Biology Commons^™

Variable Anterior Segment Dysgenesis And Cardiac Anomalies Caused By A Novel Truncating Variant Of Foxc1, Mariya R. Ahmed, Saumil Sethna, Laura A. Krueger, Michael B. Yang, Robert B. Hufnagel

Biology Graduate Research

Anterior segment dysgenesis (ASD) encompasses a wide spectrum of developmental abnormalities of the anterior ocular segment, including congenital cataract, iris hypoplasia, aniridia, iridocorneal synechiae, as well as Peters, Axenfeld, and Rieger anomalies. Here, we report a large five-generation Caucasian family exhibiting atypical syndromic ASD segregating with a novel truncating variant of FOXC1. The family history is consistent with highly variable autosomal dominant symptoms including isolated glaucoma, iris hypoplasia, aniridia, cataract, hypothyroidism, and congenital heart anomalies. Whole-exome sequencing revealed a novel variant [c.313_314insA; p.(Tyr105*)] in FOXC1 that disrupts the α-helical region of the DNA-binding forkhead box domain. In vitro studies …

Sex Differences In Desiccation Tolerance Varies By Colony In The Mesic Liverwort Plagiochila Porelloides, Juliana Da C. Silva-E-Costa, Andrea P. Luizi-Ponzo, David Nicholas Mcletchie

Biology Faculty Publications

Water scarcity, a common stress factor, negatively impacts plant performance. Strategies to cope with it, such as desiccation tolerance, are becoming increasingly important to investigate. However, phenomena, such as intraspecific variation in stress responses have not received much attention. Knowledge of this variability and the environmental drivers can be leveraged to further investigate the mechanisms of desiccation tolerance. Here we tested for variation in desiccation tolerance in Plagiochila porelloides among colonies and sexes within the same riparian zone. Field-collected dehardened plants were subjected to a desiccation event, under controlled conditions and then rehydrated. Plant water status, photosynthetic rates, net carbon …

Using Low-Fix Rate Gps Telemetry To Expand Estimates Of Ungulate Reproductive Success, Nathan D. Hooven, Kathleen E. Williams, John T. Hast, Joseph R. Mcdermott, R. Daniel Crank, Gabe Jenkins, Matthew T. Springer, John J. Cox

Forestry and Natural Resources Faculty Publications

Background

Population parameters such as reproductive success are critical for sustainably managing ungulate populations, however obtaining these data is often difficult, expensive, and invasive. Movement-based methods that leverage Global Positioning System (GPS) relocation data to identify parturition offer an alternative to more invasive techniques such as vaginal implant transmitters, but thus far have only been applied to relocation data with a relatively fine (one fix every  < 8 h) temporal resolution. We employed a machine learning method to classify parturition/calf survival in cow elk in southeastern Kentucky, USA, using 13-h GPS relocation data and three simple movement metrics, training a random forest on cows that successfully reared their calf to a week old.

Results

We developed a decision rule based upon a predicted probability threshold across individual cow time series, accurately classifying 89.5% (51/57) of cows with a known reproductive status. When used to infer status of …

Plant Canopy May Promote Seed Dispersal By Wind, Xuanping Qin, Wei Liang, Zhimin Liu, Minghu Liu, Carol C. Baskin, Jerry M. Baskin, Zhiming Xin, Zhigang Wang, Quanlai Zhou

Biology Faculty Publications

Seed dispersal has received much research attention. The plant canopy can intercept diaspores, but the effect of the plant canopy (the aboveground portion of a plant consisting of branches and leaves) on dispersal distance has not been explored empirically. To determine the effect of plant canopy on seed dispersal distance, a comparison of diaspores falling through open air and through plant canopy was made in a wind tunnel using three wind speeds and diaspores with various traits. Compared with diaspores falling through open air, the dispersal distance of diaspores falling through plant canopy was decreased or increased, depending on wind …

The Ecology And Evolution Of Human Reproductive Behavior, Kaylynne Glover

Theses and Dissertations--Biology

The complexity of human reproductive behavior has necessitated its examination through a variety of scientific disciplines, each focusing on specific elements of our biology, behavior, and society. However, this complexity also necessitates that we reintegrate the information learned from each discipline into a single framework, one rooted in the evolutionary principles that have shaped the development of all life on earth. In this dissertation, I use this framework to explore human reproductive behavior, with a particular focus on sexual coercion and fertility-mediated sexual behavior.

