Integrated transcriptomic and proteomic analyses ofP. falciparumgametocytes: molecular insight into sex-specific processes and translational repression

Sexual differentiation of malaria parasites into gametocytes in the vertebrate host and subsequent gamete fertilization in mosquitoes is essential for the spreading of the disease. The molecular processes orchestrating these transitions are far from fully understood. Here, we report the first transcriptome analysis of male and female Plasmodium falciparum gametocytes coupled with a comprehensive proteome analysis. In male gametocytes there is an enrichment of proteins involved in the formation of flagellated gametes; proteins involved in DNA replication, chromatin organization and axoneme formation. On the other hand, female gametocytes are enriched in proteins required for zygote formation and functions after fertilization; protein-, lipid- and energy-metabolism. Integration of transcriptome and proteome data revealed 512 highly expressed maternal transcripts without corresponding protein expression indicating large scale translational repression in P. falciparum female gametocytes for the first time. Despite a high degree of conservation between Plasmodium species, 260 of these 'repressed transcripts' have not been previously described. Moreover, for some of these genes, protein expression is only reported in oocysts and sporozoites indicating that repressed transcripts can be partitioned into short- and long-term storage. Finally, these data sets provide an essential resource for identification of vaccine/drug targets and for further mechanistic studies

A genome-wide association study of rheumatoid arthritis without antibodies against citrullinated peptides

Introduction. Rheumatoid arthritis (RA) patients can be classified based on presence or absence of anticitrullinated peptide antibodies (ACPA) in their serum. This heterogeneity among patients may reflect important biological differences underlying the disease process. To date, the majority of genetic studies have focused on the ACPA-positive group. Therefore, our goal was to analyse the genetic risk factors that contribute to ACPA-negative RA. Methods. We performed a large-scale genome-wide association study (GWAS) in three Caucasian European cohorts comprising 1148 ACPA-negative RA patients and 6008 controls. All patients were screened using the Illumina Human Cyto-12 chip, and controls were genotyped using different genome-wide platforms. Population-independent analyses were carried out by means of logistic regression. Meta-analysis with previously published data was performed as follow-up for selected signals (reaching a total of 1922 ACPA-negative RA patients and 7087 controls). Imputation of classical HLA alleles, aminoacid residues and single nucleotide polymorphisms was undertaken. Results. The combined analysis of the studied cohorts resulted in identification of a peak of association in the HLA-region and several suggestive non-HLA associations. Meta-analysis with previous reports confirmed the association of the HLA region with this subset and an observed association in the CLYBL locus remained suggestive. The imputation and deep interrogation of the HLA region led to identification of a two aminoacid model (HLA-B at position 9 and HLA-DRB1 at position 11) that accounted for the observed genome-wide associations in this region. Conclusions. Our study shed light on the influence of the HLA region in ACPA-negative RA and identified a suggestive risk locus for this condition

Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases

OBJECTIVE: Immune-mediated inflammatory diseases (IMIDs) are heterogeneous and complex conditions with overlapping clinical symptoms and elevated familial aggregation, which suggests the existence of a shared genetic component. In order to identify this genetic background in a systematic fashion, we performed the first cross-disease genome-wide meta-analysis in systemic seropositive rheumatic diseases, namely, systemic sclerosis, systemic lupus erythematosus, rheumatoid arthritis and idiopathic inflammatory myopathies. METHODS: We meta-analysed ~6.5 million single nucleotide polymorphisms in 11 678 cases and 19 704 non-affected controls of European descent populations. The functional roles of the associated variants were interrogated using publicly available databases. RESULTS: Our analysis revealed five shared genome-wide significant independent loci that had not been previously associated with these diseases: NAB1, KPNA4-ARL14, DGQK, LIMK1 and PRR12. All of these loci are related with immune processes such as interferon and epidermal growth factor signalling, response to methotrexate, cytoskeleton dynamics and coagulation cascade. Remarkably, several of the associated loci are known key players in autoimmunity, which supports the validity of our results. All the associated variants showed significant functional enrichment in DNase hypersensitivity sites, chromatin states and histone marks in relevant immune cells, including shared expression quantitative trait loci. Additionally, our results were significantly enriched in drugs that are being tested for the treatment of the diseases under study. CONCLUSIONS: We have identified shared new risk loci with functional value across diseases and pinpoint new potential candidate loci that could be further investigated. Our results highlight the potential of drug repositioning among related systemic seropositive rheumatic IMIDs

