence of this lineage from the clade that includes P. falciparum and P. reichenowi (21+/-9 Myrs ago using Bayesian methods and considering that the divergence between P. falciparum and P. reichenowi occurred 4 to 7 million years ago as generally considered in the literature). This time frame would be congruent with the radiation of hominoids, suggesting that this Plasmodium lineage might have been present in early hominoids and that they may both have experienced a simultaneous diversification. Investigation of the nuclear genome of this new species will further the understanding of the genetic adaptations of P. falciparum to humans. The risk of transfer and emergence of this new species in humans must be now seriously considered given that it was found in two chimpanzees living in contact with humans and its close relatedness to the most virulent agent of malaria.

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Oldest Evidence of Leprosy Found in India

Thursday, May 28th, 2009

Leprosy Leprosy is a debilitating but treatable disease caused by infection with Mycobacterium leprae. Although popular conceptions of leprosy are focused primarily on images from Biblical or Medieval times, one quarter of a million people worldwide were still suffering from the disease in 2007. The history of leprosy is “interwoven with civilization itself”. An understanding of the origin and transmission routes of this disease can potentially lead to new insights about the evolution of infectious diseases and eradication efforts. However, the organism responsible is difficult to culture in the laboratory and much about leprosy is still poorly understood, including the origin, initial transmission routes and timing of the spread of the disease in the Old World.

A new cross-disciplinary report describes the analysis of a 4000-year-old skeleton from India bearing evidence of leprosy. This skeleton represents both the earliest archaeological evidence for human infection with M. leprae in the world and the first evidence for the disease in prehistoric India. This work demonstrates that leprosy was present in human populations in India by the end of the mature phase of the Indus Civilization (2000 B.C.) and provides support for one hypothesis about prehistoric transmission routes for the disease. The findings also support the hypothesis that the Sanskrit Atharva Veda, composed before the first millennium B.C., is the earliest written reference to the disease and that burial traditions in the second millennium B.C. in one northwestern Indian village bear some resemblance to practices in Hindu tradition today.

As infectious diseases go, leprosy is still one of the least well-understood, in part because the M. leprae is difficult to culture for research and it has only one other animal host, the nine banded armadillo. An Indian or African origin for the disease has often been assumed based on historical sources that support an initial spread of the disease from Asia to Europe with Alexander the Great’s army after 400 B.C. Skeletal evidence for the disease was previously limited to 300-400 B.C. in Egypt and Thailand. A report on genomics of Mycobacterium published in the magazine Science in 2005 suggested the disease may have originated in Africa during the Late Pleistocene and that M. leprae spread out of Africa sometime after 40,000 years ago, when human population densities were small. A counter hypothesis was proposed in the same volume of Science by Pinhasi and colleagues suggesting that the same data could be interpreted as evidence for a Late Holocene migration of the disease out of India after the development of large urban centers. The new work describes a case of leprosy recorded in a skeleton buried around 2000 B.C. in Rajasthan, India, at the site of Balathal. From 3700-1800 B.C. Balathal was a large agrarian settlement at the margins of the Indus Civilization. The mature phase of the Indus Civilization during the latter half of the third millennium B.C., was a period of social complexity characterized by urbanization, a system of writing, standardized weights and measures, monumental architecture, and trade networks that stretched to Mesopotamia and beyond. The presence of leprosy in India toward the end of this period indicates that M. leprae existed in South Asia at least 4000 years ago. This suggests that there may be some validity to the hypothesis that the disease spread between Africa and Asia during a period of incipient urbanization, increasing population density, and regular inter-continental trade networks.

