Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity

Phenotypic plasticity is the variation in phenotype that a single genotype can produce in different environments and, as such, is an important component of individual fitness. However, whether the effect of new mutations, and hence evolution, depends on the direction of plasticity remains controversial. Here, we identify the cis-acting modifications that have reshaped gene expression in response to dehydration stress in three Arabidopsis species. Our study shows that the direction of effects of most cis-regulatory variants differentiating the response between A. thaliana and the sister species A. lyrata and A. halleri depends on the direction of pre-existing plasticity in gene expression. A comparison of the rate of cis-acting variant accumulation in each lineage indicates that the selective forces driving adaptive evolution in gene expression favors regulatory changes that magnify the stress response in A. lyrata. The evolutionary constraints measured on the amino-acid sequence of these genes support this interpretation. In contrast, regulatory changes that mitigate the plastic response to stress evolved more frequently in A. halleri. Our results demonstrate that pre-existing plasticity may be a stepping stone for adaptation, but its selective remodeling differs between lineages.

Actin modulates shape and mechanics of tubular membranes

The actin cytoskeleton shapes cells and also organizes internal membranous compartments. In particular, it interacts with membranes for intracellular transport of material in mammalian cells, yeast, or plant cells. Tubular membrane intermediates, pulled along microtubule tracks, are formed during this process and destabilize into vesicles. While the role of actin in tubule destabilization through scission is suggested, literature also provides examples of actin-mediated stabilization of membranous structures. To directly address this apparent contradiction, we mimic the geometry of tubular intermediates with preformed membrane tubes. The growth of an actin sleeve at the tube surface is monitored spatiotemporally. Depending on network cohesiveness, actin is able to entirely stabilize or locally maintain membrane tubes under pulling. On a single tube, thicker portions correlate with the presence of actin. These structures relax over several minutes and may provide enough time and curvature geometries for other proteins to act on tube stability.

Water, sanitation and hygiene risk factors for the transmission of cholera in a changing climate: using a systematic review to develop a causal process diagram

Cholera is a severe diarrhoeal disease affecting vulnerable communities. A long-term solution to cholera transmission is improved access to and uptake of water, sanitation and hygiene (WASH). Climate change threatens WASH. A systematic review and meta-analysis determined five overarching WASH factors incorporating 17 specific WASH factors associated with cholera transmission, focussing upon community cases. Eight WASH factors showed lower odds and six showed higher odds for cholera transmission. These results were combined with findings in the climate change and WASH literature, to propose a health impact pathway illustrating potential routes through which climate change dynamics (e.g. drought, flooding) impact on WASH and cholera transmission. A causal process diagram visualising links between climate change dynamics, WASH factors, and cholera transmission was developed. Climate change dynamics can potentially affect multiple WASH factors (e.g. drought-induced reductions in handwashing and rainwater use). Multiple climate change dynamics can influence WASH factors (e.g. flooding and sea-level rise affect piped water usage). The influence of climate change dynamics on WASH factors can be negative or positive for cholera transmission (e.g. drought could increase pathogen desiccation but reduce rainwater harvesting). Identifying risk pathways helps policymakers focus on cholera risk mitigation, now and in the future.

Arabidopsis species deploy distinct strategies to cope with drought stress

BACKGROUND AND AIMS

Water limitation is an important determinant of the distribution, abundance and diversity of plant species. Yet, little is known about how the response to limiting water supply changes among closely related plant species with distinct ecological preferences. Comparison of the model annual species Arabidopsis thaliana with its close perennial relatives A. lyrata and A. halleri, can help disentangle the molecular and physiological changes contributing to tolerance and avoidance mechanisms, because these species must maintain tolerance and avoidance mechanisms to increase long-term survival, but they are exposed to different levels of water stress and competition in their natural habitat.

METHODS

A dry-down experiment was conducted to mimic a period of missing precipitation. The covariation of a progressive decrease in soil water content (SWC) with various physiological and morphological plant traits across a set of representative genotypes in A. thaliana, A. lyrata and A. halleri was quantified. Transcriptome changes to soil dry-down were further monitored.

