Digital Commons Network^™

Draft Genome Sequencing Of Three Glutaraldehyde-Tolerant Bacteria From Produced Water From Hydraulic Fracturing, Stephen Techtmann, Andrew L. Baldwin, Dotun Aluko, Justin Andersen, Cole Becker, Grace Chandler, Steve Forgrave, Madelyn Jones, Ina Klasner, Jared Martini, Noah Mason, Ryleigh Parsons, Nick Peterson, Erik Reynolds, Lydia Schroeder

Michigan Tech Publications, Part 1

Here, we report the draft genome sequence of three glutaraldehyde-resistant isolates from produced water from hydraulic fracturing operations. The three strains were identified as sp. strain G11, sp. strain G15, and sp. strain G16. The genome sequences of these isolates will provide insights into biocide resistance in hydraulic fracturing operations.

An Exploration Of Trex1 Variants Of Uncertain Significance And Their Potential Impact On Autoimmunity In Systemic Lupus Erythematosus And Aicardi-Goutieres Syndrome, Jordan Peters

JSU Student Symposium 2022

TREX1 is a gene responsible for encoding a 3'-to-5' DNA exonuclease in human cells. Under normal conditions TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair. Mutations in TREX1, which result in the absence of the 3'-to-5' DNA exonuclease and the intracellular accumulation of unneeded DNA and RNA, have been shown to trigger immune dysfunction leading to diseases such as systemic lupus erythematosus (SLE) and Aicardi-Goutières Syndrome (AGS). The goal of this study is to determine the potential impact of a TREX1 missense mutation with uncertain clinical significance (VUS). …

Deficiency Of Ataxia Telangiectasia-Mutated Kinase (Atm) Preserves Heart Function By Affecting Cardiac Remodeling In Response To Western-Type Diet (Wd) In Female Mice, Paulina Ramirez

Tennessee Posters at the Capitol [2022]

WD and deficiency of ATM protein independently associates with heart disease. Previous work demonstrated that WD in male ATM deficient mice induces accelerated body weight gain and heart dysfunction (Am J Physiol Heart Circ Physiol. 2021;320:H2324-H2338). Conversely, WD in female ATM deficient mice attenuates weight gain and preserves heart function (unpublished). Here, we investigated the mechanism by which ATM deficiency preserves heart function in female mice. Female wild-type (WT) and ATM heterozygous knockout (hKO) mice, aged 6 weeks, were fed with normal chow (NC) or WD for 14 weeks. Heart sections were stained with Masson’s trichrome to quantify fibrosis, TUNEL-stained …

Long Term Estrogen Loss Worsens Heart Function In Aged Female Mice, Pamela Avendaño-Rubí

Tennessee Posters at the Capitol [2022]

Heart disease is the leading cause of death worldwide and according to the American Heart Association, the risk of HD in aging menopausal women doubles compared to men of the same age. Excessive contractility of blood vessels is a common feature in heart disease. Clinical and animal studies further support that estrogen loss worsen the contractility in the heart but the details remain unclear. Thus, the overall goal of this work was to examine how the timing and duration of estrogen loss affects heart failure. Our hypothesis is that long-term estrogen loss following heart failure worsens cardiac function of the …

Effects Of Specific Blocking Buffers On Histone H2b Antibodies, Noha Al-Saadi, Grace Mix, Mardasia Thompson, Elin Zaman

JSU Student Symposium 2022

Mammalian histones have been known to be one of the most highly alkaline proteins found in the nuclei. Their main function is to organize DNA into chromosomes and regulate transcription. An example of a histone would be Histone H2B, which this project focuses heavily on. Histone H2B has been seen to bind poorly to antibodies and result in a weak signal. The goal of this project is to test a multitude of blocking buffers, in triplicate, in order to find a blocking buffer that can obtain the strongest signal from the antibodies being tested. Through the use of protein gel …

Antioxidant Content In Plant-Based Diets Versus Meat-Based Diets, Lia Meadows, Peeper Walker, Reveca Tomas

JSU Student Symposium 2022

The result of naturally occurring free radicals in the body are oxidative-stress-related damages to cells, tissues, and biomolecules. Oxidative stress occurs when the balance between reactive oxygen species (ROS) outnumbers antioxidants, producing negative effects. Antioxidants exist as a natural defense mechanism utilized by the body. This defense exists in two distinct forms: enzymatic and non-enzymatic antioxidants. Non-enzymatic antioxidants consist of vitamins and bioactive compounds, such as phenols. In previous studies, plant-based diets showed promising results in reducing damage caused by oxidative-stress. The purpose of this study was to determine the extent to which antioxidant concentration differs between meat-based diet and …

Genetic Assessment Of Congenital Stationary Night Blindness-Associated Trpm1 Variants Of Uncertain Significance In C. Elegans, Sara Morris