The team is currently attempting to recover ancient DNA from the skeleton to determine if the strain of M. leprae infecting the individual from Balathal is similar to strains common in Africa, Asia and Europe today. If it is successful, this work could shed additional light on the origin and transmission routes of this disease. Understanding more about the disease can help clear up some of the many popular misconceptions about leprosy. It is generally associated with outcast and neglected people suffering their contagion on the margins of urban centers in late Biblical or Medieval times. In reality, leprosy is transmitted only through prolonged close contact with nasal droplets or infected regions of the body. It is not highly contagious and the infection can remain latent for decades. In fact, most people infected with M. leprae have few or very mild symptoms. Because leprosy is not highly contagious and its survival is likely dependent upon dense populations, the association with urban environments is possibly the only accurate part of the popular perception.

The presence of leprosy at Balathal 4000 years ago also supports translations of the Eber’s papyrus in Egypt and a Sanskrit text in India (the Atharva Veda) that refer to the disease as early as 1550 B.C. The Atharva Veda is a set of Sanskrit hymns devoted to describing health problems, their causes and treatments available in ancient India. Translations of leprosy have been questioned because it is difficult to perform a differential diagnosis on descriptions in such ancient texts particularly since diagnosis was not why the conditions were being described. The evidence from Balathal indicates that it is possible that the authors were describing leprosy as the disease was present in the subcontinent in prehistoric times. Furthermore, in contemporary Hindu tradition burial is uncommon unless an individual is a highly respected member of the community (like an ascetic) or is an individual seen as unfit to be sacrificed through cremation. These latter individuals are buried, including outcastes, pregnant women, children under 5, victims of magic or curses, and lepers. During the second millennium B.C., when there was disintegration of Indus settlements and new, smaller settlements sprang up all over the western half of peninsular India, adult burial becomes rare, children under 5 begin to predominate in the skeletal assemblages, and this early leper was one of only five individuals buried at the site of Balathal. Thus there is a similarity in terms of the demography of the burial populations from the second millennium and Vedic tradition. In addition, another feature of this burial that resembles Vedic symbolism is the burial site itself. The leper’s skeleton was interred within a large stone enclosure that had been filled with vitrified ash from burned cow dung, the most sacred and purifying of substances in Vedic tradition. The presence of this skeleton at Balathal, the manner in which it was interred, and the preponderance of children in burial assemblages from this time period throughout western India suggest deep time for the origin of these practices still common in Vedic tradition today.

Ancient Skeletal Evidence for Leprosy in India (2000 BC). 2009 PLoS ONE 4(5): e5669
Leprosy is a chronic infectious disease caused by Mycobacterium leprae that affects almost 250,000 people worldwide. The timing of first infection, geographic origin, and pattern of transmission of the disease are still under investigation. Comparative genomics research has suggested M. leprae evolved either in East Africa or South Asia during the Late Pleistocene before spreading to Europe and the rest of the World. The earliest widely accepted evidence for leprosy is in Asian texts dated to 600 B.C. We report an analysis of pathological conditions in skeletal remains from the second millennium B.C. in India. A middle aged adult male skeleton demonstrates pathological changes in the rhinomaxillary region, degenerative joint disease, infectious involvement of the tibia (periostitis), and injury to the peripheral skeleton. The presence and patterning of lesions was subject to a process of differential diagnosis for leprosy including treponemal disease, leishmaniasis, tuberculosis, osteomyelitis, and non-specific infection. Results indicate that lepromatous leprosy was present in India by 2000 B.C. This evidence represents the oldest documented skeletal evidence for the disease. Our results indicate that Vedic burial traditions in cases of leprosy were present in northwest India prior to the first millennium B.C. Our results also support translations of early Vedic scriptures as the first textual reference to leprosy. The presence of leprosy in skeletal material dated to the post-urban phase of the Indus Age suggests that if M. leprae evolved in Africa, the disease migrated to India before the Late Holocene, possibly during the third millennium B.C. at a time when there was substantial interaction among the Indus Civilization, Mesopotamia, and Egypt. This evidence should be impetus to look for additional skeletal and molecular evidence of leprosy in India and Africa to confirm the African origin of the disease.

