PfHPRT: a new biomarker candidate of acute Plasmodium falciparum infection.

Plasmodium falciparum is a protozoan parasite that causes human malaria. This parasitic infection accounts for approximately 655,000 deaths each year worldwide. Most deaths could be prevented by diagnosing and treating malaria promptly. To date, few parasite proteins have been developed into rapid diagnostic tools. We have combined a shotgun and a targeted proteomic strategy to characterize the plasma proteome of Gambian children with severe malaria (SM), mild malaria, and convalescent controls in search of new candidate biomarkers. Here we report four P. falciparum proteins with a high level of confidence in SM patients, namely, PF10_0121 (hypoxanthine phosphoribosyltransferase, pHPRT), PF11_0208 (phosphoglycerate mutase, pPGM), PF13_0141 (lactate dehydrogenase, pLDH), and PF14_0425 (fructose bisphosphate aldolase, pFBPA). We have optimized selected reaction monitoring (SRM) assays to quantify these proteins in individual patients. All P. falciparum proteins were higher in SM compared with mild cases or control subjects. SRM-based measurements correlated markedly with clinical anemia (low blood hemoglobin concentration), and pLDH and pFBPA were significantly correlated with higher P. falciparum parasitemia. These findings suggest that pHPRT is a promising biomarker to diagnose P. falciparum malaria infection. The diagnostic performance of this marker should be validated prospectively

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct

Plasmodium P-type cyclin CYC3 modulates endomitotic growth during oocyst development in mosquitoes

Cell-cycle progression and cell division in eukaryotes are governed in part by the cyclin family and their regulation of cyclin-dependent kinases (CDKs). Cyclins are very well characterised in model systems such as yeast and human cells, but surprisingly little is known about their number and role in Plasmodium, the unicellular protozoan parasite that causes malaria. Malaria parasite cell division and proliferation differs from that of many eukaryotes. During its life cycle it undergoes two types of mitosis: endomitosis in asexual stages and an extremely rapid mitotic process during male gametogenesis. Both schizogony (producing merozoites) in host liver and red blood cells, and sporogony (producing sporozoites) in the mosquito vector, are endomitotic with repeated nuclear replication, without chromosome condensation, before cell division. The role of specific cyclins during Plasmodium cell proliferation was unknown. We show here that the Plasmodium genome contains only three cyclin genes, representing an unusual repertoire of cyclin classes. Expression and reverse genetic analyses of the single Plant (P)-type cyclin, CYC3, in the rodent malaria parasite, Plasmodium berghei, revealed a cytoplasmic and nuclear location of the GFP-tagged protein throughout the lifecycle. Deletion of cyc3 resulted in defects in size, number and growth of oocysts, with abnormalities in budding and sporozoite formation. Furthermore, global transcript analysis of the cyc3-deleted and wild type parasites at gametocyte and ookinete stages identified differentially expressed genes required for signalling, invasion and oocyst development. Collectively these data suggest that cyc3 modulates oocyst endomitotic development in Plasmodium berghei

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features.

Toxoplasma gondii is an important protozoan parasite that infects all warm-blooded animals and causes opportunistic infections in immuno-compromised humans. Its closest relative, Neospora caninum, is an important veterinary pathogen that causes spontaneous abortion in livestock. Comparative genomics of these two closely related coccidians has been of particular interest to identify genes that contribute to varied host cell specificity and disease. Here, we describe a manual evaluation of these genomes based on strand-specific RNA sequencing and shotgun proteomics from the invasive tachyzoite stages of these two parasites. We have corrected predicted structures of over one third of the previously annotated gene models and have annotated untranslated regions (UTRs) in over half of the predicted protein-coding genes. We observe distinctly long UTRs in both the organisms, almost four times longer than other model eukaryotes. We have also identified a putative set of cis-natural antisense transcripts (cis-NATs) and long intergenic non-coding RNAs (lincRNAs). We have significantly improved the annotation quality in these genomes that would serve as a manually curated dataset for Toxoplasma and Neospora research communities

Changes in cytokine, filarial antigen, and DNA levels associated with adverse events following treatment of lymphatic filariasis

Mild to moderate adverse events (AEs) are common after treatment of lymphatic filariasis (LF) and pose a major challenge for the global LF elimination program. We studied changes in cytokine levels and filarial worm components in plasma of subjects with and without AEs following treatment of LF. Participants (n = 24) were hospitalized and monitored for AEs following treatment. Cytokines (27), filarial DNA, circulating filarial antigen (CFA), and immune complexes were measured in plasma samples collected before and after treatment. Levels for 16 cytokines increased after treatment in individuals with moderate AEs compared to individuals with no and/or mild AEs. These included 3 major proinflammatory cytokines (interleukin 6, tumor necrosis factor α, and interleukin 1β). Eotaxin-1 levels were elevated at baseline in individuals who developed moderate AEs after treatment; thus, eotaxin-1 is a potential biomarker for AE risk. CFA and filarial DNA levels increased more in individuals with moderate AEs after treatment than in people with no/mild AEs. Increases in cytokine, filarial DNA, and CFA levels were associated with development of AEs following treatment of LF. Improved understanding of the pathogenesis of AEs may lead to improved methods for their prevention or management that could increase compliance in elimination programs

