Life Sciences Commons^™

Parasitic Infection Surveillance In Mississippi Delta Children, Richard S. Bradbury, Irene Arguello, Meredith Lane, Gretchen Cooley, Sukwan Handali, Silvia D. Dimitrova, Fernanda S. Nascimento, Sam Jameson, Kathryn Hellmann, Michelle Tharp, Paul Byers, Susan P. Montgomery, Lisa Haynie, Brian Kirmse, Nils Pilotte, Steven A. Williams, Charlotte V. Hobbs

Biological Sciences: Faculty Publications

Some recent studies suggest ongoing transmission of parasitic diseases in the American South; however, surveys in Mississippi children are lacking. We enrolled 166 children (median age 8 years, range 4–13 years) from the Mississippi Delta region and carried out multi-parallel real-time polymerase chain reaction (PCR) for Necator americanus, Ascaris lumbricoides, and Strongyloides stercoralis on their stool samples. Dried blood spots were obtained for multiplex serology antibody detection. Of 166 children, all reported having flushable toilets, 11% had soil exposure, and 34% had a pet dog or cat. None had prior diagnosis or treatment of parasitic disease. Multi-parallel real-time PCRs were …

Rectal Swabs As An Alternative Sample Collection Method To Bulk Stool For The Real-Time Pcr Detection Of Giardia Duodenalis, Jacqueline R.M.A. Maasch, Ahmed M. Arzika, Catherine Cook, Elodie Lebas, Nils Pilotte, Jessica R. Grant, Steven A. Williams, Jeremy D. Keenan, Thomas M. Lietman, Kristen Aiemjoy

Biological Sciences: Faculty Publications

Though bulk stool remains the gold standard specimen type for enteropathogen diagnosis, rectal swabs may offer comparable sensitivity with greater ease of collection for select pathogens. This study sought to evaluate the validity and reproducibility of rectal swabs as a sample collection method for the molecular diagnosis of Giardia duodenalis. Paired rectal swab and bulk stool samples were collected from 86 children ages 0–4 years living in southwest Niger, with duplicate samples collected among a subset of 50 children. Infection was detected using a previously validated real-time PCR diagnostic targeting the small subunit ribosomal RNA gene. Giardia duodenalis was …

Consequences Of The Misidentification Of Museum Specimens: The Taxonomic Status Of Canis Lupaster Soudanicus, Andrew C. Kitchener, Fabio A. Machado, Virginia Hayssen, Patricia D. Moehlman, Suvi Viranta

Biological Sciences: Faculty Publications

Researchers are increasingly using museum collections for taxonomy, systematics, phylogenetics, and faunal analyses, and they assume that taxonomic identifications on museum labels are correct. However, identifications may be incorrect or out of date, which could result in false conclusions from subsequent research. A recent geometric morphometrics analysis of skulls of African canids by Machado and Teta (2020) suggested that Canis lupaster soudanicus is a junior synonym of Lupulella adusta. However, the holotype of soudanicus was not measured and further investigation of the putative soudanicus specimens used in this study showed that these originally were identified as L. adusta. …

Leaf Carbon Export And Nonstructural Carbohydrates In Relation To Diurnal Water Dynamics In Mature Oak Trees, Jess T. Gersony, Uri Hochberg, Fulton E. Rockwell, Maria Park, Paul P.G. Gauthier, N. Michele Holbrook

Biological Sciences: Faculty Publications

Trees typically experience large diurnal depressions in water potential, which may impede carbon export from leaves during the day because the xylem is the source of water for the phloem. As water potential becomes more negative, higher phloem osmotic concentrations are needed to draw water in from the xylem. Generating this high concentration of sugar in the phloem is particularly an issue for the ∼50% of trees that exhibit passive loading. These ideas motivate the hypothesis that carbon export in woody plants occurs predominantly at night, with sugars that accumulate during the day assisting in mesophyll turgor maintenance or being …

A Novel Quantitative Real-Time Pcr Diagnostic Assay For Fecal And Nasal Swab Detection Of An Otariid Lungworm, Parafilaroides Decorus, Kalani M. Williams, M. K. Fessler, R. A. Bloomfield, William D. Sandke, Clara R. Malekshahi, Caroline D. Keroack, Pádraig J. Duignan, Samantha D. Torquato, Steven A. Williams