Identification of Novel Genetic Markers Associated with Clinical Phenotypes of Systemic Sclerosis through a Genome-Wide Association Strategy

Contains fulltext : 97006.pdf (publisher's version ) (Open Access)The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (lcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (P = 2.32x10(-12), OR = 0.75). Also, rs12540874 in GRB10 gene (P = 1.27 x 10(-6), OR = 1.15) and rs11047102 in SOX5 gene (P = 1.39x10(-7), OR = 1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (P = 1.79x10(-61), OR = 2.48), in the HLA-DPA1/B1 loci with ATA (P = 4.57x10(-76), OR = 8.84), and in NOTCH4 with ACA P = 8.84x10(-21), OR = 0.55) and ATA (P = 1.14x10(-8), OR = 0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and auto-antibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc

Antibiotic resistant bacteria in surface water in an area with a high density of animal farms in the Netherlands

In oppervlaktewater en slib in veeteeltrijk gebied komen hoge percentages bacterien voor die resistent zijn tegen een of meerdere antibiotica. Dit blijkt uit verkennend onderzoek van het RIVM. De herkomst van deze bacterien in het onderzochte gebied is in deze studie niet onderzocht. Wel zijn er aanwijzingen dat ten minste een deel van de bacterien afkomstig is uit mest van nabijgelegen veeteeltbedrijven. Onderzoek naar de mate waarin antibioticumresistente bacterien in oppervlaktewater voorkomen is van belang om te kunnen inschatten in hoeverre mensen via het milieu worden blootgesteld aan deze bacterien. Er zijn meerdere oorzaken waardoor antibioticaresistente bacterien in oppervlaktewater terechtkomen. Bijvoorbeeld doordat mest van dieren die met antibiotica zijn behandeld, afspoelt naar het oppervlaktewater. Een andere oorzaak kan zijn dat gedeeltelijk gezuiverd of ongezuiverd afvalwater in oppervlaktewater wordt geloosd, bijvoorbeeld door ziekenhuizen waar mensen zijn behandeld met antibiotica. Als mensen met verontreinigd oppervlaktewater in aanraking komen, zoals tijdens recreatie, kunnen zij worden blootgesteld aan bacterien die resistent zijn tegen een of meerdere antibiotica. Dit brengt mogelijk volksgezondheidrisico's met zich mee omdat deze antibiotica belangrijk kunnen zijn om infecties te behandelen. De risico's kunnen zich op twee manieren manifesteren. Mensen die aan antibioticaresistente bacterien worden blootgesteld, kunnen zelf het risico lopen ziek te worden van deze - moeilijker te bestrijden - bacterien. Daarnaast is het mogelijk dat mensen zelf niet ziek worden van de resistente bacterien maar ze overdragen aan mensen met verminderde weerstand, zoals ziekenhuispatienten. Deze categorie mensen kan hier vervolgens wel ziek van worden.High percentages of bacteria with resistence to one ore more antibiotics are present in surface water and sludge in an agricultural area with a high density of animal farms. This was demonstrated in an exploratory study performed at the RIVM. Although the origin of the bacteria in the area under study was not investigated, there are indications that at least part of the bacteria originates from manure from nearby farms. Research on the prevalence of antibiotic resistant bacteria in surface water is necessary to estimate the contribution of the environment to human exposure to these bacteria. Antibiotic resistant bacteria can end up in surface water by different routes. Manure of animals treated with antibiotics can run off from land into surface water. Another route is via discharge of partially treated or untreated waste water onto surface water, for instance from hospitals were people are treated with antibiotics. If they come into contact with contaminated surface water, for instance during recreation, people risk exposure to bacteria that are resistant to one or more antibiotics. Since these antibiotics can be relevant for treatment of human infections, public health risks may be involved. These risks can manifest themselves in two ways. People who are exposed to antibiotic resistant bacteria are at risk of developing disease caused by these bacteria, which is therefore harder to treat. Additionally, if people do not get ill from the resistant bacteria they can transfer them to people who are more vulnerable, such as hospital patients. Subsequently, this category of people can develop disease.VROM-Inspecti