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Lessons from the Vaccine–Autism Wars

Wednesday, May 27th, 2009

Researchers long ago rejected the theory that vaccines cause autism, yet many parents don’t believe them. Can scientists bridge the gap between evidence and doubt? This week PLoS Biology investigates why the debunked vaccine-autism theory won’t go away. Liza Gross talks to medical anthropologists, science historians, vaccine experts, social scientists and pediatricians to explore the factors keeping the dangerous notion alive – and its proponents so vitriolic:

A Broken Trust: Lessons from the Vaccine–Autism Wars. 2009 PLoS Biol 7(5): e1000114

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Specific pneumococcus serotypes associated with increased mortality

Tuesday, May 26th, 2009

Streptococcus pneumoniae Invasive pneumococcal disease (IPD) remains a major cause of morbidity and mortality worldwide despite the availability of antibiotic therapy and vaccines. Developing countries bear the major burden of IPD along with significantly higher rates of death and disability. The introduction of a 7-valent pneumococcal conjugate vaccine (PCV7) for infants has significantly reduced rates of bacteremic and nonbacteremic pneumococcal disease in the United States and other industrialized countries, yet the emergence of nonvaccine pneumococcal serotypes may threaten the continued efficacy of conjugate vaccines. Unfortunately, since the prevalence of pneumococcal serotypes varies among geographical regions, the formulation of PCV7 is not optimal against the most prevalent serotypes found in the developing world. In addition, some controversy surrounds the use of the available 23-valent polysaccharide vaccine (PPV23), which is recommended for patients of 2 years and older with high-risk conditions and for the elderly, since controlled trials were inconclusive and observational data suggested that PPV23 may prevent bacteremic but not non-bacteremic disease.

In research published this week, doctors analyzed population-based data collected over 30 years in more than 18,000 patients with invasive pneumococcal infection, finding specific pneumococcal serotypes to be associated with increased mortality. The results confirm that age, co-existing conditions and clinical presentation affect the serotype distribution as well as determine outcomes from IPD. This work is the largest and most comprehensive population-based study to date that evaluates short-term mortality associated with invasive pneumococcal serotypes after adjustment for possible confounders. The results support the hypothesis that specific pneumococcal capsular serotypes are significantly and independently associated with short-term mortality in patients with IPD. This is of particular interest in the era of conjugate vaccination, because a limited number of serotypes are included in the vaccines and because of the current emergence of nonvaccine serotypes.

Pneumococcal Serotypes and Mortality following Invasive Pneumococcal Disease: A Population-Based Cohort Study. PLoS Med 6(5): e1000081
Pneumococcal disease is a leading cause of morbidity and mortality worldwide. The aim of this study was to investigate the association between specific pneumococcal serotypes and mortality from invasive pneumococcal disease (IPD). In a nationwide population-based cohort study of IPD in Denmark during 1977–2007, 30-day mortality associated with pneumococcal serotypes was examined by multivariate logistic regression analysis after controlling for potential confounders. A total of 18,858 IPD patients were included. Overall 30-day mortality was 18%, and 3% in children younger than age 5 y. Age, male sex, meningitis, high comorbidity level, alcoholism, and early decade of diagnosis were significantly associated with mortality. Among individuals aged 5 y and older, serotypes 31, 11A, 35F, 17F, 3, 16F, 19F, 15B, and 10A were associated with highly increased mortality as compared with serotype 1. In children younger than 5 y, associations between serotypes and mortality were different than in adults but statistical precision was limited because of low overall childhood-related mortality. Specific pneumococcal serotypes strongly and independently affect IPD associated mortality.

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You are what you eat – but what are you eating?

Monday, May 25th, 2009

Salad Despite improvements in agricultural practices, leafy greens, tomatoes, salad crops and nuts were among the foods linked to recent outbreaks of gastrointestinal illnesses caused by Escherichia coli O157:H7 and non-typhoidal Salmonella (Human enteric pathogens in produce: un-answered ecological questions with direct implications for food safety. Curr Opin Biotechnol. April 4 2009). Because plants are not traditionally considered as hosts for human enteric pathogens, recent produce-associated outbreaks highlight important deficiencies in our understanding of the ecology of enteric pathogens outside of their human and animal hosts. The ongoing food safety debate focuses on answering the question whether plants are true alternate hosts for Salmonella or E. coli, or whether they are simply matrices where these organisms persist.

