Biology subjects

Grigg, M. E.

Publications and source records attributed to Grigg, M. E..

17 recordsLinked to original sources

bioRxiv2026

The live attenuated DGAT1-knockout whole-cell Toxoplasma vaccine confers protective immunity against acute and chronic toxoplasmosis

The intravacuolar parasite Toxoplasma gondii scavenges fatty acids from host mammalian cells and stores excess in lipid droplets. To investigate the physiological relevance of neutral lipid storage in Toxoplasma, we generated a mutant lacking DGAT1, an ER-localized enzyme that synthesizes triacylglycerols, from the virulent type I RH strain of T. gondii. Compared to WT, RH {Delta}DGAT1 parasites grow poorly in mammalian cells, form few LD, suffer from lipotoxicity, and do not cause disease or lethality in immunocompetent or immunodeficient mice. Importantly, mice immunized with RH {Delta}DGAT1 parasites mount strong, long-term immune responses involving both cellular and humoral components, with higher levels of T. gondii-specific IgG antibodies, effector memory T cells, and both pro-inflammatory and anti-inflammatory cytokines, indicating a mixed Th1/Th2 response with Th1 predominance. This immunity provides complete, long-lasting protection (up to 6 months) against rechallenge from homologous type I (acute infection) and heterologous cyst-forming type II (chronic infection) T. gondii strains. Additional analyses reveal that IFN-{gamma}, CD8+ T cells, as well as B cells are crucial for defending against type I T. gondii in immunized mice. Overall, our live-attenuated RH {Delta}DGAT1 strain is a promising vaccine candidate and a model for studying immune responses that control T. gondii infections.

microbiology↗

bioRxiv2026

Restraint of Powassan virus replication by TRIM5α facilitates viral avoidance of antiviral immunity

TRIpartite Motif (TRIM) protein 5 alpha (TRIM5) is a well characterized cellular inhibitor of lentivirus replication that limits transmission of related viruses between primates. We previously reported that TRIM5 derived from humans and rhesus macaques inhibits replication of orthoflaviviruses belonging to the tick-borne encephalitis virus (TBEV) serocomplex, including TBEV, Kyasanur forest disease virus and Langat virus (LGTV), but interestingly not the tick-borne Powassan virus (POWV). To further characterize the primate TRIM5 and orthoflavivirus interface, we screened TRIM5 variants from representative old- and new-world primates for restriction capacity. TRIM5 from old-world African green monkey, De Brazzas monkey and chimpanzee demonstrated virus-specific restriction of tick-borne orthoflaviviruses. Efforts to determine why TRIM5 fails to inhibit POWV revealed that our lab stock had acquired a non-synonymous mutation in NS3 that, when introduced into a POWV molecular clone, facilitated virus replication in the presence of all inhibitory primate TRIM5 proteins. Infection of human dendritic cells with TRIM5-resistant POWV resulted in high early replication and strong induction of interferon responses that limited replication compared with the wild-type virus. Thus, primate TRIM5 functions as a potent cellular barrier to infection with tick-borne orthoflaviviruses that restrains replication to a level that may help avoid early innate immune recognition.

microbiology↗

bioRxiv2025

Toxoplasma induced cytokine release syndrome is critically dependent on the expression of pore-forming Perforin-Like Protein-1

