Biology Commons^™

Sequence-Based Bioinformatics Approaches To Predict Virus–Host Relationships In Archaea And Eukaryotes, Yingshan Li

School of Computing: Dissertations, Theses, and Student Research

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

Mitochondrial Functions Are Major Targets Of Isocyanide Activity In Saccharomyces Cerevisiae, Morgan A. Siemek

School of Biological Sciences: Dissertations, Theses, and Student Research

The isocyanide functional group is important in the synthesis of many organic compounds and is found in natural products produced by plants, bacteria, marine invertebrates, and fungi. The antimicrobial activities of isocyanide compounds have been documented for almost 70 years, however, the biochemical targets and mechanisms of action remain poorly defined. We report antimicrobial activity of 4-para-nitrophenyl-isocyanide (p-NPIC) against a model fungus, Saccharomyces cerevisiae, and the human fungal pathogen Candida albicans. To identify the cellular and molecular targets of p-NPIC, we screened the non-essential single gene-deletion collection of S. cerevisiae. We …

Exercise Facilitates Regeneration After Severe Nerve Transection And Further Modulates Neural Plasticity, Yunfan Kong, Mitchell Kuss, Yu Shi, Fang Fang, Wen Xue, Wen Shi, Yutong Liu, Chi Zhang, Peng Zhong, Bin Duan

School of Biological Sciences: Faculty Publications

Patients with severe traumatic peripheral nerve injury (PNI) always suffer from incomplete recovery and poor functional outcome. Physical exercise-based rehabilitation, as a non-invasive interventional strategy, has been widely acknowledged to improve PNI recovery by promoting nerve regeneration and relieving pain. However, effects of exercise on chronic plastic changes following severe traumatic PNIs have been limitedly discussed. In this study, we created a long-gap sciatic nerve transection followed by autograft bridging in rats and tested the therapeutic functions of treadmill running with low intensity and late initiation. We demonstrated that treadmill running effectively facilitated nerve regeneration and prevented muscle atrophy and …

Strategies Of Protected Area Use By Asian Elephants In Relation To Motivational State And Social Affiliations, Anastasia E. Madsen, Christin Minge, T.V. Pushpakumara, U. Sameera Weerathunga, U. K. Padmalal, Devaka K. Weerakoon, Shermin De Silva

School of Biological Sciences: Faculty Publications

Animals’ space requirements may vary according to life-history and social considerations. We observed 516 wild adult Asian elephants from both sexes, over 9 years, to investigate how life-history traits and social behavior influence protected-area (PA) use at Udawalawe National Park, Sri Lanka. Male PA-use, quantified in terms of average between-sightings-interval (BSI), was significantly influenced by the interaction of age class and motivational state (i.e. reproduction vs. foraging). Musth lengthened with age, with a median of 24.5 days for ages 21–30, 32.5 days for ages 31–40, and 45 days for those > 40. A minority (11%) used it exclusively during musth, while …

Strategies Of Protected Area Use By Asian Elephants In Relation To Motivational State And Social Affiliations, Anastasia E. Madsen, Christin Minge, T. V. Pushpakumara, U. Sameera Weerathunga, U. K. Padmalal, Devaka K. Weerakoon, Shermin De Silva

School of Biological Sciences: Faculty Publications

Animals’ space requirements may vary according to life-history and social considerations. We observed 516 wild adult Asian elephants from both sexes, over 9 years, to investigate how life-history traits and social behavior influence protected-area (PA) use at Udawalawe National Park, Sri Lanka. Male PA-use, quantified in terms of average between-sightings-interval (BSI), was significantly influenced by the interaction of age class and motivational state (i.e. reproduction vs. foraging). Musth lengthened with age, with a median of 24.5 days for ages 21–30, 32.5 days for ages 31–40, and 45 days for those > 40. A minority (11%) used it exclusively during musth, while …

Subtype C Hiv-1 Reservoirs Throughout The Body In Art-Suppressed Individuals, Zhou Liu, Peter Julius, Guobin Kang, John T. West, Charles Wood

