The 12th International Workshops on Opportunistic Protists (IWOP‐12)

The 12th International Workshops on Opportunistic Protists (IWOP‐12) was held in August 2012 in Tarrytown, New York. The objectives of the IWOP meetings are to: (1) serve as a forum for exchange of new information among active researchers concerning the basic biology, molecular genetics, immunology, biochemistry, pathogenesis, drug development, therapy, and epidemiology of these immunodeficiency‐associated pathogenic eukaryotic microorganisms that are seen in patients with AIDS and (2) foster the entry of new and young investigators into these underserved research areas. The IWOP meeting focuses on opportunistic protists, e.g. the free‐living amoebae, Pneumocystis, Cryptosporidium, Toxoplasma, the Microsporidia, and kinetoplastid flagellates. This conference represents the major conference that brings together research groups working on these opportunistic pathogens. Slow but steady progress is being achieved on understanding the biology of these pathogenic organisms, their involvement in disease causation in both immune‐deficient and immune‐competent hosts, and is providing critical insights into these emerging and reemerging pathogens. This IWOP meeting demonstrated the importance of newly developed genomic level information for many of these pathogens and how analysis of such large data sets is providing key insights into the basic biology of these organisms. A great concern is the loss of scientific expertise and diversity in the research community due to the ongoing decline in research funding. This loss of researchers is due to the small size of many of these research communities and a lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms.     

Highlights and summaries of the 11th International Workshops on Opportunistic Protists

The 11th in the series of International Workshops on Opportunistic Protists (IWOP-11) was held in August 2010 on the Big Island of Hawaii. These meetings are devoted to agents of infections that cause serious problems in AIDS patients and other individuals with defective immune systems. International Workshops on Opportunistic Protists serves as a forum for exchange of current research information on Pneumocystis, Cryptosporidium and the Microsporidia, Toxoplasma, free-living amoebae, kinetoplastid flagellates and other pathogens that are particularly pathogenic in immunodeficient hosts. Studies on interactions between host and pathogen, especially host responses, were highlighted in this year's symposium. The lack of in vitro cultivation methods for luxuriant growth of Pneumocystis, Cryptosporidium and the Enterocytozoon bieneusi remains a major hindrance to understanding the basic biology of these organisms and precludes genetic manipulations. However, slow but steady progress is being achieved by hard work including data mining of some completed or partially completed genome sequencing of several IWOP organisms. Of great concern is evidence for dramatic decline in research funding for these pathogens and the lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms that can provide critical insight into emerging and reemerging pathogens.     

From Virus Research to Molecular Biology: Tobacco Mosaic Virus in Germany, 1936-1956

In 1937, a group of researchers in Nazi Germany began investigating tobacco mosaic virus (TMV) with the hope of using the virus as a model system for understanding gene behavior in higher organisms. They soon developed a creative and interdisciplinary work style and were able to continue their research in the postwar era, when they made significant contributions to the history of molecular biology. This group is significant for two major reasons. First, it provides an example of how researchers were able to produce excellent scientific research in the midst of dictatorship and war.Coupled with the group's ongoing success in postwar Germany, the German TMV investigators provide a dramatic example of how scientific communities deal with adversity as well as rapid political and social change. Second, since the researchers focused heavily (though no exclusively) on TMV, their story allows us to analyze how an experimental system other than phage contributed to the emergence of molecular biology.     

Human genome diversity: Ethics and practice in Australia

Researchers who propose projects about the human past frequently fail to distinguish between scientific value and the impact of both the proposal and the possible outcome for participant groups. It is only in recent years, and still in relatively few cases, that Aboriginal Australians have been directly involved in projects about themselves. The legacy of previous research experiences is a lingering distrust of ‘white’ researchers who visit communities briefly, take material/information, publish papers, and are rarely seen again. This distrust is understandable but in turn becomes a barrier which many well-intentioned researchers are unable or unwilling to overcome. The expectations of the scientific community, particularly in the field of molecular biology, simply do not make allowances in terms of time or funding to build a trusting relationship between the researchers and the researched. Sensitivity to indigenous rights and expectations with regard to scientific research brings obligations to scientific investigators with which few are well prepared to deal. The direct involvement of indigenous people in research about themselves is essential to the development of trusting working relationships likely to result in valuable outcomes for all participants and increased opportunities for ongoing research. Well negotiated, co-operative research can provide information of value to both scientific investigators and local participants, but adequate and ongoing consultation, as well as the return of results to the communities in an accurate and appropriate form must be part of research strategy. For example, information about mitochondrial DNA studies may assist Indigenous Australian people, whose families were dispersed during colonisation by Europeans, to trace links with the past, find ‘stolen children’ and by association with other anthropological, linguistic and archaeological data, repossess some remnants of traditional knowledge, but researchers must ensure that participants have a realistic understanding of the limitations of the research.     

