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Articles 121 - 150 of 340

Full-Text Articles in Biology

Pooling As A Strategy For The Timely Diagnosis Of Soil-Transmitted Helminths In Stool: Value And Reproducibility, Marina Papaiakovou, James Wright, Nils Pilotte, Darren Chooneea, Fabian Schär, James E. Truscott, Julia C. Dunn, Iain Gardiner, Judd L. Walson, Steven A. Williams, D. Timothy J. Littlewood Sep 2019

Pooling As A Strategy For The Timely Diagnosis Of Soil-Transmitted Helminths In Stool: Value And Reproducibility, Marina Papaiakovou, James Wright, Nils Pilotte, Darren Chooneea, Fabian Schär, James E. Truscott, Julia C. Dunn, Iain Gardiner, Judd L. Walson, Steven A. Williams, D. Timothy J. Littlewood

Biological Sciences: Faculty Publications

Background: The strategy of pooling stool specimens has been extensively used in the field of parasitology in order to facilitate the screening of large numbers of samples whilst minimizing the prohibitive cost of single sample analysis. The aim of this study was to develop a standardized reproducible pooling protocol for stool samples, validated between two different laboratories, without jeopardizing the sensitivity of the quantitative polymerase chain reaction (qPCR) assays employed for the detection of soil-transmitted helminths (STHs). Two distinct experimental phases were recruited. First, the sensitivity and specificity of the established protocol was assessed by real-time PCR for each one …


Genome Analyses Of The New Model Protist Euplotes Vannus Focusing On Genome Rearrangement And Resistance To Environmental Stressors, Xiao Chen, Yaohan Jiang, Feng Gao, Weibo Zheng, Timothy J. Krock, Naomi A. Stover, Chao Lu, Laura A. Katz, Weibo Song Sep 2019

Genome Analyses Of The New Model Protist Euplotes Vannus Focusing On Genome Rearrangement And Resistance To Environmental Stressors, Xiao Chen, Yaohan Jiang, Feng Gao, Weibo Zheng, Timothy J. Krock, Naomi A. Stover, Chao Lu, Laura A. Katz, Weibo Song

Biological Sciences: Faculty Publications

As a model organism for studies of cell and environmental biology, the free-living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), “gene-sized” chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high-quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) …


Causative Agent Of Canine Heartworm (Dirofilaria Immitis) Detected In Wild Lemurs, Sarah Zohdy, Kim Valenta, Bernadette Rabaoarivola, Weam I. Zaky, Nils Pilotte, Steven A. Williams, Colin A. Chapman, Zach J. Farris Aug 2019

Causative Agent Of Canine Heartworm (Dirofilaria Immitis) Detected In Wild Lemurs, Sarah Zohdy, Kim Valenta, Bernadette Rabaoarivola, Weam I. Zaky, Nils Pilotte, Steven A. Williams, Colin A. Chapman, Zach J. Farris

Biological Sciences: Faculty Publications

The lemurs of Madagascar are threatened by human activities. We present the first molecular detection of canine heartworm (Dirofilaria immitis) in a wild non-human primate, the mouse lemur (Microcebus rufus). Zoonotic D. immitis infection has been associated with clinical pathology that includes serious and often fatal cardiac and pulmonary reactions. With human encroachment and associated increases in free-roaming dog populations in Madagascar, we examined lemurs for zoonotic canid pathogens. D. immitis presents a new potential conservation threat to lemurs. We highlight the need for wide-ranging and effective interventions, particularly near protected areas, to address this growing …


Phylotol: A Taxon/Gene-Rich Phylogenomic Pipeline To Explore Genome Evolution Of Diverse Eukaryotes, Mario A. Cerón-Romero, Xyrus X. Maurer-Alcalá, Jean David Grattepanche, Ying Yan, Miguel M. Fonseca, Laura A. Katz, Fabia Ursula Battistuzz Aug 2019

Phylotol: A Taxon/Gene-Rich Phylogenomic Pipeline To Explore Genome Evolution Of Diverse Eukaryotes, Mario A. Cerón-Romero, Xyrus X. Maurer-Alcalá, Jean David Grattepanche, Ying Yan, Miguel M. Fonseca, Laura A. Katz, Fabia Ursula Battistuzz