Making connections: technological interventions to support students in using, and tutors in creating, assessment feedback

This paper explores the potential of technology to enhance the assessment and feedback process for both staff and students. The ‘Making Connections’ project aimed to better understand the connections that students make between the feedback that they receive and future assignments, and explored whether technology can help them in this activity. The project interviewed 10 tutors and 20 students, using a semi-structured approach. Data were analysed using a thematic approach, and the findings have identified a number of areas in which improvements could be made to the assessment and feedback process through the use of technology. The findings of the study cover each stage of the assessment process from the perspective of both staff and students. The findings are discussed in the context of current literature, and special attention is given to projects from the UK higher education sector intended to address the same issues. Keywords: feed-forward; assessment; practices; technology; technology-enhanced learnin

MRE11 Is Crucial for Malaria Parasite Transmission and Its Absence Affects Expression of Interconnected Networks of Key Genes Essential for Life

The meiotic recombination 11 protein (MRE11) plays a key role in DNA damage response and maintenance of genome stability. However, little is known about its function during development of the malaria parasite Plasmodium. Here, we present a functional, ultrastructural and transcriptomic analysis of Plasmodium parasites lacking MRE11 during its life cycle in both mammalian and mosquito vector hosts. Genetic disruption of Plasmodium berghei mre11 (PbMRE11) results in significant retardation of oocyst development in the mosquito midgut associated with cytoplasmic and nuclear degeneration, along with concomitant ablation of sporogony and subsequent parasite transmission. Further, absence of PbMRE11 results in significant transcriptional downregulation of genes involved in key interconnected biological processes that are fundamental to all eukaryotic life including ribonucleoprotein biogenesis, spliceosome function and iron-sulfur cluster assembly. Overall, our study provides a comprehensive functional analysis of MRE11's role in Plasmodium development during the mosquito stages and offers a potential target for therapeutic intervention during malaria parasite transmission

The spectrum of (136199) Eris between 350 and 2350 nm: Results with X-Shooter

X-Shooter is the first second-generation instrument for the ESO-VLT. It as a spectrograph covering the 300 - 2480 nm spectral range at once with a high resolving power. These properties enticed us to observe (136199) Eris during the science verification of the instrument. The target has numerous absorption features in the optical and near-infrared domain which has been observed by different authors, showing differences in their positions and strengths. We attempt at constraining the existence of super-volatiles, e.g., CH4, CO and N2, and in particular try to understand the physical-chemical state of the ices on Eris' surface. We observed Eris in the 300-2480 nm range and compared the newly obtained spectra with those available in the literature. We identified several absorption features, measuring their positions and depth and compare them with those of reflectance of pure methane ice obtained from the optical constants of this ice at 30 K to study shifts in their positions and find a possible explanation for their origin. We identify several absorption bands in the spectrum all consistent with the presence of CH4 ice. We do not identify bands related with N2 or CO. We measured the central wavelengths of the bands and find variable shifts, with respect to the spectrum of pure CH4 at 30 K. Conclusions. Based on these wavelength shifts we confirm the presence of a dilution of CH4 in other ice on the surface of Eris and the presence of pure CH4 spatially segregated. The comparison of the centers and shapes of these bands with previous works suggest that the surface is heterogeneous. The absence of the 2160 nm band of N2 can be explained if the surface temperature is below 35.6 K, the transition temperature between the alpha and beta phases of this ice. Our results, including the reanalysis of data published elsewhere, point to an heterogeneous surface on Eris.Comment: 15 pages, 5 figure

Widening Access to Applied Machine Learning with TinyML

Broadening access to both computational and educational resources is critical to diffusing machine-learning (ML) innovation. However, today, most ML resources and experts are siloed in a few countries and organizations. In this paper, we describe our pedagogical approach to increasing access to applied ML through a massive open online course (MOOC) on Tiny Machine Learning (TinyML). We suggest that TinyML, ML on resource-constrained embedded devices, is an attractive means to widen access because TinyML both leverages low-cost and globally accessible hardware, and encourages the development of complete, self-contained applications, from data collection to deployment. To this end, a collaboration between academia (Harvard University) and industry (Google) produced a four-part MOOC that provides application-oriented instruction on how to develop solutions using TinyML. The series is openly available on the edX MOOC platform, has no prerequisites beyond basic programming, and is designed for learners from a global variety of backgrounds. It introduces pupils to real-world applications, ML algorithms, data-set engineering, and the ethical considerations of these technologies via hands-on programming and deployment of TinyML applications in both the cloud and their own microcontrollers. To facilitate continued learning, community building, and collaboration beyond the courses, we launched a standalone website, a forum, a chat, and an optional course-project competition. We also released the course materials publicly, hoping they will inspire the next generation of ML practitioners and educators and further broaden access to cutting-edge ML technologies.Comment: Understanding the underpinnings of the TinyML edX course series: https://www.edx.org/professional-certificate/harvardx-tiny-machine-learnin