JSU Student Symposium 2022

Congenital stationary night blindness (CSNB) is a disorder of the eye that impacts the ability to see in low to no light conditions. It occurs in horses and humans. TRPM1 encodes for a member of the transient receptor potential melastatin subfamily of transient receptor potential ion channels. Mutations in TRPM1 have been identified by previous researchers in horses with leopard complex pattern (LCP) suffering also from CSNB. Phenotypic changes in these horses are a loss of spotted coat pattern. An attempt was made to locate variants of uncertain significance (VUS) in TRPM1 that had been previously identified in horses with …

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

Silver Nanoparticles Synthesized By Nd: Yag Laser Ablation Technique: Characterization And Antibacterial Activity, Sahar Naji Rashid Msc., Kadhim A. Aadim Ph.D., Awatif Sabir Jasim Ph.D.

Karbala International Journal of Modern Science

The pulsed laser ablation in liquid (PLAL) technique can produce high purity nanoparticles, it is a top-down physical method based on the principle of dividing metal ion bulk precursors into metal atoms, this method was used in this work to synthesize silver nanoparticles (AgPNs) by using Nd: YAG laser with two wavelengths (355 nm) and (532 nm) at energies (500 mJ) and (600 mJ) respectively, with the number of pulses (500, 600, 700, 800, and 900 pulses) for each wavelength. The properties of the prepared nanoparticles were investigated by UV-Vis, XRD, SEM with EDX, AFM, and FTIR analysis and then …

Simulation And Improvement Of The Efficiency Of The Cfts Solar Cell Using Scaps-1d, Hardan T. Ghanem Dr., Ayed N. Saleh, Muaamer A. Kamil

Karbala International Journal of Modern Science

A simulation of the AZO/i-ZnO/CdS/CFTS solar cell was carried out using SCAPS software. The results were obtained (Voc=0.55 V, Jsc=6.2 mA/cm², FF=39 %, ɳ=1.35 %). Simulation results were compared with experimental research and we got convergence in the results (Voc=0.56 V, Jsc=6.5 mA/cm², FF=37 %, ɳ=1.37 %). The simulated solar cell is improved by increasing the doping concentration and thickness of the buffer and absorption layers. The efficiency of the solar cell was improved to ɳ=4.29%, fill factor FF=52.92%, open circuit voltage Voc=0.74 V and short circuit current Jsc=10.8 mA/cm²

Molecular Characterization Of Wild Pleurotus Ostreatus (Mw457626) And Evaluation Of Β-Glucans Polysaccharide Activities, Ghazwan Q. Hasan Ph.D., Shimal Y. Abdulhadi Ph.D.

Karbala International Journal of Modern Science

Pleurotus ostreatus is a common cultivated edible mushroom worldwide. The fruiting bodies of P. ostreatus is a rich source of a β-glucans polysaccharide. The current study aimed to investigate the effectiveness of β-glucans as a natural polysaccharide produced by P. ostreatus as an antioxidant, antimicrobial, and anticancer. The molecular identification of P. ostreatus isolate was confirmed by Internal Transcribed Spacer (ITS) sequence. The sequence alignment and phylogenetic evolutionary relationship of studied ITS sequence were performed against some deposited sequences in GenBank. The analysis of high-performance liquid chromatography (HPLC) as well as the result of fourier transform infrared spectroscopy …

Using Ecological Niche Modeling To Predict The Response Of Hydrocotyle Bonariensis To Global Climate Change, Rachel Bonner, Laura K. Dease, Elizabeth A. Hughston

JSU Student Symposium 2022

Coastal dune habitats provide valuable ecosystem services but are declining globally due to the interacting effects of multiple stressors, including global climate change (GCC). To explore the potential severity of the effects of GCC on dune plant communities of the Northern Gulf of Mexico and surrounding areas, we modeled the fundamental bioclimatic niche of a dune plant species, largeleaf pennywort (Hydrocotyle bonariensis Comm. ex Lam.), in this region. We then projected its niche to estimate habitat suitability under current and future environmental conditions. Occurrence records were mined from the Global Biodiversity Information Facility, cleaned, then thinned by spatial filtering, …

Characterization Of Anti-Microbial Properties Of Excrement And Functional Microbiome Of New World Vultures In Alabama, Bridgette Gray

JSU Student Symposium 2022

Two distinct species of New World vultures are native to North America and inhabit Alabama, black vultures (Coragyps atratus) and turkey vultures (Cathartes aura). They are scavengers that consume decaying carcasses or carrion, which helps reduce the spread of disease. Vultures are susceptible to declining population numbers as they have been trapped and killed due to the belief that they spread disease, additionally contact with poisons and habitat destruction have also led to their decline. Currently, these two vultures are one of the seven vulture species with least concern and stable in Alabama and the world. However, it is important …

