Biology Commons^™

Depth-Discrete Metagenomics Reveals The Roles Of Microbes In Biogeochemical Cycling In The Tropical Freshwater Lake Tanganyika, Patricia Q. Tran, Samantha C. Bachand, Peter B. Mcintyre, Benjamin M. Kraemer, Yvonne Vadeboncoeur, Ismael A. Kimirei, Rashid Tamatamah, Katherine D. Mcmahon, Karthik Anantharaman

Biological Sciences Faculty Publications

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed …

Public Discussion Of Anthrax On Twitter: Using Machine Learning To Identify Relevant Topics And Events, Michele Miller, William Lee Romine, Terry L. Oroszi

Biological Sciences Faculty Publications

Background: Social media allows researchers to study opinions and reactions to events in real time. One area needing more study is anthrax-related events. A computational framework that utilizes machine learning techniques was created to collect tweets discussing anthrax, further categorize them as relevant by the month of data collection, and detect discussions on anthrax-related events. Objective: The objective of this study was to detect discussions on anthrax-related events and to determine the relevance of thetweets and topics of discussion over 12 months of data collection. Methods: This is an infoveillance study, using tweets in English containing the keyword “Anthrax” and …

A Novel Thin-Film Technique To Improve Accuracy Of Fluorescence-Based Estimates For Periphytic Biofilms, Leon Katona, Yvonne Vadeboncoeur, Christopher T. Nietch, Katie Hossler

Biological Sciences Faculty Publications

Recent studies suggest that photophysiological parameters for intact substrates with depth (e.g., periphytic biofilms, microphytobenthos) are overestimated by pulse-amplitude modulated (PAM) fluorometry. This overestimation results from depth-integration effects, following the activation of deeper photosynthesizing layers by an attenuated light signal. To mitigate this error, we propose a novel slide-based thin-film technique in which fluorescence is measured on a vertically representative subsample of the biofilm, spread evenly on a microscope slide. We compared bias and precision for photosynthetic parameters estimated through conventional PAM fluorometry on intact biofilms and through our novel slide-based technique, both theoretically and empirically. Numerical simulations confirmed the …

Long-Read Assembly Of A Great Dane Genome Highlights The Contribution Of Gc-Rich Sequence And Mobile Elements To Canine Genomes, Julia V. Halo, Amanda L. Pendleton, Feichen Shen, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd

Biological Sciences Faculty Publications

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of …

Evolutionary Dynamics And Structural Consequences Of De Novo Beneficial Mutations And Mutant Lineages Arising In A Constant Environment, Margie Kinnersley, Katja Schwartz, Dong Dong Yang, Gavin Sherlock, Frank Rosenzweig

Biological Sciences Faculty Publications

Background: Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. Results: We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor …

Building Excellence In Scientific Teaching: How Important Is The Evidence For Evidence-Based Teaching When Training Stem Tas?, Lorelei E. Patrick, Hillary A. Barron, Julie C. Brown, Sehoya Cotner

Biological Sciences Faculty Publications

Evidence-based teaching practices (EBTP)—like inquiry-based learning, inclusive teaching, and active learning (AL)—have been shown to benefit all students, especially women, first-generation, and traditionally minoritized students in science fields. However, little research has focused on how best to train teaching assistants (TAs) to use EBTP or on which components of professional development are most important. We designed and experimentally manipulated a series of presemester workshops on AL, dividing subjects into two groups. The Activity group worked in teams to learn an AL technique with a workshop facilitator. These teams then modeled the activity, with their peers acting as students. In the …

Improved De Novo Alignment Of A Girardia Dorotocephala Ma-C2 (2n = 24) Transcriptome, Labib Rouhana, J F. Ryan, Eugene M. P. Almazan

Biological Sciences Faculty Publications

Improved De novo alignment of a Girardia dorotocephala MA-C2 (2n = 24) transcriptome.

