Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum

The RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.

An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum

Establishing robust genome engineering methods in the malarial parasite, Plasmodium falciparum, has the potential to substantially improve the efficiency with which we gain understanding of this pathogen’s biology to propel treatment and elimination efforts. Methods for manipulating gene expression and engineering the P. falciparum genome have been validated. However, a significant barrier to fully leveraging these advances is the difficulty associated with assembling the extremely high AT content DNA constructs required for modifying the P. falciparum genome. These are frequently unstable in commonly-used circular plasmids. We address this bottleneck by devising a DNA assembly framework leveraging the improved reliability with which large AT-rich regions can be efficiently manipulated in linear plasmids. This framework integrates several key functional genetics outcomes via CRISPR/Cas9 and other methods from a common, validated framework. Overall, this molecular toolkit enables P. falciparum genetics broadly and facilitates deeper interrogation of parasite genes involved in diverse biological processes.

Toxoplasma gondii Intravacuolar-Network-Associated Dense Granule Proteins Regulate Maturation of the Cyst Matrix and Cyst Wall

Little is known regarding how the chronic Toxoplasma gondii cyst develops. Here, we investigated intravacuolar-network-associated dense granule (GRA) proteins GRA1, GRA2, GRA4, GRA6, GRA9, and GRA12 during cyst development in vitro after differentiation of the tachyzoite-stage parasitophorous vacuole. By day 1 postdifferentiation, GRA1, GRA4, GRA6, GRA9, and GRA12 colocalized with Dolichos biflorus agglutinin stain at the cyst periphery. In contrast, GRA2 remained in the cyst matrix. By day 2 postdifferentiation, coinciding with localization of GRA2 to the cyst periphery, GRA1, GRA4, GRA6, and GRA9 established a continuous matrix pattern in the cyst. In contrast, GRA2 and GRA12 were colocalized in prominent cyst matrix puncta throughout cyst development. While GRA2, GRA6, and GRA12 localized in outer and inner layers of the cyst wall, GRA1, GRA4, and GRA9 localized predominantly in the inner layers of the cyst wall. GRA2 and GRA12 were colocalized in the cyst wall by day 7 postdifferentiation. However, by day 10 postdifferentiation, GRA12 was relocalized from the cyst wall to puncta in the cyst matrix. Differentiation of Δgra2 parasites revealed a defect in the ability to establish a normal cyst matrix. In addition, the deletion of any intravacuolar-network-associated GRA protein, except GRA1, reduced the rate of accumulation of cyst wall proteins at the cyst periphery relative to the cyst interior. Our findings reveal dynamic patterns of GRA protein localization during cyst development and suggest that intravacuolar-network-associated GRA proteins regulate the formation and maturation of the cyst matrix and cyst wall structures.IMPORTANCEToxoplasma gondii establishes chronic infection in humans by forming thick-walled cysts that persist in the brain. If host immunity wanes, cysts reactivate to cause severe, and often lethal, toxoplasmic encephalitis. There is no available therapy to eliminate cysts or to prevent their reactivation. Moreover, how the vital and characteristic cyst matrix and cyst wall structures develop is poorly understood. Here, we visualized and tracked the localization of Toxoplasma intravacuolar-network-associated dense granule (GRA) proteins during cyst development in vitro Intravacuolar-network GRAs were present within the cyst matrix and at the cyst wall in developing cysts, and genetic deletion of intravacuolar-network-associated GRAs reduced the rate of accumulation of cyst wall material at the cyst periphery. Our results show that intravacuolar-network-associated GRAs, particularly GRA2 and GRA12, play dynamic and essential roles in the development and maturation of the cyst matrix and the cyst wall structures.

