Biology Commons^™

The Role Of Landscape Variation In Shaping The Evolutionary Diversification Of Chimpanzees (Pan Troglodytes) In A Biodiversity Hotspot, Matthew William Mitchell

Legacy Theses & Dissertations (2009 - 2024)

In this dissertation, I combine population genetic and demographic history analyses of autosomal, mitochondrial and Y-chromosome genetic markers with spatially explicit modeling techniques to study the biogeographic mechanisms responsible for shaping patterns of genetic diversity among chimpanzees in Cameroon and eastern Nigeria. I also describe a new software tool, TESS Ad-Mixer, that I developed early on in this study to help visualize the geographic distribution of demes recovered from population cluster analyses.

The Role Of Igf-Ii In Memory Enhancement : Implications For Autism Spectrum Disorders, Amy S. Kohtz

Legacy Theses & Dissertations (2009 - 2024)

Cognitive and memory impairments significantly affect multiple domains in life and play major roles in disease. Identifying critical mechanisms and factors that mediate memory consolidation and enhancement may represent an important approach for increasing cognition in normal adults and preventing or treating cognitive impairments. The expression of the C/EBP- target gene insulin-like growth factor 2, (IGF-II) is required for memory consolidation; furthermore, IGF-II administration during memory consolidation produces memory enhancement, increased memory persistence and prevents forgetting. In this thesis, I investigated the therapeutic potential of IGF-II to promote memory consolidation when administered systemically. In addition, I investigated one particularly interesting …

Origins Of The Classical Gene Concept, 1900–1950: Genetics, Mechanistic, Philosophy, And The Capitalization Of Agriculture, Garland E. Allen

Biology Faculty Research

In the period of “classical genetics” (roughly 1915–1950), the common view of the gene was mechanistic—that is, genes were seen as individual, atomistic units, as material components of the chromosomes. Although it was recognized early on that genes could interact and influence each other’s expression, they were still regarded as individually functioning units, much like the chemists’ atoms or molecules. Although geneticists in particular knew the story was more complex, the atomistic gene remained the central view for a variety of reasons. It fit the growing philosophy of mechanistic materialism in the life sciences, as biologists tried to make their …

Identification Of Set1 Target Genes, William Beyer, Scott D. Briggs

The Summer Undergraduate Research Fellowship (SURF) Symposium

The Set1 complex, a histone methyltransferase complex found in S. cerevisiae (budding yeast), is the only histone methyltransferase responsible for catalyzing methylation of histone H3 at Lysine 4. It possesses homologues in other species, humans included. While yeast only have the Set1 complex, the human homologues of the yeast Set1 complex include mixed-lineage leukemia family (MLL1-4), Set1 A, Set1 B, among others. MLL1-4 has been shown to play a role in transcription, cell type specification, and the development of leukemia. One application of characterizing the role of a protein is that the information gained can provide insight into the function …

Dirigent Domain-Containing Protein Is Part Of The Machinery Required For Formation Of The Lignin-Based Casparian Strip In The Root, Prashant S. Hosmani, Takehiro Kamiya, John Danku, Sadaf Naseer, Niko Geldner, Mary Lou Guerinot, David Salt

Dartmouth Scholarship

The endodermis acts as a "second skin" in plant roots by providing the cellular control necessary for the selective entry of water and solutes into the vascular system. To enable such control, Casparian strips span the cell wall of adjacent endodermal cells to form a tight junction that blocks extracellular diffusion across the endodermis. This junction is composed of lignin that is polymerized by oxidative coupling of monolignols through the action of a NADPH oxidase and peroxidases. Casparian strip domain proteins (CASPs) correctly position this biosynthetic machinery by forming a protein scaffold in the plasma membrane at the site where …

Development Of Tools To Assess The Effects Of Lunasin On Normal Development And Tumor Progression In Drosophila Melanogaster, Gillian E. Jones

Masters Theses & Specialist Projects

Soy contains many bioactive molecules known to elicit anti-cancer effects. One such peptide, Lunasin, has been shown to selectively act on newly transformed cells while having no cytotoxic effect on non-tumorigenic or established cancer cell lines. In this study we attempt to understand the developmental effects of Lunasin overexpression in vivo and create reagents that will help us understand Lunasin’s anti tumorigenic effects in an intact organism. cDNA encoding lunasin and EGFP-lunasin were cloned into pUAST and microinjected into Drosophila embryos. Tissue-specific overexpression of EGFP-Lun in the resulting transgenic lines was accomplished by crossing transgenics to various GAL4 driver lines. …

The Ecology And Genetics Of Schoenoplectus Maritimus, An Important Emergent Macrophyte, Across Diverse Hydrologic Conditions—Implications For Restoration, Amanda Clare Sweetman

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Wetlands in the Intermountain West are typically dominated by large monotypic stands of emergent wetland plants, are highly productive, and support millions of migratory birds as important stops along the Pacific Flyway. In systems with low species diversity, such as these, diversity within a species (intraspecific diversity) can play an important role in population fitness and ecosystem functioning and can impact restoration success. Our research was designed to inform future restoration and management activities by studying the pattern of diversity within and among natural plant populations, and by studying how hydrology and plant materials used in restoration (source and diversity …

The Importance Of Epigenetic Phenomena In Regulating Activity Of The Genetic Material, Sin Chan

Senior Honors Projects

Genetics has taught us that genes are represented as discrete sequences within a larger DNA molecule found embedded within the chromosomes of a living cell. Collectively these chromosomes and their associated genes carry all of the instructions for life. Until recently, the prevailing thought has been that genes are destiny in the life of an individual since the genes carry the information that determines the general traits and characteristics associated with that individual. The relatively recent understanding of mechanisms that underlie epigenetic phenomena has led to a rethinking of this concept. Epigenetics describes cellular mechanisms that explain how two individuals …

