Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in \u3cem\u3ePlasmodium falciparum\u3c/em\u3e

Background: Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration. Results: Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle. Conclusions: We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c), a Zinc finger transcription factor (PFL0465c) both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c)

Online Learning

K-12 Online Learning has exponentially grown in the last 15 years. An estimated 1.2 million K-12 students took online classes last year; 45 states currently have some form of online learning at the state-level; and some states mandate some sort of online experience prior to high school graduation. Given its dramatic growth and ubiquity in K-12 schooling, it is critical that administrators learn more about K-12 schooling and the role it may play in their district or building. Unfortunately, there is not one single model of K-12 online schooling. Therefore, there is not one suggested set of recommendations, learnings, or best practices administrators should pay attention to. The purpose of this chapter is to introduce administrators to some of the more generic models of K-12 virtual schooling, the new roles that are created with this innovative form of teaching and learning, and any research that might impact decision-making at the building or district levels

Stable evolutionary signal in a Yeast protein interaction network

BACKGROUND: The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-protein interaction data casts doubt on the broader usefulness of these interaction sets. Approaches focusing on one-protein-at-a-time have been powerfully employed to demonstrate the high degree of conservation of proteins participating in numerous interactions; here, we expand his 'node' focused paradigm to investigate the relative persistence of 'link' based evolutionary signals in a protein interaction network of S. cerevisiae and point out the value of this relatively untapped source of information. RESULTS: The trend for highly connected proteins to be preferably conserved in evolution is stable, even in the context of tremendous noise in the underlying protein interactions as well as in the assignment of orthology among five higher eukaryotes. We find that local clustering around interactions correlates with preferred evolutionary conservation of the participating proteins; furthermore the correlation between high local clustering and evolutionary conservation is accompanied by a stable elevated degree of coexpression of the interacting proteins. We use this conserved interaction data, combined with P. falciparum /Yeast orthologs, as proof-of-principle that high-order network topology can be used comparatively to deduce local network structure in non-model organisms. CONCLUSION: High local clustering is a criterion for the reliability of an interaction and coincides with preferred evolutionary conservation and significant coexpression. These strong and stable correlations indicate that evolutionary units go beyond a single protein to include the interactions among them. In particular, the stability of these signals in the face of extreme noise suggests that empirical protein interaction data can be integrated with orthologous clustering around these protein interactions to reliably infer local network structures in non-model organisms

Expression of the essential Kinase PfCDPK1 from Plasmodium falciparum in Toxoplasma gondii facilitates the discovery of novel antimalarial drugs

We have previously shown that genetic disruption of Toxoplasma gondii calcium-dependent protein kinase 3 (TgCDPK3) affects calcium ionophore-induced egress. We examined whether Plasmodium falciparum CDPK1 (PfCDPK1), the closest homolog of TgCDPK3 in the malaria parasite P. falciparum, could complement a TgCDPK3 mutant strain. PfCDPK1 is essential and plays critical roles in merozoite development, motility, and secretion. We show that expression of PfCDPK1 in the TgCDPK3 mutant strain rescues the egress defect. This phenotypic complementation requires the localization of PfCDPK1 to the plasma membrane and kinase activity. Interestingly, PfCDPK1-expressing Toxoplasma becomes more sensitive to egress inhibition by purfalcamine, a potent inhibitor of PfCDPK1 with low activity against TgCDPK3. Based on this result, we tested eight small molecules previously determined to inhibit the kinase activity of recombinant PfCDPK1 for their abilities to inhibit ionophore-induced egress in the PfCDPK1-expressing strain. While two of these chemicals did not inhibit egress, we found that six drugs affected this process selectively in PfCDPK1-expressing Toxoplasma. Using mutant versions of PfCDPK1 and TgCDPK3, we show that the selectivities of dasatinib and PLX-4720 are regulated by the gatekeeper residue in the ATP binding site. Importantly, we have confirmed that the three most potent inhibitors of egress in the PfCDPK1-expressing strain effectively kill P. falciparum. Thus, we have established and validated a recombinant strain of Toxoplasma that can be used as a surrogate for the discovery and analysis of PfCDPK1-specific inhibitors that can be developed as antimalarials

Patterns of Morphological Variation of \u3ci\u3eSalsuginus yutanensis\u3c/i\u3e (Monogenea: Ancyrocephalidae) over Space and Time

Salsuginus yutanensis occurs on the gills of the Plains topminnow Fundulus sciadicus Cope. The fish of this species have been found to vary morphologically and biochemically among disjunct populations. Morphological characteristics of the sclerotized parts of S. yutanensis were examined from three localities in Nebraska, over a 2-yr collecting period. Analysis of variance was used to assess morphological variation with respect to site and date. Worms from two localities, Keith and Saunders counties, differed significantly for most characters considered. A third site, also in Keith County, contained worms for which measurement means tended to be intermediate between those in the other two sites. This site-related difference was maintained over a pattern of broad seasonal variation and suggests that the site-related differences are of evolutionary origin. If this interpretation is true, then the parasite populations likely are isolated in a manner analogous to those of the host. However, differences due to effects of temperature on worm development were not ruled out as possible explanations for the observations although consistent temperature differences between the sites are unlikely, given the nature of the habitats studied