School of Biological Sciences: Faculty Publications

Subtype B HIV-1 reservoirs have been intensively investigated, but reservoirs in other subtypes and how they respond to antiretroviral therapy (ART) is substantially less established. To characterize subtype C HIV-1 reservoirs, we implemented postmortem frozen, as well as formalin fixed paraffin embedded (FFPE) tissue sampling of central nervous system (CNS) and peripheral tissues. HIV-1 LTR, gag, envelope (env) DNA and RNA was quantified using genomic DNA and RNA extracted from frozen tissues. RNAscope was used to localize subtype C HIV-1 DNA and RNA in FFPE tissue. Despite uniform viral load suppression in our cohort, PCR results …

Mate Sampling Behavior Determines The Density Dependence Of Sexual Selection, J. Colton Watts, Eileen A. Hebets, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Theory predicts that the strength of sexual selection (i.e., how well a trait predicts mating or fertilization success) should increase with population density, yet empirical support remains mixed. We explore how this discrepancy might reflect a disconnect between current theory and our understanding of the strategies individuals use to choose mates. We demonstrate that the density dependence of sexual selection predicted by previous theory arises from the assumption that individuals automatically sample more potential mates at higher densities. We provide an updated theoretical framework for the density dependence of sexual selection by (1) developing models that clarify the mechanisms through …

Access To Online Formative Assessments In Lower-Division Undergraduate Biology Courses: Investigating Barriers To Student Engagement, Allison M. Upchurch, Dana L. Kirkwood-Watts, Kathleen R. Brazeal, Lorey A. Wheeler, Brian A. Couch, Gabrielle B. Johnson, Sarah K. Spier

School of Biological Sciences: Faculty Publications

Instructors use a variety of online formative assessment (FA) activities to support learning outside class. Previous studies have revealed barriers for students in online courses, but little is known about the barriers students experience when completing online FA assignments. Understanding these barriers to access is critical to fostering more inclusive learning for all students. Using a framework from previous work in online learning, we examined student perceptions of online FA access with respect to five barrier categories: technical resources, instructor organization, social interactions, personal engagement, and learning environment. We developed and administered a survey to more than 1,200 undergraduate biology …

Editorial: C. Elegans Host-Microbiome Interactions: From Medical To Ecological And Evolutionary Model, Michael A. Herman, Javier E. Irazoqui, Buck S. Samuel, Nic Vega

School of Biological Sciences: Faculty Publications

Microbiomes often form specific functional associations with their hosts. Correlations between microbiome membership and states of host health and disease abound in many systems. However, there are few systems that allow for in depth functional studies that include precise manipulation and interrogation of both microbiome composition and host function. Recently the nematode Caenorhabditis elegans - an excellent genetic model organism for studying many fields of biology, including neurobiology and behavior, development, cell biology, and innate immunity - has proven to be a robust system to probe microbiome interactions and their effect on host physiology.

Editorial: C. Elegans Hostmicrobiome Interactions: From Medical To Ecological And Evolutionary Model, Michael A. Herman, Javier E. Irazoqui, Buck S. Samuel, Nic Vega

School of Biological Sciences: Faculty Publications

No abstract provided.

Temperature Has A Unimodal Effect On The Functional Response Of Wolf Spiders, John Delong, Stella F. Uiterwaal, Alondra Magallanes

School of Biological Sciences: Faculty Publications

The response of biotic interactions to changes in temperature will play a large role in determining the impact of climate change on ecological communities. In particular, how warming alters predator-prey interactions will influence population stability, food web connectivity, and the movement of energy across trophic levels. The functional response relates predator foraging rates to prey availability, and it is often predicted to increase monotonically with temperature, at least within the limits of predator function. However, some studies suggest that functional responses peak and then decline, and such a difference has critical implications for the effect of warming on ecological communities. …

Ecological Interactions Disrupted By Habitat Alteration In The Neotropics, Aniko Toth, Andrew Allen, S. Kathleen Lyons, John Alroy