Biological Sciences: Faculty Publications

Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have focused on specific clades, with greatest attention paid to plants, animals, and fungi. The rapid increase in high-throughput sequencing (HTS) data from diverse lineages now provides opportunities to estimate evolutionary relationships and gene family evolution across the eukaryotic tree of life. At the same time, these types of data are known to be error-prone (e.g., substitutions, contamination). To address these opportunities and challenges, we have refined a phylogenomic pipeline, now named PhyloToL, to allow easy incorporation …


Hybrid Genome Assembly Of A Neotropical Mutualistic Ant, Juliane Hartke, Tilman Schell, Evelien Jongepier, Hanno Schmidt, Philipp P. Sprenger, Juraj Paule, Erich Bornberg-Bauer, Thomas Schmitt, Florian Menzel, Markus Pfenninger, Barbara Feldmeyer, Laura A. Katz Aug 2019

Hybrid Genome Assembly Of A Neotropical Mutualistic Ant, Juliane Hartke, Tilman Schell, Evelien Jongepier, Hanno Schmidt, Philipp P. Sprenger, Juraj Paule, Erich Bornberg-Bauer, Thomas Schmitt, Florian Menzel, Markus Pfenninger, Barbara Feldmeyer, Laura A. Katz

Biological Sciences: Faculty Publications

The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labor. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component of this communication system. Two cryptic Crematogaster species, which share their nest with Camponotus ants, show striking diversity in their cuticular hydrocarbon (CHC) profile. This mutualistic system therefore offers a great opportunity to study the genetic basis of CHC divergence between sister species. As a basis for further genome-wide studies high-quality genomes …


Frankia-Enriched Metagenomes From The Earliest Diverging Symbiotic Frankia Cluster: They Come In Teams, Thanh Van Nguyen, Daniel Wibberg, Theoden Vigil-Stenman, Fede Berckx, Kai Battenberg, Kirill N. Demchenko, Jochen Blom, Maria P. Fernandez, Takashi Yamanaka, Alison M. Berry, Jörn Kalinowski, Andreas Brachmann, Katharina Pawlowski, Laura A. Katz Aug 2019

Frankia-Enriched Metagenomes From The Earliest Diverging Symbiotic Frankia Cluster: They Come In Teams, Thanh Van Nguyen, Daniel Wibberg, Theoden Vigil-Stenman, Fede Berckx, Kai Battenberg, Kirill N. Demchenko, Jochen Blom, Maria P. Fernandez, Takashi Yamanaka, Alison M. Berry, Jörn Kalinowski, Andreas Brachmann, Katharina Pawlowski, Laura A. Katz

Biological Sciences: Faculty Publications

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show …


Targeting A Highly Repeated Germline Dna Sequence For Improved Real-Time Pcr-Based Detection Of Ascaris Infection In Human Stool, Nils Pilotte, Jacqueline R.M.A. Maasch, Alice V. Easton, Eric Dahlstrom, Thomas B. Nutman, Steven A. Williams Jul 2019

Targeting A Highly Repeated Germline Dna Sequence For Improved Real-Time Pcr-Based Detection Of Ascaris Infection In Human Stool, Nils Pilotte, Jacqueline R.M.A. Maasch, Alice V. Easton, Eric Dahlstrom, Thomas B. Nutman, Steven A. Williams

Biological Sciences: Faculty Publications

Background: With the expansion of soil transmitted helminth (STH) intervention efforts and the corresponding decline in infection prevalence, there is an increased need for sensitive and specific STH diagnostic assays. Previously, through next generation sequencing (NGS)-based identification and targeting of non-coding, high copy-number repetitive DNA sequences, we described the development of a panel of improved quantitative real-time PCR (qPCR)-based assays for the detection of Necator americanus, Ancylostoma duodenale, Ancylostoma ceylanicum, Trichuris trichiura, and Strongyloides stercoralis. However, due to the phenomenon of chromosome diminution, a similar assay based on high copy-number repetitive DNA was not developed for the detection of Ascaris …