KEY RESULTS

The analysis of trait covariation demonstrates that the three species differ in the strategies they deploy to respond to drought stress. Arabidopsis thaliana showed a drought avoidance reaction but failed to survive wilting. Arabidopsis lyrata efficiently combined avoidance and tolerance mechanisms. In contrast, A. halleri showed some degree of tolerance to wilting but it did not seem to protect itself from the stress imposed by drought. Transcriptome data collected just before plant wilting and after recovery corroborated the phenotypic analysis, with A. lyrata and A. halleri showing a stronger activation of recovery- and stress-related genes, respectively.

CONCLUSIONS

The response of the three Arabidopsis species to soil dry-down reveals that they have evolved distinct strategies to face drought stress. These strategic differences are in agreement with the distinct ecological priorities of the stress-tolerant A. lyrata, the competitive A. halleri and the ruderal A. thaliana.

Emerging pathogens and deliberate attacks on European water supplies: a scenario planning workshop

Microbiological contamination of drinking water supplies is an ever-present concern for water utility managers. Most such threats are routine, well-recognised and described. Therefore, they can usually be prevented using standard protection measures. Incidents involving emerging pathogens and malicious attacks are inherently less predictable. In a multi-stage process over one day, participants with backgrounds in microbiology, medicine, infrastructure, data analysis, environmental or public health and facility management developed qualitative scenarios on potential threats posed by either an emergent pathogen in or a microbiological attack on drinking water supplies in a European country. Participants were guided via structured activities to identify key factors that would impact the magnitude and severity of such an emergency. Plausible variant states for each key factor were determined, and participants constructed sequences of events to create scenario outlines. Five scenarios in outline form are reported which incorporate genuine possible future events as well as pathogens of international concern. Common features that would exacerbate all scenarios were under-investment in public services, inadequate water quality testing, and monitoring and lack of resources to keep water supplies safe. Participant evaluation of their scenario planning experience was broadly very positive and the scenario planning process was received as credible and relevant.

Giardia secretome highlights secreted tenascins as a key component of pathogenesis

Background

Giardia is a protozoan parasite of public health relevance that causes gastroenteritis in a wide range of hosts. Two genetically distinct lineages (assemblages A and B) are responsible for the human disease. Although it is clear that differences in virulence occur, the pathogenesis and virulence of Giardia remain poorly understood.

Results

The genome of Giardia is believed to contain open reading frames that could encode as many as 6000 proteins. By successfully applying quantitative proteomic analyses to the whole parasite and to the supernatants derived from parasite culture of assemblages A and B, we confirm expression of ∼1600 proteins from each assemblage, the vast majority of which are common to both lineages. To look for signature enrichment of secreted proteins, we considered the ratio of proteins in the supernatant compared with the pellet, which defined a small group of enriched proteins, putatively secreted at a steady state by cultured growing trophozoites of both assemblages. This secretome is enriched with proteins annotated to have N-terminal signal peptide. The most abundant secreted proteins include known virulence factors such as cathepsin B cysteine proteases and members of a Giardia superfamily of cysteine-rich proteins that comprise variant surface proteins, high-cysteine membrane proteins, and a new class of virulence factors, the Giardia tenascins. We demonstrate that physiological function of human enteric epithelial cells is disrupted by such soluble factors even in the absence of the trophozoites.

Conclusions

We are able to propose a straightforward model of Giardia pathogenesis incorporating key roles for the major Giardia-derived soluble mediators.

Risk factors for Cryptosporidium infection in low and middle income countries: A systematic review and meta-analysis

BACKGROUND

Cryptosporidium infection causes gastrointestinal disease and has a worldwide distribution. The highest burden is in developing countries.

OBJECTIVES

We sought to conduct a systematic review and meta-analysis to identify Cryptosporidium risk factors in Low and Middle Income countries (LMICs).

METHODS

Medline Ovid and Scopus databases were searched with no restriction on year or language of publication. All references were screened independently in duplicate and were included if they presented data on at least 3 risk factors. Meta-analyses using random effects models were used to calculate overall estimates for each exposure.

RESULTS

The most frequently reported risk factors in the 15 included studies were overcrowding, household diarrhoea, poor quality drinking water, animal contact, open defecation/ lack of toilet and breastfeeding. The combined odds ratio for animal contact was 1.98 (95%CI: 1.11-3.54) based on 11 studies and for diarrhoea in the household 1.98 (95%CI: 1.13-3.49) based on 4 studies. Open defecation was associated with a pooled odds ratio of 1.82 (95%CI: 1.19-2.8) based on 5 studies. Poor drinking water quality was not associated with a significant Cryptosporidium risk, odds ratio 1.06 (95%CI: 0.77-1.47). Breastfeeding was protective with pooled odds ratio 0.4 (95%CI: 0.13-1.22), which was not statistically significant.

