Life Sciences Commons^™

Miniscule Differences Between Sex Chromosomes In The Giant Genome Of A Salamander, Melissa C. Keinath, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, S. Randal Voss, Jeramiah J. Smith

Biology Faculty Publications

In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, …

Effect Of Temperature Change On Synaptic Transmission At Crayfish Neuromuscular Junctions, Yuechen Zhu, Leo De Castro, Robin L. Cooper

Biology Faculty Publications

Ectothermic animals in areas characterised by seasonal changes are susceptible to extreme fluctuations in temperature. To survive through varied temperatures, ectotherms have developed unique strategies. This study focuses on synaptic transmission function at cold temperatures, as it is a vital component of ectothermic animals' survival. For determining how synaptic transmission is influenced by an acute change in temperature (20°C to 10°C within a minute) and chronic cold (10°C), the crayfish (Procambarus clarkii) neuromuscular junction (NMJ) was used as a model. To simulate chronic cold conditions, crayfish were acclimated to 15°C for 1 week and then to 10°C for …

Canvass: A Crowd-Sourced, Natural-Product Screening Library For Exploring Biological Space, Sara E. Kearney, Gergely ZahoráNszky-KőHalmi, Kyle R. Brimacombe, Mark J. Henderson, Caitlin Lynch, Tongan Zhao, Kanny K. Wan, Zina Itkin, Christopher Dillon, Min Shen, Dorian M. Cheff, Tobie D. Lee, Danielle Bougie, Ken Cheng, Nathan P. Coussens, Dorjbal Dorjsuren, Richard T. Eastman, Ruili Huang, Michael J. Iannotti, Surendra Karavadhi, Carleen Klumpp-Thomas, Jacob S. Roth, Srilatha Sakamuru, Wei Sun, Steven A. Titus, Adam Yasgar, Ya-Qin Zhang, Jinghua Zhao, Rodrigo B. Andrade, M. Kevin Brown, Robert B. Grossman

Chemistry Faculty Publications

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The …

Meta-Analysis Challenges A Textbook Example Of Status Signalling And Demonstrates Publication Bias, Alfredo Sánchez-Tójar, Shinichi Nakagawa, Moisès Sánchez-Fortún, Dominic A. Martin, Sukanya Ramani, Antje Girndt, Veronika Bókony, Bart Kempenaers, András Liker, David F. Westneat, Terry Burke, Julia Schroeder

Biology Faculty Publications

The status signalling hypothesis aims to explain within-species variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of male house sparrows (Passer domesticus). We conducted a systematic review, and obtained primary data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, the overall effect size (i.e. meta-analytic mean) was small and uncertain. Furthermore, we found several biases in the literature that further question the support available …

The Mitochondrial Genome Of The Endemic Brazilian Paradoxial Frog Pseudis Tocantins (Hylidae), Kaleb Pretto Gatto, Jeramiah J. Smith, Luciana Bolsoni Lourenço

Biology Faculty Publications

In this work, we present for the first time the mitochondrial genome of a paradoxical frog (Pseudis tocantins). This genome is 15.56 kb, excluding the control region, and is similar in gene content to other hylid mitogenomes. Maximum likelihood analysis, using the mitogenomes of several anurans, indicated P. tocantins as closely related to other hylid species.

Seqothello: Querying Rna-Seq Experiments At Scale, Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian, Jinze Liu

Computer Science Faculty Publications

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.

Using Transcriptomics To Enable A Plethodontid Salamander (Bolitoglossa Ramosi) For Limb Regeneration Research, Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss, Jean Paul Delgado

Biology Faculty Publications

Background: Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration.

