The development of vaccines: how the past led to the future

The history of vaccine development has seen many accomplishments, but there are still many diseases that are difficult to target, and new technologies are being brought to bear on them. Past successes have been largely due to elicitation of protective antibodies based on predictions made from the study of animal models, natural infections and seroepidemiology. Those predictions have often been correct, as indicated by the decline of many infections for which vaccines have been made over the past 200 years.     

Alkaloid toxins in endophyte-infected grasses.

Grasses infected with clavicipitaceous fungi have been associated with a variety of diseases including classical ergotism in humans and animals, fescue foot and summer syndrome in cattle, and rye-grass staggers in sheep. During the last decade it has been recognized that many of these fungal infections are endophytic; a fungal endophyte is a fungus that grows entirely within the host plant. Inspection of field collections and herbarium specimens has revealed that such infections are widespread in grasses. The chemistry associated with these grass-fungal interactions has proved to be interesting and complex, as each grass-fungal pair results in a unique "fingerprint" of various alkaloids, of which some are highly toxic to herbivores. In many cases the presence of an endophyte appears to benefit the plant by increasing drought resistance, or by increasing resistance to attack by insects, thus improving the overall survivability of the grass. This review will focus on alkaloids that have been reported in endophyte-infected grasses.     

Th17 Down-regulation Is Involved in Reduced Progression of Schistosomiasis Fibrosis in ICOSL KO Mice

Background

Granulomatous and fibrosing inflammation in response to parasite eggs is the main pathology that occurs during infection with Schistosoma spp. CD4+ T cells play critical roles in both host immune responses against parasitic infection and immunopathology in schistosomiasis,and coordinate many types of immune cells that contribute to fibrosis. ICOSL plays an important role in controlling specific aspects of T cell activation, differentiation, and function. Previous work has suggested that ICOS is essential for Th17 cell development. However, the immunopathogenesis of this pathway in schistosomiasis fibrosisis still unclear.

Methodology/Principal Findings

Using models of schistosomiasis in ICOSL KO and the C57BL/6 WT mice, we studied the role of the ICOSL/ICOS interaction in the mediation of the Th17 response in host granulomatous inflammation, particularly in liver fibrosis during S. japonicum infection, and investigated the immune responses and pathology of ICOSL KO mice in these models. The results showed that ICOSL KO mice exhibited improved survival, reduced liver granulomatous inflammation around parasite eggs, markedly inhibited hepatic fibrosis development, lower levels of Th17-related cytokines (IL-17/IL-21), Th2-related cytokines (IL-4/IL-6/IL-10), a pro-fibrotic cytokine (IL-13), and TGF-β1, but higher level of Th1-related cytokine (IFN-γ) compared to wild-type (WT) mice. The reduced progression of fibrogenesis was correlated with the down-regulation of Th17 and Th2 and the elimination of ICOSL/ICOS interactions.

Conclusions/Significance

Our findings suggest that IL-17-producing cells contribute to the hepatic granulomatous inflammation and subsequent fibrosis. Importantly, there was a clearly positive correlation between the presence of IL-17-producing cells and ICOS expression in ICOSL KO mice, and additional results indicated that Th17 was involved in the pathological tissue remodeling in liver fibrosis induced by schistosomiasis.     

Schistosomes: unanswered questions on the basic biology of the host-parasite relationship

As is the case in many parasite infections, research into schistosomiasis has not yet yielded a vaccine and, although chemotherapy with praziquantel is very effective, the mechanism of action of this drug is unknown. John Kusel and colleagues here suggest that an understanding of basic biological phenomena, such as the role of Ca(2+) in skin penetration and the function of the adult excretory system, might lead to important breakthroughs. Other crucial questions are also addressed, with the hope of stimulating debate. They invite suggestions and correspondence from others working in related fields.     

A career pathway in protein folding: from model peptides to postreductionist protein science

This review discusses the inherent challenge of linking "reductionist" approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-"postreductionist" approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.     

S. haematobium as a Common Cause of Genital Morbidity in Girls: A Cross-sectional Study of Children in South Africa

Background

Schistosoma (S.) haematobium infection is a common cause of genital morbidity in adult women. Ova in the genital mucosal lining may cause lesions, bleeding, pain, discharge, and the damaged surfaces may pose a risk for HIV. In a heterogeneous schistosomiasis endemic area in South Africa, we sought to investigate if young girls had genital symptoms and if this was associated with urinary S. haematobium.