CONCLUSIONS

Based on the included studies, crowded living conditions, animal contact and open defecation are responsible for the majority of Cryptosporidium cases in LMICs. Future studies investigating Cryptosporidium risk factors should have a good study design and duration, include appropriate number of cases, select suitable controls, investigate multiple relevant risk factors, fully report data and perform multivariate analysis.

What is the impact of water sanitation and hygiene in healthcare facilities on care seeking behaviour and patient satisfaction? A systematic review of the evidence from low-income and middle-income countries

Patient satisfaction with healthcare has clear implications on service use and health outcomes. Barriers to care seeking are complex and multiple and delays in seeking care are associated with significant morbidity and mortality. We sought to assess the relationship between water, sanitation and hygiene (WASH) provision in healthcare facilities (HCF) and patient satisfaction/care seeking behaviour in low-income and middle-income countries. Pubmed and Medline Ovid were searched using a combination of search terms. 984 papers were retrieved and only 21 had a WASH component warranting inclusion. WASH was not identified as a driver of patient satisfaction but poor WASH provision was associated with significant patient dissatisfaction with infrastructure and quality of care. However, this dissatisfaction was not sufficient to stop patients from seeking care in these poorly served facilities. With specific regard to maternal health services, poor WASH provision was the reason for women choosing home delivery, although providers' attitudes and interpersonal behaviours were the main drivers of patient dissatisfaction with maternal health services. Patient satisfaction was mainly assessed via questionnaires and studies reported a high risk of courtesy bias, potentially leading to an overestimation of patient satisfaction. Patient satisfaction was also found to be significantly affected by expectation, which was strongly influenced by patients' socioeconomic status and education. This systematic review also highlighted a paucity of research to describe and evaluate interventions to improve WASH conditions in HCF in low-income setting with a high burden of healthcare-associated infections. Our review suggests that improving WASH conditions will decrease patience dissatisfaction, which may increase care seeking behaviour and improve health outcomes but that more rigorous research is needed.

Climate change and the emergence of vector-borne diseases in Europe: case study of dengue fever

BACKGROUND

Dengue fever is the most prevalent mosquito-borne viral disease worldwide. Dengue transmission is critically dependent on climatic factors and there is much concern as to whether climate change would spread the disease to areas currently unaffected. The occurrence of autochthonous infections in Croatia and France in 2010 has raised concerns about a potential re-emergence of dengue in Europe. The objective of this study is to estimate dengue risk in Europe under climate change scenarios.

METHODS

We used a Generalized Additive Model (GAM) to estimate dengue fever risk as a function of climatic variables (maximum temperature, minimum temperature, precipitation, humidity) and socioeconomic factors (population density, urbanisation, GDP per capita and population size), under contemporary conditions (1985-2007) in Mexico. We then used our model estimates to project dengue incidence under baseline conditions (1961-1990) and three climate change scenarios: short-term 2011-2040, medium-term 2041-2070 and long-term 2071-2100 across Europe. The model was used to calculate average number of yearly dengue cases at a spatial resolution of 10 × 10 km grid covering all land surface of the currently 27 EU member states. To our knowledge, this is the first attempt to model dengue fever risk in Europe in terms of disease occurrence rather than mosquito presence.

RESULTS

The results were presented using Geographical Information System (GIS) and allowed identification of areas at high risk. Dengue fever hot spots were clustered around the coastal areas of the Mediterranean and Adriatic seas and the Po Valley in northern Italy.

CONCLUSIONS

This risk assessment study is likely to be a valuable tool assisting effective and targeted adaptation responses to reduce the likely increased burden of dengue fever in a warmer world.

The effectiveness of public health interventions to reduce the health impact of climate change: a systematic review of systematic reviews

BACKGROUND

Climate change is likely to be one of the most important threats to public health in the coming years. Yet despite the large number of papers considering the health impact of climate change, few have considered what public health interventions may be of most value in reducing the disease burden. We aimed to evaluate the effectiveness of public health interventions to reduce the disease burden of high priority climate sensitive diseases.