Effects Of Single And Integrated Water, Sanitation, Handwashing, And Nutrition Interventions On Child Soil-Transmitted Helminth And Giardia Infections: A Cluster-Randomized Controlled Trial In Rural Kenya, Amy J. Pickering, Sammy M. Njenga, Lauren Steinbaum, Jenna Swarthout, Audrie Lin, Benjamin F. Arnold, Christine P. Stewart, Holly N. Dentz, Maryanne Mureithi, Benard Chieng, Marlene Wolfe, Ryan Mahoney, Jimmy Kihara, Kendra Byrd, Gouthami Rao, Theodora Meerkerk, Priscah Cheruiyot, Marina Papaiakovou, Nils Pilotte, Steven A. Williams, John M. Colford Jr., Clair Null Jun 2019

Effects Of Single And Integrated Water, Sanitation, Handwashing, And Nutrition Interventions On Child Soil-Transmitted Helminth And Giardia Infections: A Cluster-Randomized Controlled Trial In Rural Kenya, Amy J. Pickering, Sammy M. Njenga, Lauren Steinbaum, Jenna Swarthout, Audrie Lin, Benjamin F. Arnold, Christine P. Stewart, Holly N. Dentz, Maryanne Mureithi, Benard Chieng, Marlene Wolfe, Ryan Mahoney, Jimmy Kihara, Kendra Byrd, Gouthami Rao, Theodora Meerkerk, Priscah Cheruiyot, Marina Papaiakovou, Nils Pilotte, Steven A. Williams, John M. Colford Jr., Clair Null

Biological Sciences: Faculty Publications

Helminth and protozoan infections affect more than 1 billion children globally. Improving water quality, sanitation, handwashing, and nutrition could be more sustainable control strategies for parasite infections than mass drug administration, while providing other quality of life benefits.


Heatwaves And Novel Host Consumption Increase Overwinter Mortality Of An Imperiled Wetland Butterfly, Mariana Abarca, Elise A. Larsen, Leslie Ries Jun 2019

Heatwaves And Novel Host Consumption Increase Overwinter Mortality Of An Imperiled Wetland Butterfly, Mariana Abarca, Elise A. Larsen, Leslie Ries

Biological Sciences: Faculty Publications

Disruptive effects of climate change include range shifts, phenological mismatches among consumers and producers, and population declines. While these biological alterations have been widely documented, studies identifying specific mechanisms linking climate change to population declines are scarce. Extreme events, such as heatwaves can have devastating effects on living organisms and are increasing in frequency as Earth warms. Hence, understanding the effects of heatwaves on insects is necessary to inform conservation efforts and to develop predictions of population dynamics under future climate scenarios. Here, we experimentally evaluated the effects of heatwaves on the survival and phenology of the Baltimore Checkerspot (Euphydryas …


Incubation And Grazing Effects On Spirotrich Ciliate Diversity Inferred From Molecular Analyses Of Microcosm Experiments, Jean David Grattepanche, Doris L. Juarez, Cameah C. Wood, George B. Mcmanus, Laura A. Katz May 2019

Incubation And Grazing Effects On Spirotrich Ciliate Diversity Inferred From Molecular Analyses Of Microcosm Experiments, Jean David Grattepanche, Doris L. Juarez, Cameah C. Wood, George B. Mcmanus, Laura A. Katz

Biological Sciences: Faculty Publications

We used an experimental approach of analyzing marine microcosms to evaluate the impact of both predation (top-down) and food resources (bottom-up) on spirotrich ciliate communities. To assess the diversity, we used two molecular methods-denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS). We carried out two types of experiments to measure top-down (adult copepods as predators) and bottom-up effects (phytoplankton as food resources) on the spirotrich ciliates. We observed both strong incubation effects (untreated controls departed from initial assessment of diversity) and high variability across replicates within treatments, particularly for the bottom-up experiments. This suggests a rapid community turn-over during …


Phylochromomap, A Tool For Mapping Phylogenomic History Along Chromosomes, Reveals The Dynamic Nature Of Karyotype Evolution In Plasmodium Falciparum, Mario A. Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A. Katz Jan 2019

Phylochromomap, A Tool For Mapping Phylogenomic History Along Chromosomes, Reveals The Dynamic Nature Of Karyotype Evolution In Plasmodium Falciparum, Mario A. Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A. Katz