Results: Using paired-end Illumina sequencing technology and Trinity …

Physiological Changes As A Measure Of Crustacean Welfare Under Different Standardized Stunning Techniques: Cooling And Electroshock, Kristin Weineck, Andrew J. Ray, Leo J. Fleckenstein, Meagan Medley, Nicole Dzubuk, Elena Piana, Robin L. Cooper

Biology Faculty Publications

Stunning of edible crustaceans to reduce sensory perception prior and during slaughter is an important topic in animal welfare. The purpose of this project was to determine how neural circuits were affected during stunning by examining the physiological function of neural circuits. The central nervous system circuit to a cardiac or skeletal muscle response was examined. Three commercially important crustacean species were utilized for stunning by immersion in an ice slurry below 4 °C and by electrocution; both practices are used in the seafood industry. The blue crab (Callinectes sapidus), the red swamp crayfish (Procambarus clarkii), …

Transcriptional Response Of Honey Bee (Apis Mellifera) To Differential Nutritional Status And Nosema Infection, Farida Azzouz-Olden, Arthur G. Hunt, Gloria Degrandi-Hoffman

Plant and Soil Sciences Faculty Publications

Background: Bees are confronting several environmental challenges, including the intermingled effects of malnutrition and disease. Intuitively, pollen is the healthiest nutritional choice, however, commercial substitutes, such as Bee-Pro and MegaBee, are widely used. Herein we examined how feeding natural and artificial diets shapes transcription in the abdomen of the honey bee, and how transcription shifts in combination with Nosema parasitism.

Results: Gene ontology enrichment revealed that, compared with poor diet (carbohydrates [C]), bees fed pollen (P > C), Bee-Pro (B > C), and MegaBee (M > C) showed a broad upregulation of metabolic processes, especially lipids; however, pollen feeding promoted more functions, and …

Why Large Seeds With Physical Dormancy Become Nondormant Earlier Than Small Ones, Ailton G. Rodrigues-Junior, Ana Caroline M. P. Mello, Carol C. Baskin, Jerry M. Baskin, Denise M. T. Oliveira, Queila S. Garcia

Biology Faculty Publications

Under natural conditions, large seeds with physical dormancy (PY) may become water permeable earlier than small ones. However, the mechanism for this difference has not been elucidated. Thus, our aim was to evaluate the traits associated with PY in seeds of Senna multijuga (Fabaceae) and to propose a mechanism for earlier dormancy-break in large than in small seeds. Two seedlots were collected and each separated into large and small seeds. Seed dry mass, water content, thickness of palisade layer in the hilar and distal regions and the ratio between palisade layer thickness (P) in the lens fissure and seed mass …

High-Density Lipoprotein Inhibits Serum Amyloid A-Mediated Reactive Oxygen Species Generation And Nlrp3 Inflammasome Activation, Preetha Shridas, Maria C. De Beer, Nancy R. Webb

Internal Medicine Faculty Publications

Serum amyloid A (SAA) is a high-density apolipoprotein whose plasma levels can increase more than 1000-fold during a severe acute-phase inflammatory response and are more modestly elevated in chronic inflammation. SAA is thought to play important roles in innate immunity, but its biological activities have not been completely delineated. We previously reported that SAA deficiency protects mice from developing abdominal aortic aneurysms (AAAs) induced by chronic angiotensin II (AngII) infusion. Here, we report that SAA is required for AngII-induced increases in interleukin-1β (IL-1β), a potent proinflammatory cytokine that is tightly controlled by the Nod-like receptor protein 3 (NLRP3) inflammasome and …

Hyperpolarization By Activation Of Halorhodopsin Results In Enhanced Synaptic Transmission: Neuromuscular Junction And Cns Circuit, Matthew Mattingly, Kristin Weineck, Jennifer Costa, Robin L. Cooper

Biology Faculty Publications

Optogenetics offers a unique method to regulate the activity of select neural circuits. However, the electrophysiological consequences of targeted optogenetic manipulation upon the entire circuit remain poorly understood. Analysis of the sensory-CNS-motor circuit in Drosophila larvae expressing eHpHR and ChR2-XXL revealed unexpected patterns of excitability. Optical stimulation of motor neurons targeted to express eNpHR resulted in inhibition followed by excitation of body wall contraction with repetitive stimulation in intact larvae. In situ preparations with direct electrophysiological measures showed an increased responsiveness to excitatory synaptic activity induced by sensory stimulation within a functional neural circuit. To ensure proper function of eNpHR …

Capn5 Expression In The Healthy And Regenerating Zebrafish Retina, Cagney E. Coomer, Ann C. Morris

