Biology Commons^™

A Mutation Affecting Polycystin-1 Mediated Heterotrimeric G-Protein Signaling Causes Pkd, Stephen C. Parnell, Brenda S. Magenheimer, Robin L. Maser, Tengis S. Pavlov, Mallory A. Havens, Michelle L. Hastings, Stephen F. Jackson, Christopher J. Ward, Kenneth R. Peterson, Alexander Staruschenko, James P. Calvet

Biology Department Faculty Articles

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the growth of renal cysts that ultimately destroy kidney function. Mutations in the PKD1 and PKD2 genes cause ADPKD. Their protein products, polycystin-1 (PC1) and polycystin-2 (PC2) have been proposed to forma calcium-permeable receptor-channel complex; however the mechanisms by which they function are almost completely unknown. Most mutations in PKD1 are truncating loss-of-function mutations or affect protein biogenesis, trafficking or stability and reveal very little about the intrinsic biochemical properties or cellular functions of PC1. An ADPKD patient mutation (L4132D or DL), resulting in a single amino acid deletion in a …

Sources And Fates Of Carbamyl Phosphate: A Labile Energy-Rich Molecule With Multiple Facets., Dashuang Shi, Ljubica Caldovic, Mendel Tuchman

Genomics and Precision Medicine Faculty Publications

Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether

Systematics And Diversification Of The Pantropical Avian Order Coraciiformes, Jenna Merle Mccullough

Biology ETDs

How and why species diversify is a central theme of evolutionary biology. Species-rich, morphologically diverse, pantropical clades provide rare opportunities to explore questions about drivers of diversification in the tropics. Here, we present the first complete species tree of Coraciiformes (6 families, ~177 species of kingfishers, motmots, bee-eaters, and allies), produced with thousands of ultraconserved elements. We recovered a well-supported tree which shows that there are two clades within Coraciiformes: 1) bee-eaters sister to rollers + ground- rollers and 2) todies sister to motmots + kingfishers. We estimated the biogeographical history of the group, explored bill shape evolution with a …

Completion Of Dna Replication In Escherichia Coli, Brian Michael Wendel

Dissertations and Theses

To maintain genomic integrity, all cells must accurately duplicate their genetic material in order to provide intact and complete copies to each daughter cell following cell division. Successful inheritance of chromosomal information without changing even a single nucleotide requires accurate and robust DNA replication. This requires that cells tightly control replication initiation from the origin(s), processive elongation of the replisome, and the completion of DNA replication by resolving convergent replication forks ensuring that each sequence is duplicated without alteration. Unlike initiation and elongation, the process by which replication forks converge and are resolved into two discrete, inheritable DNA molecules is …

Population Genetics And Bumble Bee Conservation: Saving Species By Thinking Small, Cady Greenslit

Lawrence University Honors Projects

Pollinators have experienced a severe decline over the last few decades, and this includes bumble bee populations (g. Bombus). Bumble bees are important native pollinators, and here I investigate the health of local populations with molecular tools. The field of conservation genetics has created useful methodology for investigating the health and informing management strategies of threatened populations. This work investigates and describes the applications of population genetics, which uses span across the board. These applications are then brought back into the context of bumble bee conservation, and how they fit into the experimental plan I originally designed. I designed …

Population Structure, Demographic History, And Environmental Niche Of The Sand Fly Disease Vector Lutzomyia Shannoni (Dyar) (Diptera: Psychodidae) In The U.S., Mexico, And Colombia, Matthew E. Wolkoff

Biology Theses

Lutzomyia shannoni (Dyar, 1929) (Diptera: Psychodidae) is the only known sand fly vector of vesicular stomatitis virus, a putative leishmaniasis vector, and also boasts the widest distribution of any sand fly in the New World. Research on Lu. shannoni in Central and South America has revealed genetically divergent subpopulations; however, tentative analysis of Lu. shannoni in the U.S. has failed to detect any significant population structure, even between specimens collected from highly disparate localities.

