Biology Commons^™

Life In The Underworld: Anchialine Cave Biology In The Era Of Speleogenomics, Jorge L. Pérez-Moreno, Thomas M. Iliffe, Heather D. Bracken-Grissom

International Journal of Speleology

Anchialine caves contain haline bodies of water with underground connections to the ocean and limited exposure to open air. Despite being found on islands and peninsular coastlines around the world, the isolation of anchialine systems has facilitated the evolution of high levels of endemism among their inhabitants. The unique characteristics of anchialine caves and of their predominantly crustacean biodiversity nominate them as particularly interesting study subjects for evolutionary biology. However, there is presently a distinct scarcity of modern molecular methods being employed in the study of anchialine cave ecosystems. The use of current and emerging molecular techniques, e.g., next-generation sequencing …

Successful Enrichment And Recovery Of Whole Mitochondrial Genomes From Ancient Human Dental Calculus, Andrew T. Ozga, Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, Christina Warinner

Biology Faculty Articles

Objectives

Archaeological dental calculus is a rich source of host‐associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.

Materials and …

A Novel Variant In Cmah Is Associated With Blood Type Ab In Ragdoll Cats, Barbara Gandolfi, Robert Grahn, Nicholas Gustafson, Daniela Proverbio, Eva Spada, Badri Adhikari, Janling Cheng, Gordon Andrews, Leslie Lyons, Chris Helps

Computer Science Faculty Works

The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood …

Embryonic And Post-Embryonic Hoxa13 Expression In The Four-Toed Salamander, Hemidactylium Scutatum., Breanna R. Lee

Senior Honors Projects, 2010-2019

The process of somitogenesis occurs during embryological development and results in the definition of persisting axial segments. The four toed salamander, Hemidactylium scutatum, exhibits post-embryonic segmentation while most other vertebrates stop segmentation at the end of embryological development. HoxA13, a transcription factor expressed along the developing anteroposterior axis, plays a role in specifying caudal segmental identity, cell ingression into the pre-somitic mesoderm (PSM), and PSM truncation. HoxA13’s responsibilities in influencing embryological development make it an interesting candidate for involvement in post-embryonic segment addition mechanisms. This study explores the role of HoxA13 in tail segmentation in H. scutatum embryonic, larval, …

Reverse Genetic Screening Of Innexin Gap Junction Proteins In Drosophila Neurons, Shannon P. Fox

Senior Honors Projects, 2010-2019

The reflexive response and perception of pain (nociception) is an evolutionarily conserved process in animals. Pain can be a major health concern and current treatments often prove insufficient, especially in regards to chronic pain. Greater understanding of the molecular processes underlying pain sensation could lead to new and more effective treatments. The aim of this study is to investigate the molecular mechanisms of cold nociception in Drosophila melanogaster. A specific subset of peripheral sensory neurons (Class III dendritic arborization (da) neurons), are implicated in Drosophila larvae’s response to noxious cold.

Previous literature has associated a family of gap junction protein, …

Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. 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 the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene …

Rac1 And Ire1 Are Required To Prevent Early Loss Of Intestinal Homeostasis In Drosophila Melanogaster, Mauricio M. Ortega

Dissertations, Masters Theses, Capstones, and Culminating Projects

No abstract available

A Comparative Study Of Isolation In Headwater Fishes, Bjorn Victor Schmidt

Dissertations

Headwater resident fishes may be prone to a high rate of population fragmentation within river networks because large streams have habitat conditions outside of their preferred ecological niche and may limit gene flow in the dendritic ecological network. To investigate patterns of population structure, asymmetrical gene flow, and influences on genetic distance and isolation from connecting habitat pathways, species specific ecological traits, and basin scale characteristics, a multi-species, multi-regional study was performed. Six headwater species of fish from four taxonomic groupings were sampled for genetic material in three regions of paired neighbor drainages and then genotyped for eight microsatellite loci. …

Rheb1 Expression In Embryonic And Postnatal Mouse, Qi Tian, James L. Smart, Joachim H. Clement, Yingming Wang, Alex Derkatch, Harald Schubert, Michael V. Danilchik, Daniel L. Marks, Lev M. Federov

Faculty Publications - Department of Biological & Molecular Science

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres-sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu-nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde-pendent methods revealed similar RHEB1 expression pat-terns during both embryonic and postnatal developments. …

Hybridization, Population Genetic Structure And Gene Expression In The Genus Boechera, Martin Peter Schilling

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

When we look at life on earth, we can see a lot of different life forms, but we still do not fully understand how these different life forms came to be and at which points in time these life forms began to be different enough from each other so we could call them by different names, or species. Some groups of species on earth, especially plants, seem to reproduce with each other, even though they are already very different from each other so that we call them different species. This process is called hybridization, and it can stir up the …