Biological Sciences: Faculty Publications

The genome of Plasmodium falciparum, the causative agent of malaria in Africa, has been extensively studied since it was first fully sequenced in 2002. However, many open questions remain, including understanding the chromosomal context of molecular evolutionary changes (e.g., relationship between chromosome map and phylogenetic conservation, patterns of gene duplication, and patterns of selection). Here, we present PhyloChromoMap, a method that generates a phylogenomic map of chromosomes from a custom-built bioinformatics pipeline. Using P. falciparum 3D7 as a model, we analyze 2,116 genes with homologs in up to 941 diverse eukaryotic, bacterial and archaeal lineages. We estimate the level of …


Effects Of Thermal Stress On Amount, Composition, And Antibacterial Properties Of Coral Mucus, Rachel M. Wright, Marie E. Strader, Heather M. Genuise, Mikhail Matz Jan 2019

Effects Of Thermal Stress On Amount, Composition, And Antibacterial Properties Of Coral Mucus, Rachel M. Wright, Marie E. Strader, Heather M. Genuise, Mikhail Matz

Biological Sciences: Faculty Publications

Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, United States of America ABSTRACT The surface mucus layer of reef-building corals supports feeding, sediment clearing, and protection from pathogenic invaders. As much as half of the fixed carbon supplied by the corals' photosynthetic symbionts is incorporated into expelled mucus. It is therefore reasonable to expect that coral bleaching (disruption of the coralfialgal symbiosis) would affect mucus production. Since coral mucus serves as an important nutrient source for the entire reef community, this could have substantial ecosystemwide consequences. In this study, we examined the effects of heat …


Laboratory Evaluation Of Molecular Xenomonitoring Using Mosquito And Tsetse Fly Excreta/Feces To Amplify Plasmodium, Brugia, And Trypanosoma Dna, Nils Pilotte, Darren A.N. Cook, Joseph Pryce, Michael F. Zulch, Corrado Minetti, Lisa J. Reimer, Steven A. Williams Jan 2019

Laboratory Evaluation Of Molecular Xenomonitoring Using Mosquito And Tsetse Fly Excreta/Feces To Amplify Plasmodium, Brugia, And Trypanosoma Dna, Nils Pilotte, Darren A.N. Cook, Joseph Pryce, Michael F. Zulch, Corrado Minetti, Lisa J. Reimer, Steven A. Williams

Biological Sciences: Faculty Publications

Background: Results from an increasing number of studies suggest that mosquito excreta/feces (E/F) testing has considerable potential to serve as a supplement for traditional molecular xenomonitoring techniques. However, as the catalogue of possible use-cases for this methodology expands, and the list of amenable pathogens grows, a number of fundamental methods-based questions remain. Answering these questions is critical to maximizing the utility of this approach and to facilitating its successful implementation as an effective tool for molecular xenomonitoring. Methods: Utilizing E/F produced by mosquitoes or tsetse flies experimentally exposed to Brugia malayi, Plasmodium falciparum, or Trypanosoma brucei brucei, factors such as …


Quantifying Protein Copy Number In Super-Resolution Using An Imaging Invariant Calibration, Francesca Cella Zanacchi, Carlo Manzo, Raffaella Magrassi, Nathan D. Derr, Melike Lakadamyali Jan 2019

Quantifying Protein Copy Number In Super-Resolution Using An Imaging Invariant Calibration, Francesca Cella Zanacchi, Carlo Manzo, Raffaella Magrassi, Nathan D. Derr, Melike Lakadamyali

Biological Sciences: Faculty Publications

The use of super-resolution microscopy in recent years has revealed that proteins often form small assemblies inside cells and are organized in nanoclusters. However, determining the copy number of proteins within these nanoclusters constitutes a major challenge because of unknown labeling stoichiometries and complex fluorophore photophysics. We previously developed a DNA-origami-based calibration approach to extract protein copy number from super-resolution images. However, the applicability of this approach is limited by the fact that the calibration is dependent on the specific labeling and imaging conditions used in each experiment. Hence, the calibration must be repeated for each experimental condition, which is …


Backpack Pcr: A Point-Of-Collection Diagnostic Platform For The Rapid Detection Of Brugia Parasites In Mosquitoes, Weam I. Zaky, Francesca R. Tomaino, Nils Pilotte, Sandra J. Laney, Steven A. Williams Nov 2018

Backpack Pcr: A Point-Of-Collection Diagnostic Platform For The Rapid Detection Of Brugia Parasites In Mosquitoes, Weam I. Zaky, Francesca R. Tomaino, Nils Pilotte, Sandra J. Laney, Steven A. Williams

Biological Sciences: Faculty Publications

No abstract provided.