Diving Into The Unknown: A Genetic Investigation Of Type-2 Diabetes-Associated Insr Variants Of Uncertain Significance, Trinity Elston

JSU Student Symposium 2022

Type 2 diabetes is a complex metabolic disorder with interactions between genetic and environmental factors, making it more complicated to understand the clinical implications of identified genetic variants and disease pathology. Many of the diabetes-associated variants are currently classified as VUS and occur within the genes involved in insulin signaling and regulation, so we turned our focus on the human INSR gene. INSR encodes the insulin receptor protein that plays a major role in insulin signaling. Furthermore, C. elegans provides a simple model system to examine the functional consequences of these diabetes-associated VUS. We examined INSR diabetes-associated VUS through the …

Butterfly Eyespots Evolved Via Cooption Of An Ancestral Gene-Regulatory Network That Also Patterns Antennae, Legs, And Wings, Suriya Narayanan Murugesan, Heidi Connahs, Yuji Matsuoka, Mainak Das Gupta, Galen J. Tiong, Manizah Huq, Thomas Werner, Et. Al.

Michigan Tech Publications, Part 1

Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via cooption of parts of an ancestral appendage gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster most closely with antennae, relative to multiple other tissues. Furthermore, three genes essential for eyespot development, (), (), and (), share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of -regulatory elements (CREs) for and led to the loss of eyespots, antennae, legs, and also wings, demonstrating that these CREs are highly …

Summer Distribution And Day Roost Characteristics Of Eastern Small-Footed Bats (Myotis Leibii) In West-Central Arkansas, Valerie Marie Kearny

Student Theses and Dissertations

Information on summer distribution and diurnal roosting is lacking for the imperiled, rock-roosting Myotis leibii, a species threatened by habitat loss and White-nose Syndrome. I aimed to 1) identify diurnal, summer roost locations in the greater Ouachita Mountains of Arkansas, and 2) determine roost habitat characteristics at the local, landscape, and roost-level scales. Using acoustic monitoring, rock searches, mist-netting, and temperature monitoring in 2019 and 2020, I found M. leibii in an aggregated distribution across the landscape roosting either solitarily or in small groups in the Rich Mountain-Black Fork Mountain, Mount Magazine, and Mount Nebo areas under sparse canopy cover, …

Migration Ecology Of Female Indiana Bats, Arin Michelle Vann

Student Theses and Dissertations

The Indiana bat (Myotis sodalis) has been listed as a federally endangered species since 1967 due to numerous natural and anthropogenic threats. Research on the species has focused on hibernacula and maternity colonies, but data gaps exist in portions of their range. To prevent further decline, migration resources need protection, but management practices are difficult to implement without having precise data on migration routes. I documented spring migration in Arkansas using aerial and ground telemetry during 2017–2018. Radio transmitters were affixed to 52 female M. sodalis during 2017 and 2018 of which 23 were successfully tracked. I located roost trees …

Relationship Between Oxidative Stress And Lifespan In Daphnia Pulex, Benedicth Ukhueduan, Charles Schumpert, Eunsuk Kim, Jeffry L. Dudycha, Rekha C. Patel

Faculty Publications

Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the …

Understanding The Modus Operandi Of Class Ii Knox Transcription Factors In Secondary Cell Wall Biosynthesis, Akula Nookaraju, Shashank K. Pandey, Yogesh Ahlawat, Chandrashekhar P. Joshi

Michigan Tech Publications, Part 1

Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are …

Diversity, Biology, And History Of Psilocybin-Containing Fungi: Suggestions For Research And Technological Development, R. C. Van Court, K. W. Meyer, M. S. Wiseman, Daniel J. Ballhorn, K. R. Amses, J. C. Slot, B.T. M. Dentinger, R. Garibay-Orijel, J. K. Uehling

Biology Faculty Publications and Presentations

Therapeutic use of psilocybin has become a focus of recent international research, with preliminary data showing promise to address a range of treatment-resistant mental health conditions. However, use of psilocybin as a healing entheogen has a long history through traditional consumption of mushrooms from the genus Psilocybe. The forthcoming adoption of new psilocybin-assisted therapeutic practices necessitates identification of preferred sources of psilocybin; consequently, comprehensive understanding of psilocybin-containing fungi is fundamental to consumer safety. Here we examine psilocybin producing fungi, discuss their biology, diversity, and ethnomycological uses. We also review recent work focused on elucidation of psilocybin biosynthetic production pathways, especially …

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 …

Detection Of Methicillin-Resistant Staphylococcus Aureus Infections Using Molecular Methods, Fred C. Tenover, Isabella A. Tickler