In Chapter 1, I introduce the approach taken in this document, identify several key limitations, and …

Estrogen Regulation Of Daily Metabolic Rhythms In Female Mice, Oluwabukola Omotola

Theses and Dissertations--Biology

Circadian rhythms are approximately 24-hour cycles of behavior, physiology, and gene expression. In mammals, these circadian rhythms are generated by clocks located in nearly every tissue in the body. The function of circadian clocks is to synchronize physiology and behavior with environmental cycles such as the light-dark cycle. After menopause, when circulating levels of estrogens are very low, women are more susceptible to obesity comorbidities such as metabolic syndrome and cardiovascular disease, suggesting that estrogens regulate these processes. Estrogens could protect females from metabolic dysfunction by regulating circadian rhythms. Consumption of diets that are high in fat contribute to obesity. …

Understanding The Effects Of Embryonic Hyperglycemia On Retinal Development And Maintenance, Kayla Titialii-Torres

Theses and Dissertations--Biology

Hundreds of millions of people are affected by diabetes worldwide. Whether they are diagnosed with prediabetes or Type I or II diabetes, there are a variety of mechanisms in the pathogenesis of diabetes. Diabetes is a disease which consists of recurring states of hyperglycemia that can be difficult to manage due to either lack of insulin production or improper utilization of insulin. While these mechanisms of action differ, complications induced by diabetes occur in both poorly regulated Type I and II. Common complications of diabetes include nerve damage, kidney damage, and eye damage. Eye damage specifically is called diabetic retinopathy …

Understanding The Cellular And Physiological Mechanisms Of Fertilization And Early-Stage Seed Development, Mohammad Foteh Ali

Theses and Dissertations--Plant and Soil Sciences

Flowering plants have evolved a unique double-fertilization process. Two sperm cells fuse with two female gametophytic cells, the egg and central cells within the ovule, giving rise to the embryo and endosperm, respectively. Sperm cells in flowering plants are nonmotile and delivered in close proximity to the egg and central cells by the pollen tube. Flowering plants have established filamentous actin (F-actin) based sperm nuclear migration system for successful fertilization. Prior to fertilization, the female gamete forms a mesh-like structure of F-actin that shows constant inward movement from the plasma membrane periphery to the center of the cell where the …

Global Patterns Of Potential Future Plant Diversity Hidden In Soil Seed Banks, Xuejun Yang, Carol C. Baskin, Jerry M. Baskin, Robin J. Pakeman, Zhenying Huang, Ruiru Gao, Johannes H. C. Cornelissen

Biology Faculty Publications

Soil seed banks represent a critical but hidden stock for potential future plant diversity on Earth. Here we compiled and analyzed a global dataset consisting of 15,698 records of species diversity and density for soil seed banks in natural plant communities worldwide to quantify their environmental determinants and global patterns. Random forest models showed that absolute latitude was an important predictor for diversity of soil seed banks. Further, climate and soil were the major determinants of seed bank diversity, while net primary productivity and soil characteristics were the main predictors of seed bank density. Moreover, global mapping revealed clear spatial …

[Review Of] What Is A Complex System? By James Ladyman And Karoline Wiesner. New Haven (Connecticut): Yale University Press. $35.00 (Paper). Xi + 169 P.; Ill.; Index. Isbn: 978-0-300-25110-4. 2020., Joseph Robert Burger

Biology Faculty Publications

No abstract provided.