Acute virulence in Toxoplasma gondii is linked to an excessive proinflammatory cytokine cascade during laboratory murine infection. Previous work showed that T. gondii secretes a pore forming protein, PLP1, that is required for efficient cytolytic egress from host cells. Deletion of the PLP1 gene results in defective egress from infected culture cells and a marked reduction in parasite virulence. The goal of the present study was to gain insight into the nature of the attenuated virulence observed in PLP1 knockout compared to wild type (WT) RH parasites. Using in vivo bioluminescence imaging, we show that parasites lacking PLP1 establish an acute infection and disseminate throughout the infected mice. Histological tissue analysis indicates that parasites cause severe pathology, even in the absence of PLP1. However, mice infected with{Delta} plp1 parasites evoke a protective inflammatory response, demonstrated by mouse survival and control of infection. Flow cytometric analysis was used to determine cellular changes occurring during both WT and {Delta}plp1 parasite infection. Parasite control in the{Delta} plp1 infection was associated with earlier activation of myeloid cells and a moderate neutrophil response that, by comparison, becomes the dominant infiltrating cell type of WT infection. Positive disease outcome during{Delta} plp1 parasite infection is also associated with regulated induction of proinflammatory cytokines, including IFN-{gamma} and TNF-, and an earlier IL-10 regulatory response that is dysregulated during WT infection. Together these findings suggest a key role for Toxoplasma PLP1 in promoting a lethal inflammatory immune response during acute infection with a virulent strain of the parasite. Author SummaryPore-forming proteins are virulence determinants expressed by multiple different pathogens, with varied roles including cellular invasion and escape, immune cell destruction, and the hijack of host cell defenses. The pathogen, Toxoplasma gondii, expresses a pore-forming protein PLP1, that is required for cell lysis and acute virulence in mice. Here, we investigate the potential mechanisms by which this pore-forming protein promotes parasite virulence; from parasite replication and dissemination to immunologic outcomes after infection. In vivo infections demonstrate that parasites replicate, disseminate, and stimulate a protective immune response when PLP1 is not expressed. We show that PLP1 expression induces a parasite driven dysregulation of cell populations and cytokine/chemokine responses, resulting in cytokine release syndrome. In a broader context, Toxoplasmas PLP1 is comparable to other pathogen pore-forming proteins that function as virulence determinants by their ability to alter host immune responses.

microbiology↗

bioRxiv2024

Rapid detection, quantification and speciation of Leishmania using real-time PCR and DNA sequencing at the rRNA Internal Transcribed Spacer 2

The ability to discriminate infection between closely related Leishmania species within the Viannia species complex, specifically L. braziliensis, L. guyanensis and L. panamensis is critical to inform the clinical diagnosis and determine the most efficacious treatment modality. We designed a nested primer set targeting the rRNA Internal Transcribed Spacer 2 (ITS2), located on Chromosome 27, to distinguish among all human infective Leishmania species. Separate nested and single primer pairs were developed for conventional and quantitative PCR approaches respectively. Species-specific single nucleotide polymorphisms and indels located within the PCR products were identified by Sanger sequencing. This single locus approach provides a sensitive and specific platform to identify the species of Leishmania causing infection.

microbiology↗

bioRxiv2024

Human ESCRT-I and ALIX function as scaffolding helical filaments in vivo

The Endosomal Sorting Complex Required for Transport (ESCRT) is an evolutionarily conserved machinery that performs reverse-topology membrane scission in cells universally required from cytokinesis to budding of enveloped viruses. Upstream acting ESCRT-I and ALIX control these events and link recruitment of viral and cellular partners to late-acting ESCRT-III CHMP4 through incompletely understood mechanisms. Using structure-function analyses combined with super-resolution imaging, we show that ESCRT-I and ALIX function as distinct helical filaments in vivo. Together, they are essential for optimal structural scaffolding of HIV-1 nascent virions, the retention of viral and human genomes through defined functional interfaces, and recruitment of CHMP4 that itself assembles into corkscrew-like filaments intertwined with ESCRT-I or ALIX helices. Disruption of filament assembly or their conformationally clustered RNA binding interfaces in human cells impaired membrane abscission, resulted in major structural instability and leaked nucleic acid from nascent virions and nuclear envelopes. Thus, ESCRT-I and ALIX function as helical filaments in vivo and serve as both nucleic acid-dependent structural scaffolds as well as ESCRT-III assembly templates. Significance statementWhen cellular membranes are dissolved or breached, ESCRT is rapidly deployed to repair membranes to restore the integrity of intracellular compartments. Membrane sealing is ensured by ESCRT-III filaments assembled on the inner face of membrane; a mechanism termed inverse topology membrane scission. This mechanism, initiated by ESCRT-I and ALIX, is universally necessary for cytokinesis, wound repair, budding of enveloped viruses, and more. We show ESCRT-I and ALIX individually oligomerize into helical filaments that cluster newly discovered nucleic acid-binding interfaces and scaffold-in genomes within nascent virions and nuclear envelopes. These oligomers additionally appear to serve as ideal templates for ESCRT-III polymerization, as helical filaments of CHMP4B were found intertwined ESCRT-I or ALIX filaments in vivo. Similarly, corkscrew-like filaments of ALIX are also interwoven with ESCRT-I, supporting a model of inverse topology membrane scission that is synergistically reinforced by inward double filament scaffolding.

cell biology↗

bioRxiv2024

Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity

Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover [~]92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.

genomics↗

bioRxiv2024

WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp.