METHODS AND FINDINGS

For each disease, we performed a systematic search with no restriction on date or language of publication on Medline, Web of Knowledge, Cochrane CENTRAL and SCOPUS up to December 2010 to identify systematic reviews of public health interventions. We retrieved some 3176 records of which 85 full papers were assessed and 33 included in the review. The included papers investigated the effect of public health interventions on various outcome measures. All interventions were GRADE assessed to determine the strength of evidence. In addition we developed a systematic review quality score. The interventions included environmental interventions to control vectors, chemoprophylaxis, immunization, household and community water treatment, greening cities and community advice. For most reviews, GRADE showed low quality of evidence because of poor study design and high heterogeneity. Also for some key areas such as floods, droughts and other weather extremes, there are no adequate systematic reviews of potential public health interventions.

CONCLUSION

In conclusion, we found the evidence base to be mostly weak for environmental interventions that could have the most value in a warmer world. Nevertheless, such interventions should not be dismissed. Future research on public health interventions for climate change adaptation needs to be concerned about quality in study design and should address the gap for floods, droughts and other extreme weather events that pose a risk to health.

A new heterogeneous family of telomerically encoded Cryptosporidium proteins

Cryptosporidiosis is predominantly caused by two closely related species of protozoan parasites the zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis which diverge phenotypically in respect to host range and virulence. Using comparative genomics we identified two genes displaying overt heterogeneity between species. Although initial work suggested both were species specific, Cops-1 for C. parvum and Chos-1 for C. hominis, subsequent study identified an abridged ortholog of Cops-1 in C. hominis. Cops-1 and Chos-1 showed limited, but significant, similarity to each other and share common features: (i) telomeric location: Cops-1 is the last gene on chromosome 2, whilst Chos-1 is the first gene on chromosome 5, (ii) encode circa 50-kDa secreted proteins with isoelectric points above 10, (iii) are serine rich, and (iv) contain internal nucleotide repeats. Importantly, Cops-1 sequence contains specific SNPs with good discriminatory power useful epidemiologically. C. parvum-infected patient sera recognized a 50-kDa protein in antigen preparations of C. parvum but not C. hominis, consistent with Cops-1 being antigenic for patients. Interestingly, anti-Cops-1 monoclonal antibody (9E1) stained oocyst content and sporozoite surface of C. parvum only. This study provides a new example of protozoan telomeres as rapidly evolving contingency loci encoding putative virulence factors.

Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci

Background

Cryptosporidium is a protozoan parasite that causes diarrheal illness in a wide range of hosts including humans. Two species, C. parvum and C. hominis are of primary public health relevance. Genome sequences of these two species are available and show only 3-5% sequence divergence. We investigated this sequence variability, which could correspond either to sequence gaps in the published genome sequences or to the presence of species-specific genes. Comparative genomic tools were used to identify putative species-specific genes and a subset of these genes was tested by PCR in a collection of Cryptosporidium clinical isolates and reference strains.

Results

The majority of the putative species-specific genes examined were in fact common to C. parvum and C. hominis. PCR product sequence analysis revealed interesting SNPs, the majority of which were species-specific. These genetic loci allowed us to construct a robust and multi-locus analysis. The Neighbour-Joining phylogenetic tree constructed clearly discriminated the previously described lineages of Cryptosporidium species and subtypes.

Conclusions

Most of the genes identified as being species specific during bioinformatics in Cryptosporidium sp. are in fact present in multiple species and only appear species specific because of gaps in published genome sequences. Nevertheless SNPs may offer a promising approach to studying the taxonomy of closely related species of Cryptosporidia.

Occurrence of Culicoides spp. (Diptera: Ceratopogonidae) in Tunisia, with emphasis on the bluetongue vector Culicoides imicola

Following the bluetongue (BT) outbreaks in Tunisia from 1999 to 2002, BTV (bluetongue virus) serotype 2 was isolated; however, no entomological investigation was performed. In the study presented here, we assessed the Culicoides species populations (particularly C. imicola) in proximity to the BT outbreaks locations, both as a retrospective analysis and to update the list of Culicoides species present in Tunisia. The insects were caught using light traps and the species identification was performed according to the standard entomological methods. This study reveaaled the presence of significant numbers of C. imicola in all the tested locations. In addition, we reported a new Culicoides species for the Tunisian fauna C. punctatus.