The present study used four molecular markers to more closely investigate the population structure of Lu. shannoni in the U.S., and assess the species’ relationships with …

Investigating The Role Of Genomic Variation In Susceptibility To Environmental Chemicals Across Populations, Lindsay Adrian Holden

Dissertations and Theses

No two individuals are identical. This is true at the genetic level and at the phenotypic level. One of the traits that varies between populations is toxicant susceptibility: some individuals are sensitive to the effects of environmental chemical exposure, and others are resistant. This body of work aims to address the impact of genomic copy number variants (CNV)--large (>1 Kb) duplications or deletions across the genome--on the toxicant-susceptibility phenotype.

Herein copy number variants were characterized across three commonly used laboratory strains of zebrafish (Danio rerio) and mRNA expression phenotypes were identified in the same strains. It was found that …

Cannibalism In Blepharisma Americanum : A Genome Comparison, Bethaney Gulla-Devaney

Theses, Dissertations, and Projects

Cannibalism is a process in which an organism consumes a member of its own species. The process is intraspecies while predation is interspecies. Unlike predation, literature on the process of cannibalism is largely understudied, particularly in the microbial world. This study focuses on Blepharisma americanum, a species of eukaryotic microbe. In this species, cannibalism can be confirmed visually by a giant cannibal cell digesting victim cells within the food vacuoles. Cannibalism is regularly practiced in B. americanum and I attempt to elucidate the genetic differences between life states: cannibal and vegetative cells. I investigate using bioinformatic approaches: whole transcriptome amplification, …

Analysis Of Genes Encoded By A Chromosomal Insert In Rickettsia Philipii, Sydney A. Wright

Honors College Theses

Background: Spotted Fever group rickettsiae are obligate intracellular arthropod-borne bacteria. Rickettsiae are globally distributed yet typically confined to the distribution of their vector(s). Rickettsia rickettsii and Rickettsia philipii are closely related human pathogens endemic to the United States and cause similar febrile illness with differing morbidity and mortality. Genomic comparison found the presence of a 19 kilobase insert containing eleven genes in Rickettsia philipii. The functions of proteins encoded by this insert are speculated to affect virulence and pathogenicity.

Materials and Methods: Bioinformatic analysis was performed to identify functional motifs in four proteins encoded by the insert. Homologous proteins …

Landscape Genetics Of Ambystoma Opacum In Mammoth Cave National Park, Haley Austin

Mahurin Honors College Capstone Experience/Thesis Projects

No abstract provided.

Evolution Of Voltage-Gated Ion Channels, Kevin Gregory Bennett, Kevin Bennett

Master of Science in Integrative Biology Theses

Voltage-gated Ion Channels (VICs) form a superfamily of energy-independent membrane transporters that facilitate the transfer of charged sodium, calcium, and potassium ions across the cell membrane (Hodgkin & Huxley 1952). The channels contain a selective ion-conducting pore along with several other structural and gating features that come together to form a functional hetero- or homotetramer. A comprehensive phylogenetic study of all available proteins aimed at finding unknown distribution and illuminating evolutionary paths would be immensely useful in understanding relationships of structure, function, and organismal distribution. This phylogenetic analysis of VICs will be immensely useful in characterizing functional and structural distribution, …

Pyruvate Kinase Isoform M2 Influences Autophagy And Related Processes In Hepatocellular Carcinoma Cells, Matthew Lin

University Scholar Projects

Hepatocellular carcinoma (HCC) is the most common form of liver cancer that affects ~14 million people in the world. Like all cancers, HCC is a disease that arises from unstinted cellular growth initiated by genetic alterations, metabolic changes, and dysregulation in key cellular pathways. Of interest is the relationship between metabolism and cell proliferation/degradation for therapeutic targeting. Pyruvate kinase M2 is a dimeric, glycolytically inactive isoform of the final enzyme involved in glycolysis, that is often upregulated in cancerous tissue. It is thought that the enzymatic function of PKM2 outside of glycolysis contributes to the biosynthesis of anabolic intermediates used …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