Biology Faculty Publications

PURPOSE. Autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) is a devastating inherited autoimmune disease of the eye that displays features commonly seen in other eye diseases, such as retinitis pigmentosa and diabetic retinopathy. ADNIV is caused by a gain-of-function mutation in Calpain-5 (CAPN5), a calcium-dependent cysteine protease. Very little is known about the normal function of CAPN5 in the adult retina, and there are conflicting results regarding its role during mammalian embryonic development. The zebrafish (Danio rerio) is an excellent animal model for studying vertebrate development and tissue regeneration, and represents a novel model to explore the …

Screening Of Multimeric Β-Xylosidases From The Gut Microbiome Of A Higher Termite, Globitermes Brachycerastes, Chunyan Liu, Gen Zou, Xing Yan, Xuguo Zhou

Entomology Faculty Publications

Termite gut microbiome is a rich reservoir for glycoside hydrolases, a suite of enzymes critical for the degradation of lignocellulosic biomass. To search for hemicellulases, we screened 12,000 clones from a fosmid gut library of a higher termite, Globitermes brachycerastes. As a common Southeastern Asian genus, Globitermes distributes predominantly in tropical rain forests and relies on the lignocellulases from themselves and bacterial symbionts to digest wood. In total, 22 positive clones with β-xylosidase activity were isolated, in which 11 representing different restriction fragment length polymorphism (RFLP) patterns were pooled and subjected to 454 pyrosequencing. As a result, eight putative β-xylosidases …

In Vivo Structures Of The Helicobacter Pylori Cag Type Iv Secretion System, Yi-Wei Chang, Carrie L. Shaffer, Lee A. Rettberg, Debnath Ghosal, Grant J. Jensen

Veterinary Science Faculty Publications

The type IV secretion system (T4SS) is a versatile nanomachine that translocates diverse effector molecules between microbes and into eukaryotic cells. Here, using electron cryotomography, we reveal the molecular architecture of the Helicobacter pylori cag T4SS. Although most components are unique to H. pylori, the cag T4SS exhibits remarkable architectural similarity to other T4SSs. Our images revealed that, when H. pylori encounters host cells, the bacterium elaborates membranous tubes perforated by lateral ports. Sub-tomogram averaging of the cag T4SS machinery revealed periplasmic densities associated with the outer membrane, a central stalk, and peripheral wing-like densities. Additionally, we resolved pilus-like …

The Evolutionary History Of Nebraska Deer Mice: Local Adaptation In The Face Of Strong Gene Flow, Susanne P Pfeifer, Stefan Laurent, Vitor C. Sousa, Catherine R. Linnen, Matthieu Foll, Laurent Excoffier, Hopi E. Hoekstra, Jeffrey D. Jensen

Biology Faculty Publications

The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, …

Morphogenetic Defects Underlie Superior Coloboma, A Newly Identified Closure Disorder Of The Dorsal Eye, Jennifer C. Hocking, Jakub K. Famulski, Kevin H. Yoon, Sonya A. Widen, Cassidy S. Bernstein, Sophie Koch, Omri Weiss, Forge Canada Consortium, Canada, Seema Agarwala, Adi Inbal, Ordan J. Lehmann, Andrew J. Waskiewicz

Biology Faculty Publications

The eye primordium arises as a lateral outgrowth of the forebrain, with a transient fissure on the inferior side of the optic cup providing an entry point for developing blood vessels. Incomplete closure of the inferior ocular fissure results in coloboma, a disease characterized by gaps in the inferior eye and recognized as a significant cause of pediatric blindness. Here, we identify eight patients with defects in tissues of the superior eye, a congenital disorder that we term superior coloboma. The embryonic origin of superior coloboma could not be explained by conventional models of eye development, leading us to …

The Premammillary Nucleus Of The Hypothalamus Is Not Necessary For Photoperiodic Timekeeping In Female Turkeys (Meleagris Gallopavo), Ashli F. Moore, Vincent M. Cassone, Kevin D. Alloway, Paul A. Bartell