Biological Sciences: Faculty Publications

Parafilaroides decorus, also known as sea lion lungworm, is a metastrongyloid nematode that infects otariid hosts, such as the charismatic California sea lion, Zalophus californianus. P. decorus causes bronchointerstitial pneumonia, respiratory distress, reduced ability to swim, dive and hunt and as a result, increased mortality particularly in young animals. Respiratory disease is a leading cause of stranding and admission to rehabilitation centers on the Pacific coast. Low-coverage genomic sequencing of four P. decorus individuals analyzed through Galaxy's RepeatExplorer identified a novel repeat DNA family we employed to design a sensitive quantitative PCR (qPCR) assay for diagnosing infections from fecal or …

High Diversity Of Testate Amoebae (Amoebozoa, Arcellinida) Detected By Hts Analyses In A New England Fen Using Newly Designed Taxon-Specific Primers, Alistaire Ruggiero, Jean David Grattepanche, Agnes K.M. Weiner, Laura A. Katz

Biological Sciences: Faculty Publications

Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36-cm horizontal transects and vertical cores; and (2) 26-m horizontal transects fractioned into four size classes (2–10, 10–35, 35–100, and 100–300 μm). Analyses of these data show the following: (1) …

First International External Quality Assessment Scheme Of Nucleic Acid Amplification Tests For The Detection Of Schistosoma And Soil-Transmitted Helminths, Including Strongyloides: A Pilot Study, Piet Cools, Lisette Van Lieshout, Rob Koelewijn, David Addiss, Sitara S.R. Ajjampur, Mio Ayana, Richard S. Bradbury, Jason L. Cantera, Daniel Dana, Kerstin Fischer, Rubina Imtiaz, Joyce Kabagenyi, James Lok, James Mccarthy, Rojelio Mejia, Zeleke Mekonnen, Sammy M. Njenga, Nurulhasanah Othman, Hongguang Shao, Rebecca Traub, Marjan Van Esbroeck, Jozef Vercruysse, Johnny Vlaminck, Steven A. Williams, Jaco J. Verweij, Jaap J. Van Hellemond, Bruno Levecke

Biological Sciences: Faculty Publications

Background Nucleic acid amplification tests (NAATs) are increasingly being used as diagnostic tools for soil-transmitted helminths (STHs; Ascaris lumbricoides, Trichuris trichiura, Necator ameri-canus, Ancylostoma duodenale and A. ceylanicum), Strongyloides stercoralis and Schisto-soma in human stool. Currently, there is a large diversity of NAATs being applied, but an external quality assessment scheme (EQAS) for these diagnostics is lacking. An EQAS involves a blinded process where test results reported by a laboratory are compared to those reported by reference or expert laboratories, allowing for an objective assessment of the diagnostic performance of a laboratory. In the current study, we piloted an international …

Selection And Exploitation Of Prevalent, Tandemly Repeated Genomic Targets For Improved Real-Time Pcr-Based Detection Of Wuchereria Bancrofti And Plasmodium Falciparum In Mosquitoes, Michael F. Zulch, Nils Pilotte, Jessica R. Grant, Corrado Minetti, Lisa J. Reimer, Steven A. Williams

Biological Sciences: Faculty Publications

Background Optimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control …

Comparison Of Multi-Parallel Qpcr And Double-Slide Kato-Katz For Detection Of Soil-Transmitted Helminth Infection Among Children In Rural Bangladesh, Jade Benjamin-Chung, Nils Pilotte, Ayse Ercumen, Jessica R. Grant, Jacqueline R.M.A. Maasch, Andrew M. Gonzalez, Ashanta C. Ester, Benjamin F. Arnold, Mahbubur Rahman, Rashidul Haque, Alan E. Hubbard, Stephen P. Luby, Steven A. Williams, John M. Colford

Biological Sciences: Faculty Publications

There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2–12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for …

Symbiont Community Diversity Is More Variable In Corals That Respond Poorly To Stress, Lauren I. Howe-Kerr, Benedicte Bachelot, Rachel M. Wright, Carly D. Kenkel, Line K. Bay, Adrienne M.S. Correa

Biological Sciences: Faculty Publications

Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts—the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four ‘best performer’ …