Toxoplasma gondii Parasitophorous Vacuole Membrane-Associated Dense Granule Proteins Orchestrate Chronic Infection and GRA12 Underpins Resistance to Host Gamma Interferon

Toxoplasma gondii evades host immunity to establish a chronic infection. Here, we assessed the role of parasitophorous vacuole (PV) membrane (PVM)- and intravacuolar network (IVN) membrane-localized dense granule (GRA) proteins in the development of acute and chronic Toxoplasma infection. Deletion of PVM-associated GRA3, GRA7, GRA8, and GRA14 or IVN membrane-associated GRA2, GRA9, and GRA12 in the low-virulence type II Prugniaud (Pru) strain induced severe defects in the development of chronic-stage cysts in vivo without affecting the parasite growth rate or the ability to differentiate into cysts in vitro Acute virulence of the PruΔgra2, PruΔgra3, and PruΔgra4 mutants was reduced but not abolished. In contrast, the PruΔgra12 mutant was avirulent in mice and PruΔgra12 parasites failed to establish a chronic infection. High-virulence type I strain RHΔgra12 parasites also exhibited a major defect in acute virulence. In gamma interferon (IFN-γ)-activated macrophages, type I RHΔgra12 and type II PruΔgra12 parasites resisted the coating of the PVM with host immunity-related GTPases as effectively as the parental type I RHΔku80 and type II PruΔku80 strains, respectively. Despite this resistance, Δgra12 PVs ultimately succumbed to IFN-γ-activated host cell innate immunity. Our findings uncover a key role for GRA12 in mediating resistance to host IFN-γ and reveal that many other IVN membrane-associated GRA proteins, as well as PVM-localized GRA proteins, play important roles in establishing chronic infection.IMPORTANCEToxoplasma gondii cysts reactivate during immune deficiency and cause fatal encephalitis. Parasite molecules that coordinate the development of acute and chronic infection are poorly characterized. Here, we show that many intravacuolar network membrane and parasitophorous vacuole membrane-associated dense granule (GRA) proteins orchestrate the development of chronic cysts in vivo A subset of these GRA proteins also modulate acute virulence, and one protein that associates with the intravacuolar network membranes, namely GRA12, was identified as a major virulence factor required for parasite resistance to host gamma interferon (IFN-γ). Our results revealed that many parasitophorous vacuole membrane and intravacuolar network membrane-associated GRA proteins are essential for successful chronic infection.

The role of the general practitioner in the screening and clinical management of chronic viral hepatitis in six EU countries

INTRODUCTION

Chronic viral hepatitis is still a major public health concern in the EU. In order to halt the progression of the disease and to prevent onward transmission, timely recognition and accurate clinical management are crucial. The aim of the present study was to investigate the role of the general practitioner (GP) in the screening of persons at risk and in the clinical management of chronic viral hepatitis patients in six EU countries.

METHODS

An online survey among GPs and secondary-care specialists was conducted in the UK, Germany, the Netherlands, Hungary, Italy and Spain. In the GP survey, we used a four-point Likert scale to find out how commonly risk groups are screened. In both surveys, we measured GPs involvement in monitoring clinical indicators in patients undergoing antiviral treatment, and explored whether patients in four clinical scenarios are referred back to primary care.

RESULTS

Between five and 10 experts per professional group were surveyed, except for Spain (GPs: n = 2; Specialists: n = 4) and, in the case of the GP survey, Hungary (GPs: n = 1) and Germany (GPs: n = 4). Migrants are variably or not routinely screened for hepatitis B/C in the majority of cases. The majority of GPs reported that hepatitis B/C screening was routinely offered to people who inject drugs. In Hungary, Italy and in the Netherlands, screening sex workers is not a regular practice. As to whether GPs offer screening to men who have sex with men, responses varied; in Germany, the Netherlands and Italy, screening was "variably" or "commonly" implemented, while in Hungary the practice seems to be sporadic. In the UK, screening for hepatitis B seems to be common practice among GPs, while hepatitis C testing is only occasionally offered to this risk group. Most GPs (> 44%) in all countries except Hungary reported that hepatitis B/C screening was very commonly offered to HIV patients. The role of GPs in monitoring hepatitis cases and the referral of cases back to GPs by specialists varied both within and between countries. GPs are unlikely to monitor clinical outcomes other than side effects in patients undergoing treatment. Patients who have had a sustained virological response are usually referred back to GPs, whereas patients undergoing antiviral treatment and those who do not respond to treatment are rarely referred back.

CONCLUSIONS

The GP's decision to offer screening to risk groups often seems to be an individual choice of the healthcare professional. Raising GPs' awareness of the disease, for example through the adoption of effective strategies for the dissemination and implementation of the existing guidelines for general practice, is strongly needed. The role of GPs and specialists involved in the management of chronically infected patients should also be clarified, as opinions sometimes differ markedly even within each professional group.