Plastid Phylogenomics Of The Gynoxoid Group (Senecioneae, Asteraceae) Highlights The Importance Of Motif-Based Sequence Alignment Amid Low Genetic Distances, Belen Escobari, Thomas Borsch, Taylor Quedensley, Michael Gruenstaeudl

Biological Sciences Faculty Publications

Premise The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it. Methods We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on …

Airpg: Automatically Accessing The Inverted Repeats Of Archived Plastid Genomes, Tilman Mehl, Michael Gruenstaeudl

Biological Sciences Faculty Publications

In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly …

Quantitative Assessment Of Aphid Parasitoids And Predators In Central Oklahoma Wheat Fields During Five Growing Seasons, Norman C. Elliott, Kristopher L. Giles, Kristen A. Baum, Sarah Elzay

Biological Sciences Faculty Publications

Winter wheat (Triticum aestivum L.) is the most widely grown crop in Oklahoma and typically is planted in autumn and harvested in June. Wheat in Oklahoma is often infested by insect pests, the most important of which are the cereal aphids – greenbug, Schizaphis graminum (Rondani), and bird cherry-oat aphid, Rhopalosiphum padi (L.). We sampled a total of 69 wheat fields in central Oklahoma during five wheat-growing seasons. The number of wheat fields sampled ranged from seven in the 2016-2017 growing season to 24 fields in the 2009-2010 growing season. We used a D-vac suction sampler to collect aphids …

The Structure Of The Cysteine-Rich Region From Human Histone-Lysine N-Methyltransferase Ehmt2 (G9a), Keshia M. Kerchner, Tung-Chung Mou, Yizhi Sun, Domniţa-Valeria Rusnac, Stephen R. Sprang, Klára Briknarová

Biological Sciences Faculty Publications

Euchromatic histone-lysine N-methyltransferase 1 (EHMT1; G9a-like protein; GLP) and euchromatic histone-lysine N-methyltransferase 2 (EHMT2; G9a) are protein lysine methyltransferases that regulate gene expression and are essential for development and the ability of organisms to change and adapt. In addition to ankyrin repeats and the catalytic SET domain, the EHMT proteins contain a unique cysteine-rich region (CRR) that mediates protein-protein interactions and recruitment of the methyltransferases to specific sites in chromatin. We have determined the structure of the CRR from human EHMT2 by X-ray crystallography and show that the CRR adopts an unusual compact fold with four bound zinc atoms. The …

Incorporation Of Feeding Functional Group Information Informs Explanatory Patterns Of Long-Term Population Changes In Fish Assemblages, Jason C. Doll, Stephen J. Jacquemin

Biological Sciences Faculty Publications

The objective of this study was to evaluate long term trends of fish taxa in southern Lake Michigan while incorporating their functional roles to improve our understanding of ecosystem level changes that have occurred in the system over time. The approach used here highlighted the ease of incorporating ecological mechanisms into population models so researchers can take full advantage of available long-term ecosystem information. Long term studies of fish assemblages can be used to inform changes in community structure resulting from perturbations to aquatic systems and understanding these changes in fish assemblages can be better contextualized by grouping species according …

Vertebrate Subfossil Localities In Taylorsville Metropark, Montgomery County, Ohio, Usa, Ryan Shell, Kristin Zimmerman, David Peterman, Charles Ciampaglio, Lauren Fuelling, Stephen J. Jacquemin

Biological Sciences Faculty Publications

Karst features in the Silurian dolomites of Taylorsville MetroPark (Dayton Metropolitan Area, Ohio, United States) were explored from 2017 to 2018 to identify sites of paleontological interest. Initial landscape surveys recovered 124 skeletal elements (from 12 sites) that were attributed to 17 vertebrate species--including evidence of such extirpated animals as bobcats (Lynx rufus) and rattlesnakes (Crotalus sp.). Of the 12 sites, 9 sites contained remains from the historical era and 3 sites contained much older remains (n = 17) that were radiocarbon dated to approximately 1,400 years before present (YBP). Human remains at one site, butchered bones at another, and …

Evaluating Winter Malting Barley Grain Yield With Fractional Green Canopy Cover, Gregory J. Mcglinch, Stephen J. Jacquemin, Laura E. Lindsey