Biology Faculty Publications

In birds, seasonal reproduction is regulated by day length, with long days in the spring activating the hypothalamic-pituitary-gonadal axis and reproductive behaviors. The photoreceptors mediating this process remain unknown, but recently, the premammillary nucleus (PMM) of the hypothalamus has been implicated as the site of photoperiodic signaling in turkeys. We performed electrolytic lesions of the PMM to elucidate its role in the photoactivation and maintenance of egg production in female turkeys. Our results show that ablation of the PMM does not alter the normal lay cycle. No differences were found between lesioned birds and sham controls in the latency to …

Effects Of Predispersal Insect Seed Predation On The Early Life History Stages Of A Rare Cold Sand-Desert Legume, Yi J. Han, Jerry M. Baskin, Dun Y. Tan, Carol C. Baskin, Ming Y. Wu

Biology Faculty Publications

Seed predation by insects is common in seeds of Fabaceae (legume) species with physical dormancy (PY). However, the consequences of insect seed predation on the life history of legumes with PY have been little studied. In the largest genus of seed plants, Astragalus (Fabaceae), only one study has tested the effects of insect predation on germination, and none has tested it directly on seedling survival. Thus, we tested the effects of insect predation on seed germination and seedling growth and survival of Astragalus lehmannianus, a central Asian sand-desert endemic. Under laboratory conditions, seeds lightly predated in the natural habitat …

Highly Conserved Molecular Pathways, Including Wnt Signaling, Promote Functional Recovery From Spinal Cord Injury In Lampreys, Paige E. Herman, Angelos Papatheodorou, Stephanie A. Bryant, Courtney K. M. Waterbury, Joseph R. Herdy, Anthony A. Arcese, Joseph D. Buxbaum, Jeramiah J. Smith, Jennifer R. Morgan, Ona Bloom

Biology Faculty Publications

In mammals, spinal cord injury (SCI) leads to dramatic losses in neurons and synaptic connections, and consequently function. Unlike mammals, lampreys are vertebrates that undergo spontaneous regeneration and achieve functional recovery after SCI. Therefore our goal was to determine the complete transcriptional responses that occur after SCI in lampreys and to identify deeply conserved pathways that promote regeneration. We performed RNA-Seq on lamprey spinal cord and brain throughout the course of functional recovery. We describe complex transcriptional responses in the injured spinal cord, and somewhat surprisingly, also in the brain. Transcriptional responses to SCI in lampreys included transcription factor networks …

Effects Of Clove Oil (Eugenol) On Proprioceptive Neurons, Heart Rate, And Behavior In Model Crustaceans, Samuel Wycoff, Kristin Weineck, Shannon Conlin, Chinni Suryadevara, Elizabeth Grau, Alec Bradley, Danielle Cantrell, Samantha Eversole, Carolyn Grachen, Kaylee Hall, Danielle Hawthorne, Claire Kinmon, Paula Ortiz Guerrero, Bhavik Patel, Kaitlyn Samuels, Gia Valdes, Andrew J. Ray, Leo J. Fleckenstein, Elena Piana, Robin L. Cooper

Biology Faculty Publications

Clove oil contains eugenol as an active ingredient and is used as a topical anesthetic in mammals to remedy pain and to anesthetize fish and other seafood for short periods; however, the exact mechanism of action of eugenol is not fully understood. We examined use of eugenol as a reversible anesthetic in crustaceans by examining its effect on sensory and motor neurons in the Red Swamp crayfish (Procambarus clarkii), Blue crab (Callinectes sapidus) and Whiteleg shrimp (Litopenaeus vannamei) with electrophysiological recordings. The neurogenic heart rate in the three species was also monitored along with …

Cycads, Flying Foxes, And Brain Disease In Humans, Logan Disney

Lewis Honors College Capstone Collection

Cycads are a group of ancient gymnosperms with a rich fossil history. While they once dominated the world’s forests, their adaptation to warm climates has now restricted them to tropical areas. They are not widely eaten by humans due to their known toxicity, but some indigenous groups of the Pacific Islands, such as the Chamorro people of Guam, have developed methods of washing the seeds for safe consumption. Cycad seeds are a common dietary item of several mammals. One such mammal, the flying fox, is considered a delicacy to several indigenous groups. In the mid-twentieth century, these groups also expressed …