Synthetic RNA-protein modules integrated with native translation mechanisms to control gene expression in malaria parasites

Synthetic posttranscriptional regulation of gene expression is important for understanding fundamental biology and programming new cellular processes in synthetic biology. Previous strategies for regulating translation in eukaryotes have focused on disrupting individual steps in translation, including initiation and mRNA cleavage. In emphasizing modularity and cross-organism functionality, these systems are designed to operate orthogonally to native control mechanisms. Here we introduce a broadly applicable strategy for robustly controlling protein translation by integrating synthetic translational control via a small-molecule-regulated RNA–protein module with native mechanisms that simultaneously regulate multiple facets of cellular RNA fate. We demonstrate that this strategy reduces ‘leakiness' to improve overall expression dynamic range, and can be implemented without sacrificing modularity and cross-organism functionality. We illustrate this in Saccharomyces cerevisae and the non-model human malarial parasite, Plasmodium falciparum. Given the limited functional genetics toolkit available for P. falciparum, we establish the utility of this strategy for defining essential genes.

Current strategies for regulatory control of gene expression are orthogonal to the host organism mechanisms. Here the authors demonstrate an RNA aptamer controlled system integrated into native regulatory pathways in the parasite Plasmodium falciparum.

Genetic manipulation in Δku80 strains for functional genomic analysis of Toxoplasma gondii

Targeted genetic manipulation using homologous recombination is the method of choice for functional genomic analysis to obtain a detailed view of gene function and phenotype(s). The development of mutant strains with targeted gene deletions, targeted mutations, complemented gene function, and/or tagged genes provides powerful strategies to address gene function, particularly if these genetic manipulations can be efficiently targeted to the gene locus of interest using integration mediated by double cross over homologous recombination.

Due to very high rates of nonhomologous recombination, functional genomic analysis of Toxoplasma gondii has been previously limited by the absence of efficient methods for targeting gene deletions and gene replacements to specific genetic loci. Recently, we abolished the major pathway of nonhomologous recombination in type I and type II strains of T. gondii by deleting the gene encoding the KU80 protein^1,2. The Δku80 strains behave normally during tachyzoite (acute) and bradyzoite (chronic) stages in vitro and in vivo and exhibit essentially a 100% frequency of homologous recombination. The Δku80 strains make functional genomic studies feasible on the single gene as well as on the genome scale^1-4.

Here, we report methods for using type I and type II Δku80Δhxgprt strains to advance gene targeting approaches in T. gondii. We outline efficient methods for generating gene deletions, gene replacements, and tagged genes by targeted insertion or deletion of the hypoxanthine-xanthine-guanine phosphoribosyltransferase (HXGPRT) selectable marker. The described gene targeting protocol can be used in a variety of ways in Δku80 strains to advance functional analysis of the parasite genome and to develop single strains that carry multiple targeted genetic manipulations. The application of this genetic method and subsequent phenotypic assays will reveal fundamental and unique aspects of the biology of T. gondii and related significant human pathogens that cause malaria (Plasmodium sp.) and cryptosporidiosis (Cryptosporidium).

Sequence analysis of the spliced-leader intergenic region (SL-IR) and random amplified polymorphic DNA (RAPD) of Trypanosoma rangeli strains isolated from Rhodnius ecuadoriensis, R. colombiensis, R. pallescens and R. prolixus suggests a degree of co-evolution between parasites and vectors

Spliced leader intergenic region (SL-IR) sequences from 23 Trypanosoma rangeli strains isolated from the salivary glands of Rhodnius colombiensis, R. ecuadoriensis, R. pallescens and R. prolixus and two human strains revealed the existence of 4 genotypes with CA, GT, TA, ATT and GTAT microsatellite repeats and the presence of insertions/deletions (INDEL) and single nucleotide polymorphism (SNP) characterizing each genotype. The strains isolated from the same vector species or the same Rhodnius evolutionary line presented the same genotypes, even in cases where strains had been isolated from vectors captured in geographically distant regions. The dendrogram constructed from the SL-IR sequences separated all of them into two main groups, one with the genotypes isolated from R. prolixus and the other group containing three well defined sub-groups with the genotypes isolated from R. pallescens, R. colombiensis and R. ecuadoriensis. Random amplified polymorphic DNA (RAPD) analysis showed the same two main groups and sub-groups supporting strict T. rangeli genotypes' association with Rhodnius species. Combined with other studies, these results suggest a possible co-evolutionary association between T. rangeli genotypes and their vectors.