Biological Sciences Faculty Publications

Because of growth in the craft brewing industry, farmers in the eastern United States are planting winter malting barley (Hordeum vulgare L.) to meet demands for locally sourced grain. However, given that barley is a relatively new crop in this region, basic agronomic information relating to stand assessment is needed. This is particularly relevant in this region, as climatic variability from extreme temperature fluctuations during the winter and spring can reduce a barley stand, creating the need for farmers to estimate grain yield potential. The objective of the research was to evaluate the relationship between spring stem counts, fractional …

Importance Of Fossil And Archaeological Occurrence Data For Understanding The Evolution And Distribution Of The Freshwater Drum (A. Grunniens)., Stephen J. Jacquemin, Lauren J. Fuelling, G. Stringer, A. Smith, Charles N. Ciampaglio

Biological Sciences Faculty Publications

No abstract provided.

Importance And Challenges Of Monitoring Harmful Algal Blooms In Grand Lake St Marys, Stephen J. Jacquemin, M. Morden, C. Ewing, J. C. Doll

Biological Sciences Faculty Publications

No abstract provided.

Response Of Fish And Invertebrate Larvae To Backreef Sounds At Varying Distances: Implications For Habitat Restoration, Emily R. Anderson, Jack Butler, Mark J. Butler

Biological Sciences Faculty Publications

Underwater sound is used by many marine larvae to orient to coastal habitats including backreef, sponge-dominated hardbottom habitat in the Florida Keys (FL, United States)—a particularly “noisy” coastal habitat. However, the distance over which acoustic cues are attractive to settlement-stage larvae is generally unknown. We examined this phenomenon in a region of the Florida Keys where mass sponge die-offs have diminished both underwater soundscapes and larval settlement. The absence of pronounced hardbottom-associated sound over such a large area allowed us to experimentally test in situ the response of fish and invertebrate larvae to broadcasted sounds at different distances from their …

Tick Ecdysteroid Hormone, Global Microbiota/Rickettsia Signaling In The Ovary Versus Carcass During Vitellogenesis In Part-Fed (Virgin) American Dog Ticks, Dermacentor Variabilis, Loganathan Ponnusamy, Haley Sutton, Robert D. Mitchell Iii, Daniel E. Sonenshine, Charles S. Apperson, Richard Michael Roe

Biological Sciences Faculty Publications

The transovarial transmission of tick-borne bacterial pathogens is an important mechanism for their maintenance in natural populations and transmission, causing disease in humans and animals. The mechanism for this transmission and the possible role of tick hormones facilitating this process have never been studied. Injections of physiological levels of the tick hormone, 20-hydroxyecdysone (20E), into part-fed (virgin) adult females of the American dog tick, Dermacentor variabilis, attached to the host caused a reduction in density of Rickettsia montanensis in the carcass and an increase in the ovaries compared to buffer-injected controls. This injection initiates yolk protein synthesis and uptake …

Patterns Of Genetic Divergence Across Geographically Variable Populations Of Xanthisma Gracile (Asteraceae), Lavanya Challagundla, Lisa E. Wallace

Biological Sciences Faculty Publications

Premise of research. Numerous biotic and abiotic factors can contribute to local selection and lead to geographic structure and genetic divergence between populations. The southwestern United States contains many distinctive plant communities, ranging from woodlands to desert scrub, that are shaped by species adapting to local variation in elevation, precipitation, seasonality, and soils. Given this variation, species occurring across diverse habitats are expected to harbor high genetic diversity and exhibit significant genetic differences associated with environmental variation.

Methodology. Here, we studied the genetic divergence of populations of Xanthisma gracile (Asteraceae) across Arizona using amplified fragment length polymorphisms and evaluated associations …

Effects Of Weather On Foraging Success And Hunting Frequency In Winter-Irruptive Snowy Owls (Bubo Scandiacus) In Upstate New York, Russell E. Winter, William M. Shields

Biological Sciences Faculty Publications

The effects of weather on an individual can often alter the population dynamics of a species. Knowledge of how weather influences individual behavior is therefore essential in understanding its full impact in the context of population ecology. Snowy Owls (Bubo scandiacus) exhibit expensive long-distance migrations in winters following population irruptions. During irruptive movements, many owls migrate past the southernmost extent of their traditional wintering grounds, the mechanism for which is still debated. We propose and test the “milder climate” hypothesis; Snowy Owls wintering in lower latitudes are better able to meet their metabolic demands due to higher temperatures …