The effect of weather on the microbiological quality of rainwater used for toilet flushing and cleaning

Onderzoek naar de microbiologische kwaliteit van opgevangen regenwater dat bewaard werd in reservoirs toonde aan dat dit water altijd fecaal verontreinigd was en soms ziekteverwekkende micro-organismen zoals Campylobacter, Legionella, Cryptosporidium of Giardia bevatte. De mate van fecale verontreiniging van het water werd beinvloed door de hoeveelheid neerslag en de neerslagintensiteit. Als vervolg op een in 2005 uitgevoerd inventariserend onderzoek naar de microbiologische kwaliteit van opgevangen regenwater werd in 2006 het effect van omgevingsfactoren op de microbiologische kwaliteit van opgevangen regenwater onderzocht. Uit drie regenwaterreservoirs werden onder verschillende omstandigheden monsters genomen, zodat de mogelijke invloed van droogte, (hevige) neerslag, al dan niet na een periode van droogte, en temperatuur bestudeerd kon worden. De aanwezigheid van Campylobacter, Salmonella, Vibrio, Legionella, Cryptosporidium, Giardia en enterovirussen werd onderzocht. Bij een hoge neerslagintensiteit na een periode van droogte steeg het aantal fecale indicatorbacterien in het water in de reservoirs en werden ziekteverwekkende bacterien zoals Campylobacter gevonden. Door afspoeling van vogelfeces vanaf de daken kunnen hoge aantallen Campylobacter in de reservoirs terechtkomen, waardoor het denkbaar is dat bij gebruik van het opgevangen regenwater voor toiletspoeling niet aan het in het Waterleidingbesluit gestelde infectierisico van 1 per 10.000 personen per jaar wordt voldaan.A 2006 study of the microbiological quality of rainwater collected in reservoirs demonstrated that this water was fecally contaminated at all instances and sometimes contained pathogenic micro-organisms such as Campylobacter, Legionella, Cryptosporidium or Giardia. The amount of rainfall and rainfall intensity influenced the level of faecal contamination of the water. The study reported here - a follow up to a pilot study on the microbiological quality of collected rainwater carried out in 2005 - dealt specifically with the effect of environmental conditions on the microbiological quality of collected rainwater. Samples were taken from three reservoirs at various environmental conditions to study the effect of drought, heavy and normal rainfall (whether or not after a period of drought) and temperature. The presence of Campylobacter, Salmonella, Vibrio, Legionella, Cryptosporidium, Giardia and enteroviruses was determined. The number of faecal indicator bacteria in the reservoirs increased with high rainfall intensity, especially after a period of drought, and pathogenic micro-organisms such as Campylobacter were detected. Considering the high numbers of Campylobacter found in the reservoirs due to the runoff of bird faeces from roofs, it is conceivable that the requirement of one infection in 10,000 persons per year, as outlined in the Dutch Drinking Water Act, will not be met.VROM-Inspecti

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant

Legionella pneumophila in potable water installations poses a potential health risk, but quantitative information about its replication in biofilms in relation to water quality is scarce. Therefore, biofilm formation on the surfaces of glass and chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34 to 39°C was investigated under controlled hydraulic conditions in a model system inoculated with biofilm-grown L. pneumophila. The biofilm on glass (average steady-state concentration, 23 ± 9 pg ATP cm -2 ) exposed to treated aerobic groundwater (0.3 mg C liter -1 ; 1 μg assimilable organic carbon [AOC] liter -1 ) did not support growth of the organism, which also disappeared from the biofilm on CPVC (49 ± 9 pg ATP cm -2 ) after initial growth. L. pneumophila attained a level of 4.3 log CFU cm -2 in the biofilms on glass (1,055 ± 225 pg ATP cm -2 ) and CPVC (2,755± 460 pg ATP cm -2 ) exposed to treated anaerobic groundwater (7.9 mg C liter -1 ; 10 μg AOC liter -1 ). An elevated biofilm concentration and growth of L. pneumophila were also observed with tap water from the laboratory. The Betaproteobacteria Piscinibacter and Methyloversatilis and amoeba-resisting Alphaproteobacteria predominated in the clones and isolates retrieved from the biofilms. In the biofilms, the Legionella colony count correlated significantly with the total cell count (TCC), heterotrophic plate count, ATP concentration, and presence of Vermamoeba vermiformis. This amoeba was rarely detected at biofilm concentrations of <100 pg ATP cm -2 . A threshold concentration of approximately 50 pg ATP cm -2 (TCC = 1 × 106 to 2 × 106 cells cm -2 ) was derived for growth of L. pneumophila in biofilms

