Digital Commons Network^™

Comparative Transcriptomic Analysis And Structure Prediction Of Novel Newt Proteins, Abijeet Singh Mehta, Agustin Luz-Madrigal, Jian-Liang Li, Panagiotis A. Tsonis, Amit Singh

Biology Faculty Publications

Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved …

Integrated Pest Management In The Academic Small Greenhouse Setting: A Case Study Using Solanum Spp. (Solanaceae)., Daniel S. Hayes, Ingrid E. Jordon-Thaden, Jason T. Cantley, Angela J. Mcdonnell, Christopher T. Martine

Faculty Journal Articles

Premise

Botanical faculty and staff at academic institutions are often tasked with establishing and/or caring for plant collections held in small greenhouse facilities. Once plants are in place, an especially acute challenge is managing plant pest/pathogen populations. Integrated pest management (IPM) approaches are an excellent option, but few examples exist in the literature of successful programs that have been developed in academic small greenhouse settings.

Methods and Results

Over several years, we developed an IPM program for two small research greenhouses on the campus of a primarily undergraduate institution where hundreds of plants have been grown for studies in the …

The Database Of Identified Root-Specific Genes And Their Promoters In Maize, Sorghum, And Soybean, Gleb Moisseyev, Divith Rajagopal, Alix Cui, Kiyoul Park, Edgar B. Cahoon, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Root genes are essential to plants as they dictate factors such as the strength of the plant, reproductivity success, etc. However, in the status quo, studies on root genes are simply ineffective. To be more specific, currently, there are very few online databases of root genes and promoters, which essentially deters root gene studies from being successful. To fix this problem, our lab constructed and coded an online database that contains information about the roots of maize, soybean, and sorghum. We collected 1200 root genes and assessed the strength and success of a given gene. This online database of these …

The Influence Of Mir-322 On Skeletal Muscle Differentiation, Miles Alexander Soyer

Legacy Theses & Dissertations (2009 - 2024)

Skeletal muscle plays a crucial role in coordinating voluntary movement and accounts for nearly 50% of total body mass. Dysregulation in skeletal muscle development is known to cause muscle degenerative diseases including the devastating Duchenne Muscular Dystrophy (DMD). The majority of the biological studies investigating muscle development were based on myogenic transcription factors and signaling molecules including: Pax7, Myf5, MyoD, WNT, TGF-β and BMP. After the discovery of non-coding RNAs including microRNAs, it was postulated that these molecules could regulate gene expression and thus affect differentiation and development. MicroRNAs are small non-coding RNAs (~17-25 nucleotides) that regulate gene expression negatively …

Does Thermotolerance In Daphnia Depend On The Mitochondrial Function?, Rajib Hasan

Electronic Theses and Dissertations

Thermotolerance limit in aquatic organism is set by the ability to sustain aerobic scope to sudden temperature shifts. This study tested the genetic and plastic differences in thermotolerance of Daphnia that can be explained by the differences in the ability to retain mitochondrial integrity at high temperatures. Five genotypes with different biogeographic origins were acclimated to 18^ᵒC and 25^ᵒC. We developed a rhodamine 123 in-vivo assay to measure mitochondrial membrane potential and observed higher fluorescent in heat damaged tissues as the disruption of the mitochondrial membrane potential. Significant effects on temperature tolerance were observed with CCCP …

Designing And Sample Size Calculation In Presence Of Heterogeneity In Biological Studies Involving High-Throughput Data., Sudhir Srivastava

Electronic Theses and Dissertations

The designing and determination of sample size are important for conducting high-throughput biological experiments such as proteomics experiments and RNA-Seq expression studies, thus leading to better understanding of complex mechanisms underlying various biological processes. The variations in the biological data or technical approaches to data collection lead to heterogeneity for the samples under study. We critically worked on the issues of technical and biological heterogeneity. The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values (MVs) and data heterogeneity. We considered a proteomics data set generated from human kidney …

The Transcriptome Of The Veiled Chameleon (Chamaeleo Calyptratus): A Resource For Studying The Evolution And Development Of Vertebrates, Brendan John Pinto, Daren C. Card, Todd A. Castoe, Raul E. Diaz Jr., Stuart V. Nielsen, Paul A. Trainor, Tony Gamble

Biological Sciences Faculty Research and Publications

Purpose

The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo‐devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking.