Rapid And Direct Action Of Lipopolysaccharide (Lps) On Skeletal Muscle Of Larval Drosophila, Rachel Potter, Alexis Meade, Samuel Potter, Robin L. Cooper

Biology Faculty Publications

The endotoxin lipopolysaccharide (LPS) from Gram-negative bacteria exerts a direct and rapid effect on tissues. While most attention is given to the downstream actions of the immune system in response to LPS, this study focuses on the direct actions of LPS on skeletal muscle in Drosophila melanogaster. It was noted in earlier studies that the membrane potential rapidly hyperpolarizes in a dose-dependent manner with exposure to LPS from Pseudomonas aeruginosa and Serratia marcescens. The response is transitory while exposed to LPS, and the effect does not appear to be due to calcium-activated potassium channels, activated nitric oxide synthase …

The Effect Of Calcium Ions On Mechanosensation And Neuronal Activity In Proprioceptive Neurons, Devan E. Atkins, Kimberly L. Bosh, Grace W. Breakfield, Sydney E. Daniels, Makayla J. Devore, Hailey E. Fite, Landys Z. Guo, Danielle K. J. Henry, Alana K. Kaffenberger, Katherine S. Manning, Tatum E. Mowery, Cecilia L. Pankau, Nyla Parker, Malina E. Serrano, Yamaan Shakhashiro, Hannah N. Tanner, Ruth. A. Ward, Aubrey H. Wehry, Robin L. Cooper

Biology Faculty Publications

Proprioception of all animals is important in being able to have coordinated locomotion. Stretch activated ion channels (SACs) transduce the mechanical force into electrical signals in the proprioceptive sensory endings. The types of SACs vary among sensory neurons in animals as defined by pharmacological, physiological and molecular identification. The chordotonal organs within insects and crustaceans offer a unique ability to investigate proprioceptive function. The effects of the extracellular environment on neuronal activity, as well as the function of associated SACs are easily accessible and viable in minimal saline for ease in experimentation. The effect of extracellular [Ca²⁺] on …

The Effect Of Optogenetically Activating Glia On Neuronal Function, Cecilia Pankau, Shelby Mccubbin, Robin L. Cooper

Biology Faculty Publications

Glia, or glial cells, are considered a vital component of the nervous system, serving as an electrical insulator and a protective barrier from the interstitial (extracellular) media. Certain glial cells (i.e., astrocytes, microglia, and oligodendrocytes) within the CNS have been shown to directly affect neural functions, but these properties are challenging to study due to the difficulty involved with selectively-activating specific glia. To overcome this hurdle, we selectively expressed light-sensitive ion channels (i.e., channel rhodopsin, ChR2-XXL) in glia of larvae and adult Drosophila melanogaster. Upon activation of ChR2, both adults and larvae showed a rapid contracture of body wall …

Against The Odds: Hybrid Zones Between Mangrove Killifish Species With Different Mating Systems, Waldir M. Berbel-Filho, Andrey Tatarenkov, George Pacheco, Helder M. V. Espírito-Santo, Mateus G. Lira, Carlos Garcia De Leaniz, John C. Avise, Sergio M. Q. Lima, Carlos M. Rodriguez Lopez, Sofia Consuegra

Horticulture Faculty Publications

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization …

Is The Life History Flexibility Of Cold Desert Annuals Broad Enough To Cope With Predicted Climate Change? The Case Of Erodium Oxyrhinchum In Central Asia, Huiliang Liu, Yanfeng Chen, Lingwei Zhang, Jerry M. Baskin, Carol C. Baskin, Lan Zhang, Yan Liu, Daoyuan Zhang, Yuanming Zhang

Biology Faculty Publications

Interannual seasonal variability in precipitation may strongly affect the life history and growth of desert annual plants. We compared the effects of dry and wet springs and dry and wet autumns on growth and F2 seed dormancy of plants from spring (SG)- and autumn (AG)-germinated seeds of the cold desert annual Erodium oxyrhinchum. Vegetative and reproductive growth and F2 seed dormancy and germination were monitored from September 2016 to November 2020 in the sandy Gurbantunggut Desert in NW China in Central Asia. Dry autumns decreased the density of AG plants, and dry springs decreased the density of SG plants …