School of Biological Sciences: Faculty Publications

Ecological interactions help determine the distribution of species across landscapes and play crucial roles in ecosystem services such as pollination, seed dispersal, and pest control1. Human disturbances, particularly habitat alteration, have the potential to modify or erase ecological interactions^2,3 and so jeopardise the processes they control. While examples of interactions becoming rewired under human influence have been recorded, studies of this process for speciose assemblages at regional to continental scales are uncommon⁴ and obstructed by logistical difficulties2. The consequences for ecological communities and people are therefore poorly understood. Here we show that human habitat alteration is associated with …

Multiple Generations Of Antibiotic Exposure And Isolation Influence Host Fitness And The Microbiome In A Model Zooplankton Species, Reilly O. Cooper, Sarah Tjards, Jessica Rischling, David T. Nguyen, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Background

Chronic antibiotic exposure impacts host health through changes to the microbiome, increasing disease risk and reducing the functional repertoire of community members. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied. However, much less is understood about the multigenerational effects of antibiotic exposure and how the microbiome may recover across host generations.

Results

In this study, we examined microbiome composition and host fitness across five generations of exposure to a suite of three antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where …

Species Distribution Models And Climatic Niche Comparisons Provide Clues On The Geographic Origin Of A Spider Invasion In The Americas, Laura Segura‑Hernandez, Gilbert Barrantes, Eduardo Chacon‑Madrigal, Adrián Garcia‑Rodriguez

School of Biological Sciences: Faculty Publications

Identifying the source population of alien species is important to assess the distribution and potential effects in the invaded area. The araneid spider Cyrtophora citricola is widely distributed in Europe, Asia, and Africa; however, in the last 26 years, it has been reported in several countries across the Americas. To date, the geographic origin of the populations established in the Americas remains unclear, but considering the successful colonization after its recent arrival, assessing climatic similarities between the invaded and native geographic ranges could be useful to address this question. In this study, we used a combination of Species Distribution Models …

Quantitative Assay For Farnesol And The Aromatic Fusel Alcohols From The Fungus Candida Albicans, Cory H. T. Boone, Daniel Gutzmann, Jaxon J. Kramer, Audrey L. Atkin, Kenneth Nickerson

School of Biological Sciences: Faculty Publications

The dimorphic fungus Candida albicans is a commensal and opportunistic fungal pathogen of humans. It secretes at least four small lipophilic molecules, farnesol and three aromatic fusel alcohols. Farnesol has been identified as both a quorum sensing molecule (QSM) and a virulence factor. Our gas chromatography (GC)-based assay for these molecules exhibits high throughput, prevention of analyte loss by avoiding filtration and rotary evaporation, simultaneous cell lysis and analyte extraction by ethyl acetate, and the ability to compare whole cultures with their cell pellets and supernatants. Farnesol synthesis and secretion were separable phenomena and pellet:supernatant ratios for farnesol were high, …

The Global Spread Of Misinformation On Spiders, Stefano Mammola, Jagoba Malumbres-Olarte, Valeria Arabesky, Diego Alejandro Barrales-Alcalá, Aimee Lynn Barrion-Dupo, Marco Antonio Benamú, Tharina L. Bird, Maria Bogomolova, Pedro Cardoso, Maria Chatzaki, Ren Chung Cheng, Tien Ai Chu, Leticia M. Classen-Rodríguez, Iva Čupić, Naufal Urfi Dhiya'ulhaq, André Philippe Drapeau Picard, Hisham K. El-Hennawy, Mert Elverici, Caroline S. Fukushima, Zeana Ganem, Efrat Gavish-Regev, Naledi T. Gonnye, Axel Hacala, Charles R. Haddad, Thomas Hesselberg, Tammy Ai Tian Ho, Thanakorn Into, Marco Isaia, Dharmaraj Jayaraman, Nanguei Karuaera, Rajashree Khalap, Kiran Khalap, Dongyoung Kim, Tuuli Korhonen, Laura Segura-Hernández, Et Al.