Methods

To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) …

Shallow- Water Hardbottom Communities Support The Separation Of Biogeographic Provinces On The West- Central Florida Gulf Coast, Shelby Eagan

HCNSO Student Theses and Dissertations

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral …

Comparative Analysis Of The Aroma Components In Mainstream Aerosol Of Heat-Not-Burn Tobacco Products, Wang Ying, Yang Wenbin, Wang Chong, Chen Jiabin, Li Jianzheng, Xie Tao, Ji Xiong

Food and Machinery

In order to investigate the release characteristics of aroma components in mainstream aerosol of heat-not-burn tobacco products, three popular commercial products were smoked. The aroma components were analyzed by gas chromatography-mass spectrometry (GC/MS). The results showed that: ① The release of neutral and basic aroma components per unit puff was higher than that of acids flavors. ② The total release of aroma components per unit puff of sample I was higher than that of sample L which was higher than that of sample G. ③ The quality and quantity of aroma components which originated from natural tobacco leaves, were lower …

Life-History Parameters Of Striacosta Albicosta (Lepidoptera: Noctuidae) Under Laboratory Conditions, Débora G. Montezano, Thomas E. Hunt, Alexandre Specht, Priscila M. C. Luz, Julie A. Peterson

Department of Entomology: Faculty Publications

Striacosta albicosta (Smith) is a key pest of maize and dry beans in North America. It has expanded its distribution from the western Great Plains of the United States to the Great Lakes region in the United States and Canada. There has been limited research on the baseline biological aspects of this insect under controlled conditions. The objective of this study was to detail the biological parameters of S. albicosta feeding on an artificial diet under laboratory conditions. Overall survival from neonate to adult at 26.6 ± 1°C was 36.72% and the total developmental time was approximately 110 d. Survival …

Tropic Transfer And Bioaccumulation Of Lead Along Soil-Plant-Aphid-Ladybird Food Chain, Mohod Irfan Naikoo, Mudasir Ifran Dar, Fareed Ahmad Khan, Fariha Raghib, N. Rajakaruna

Biological Sciences

Lead (Pb) contamination of agroecosystems is a serious issue as Pb is a persistent pollutant that is retained in soil for long, causing toxicities to organisms. This study examines biotransfer of Pb from soils treated with different concentrations of Pb through a broad bean (Vicia faba L.)–aphid (Aphis fabae Scop.)–ladybird (Coccinella transversalis Fabricius) food chain and its consequent inference for natural biological control, the ladybird. The soil was amended with Pb at the rates of 0, 25, 50, 75 and 100 mg kg⁻¹(w/w). The amount of Pb in plant, aphid and ladybird increased in a dose-dependent manner …

Review Of Grosphus Simon, 1880, With Description Of Teruelius Gen. N., A New Buthid Genus From Madagascar (Scorpiones: Buthidae), Graeme Lowe, František Kovařík

Euscorpius

We review the taxonomy of the Madagascar endemic buthid genus Grosphus Simon, 1880. We split the genus and describe Teruelius gen. n. on the basis of nine morphological characters, six of them new for Grosphus: positions of trichobothria d₂ on pedipalp femur and Eb₃ on chela manus, number of pectine teeth, shape of female basal pectinal tooth, form of hemispermatophore capsule posterior lobe, spiracle shape, metasoma I ventromedian carination, telotarsal setation and UV fluorescence. We discuss functional and taxonomic aspects of these characters, and propose that Teruelius gen. n. is monophyletic, while Grosphus (sensu stricto) is paraphyletic. …

Play Behavior And The Development Of Boldness And Caution In Juvenile Belding’S Ground Squirrels (Urocitellus Beldingi), Madelene Shehan

Master's Theses

The ubiquity of play among juvenile mammals suggests it provides adaptive benefits, potentially through influences on the development of temperament in young animals. Juvenile Belding’s ground squirrels (Urocitellus beldingi) must balance competing demands for boldness and caution imposed by the fundamental trade-off between their short active season and their vulnerability to predation. In this study, I evaluated whether play helps to facilitate the development of an appropriate balance between boldness and caution in juvenile U. beldingi.I observed the play behavior of juvenile U. beldingiand conducted flight-initiation distance tests to measure boldness-caution at the beginning and toward …

The Evolutionary And Functional Roles Of Synonymous Codon Usage In Eukaryotes, Zhen Peng

Arts & Sciences Graduate Student Theses and Dissertations

Most amino acids are encoded by multiple synonymous codons. Although alternative usage of synonymous codons does not affect the amino acid sequences of proteins, researchers have been reporting evidence for functional synonymous codon usage at the species- and gene-specific levels for over four decades. It has been shown that variations in synonymous codon usage can affect phenotypes through diverse mechanisms such as shaping translation efficiency and mRNA stability. On the other hand, the common view that cellular and organismal phenotypes are primarily determined by proteins whose functions are primarily determined by amino acid sequences, often drives the assumption that synonymous …

Mesopredator Distribution, Abundance And Potential Competition With The American Burying Beetle (Nicrophorus Americanus) At Fort Chaffee Joint Maneuver Training Center, Karisa Fenton