First Colombian multicentric newborn screening for congenital toxoplasmosis

Aims

To determine the incidence of congenital toxoplasmosis in Colombian newborns from 19 hospital or maternal child health services from seven different cities of five natural geographic regions (Caribbean, Central, Andean, Amazonia and Eastern).

Materials and Methods

We collected 15,333 samples from umbilical cord blood between the period of March 2009 to May 2010 in 19 different hospitals and maternal-child health services from seven different cities. We applied an IgM ELISA assay (Vircell, Spain) to determine the frequency of IgM anti Toxoplasma. The results in blood cord samples were confirmed either by western blot and repeated ELISA IgM assay. In a sub-sample of 1,613 children that were negative by the anti-Toxoplasma IgM assay, the frequency of specific anti-Toxoplasma IgA by the ISAGA assay was determined. All children with positive samples by IgM, IgA, clinical diagnosis or treatment during pregnancy were recalled for confirmatory tests after day 10 of life.

Results

61 positive samples for specific IgM (0.39%) and 9 positives for IgA (0.5%) were found. 143 questionnaires were positive for a clinical diagnosis or treatment for toxoplasmosis during pregnancy. 109 out of the 218 children that had some of the criteria for postnatal confirmatory tests were followed. Congenital toxoplasmosis infection was confirmed in 15 children: 7 were symptomatic, and three of them died before the first month of life (20% of lethality). A significant correlation was found between a high incidence of markers for congenital toxoplasmosis and higher mean annual rainfall for the city.

Conclusions

Incidence for congenital toxoplasmosis is significantly different between hospitals or maternal child health services from different cities in Colombia. Mean annual rainfall was correlated with incidence of congenital toxoplasmosis.

Congenital toxoplasmosis can result in permanent sequel as blindness or neurological damage in children and it seems to be more severe in South America than in other continents. There is a lack of information about this frequency in Colombia, where no control program is established, although it is a recognized cause of potentially preventable congenital blindness. We propose the first Colombian multicentric study to determine the frequency and impact of congenital toxoplasmosis. More than 15,000 newborns in seven cities were studied. Newborns were tested at birth by doing a cord blood test for toxoplasmosis. Additionally, children from mothers with history of toxoplasmosis acquired during pregnancy were recalled for a follow-up. The program identified fifteen children otherwise undiagnosed; three of these children died as consequence of congenital toxoplasmosis. The frequency of the congenital infection varied significantly between cities, being higher in Armenia and Florencia, intermediate in Bogota, Bucaramanga and Barranquilla and very low in western cities such as Cucuta and Riohacha. For the first time a significant correlation was found between mean rainfall at the city and the incidence of this congenital infection.

Genetic Variability and Phylogenetic Relationships within Trypanosoma cruzi I Isolated in Colombia Based on Miniexon Gene Sequences

Phylogenetic studies of Trypanosoma cruzi have identified the existence of two groups: T. cruzi I and T. cruzi II. There are aspects that still remain unknown about the genetic variability within the T. cruzi I group. Given its epidemiological importance, it is necessary to have a better understanding of T. cruzi transmission cycles. Our purpose was to corroborate the existence of haplotypes within the T. cruzi I group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs) found in the miniexon gene intergenic region, for the isolates from different hosts and epidemiological transmission cycles in Colombian regions. 31 T. cruzi isolates were molecularly characterized. Phylogenetic relationships within T. cruzi I isolates showed four haplotype groups (Ia-Id), associated with their transmission cycle. In previous studies, we reported that haplotype Ia is mainly associated with the domestic cycle and domiciliated Rhodnius prolixus. Haplotype Ib is associated with the domestic cycle and peridomestic cycle, haplotype Ic is closely related with the peridomestic cycle, and haplotype Id is strongly associated with the sylvatic cycle. The phylogenetic methodologies applied in this study are tools that bolster the associations among isolates and thus shed light on Chagas disease epidemiology.