Re-thinking organisms: The impact of databases on model organism biology

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species.     

A prevalence survey for zoonotic enteric bacteria in a research monkey colony with specific emphasis on the occurrence of enteric Yersinia

Transmissible pathogenic and opportunistic zoonotic enteric bacteria comprise a recognized occupational health threat to exposed humans from non-human primates (NHPs). In an effort to evaluate the occurrence of selected enteric organisms with zoonotic and biohazard potential in a research colony setting, we performed a prevalence study examining 61 juvenile and young adult rhesus macaques participating in a transplant immunology project. Primary emphasis was directed specifically to detection of pathogenic enteric Yersinia, less well-documented and reported NHP pathogens possessing recognized significant human disease potential. NHPs were surveyed by rectal culture during routine health monitoring on three separate occasions, and samples incubated using appropriate media and specific selective culture methods. Enteric organisms potentially transmissible to humans were subcultured and identified to genus and species. Significant human pathogens of the Salmonella/Shigella, Campylobacter, and enteric Yersinia groups were not isolated throughout the survey, suggesting prevalence of these organisms may generally be quite low.     

The prevalence of opportunistic pathogens associated with intraoral implants

Aims: The aim of this study was to determine the prevalence and proportions of opportunistic pathogens harboured on orthodontic retainers. Methods and Results: First, Staphylococcus spp. and Candida spp. were isolated from the retainer’s inner surface and from other mucosal surfaces of the subject’s mouth by routine bacterial culture. The prevalence and proportions of these micro‐organisms on retainers was compared in different areas of the mouth within a group of retainer wearers, and mucosal carriage was compared to a group of nonretainer wearers. Staphylococcus spp. were isolated from 50% of the retainers and comprised on average 8·4% of the viable microbiota. Candida spp. comprised 0·13% of the viable microbiota and were recovered from 66·7% of the retainers. Neither genus was isolated from nonretainer wearers. Second, the two most commonly worn retainers manufactured from different materials were sampled; again Staphylococcus spp. and Candida spp. were recovered; however, no statistical differences were observed between the devices. Conclusions: Opportunistic, nonoral, pathogenic micro‐organisms were recovered from orthodontic retainers. Significance and Impact of the Study: It is possible that an orthodontic retainer could be a reservoir for opportunistic pathogens and act as a source of cross‐, self‐ and re‐infection.     

Growing weed, producing knowledge: an epistemic history of Arabidopsis thaliana

Arabidopsis is currently the most popular and well-researched model organism in plant biology. This paper documents this plant's rise to scientific fame by focusing on two interrelated aspects of Arabidopsis research. One is the extent to which the material features of the plant have constrained research directions and enabled scientific achievements. The other is the crucial role played by the international community of Arabidopsis researchers in making it possible to grow, distribute and use plant specimen that embody these material features. I argue that at least part of the explosive development of this research community is due to its successful standardisation and to the subsequent use of Arabidopsis specimen as material models of plants. I conclude that model organisms have a double identity as both samples of nature and artifacts representing nature. It is the resulting ambivalence in their representational value that makes them attractive research tools for biologists.     

Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)

Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six‐sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco‐epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long‐term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long‐term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green‐ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores' immune and behavioural responses to anthrax risk, interact to produce regular ‘anthrax seasons’ that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats.     

Why flies? Inexpensive public engagement exercises to explain the value of basic biomedical research on Drosophila melanogaster

Invertebrate model organisms are powerful systems for uncovering conserved principles of animal biology. Despite widespread use in scientific communities, invertebrate research is often severely undervalued by laypeople. Here, we present a set of simple, inexpensive public outreach exercises aimed at explaining to the public why basic research on one particular invertebrate, the insect Drosophila melanogaster, is valuable. First, we designed seven teaching modules that highlight cutting-edge research in Drosophila genetics, metabolism, physiology, and behavior. We then implemented these exercises in a public outreach event that included both children and adults. Quantitative evaluation of participant feedback suggests that these exercises 1) teach principles of animal biology, 2) help laypeople better understand why researchers study fruit flies, and 3) are effective over a wide range of age groups. Overall, this work provides a blueprint for how to use Drosophila as a vehicle for increasing public awareness and appreciation of basic research on genetically tractable insects in particular and invertebrates in general.     