Trends And Opportunities In Tick-Borne Disease Geography, Catherine A. Lippi, Sadie J. Ryan, Alexis L. White, Holly D. Gaff, Colin J. Carlson

Biological Sciences Faculty Publications

Tick-borne diseases are a growing problem in many parts of the world, and their surveillance and control touch on challenging issues in medical entomology, agricultural health, veterinary medicine, and biosecurity. Spatial approaches can be used to synthesize the data generated by integrative One Health surveillance systems, and help stakeholders, managers, and medical geographers understand the current and future distribution of risk. Here, we performed a systematic review of over 8,000 studies and identified a total of 303 scientific publications that map tick-borne diseases using data on vectors, pathogens, and hosts (including wildlife, livestock, and human cases). We find that the …

Fast And Pervasive Transcriptomic Resilience And Acclimation Of Extremely Heat-Tolerant Coral Holobionts From The Northern Red Sea, Romain Savary, Daniel J. Barshis, Christian R. Voolstra, Anny Cárdenas, Nicolas R. Evensen, Guilhem Banc-Prandi, Maoz Fine, Anders Meiborn

Biological Sciences Faculty Publications

Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were …

Antibodies Against Egf-Like Domains In Ixodes Scapularis Bm86 Orthologs Impact Tick Feeding And Survival Of Borrelia Burgdorferi, Juraj Koči, Sandhya Bista, Payal Chirania, Xiuli Yang, Chrysoula Kitsou, Vipin Singh Rana, Ozlem Buyuktanir Yas, Daniel E. Sonenshine, Utpal Pal

Biological Sciences Faculty Publications

Ixodes scapularis ticks transmit multiple pathogens, including Borrelia burgdorferi sensu stricto, and encode many proteins harboring epidermal growth factor (EGF)-like domains. We show that I. scapularis produces multiple orthologs for Bm86, a widely studied tick gut protein considered as a target of an anti-tick vaccine, herein termed as Is86. We show that Is86 antigens feature at least three identifiable regions harboring EGF-like domains (termed as EGF-1, EGF-2, and EGF-3) and are differentially upregulated during B. burgdorferi infection. Although the RNA interference-mediated knockdown of Is86 genes did not show any influences on tick engorgement or B. burgdorferi sensu stricto persistence, the …

Double Anus In An Ixodes Scapularis Nymph, A Medically Important Tick Vector, Vikas Taank, Frank A. Lattanzio, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Background: Ixodes scapularis ticks are medically important arthropod vectors that transmit several pathogens to humans. The observations of morphological abnormalities, including nanism, missing leg, extra leg, and gynandromorphism, have been reported in these ticks. In this study, we report the presence of two anuses in a laboratory-reared I. scapularis nymph.

Results: Larval ticks were allowed to feed on mice and to molt to nymphs. Two anuses were observed in one of the freshly molted nymphs. Stereo and scanning electron microscopy confirmed the presence of two anuses in one nymph within a single anal groove.

Conclusions: This report confirms the rare …

Focus Stacking Images Of Morphological Character States For Differentiating The Adults Of Ixodes Affinis And Ixodes Scapularis (Acari: Ixodidae) In Areas Of Sympatry, Robyn M. Nadolny, Marcée Toliver, Holly D. Gaff, John G. Snodgrass, Richard G. Robbins

Biological Sciences Faculty Publications

Adult females and males of Ixodes affinis and Ixodes scapularis are illustrated by focus stacking image photography, and morphological character states are described that reliably differentiate the two species. In conjunction with other environmental cues, such as the questing phenology of adults, these characteristics will enable the rapid identification of adults of either sex along the southern Coastal Plain of the United States, where these species are sympatric.