Nocturnal Foraging Enhanced By Enlarged Secondary Eyes In A Net-Casting Spider, Jay A. Stafstrom, Eileen A. Hebets

Eileen Hebets Publications

Animals that possess extreme sensory structures are predicted to have a related extreme behavioral function. This study focuses on one such extreme sensory structure—the posterior median eyes of the net-casting spider Deinopis spinosa. Although past research has implicated the importance of vision in the nocturnal foraging habits of Deinopis, no direct link between vision in the enlarged eyes and nocturnal foraging has yet been made. To directly test the hypothesis that the enlarged posterior median eyes facilitate visually based nocturnal prey capture, we conducted repeated-measures, visual occlusion trials in both natural and laboratory settings. Our results indicate that D. …

Novel Interactome Of Saccharomyces Cerevisiae Myosin Type Ii Identified By A Modified Integrated Membrane Yeast Two-Hybrid (Imyth) Screen, Ednalise Santiago, Pearl Akamine, Jamie Snider, Victoria Wong, Matthew Jessulat, Viktor Deineko, Alla Gagarinova, Hiroyuki Aoki, Zoran Minic, Sadhna Phanse, Andrea San Antonio, Luis A Cubano, Brian C. Rymond, Mohan Babu, Igor Stagljar, Jose R. Rodriguez-Medina

Biology Faculty Publications

Nonmuscle myosin type II (Myo1p) is required for cytokinesis in the budding yeast Saccharomyces cerevisiae. Loss of Myo1p activity has been associated with growth abnormalities and enhanced sensitivity to osmotic stress, making it an appealing antifungal therapeutic target. The Myo1p tail-only domain was previously reported to have functional activity equivalent to the full-length Myo1p whereas the head-only domain did not. Since Myo1p tail-only constructs are biologically active, the tail domain must have additional functions beyond its previously described role in myosin dimerization or trimerization. The identification of new Myo1p-interacting proteins may shed light on the other …

Rhebi Expression In Embryonic And Postnatal Mouse, Qi Tian, James L. Smart, Joachim H. Clement, Yingming Wang, Alex Derkatch, Harald Schubert, Michael V. Danilchik, Daniel L. Marks, Lev M. Fedorov

Faculty Publications - Department of Biological & Molecular Science

Ras homolog enriched in brain (RHEB1) is a member within the superfamily of GTP-binding proteins encoded by the RAS oncogenes. RHEB1 is located at the crossroad of several important pathways including the insulin-signaling pathways and thus plays an important role in different physiological processes. To understand better the physiological relevance of RHEB1 protein, the expres- sion pattern of RHEB1 was analyzed in both embryonic (at E3.5–E16.5) and adult (1-month old) mice. RHEB1 immu- nostaining and X-gal staining were used for wild-type and Rheb1 gene trap mutant mice, respectively. These inde- pendent methods revealed similar RHEB1 expression pat- terns during both …

Social And Scientific Implications Of Genetic Testing In The Digital Age, Yaruska A. Ordinola

Senior Honors Projects

From Mendel’s law of inheritance in the 19th century through Watson and Crick’s revolutionary observations of the double helix in the 20th century, genetics has been a fascinating and continuing topic of discussion in the field of science (Collins & McKusick, 2001). Major studies like the Human Genome Project (HGP), initiated in 1990 and completed in 2003, provided a starting point from which scientists could more thoroughly investigate the human condition on a genetic level. Arising from this study, personal genomics is considered a blooming field in genetics- in which rapidly developing technological advances are able to provide easier and …

The Role Of Cellulose Synthase-Like D Genes In Tip Growth Of Physcomitrella Patens, Erin E. Killeavy, Arielle Chaves, Alison Roberts

Senior Honors Projects

Physcomitrella patens is a non-vascular plant with a relatively small genome and is amongst the few eukaryotic organisms that have a high rate of homologous recombination. This is valuable in biological research because it allows for targeted genetic modification of the organism. In vascular plants like Arabidopsis thaliana, a model organism, Cellulose Synthase-like D (CSLD) genes have been discovered to be important in tip growth. This type of growth is observed in the pollen tubes and root hairs of these plant types. The CSLD genes in Arabidopsis were found to play a crucial role in the growth of …

Alzheimer's Disease: The Silver Tsunami Of The 21st Century, Ankita Sarkar, Madison Irwin, Aditi Singh, Matthew Riccetti, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD), a fatal progressive neurodegenerative disorder, has no cure to date. One of the causes of AD is the accumulation of amyloid-beta 42 (Aß42) plaques, which result in the onset of neurodegeneration. It is not known how these plaques trigger the onset of neurodegeneration. There are several animal models developed to (i) study etiology of disease, (ii) look for genetic modifiers, and (iii) identify chemical inhibitors that can block neurodegeneration and help to find cure for this disease. An insect model of Drosophila melanogaster has also provided new insights into the disease. Here we will discuss the utility …

