1,720,972 research outputs found
Novel insights into telomere biology and virulence gene expression in plasmodium falciparum
Get PDFPlasmodium falciparum malaria is still one of the most preeminent and deadliest infectious diseases worldwide, imposing a tremendous health and economic burden on endemic countries. The high virulence of P. falciparum is mostly attributable to the expression of P. falciparum erythrocyte membrane protein 1 (PfEMP1) on the surface of infected red blood cells. PfEMP1 mediates intravascular parasite sequestration in vital organs, which contributes substantially to severe disease and death. Mutually exclusive transcription of the 60 var genes (encoding PfEMP1) and switching to formerly silenced variants results in antigenic variation and allows the parasite to efficiently evade host immune responses and to establish chronic infection.
Members of the var multigene family are predominantly positioned close to chromosome ends. Characteristically, these regions are transcriptionally inert and demarcated by the repressive histone mark H3K9me3 and the evolutionary conserved silencing factor P. falciparum heterochromatin protein 1 (PfHP1). It is believed that this specialised environment at chromosome ends generates a structural framework for the epigenetic control of var gene expression. Moreover, telomeres play a crucial role in preserving genome integrity by protecting chromosome ends from inappropriate fusion and recombination events, as well as in regulating telomere length.
However, we still lack a detailed functional understanding of the underlying molecular mechanisms that regulate Plasmodium chromosome end biology. During my PhD thesis, I tackled chromosome end biology from three different angles to improve our understanding of how virulence gene expression is regulated and how genome integrity is preserved.
In a first project I performed an in-depth functional analysis of the epigenetic silencing factor PfHP1 by generating an inducible loss-of-function mutant. We showed that upon PfHP1 depletion parasites display a complete breakdown of mutually exclusive var expression and antigenic variation. Intriguingly, we also found that over 50% of PfHP1-deprived parasites represented viable gametocytes that complete sexual development up to stage V maturity. This high conversion rate was linked to the targeted de-repression of the ap2-g locus that codes for the ApiAP2 transcription factor AP2-G, which is essential for gametocyte conversion. Thus, our data unveiled PfHP1 not only as a master regulator of variegated expression of exported virulence factors, but also as a crucial factor in the regulation of sexual cell differentiation.
In a second project I aimed at the functional characterisation of the chromosome-end associated protein PfSIP2, which was shown to specifically interact with SPE2 elements in subtelomeric regions. In-depth analysis of the expression profile of endogenous PfSIP2 revealed that this protein is only expressed during a very narrow time window of approximately 10hrs in late stage parasites, which coincides with intra-erythrocytic schizogony. Genome-wide ChIP-Seq experiments confirmed the exclusive binding of endogenous PfSIP2 to subtelomeric SPE2 landmarks in upsB var promoter regions and subtelomeric non-coding regions. Surprisingly, however, neither phenotypic changes nor differential gene expression were observed in a conditional PfSIP2-loss-of-function mutant and hence this approach didn’t uncover novel insights into the function of this ApiAP2 factor.
In a third project I aimed at the identification of the telomere repeat-binding factor (TRF) in P. falciparum. Although TRFs are highly conserved and play essential roles in preserving chromosome integrity and regulating chromosome length in model eukaryotes, so far no TRF homologue has been found in the malaria parasites. My work reports about the successful de novo identification of the P. falciparum telomere repeat-binding protein (PfTRF). Intriguingly, this protein appears to be evolutionary distinct from TRFs in other eukaryotes as it binds to telomere repeat DNA via a C-terminal C2H2-type zinc finger domain instead of a MYB domain. Genome-wide mapping by ChIP-Seq experiments not only confirmed that PfTRF indeed binds to all chromosome termini in vivo, but as well revealed an unexpected second binding hotspot at telomere repeat-like sequences found in subtelomeric var gene promoters. A comprehensive characterisation of PfTRF using a conditional loss-of-function mutant identified essential roles for this protein in mitotic cell cycle progression and telomere length regulation. Hence, our findings provide important new insight into mechanisms underlying genome maintenance and possibly virulence gene silencing in P. falciparum. They further suggest that malaria parasites employ an evolutionary divergent molecular complex to preserve telomere function.
In summary, my results provide important new and detailed understanding of the molecular processes involved in genome maintenance, virulence gene expression and sexual conversion in P. falciparum, processes that are highly relevant for malaria pathogenesis, parasite viability and malaria transmission. I am confident that these findings have important implications for the development of intervention strategies targeting parasite propagation and transmission
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Investigating the link between nutrient sensing and gametocyte formation in the malaria parasite Plasmodium falciparum
No full textMalaria is an infectious disease and causes over 600’000 deaths annually. To ensure host-to-host transmission, malaria parasites rely on specialized stages, called gametocytes. The formation of these sexual precursor cells is initiated by commitment of asexual blood stage parasites to the sexual differentiation pathway. Plasmodium falciparum, the most virulent of six parasite species infecting humans, employs nutrient sensing to adapt the rate of sexual commitment. The parasite monitors the levels of the host-derived lipid lysophosphatidylcholine (lysoPC) to control the epigenetically regu-lated expression of the transcription factor AP2-G, the master regulator of sexual commitment. The molecular mechanisms linking lysoPC sensing to AP2-G expression, however, are poorly under-stood. In this PhD project, I aimed at identifying factors linking nutrient sensing and sexual commit-ment in P. falciparum. To this end, I investigated the effect of a set of chemical compounds and 12 selected genes on sexual commitment rates. In a first study, I assessed the effect of drug treatment on sexual commitment rates using a high content imaging-based assay to clarify the longstanding question of whether antimalarial drug treatment increases gametocyte formation. By screening a comprehensive set of pharmaceuticals using both drug sensitive and drug resistant parasite strains, we show that drug treatment indeed can increase sexual commitment rates, but only rarely results in a net increase in gametocyte production. Our results suggest that general stress, rather than drug-specific activities, promotes sexual commitment. This finding was crucial to interpret the results of a second study, in which we screened compounds of inhibitor libraries to identify molecules influenc-ing sexual commitment. We then employed mass spectrometry-based cellular thermal shift assays (MS-CETSA) to identify the cellular target of selected hit compounds. Thereby, we identified high-confidence candidate targets and assessed their role during sexual commitment using reverse genet-ics approaches. We found indication for an involvement of cyclic adenosine monophosphate (cAMP)-dependent signaling and protein kinase A (PKA) in regulating commitment to gametocyte formation. Based on reverse genetics experiments and chemical perturbation assays, we hypothesize that PKA acts as a repressor of AP2-G expression under lysoPC-free conditions and thus links nutri-ent sensing to the epigenetic regulation of AP2-G. However, more experiments are required to con-firm this hypothesis. In a third project, we assessed the function the FK506-binding protein 35 (FKBP35) – another putative target of a commitment-inducing compound – by combining reverse genetics with transcriptional and proteomic profiling. While we did not find evidence for a role in sexual commitment, we show that limiting FKBP35 levels are lethal to P. falciparum and result in a delayed death-like phenotype that is characterized by defective ribosome homeostasis and stalled protein synthesis. Our data furthermore suggest that the antiplasmodial activity of the well-characterized FKBP inhibitor FK506 is independent of FKBP35, which has implications for the de-velopment of FK506-derived molecules as antimicrobial drugs. In summary, this thesis offers a test-able model to further investigate the link between nutrient sensing and sexual commitment and pro-vides new insights into the function of FKBP35
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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