Methodology

In a cross-sectional study of 18 randomly chosen primary schools, we included 1057 schoolgirls between the age of 10 and 12 years. We interviewed assenting girls, whose parents had consented to their participation and examined three urines from each of them for schistosome ova.

Principal findings

One third of the girls reported to have a history of genital symptoms. Prior schistosomal infection was reported by 22% (226/1020), this was associated with current genital symptoms (p<0.001). In regression analysis the genital symptoms were significantly associated both with urinary schistosomiasis (p<0.001) and water contact (p<0.001).

Conclusions

Even before sexually active age, a relatively large proportion of the participating girls had similar genital symptoms to those reported for adult genital schistosomiasis previously. Anti-schistosomal treatment should be considered at a young age in order to prevent chronic genital damage and secondary infections such as HIV, sexually transmitted diseases and other super-infections.     

机器学习在蛋白质功能预测领域的研究进展

蛋白质是有机生命体内不可或缺的化合物,在生命活动中发挥着多种重要作用,了解蛋白质的功能有助于医学和药物研发等领域的研究。此外,酶在绿色合成中的应用一直备受人们关注,但是由于酶的种类和功能多种多样,获取特定功能酶的成本高昂,限制了其进一步的应用。目前,蛋白质的具体功能主要通过实验表征确定,该方法实验工作繁琐且耗时耗力,同时,随着生物信息学和测序技术的高速发展,已测序得到的蛋白质序列数量远大于功能获得注释的序列数量,高效预测蛋白质功能变得至关重要。随着计算机技术的蓬勃发展,由数据驱动的机器学习方法已成为应对这些挑战的有效解决方案。本文对蛋白质功能及其注释方法以及机器学习的发展历程和操作流程进行了概述,聚焦于机器学习在酶功能预测领域的应用,对未来人工智能辅助蛋白质功能高效研究的发展方向提出了展望。     

Real-time PCR Demonstrates High Prevalence of Schistosoma japonicum in the Philippines: Implications for Surveillance and Control

Background

The Philippines has a population of approximately 103 million people, of which 6.7 million live in schistosomiasis-endemic areas with 1.8 million people being at risk of infection with Schistosoma japonicum. Although the country-wide prevalence of schistosomiasis japonica in the Philippines is relatively low, the prevalence of schistosomiasis can be high, approaching 65% in some endemic areas. Of the currently available microscopy-based diagnostic techniques for detecting schistosome infections in the Philippines and elsewhere, most exhibit varying diagnostic performances, with the Kato-Katz (KK) method having particularly poor sensitivity for detecting low intensity infections. This suggests that the actual prevalence of schistosomiasis japonica may be much higher than previous reports have indicated.

Methodology/Principal Findings

Six barangay (villages) were selected to determine the prevalence of S. japonicum in humans in the municipality of Palapag, Northern Samar. Fecal samples were collected from 560 humans and examined by the KK method and a validated real-time PCR (qPCR) assay. A high S. japonicum prevalence (90.2%) was revealed using qPCR whereas the KK method indicated a lower prevalence (22.9%). The geometric mean eggs per gram (GMEPG) determined by the qPCR was 36.5 and 11.5 by the KK. These results, particularly those obtained by the qPCR, indicate that the prevalence of schistosomiasis in this region of the Philippines is much higher than historically reported.

Conclusions/Significance

Despite being more expensive, qPCR can complement the KK procedure, particularly for surveillance and monitoring of areas where extensive schistosomiasis control has led to low prevalence and intensity infections and where schistosomiasis elimination is on the horizon, as for example in southern China.     

Saint Lucia revisited

The eastern Caribbean island of Saint Lucia is now famous in parasitological history as the setting for a major programme of schistosomiasis control'. Perhaps less well-known are the island's effective control of many intestinal parasites, and elimination of malaria, such that the current patterns of mortality and other demographic indicators now resemble those of industrialized countries. More recently, the island has become the focus for another community-based health programme as the Caribbean region again comes to grips with Aedes aegypti and its recently imported relative, Aedes albopictus, important vectors of yellow fever and dengue viruses (see Box 1).     