Field Evaluation Of Dna Detection Of Human Filarial And Malaria Parasites Using Mosquito Excreta/Feces, Corrado Minetti, Nils Pilotte, Michael Zulch, Tiago Canelas, Edward J. Tettevi, Francis B.D. Veriegh, Mike Yaw Osei-Atweneboana, Steven A. Williams, Lisa J. Reimer

Biological Sciences: Faculty Publications

We recently developed a superhydrophobic cone-based method for the collection of mosquito excreta/feces (E/F) for the molecular xenomonitoring of vector-borne parasites show-ing higher throughput compared to the traditional approach. To test its field applicability, we used this platform to detect the presence of filarial and malaria parasites in two villages of Ghana and compared results to those for detection in mosquito carcasses and human blood. We compared the molecular detection of three parasites (Wuchereria bancrofti, Plas-modium falciparum and Mansonella perstans) in mosquito E/F, mosquito carcasses and human blood collected from the same households in two villages in the Savannah Region …

De Novo Sequencing, Assembly, And Annotation Of The Transcriptome For The Free-Living Testate Amoeba Arcella Intermedia, Giulia M. Ribeiro, Alfredo L. Porfírio-Sousa, Xyrus X. Maurer-Alcalá, Laura A. Katz, Daniel J.G. Lahr

Biological Sciences: Faculty Publications

Arcella, a diverse understudied genus of testate amoebae is a member of Tubulinea in Amoebozoa group. Transcriptomes are a powerful tool for charac- terization of these organisms as they are an efficient way of characterizing the protein-coding potential of the genome. In this work, we employed both sin- gle-cell and clonal populations transcriptomics to create a reference transcrip- tome for Arcella. We compared our results with annotations of Dictyostelium discoideum, a model Amoebozoan. We assembled a pool of 38 Arcella inter- media transcriptomes, which after filtering are composed of a total of 14,712 translated proteins. There are GO categories enriched …

Top-Down And Bottom-Up Controls On Microeukaryotic Diversity (I.E., Amplicon Analyses Of Sar Lineages) And Function (I.E., Metatranscriptome Analyses) Assessed In Microcosm Experiments, Jean David Grattepanche, Laura A. Katz

Biological Sciences: Faculty Publications

The availability of high-throughput sequencing (HTS) has transformed our understanding of the diversity of microbial eukaryotes (i.e., protists) across diverse habitats. Yet relating this biodiversity to function remains a challenge, particularly in the context of microbial food webs. Here we perform a set of microcosm experiments to evaluate the impact of changing predator and prey concentrations on a marine protist community, focusing on SAR (Stramenopila, Alveolata, and Rhizaria) lineages. We combine an estimate of taxonomic diversity through analysis of SSU-rDNA amplicons with metatranscriptomics, a proxy for function. We assess changes in a community sampled from New England waters with varying …

What Does Soil-Transmitted Helminth Elimination Look Like? Results From A Targeted Molecular Detection Survey In Japan, Mitsuko Hasegawa, Nils Pilotte, Mihoko Kikuchi, Arianna R. Means, Marina Papaiakovou, Andrew M. Gonzalez, Jacqueline R.M.A. Maasch, Hiroshi Ikuno, Toshihiko Sunahara, Kristjana H. Ásbjörnsdóttir, Judd L. Walson, Steven A. Williams, Shinjiro Hamano

Biological Sciences: Faculty Publications

Background: Japan is one of the few countries believed to have eliminated soil-transmitted helminths (STHs). In 1949, the national prevalence of Ascaris lumbricoides was 62.9%, which decreased to 0.6% in 1973 due to improvements in infrastructure, socioeconomic status, and the implementation of national STH control measures. The Parasitosis Prevention Law ended in 1994 and population-level screening ceased in Japan; therefore, current transmission status of STH in Japan is not well characterized. Sporadic cases of STH infections continue to be reported, raising the possibility of a larger-scale recrudescence of STH infections. Given that traditional microscopic detection methods are not sensitive to …

What Does Soil-Transmitted Helminth Elimination Look Like? Results From A Targeted Molecular Detection Survey In Japan, Mitsuko Hasegawa, Nils Pilotte, Mihoko Kikuchi, Arianna R. Means, Marina Papaiakovou, Andrew M. Gonzalez, Jacqueline R.M.A. Maasch, Hiroshi Ikuno, Toshihiko Sunahara, Kristjana H. Ásbjörnsdóttir, Judd L. Walson, Steven A. Williams, Shinjiro Hamano