School of Biological Sciences: Faculty Publications

In the internet era, the digital architecture that keeps us connected and informed may also amplify the spread of misinformation. This problem is gaining global attention, as evidence accumulates that misinformation may interfere with democratic processes and undermine collective responses to environmental and health crises1,2. In an increasingly polluted information ecosystem, understanding the factors underlying the generation and spread of misinformation is becoming a pressing scientific and societal challenge3. Here, we studied the global spread of (mis-)information on spiders using a high-resolution global database of online newspaper articles on spider–human interactions, covering stories of spider–human encounters and biting events published …

Defence Mitigation By Predators Of Chemically Defended Prey Integrated Over The Predation Sequence And Across Biological Levels With A Focus On Cardiotonic Steroids, Shabnam Mohammadi, Lu Yang, Matthew Bulbert, Hannah M. Rowland

School of Biological Sciences: Faculty Publications

Predator–prey interactions have long served as models for the investigation of adaptation and fitness in natural environments. Anti-predator defences such as mimicry and camouflage provide some of the best examples of evolution. Predators, in turn, have evolved sensory systems, cognitive abilities and physiological resistance to prey defences. In contrast to prey defences which have been reviewed extensively, the evolution of predator counter-strategies has received less attention. To gain a comprehensive view of how prey defences can influence the evolution of predator counter-strategies, it is essential to investigate how and when selection can operate. In this review we evaluate how predators …

Dynamic Energy Budget Models: Fertile Ground For Understanding Resource Allocation In Plants In A Changing World, Sabrina E. Russo, Glenn Ledder, Erik B. Muller, Roger M. Nisbet

School of Biological Sciences: Faculty Publications

Climate change is having dramatic effects on the diversity and distribution of species. Many of these effects are mediated by how an organism’s physiological patterns of resource allocation translate into fitness through effects on growth, survival and reproduction. Empirically, resource allocation is challenging to measure directly and so has often been approached using mathematical models, such as Dynamic Energy Budget (DEB) models. The fact that all plants require a very similar set of exogenous resources, namely light, water and nutrients, integrates well with the DEB framework in which a small number of variables and processes linked through pathways represent an …

Constraints On The Evolution Of Toxin-Resistant Na,K-Atpases Have Limited Dependence On Sequence Divergence, Shabnam Mohammadi, Santiago Herrera-Álvarez, Lu Yang, María Del Pilar Rodrı´Guez-Ordoñez, Karen Zhang, Jay F. Storz, Susanne Dobler, Andrew J. Crawford, Peter Andolfatto

School of Biological Sciences: Faculty Publications

A growing body of theoretical and experimental evidence suggests that intramolecular epistasis is a major determinant of rates and patterns of protein evolution and imposes a substantial constraint on the evolution of novel protein functions. Here, we examine the role of intramolecular epistasis in the recurrent evolution of resistance to cardiotonic steroids (CTS) across tetrapods, which occurs via specific amino acid substitutions to the α-subunit family of Na,K-ATPases (ATP1A). After identifying a series of recurrent substitutions at two key sites of ATP1A that are predicted to confer CTS resistance in diverse tetrapods, we then performed protein engineering experiments to test …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Functional Traits’ Annual Variation Exceeds Nitrogen-Driven Variation In Grassland Plant Species, George R. Wheeler, Chad Brassil, Johannes M. H. Knops

School of Biological Sciences: Faculty Publications

Effective application of functional trait approaches to ecological questions requires understanding the patterns of trait variation within species as well as between them. However, few studies address the potential for intraspecific variation to occur on a temporal basis and, thus, for trait-based findings to be contingent upon sampling year. To quantify annual variation in the functional traits of grassland plant species, we measured specific leaf area, leaf dry matter content, plant height, and chlorophyll content in 12 shortgrass prairie plant species. We repeated these measurements across 4 years, both in long-term nitrogen addition plots and in corresponding control plots. Three …