Theses and Dissertations from 2019

The American burying beetle (Nicrophorus americanus, hereafter ABB) was listed as an endangered species in 1989 and many hypotheses have been developed to explain their rangewide decline. I investigated the carcass competition hypothesis that implicates increased competition between vertebrate scavengers and ABBs for appropriate-sized carcasses as a cause for ABB decline. Predators of medium size that occupy an intermediate trophic level (hereafter mesopredators) are potential competitors for carcasses. I used camera trapping to assess mesopredator abundances in nine different habitats at Fort Chaffee Joint Maneuver Training Center (FCJMTC) in western Arkansas because this area supports the largest known population of …

Development Of Long-Acting Nanoformulated Abacavir Protides, Zhiyi Lin, Howard E. Gendelmant

Theses & Dissertations

Combination antiretroviral therapy (cART) for treatment of human immunodeficiency virus (HIV) infection demands life-long regimen adherence. Treatment interruptions lead to a lack of virologic control and the emergence of viral mutations and drug resistance. To address these, our laboratory developed long-acting (LA) parenteral administered nanoformulated abacavir prodrug (NMABC) by formulating myristoylated abacavir (MABC) with poloxamer 407 as stabilizer, which sustained ABC levels for up to 2 weeks with low levels of active drug metabolite (CBV-TP). To more significantly extend the apparent half-life of ABC and improve its antiretroviral activities, we developed second generation long-acting ABC prodrugs by ProTide technologies. This …

Developing Targeted Therapy Against Pancreatic Cancer, Garima Kaushik

Theses & Dissertations

Not available.

Med12 Mutations Promote Castration-Resistant Prostate Cancer Through Hyperactivated Gli3/Shh Signalling, Soundharrya Muthukumar

Theses & Dissertations

When cells of the prostate gland start growing uncontrollably, it results in cancer due to genetic aberrations. The development and progression of prostate cancer depend on androgenic stimulation. Although prostate cancer is temporarily treated by depriving a tumor of androgen, the patient relapses getting a castration-resistant form of the disease called castration-resistant prostate cancer (CRPC). CRPC can specifically develop through crosstalk of androgen receptor signalling pathways. One such pathway that is of specific interest in this paper is the MED12 regulated SHH signalling pathway. The mediator is a signal processor that helps in the transduction of gene-specific transcription factors to …

A Gradient Of Pollination Specialization In Three Species Of Bolivian Centropogon, Laura Lagomarsino, Nathan Muchhala

Biology Department Faculty Works

PremiseClosely related plant species with overlapping ranges often experience competition for pollination services. Such competition can select for divergence in floral traits that attract pollinators or determine pollen placement. While most species in Centropogon(Campanulaceae: Lobelioideae) have flowers that suggest adaptation to bat or hummingbird pollination, actual pollinators are rarely documented, and a few species have a mix of traits from both pollination syndromes. We studied the pollination biology of a “mixed‐syndrome” species and its co‐occurring congeners to examine the relationship between floral traits and visitation patterns for Centropogon.Methods Fieldwork at two sites in Bolivian cloud forests involved filming floral visitors, …

Saturated Hydrocarbon Analysis Of Liberty State Park Soils, Matthew Chi-Hymn Cheung

Theses, Dissertations and Culminating Projects

Contaminated soils have been a concern in New Jersey since the Industrial Revolution (Gallagher, 2008). One site in particular has a variety of contaminants and is near the coast of Jersey City in Liberty State Park. Liberty State Park has been impacted by three significant changes. It was first a wetland in the 1600s, then became a New York dump site, and finally a railyard for the Central Railroad of New Jersey (Stanislaw, 2013). The whole land mass has mixed contaminants, including trace elements, heavy metals, organic wastes, and organic compounds. Currently, most of the state park has been dredged …

Ecometric Estimation Of Present And Past Climate Of North America Using Crown Heights Of Rodents And Lagomorphs: With Application To The Middle Miocene Climatic Optimum, Julia Schap

Electronic Theses and Dissertations

Continental scale studies on ungulate crown heights in relation to climate and habitat changes have revealed a correlation between increasing hypsodonty and a shift to more arid environments. Small mammals have been shown to adapt to changing habitats millions of years earlier than larger mammals. In this study I examined fossil localities throughout the last 37 Ma across North America. Diversity of rodents and lagomorphs were analyzed through this time period, with examination of community structure characterized by relative percentages of taxa with different crown heights. Overall, a decrease in precipitation and temperature was found across North America from 37 …

Isolation, Analysis, And Partial Characterization Of An Inhibitor Of Neisseria Gonorrhoeae, Natania Paul

Undergraduate Honors Theses

There is an emerging threat of Neisseria gonorrhoeae strains that are resistant to all antibiotics. Because of this, the purpose of this research is to isolate, analyze, and partially characterize a new inhibitor(s) of N. gonorrhoeae. Since there is an unknown molecule secreted by Candida albicans that inhibits N. gonorrhoeae, this molecule can be partially characterized using ¹H NMR Spectroscopy to assist in the development of a new antibiotic compound. It was hypothesized that quorum-sensing molecules, trans, trans- farnesol, tyrosol, phenylethyl alcohol, and tryptophol, could be possible candidates for the inhibitor. Because of this, ¹H …