Investigating The Effects Of Homocysteine As An Agonist On Invertebrate Glutamatergic Synapses, Elizabeth Grau, Alexandra E. Stanback, Alec Bradley, Danielle Cantrell, Samantha Eversole, Carolyn Grachen, Kaylee Hall, Danielle Hawthorne, Claire Kinmon, Paula Ortiz Guerrero, Bhavik Patel, Kaitlyn Samuels, Chinni Suryadevara, Gia Valdes, Samuel Wycoff, Robin L. Cooper

Biology Faculty Publications

Hyperhomocysteinemia (HHcy) in mammals can produce neurological deficits, such as memory loss. The cause of the neurological issues is assumed to be due to homocysteine (HCY) binding to glutamatergic receptors in the central nervous system (CNS). High levels of HCY in the CNS are also associated with Amyotrophic Lateral Sclerosis (ALS) and Parkinson’s disease. Thus, understanding the detailed mechanisms of HCY in model preparations could be useful in developing potential treatments to neurodegenerative diseases with overlapping symptoms to HHcy. The aim of this study is to investigate the efficacy of HCY as an agonist at glutamatergic synapses in invertebrates. The …

Functional Analysis Of Protease Adamts 6 During Vertebrate Eye Formation, Austin Taylor

Lewis Honors College Capstone Collection

Extracellular matrix (ECM) remodeling and epithelial sheet fusion occur during the development of many different tissues, including the vertebrate eye (Lu et al., 2011) (Pai et al., 2012). During morphogenesis of the eye, the ventral hemisphere of the developing retinal tissue forms an opening called the optic fissure which must undergo epithelial fusion (Pai et al., 2012). Failure of optic fissure fusion leads to a congenital blinding disorder called coloboma (Gregory-Evans, 2004). A long standing question pertaining to the mechanism of optic fissure fusion is exactly which ECM remodeling enzymes are actively involved in dismantling the ECM to allow for …

Does The Foundational Model Of Anatomy Ontology Provide A Knowledge Base For Learning And Assessment In Anatomy Education?, Melissa D. Clarkson, Mark E. Whipple

Institute for Biomedical Informatics Faculty Publications

Throughout the development of the Foundational Model of Anatomy (FMA) ontology, one of the use cases put forth has been anatomy education. In this work, we examine which types of knowledge taught to anatomy students can be supported by the FMA knowledge base. We first categorize types of anatomical knowledge, then express these patterns in the form “Given ____, state ____”. Each of the 33 patterns was evaluated for whether this type of knowledge is compatible with the modeling and scope of the FMA.

Cold Exposure Effects On Cardiac Function And Synaptic Transmission At The Neuromuscular Junction In Invertebrates, Yuechen Zhu, Robin L. Cooper

Biology Faculty Publications

This review emphasizes how ectothermic animals respond physiologically to environmental temperature changes and cold stress. Generally ectothermic animals cannot generate heat to maintain their body temperature but they can still survive in various temperature zones. Various organisms have been analyzed anatomically and physiologically in the attempt to understand the underlying mechanisms of this temperature adaptation. A few of the changes in the metabolic and molecular function of proteins are discussed. The potential of how hormonal modulation of cardiac and nervous systems which influences responses during exposure cold exposure is also addressed. The focus of this review is on the effect …

Range Expansion Of Sigmodon Hispidus (Hispid Cotton Rat) Into Reclaimed Coal Surface-Mines In Southeastern Kentucky, Brittany L. Slabach, James J. Krupa

Biology Faculty Publications

Sigmodon hispidus (Hispid Cotton Rat) is the most wide-spread species of Sigmodon in North America. In recent years, this species has expanded northward and westward in the western part of its range due to changes in habitat and climate. Evidence suggests northward expansion is also occurring in Kentucky. Since the 1980s, extensive coal mining via surface mining and mountain-top removal has transformed more than 2300 km² of hardwood forests on the Cumberland Plateau of eastern Kentucky. Mining has transformed the landscape, once characterized by forests with deep valleys, steep slopes, and narrow, winding ridgetops into reclaimed sites with a …