- ItemSupplementary materials for Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data(2023) Chou, Renee Ti; Ouattara, Amed; Takala-Harrison, Shannon; Cummings, Michael P.Intensive malaria control and elimination efforts have led to substantial reductions in malaria incidence over the past two decades. However, the reduction in Plasmodium falciparum malaria cases has led to a species shift in some geographic areas, with P. vivax predominating in many areas outside of Africa. Despite its wide geographic distribution, P. vivax vaccine development has lagged far behind that for P. falciparum, in part due to the inability to cultivate P. vivax in vitro, hindering traditional approaches for antigen identification. In a prior study, we have used a positive-unlabeled random forest (PURF) machine learning approach to identify P. falciparum antigens for consideration in vaccine development efforts. Here we integrate systems data from P. falciparum (the better-studied species) to improve PURF models to predict potential P. vivax vaccine antigen candidates. We further show that inclusion of known antigens from the other species is critical for model performance, but the inclusion of unlabeled proteins the other species can result in misdirection of the model toward predictors of species classification, rather than antigen identification. Beyond malaria, incorporating antigens from a closely related species may aid in vaccine development for emerging pathogens having few or no known antigens.
- ItemGenomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes(MDPI, 2018-12-05) Clark, Frances E.; Conte, Matthew A.; Kocher, Thomas D.B chromosomes (Bs) were discovered a century ago, and since then, most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function, and evolution of B chromosomes remain unanswered. Here, we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with or without B chromosomes. We examined the efficiency of this method, and compared results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets were identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified genes and gene fragments located on the B chromosome, some of which may regulate the segregation and maintenance of the B chromosome.
- ItemDistribution and Community Assembly of Trees Along an Andean Elevational Gradient(MDPI, 2019-09-05) Worthy, Samantha J.; Jiménez Paz, Rosa A.; Pérez, Álvaro J.; Reynolds, Alex; Cruse-Sanders, Jennifer; Valencia, Renato; Barone, John A.; Burgess, Kevin S.Highlighting patterns of distribution and assembly of plants involves the use of community phylogenetic analyses and complementary traditional taxonomic metrics. However, these patterns are often unknown or in dispute, particularly along elevational gradients, with studies finding different patterns based on elevation. We investigated how patterns of tree diversity and structure change along an elevation gradient using taxonomic and phylogenetic diversity metrics. We sampled 595 individuals (36 families; 53 genera; 88 species) across 15 plots along an elevational gradient (2440–3330 m) in Ecuador. Seventy species were sequenced for the rbcL and matK gene regions to generate a phylogeny. Species richness, Shannon–Weaver diversity, Simpson’s Dominance, Simpson’s Evenness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD) were evaluated for each plot. Values were correlated with elevation and standardized effect sizes (SES) of MPD and MNTD were generated, including and excluding tree fern species, for comparisons across elevation. Taxonomic and phylogenetic metrics found that species diversity decreases with elevation. We also found that overall the community has a non-random phylogenetic structure, dependent on the presence of tree ferns, with stronger phylogenetic clustering at high elevations. Combined, this evidence supports the ideas that tree ferns have converged with angiosperms to occupy the same habitat and that an increased filtering of clades has led to more closely related angiosperm species at higher elevations.
- ItemCooperativity and Steep Voltage Dependence in a Bacterial Channel(MDPI, 2019-09-11) Lin, Shang H.; Chang, Kai-Ti; Cherian, Nuval; Wu, Benjamin; Phee, Hyo; Cho, Christy; Colombini, MarcoThis paper reports on the discovery of a novel three-membrane channel unit exhibiting very steep voltage dependence and strong cooperative behavior. It was reconstituted into planar phospholipid membranes formed by the monolayer method and studied under voltage-clamp conditions. The behavior of the novel channel-former, isolated from Escherichia coli, is consistent with a linearly organized three-channel unit displaying steep voltage-gating (a minimum of 14 charges in the voltage sensor) that rivals that of channels in mammalian excitable membranes. The channels also display strong cooperativity in that closure of the first channel permits the second to close and closure of the second channel permits closure of the third. All three have virtually the same conductance and selectivity, and yet the first and third close at positive potentials whereas the second closes at negative potentials. Thus, is it likely that the second channel-former is oriented in the membrane in a direction opposite to that of the other two. This novel structure is named “triplin.” The extraordinary behavior of triplin indicates that it must have important and as yet undefined physiological roles.
- ItemInteractions with a Complex Microbiota Mediate a Trade-Off between the Host Development Rate and Heat Stress Resistance(MDPI, 2020-11-13) Slowinski, Samuel; Ramirez, Isabella; Narayan, Vivek; Somayaji, Medha; Para, Maya; Pi, Sarah; Jadeja, Niharika; Karimzadegan, Siavash; Pees, Barbara; Shapira, MichaelAnimals and plants host diverse communities of microorganisms, and these microbiotas have been shown to influence host life history traits. Much has been said about the benefits that host-associated microbiotas bestow on the host. However, life history traits often demonstrate tradeoffs among one another. Raising Caenorhabditis elegans nematodes in compost microcosms emulating their natural environment, we examined how complex microbiotas affect host life history traits. We show that soil microbes usually increase the host development rate but decrease host resistance to heat stress, suggesting that interactions with complex microbiotas may mediate a tradeoff between host development and stress resistance. What element in these interactions is responsible for these effects is yet unknown, but experiments with live versus dead bacteria suggest that such effects may depend on bacterially provided signals.