Decline Of A Foundation Tree Species Due To Invasive Insects Will Trigger Net Release Of Soil Organic Carbon, Danielle Ignace, Aliza Fassler, Jesse Bellemare Aug 2018

Decline Of A Foundation Tree Species Due To Invasive Insects Will Trigger Net Release Of Soil Organic Carbon, Danielle Ignace, Aliza Fassler, Jesse Bellemare

Biological Sciences: Faculty Publications

Eastern U.S. forests are witnessing an ecologically disruptive decline in one of the region’s distinctive foundation tree species, the eastern hemlock (Tsuga canadenis). The exotic insect pests hemlock woolly adelgid (Adelges tsugae, HWA) and elongate hemlock scale (Fiorinia externa) have greatly altered many forest ecosystems previously dominated by this important evergreen conifer. The consequences for ecosystem processes are far reaching because hemlock is often replaced by deciduous tree species, such as black birch (Betula lenta), which have strongly divergent effects on forest floor microenvironments and nutrient cycling. We took advantage of an accidental experiment initiated by patch-level timber harvesting ~30 …


Ancylostoma Ceylanicum Hookworm In Myanmar Refugees, Thailand, 2012–2015, Elise M. O'Connell, Tarissa Mitchell, Marina Papaiakovou, Nils Pilotte, Deborah Lee, Michelle Weinberg, Potsawin Sakulrak, Dilok Tongsukh, Georgiette Oduro-Boateng, Sarah Harrison, Steven A. Williams, William M. Stauffer, Thomas B. Nutman Aug 2018

Ancylostoma Ceylanicum Hookworm In Myanmar Refugees, Thailand, 2012–2015, Elise M. O'Connell, Tarissa Mitchell, Marina Papaiakovou, Nils Pilotte, Deborah Lee, Michelle Weinberg, Potsawin Sakulrak, Dilok Tongsukh, Georgiette Oduro-Boateng, Sarah Harrison, Steven A. Williams, William M. Stauffer, Thomas B. Nutman

Biological Sciences: Faculty Publications

During 2012–2015, US-bound refugees living in Myanmar– Thailand border camps (n = 1,839) were surveyed for hookworm infection and treatment response by using quantitative PCR. Samples were collected at 3 time points: after each of 2 treatments with albendazole and after resettlement in the United States. Baseline prevalence of Necator americanus hookworm was 25.4%, Ancylostoma duodenale 0%, and Ancylostoma ceylanicum (a zoonosis) 5.4%. Compared with N. americanus prevalence, A. ceylanicum hookworm prevalence peaked in younger age groups, and blood eosinophil concentrations during A. ceylanicum infection were higher than those for N. americanus infection. Female sex was associated with a lower …


Twisted Tales: Insights Into Genome Diversity Of Ciliates Using Single-Cell ‘Omics, Maurer-Alcala X. Xyrus X. Maurer-Alcala, Ying Yan, Olivia A. Pilling, Rob Knight, Laura A. Katz Aug 2018

Twisted Tales: Insights Into Genome Diversity Of Ciliates Using Single-Cell ‘Omics, Maurer-Alcala X. Xyrus X. Maurer-Alcala, Ying Yan, Olivia A. Pilling, Rob Knight, Laura A. Katz

Biological Sciences: Faculty Publications

The emergence of robust single-cell ‘omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a > 1 Gy old clade). Analysis of the data resulting from these single-cell ‘omics approaches show: 1) the description of the ciliates in the class Karyorelictea as “primitive”is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani’s (1890) observation …