Cryptosporidium spp. are parasites that cause severe illness in vulnerable human populations. Obtaining pure and sufficient Cryptosporidium DNA from clinical and environmental samples is a challenging task. Oocysts shed in available fecal samples can be limited in quantity, require purification (biased towards dominant strains), and yield limited DNA (<40 fg/oocyst). Here, we use updated genomic sequences from a broad diversity of Cryptosporidium species that have been found to infect humans (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to develop and validate a set of 100,000 RNA baits (CryptoCap_100k) with the aim of enriching Cryptosporidium DNA from varied samples. Compared to unenriched libraries, CryptoCap_100k increases the percentage of reads mapping to target genome sequences, increases the depth and breadth of genome coverage, and facilitates analyses of genetic variants in many samples, while decreasing overall costs.

genomics↗

bioRxiv2024

Giardia intestinalis reshapes mucosal immunity toward a Type 2 response that attenuates inflammatory bowel-like diseases

Diarrheal diseases are the second leading cause of death in children worldwide. Epidemiological studies show that co-infection with Giardia intestinalis decreases the severity of diarrhea. Here, we show that Giardia is highly prevalent in the stools of asymptomatic school-aged children. It orchestrates a Th2 mucosal immune response, characterized by increased antigen-specific Th2 cells, IL-25, Type 2-associated cytokines, and goblet cell hyperplasia. Giardia infection expanded IL-10-producing Th2 and GATA3+ Treg cells that promoted chronic carriage, parasite transmission, and conferred protection against Toxoplasma gondii-induced lethal ileitis and DSS-driven colitis by downregulating proinflammatory cytokines, decreasing Th1/Th17 cell frequency, and preventing collateral tissue damage. Protection was dependent on STAT6 signaling, as Giardia-infected STAT6-/- mice no longer regulated intestinal bystander inflammation. Our findings demonstrate that Giardia infection reshapes mucosal immunity toward a Type 2 response, which confers a mutualistic protection against inflammatory disease processes and identifies a critical role for protists in regulating mucosal defenses.

immunology↗

bioRxiv2023

Extant interspecific hybridization among trematodes within the Schistosoma haematobium species complex in Nigeria

BackgroundNatural interspecific hybridization between the human parasite (Schistosoma haematobium [Sh]) and bovine parasites (S. bovis [Sb], S. curassoni [Sc]) is increasingly reported in Africa. We developed a multi-locus PCR DNA-Seq strategy that amplifies two unlinked nuclear (transITS, BF) and two linked organellar genome markers (CO1, NAD5) to genotype S. haematobium eggs collected from infected people in Ile Oluji/Oke Igbo, Ondo State (an agrarian community) and Kachi, Jigawa State (a pastoral community) in Southwestern and Northern Nigeria, respectively. Principal FindingsWe applied this methodology against 57 isolates collected from a total of 219 participants. All patients from Jigawa state were infected with just one of two haplotypes of an S. haematobium x S. bovis hybrid based on sequences obtained at CO1, NAD5, transITS and BF markers. Whereas samples collected from Ondo state were varied. Mitonuclear discordance was observed in all 17 patients, worms possessed an Sb mitochondrial genome but one of four different haplotypes at the nuclear markers, either admixed (heterozygous between Sh x Sc or Sh x Sb) at both markers (n=10), Sh at BF and admixed at transITS (Sh x Sc) (n=5), admixed (Sh x Sc) at BF and homozygous Sc at transITS (n=1) or homozygous Sh at BF and homozygous Sc at transITS (n=1). SignificancePrevious work suggested that zoonotic transmission of S. bovis in pastoral communities, where humans and animals share a common water source, is a driving factor facilitating interspecific hybridization. However, our data showed that all isolates were hybrids, with greater diversity identified in Southwestern Nigeria, a non-pastoral site. Further, one patient possessed an S. bovis mitochondrial genome but was homozygous for S. haematobium at BF and homozygous for S. curassoni at transITS supporting at least two separate backcrosses in its origin, suggesting that interspecific hybridization may be an ongoing process. Author SummaryInterspecific hybridization between trematode parasites poses serious health risks to humans. Many systems have shown possible hybridization between different schistosome species. As evidence of natural hybridization between human S. haematobium and animal S. bovis or S. curassoni has grown in recent years, epidemiological surveys across potential hybrid zones are required, particularly in endemic African regions. According to several reports, indiscriminate human-animal water contact is a major factor contributing to hybridization of human and animal schistosomes. We collected and genotyped 57 parasite isolates from pastoral and non-pastoral communities in Kachi, Jigawa state, and Ile Oluji/Oke Igbo, Ondo state, Nigeria to screen for hybrids. In both sites, we found Schistosoma hybrids with mitonuclear discordance and repeated backcrossing between S. haematobium, S. bovis, and S. curassoni. Contrary to previous reports, Schistosoma hybrids appear to be widespread and not solely dependent on human-animal water interactions.