Biological Sciences: Faculty Publications

Background: Japan is one of the few countries believed to have eliminated soil-transmitted helminths (STHs). In 1949, the national prevalence of Ascaris lumbricoides was 62.9%, which decreased to 0.6% in 1973 due to improvements in infrastructure, socioeconomic status, and the implementation of national STH control measures. The Parasitosis Prevention Law ended in 1994 and population-level screening ceased in Japan; therefore, current transmission status of STH in Japan is not well characterized. Sporadic cases of STH infections continue to be reported, raising the possibility of a larger-scale recrudescence of STH infections. Given that traditional microscopic detection methods are not sensitive to …

Combined Genome And Transcriptome Analyses Of The Ciliate Schmidingerella Arcuata (Spirotrichea) Reveal Patterns Of Dna Elimination, Scrambling, And Inversion, Susan A. Smith, Xyrus X. Maurer-Alcalá, Ying Yan, Laura A. Katz, Luciana F. Santoferrara, George B. Mcmanus

Biological Sciences: Faculty Publications

Schmidingerella arcuata is an ecologically important tintinnid ciliate that has long served as a model species in plankton trophic ecology. We present a partial micronuclear genome and macronuclear transcriptome resource for S. arcuata, acquired using single-cell techniques, and we report on pilot analyses including functional annotation and genome architecture. Our analysis shows major fragmentation, elimination, and scrambling in the micronuclear genome of S. arcuata. This work introduces a new nonmodel genome resource for the study of ciliate ecology and genomic biology and provides a detailed functional counterpart to ecological research on S. arcuata.

Misconceptions About Conception And Other Fallacies: Historical Bias In Reproductive Biology, Virginia Hayssen

Biological Sciences: Faculty Publications

Natural selection (differential reproduction) is a major tenet of evolutionary theory. In mammals the success of reproduction is primarily controlled by females who provide the majority of offspring care via gestation and lactation. In some species, maternal care also extends post-weaning. This primacy of female reproduction in evolution has not quite crept into our understanding of organismal adaptations in anatomy, physiology, and behavior. This cultural legacy has left its mark and led to misconceptions in our understanding of reproductive biology that are especially prominent in the understanding of reproduction in the general public. Here, I give examples of such misconceptions. …

Eukaryotic Plankton Communities Across Reef Environments In Bocas Del Toro Archipelago, Panamá, Andrea M. Rodas, Rachel M. Wright, Logan K. Buie, Hannah E. Aichelman, Karl D. Castillo, Sarah W. Davies

Biological Sciences: Faculty Publications

Variation in light and temperature can influence the genetic diversity and structure of marine plankton communities. While open-ocean plankton communities receive much scientific attention, little is known about how environmental variation affects plankton communities on tropical coral reefs. Here, we characterize eukaryotic plankton communities on coral reefs across the Bocas del Toro Archipelago, Panama´. Temperature loggers were deployed, and midday light levels were measured to quantify environmental differences across reefs at four inshore and four offshore sites (Inshore = Punta Donato, Smithsonian Tropical Research Institute (STRI) Point, Cristobal, Punta Laurel and Offshore = Drago Mar, Bastimentos North, Bastimentos South, and …

Dietary Fish Oil Supplement Induces Age-Specific Contractile And Proteomic Responses In Muscles Of Male Rats, David W. Russ, Kalina Dimova, Emily Morris, Marguerite Pacheco, Sean M. Garvey, Stylianos P. Scordilis

Biological Sciences: Faculty Publications

Background: Dietary fish oil (DFO) has been identified as a micronutrient supplement with the potential to improve musculoskeletal health in old age. Few data are available for effects of DFO on muscle contractility, despite the significant negative impact of muscle weakness on age-related health outcomes. Accordingly, the effects of a DFO intervention on the contractile function and proteomic profile of adult and aged in an animal model of aging were investigated.