In a survey of several farms, up to 43% of produce sampled in the field was positive for Salmonella enterica, and the pathogen was found in the soil, irrigation water and on the hands of agricultural laborers. Following the 2006 E. coli O157:H7 spinach outbreak in the United States, the pathogen was isolated from cattle and feral swine faeces, river sediment, pasture soil, and surface water near the implicated fields. Human enteric pathogens are often recovered from surface water and untreated waste water used for irrigation. These reports establish that enteric pathogens in various environmental reservoirs may lead to food-associated outbreaks. Once deposited in soils, enteric bacteria persist for periods of time that range from a few weeks to several years. In field studies, both E. coli and Salmonella from raw manure were capable of colonizing the root zone and above ground parts of plants, supporting the hypothesis that pre-harvest contamination in the field could be a plausible route of produce contamination.

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For an enteric bacterium, it may make evolutionary sense to colonize vegetative and reproductive parts of plants that are then eaten by animals. If so, then enteric bacteria should have sophisticated, co-evolved mechanisms for getting into plants, spreading and multiplying in edible plant tissues to levels capable of populating guts of their herbivorous hosts. Salmonella enterica and enterovirulent E. coli are able to colonize tissues of plants quite effectively. This suggests that under favorable conditions enterics can exist as epi- or endophytes. If endophytic growth is truly a part of the life cycle of enterics, then this explains why current surface salad crop decontamination procedures may not be very effective. Conversely, if endo- or epiphytic growth is an important part of the life cycle of enterics, then we should be able to uncover evidence of specificity in the bacterial attachment, colonization and avoidance of plant defenses.

Recent laboratory studies identified a few of the genes and mechanisms that enterics use to colonize external surfaces of host plants. It appears that bacterial polymers and aggregative fimbriae were involved in the attachment of E. coli and/or Salmonella to plant seedlings. In their reliance on cellulose for attachment to plant surfaces, enteric pathogens are similar to plant symbiotic and pathogenic bacteria that also use cellulose fibrils to anchor themselves to plant surfaces.

Most plant pathogens and endophytes also produce hemicellulases and pectinases, enzymes that degrade polymers in plant cell walls. Unlike closely related members of the Enterobacteriaceae, Salmonella and E. coli do not seem to produce such enzymes and their genomes do not encode homologs of these enzymes. It is not yet clear whether Salmonella has unknown classes of cell wall degrading enzymes, whether it manages to gain entry and spread in plant tissues without such enzymes by moving intercellularly, or whether it relies on enzymes from the host or from other endophytes or plant pathogens to degrade plant cell walls. Regardless of their route of entry, enteric bacteria that were present inside plant seedlings were found in the intercellular spaces between host cell walls.

Although recent research has established that Salmonella and enterovirulent E. coli are capable of spending at least a part of their life cycle as plant-associated endo- or epiphytes, several important questions about the genetics and physiology of these interactions still need to be answered before plants are designated as true alternate hosts for these bacteria. Because there is evidence of specificity in the interactions of plant genotypes with enterics, defining the genetic basis and molecular markers associated with resistance to enterics may help identify crop cultivars that are less conducive to supporting growth of human pathogens. Further characterization of the attachment to plant surfaces and interactions with the resident microbiota will likely help improve pre- and post-harvest treatments to ensure safety of produce for human consumption.