microbiology↗

bioRxiv2023

The commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces B cell-modulated remodeling of the gut microbiota

Commensal protists and gut bacterial communities exhibit complex relationships, mediated at least in part through host immunity. To improve our understanding of this tripartite interplay, we investigated community and functional dynamics between the murine protist Tritrichomonas musculus (T. mu) and intestinal bacteria in healthy and B cell-deficient mice. We identified dramatic, protist-driven remodeling of resident microbiome growth and activities, in parallel with T. mu functional changes, accelerated in the absence of B cells. Metatranscriptomic data revealed nutrient-based competition between bacteria and the protist. Single cell transcriptomics identified distinct T. mu life stages, providing new evidence for trichomonad sexual replication and the formation of pseudocysts. Unique cell states were validated in situ through microscopy and flow cytometry. Our results reveal complex microbial dynamics during the establishment of a commensal protist in the gut, and provide valuable datasets to drive future mechanistic studies.

microbiology↗

bioRxiv2023

Ultrastructural identification and molecular characterization of two new parabasalid species that naturally colonize laboratory mice, Tritrichomonas musculus and Tritrichomonas casperi

Tritrichomonas muris is a flagellated protist isolated from the cecum of wild mice in the Czech Republic. This commensal protist has been shown previously to alter immune phenotypes in laboratory mice. Other trichomonads, previously referred to as Tritrichomonas musculis and Tritrichomonas rainier, also naturally colonize laboratory mice and cause immune alterations. This report formally describes two new trichomonads, Tritrichomonas musculus n. sp., and Tritrichomonas casperi n. sp., at the ultrastructural and molecular level. These two protists were isolated from laboratory mice, and were differentiated by their size and the structure of their undulating membrane and posterior flagellum. Analysis at the 18S rRNA and trans-ITS genetic loci supported their designation as distinct species, related to T. muris. To further assess the true extent of parabasalid diversity infecting laboratory mice, 135 mice were screened at the NIH using pan-parabasalid primers that amplify the trans-ITS region. Forty-four percent of mice were positive for parabasalids, encompassing a total of 8 distinct sequence types. Tritrichomonas casperi and Trichomitus-like protists were dominant. T. musculus and T. rainier were also detected, but T. muris was not. Our work establishes a previously underappreciated diversity of commensal trichomonad protists that naturally colonize the enteric cavity of laboratory mice.

microbiology↗

bioRxiv2022

Toxoplasma surface coat protein TgSRS57 (TgSAG3) regulates complement deposition, Factor H recruitment, and promotes parasite persistence