Chronic Schistosoma japonicum Infection Reduces Immune Response to Vaccine against Hepatitis B in Mice

Background

Hepatitis B and schistosomiasis are most prevalent in Africa and Asia, and co-infections of both are frequent in these areas. The immunomodulation reported to be induced by schistosome infections might restrict immune control of hepatitis B virus (HBV) leading to more severe viral infection. Vaccination is the most effective measure to control and prevent HBV infection, but there is evidence for a reduced immune response to the vaccine in patients with chronic schistosomiasis japonica.

Methodology/Principal Findings

In this paper, we demonstrate in a mouse model that a chronic Schistosoma japonicum infection can inhibit the immune response to hepatitis B vaccine (HBV vaccine) and lead to lower production of anti-HBs antibodies, interferon-γ (IFN-γ) and interleukin-2 (IL-2). After deworming with Praziquantel (PZQ), the level of anti-HBs antibodies gradually increased and the Th2-biased profile slowly tapered. At 16 weeks after deworming, the levels of anti-HBs antibodies and Th1/Th2 cytokines returned to the normal levels.

Conclusions/Significance

The results suggest that the preexisting Th2-dominated immune profile in the host infected with the parasite may down–regulate levels of anti-HBs antibodies and Th1 cytokines. To improve the efficacy of HBV vaccination in schistosome infected humans it may be valuable to treat them with praziquantel (PZQ) some time prior to HBV vaccination.     

Parasitic worms: knowledge, attitudes, and practices in Western Côte d'Ivoire with implications for integrated control

Background

In the developing world where parasitic worm infections are pervasive, preventive chemotherapy is the key strategy for morbidity control. However, local knowledge, attitudes, and practices (KAP) of parasitic worms are poorly understood, although such information is required for prevention and sustainable control.

Methods

We carried out KAP surveys in two rural communities of Côte d''Ivoire that were subjected to school-based and community-based research and control activities. We used qualitative and quantitative methods. The former included observations, in-depth interviews with key informants, and focus group discussions with school children and adults. Quantitative methods consisted of a structured questionnaire administered to household heads.

Principal Findings

Access to clean water was lacking in both communities and only a quarter of the households had functioning latrines. There was a better understanding of soil-transmitted helminthiasis than intestinal schistosomiasis, but community-based rather than school-based interventions appeared to improve knowledge of schistosomiasis. In the villages with community-based interventions, three-quarters of household interviewees knew about intestinal schistosomiasis compared to 14% in the village where school-based interventions were implemented (P<0.001). Whereas two-thirds of respondents from the community-based intervention village indicated that the research and control project was the main source of information, only a quarter of the respondents cited the project as the main source.

Conclusions/Significance

Preventive chemotherapy targeting school-aged children has limitations, as older population segments are neglected, and hence lack knowledge about how to prevent and control parasitic worm infections. Improved access to clean water and sanitation is necessary, along with health education to make a durable impact against helminth infections.     

Improved Perceptions and Practices Related to Schistosomiasis and Intestinal Worm Infections Following PHAST Intervention on Kome Island,North-Western Tanzania

Schistosomiasis and intestinal worm infections are widespread diseases of public health importance in Tanzania. A study on perceptions and practices related to schistosomiasis and intestinal worm infections was undertaken among a community population of Kome Island in Sengerema District, north-western Tanzania, where intestinal schistosomiasis and intestinal worm infections are endemic. Schistosomiasis and intestinal worm-related perceptions and practices were assessed before and 3 years after implementation of a participatory hygiene and sanitation transformation (PHAST) intervention as a control measure. Data were obtained from baseline and post-intervention knowledge, attitudes, and practices (KAP) questionnaire surveys conducted twice in 2009 and 2012 among 82 individuals aged ≥15 years. We found significant increases in respondents’ knowledge of the cause, transmission, symptoms, health consequences, and prevention of schistosomiasis and intestinal worm infections after PHAST intervention. The increase in respondents’ knowledge on almost all aspects of the said infections was translated into actions to control schistosomiasis and intestinal worm infections. This has not been achieved by chance, but due to well-designed and locally-adapted PHAST intervention. We conclude that despite criticisms, PHAST approach is still useful in empowering communities to control water, sanitation, and hygiene related infectious diseases such as schistosomiasis and intestinal worm infections.     