Time Domains Of Hypoxia Responses And -Omics Insights, James J. Yu, Amy L. Non, Erica C. Heinrich, Wanjun Gu, Joe Alcock, Esteban A. Moya, Elijah S. Lawrence, Michael S. Tift, Katie A. O'Brien, Jay F. Storz, Anthony V. Signore, Jane I. Khudyakov, William K. Milsom, Sean M. Wilson, Cynthia M. Beall, Francisco C. Villafuerte, Tsering Stobdan, Colleen G. Julian, Lorna G. Moore, Mark M. Fuster, Jennifer A. Stokes, Richard Milner, John B. West, Jiao Zhang, John Y. Shyy, Ainash Childebayeva, José Pablo Vázquez-Medina, Luu V. Pham, Omar A. Mesarwi, James E. Hall, Zachary A. Cheviron, Jeremy Sieker, Arlin B. Blood, Jason X. Yuan, Tatum S. Simonson, Et Al.

School of Biological Sciences: Faculty Publications

The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Tremblay, Pier-Luc Plante, Ellen C. Jensen, Kenneth Nickerson, Sylvain Moineau

School of Biological Sciences: Faculty Publications

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Trembly, Pier-Luc Plante, Ellen C. Jensen, Kenneth W. Nickerson, Sylvian Moineau

School of Biological Sciences: Faculty Publications

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Stabilization By Adaptive Feedback Control For Positive Difference Equations With Applications In Pest Management, J. Edholm, C. Guiver, Richard Rebarber, Brigitte Tenhumberg, S. Townley

School of Biological Sciences: Faculty Publications

An adaptive feedback control scheme is proposed for stabilizing a class of forced nonlinear positive difference equations. The adaptive scheme is based on so-called high-gain adaptive controllers and contains substantial robustness with respect to model uncertainty as well as with respect to persistent forcing signals, including measurement errors. Our results take advantage of the underlying positive systems structure and ideas from input-to-state stability from nonlinear control theory. Our motivating application is to pest or weed control, and in this context the present work substantially strengthens previous work by the authors. The theory is illustrated with examples.

Long-Distance Vocalizations Of Spotted Hyenas Contain Individual, But Not Group, Signatures, Kenna D.S. Lehmann, Frants H. Jensen, Andrew Gersick, Ariana Strandburg-Peshkin, Kay E. Holekamp

School of Biological Sciences: Faculty Publications

In animal societies, identity signals are common, mediate interactions within groups, and allow individuals to discriminate group-mates from out-group competitors. However, individual recognition becomes increasingly challenging as group size increases and as signals must be transmitted over greater distances. Group vocal signatures may evolve when successful in-group/out-group distinctions are at the crux of fitness-relevant decisions, but group signatures alone are insufficient when differentiated within-group relationships are important for decision-making. Spotted hyenas are social carnivores that live in stable clans of less than 125 individuals composed of multiple unrelated matrilines. Clan members cooperate to defend resources and communal territories from neighbouring …

Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) are the most sought-after deer species in America. The antlers of mammals, such as deer, are one of the fastest regenerative tissues in the world and are grown and naturally cast every year. Research on cast antlers have been used for a variety of purposes including population comparisons and impacts of deer health due to climatic stressors. When investigating cast antlers, it is important to confirm individuality of match sets in addition to antlers of the same individual between years. Therefore, individuality must be confirmed genetically, and protocols must be developed and established to …

Access To Online Formative Assessments In Introductory Biology Courses: Investigating Barriers To Student Engagement, Allison M. Upchurch

School of Biological Sciences: Dissertations, Theses, and Student Research

Instructors use a variety of online formative assessment (FA) activities to support learning outside of class. Previous studies have revealed barriers for students in online courses, but little is known about the barriers students experience when completing online FA assignments. Understanding these barriers to access is critical to fostering more inclusive learning for all students. Using a framework from previous work in online learning, we examined student perceptions of online FA access with respect to five barrier categories: technical resources, instructor organization, social interactions, personal engagement, and learning environment. We developed and administered a survey to over 1200 undergraduate biology …