Genomic Drivers Of Cutaneous Squamous Cell Carcinoma Development, Vida Chitsazzadeh

Dissertations and Theses (Open Access)

Skin cancer is the most common malignancy in humans. Annually, in U.S. there are over 3 million cases with an estimated overall economic impact of $2 billion. Cutaneous Squamous Cell Carcinoma (cuSCC) comprises 15-20% of all skin cancers. cuSCC has the best-defined progression from a distinct precancerous lesion, the Actinic Keratosis (AK), to invasive cuSCC. Destructive therapies for AK treatment must be used repetitively, causing significant morbidity. There is a tremendous need for targeted diagnostics and therapy for AKs, representing an important opportunity for secondary skin cancer prevention. Our knowledge of the molecular and cellular events that lead to the …

Insights Into The Introduction Histories And Population Genetic Dynamics Of The Nile Monitor (Varanus Niloticus) And Argentine Black And White Tegu (Salvator Merianae) In Florida., Jared Price Wood

Electronic Theses and Dissertations

This dissertation examines the population genetic dynamics of two Florida invasives: the Nile monitor (Varanus niloticus) and Argentine black and white tegu (Salvator merianae). I also provide insights into the introduction histories of both species. This study was developed as part of a collaborative effort with the Florida Wildlife Commission to expand our knowledge of these highly detrimental, invasive lizards. All research activities involving animals and animal tissues were approved by the University of Louisville’s Institutional Animal Care and Use Committee (IACUC Proposal #: 12024). I start with a brief introduction into what makes invasive species …

Epigenetic Profiles Signify Cell Fate Plasticity In Unipotent Spermatogonial Stem And Progenitor Cells, Ying Liu, Eugenia G. Giannopoulou, Duacheng Wen, Ilaria Falciatori, Oliver Elemento, C. David Allis, Shahin Rafii, Marco Seandel

Publications and Research

Spermatogonial stem and progenitor cells (SSCs) generate adult male gametes. During in vitro expansion, these unipotent murine cells spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs). Here we investigate this conversion process through integrative transcriptomic and epigenomic analyses. We find in SSCs that promoters essential to maintenance and differentiation of embryonic stem cells (ESCs) are enriched with histone H3-lysine4 and -lysine 27 trimethylations. These bivalent modifications are maintained at most somatic promoters after conversion, bestowing MASCs an ESC-like promoter chromatin. At enhancers, the core pluripotency circuitry is activated partially in SSCs and completely in MASCs, concomitant with loss of …

Global Genetic Connectivity And Diversity In A Shark Of High Conservation Concern, The Oceanic Whitetip, Carcharhinus Longimanus, Cassandra L. Ruck

HCNSO Student Theses and Dissertations

The oceanic whitetip shark, Carcharhinus longimanus, is a circumtropical pelagic shark of high conservation concern (IUCN Red List: “Critically Endangered” in the Western North and Western Central Atlantic and “Vulnerable” globally). I present the first, population genetic assessment of the oceanic whitetip shark on a global scale, based on analysis of two mitochondrial genome regions (entire 1066-1067 bp control region and 784 bp partial ND4 gene), and nine nuclear microsatellite loci. No population structure was detected within the Western Atlantic. However, highly significant population structure was detected between Western Atlantic and Indo-Pacific Ocean sharks across all markers. Additionally, a …

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Evolution Of Kaic-Dependent Timekeepers: A Proto-Circadian Timing Mechanism Confers Adaptive Fitness In The Purple Bacterium Rhodopseudomonas Palustris, Peijun Ma, Tetsuya Mori, Chi Zhao, Teresa Thiel, Carl Johnson

Biology Department Faculty Works

Circadian (daily) rhythms are a fundamental and ubiquitous property of eukaryotic organisms. However, cyanobacteria are the only prokaryotic group for which bona fide circadian properties have been persuasively documented, even though homologs of the cyanobacterial kaiABC central clock genes are distributed widely among Eubacteria and Archaea. We report the purple non-sulfur bacterium Rhodopseudomonas palustris (that harbors homologs of kaiB and kaiC) only poorly sustains rhythmicity in constant conditions–a defining characteristic of circadian rhythms. Moreover, the biochemical characteristics of the Rhodopseudomonas homolog of the KaiC protein in vivo and in vitro are different from those of cyanobacterial KaiC. Nevertheless, R. palustris …