Inclusion Of Host Quality Data Improves Predictions Of Herbivore Phenology, Mariana Abarca, Elise A. Larsen, John T. Lill, Martha Weiss, Eric Lind, Leslie Ries Jul 2018

Inclusion Of Host Quality Data Improves Predictions Of Herbivore Phenology, Mariana Abarca, Elise A. Larsen, John T. Lill, Martha Weiss, Eric Lind, Leslie Ries

Biological Sciences: Faculty Publications

Understanding the correspondence between ambient temperature and insect development is necessary to forecast insect phenology under novel environments. In the face of climate change, both conservation and pest control efforts require accurate phenological predictions. Here, we compare a suite of degree-day models to assess their ability to predict the phenology of a common, oligophagous butterfly, the silver-spotted skipper, Epargyreus clarus (Cramer) (Lepidoptera: Hesperiidae). To estimate model parameters, we used development time of eggs and larvae reared in the laboratory at six constant temperatures ranging from 8 to 38 °C and on two host plants of contrasting quality (kudzu and wisteria). …


Seed Bank And Seasonal Patterns Of The Eukaryotic Sar (Stramenopila, Alveolata And Rhizaria) Clade In A New England Vernal Pool, Chip Sisson, Bethaney Gulla-Devaney, Laura A. Katz, Jean-David Grattepanche Jun 2018

Seed Bank And Seasonal Patterns Of The Eukaryotic Sar (Stramenopila, Alveolata And Rhizaria) Clade In A New England Vernal Pool, Chip Sisson, Bethaney Gulla-Devaney, Laura A. Katz, Jean-David Grattepanche

Biological Sciences: Faculty Publications

Vernal pools are dynamic freshwater ecosystems that dry during the summer. These unique habitats are vital to a number of well-studied animal species but there is little documentation of the diversity of the SAR—Stramenopila, Alveolata and Rhizaria—clade in vernal pools. Here, we characterize the protist community over a portion of the hydroperiod as the vernal pool transitions from its winter stage through its drying out in late summer. Our study focuses on the SAR clade, which encompasses a broad range of morphological diversity and a variety of trophic modes within the microbial food web. Using high-throughput sequencing, we investigate the …


Deconvoluting The Effects Of Surface Chemistry And Nanoscale Topography: Pseudomonas Aeruginosa Biofilm Nucleation On Si-Based Substrates, Jing Zhang, Jingling Huang, Carmen Say, Robert L. Dorit, Kate Queeney Jun 2018

Deconvoluting The Effects Of Surface Chemistry And Nanoscale Topography: Pseudomonas Aeruginosa Biofilm Nucleation On Si-Based Substrates, Jing Zhang, Jingling Huang, Carmen Say, Robert L. Dorit, Kate Queeney

Chemistry: Faculty Publications

Hypothesis

The nucleation of biofilms is known to be affected by both the chemistry and topography of the underlying substrate, particularly when topography includes nanoscale (nm) features. However, determining the role of topography vs. chemistry is complicated by concomitant variation in both as a result of typical surface modification techniques. Analyzing the behavior of biofilm-forming bacteria exposed to surfaces with systematic, independent variation of both topography and surface chemistry should allow differentiation of the two effects.

Experiments

Silicon surfaces with reproducible nanotopography were created by anisotropic etching in deoxygenated water. Surface chemistry was varied independently to create hydrophilic (OH- terminated) …


Cannibalism In Blepharisma Americanum : A Genome Comparison, Bethaney Gulla-Devaney May 2018

Cannibalism In Blepharisma Americanum : A Genome Comparison, Bethaney Gulla-Devaney

Theses, Dissertations, and Projects

Cannibalism is a process in which an organism consumes a member of its own species. The process is intraspecies while predation is interspecies. Unlike predation, literature on the process of cannibalism is largely understudied, particularly in the microbial world. This study focuses on Blepharisma americanum, a species of eukaryotic microbe. In this species, cannibalism can be confirmed visually by a giant cannibal cell digesting victim cells within the food vacuoles. Cannibalism is regularly practiced in B. americanum and I attempt to elucidate the genetic differences between life states: cannibal and vegetative cells. I investigate using bioinformatic approaches: whole transcriptome amplification, …