Chronic hepatosplenomegaly in African school children: a common but neglected morbidity associated with schistosomiasis and malaria

Chronic hepatosplenomegaly, which is known to have a complex aetiology, is common amongst children who reside in rural areas of sub-Saharan Africa. Two of the more common infectious agents of hepatosplenomegaly amongst these children are malarial infections and schistosomiasis. The historical view of hepatosplenomegaly associated with schistosomiasis is that it is caused by gross periportal fibrosis and resulting portal hypertension. The introduction of ultrasound examinations into epidemiology studies, used in tandem with clinical examination, showed a dissociation within endemic communities between presentation with hepatosplenomegaly and ultrasound periportal fibrosis, while immuno-epidemiological studies indicate that rather than the pro-fibrotic Th2 response that is associated with periportal fibrosis, childhood hepatosplenomegaly without ultrasound-detectable fibrosis is associated with a pro-inflammatory response. Correlative analysis has shown that the pro-inflammatory response is also associated with chronic exposure to malarial infections and there is evidence of exacerbation of hepatosplenomegaly when co-exposure to malaria and schistosomiasis occurs. The common presentation with childhood hepatosplenomegaly in rural communities means that it is an important example of a multi-factorial disease and its association with severe and subtle morbidities underlies the need for well-designed public health strategies for tackling common infectious diseases in tandem rather than in isolation.     

Hijacking mitochondria: bacterial toxins that modulate mitochondrial function

Bacterial infection has enormous global social and economic impacts stemming from effects on human health and agriculture. Although there are still many unanswered questions, decades of research has uncovered many of the pathogenic mechanisms at play. It is now clear that bacterial pathogens produce a plethora of proteins known as "toxins" and "effectors" that target a variety of physiological host processes during the course of infection. One of the targets of host targeted bacterial toxins and effectors are the mitochondria. The mitochondrial organelles are major players in many biological functions, including energy conversion to ATP and cell death pathways, which inherently makes them targets for bacterial proteins. We present a summary of the toxins targeted to mitochondria and for those that have been studied in finer detail, we also summarize what we know about the mechanisms of targeting and finally their action at the organelle.     

The Colposcopic Atlas of Schistosomiasis in the Lower Female Genital Tract Based on Studies in Malawi,Zimbabwe, Madagascar and South Africa

Background

Schistosoma (S.) haematobium is a neglected tropical disease which may affect any part of the genital tract in women. Female genital schistosomiasis (FGS) may cause abnormal vaginal discharge, contact bleeding, genital tumours, ectopic pregnancies and increased susceptibility to HIV. Symptoms may mimic those typical of sexually transmitted infections (STIs) and women with genital schistosomiasis may be incorrectly diagnosed. An expert consensus meeting suggested that the following findings by visual inspection should serve as proxy indicators for the diagnosis of schistosomiasis of the lower genital tract in women from S. haematobium endemic areas: sandy patches appearing as (1) single or clustered grains or (2) sandy patches appearing as homogenous, yellow areas, or (3) rubbery papules. In this atlas we aim to provide an overview of the genital mucosal manifestations of schistosomiasis in women.

Methodology/Principal findings

Photocolposcopic images were captured from women, between 1994 and 2012 in four different study sites endemic for S. haematobium in Malawi, Zimbabwe, South Africa and Madagascar. Images and specimens were sampled from sexually active women between 15 and 49 years of age. Colposcopic images of other diseases are included for differential diagnostic purposes.

Significance

This is the first atlas to present the clinical manifestations of schistosomiasis in the lower female genital tract. It will be freely available for online use, downloadable as a presentation and for print. It could be used for training purposes, further research, and in clinical practice.     

Human RNA “Rumor” Viruses: the Search for Novel Human Retroviruses in Chronic Disease

Summary: Retroviruses are an important group of pathogens that cause a variety of diseases in humans and animals. Four human retroviruses are currently known, including human immunodeficiency virus type 1, which causes AIDS, and human T-lymphotropic virus type 1, which causes cancer and inflammatory disease. For many years, there have been sporadic reports of additional human retroviral infections, particularly in cancer and other chronic diseases. Unfortunately, many of these putative viruses remain unproven and controversial, and some retrovirologists have dismissed them as merely “human rumor viruses.” Work in this field was last reviewed in depth in 1984, and since then, the molecular techniques available for identifying and characterizing retroviruses have improved enormously in sensitivity. The advent of PCR in particular has dramatically enhanced our ability to detect novel viral sequences in human tissues. However, DNA amplification techniques have also increased the potential for false-positive detection due to contamination. In addition, the presence of many families of human endogenous retroviruses (HERVs) within our DNA can obstruct attempts to identify and validate novel human retroviruses. Here, we aim to bring together the data on “novel” retroviral infections in humans by critically examining the evidence for those putative viruses that have been linked with disease and the likelihood that they represent genuine human infections. We provide a background to the field and a discussion of potential confounding factors along with some technical guidelines. In addition, some of the difficulties associated with obtaining formal proof of causation for common or ubiquitous agents such as HERVs are discussed.     