The Molecular Chaperone Hsp90 Promotes Notch Signaling In The Germline Of Caenorhabditis Elegans, James L. Lissemore, Elyse Connors, Ying Liu, Li Qiao, Bing Yang, Mark L. Edgley, Stephane Flibotte, Jon Taylor, Vinci Au, Donald G. Moerman, Eleanor M. Maine

2018 Faculty Bibliography

In a genetic screen to identify genes that promote GLP-1/Notch signaling in Caenorhabditis elegans germline stem cells, we found a single mutation, om40, defining a gene called ego-3. ego-3(om40) causes several defects in the soma and the germline, including paralysis during larval development, sterility, delayed proliferation of germline stem cells, and ectopic germline stem cell proliferation. Whole genome sequencing identified om40 as an allele of hsp-90, previously known as daf-21, which encodes the C. elegans ortholog of the cytosolic form of HSP90. This protein is a molecular chaperone with a central position in the protein homeostasis network, which is responsible …

Determination Of Adamts13 Susceptibility In Type Iia Von Willebrand Disease, Monica Buselli

Dissertations, Masters Theses, Capstones, and Culminating Projects

von Willebrand Disease (vWD) is a bleeding disorder caused by a deficiency in von Willebrand Factor (vWF), a large glycoprotein that assists in coagulation. Specifically, large vWF multimers in the blood stream are key components in starting the coagulation cascade. vWF is cleaved by the metalloprotease ADAMTS13, regulating the multimers size, which hinders vWF’s ability to function properly. The three main types of vWD —Type I, II, and III— are not well defined, and as a result are all similarly treated with plasma-derived vWF replacement therapy. Plasma-derived vWF is a treatment that does not cure the problem but relieves the …

Phylogeny Of The Orangethroat Darter (Etheostoma Spectabile) Species Complex In The Ozark Highlands Of Arkansas, Mckenna George

Animal Science Undergraduate Honors Theses

Darters are small, benthic fishes that live in freshwater rivers and streams and belong to the family Percidae. Pleistocene glaciations fragmented many darter species, resulting in speciation, but new species are often hard to detect if they are morphologically identical to pre-existing species. Intraspecific hybridization and resulting introgression, which occur frequently in glaciated areas, further complicate identification by introducing heterospecific genomes into mitochondrial DNA, making it difficult to accurately resolve phylogenetic relationships. The results of Bossu and Near’s 2009 study highlight this issue, showing a large degree of incongruence between mitochondrial and nuclear gene trees.

This study analyzed samples from …

Internal Validation Of Strmix™ – A Multi Laboratory Response To Pcast, Jo-Anne Bright, Rebecca Richards, Maarten Kruijver, Hannah Kelly, Catherine Mcgovern, Alan Magee, Andrew Mcwhorter, Anne Cieko, Brian Peck, Chase Baumgartner, Christina Buettner, Scott Mcwilliams, Claire Mckenna, Colin Gallacher, Ben Mallinder, Darren Wright, Deven Johnson, Dorothy Catella, Eugene Lien, Craig O'Connor, George Duncan, Jason Bundy, Jillian Echard, John Lowe, Joshua Stewart, Kathleen Corrado, Sheila Gentile, Marla Kaplan, Michelle Hassler, Naomi Mcdonald, Paul Hulme, Rachel H. Oefelein, Shawn Montpetit, Melissa Strong, Sarah Noel, Simon Malsom, Steven Myers, Susan Welti, Tamyra Moretti, Teresa Mcmahon, Thomas Grill, Tim Kalafut, Mary Margaret Greer-Ritzheimer, Vickie Beamer, Duncan A. Taylor, John S. Buckleton

Biology Faculty Articles

We report a large compilation of the internal validations of the probabilistic genotyping software STRmix™. Thirty one laboratories contributed data resulting in 2825 mixtures comprising three to six donors and a wide range of multiplex, equipment, mixture proportions and templates. Previously reported trends in the LR were confirmed including less discriminatory LRs occurring both for donors and non-donors at low template (for the donor in question) and at high contributor number. We were unable to isolate an effect of allelic sharing. Any apparent effect appears to be largely confounded with increased contributor number.