A Superhydrophobic Cone To Facilitate The Xenomonitoring Of Filarial Parasites, Malaria, And Trypanosomes Using Mosquito Excreta/Feces, Darren A.N. Cook, Nils Pilotte, Corrado Minetti, Steven A. Williams, Lisa J. Reimer Apr 2018

A Superhydrophobic Cone To Facilitate The Xenomonitoring Of Filarial Parasites, Malaria, And Trypanosomes Using Mosquito Excreta/Feces, Darren A.N. Cook, Nils Pilotte, Corrado Minetti, Steven A. Williams, Lisa J. Reimer

Biological Sciences: Faculty Publications

Background: Molecular xenomonitoring (MX), the testing of insect vectors for the presence of human pathogens, has the potential to provide a non-invasive and cost-effective method for monitoring the prevalence of disease within a community. Current MX methods require the capture and processing of large numbers of mosquitoes, particularly in areas of low endemicity, increasing the time, cost and labour required. Screening the excreta/feces (E/F) released from mosquitoes, rather than whole carcasses, improves the throughput by removing the need to discriminate vector species since non-vectors release ingested pathogens in E/F. It also enables larger numbers of mosquitoes to be processed per …


Asymmetric Interference Competition Between Herbivorous Gastropods, Introduced Littorina Littorea And Indigenous L. Obtusata, Alysha B. Putnam, Paulette Peckol Apr 2018

Asymmetric Interference Competition Between Herbivorous Gastropods, Introduced Littorina Littorea And Indigenous L. Obtusata, Alysha B. Putnam, Paulette Peckol

Biological Sciences: Faculty Publications

Competitive interactions may affect distribution and abundance of mobile organisms, such as the intertidal herbivorous gastropods Littorina littorea and L. obtusata, in areas of resource overlap. We examined intra- and interspecific competition between US New England populations by measuring effects of snail density and food availability on growth rates and abundances. We investigated mechanisms of interference, including resistance (phlorotannin) induction of fucoid algae, and impacts of snail presence, waterborne cues, and mucus on herbivory. L. obtusata density increased significantly within fucoid canopies following repeated (every 12 h for 3 d) removal of L. littorea at both study sites. In the …


Canis Aureus (Carnivore: Canidae), Patricia D. Moehlman, Virginia Hayssen Apr 2018

Canis Aureus (Carnivore: Canidae), Patricia D. Moehlman, Virginia Hayssen

Biological Sciences: Faculty Publications

Canis aureus (Linnaeus, 1758), the golden jackal, is a medium-sized, wide spread, terrestrial carnivore. It is 1 of 7 species found in the genus Canis. It ranges from Africa to Europe, the Middle East, Central Asia, and Southeast Asia. Due to its tolerance of dry habitats and its omnivorous diet, C. aureus can live in a wide variety of habitats. It normally lives in open grassland habitat but also occurs in deserts, woodlands, mangroves, and agricultural and rural habitats in India and Bangladesh. It ranges from sea level in Eritrea to 3,500 m in the Bale Mountains …


Microbial Diversity In The Eukaryotic Sar Clade: Illuminating The Darkness Between Morphology And Molecular Data, Jean David Grattepanche, Laura M. Walker, Brittany M. Ott, Daniela L. Paim Pinto, Charles F. Delwiche, Christopher E. Lane, Laura A. Katz Apr 2018

Microbial Diversity In The Eukaryotic Sar Clade: Illuminating The Darkness Between Morphology And Molecular Data, Jean David Grattepanche, Laura M. Walker, Brittany M. Ott, Daniela L. Paim Pinto, Charles F. Delwiche, Christopher E. Lane, Laura A. Katz

Biological Sciences: Faculty Publications

Despite their diversity and ecological importance, many areas of the SAR—Stramenopila, Alveolata, and Rhizaria—clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the “dark area” of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for …


A Comparative Analysis Of Preservation Techniques For The Optimal Molecular Detection Of Hookworm Dna In A Human Fecal Specimen, Marina Papaiakovou, Nils Pilotte, Benjamin Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabien Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A. Williams Jan 2018