The surface coat of Toxoplasma gondii possesses a lectin-like activity that activates host complement. Serum resistance relies on specific recruitment of host regulators Factor H (FH) and C4BP to the parasite surface to inactivate bound C3 and evade the complement system. TgSRS57 (TgSAG3) was previously reported to possess a lectin-like activity specific for sulfated proteoglycans (SPGs) that facilitated host cell attachment and parasite invasion. To investigate whether TgSRS57 actively recruits Factor H to the parasite surface to regulate the complement cascade, we generated Type I RH and Type II CZ1 knockout strains. {Delta}srs57 parasites showed a reduction in both C3 deposition and FH recruitment indicating that TgSRS57 is a C3 acceptor and regulates complement activation. However, {Delta}srs57 parasites showed no attachment defect, possessed normal extracellular survival and intracellular replication kinetics, and were more virulent than WT strains in low dose murine infections, contrary to previous findings. To better understand the genetic and cellular data, we determined the 1.59[A] resolution TgSRS57 crystal structure. Notably, TgSRS57 did not possess a dimer dependent basic surface groove as originally modeled, nor did it bind heparin. However, approximately 10 distinct parasite proteins were identified that interact specifically with SPGs. Infection studies showed that Type II {Delta}srs57 parasites achieved higher parasite burdens and elevated inflammatory responses compared to WT parasites. Infection of C3 deficient mice established that TgSRS57-dependent protection was C3-dependent and that T. gondii actively parasitizes the complement system. Our results suggest that the interaction between TgSRS57 and C3 plays a critical role in disease tolerance by controlling both parasite proliferation and persistence in vivo. AUTHOR SUMMARYThe Toxoplasma gondii surface coat is dominated by a superfamily of developmentally expressed, antigenically distinct adhesins collectively called the SRS proteins, which are structurally analogous to the Plasmodium 6-CYS surface proteins. These proteins are thought to possess lectin-like activities, facilitate parasite attachment and entry into host cells, and regulate innate effectors of the host immune response. Disease tolerance in hosts is critically dependent on the induction of sufficient immunity to limit parasite replication and promote host survival without inducing bystander immune damage. In this study we employed a combination of genetic, cellular and structural biology approaches to establish that the surface antigen TgSRS57 regulates complement C3 deposition on parasite surfaces by specifically recruiting host Factor H to actively resist serum killing and limit the formation of the C5b-9 membrane attack complex. Further, that the presence of C3 was host protective, as C3-deficient mice failed to control parasite replication. The ability of the parasites to inactivate C3 was also necessary to resist serum killing and promote chronic infection. Because complement exists as a potent inflammatory mediator, the active regulation of complement by Toxoplasma ensures that the parasite is not lysed by C3 but also limits the induction of lethal immunopathology, thereby promoting an immune balance, disease tolerance, and the long-term persistence of transmissible parasites.

microbiology↗

bioRxiv2021

ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii reveals novel virulence factors implicated in host cell invasion

The apicomplexan intracellular parasite Toxoplasma gondii is a major food borne pathogen with significant impact in children and during pregnancy. The majority of the T. gondii proteome remains uncharacterized and the organization of proteins into complexes is unclear. To overcome this knowledge gap, we utilize a biochemical fractionation strategy coupled with mass spectrometry to predict interactions by correlation profiling. Key to this approach is the integration of additional datasets based on gene co-expression as well as phylogenetic profiles that eliminate poorly supported interactions and reduce the number of false positive interactions. In addition to a supervised machine learning strategy, we employed an unsupervised approach in data integration, based on similarity network fusion, to overcome the deficit of high-quality training data in non-model organisms. The resulting high confidence network, we term ToxoNet, comprises 2,063 interactions connecting 652 proteins. Clustering of this network identifies 93 protein complexes, predicting both novel complexes as well as new components for previously known complexes. In particular, we identified clusters enriched in mitochondrial machinery that include previously uncharacterized proteins that likely represent novel adaptations to oxidative phosphorylation. Furthermore, complexes enriched in proteins localized to secretory organelles and the inner membrane complex, predict additional novel components representing novel targets for detailed functional characterization. We present ToxoNet as a publicly available resource with the expectation that it will help drive future hypotheses within the research community.

microbiology↗

bioRxiv2021

Virulence shift in a sexual clade of Type X Toxoplasma infecting Southern Sea Otters