The Role Of Merlin And Apicobasal Polarity In Endometrial Development And Homeostasis, Erin Lopez

Dissertations and Theses (Open Access)

Apicobasal polarity and cell adhesion are necessary for the proper formation and organization of epithelial tissues. Merlin couples cell polarity and adhesion through correct localization of the polarity protein Par3 and maturation of apical junctions. Merlin and Par3 are necessary for the development and homeostasis of highly regenerative tissues like the epidermis. The continual repopulation of the endometrium after each menstrual cycle requires a constant reorganization of cell polarity and adhesion. The endometrium consists of a luminal epithelium that postnatally gives rise to the distinct glandular epithelium. Endometrial glands are necessary to secrete nutrients for the pre-implantation embryo. In addition, …

Changes In The Microbial Community Of Lubomirskia Baicalensis Affected By Red Sponge Disease, Colin Rorex

Electronic Theses and Dissertations

Lake Baikal is the oldest known lake and a unique ecosystem, home to several species of fresh water sponge. A disease outbreak affecting the dominant species, Lubormirskia baialensis, was recently reported. The cause of the disease has not been determined but one of the current hypothesis is that the increase in methane concentration is correlated to the disease outbreak. This pilot study characterized the microbiomes of sick and healthy sponges through the use of 16S rRNA sequencing. Sick sponge microbiomes shared a conserved group of taxa while the healthy sponge microbiomes had greater diversity. Indicator species analysis identified two significant …

Sequencing And Analysis Of Centromere Protein B In Wallaby And The Rapid Evolution Of The Centromere, Alexander Tedeschi

Honors Scholar Theses

Using a combination of Sanger sequencing and RNA-seq data, this project aims to determine the nucleotide and amino acid sequence of Centromere Protein B (CENP-B), an important protein involved in the assembly of the kinetochore protein complex at the centromere, in several species of marsupials, specifically wallabies. Despite their recent evolutionary history, these species have been shown to have surprisingly divergent centromeric DNA sequences. Through comparative analysis of these sequences, this project, along with analysis of several other CENPs, aims to determine if this divergence extends to the proteins closely associated with these sequences and possibly even further into the …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Using Molecular Markers To Trace The Population History Of Volant Organisms At Differing Temporal Scales, Noah A. Burg

Dissertations, Theses, and Capstone Projects

Using molecular markers to test phylogenetic and phylogeographic hypotheses is critical for tracking the population origin of invasive, introduced species (Chapter 2, Chapter 4) and to identify the systematic relationships of disparate lineages at both shallow and deep evolutionary time scales (Chapters 3, Chapter 4). In this thesis, Sanger Sequencing was used to generate datasets based on fresh and preserved tissue from specimens collected in the field, as well as museum tissue vouchers granted from various institutions in the US and Europe. In combining these source materials, data were generated for three focal studies: 1) In the first research section …

A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian

Dissertations, Theses, and Capstone Projects

Gyroporus (Sclerodermatineae, Boletales, Agaricomycetes, Basidiomycota, Fungi) is a genus of ectomycorrhizal mushroom-forming fungi distributed throughout the world in suitable habitats. Previous attempts to untangle the diversity of this genus proved difficult due to the presence of semi-cryptic species and equivocal results from phylogenetic analysis of ribosomal RNA markers. To overcome these obstacles, a combined taxonomic and phylogenetic (emphasizing protein-coding genes) approach is used here to delimit species and elucidate geographic and evolutionary patterns of Gyroporus. Careful study of relevant literature and herbarium specimens was augmented by field work in North America, Australia, and East Asia for observation and collection …

Threshold-Dependent Repression Of Spl Gene Expression By Mir156/Mir157 Controls Vegetative Phase Change In Arabidopsis Thaliana, Jia He, Mingli Xu, Matthew R. Willmann, Kevin Mccormick, Tieqiang Hu, Li Yang, Colby G. Starker, Daniel F. Voytas, Blake C. Meyers, R. Scott Poethig