A Comparative Analysis Of Preservation Techniques For The Optimal Molecular Detection Of Hookworm Dna In A Human Fecal Specimen, Marina Papaiakovou, Nils Pilotte, Benjamin Baumer, Jessica Grant, Kristjana Asbjornsdottir, Fabien Schaer, Yan Hu, Raffi Aroian, Judd Walson, Steven A. Williams

Biological Sciences: Faculty Publications

Maximizing the recovery of PCR-amplifiable DNA is an important consideration in the optimization of field-ready PCR-based diagnostic techniques. Fecal specimen preservation is particularly important due to the universal use of stool for the non-invasive diagnosis of soil-transmitted helminth (STH) infections. A comprehensive and systematic assessment of methods for maintaining and preserving soil-transmitted helminth (STH) DNA, particularly from fragile eggs subjected to nuclease exposure in stool, has not been conducted previously. Through the comparative analysis of a variety of preservation techniques, the present study demonstrates that fecal samples designated for PCR-based molecular analysis maintain sample integrity for at least 60 days …


Exploration Of The Germline Genome Of The Ciliate Chilodonella Uncinata Through Single-Cell Omics (Transcriptomics And Genomics), Xyrus X. Maurer-Alcalá, Rob Knight, Laura A. Katz Jan 2018

Exploration Of The Germline Genome Of The Ciliate Chilodonella Uncinata Through Single-Cell Omics (Transcriptomics And Genomics), Xyrus X. Maurer-Alcalá, Rob Knight, Laura A. Katz

Biological Sciences: Faculty Publications

Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences. Most studies of germline genome architecture in ciliates have focused on the model ciliates Oxytricha trifallax, Paramecium tetraurelia, and Tetrahymena thermophila, for which …


Nuclear Features Of The Heterotrich Ciliate Blepharisma Americanum: Genomic Amplification, Life Cycle, And Nuclear Inclusion, Megan M. Wancura, Ying Yan, Laura A. Katz, Xyrus X. Maurer-Alcalá Jan 2018

Nuclear Features Of The Heterotrich Ciliate Blepharisma Americanum: Genomic Amplification, Life Cycle, And Nuclear Inclusion, Megan M. Wancura, Ying Yan, Laura A. Katz, Xyrus X. Maurer-Alcalá

Biological Sciences: Faculty Publications

Blepharisma americanum, a member of the understudied ciliate class Heterotrichea, has a moniliform somatic macronucleus that resembles beads on a string. Blepharisma americanum is distinguishable by its pink coloration derived from the autofluorescent pigment blepharismin and tends to have a single somatic macronucleus with 3–6 nodes and multiple germline micronuclei. We used fluorescence confocal microscopy to explore the DNA content and amplification between the somatic and germline nuclei of B. americanum through its life cycle. We estimate that the DNA content of the macronucleus and micronucleus are 43 ± 8 Gbp and 83 ± 16 Mbp respectively. This correlates with …


A Novel Quantitative Real-Time Pcr Diagnostic Assay For Seal Heartworm (Acanthocheilonema Spirocauda) Provides Evidence For Possible Infection In The Grey Seal (Halichoerus Grypus), Caroline D. Keroack, Kalani M. Williams, M. K. Fessler, Kaela E. Deangelis, Eirini Tsekitsidou, Jillian M. Tozloski, Steven A. Williams Jan 2018

A Novel Quantitative Real-Time Pcr Diagnostic Assay For Seal Heartworm (Acanthocheilonema Spirocauda) Provides Evidence For Possible Infection In The Grey Seal (Halichoerus Grypus), Caroline D. Keroack, Kalani M. Williams, M. K. Fessler, Kaela E. Deangelis, Eirini Tsekitsidou, Jillian M. Tozloski, Steven A. Williams

Biological Sciences: Faculty Publications

The distinct evolutionary pressures faced by Pinnipeds have likely resulted in strong coevolutionary ties to their parasites (Leidenberger et al., 2007). This study focuses on the phocid seal filarial heartworm speciesAcanthocheilonema spirocauda. A. spirocauda is known to infect a variety of phocid seals, but does not appear to be restricted to a single host species (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). However, to date, seal heartworm has never been reported in grey seals (Halichoerus grypus) (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). The proposed vector for seal heartworm is …