How virulent parasites are maintained in nature is an important paradigm of eukaryotic pathogenesis. Here we used population genetics and molecular methods to study the evolution and emergence of genetic variants of the protozoan parasite Toxoplasma gondii, referred collectively as Type X (HG12), recovered from a threatened marine mammal species. Specifically, 53 T. gondii strains were isolated from southern sea otters (SSO) that stranded between 1998-2004 with T. gondii infection (ranging from chronic incidental infections to fatal encephalitis). Over 74% of these SSO, collected throughout their geographic range, were infected with Type X, based on multi-locus PCR-DNA sequencing. Depending on the locus investigated, Type X strains possessed one of three allelic types that had independently assorted across the strains examined; either genetically distinct alleles, referred to as "{psi}" or "8", or a Type II allele. Phylogenetic incongruence among locus-specific trees, genome-wide CGH array and WGS analyses confirmed that Type X is a sexual clade of natural recombinants that resemble F1 progeny from a genetic cross between Type II and a mosaic of two distinct "{psi}" or "{delta}" ancestries. A single Type X genotype (19/53; 36%) that largely caused subclinical chronic infections in SSO, was highly pathogenic to mice (LD100= 1 parasite). To determine whether murine virulence genes could be mapped within this population of natural isolates, we performed a genome scan and identified four QTLs with LOD scores greater than 4.0. Targeted disruption of ROP33, the strongest candidate from among 16 genes within the highest QTL on Chromosome VIIa established ROP33 as a murine virulence locus. The ability of this highly pathogenic mouse-virulent T. gondii clone to expand its environmental niche and infect a majority of SSO supports a virulence shift model whereby generalist pathogens like T. gondii utilize their sexual cycles to produce new strains that possess an expanded biological potential. Such a trait enables pathogens to extend their host range or be naturally selected within their vast intermediate host range to maximize transmission. Our work establishes a rationale for how virulent strains can be maintained cryptically in nature across a pathogens broad host range, and act as potential reservoirs for epidemic disease. ImportanceWaterborne outbreaks of protozoal parasites are capable of causing fatal disease in a wide range of animals, including humans. Population expansion of felids in addition to anthropogenic changes near marine estuarine environments may facilitate marine wildlife exposure to highly infectious Toxoplasma gondii oocysts shed in felid feces. Infected cats shed millions of environmentally-resistant T. gondii oocysts that can be widely dispersed by storm events. In North America T. gondii is thought to possess a highly clonal population structure dominated by 4 clonal lineages (I, II, III, and X). Population genetic analysis of 53 T. gondii isolates collected longitudinally from SSO infected with T. gondii that stranded between 1998-2004 identified 74% of otters infected with Type X T. gondii, and that Type X is not a clonal lineage, but rather a recombinant clade of at least 12 distinct strains consistent with a recent genetic cross. Importantly, one Type X haplotype was isolated from 36% of southern sea otters (Enhydra lutris neries) across their geographic range in California. This haplotype was highly pathogenic to mice but caused relatively benign infections in SSO. A genome scan was performed to identify a virulence locus; a secreted serine threonine kinase (ROP33) that enhanced pathogenicity in laboratory mice, but not sea otters. Our data support a virulence shift model whereby generalist pathogens like T. gondii utilize their sexual cycles to produce virulent strains that can be maintained cryptically in nature, according to their differential capacity to cause disease within the pathogens broad intermediate host range. This type of "host selection" has important public health implications. Strains capable of causing fatal infections can persist in nature by circulating as chronic infections in resistant intermediate host species that act as reservoirs for epidemic disease.

molecular biology↗

bioRxiv2020

Extensive hybridization between pig and human Ascaris identifies a highly interbred species complex infecting humans

Human ascariasis is a major neglected tropical disease caused by the nematode Ascaris lumbricoides. We report a 296 megabase (Mb) reference quality genome comprised of 17902 protein-coding genes derived from a single, representative Ascaris worm collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of human isolates (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite Ascaris suum than to A. lumbricoides. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analysed. The nuclear genomes had extensive heterozygosity and all samples existed as genetic mosaics with either A. suum-like or A. lumbricoides-like inheritance patterns supporting a highly interbred Ascaris species genetic complex. As no barriers appear to exist for anthroponotic transmission of these "hybrid" worms, a one-health approach to control the spread of human ascariasis will be necessary.

genomics↗

bioRxiv2018

POPSICLE: A Software Suite to Study Population Structure and Ancestral Determinants of Phenotypes using Whole Genome Sequencing Data