Molecular Evolution And Functional Divergence Of Trace Amine–Associated Receptors, Seong-Il Eyun, Hideaki Moriyama, Federico G. Hoffmann, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey.We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian- specific) in addition to previously known nine …

A Colletotrichum Graminicola Mutant Deficient In The Establishment Of Biotrophy Reveals Early Transcriptional Events In The Maize Anthracnose Disease Interaction, Maria F. Torres, Noushin Ghaffari, Ester A. S. Buiate, Neil Moore, Scott Schwartz, Charles D. Johnson, Lisa J. Vaillancourt

Plant Pathology Faculty Publications

Background: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development in planta: melanized appressoria on the host surface prior to penetration; biotrophy, characterized by intracellular colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. A “Mixed Effects” Generalized Linear Model (GLM) was developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of C. graminicola gene expression during infection and colonization. Additionally, the in planta transcriptome of the wild-type was compared with that of …

Role Of Multicellular Aggregates In Biofilm Formation, Kasper N. Kragh, Jaime B. Hutchison, Gavin Melaugh, Chris Rodesney, Aled E. L. Roberts, Yasuhiko Irie, Peter Ø. Jensen, Stephen P. Diggle, Rosalind J. Allen, Vernita Gordon, Thomas Bjarnsholt

Biology Faculty Publications

In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known.

Here we use a combination of …

Bacteriophage Ems9: Preliminary Genomic Description, Hallie Rae Zimmer

Honors Projects

EMS9 is a bacteriophage that was recently isolated from an Escherichia coli strain present in horse feces. Bacteriophage EMS9 consists of 98,771 base pairs that are organized into 139 predicted open reading frames (ORFs). These predicted genes potentially encode specific bacteriophage proteins. The genomic sequence of bacteriophage EMS9 is arranged intro three groups: early, middle, and late genes. Considerable homology between the ORFs of bacteriophage EMS9 and bacteriophages T5 and H8 exists. All of these bacteriophages are believed to use a rare two-step transfer mechanism to invade host cells. This annotation of the genomic sequence of EMS9 will provide a …

Bioinformatics Comparison Of M. Ruber Mrub_2507 To E. Coli Pdxk/B1636 And M. Ruber Mrub_2888 To E. Coli Pdxh/B1638 To Determine The Orthologous Nature, Adam Bernardi, 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 the genes Mrub_2507 and Mrub_2888. We predict that Mrub_2507 encodes the enzyme pyridoxal kinase (DNA coordinates 2555521..2556402), which is in the Vitamin B₆ Metabolism pathway (KEGG map number 00750). It catalyzes the conversion of pyridoxine, pyridoxamine, or pyridoxal to pyridoxine 5’-phosphate, pyridoxamine 5’-phosphate, or pyridoxal 5’-phosphate respectively. The E. coli K12 MG1655 ortholog is predicted to be b1636, which has …

Comparing Apples And Oranges?: Next Generation Sequencing And Its Impact On Microbiome Analysis, Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O'Driscoll, Stanton Catherine, Paul D. Cotter, Marcus J. Claesson

Department of Biological Sciences Publications

Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to …

Genomic Analysis Of Meiothermus Ruber Mrub_1907 And Meiothermus Ruber Mrub_1844 With Potential Ortholog Escherichia Coli B3774 Ilvc And Escherichia Coli B3771 Ilvc Gene Through Bioinformatics, Felipe A. Hernandez, 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 the genes Mrub_1907 and Mrub_1844. We predict that Mrub__1907 encodes the enzyme ketol-acid reductoisomerase (DNA coordinates 1966630..1967649 on the reverse strand), which is the fourth step of the L-isoleucine pathway (from threonine) (KEGG map number 00290). It catalyzes the conversion of (R)-3- Hydroxy-3-methyl-2-oxopentanoate to (R)-2-3 Dihydroxy-3-methylpentanoate. The E. coli K12 MG1655 ortholog is predicted to be b3774, which has the gene …

Comparison Of Genes In Meiothermus Ruber And Escherichia Coli In The Thiamine Biosynthesis Pathway, Erin E. Frye, 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 the genes Mrub_2046 and Mrub_2041.We predict that Mrub_2046 encodes the enzyme phosphomethylpyrimidine kinase (DNA coordinates 2082772..2083572 on the reverse strand), which is the second step of the Thiamine Metabolism pathway (KEGG map number mrb00730). It catalyzes the conversion of 4-Amino-2-methyl-5-phosphomethylpyrimidine to 4-Amino-2-methyl-5-hydroxymethyl diphosphate The E. coli K12 MG1655 ortholog is predicted to be b2103, which has the gene identifier thiD. We …