Methods: This preliminary study evaluated 14 adult (8 months) and 12 aged (22 months) male, Sprague-Dawley rats consuming a DFO-supplemented diet or a control diet for 8 weeks (7 …

Comparative Studies On The Polymorphism And Copy Number Variation Of Mtssu Rdna In Ciliates (Protista, Ciliophora): Implications For Phylogenetic, Environmental, And Ecological Research, Yurui Wang, Yaohan Jiang, Yongqiang Liu, Yuan Li, Laura A. Katz, Feng Gao, Ying Yan

Biological Sciences: Faculty Publications

No abstract provided.

Molecular Detection Of Intestinal Helminths And Protozoa Among Young Children In Dosso Region, Niger, Kristen Aiemjoy, Ahmed M. Arzika, Catherine Cook, Elodie Lebas, Nils Pilotte, Jessica R. Grant, Steven A. Williams, Thomas M. Lietman, Jeremy D. Keenan

Biological Sciences: Faculty Publications

Eukaryotic parasites are significant contributors to childhood illness in Niger. While helminthiases have received national attention through mass deworming efforts, the epidemiology of intestinal protozoa in Niger remains underexamined. This study employed real-time PCR diagnostics to describe the prevalence of two schistosomes, four soil-transmitted helminths, and one protozoan parasite in Boboye Department, Dosso Region. Prevalence was assessed using bulk stool specimens collected from a population-based sample of 86 children residing in 9 communities. Anthropometric measurements were used to calculate child growth z-scores and stool consistency was graded. Helminths were absent from the study population, with the exception of a single …

The Wisdom Of A Crowd Of Near-Best Fits: Drug-Resistant Tuberculosis In The United States, Ellie Mainou, Gwen Spencer, Dylan Shepardson, Robert Dorit

Biological Sciences: Faculty Publications

Antibiotic-resistant tuberculosis (TB) strains pose a major challenge to TB eradication. Existing US epidemiological models have not fully incorporated the impact of antibiotic-resistance. To develop a more realistic model of US TB dynamics, we formulated a compartmental model integrating single-and multi-drug resistance. We fit twenty-seven parameters to twenty-two years of historical data using a genetic algorithm to minimize a non-differentiable error function. Since counts for several compartments are not available, many parameter combinations achieve very low error. We demonstrate that a crowd of near-best fits can provide compelling new evidence about the ranges of key parameters. While available data is …

Phylogenomics Of The Epigenetic Toolkit Reveals Punctate Retention Of Genes Across Eukaryotes, Agnes K.M. Weiner, Mario A. Cerón-Romero, Ying Yan, Laura A. Katz

Biological Sciences: Faculty Publications

Epigenetic processes in eukaryotes play important roles through regulation of gene expression, chromatin structure, and genome rearrangements. The roles of chromatin modification (e.g., DNA methylation and histone modification) and non-protein-coding RNAs have been well studied in animals and plants. With the exception of a few model organisms (e.g., Saccharomyces and Plasmodium), much less is known about epigenetic toolkits across the remainder of the eukaryotic tree of life. Even with limited data, previous work suggested the existence of an ancient epigenetic toolkit in the last eukaryotic common ancestor. We use PhyloToL, our taxon-rich phylogenomic pipeline, to detect homologs of epigenetic genes …

Complementary Metagenomic Approaches Improve Reconstruction Of Microbial Diversity In A Forest Soil, L. V. Alteio, F. Schulz, R. Seshadri, N. Varghese, W. Rodriguez-Reillo, E. Ryan, D. Goudeau, S. A. Eichorst, R. R. Malmstrom, R. M. Bowers, Laura A. Katz, J. L. Blanchard, T. Woyke

Biological Sciences: Faculty Publications

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific …

Engaging New Audiences With Imaging And Microscopy, Michael J. Barresi, Enrico Coen, Elisabeth Kugler, Jamie Shuda, Derek C. Sung

Biological Sciences: Faculty Publications

In this Spotlight, we hear first-hand accounts from five scientists and educators who use microscopy and imaging to engage, entertain, educate and inspire new audiences with science and the field of developmental biology in particular. The 'voices' that follow each convey each authors' own personal take on why microscopy is such a powerful tool for capturing the minds, and the hearts, of scientists, students and the public alike. They discuss how microscopy and imaging can reveal new worlds, and improve our communication and understanding of developmental biology, as well as break down barriers and promote diversity for future generations of …