The advent of new sequencing technologies has provided access to genome-wide markers which may be evaluated for their association with phenotypes. Recent studies have leveraged these technologies and sequenced hundreds and sometimes thousands of strains to improve the accuracy of genotype-phenotype predictions. Sequencing of thousands of strains is not practical for many research groups which argues for the formulation of new strategies to improve predictability using lower sample sizes and more cost-effective methods. We introduce here a novel computational algorithm called POPSICLE that leverages the local genetic variations to infer blocks of shared ancestries to construct complex evolutionary relationships. These evolutionary relationships are subsequently visualized using chromosome painting, as admixtures and as clades to acquire general as well as specific ancestral relationships within a population. In addition, POPSICLE evaluates the ancestral blocks for their association with phenotypes thereby bridging two powerful methodologies from population genetics and genome-wide association studies. In comparison to existing tools, POPSICLE offers substantial improvements in terms of accuracy, speed and automation. We evaluated POPSICLEs ability to find genetic determinants of Artemisinin resistance within P. falciparum using 57 randomly selected strains, out of 1,612 that were used in the original study. POPSICLE found Kelch, a gene implicated in the original study, to be significant (p-value 0) towards resistance to Artemisinin. We further extended this analysis to find shared ancestries among closely related P. falciparum, P. reichenowi and P. gaboni species from the Laverania subgenus of Plasmodium. POPSICLE was able to accurately infer the population structure of the Laverania subgenus and detected 4 strains from a chimpanzee in Koulamoutou with significant shared ancestries with P. falciparum and P. gaboni. We simulated 4 datasets to asses if these shared ancestries indicated a hybrid or mixed infections involving P. falciparum and P. gaboni. The analysis based on the simulated data and genome-wide heterozygosity profiles of the strains indicate these are most likely mixed infections although the possibility of hybrids cannot be ruled out. POPSICLE is a java-based utility that requires no installation and can be downloaded freely from https://popsicle-admixture.sourceforge.io/\n\nAuthor SummaryThe associations between genotypes and phenotypes have traditionally been performed using markers such as single nucleotide polymorphisms. Often, these markers are independently evaluated for their association with phenotypes. A genomic region is deemed significant if multiple markers with significance colocalize. However, multiple markers that are in linkage disequilibrium can sometimes work synergistically and contribute to phenotypic variations. These synergistic associations across markers and across subpopulations have traditionally been captured by population genetic approaches that determine local ancestries. We sought to bridge these two powerful but independent methodologies to improve genotype-phenotype predictions. We developed a new software called POPSICLE that employs an innovative approach to determine local ancestries and evaluates them for their association with phenotypes. Validity of POPSICLE in determining the genes that are responsible for Plasmodium Falciparums resistance to Artemisinin and in determining the population structure of Laverania subgenus of Plasmodium are discussed.

bioinformatics↗

bioRxiv2017

Toxoplasma gondii microneme proteins 1 and 4 bind to Toll-like receptors 2 and 4 N-glycans triggering innate immune response

Infection of host cells by Toxoplasma gondii is an active process, which is regulated by secretion of microneme (MICs) and rhoptry proteins (ROPs and RONs) from specialized organelles in the apical pole of the parasite. MIC1, MIC4 and MIC6 assemble into an adhesin complex, secreted on the parasite surface and function to promote infection competency. MIC1 and MIC4 are known to bind terminal sialic acid residues and galactose residues, respectively and to induce IL-12 production from splenocytes. Here we show that rMIC1- and rMIC4-stimulated dendritic cells and macrophages to produce proinflammatory cytokines, and they do so by engaging TLR2 and TLR4. This process depends on sugar recognition, since point mutations in the carbohydrate-recognition domains (CRD) of rMIC1 and rMIC4 inhibit innate immune cells activation. HEK cells transfected with TLR2 glycomutants were selectively unresponsive to MICs. Following in vitro infection, parasites lacking MIC1 or MIC4, as well as expressing MIC proteins with point mutations in their CRD, failed to induce wild-type (WT) levels of IL-12 secretion by innate immune cells. However, only MIC1 was shown to impact systemic levels of IL-12 and IFN-{gamma} in vivo. Together, our data show that MIC1 and MIC4 interact physically with TLR2 and TLR4 N-glycans to trigger IL-12 responses, and MIC1 is playing a significant role in vivo by altering T. gondii infection competency and murine pathogenesis.\n\nAUTHOR SUMMARYToxoplasmosis is caused by the protozoan Toxoplasma gondii, belonging to the Apicomplexa phylum. This phylum comprises important parasites able to infect a broad diversity of animals, including humans. A particularity of T. gondii is its ability to invade virtually any nucleated cell of all warm-blooded animals through an active process, which depends on the secretion of adhesin proteins. These proteins are discharged by specialized organelles localized in the parasite apical region, and termed micronemes and rhoptries. We show in this study that two microneme proteins from T. gondii utilize their adhesion activity to stimulate innate immunity. These microneme proteins, denoted MIC1 and MIC4, recognize specific sugars on receptors expressed on the surface of mammalian immune cells. This binding activates these innate immune cells to secrete cytokines, which promotes efficient host defense mechanisms against the parasite and regulate their pathogenesis. This activity promotes a chronic infection by controlling parasite replication during acute infection.

immunology↗