Antibioticaresistente bacterien in Nederlands oppervlaktewater in veeteeltrijk gebied

In oppervlaktewater en slib in veeteeltrijk gebied komen hoge percentages bacterien voor die resistent zijn tegen een of meerdere antibiotica. Dit blijkt uit verkennend onderzoek van het RIVM. De herkomst van deze bacterien in het onderzochte gebied is in deze studie niet onderzocht. Wel zijn er aanwijzingen dat ten minste een deel van de bacterien afkomstig is uit mest van nabijgelegen veeteeltbedrijven. Onderzoek naar de mate waarin antibioticumresistente bacterien in oppervlaktewater voorkomen is van belang om te kunnen inschatten in hoeverre mensen via het milieu worden blootgesteld aan deze bacterien. Er zijn meerdere oorzaken waardoor antibioticaresistente bacterien in oppervlaktewater terechtkomen. Bijvoorbeeld doordat mest van dieren die met antibiotica zijn behandeld, afspoelt naar het oppervlaktewater. Een andere oorzaak kan zijn dat gedeeltelijk gezuiverd of ongezuiverd afvalwater in oppervlaktewater wordt geloosd, bijvoorbeeld door ziekenhuizen waar mensen zijn behandeld met antibiotica. Als mensen met verontreinigd oppervlaktewater in aanraking komen, zoals tijdens recreatie, kunnen zij worden blootgesteld aan bacterien die resistent zijn tegen een of meerdere antibiotica. Dit brengt mogelijk volksgezondheidrisico's met zich mee omdat deze antibiotica belangrijk kunnen zijn om infecties te behandelen. De risico's kunnen zich op twee manieren manifesteren. Mensen die aan antibioticaresistente bacterien worden blootgesteld, kunnen zelf het risico lopen ziek te worden van deze - moeilijker te bestrijden - bacterien. Daarnaast is het mogelijk dat mensen zelf niet ziek worden van de resistente bacterien maar ze overdragen aan mensen met verminderde weerstand, zoals ziekenhuispatienten. Deze categorie mensen kan hier vervolgens wel ziek van worden

Slowly biodegradable organic compounds impact the biostability of non-chlorinated drinking water produced from surface water

It is possible to distribute drinking water without a disinfectant residual when the treated water is biologically stable. The objective of this study was to determine the impact of easily and slowly biodegradable compounds on the biostability of the drinking water at three full-scale production plants which use the same surface water, and on the regrowth conditions in the related distribution systems. Easily biodegradable compounds in the drinking water were determined with AOC-P17/Nox during 2012–2015. Slowly biodegradable organic compounds measured as particulate and/or high-molecular organic carbon (PHMOC), were monitored at the inlet and after the different treatment stages of the three treatments during the same period. The results show that PHMOC (300–470 μg C L−1) was approximately 10% of the TOC in the surface water and was removed to 50–100 μg C L−1. The PHMOC in the water consisted of 40–60% of carbohydrates and 10% of proteins. A significant and strong positive correlation was observed for PHMOC concentrations and two recently introduced bioassay methods for slowly biodegradable compounds (AOC-A3 and biomass production potential, BPC14). Moreover, these three parameters in the biological active carbon effluent (BACF) of the three plants showed a positive correlation with regrowth in the drinking water distribution system, which was assessed with Aeromonas, heterotrophic plate counts, coliforms and large invertebrates. In contrast, the AOC-P17/Nox concentrations did not correlate with these regrowth parameters. We therefore conclude that slowly biodegradable compounds in the treated water from these treatment plants seem to have a greater impact on regrowth in the distribution system than easily biodegradable compounds