Defining dysbiosis and its influence on host immunity and disease

Mammalian immune system development depends on instruction from resident commensal microorganisms. Diseases associated with abnormal immune responses towards environmental and self antigens have been rapidly increasing over the last 50 years. These diseases include inflammatory bowel disease (IBD), multiple sclerosis (MS), type I diabetes (T1D), allergies and asthma. The observation that people with immune mediated diseases house a different microbial community when compared to healthy individuals suggests that pathogenesis arises from improper training of the immune system by the microbiota. However, with hundreds of different microorganisms on our bodies it is hard to know which of these contribute to health and more importantly how? Microbiologists studying pathogenic organisms have long adhered to Koch's postulates to directly relate a certain disease to a specific microbe, raising the question of whether this might be true of commensal–host relationships as well. Emerging evidence supports that rather than one or two dominant organisms inducing host health, the composition of the entire community of microbial residents influences a balanced immune response. Thus, perturbations to the structure of complex commensal communities (referred to as dysbiosis) can lead to deficient education of the host immune system and subsequent development of immune mediated diseases. Here we will overview the literature that describes the causes of dysbiosis and the mechanisms evolved by the host to prevent these changes to community structure. Building off these studies, we will categorize the different types of dysbiosis and define how collections of microorganisms can influence the host response. This research has broad implications for future therapies that go beyond the introduction of a single organism to induce health. We propose that identifying mechanisms to re‐establish a healthy complex microbiota after dysbiosis has occurred, a process we will refer to as rebiosis, will be fundamental to treating complex immune diseases.     

Molecular analysis of shower curtain biofilm microbes

Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the alpha-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.     

If we build – they mostly come: partial functional recovery but persistent compositional differences in wetland beetle community restoration

There is growing evidence of restoration success for wetland plant communities. However, little research has been done on the associated invertebrate community. We test whether restoring plant communities after peat extraction is sufficient for restoring the taxonomic and functional composition of beetle communities. We monitored taxonomic and trait‐based community metrics for beetle assemblages on restoration islands that were up to 13 years old and compared these with the adjacent “target” undisturbed peat bog. Recovery of beetle abundance, species richness, and trophic structure on the islands was remarkably rapid (i.e. within a decade) and converged on that of the undisturbed peat bog within 13 years after restoration commenced. In contrast, small, native, and poor‐dispersing taxa were persistently less abundant on the islands than in the undisturbed peat bog, causing persistent differences in species composition, even on the oldest islands. These poor‐dispersers probably need assistance to reach the islands and possibly ongoing intervention to allow them to survive there. Our findings emphasize the potential for functional trait analysis to reveal barriers to full restoration of insect community composition.     

Effects of polymicrobial communities on host immunity and response

Microorganisms grow as members of microbial communities in unique niches, such as the mucosal surfaces of the human body. These microbial communities, containing both commensals and opportunistic pathogens, serve to keep individual pathogens 'in check' through a variety of mechanisms and complex interactions, both between the microorganisms themselves and the microorganisms and the host. Recent studies shed new light on the diversity of microorganisms that form the human microbial communities and the interactions these microbial communities have with the host to stimulate immune responses. This occurs through their recognition by dendritic cells or their ability to induce differential cytokine and defensin profiles. The differential induction of defensins by commensals and pathogens and the ability of the induced defensins to interact with the antigens from these microorganisms may attenuate proinflammatory signaling and trigger adaptive immune responses to microbial antigens in a multistep process. Such an activity may be a mechanism that the host uses to sense what is on its mucosal surfaces, as well as to differentiate among commensals and pathogens.     