Remarkably High And Consistent Tolerance Of A Red Sea Coral To Acute And Chronic Thermal Stress Exposures, Nicolas R. Evensen, Maoz Fine, Gabriela Perna, Christian R. Voolstra, Daniel J. Barshis

Biological Sciences Faculty Publications

Global warming is resulting in unprecedented levels of coral mortality due to mass bleaching events and, more recently, marine heatwaves, where rapid increases in seawater temperature cause mortality within days. Here, we compare the response of a ubiquitous scleractinian coral, Stylophora pistillata, from the northern Red Sea to acute (7 h) and chronic (7-11 d) thermal stress events that include temperature treatments of 27 degrees C (i.e., the local maximum monthly mean), 29.5 degrees C, 32 degrees C, and 34.5 degrees C, and assess recovery of the corals following exposure. Overall, S. pistillata exhibited remarkably similar responses to acute …

Dietary Protein Content And Digestibility Influences Discrimination Of Amino Acid Nitrogen Isotope Values In A Terrestrial Omnivorous Mammal, John P. Whiteman, Mauriel Rodriguez Curras, Kelli L. Feeser, Seth D. Newsome

Biological Sciences Faculty Publications

RATIONALE: Ecologists increasingly determine the δ¹⁵N values of amino acids (AA) in animal tissue; "source" AA typically exhibit minor variation between diet and consumer, while "trophic" AA have increased δ¹⁵N values in consumers. Thus, trophic-source δ¹⁵N offsets (i.e., Δ¹⁵N_T-S) reflect trophic position in a food web. However, even minor variation in δ¹⁵N_{source AA} values may influence the magnitude of offset that represents a trophic step, known as the trophic discrimination factor (i.e., TDF_T-S). Diet digestibility and protein content can influence the δ¹⁵N values …

Tick Extracellular Vesicles Enable Arthropod Feeding And Promote Distinct Outcomes Of Bacterial Infection, Adela S. Oliva Chávez, Xiaowei Wang, Liron Marnin, Nathan K. Archer, Holly L. Hammond, Erin E. Mcclure Carroll, Dana K. Shaw, Brenden G. Tully, Amanda D. Buskirk, Shelby L. Ford, L. Rainer Butler, Preeti Shahi, Kateryna Morozova, Cristina C. Clement, Lauren Lawres, Anya J. O'Neal, Choukri Ben Mamoun, Kathleen L. Mason, Brandi E. Hobbs, Glen A. Scoles, Eileen M. Barry, Daniel E. Sonenshine, Utpal Pal, Jesus G. Valenzuela, Marcelo B. Sztein, Marcela F. Pasetti, Michael L. Levin, Michail Kotsyfakis, Steven M. Jay, Jason F. Huntley, Lloyd S. Miller, Laura Santambrogio, Joao H.F. Pedra

Biological Sciences Faculty Publications

Extracellular vesicles are thought to facilitate pathogen transmission from arthropods to humans and other animals. Here, we reveal that pathogen spreading from arthropods to the mammalian host is multifaceted. Extracellular vesicles from Ixodes scapularis enable tick feeding and promote infection of the mildly virulent rickettsial agent Anaplasma phagocytophilum through the SNARE proteins Vamp33 and Synaptobrevin 2 and dendritic epidermal T cells. However, extracellular vesicles from the tick Dermacentor andersoni mitigate microbial spreading caused by the lethal pathogen Francisella tularensis. Collectively, we establish that tick extracellular vesicles foster distinct outcomes of bacterial infection and assist in vector feeding by acting …

Global Extinction Risk For Seahorses, Pipefishes And Their Near Relatives (Syngnathiformes), Riley A. Pollom, Gina M. Ralph, Caroline M. Pollock, Amanda C.J. Vincent

Biological Sciences Faculty Publications

Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are …

Diet Of Long-Eared Owl And Common Kestrel In An Urban Landscape (Ukraine), Ivan Zahorodnyi, Oleksii Dubovyk, Ivan Komarnytskyi, Ihor Dykyy

Biological Sciences Faculty Publications

In the present study we performed a comparative dietary analysis of two predatory birds, the Long-eared Owl (Asio otus) and the Common Kestrel (Falco tinnunculus) in the district of Lviv city. We found that the Long-eared Owl and the Common Kestrel are typical small mammal specialists within the urban ecosystem. Considering the abundance and biomass of prey, small mammals comprise 98.4% of the Long-eared Owl’s diet. The species composition of mammals coincides almost 50% in the food intake comparison of the two birds. It has been established that the main prey of both species is the …