Age-Related Tick Infestation Patterns In Springtime Migratory Passerines, Matthew Dunning

Honors Theses

To test the hypothesis that younger migrants are more prone to arrive at stopover sites on the northern coast of the Gulf of Mexico with ticks than adult migrants, 2177 migratory passerines were screened for ticks at Gulf Coast sites in Texas and Louisiana. Fifty eight (2.7%) were infested with ticks with 28 (1.3%) being young birds and 30 (1.4%) being adult birds. The body condition of the birds was assessed to determine if tick infestation had negative consequences and if the severity of consequences varied between ages. I found no relationship of age with the prevalence of a tick …

All For One And One For All: The Emergent Intelligence Of Ant Colonies, Kristen Pitts

Scientific Kenyon: The Neuroscience Edition

No abstract provided.

Genomic Signatures Of Extensive Inbreeding In Isle Royale Wolves, A Population On The Threshold Of Extinction, Jacqueline A. Robinson, Jannikke Raikkonen, Leah Vucetich, John A. Vucetich, Rolf O. Peterson, Kirk Lohmueller, Robert Wayne

Michigan Tech Publications, Part 1

The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression …

Taxonomy And The History Of Science: A Critical Analysis Of Four Historic Publications, Christopher M. Rogers

KSU Journey Honors College Capstones and Theses

The history of taxonomy is not usually taught in modern biology classes, but it is necessary to understand the history of classification and science as a whole in order to better understand the processes of classification and thinking that are commonly taught at the college level. Through the exploration of the difficulties of publishing, Linnaeus' Species Plantarum, and three pre-Linnaean works from Pliny the Elder, Nehemiah Grew, and Rembert Dodoens, I have found that the history of the sciences has been largely distorted. The distortion appears to be of many factors, including the replacement of ideas, censorship from scholarly …

Relative Importance Of Ions And Particles In Silver Nanoparticle Uptake And Accumulation In Keystone Estuarine Organisms; Prorocentrum Minimum And Crassostrea Virginica, Shelby Victoria Butz

Theses and Dissertations

In marine systems, silver is regarded as being one of the most toxic and readily accumulated metals, and is known to be taken up and accumulate within marine invertebrates, fish, phytoplankton and seaweeds. Reported open ocean concentrations of silver range from 0.1 – 2 ng L-1 while silver concentrations in coastal waters are typically 5 to 10 times higher than open ocean values (0.1 - 50 ng L-1). The determination of silver in marine and coastal waters presents several challenges including low concentrations and matrix complexity of seawater, which creates interferences and other challenges for many instrumental techniques creating a …

White Shark Genome Reveals Ancient Elasmobranch Adaptations Associated With Wound Healing And The Maintenance Of Genome Stability, Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina D. Pavinski Bitar, Vincent P. Richards, Aleksey S. Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen James O'Brien, Agostinho Antunes, Salvador Jorgensen, Mahmood S. Shivji

Biology Faculty Articles

The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability …

Cophosk: A Method For Comprehensive Kinase Substrate Annotation Using Co-Phosphorylation Analysis, Marzieh Ayati, Danica D. Wiredja, Daniela M. Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance

Faculty Scholarship

We present CoPhosK to predict kinase-substrate associations for phosphopeptide substrates detected by mass spectrometry (MS). The tool utilizes a Naïve Bayes framework with priors of known kinase-substrate associations (KSAs) to generate its predictions. Through the mining of MS data for the collective dynamic signatures of the kinases’ substrates revealed by correlation analysis of phosphopeptide intensity data, the tool infers KSAs in the data for the considerable body of substrates lacking such annotations. We benchmarked the tool against existing approaches for predicting KSAs that rely on static information (e.g. sequences, structures and interactions) using publically available MS data, including breast, colon, …

Demographic Analyses Of The Data Limited Silky Shark Population In The Indian Ocean Using A Two-Sex Stochastic Matrix Framework, Wen-Pei Tsai, Yen-Jun Wang, Atsuko Yamaguchi

Journal of Marine Science and Technology–Taiwan

The silky shark, Carcharhinus falciformis, is a common bycatch species of tuna and swordfish longline fishing in the Indian Ocean. The high value of its fins makes it one of the most heavily fished shark species in the world. Concern over declining populations and the uncertainty surrounding its population dynamics has increased the urgency of developing appropriate methods to assess its stock status. This study developed a two-sex stage-based structured matrix model with Monte Carlo simulations to examine silky shark demography and population dynamics. The simulations indicate that, without mortality from fishing, the stock will increase slightly (sex combined mean …