我国南北区域城市污水处理系统内真菌群落的差异

【背景】微生物是污水处理系统内污染物去除的主体,真菌作为其中不可或缺的一部分,在去除有毒化合物、提高生物转化等方面发挥着重要作用,应引起人们的关注。【目的】明确我国南北区域城市污水处理系统内真菌群落的多样性、组成差异及其影响因素。【方法】采集我国北方23个污水处理厂的90份活性污泥样品和南方37个污水处理厂的121份活性污泥样品,提取上述样本的总DNA,并应用Illumina MiSeq平台进行ITS高通量测序,结合多种数量生态学分析方法对数据进行分析。【结果】我国南北区域城市污水处理系统内真菌群落结构存在显著差异,真菌群落多样性南方显著高于北方;我国南北区域真菌群落的组成差异显著,南方群落以Sordariomycetes和Glomeromycetes为优势菌纲,以Ophiocordycep和Alternaria为优势菌属,北方群落以Tremellomycetes和Saccharomycetes为优势菌纲,以Trichosporon和Saccharomyces为优势菌属,其中Tremellomycetes和Sordariomycetes是常见的病原菌,对下游生物或者人类的健康具有潜在威胁,Trichosporon属的丝状真菌若大量异常增殖会引发污泥膨胀现象,影响系统的稳定运行;地理纬度、年平均气温、进水NH_4~+浓度、进水总氮浓度是导致我国南北区域真菌群落存在差异的重要影响因子。【结论】我国南北区域真菌群落多样性、组成存在显著差异,地理因素、所在城市的气候因素和进水污染物浓度对真菌群落结构影响显著。针对南北区域,应合理调控相应区域内的重要功能菌群,以调控污水处理厂的高效稳定运行,同时密切关注其中的条件致病菌和易引发污泥膨胀的菌群,建立面向种群的优化控制系统以管控风险。     

Molecular Analysis of Shower Curtain Biofilm Microbes

Households provide environments that encourage the formation of microbial communities, often as biofilms. Such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. One household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. Over time, vinyl shower curtains accumulate films, commonly referred to as “soap scum,” which microscopy reveals are constituted of lush microbial biofilms. To determine the kinds of microbes that constitute shower curtain biofilms and thereby to identify potential opportunistic pathogens, we conducted an analysis of rRNA genes obtained by PCR from four vinyl shower curtains from different households. Each of the shower curtain communities was highly complex. No sequence was identical to one in the databases, and no identical sequences were encountered in the different communities. However, the sequences generally represented similar phylogenetic kinds of organisms. Particularly abundant sequences represented members of the α-group of proteobacteria, mainly Sphingomonas spp. and Methylobacterium spp. Both of these genera are known to include opportunistic pathogens, and several of the sequences obtained from the environmental DNA samples were closely related to known pathogens. Such organisms have also been linked to biofilm formation associated with water reservoirs and conduits. In addition, the study detected many other kinds of organisms at lower abundances. These results show that shower curtains are a potential source of opportunistic pathogens associated with biofilms. Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals.     

Molecular approaches to malaria: seeking the whole picture

This year, Australia hosted its first major international conference on malaria - Molecular Approaches to Malaria in Lorne, Victoria, 2-5 February 2000 (MAM2000). The worldwide research effort toward a better understanding of the pathogenesis and control of malaria in the post-genomic era was discussed and debated by over 250 researchers from 18 countries during four days packed with molecular biology, cell biology, genomics, vaccines and pathogenic mechanisms. This special malaria edition of Parasitology Today is an attempt to capture and summarize the quality and breadth of work presented at the conference and place this in the context of the current global malaria research effort; eight of the nine Reviews in this issue have been written by session chairs or presenters at MAM2000.     

An emerging synthesis between community ecology and evolutionary biology

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.     

Exosomes and other microvesicles in infection biology: organelles with unanticipated phenotypes

The release of exosomes and other microvesicles by diverse prokaryotic and eukaryotic cells and organisms was first appreciated early in the 20th century. The functional properties of these organelles, however, have only recently been the focus of rigorous investigation. In this review, we discuss the release of microvesicles of varying complexity by diverse microbial pathogens. This includes vesicle secretion by Gram-negative bacteria, eukaryotic parasites of the kinetoplast lineage and opportunistic fungal pathogens of both the ascomycetes and basidiomycetes lineages. We also discuss vesicle release from mammalian cells brought about as a result of infection with bacteria, viruses and prions. In addition, we review the evidence showing that in their specific microenvironments, release of these organelles from diverse pathogens contributes to pathogenesis. Germane to this and based upon recent findings with Leishmania, we propose a model whereby exosome release by an intracellular pathogen serves as a general mechanism for effector molecule delivery from eukaryotic pathogen to host cell cytosol. These new findings linking exosomes and other microvesicles to infection biology have important implications for understanding the immune response to infection and for the design of research strategies aimed at the development of novel therapeutics and vaccines.