Biogenic amines and the control of neuromuscular signaling in schistosomes

Biogenic amines are small cationic monoamines that function broadly as neurotransmitters and/or neuromodulators in every animal phylum. They include such ubiquitous substances as serotonin, dopamine and invertebrate-specific phenolamines (tyramine, octopamine), among others. Biogenic amines are important neuroactive agents in all the flatworms, including blood flukes of the genus Schistosoma, the etiological agents of human schistosomiasis. A large body of evidence spanning nearly five decades identifies biogenic amines as major modulators of neuromuscular function in schistosomes, controlling movement, attachment to the host and other fundamental behaviors. Recent advances in schistosome genomics have made it possible to dissect the molecular mechanisms responsible for these effects and to identify the proteins involved. These efforts have already provided important new information about the mode of action of amine transmitters in the parasite. Moreover, these advances are continuing, as the field moves into a post-genomics era, and new molecular tools for gene and protein analysis are becoming available. Here, we review the current status of this research and discuss future prospects. In particular, we focus our attention on the receptors that mediate biogenic amine activity, their structural characteristics, functional properties and "druggability" potential. One of the themes that will emerge from this discussion is that schistosomes have a rich diversity of aminergic receptors, many of which share little sequence homology with those of the human host, making them ideally suited for selective drug targeting. Strategies for the characterization of these important parasite proteins will be discussed.     

Translational Bioinformatics:Past,Present, and Future

Though a relatively young discipline, translational bioinformatics (TBI) has become a key component of biomedical research in the era of precision medicine. Development of high-throughput technologies and electronic health records has caused a paradigm shift in both healthcare and biomedical research. Novel tools and methods are required to convert increasingly voluminous datasets into information and actionable knowledge. This review provides a definition and contex-tualization of the term TBI, describes the discipline’s brief history and past accomplishments, as well as current foci, and concludes with predictions of future directions in the field.     

Predictors of bovine Schistosoma japonicum infection in rural Sichuan,China

In China, bovines are believed to be the most common animal source of human schistosomiasis infections, though little is known about what factors promote bovine infections. The current body of literature features inconsistent, and sometimes contradictory results, and to date, few studies have looked beyond physical characteristics to identify the broader environmental conditions that predict bovine schistosomiasis. Because schistosomiasis is a sanitation-related, water-borne disease transmitted by many animals, we hypothesised that several environmental factors – such as the lack of improved sanitation systems, or participation in agricultural production that is water-intensive – could promote schistosomiasis infection in bovines. Using data collected as part of a repeat cross-sectional study conducted in rural villages in Sichuan, China from 2007 to 2016, we used a Random Forests, machine learning approach to identify the best physical and environmental predictors of bovine Schistosoma japonicum infection. Candidate predictors included: (i) physical/biological characteristics of bovines, (ii) human sources of environmental schistosomes, (iii) socio-economic indicators, (iv) animal reservoirs, and (v) agricultural practices. The density of bovines in a village and agricultural practices such as the area of rice and dry summer crops planted, and the use of night soil as an agricultural fertilizer, were among the top predictors of bovine S. japonicum infection in all collection years. Additionally, human infection prevalence, pig ownership and bovine age were found to be strong predictors of bovine infection in at least 1 year. Our findings highlight that presumptively treating bovines in villages with high bovine density or human infection prevalence may help to interrupt transmission. Furthermore, village-level predictors were stronger predictors of bovine infection than household-level predictors, suggesting future investigations may need to apply a broad ecological lens to identify potential underlying sources of persistent transmission.     

Medaka as a research organism: past, present and future

This introductory review briefly describes the history of medaka as a research organism and the previous accomplishments of the medaka field. The medaka genome project currently underway through the efforts of an international consortium, the Medaka Genome Initiative, and the future prospects for medaka research, particularly for genomic analyses, are also discussed.