Diminishing Opportunities For Sustainability Of Coastal Cities In The Anthropocene: A Review, John W. Day, Joel D. Gunn, Joseph Robert Burger

Biology Faculty Publications

The world is urbanizing most rapidly in tropical to sub-temperate areas and in coastal zones. Climate change along with other global change forcings will diminish the opportunities for sustainability of cities, especially in coastal areas in low-income countries. Climate forcings include global temperature and heatwave increases that are expanding the equatorial tropical belt, sea-level rise, an increase in the frequency of the most intense tropical cyclones, both increases and decreases in freshwater inputs to coastal zones, and increasingly severe extreme precipitation events, droughts, freshwater shortages, heat waves, and wildfires. Current climate impacts are already strongly influencing natural and human systems. …

Persistent Miscalibration For Low And High Achievers Despite Practice Test Feedback In An Introductory Biology Course, Jennifer L. Osterhage

Biology Faculty Publications

Students' ability to accurately judge their knowledge is crucial for effective learning. However, students' perception of their current knowledge is often misaligned with their actual performance. The relationship between learners' perception of their performance and their actual performance on a task is defined as calibration. Previous studies have shown significant student miscalibration in an introductory biology course: students' predicted exam scores were, on average, significantly higher than their actual scores. The goal of this study was to determine whether completion of a practice test before exams would result in better performance and calibration. The hypothesis was that students who completed …

Set1 Targets Genes With Essential Identity And Tumor-Suppressing Functions In Planarian Stem Cells, Prince Verma, Courtney K. M. Waterbury, Elizabeth M. Duncan

Biology Faculty Publications

Tumor suppressor genes (TSGs) are essential for normal cellular function in multicellular organisms, but many TSGs and tumor-suppressing mechanisms remain unknown. Planarian flatworms exhibit particularly robust tumor suppression, yet the specific mechanisms underlying this trait remain unclear. Here, we analyze histone H3 lysine 4 trimethylation (H3K4me3) signal across the planarian genome to determine if the broad H3K4me3 chromatin signature that marks essential cell identity genes and TSGs in mammalian cells is conserved in this valuable model of in vivo stem cell function. We find that this signature is indeed conserved on the planarian genome and that the lysine methyltransferase Set1 …

Zebrafish Blunt-Force Tbi Induces Heterogenous Injury Pathologies That Mimic Human Tbi And Responds With Sonic Hedgehog-Dependent Cell Proliferation Across The Neuroaxis, James Hentig, Kaylee Cloghessy, Manuela Lahne, Yoo Jin Jung, Rebecca A. Petersen, Ann C. Morris, David R. Hyde

Biology Faculty Publications

Blunt-force traumatic brain injury (TBI) affects an increasing number of people worldwide as the range of injury severity and heterogeneity of injury pathologies have been recognized. Most current damage models utilize non-regenerative organisms, less common TBI mechanisms (penetrating, chemical, blast), and are limited in scalability of injury severity. We describe a scalable blunt-force TBI model that exhibits a wide range of human clinical pathologies and allows for the study of both injury pathology/progression and mechanisms of regenerative recovery. We modified the Marmarou weight drop model for adult zebrafish, which delivers a scalable injury spanning mild, moderate, and severe phenotypes. Following …

The Anti-Dipsogenic And Anti-Natriorexigenic Effects Of Estradiol, But Not The Anti-Pressor Effect, Are Lost In Aged Female Rats, Jessica Santollo, Jason A. Collett, Andrea A. Edwards

Biology Faculty Publications

Estradiol (E2) inhibits fluid intake in several species, which may help to defend fluid homeostasis by preventing excessive extracellular fluid volume. Although this phenomenon is well established using the rat model, it has only been studied directly in young adults. Because aging influences the neuronal sensitivity to E2 and the fluid intake effects of E2 are mediated in the brain, we tested the hypothesis that aging influences the fluid intake effects of E2 in female rats. To do so, we examined water and NaCl intake in addition to the pressor effect after central angiotensin II treatment in young (3-4 months), …