Haplotype identification within Trypanosoma cruzi I in Colombian isolates from several reservoirs, vectors and humans

Genetic variability in the Trypanosoma cruzi I group has recently been revealed in Colombian isolates from humans, reservoirs and vectors. Genomic rearrangements and the polymorphic regions in taxonomic markers, such as the miniexon gene, have led to the development of molecular tools to identify phylogenetic haplotypes in T. cruzi isolates. From genetic polymorphisms found in T. cruzi I isolates, they have been classified into four haplotypes according to their epidemiologic transmission cycles. Haplotype Ia is associated with domestic isolates, from Rhodnius prolixus; haplotype Ib, with the domestic and peridomestic cycle, mainly associated with Triatoma dimidiata; haplotype Ic is a poorly characterized group, which has been associated with the peridomestic cycle; and haplotype Id has been related to the sylvatic cycle. In order to demonstrate that the circulating T. cruzi I isolates in Colombia can be classified in the four proposed haplotypes, specific primers were designed on polymorphic regions of the miniexon gene's intergenic sequences. This set of primers allowed the molecular characterization of 33 Colombian isolates, classifying them into three of the four proposed haplotypes (Ia, Ib and Id). Results obtained from maximum parsimony and maximum-likelihood-based phylogenetic analyses correlated with the molecular classification of the isolates and their transmission cycles. This study brings insights into the Chagas disease epidemiology and the parasite's transmission dynamics.

Cardiac perforation from central venous catheters: survival after cardiac tamponade in an infant

A 2,210-g infant suffered cardiac tamponade, which resulted from atrial perforation by a central venous catheter. The infant survived due to timely diagnostic and therapeutic intervention. Cardiac tamponade should be suspected in any patient with a central venous catheter whose condition deteriorates suddenly. Immediate chest roentgenogram and echocardiogram may be performed to support the diagnosis; but when the patient's condition is deteriorating, a diagnostic (and therapeutic as well!) pericardiocentesis should be performed without waiting for other diagnostic measures. A review of clinical recognition and diagnostic measures for cardiac perforation and tamponade is presented. Preventive measures to avoid this fatal complication of central venous catheters are suggested, and therapeutic interventions are outlined.

Management of intractable and extensive tracheal stenosis by implantation of cartilage graft

A variety of methods have been developed to solve the problem of extensive tracheal stenosis. Endoscopic resection with injection of steroids was performed with some success. Resection with end-to-end anastomosis has been attempted in localized tracheal stenosis, but it is not practical in extensive tracheal stenosis. As an alternative to the above procedures, we performed a simpler operation to increase the diameter of the narrow trachea. We treated three children (a 7-month-old, a 2-year-old, and a 3-year-old) who had severe tracheal stenosis. The trachea was explored through a cervical transverse incision. The anterior wall of the trachea at the level of the stenosis was opened longitudinally and the scar in the tracheal lumen was resected. A free-cartilage graft measuring 1 X 4 cm was taken from the third costochondral junction and was wedged and sutured in place into the tracheal opening. This resulted in increasing the internal diameter of the stenotic trachea. A nasotracheal tube was left in place at the end of the procedure for 48 hours. The children are still asymptomatic 19, 10, and 8 months postoperatively. The careful selection and preparation of the patients for this procedure is discussed.

Selective spermatic arteriography for localization of an impalpable undescended testis

Thirty patients with undescended testes, including 15 children, were studied by selective spermatic angiography. Six patients had both arteriography and venography, and 24 had bilateral arteriography for assessment of testicular size. In 7 patients, arteriography revealed an impalpable testis following unsuccessful surgical exploration. In 17, subsequent surgery confirmed the angiographic findings; testicular agenesis was diagnosed in 7, and catheterization failed in 2. There were no complications. Preoperative testicular arteriography localizes the testis, facilitates surgery, and may aid in tumor detection. Angiographic identification of testicular agenesis precludes exploration. Arteriography is more accurate, simpler, and less complicated than venography.