A statistical approach to finding overlooked genetic associations

<p>Abstract</p> <p>Background</p> <p>Complexity and noise in expression quantitative trait loci (eQTL) studies make it difficult to distinguish potential regulatory relationships among the many interactions. The predominant method of identifying eQTLs finds associations that are significant at a genome-wide level. The vast number of statistical tests carried out on these data make false negatives very likely. Corrections for multiple testing error render genome-wide eQTL techniques unable to detect modest regulatory effects.</p> <p>We propose an alternative method to identify eQTLs that builds on traditional approaches. In contrast to genome-wide techniques, our method determines the significance of an association between an expression trait and a locus with respect to the set of all associations to the expression trait. The use of this specific information facilitates identification of expression traits that have an expression profile that is characterized by a single exceptional association to a locus.</p> <p>Our approach identifies expression traits that have exceptional associations regardless of the genome-wide significance of those associations. This property facilitates the identification of possible false negatives for genome-wide significance. Further, our approach has the property of prioritizing expression traits that are affected by few strong associations. Expression traits identified by this method may warrant additional study because their expression level may be affected by targeting genes near a single locus.</p> <p>Results</p> <p>We demonstrate our method by identifying eQTL hotspots in <it>Plasmodium falciparum </it>(malaria) and <it>Saccharomyces cerevisiae </it>(yeast). We demonstrate the prioritization of traits with few strong genetic effects through Gene Ontology (GO) analysis of Yeast. Our results are strongly consistent with results gathered using genome-wide methods and identify additional hotspots and eQTLs.</p> <p>Conclusions</p> <p>New eQTLs and hotspots found with this method may represent regions of the genome or biological processes that are controlled through few relatively strong genetic interactions. These points of interest warrant experimental investigation.</p

Quantitative Dissection of Clone-Specific Growth Rates in Cultured Malaria Parasites

Measurement of parasite proliferation in cultured red blood cells underpins many facets of malaria research, from drug sensitivity assays to assessing the impact of experimentally altered genes on parasite growth, virulence, and fitness. Pioneering efforts to grow Plasmodium falciparum in cultured red blood cells revolutionized malaria research and spurred the development of semi-high throughput growth assays using radio-labeled hypoxanthine, an essential nucleic acid precursor, as a reporter of whole-cycle proliferation (Trager and Jensen, 1976; Desjardins et al., 1979). Use of hypoxanthine (Hx) and other surrogate readouts of whole-cycle proliferation remains the dominant choice in malaria research. While amenable to high-throughput inference of bulk proliferation rates, these assays are blind to the underlying developmental and cellular steps of growth in human red blood cells. Modern whole-genome methods promise to reveal much about basic parasite biology, but progress is hindered by limitations of our ability to precisely quantify the specific development and growth events within the erythrocytic cycle. Here we build on standard visual and Hx-incorporation measures of growth by quantifying sub-phenotypes of a rapid proliferator, the multi-drug resistant clone Dd2, from a standard wild type clone, HB3. These data illustrate differences in cycle duration, merozoite production, and invasion rate and efficiency that underpin Dd2’s average 2-fold proliferation advantage over HB3 per erythrocytic cycle. The ability to measure refined growth phenotypes can inform the development of high-throughput methods to isolate molecular and developmental determinants of differential parasite growth rates

SITE Joint SIG Symposia: A Collaboration Between the K-12 Online Learning SIG and Distance Learning SIG: How Higher Education and K-12 Online Learning Research Can Impact Each Other

Facilitated by Rick Ferdig of Kent State University and editor of JTATE, this Symposia brings together the work of the K-12 Online Learning SIG and the Distance Learning SIG communities and focuses on presentations from scholars in the field whose work has implications for both higher education and K-12 online learning. This Symposia will have nine panelists who will each present their work and then talk specifically about how their work can inform both K-12 and HE. Included in the list of Higher Education-focused panelists are Trisha Litz of Regis University, Maggie Niess of Oregon State University, Antoinette Davis of Eastern Kentucky University, and David Marcovitz of Loyola University Maryland. Included in the list of K-12-focused panelists are Leanna Archambault of Arizona State University, Kerry Rice of Boise State University, Michael Barbour of Touro University, Amy Garrett Dikkers of the University of North Carolina at Charlotte, and Aimee Whiteside of the University of Tampa

Guanabenz repurposed as an antiparasitic with activity against acute and latent toxoplasmosis

Toxoplasma gondii is a protozoan parasite that persists as a chronic infection. Toxoplasma evades immunity by forming tissue cysts, which reactivate to cause life-threatening disease during immune suppression. There is an urgent need to identify drugs capable of targeting these latent tissue cysts, which tend to form in the brain. We previously showed that translational control is critical during infections with both replicative and latent forms of Toxoplasma. Here we report that guanabenz, an FDA-approved drug that interferes with translational control, has antiparasitic activity against replicative stages of Toxoplasma and the related apicomplexan parasite Plasmodium falciparum (a malaria agent). We also found that inhibition of translational control interfered with tissue cyst biology in vitro. Toxoplasma bradyzoites present in these abnormal cysts were diminished and misconfigured, surrounded by empty space not seen in normal cysts. These findings prompted analysis of the efficacy of guanabenz in vivo by using established mouse models of acute and chronic toxoplasmosis. In addition to protecting mice from lethal doses of Toxoplasma, guanabenz has a remarkable ability to reduce the number of brain cysts in chronically infected mice. Our findings suggest that guanabenz can be repurposed into an effective antiparasitic with a unique ability to reduce tissue cysts in the brain