Biology Faculty Publications

The application of molecular detection methods for bacterial pathogens has dramatically improved the outcomes of septic patients, including those with methicillin-resistant Staphylococcus aureus (MRSA) infections. Molecular methods can be applied to a variety of clinical specimens including nasal swabs, growth in blood culture bottles, and wounds. While data show that the overall accuracy of molecular tests for MRSA is high, results can be confounded by the presence of multiple staphylococcal species in a specimen, insertions and deletions of DNA in and around the Staphylococcal Cassette Chromosome mec (SCCmec) element, and point mutations in mecA. Herein, we explore the complexities of …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Spring Migration Behavior And Summer Habitat Associations Of Female Indiana Bats (Myotis Sodalis) In Arkansas, Heather N. Custer

Student Theses and Dissertations

Since 1967, the Indiana bat (Myotis sodalis) has been federally listed. Range-wide research continues to expand our understanding of the behaviors of the species, but knowledge gaps still remain. Specifically, information regarding spring migration behavior and associated summer habitat of female Indiana bats that overwinter in Arkansas is lacking. Accordingly, objectives of this research included determining direction and distance of migrating female Indiana bats, locating maternity colonies and roosts, estimating maternity colony size, home ranges, and core areas. Migration directions and distances varied among bats, and a maternity colony was located in Arkansas in 2019 that subsequently used artificial roosts …

Helminths Of Thomomys Species (Rodentia: Geomyidae) Of Oregon, Malorri Rene Hughes

Dissertations and Theses

Although often viewed as inconsequential, parasites have significant ecological and evolutionary importance, and studying them can generate knowledge regarding their environments and their hosts. Helminths (intestinal parasites) infecting Western pocket gophers (Thomomys species) in Oregon had been documented based only on morphology prior to this study. Basing parasite identification solely on morphology is problematic because the characteristics used to identify species can be vague or similar, leading to misidentification or obscuring the true biodiversity present. Using molecular markers to verify species present not only is more reliable but also can be informative in terms of the host-parasite association. To …

To Better Engage Students, Instructors Should Create Lab Exercises With Real-World Examples., Autumn Kelsch

Research on Capitol Hill

USU senior Autumn studies biology here in Logan and led and funded this project herself through a student grant. ‘Elementary Microbiology’ is a required course for many medical fields, and traditionally relies on several pre-determined research projects in class. However, educators suggest that students gain more from open-ended projects where the answer is unknown and the students’ findings contribute to our knowledge on the subject. When Autumn was hired as a teaching assistant for this course at USU, she developed and created a project where students look for bacteria in soil samples that may help fight infections. She now hopes …

Understanding The Decline In Successful Cattle Pregnancies, Andre Tu Nguyen

Research on Capitol Hill

USU junior Andre, a local Loganer, studies computer science and biology.He has been working in an animal science lab. Over time, we have seen a decline in successful dairy cattle pregnancies. This is a huge cause for concern for Utah, with milk sales at an estimated value of $405 million in 2020. Andre’s work has been in studying a certain protein in pregnant cattle; now that he has determined there is a decrease in this protein over the course of the pregnancy, he hopes to see whether that might impact its viability. Andre got involved in research in a high …

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 …

Temperature-Induced Multi-Species Cohort Effects In Sympatric Snakes, Richard B. King

Faculty Articles, Papers, and Other Scholarship

In reptiles, reproductive maturity is often determined by size rather than age. Consequently, growth early in life may influence population dynamics through effects on generation time and survival to reproduction. Because reproductive phenology and pre- and post-natal growth are temperature dependent, environmental conditions may induce multi-species cohort effects on body size in sympatric reptiles. I present evidence of this using 10 years of neonatal size data for three sympatric viviparous snakes, Dekay's Brown snakes (Storeria dekayi), Red-bellied Snakes (S. occipitomaculata), and Common Garter snakes (Thamnophis sirtalis). End-of-season neonatal size varied in parallel across species such that snout–vent length was 36%–61% …

Retinal Horizontal Cells Use Different Synaptic Sites For Global Feedforward And Local Feedback Signaling, Christian Behrens, Shubhash Chandra Yadav, Maria M Korympidou, Yue Zhang, Silke Haverkamp, Stephan Irsen, Anna Schaedler, Xiaoyu Lu, Zhuohe Liu, Jan Lause, François St-Pierre, Katrin Franke, Anna Vlasits, Karin Dedek, Robert G Smith, Thomas Euler, Philipp Berens, Timm Schubert

Faculty, Staff and Students Publications

In the outer plexiform layer (OPL) of the mammalian retina, cone photoreceptors (cones) provide input to more than a dozen types of cone bipolar cells (CBCs). In the mouse, this transmission is modulated by a single horizontal cell (HC) type. HCs perform global signaling within their laterally coupled network but also provide local, cone-specific feedback. However, it is unknown how HCs provide local feedback to cones at the same time as global forward signaling to CBCs and where the underlying synapses are located. To assess how HCs simultaneously perform different modes of signaling, we reconstructed the dendritic trees of five …