Faculty Publications

Vegetative phase change is regulated by a decrease in the abundance of the miRNAs, miR156 and miR157, and the resulting increase in the expression of their targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. To determine how miR156/miR157 specify the quantitative and qualitative changes in leaf morphology that occur during vegetative phase change, we measured their abundance in successive leaves and characterized the phenotype of mutations in different MIR156 and MIR157 genes. miR156/miR157 decline rapidly between leaf 1&2 and leaf 3 and decrease more slowly after this point. The amount of miR156/miR157 in leaves 1&2 greatly exceeds the …

Testing Viability Of Oligonucleotide Primers On Microsatellite Markers Amplified By Polymerase Chain Reaction On Dermacentor Variabilis Samples From The Bulloch County Region Of Georgia, Usa, Danielle Souza

Honors College Theses

Dermacentor variabilis, more commonly known as the wood tick, or the American dog tick, can be found all over North America. D. variabilis is a common tick in Bulloch county, Georgia, USA, and little is known about the population structure of this population of the species. Microsatellite markers are able to locate sections of the genome and can aid in estimating relatedness among individuals in a population. Six different oligonucleotide primer pairs were published for D. variabilis, however, published and non-published works indicated that not all of those primer pairs were working equally well for PCR. This study is …

Skeletal, Cardiac, And Respiratory Muscle Function And Histopathology In The P448lneo- Mouse Model Of Fkrp-Deficient Muscular Dystrophy., Qing Yu, Melissa Morales, Ning Li, Alexander G Fritz, Ren Ruobing, Anthony Blaeser, Ershia Francois, Qi-Long Lu, Kanneboyina Nagaraju, Christopher F Spurney

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Fukutin-related protein (FKRP) mutations are the most common cause of dystroglycanopathies known to cause both limb girdle and congenital muscular dystrophy. The P448Lneo- mouse model has a knock-in mutation in the FKRP gene and develops skeletal, respiratory, and cardiac muscle disease.

METHODS: We studied the natural history of the P448Lneo- mouse model over 9 months and the effects of twice weekly treadmill running. Forelimb and hindlimb grip strength (Columbus Instruments) and overall activity (Omnitech Electronics) assessed skeletal muscle function. Echocardiography was performed using VisualSonics Vevo 770 (FujiFilm VisualSonics). Plethysmography was performed using whole body system (ADInstruments). Histological evaluations included …

Characterizing The Role Of Cp1 In Drosophila Melanogaster: Its Effects On Basement Membrane Degradation And Signaling, Dane Alan Flinchum

Masters Theses & Specialist Projects

CP1 is a well-conserved cathepsin L-like protease essential for proper growth and development in Drosophila melanogaster. Previous research has demonstrated that CP1 has the ability to break down the extracellular matrix. Using the UAS-GAL4 system, immunohistochemistry, and antibody-staining, this research attempts to characterize the role of CP1 and its effects on basement membrane degradation and signaling. These effects include actions at the cellular level and on a known signaling pathway. The genes involved in this pathway are known to be required for proper development of the wing disc into the adult wing. We have demonstrated the collagenase activity of CP1 …

Genetic Interactions Between Bob1 And Multiple 26s Proteasome Subunits Suggest A Role For Proteostasis In Regulating Arabidopsis Development, Elan W. Silverblatt-Buser , '12, Melissa A. Frick , '12, Christina Rabeler, Nicholas J. Kaplinsky

Biology Faculty Works

Protein folding and degradation are both required for protein quality control, an essential cellular activity that underlies normal growth and development. We investigated how BOB1, an Arabidopsis thaliana small heat shock protein, maintains normal plant development. bob1 mutants exhibit organ polarity defects and have expanded domains of KNOX gene expression. Some of these phenotypes are ecotype specific suggesting that other genes function to modify them. Using a genetic approach we identified an interaction between BOB1 and FIL, a gene required for abaxial organ identity. We also performed an EMS enhancer screen using the bob1-3 allele to identify pathways that are …

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, …

Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh

Biology Faculty Publications

The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation. However, there are not any Gal4 drivers available to observe the gain- of- function or loss- of- function of a …