Detection and surveillance of waterborne protozoan parasites

The majority of the world's population still live without access to healthy water and the contamination of drinking water with protozoan pathogens poses a serious threat to millions of people in the developing world. Even in the developed world periodic outbreaks of diarrhoeal diseases are caused by the protozoan parasites Cryptosporidium sp., Giardia duodenalis and Entamoeba histolytica. Thus, surveillance of drinking water is imperative to minimize such contaminations and ensure continuous supplies of healthy water world-wide. This article reviews the progress in technology for detection and surveillance of these important waterborne parasites.

Different distribution of H1-H2 Epstein-Barr virus variant in oropharyngeal virus and in biopsies of Hodgkin's disease and in nasopharyngeal carcinoma from Algeria

In a previous study of Epstein-Barr virus (EBV) strains in North African nasopharyngeal carcinoma (N PC) biopsies, we have found that the viral strain present was of A/F/W'-I'/Xhol kept/H1-H2 type, while the strain associated with Chinese NPC was the A/"f"/W'I'/Xhol lost/H type. Using the restriction fragment length polymorphism (RFLP) and PCR-RFLP methods, the present study analyzed the H1-H2 variant in different clinical samples from Algeria, including the saliva of healthy EBV-positive individuals and patients with NPC or Hodgkin's disease (HD), as well as HD biopsies and lymphoblastoid cell lines (LCLs) established from the oropharyngeal virus-infected cells. Our results demonstrate that, in contrast to the H1-H2 variant found in NPC biopsies, the H genotype was dominant in HD biopsies. Moreover, H genotype was also dominant in the oropharynx of healthy EBV-positive individuals, of patients with NPC and with HD. Our results clearly indicate that in North Africa the EBV strain present of NPC biopsies is different from that shed in the oropharynx. This may suggest a specific distribution of the H1-H2 variant in the NPC epithelial tumor, whereas the H genotype is dominant in HD biopsies and in the oropharynx. The specific association of both viral strains with these 2 distinct diseases in North Africa may reflect a difference in tumorigenicity.

Epstein-Barr virus genotypes in NPC biopsies from north Africa

The genotypes of Epstein-Barr virus (EBV) were investigated in North African nasopharyngeal carcinoma (NPC) biopsies, nasopharyngeal chronic inflammation (NCI) biopsies, and saliva of healthy individuals from Algeria and Tunisia where there is an intermediate incidence of NPC. The prevalence of A-type virus in NPC, NCI biopsies and saliva of healthy individuals was found in these regions by means of a PCR assay. Restriction enzyme polymorphism analysis by Southern blotting revealed that all North African EBV variants have a conserved restriction site on BamHI W'-I' and XhoI LMP gene. No additional BamHI enzyme site on the BamHI-F fragment was observed; however, the presence of an extra BamHI site on the BamHI-H fragment giving 2 HI and H2 fragment-like EBV M-ABA strains was found. All EBV strains present in NPC or NCI biopsies at all ages were homogeneous in these polymorphisms and no correlation was observed between the EBV genotypes from NPC patients and clinical stages of the cancer. These characteristics revealed a significant difference between the EBV variants common in Chinese NPC and those in North African NPC.

Co-existence of the A and B types of Epstein-Barr virus DNA in lymph node biopsies from Algerian patients with Hodgkin's disease and non-Hodgkin's lymphoma

The association of Epstein-Barr virus (EBV) with Hodgkin's disease (HD) and non-Hodgkin's lymphoma (NHL) was examined in Algerian patients. The DNA extracted from fresh lymph node biopsies of 17 HD and five NHL was analysed by polymerase chain reaction (PCR). Fifteen out of 17 biopsies (88%) from HD contained EBV genome. Viral type analysis showed the coexistence of A and B types of EBV in 14 biopsies (93%), and the sole presence of A type virus in one biopsy. Among five NHL biopsies examined, four biopsies contained both A and B types of EBV, while one revealed A type-virus only. This co-infection of Algerian HD and NHL patients does not seem to be related with any histologic form of these diseases. The analysis of viral types in the saliva from 12 Algerian healthy individuals revealed six EBV positives with only one A type. Two types of lymphoma in Algeria therefore are closely associated with EBV, and are characterized by coinfection with A and B types of EBV.