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MicroRNA regulation of tumor-killing viruses

Friday, May 22nd, 2009

Adenoviruses Attenuated viruses have found important applications in medicine, including their use as vaccines (notably for measles, mumps, polio, influenza, and chicken pox) and their experimental development as selective cancer-killing agents, so-called “virotherapy”. Wild-type versions are often most effective in both of these settings; however, attenuated viruses have usually been developed to decrease the risk of significant viral pathology. Recent advances in understanding regulation of gene expression by microRNA now afford the possibility to design viruses that are “selectively attenuated” in sites of potential pathology, by engineering them for inhibition by micro-RNA molecules that are expressed there. A new paper describes how researchers have engineered wild-type adenovirus for recognition by a microRNA expressed in hepatocytes, producing a virus that retains wild-type infection and replication at sites of therapeutic activity (such as cancer cells) but is severely attenuated in hepatocytes, both in vitro and in vivo. This virus caused no significant liver toxicity to mice even when applied at ten times the lethal dose of wild-type virus. The ability to produce replication-competent viruses with key toxicities removed should provide a new platform for development of improved cancer treatments and better vaccines for a broad range of virus diseases.

Cellular microRNA molecules regulate the stability of mRNA in different cell types, and this newly-understood mechanism provides the possibility to engineer viruses for cell-specific inactivation. Adenovirus is a DNA virus widely used in cancer therapy but which causes hepatic disease in mice. Researchers found that introducing sites into the virus genome that are recognized by microRNA 122 leads to hepatic degradation of important viral mRNA, thereby diminishing the virus’ ability to adversely affect the liver, while maintaining its ability to replicate in and kill tumor cells. Tumor-killing replicating viruses are a hot topic in the biotherapeutics arena, with many clinical trials ongoing worldwide. They have now defined a mechanism whereby wild type virus potency could be maintained in tumor cells but the virus could be “turned off” in tissues vulnerable to pathology adds important information to the current base of knowledge.

This approach is surprisingly effective and quite versatile. It could find a range of applications in controlling the activity of therapeutic viruses, both for cancer research and also to engineer a new generation of conditionally-replicating vaccines, where the vaccine pathogen is disabled in its primary sites of toxicity. The present study was intended mainly to explore and demonstrate the potential of this new mechanism to regulate virus activity. Although the current tumor-killing virus is useful in mice, transfer of the technology into the clinical setting will require re-engineering of the virus to overcome virus pathologies seen in humans, and it will be at least two years before this can be tested in the clinics.

Use of Tissue-Specific MicroRNA to Control Pathology of Wild-Type Adenovirus without Attenuation of Its Ability to Kill Cancer Cells. PLoS Pathog 5(5): e1000440
Replicating viruses have broad applications in biomedicine, notably in cancer virotherapy and in the design of attenuated vaccines; however, uncontrolled virus replication in vulnerable tissues can give pathology and often restricts the use of potent strains. Increased knowledge of tissue-selective microRNA expression now affords the possibility of engineering replicating viruses that are attenuated at the RNA level in sites of potential pathology, but retain wild-type replication activity at sites not expressing the relevant microRNA. To assess the usefulness of this approach for the DNA virus adenovirus, we have engineered a hepatocyte-safe wild-type adenovirus 5 (Ad5), which normally mediates significant toxicity and is potentially lethal in mice. To do this, we have included binding sites for hepatocyte-selective microRNA mir-122 within the 39 UTR of the E1A transcription cassette. Imaging versions of these viruses, produced by fusing E1A with luciferase, showed that inclusion of mir-122 binding sites caused up to 80-fold decreased hepatic expression of E1A following intravenous delivery to mice. Animals administered a ten-times lethal dose of wild-type Ad5 (561010 viral particles/mouse) showed substantial hepatic genome replication and extensive liver pathology, while inclusion of 4 microRNA binding sites decreased replication 50-fold and virtually abrogated liver toxicity. This modified wild-type virus retained full activity within cancer cells and provided a potent, liver-safe oncolytic virus. In addition to providing many potent new viruses for cancer virotherapy, microRNA control of virus replication should provide a new strategy for designing safe attenuated vaccines applied across a broad range of viral diseases.

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Bacteria – amazing communications

Thursday, May 21st, 2009

Bacteria “talk” to each other using a chemical language (“quorum sensing”) that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry and our understanding of ourselves.

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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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