Effect Of Nitrogen Addition On Selection Of Germination Trait In An Alpine Meadow On The Tibet Plateau, Kun Liu, Yang Liu, Zhilong Zhang, Shiting Zhang, Carol C. Baskin, Jerry M. Baskin, Ting Liang, Haiyan Bu, Shuxia Li, Tingting Zhang, Xianliang Cui, Sa Xiao

Biology Faculty Publications

Seed germination requirements may determine the kinds of habitat in which plants can survive. We tested the hypothesis that nitrogen (N) addition can change seed germination trait-environmental filter interactions and ultimately redistribute seed germination traits in alpine meadows. We determined the role of N addition on germination trait selection in an alpine meadow after N addition by combining a 3-year N addition experiment in an alpine meadow and laboratory germination experiments. At the species level, germination percentage, germination rate (speed) and breadth of temperature niche for germination (BTN) were positively related to survival of a species in the fertilized community. …

The Giant Axolotl Genome Uncovers The Evolution, Scaling, And Transcriptional Control Of Complex Gene Loci, Siegfried Schloissnig, Akane Kawaguchi, Sergej Nowoshilow, Francisco Falcon, Leo Otsuki, Pietro Tardivo, Nataliya Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith, S. Randal Voss, Elly M. Tanaka

Biology Faculty Publications

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth …

Most Published Selection Gradients Are Underestimated: Why This Is And How To Fix It, Niels Jeroen Dingemanse, Yimen G. Araya-Ajoy, David F. Westneat

Biology Faculty Publications

Ecologists and evolutionary biologists routinely estimate selection gradients. Most researchers seek to quantify selection on individual phenotypes, regardless of whether fixed or repeatedly expressed traits are studied. Selection gradients estimated to address such questions are attenuated unless analyses account for measurement error and biological sources of within-individual variation. Estimates of standardized selection gradients published in Evolution between 2010 and 2019 were primarily based on traits measured once (59% of 325 estimates). We show that those are attenuated: bias increases with decreasing repeatability but differently for linear versus nonlinear gradients. Others derived individual-mean trait values prior to analyses (41%), typically using …

Physical Mapping Of The Anopheles (Nyssorhynchus) Darlingi Genomic Scaffolds, Míriam Silva Rafael, Leticia Cegatti Bridi, Igor V. Sharakhov, Osvaldo Marinotti, Maria V. Sharakhova, Vladimir A. Timoshevskiy, Giselle Moura Guimarães-Marques, Valéria Silva Santos, Carlos Gustavo Nunes Da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei

Biology Faculty Publications

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping …

Intragenic Dna Methylation Regulates Insect Gene Expression And Reproduction Through The Mbd/Tip60 Complex, Guanfeng Xu, Hao Lyu, Yangqin Yi, Yuling Peng, Qili Feng, Qisheng Song, Chengcheng Gong, Xuezhen Peng, Subba Reddy Palli, Sichun Zheng

Entomology Faculty Publications

DNA methylation is an important epigenetic modification. However, the regulations and functions of insect intragenic DNA methylation remain unknown. Here, we demonstrate that a regulatory mechanism involving intragenic DNA methylation controls ovarian and embryonic developmental processes in Bombyx mori. In B. mori, DNA methylation is found near the transcription start site (TSS) of ovarian genes. By promoter activity analysis, we observed that 5′ UTR methylation enhances gene expression. Moreover, methyl-DNA-binding domain protein 2/3 (MBD2/3) binds to the intragenic methyl-CpG fragment and recruits acetyltransferase Tip60 to promote histone H3K27 acetylation and gene expression. Additionally, genome-wide analyses showed that the peak …

Effect Of Temperature On Heart Rate For Phaenicia Sericata And Drosophila Melanogaster With Altered Expression Of The Trpa1 Receptors, Nicole T. Marguerite, Jate Bernard, Douglas A. Harrison, David Harris, Robin L. Cooper

Biology Faculty Publications

The transient receptor potential (TrpA—ankyrin) receptor has been linked to pathological conditions in cardiac function in mammals. To better understand the function of the TrpA1 in regulation of the heart, a Drosophila melanogaster model was used to express TrpA1 in heart and body wall muscles. Heartbeat of in intact larvae as well as hearts in situ, devoid of hormonal and neural input, indicate that strong over-expression of TrpA1 in larvae at 30 or 37 °C stopped the heart from beating, but in a diastolic state. Cardiac function recovered upon cooling after short exposure to high temperature. Parental control larvae (UAS-TrpA1) …

Mechanisms Of Cadmium-Induced And Epidermal Growth Factor Receptor Mutation-Driven Lung Tumorigenesis, Hsuan-Pei Lin

Theses and Dissertations--Toxicology and Cancer Biology

Cadmium (Cd) is a ubiquitous pollutant in the environment and a known carcinogen for lung cancer. Cd has been shown to act as a weak mutagen, which suggests that it may exert tumorigenic effect through non-genotoxic ways, such as epigenetic mechanisms. The goal of this project is to investigate the mechanisms of Cd carcinogenesis focusing on the role of lncRNA dysregulations. The Cd-exposed cells formed significantly more colonies in soft agar, displayed cancer stem cell (CSC)-like property and formed tumors in nude mice. Mechanistically, the lncRNA microarray analysis revealed that chronic Cd exposure dysregulates lncRNA expressions. Q-PCR analysis confirmed the …

Effects Of Sleep Fragmentation On The Progression Of Alzheimer’S Disease, Lindsay Beechem

Lewis Honors College Capstone Collection

Alzheimer’s Disease (AD) is a neurodegenerative disease that is characterized by amyloid-beta (Aβ) plaques, neurofibrillary tangles, neuronal death, and profound cognitive impairment. Previous studies have indicated that increased Aβ and alterations in the daily sleep-wake cycle are early risk factors and possible predictors of AD. Acute sleep deprivation decreases Aβ clearance, and increased Aβ levels stimulate neuroinflammation and accelerate loss of neurons and synapses. Likewise, it has been shown that there are higher rates of sleep disorders in AD patients. However, limited studies have investigated whether sleep fragmentation accelerates the progression of AD pathology. This partial review will discuss experiments …

An Exploration Of Sleep Fragmentation And Sleep Enhancement In Mice, Frannie Salisbury

Lewis Honors College Capstone Collection

Alzheimer’s Disease (AD) is a neurodegenerative disease that is can be defined by amyloid beta (Aβ) plaques, neurofibrillary tangles, and neuronal death. AD patients have characteristically fragmented sleep, with frequent nighttime awakenings and daytime naps. Decreased clearance of Aβ from disrupted sleep may be a contributing factor in the progression of AD. This study investigated how sleep fragmentation effected the progression of AD in 3xTgAD mice. Results showed that sleep fragmented mice had significantly more Aβ build-up in the hippocampus and thus greater progression of AD when compared to control mice. Improving sleep may be one way to reduce the …

Seed Priming With Phytohormones: An Effective Approach For The Mitigation Of Abiotic Stress, Mohammad Saidur Rhaman, Shahin Imran, Farjana Rauf, Mousumi Khatun, Carol C. Baskin, Yoshiyuki Murata, Mirza Hasanuzzaman

Biology Faculty Publications

Plants are often exposed to abiotic stresses such as drought, salinity, heat, cold, and heavy metals that induce complex responses, which result in reduced growth as well as crop yield. Phytohormones are well known for their regulatory role in plant growth and development, and they serve as important chemical messengers, allowing plants to function during exposure to various stresses. Seed priming is a physiological technique involving seed hydration and drying to improve metabolic processes prior to germination, thereby increasing the percentage and rate of germination and improving seedling growth and crop yield under normal and various biotic and abiotic stresses. …