Oxidative Stress Disruption Of Receptor-Mediated Calcium Signaling Mechanisms, Tso-Hao Tang, Chiung-Tan Chang, Hsiu-Jen Wang, Joshua Erickson, Rhett A. Reichard, Alexis Martin, Erica Shannon, Adam L. Martin, Yue-Wern Huang, Robert Aronstam

Biological Sciences Faculty Research & Creative Works

Background: Oxidative stress increases the cytosolic content of calcium in the cytoplasm through a combination of effects on calcium pumps, exchangers, channels and binding proteins. In this study, oxidative stress was produced by exposure to tert-butyl hydroperoxide (tBHP); cell viability was assessed using a dye reduction assay; receptor binding was characterized using [³H]N-methylscopolamine ([³H]MS); and cytosolic and luminal endoplasmic reticulum (ER) calcium concentrations ([Ca²⁺]_i and [Ca²⁺]_L, respectively) were measured by fluorescent imaging.

Results: Activation of M3 muscarinic receptors induced a biphasic increase in [Ca²⁺] …

Use Of Image Cytometry For Quantification Of Pathogenic Fungi In Association With Host Cells, Charlotte A. Berkes, Leo Li-Ying Chan, Alisha Wilkinson, Benjamin Paradis

Biology Faculty Publications

Studies of the cellular pathogenesis mechanisms of pathogenic yeasts such as Candida albicans, Histoplasma capsulatum, and Cryptococcus neoformans commonly employ infection of mammalian hosts or host cells (i.e. macrophages) followed by yeast quantification using colony forming unit analysis or flow cytometry. While colony forming unit enumeration has been the most commonly used method in the field, this technique has disadvantages and limitations, including slow growth of some fungal species on solid media and low and/or variable plating efficiencies, which is of particular concern when comparing growth of wild-type and mutant strains. Flow cytometry can provide rapid quantitative information regarding yeast …

Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May

Biology Faculty Publications

Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …

Apoptotic And Epigenetic Induction Of Embryo Failure Following Somatic Cell Nuclear Transfer, Aaron Patrick Davis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The cloning of domestic species has tremendous potential, as the technology can be used in selective breeding, conservation, and the production of transgenic animals. The technique of cloning involves the transplant of DNA from a cell to a recipient gamete. Following transfer to a surrogate, the cloned embryo may successfully complete development to a live offspring. Despite intensive research, the success rate of cloning remains prohibitively low, and the potential benefits of cloning have not yet been realized. Embryos produced from cloning suffer from high rates of embryo degradation, implantation failure, and abortion. The goal of this dissertation research project …

In Vitro Characterization Of Avian Influenza Virus Isolates With A Truncated Ns1 Gene Segment, Aaron Dick

Honors Scholar Theses

Avian Influenza Virus represents a significant threat to the world poultry population, and is a potential threat to humans due to the possibility of cross-species AIV infection. Our approach is to characterize a number of avian virus populations with respect to their content of biologically active particles that include hemagglutinating particles (HAP), plaque forming particles (PFP), interferon inducing particles (IFP), interferon induction-suppressing particles (ISP), defective-interfering particles (DIP), cell-killing particles (CKP) and non-infectious cell killing particles (niCKP) using unique in vitro assays developed for avian influenza virus in the Marcus-Sekellick Laboratory. Specifically, we will use a strain of Avian influenza virus, …

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Septin Phosphorylation And Coiled-Coil Domains Function In Cell And Septin Ring Morphology In The Filamentous Fungus Ashbya Gossypii, Rebecca A. Meseroll, Patricia Occhipinti, Amy S. Gladfelter

Dartmouth Scholarship

Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures in vivo. The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus, Ashbya gossypii, are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites …

Landscape Of Transcription In Human Cells, Jainab Khatun

Biology Faculty Publications and Presentations

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, …

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Winter Habitat Selection And Genetic Relatedness Of Southern Flying Squirrels In Southwest Michigan, Sheila M. Miara

Masters Theses

Few studies have examined winter habitat selection for southern flying squirrels (Glaucomys volans) in northern latitudes where winter conditions are harsher than southern latitudes and resource availability is particularly limiting. Winter den tree characteristics and use by 19 southern flying squirrels (10 females and 9 males) were investigated from November through February in 2010-2011 and 2011-2012. The mean home range size using 100% minimum convex polygon for 18 individuals was 3.40 ha (±0.46 0.46 SE) and there was no significant difference between genders (P= 0.56) or ages (P=0.50). The mean 95% fixed kernel home range size was 0.15 …

Pf19 Encodes The P60 Catalytic Subunit Of Katanin And Is Required For Assembly Of The Flagellar Central Apparatus In Chlamydomonas, Erin E. Dymek, Elizabeth F. Smith

Dartmouth Scholarship

For all eukaryotic cilia the basal bodies provide a template for the assembly of the doublet microtubules, and intraflagellar transport provides a mechanism for transport of axonemal components into the growing cilium. What is not known is how the central pair of microtubules is nucleated or how their associated polypeptides are assembled. Here we report that the Chlamydomonas pf19 mutation results in a single amino acid change within the p60 catalytic subunit of katanin, and that this mutation prevents microtubule severing activity. The pf19 mutant has paralyzed flagella that lack the central apparatus. Using a combination of mutant analysis, RNAi-mediated …

Reducing False-Positive Prediction Of Minimotifs With A Genetic Interaction Filter, Jerlin Camilus Merlin, Sanguthevar Rajasekaran, Tian Mi, Martin Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists.

Methods and Findings

We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target …

The Molecular And Genetic Characterization Of L(3)Hem2 And L(3)Hem1, Putative Novel Alleles Of The Neurogenic Gene, Neuralized, Maria A. Otazo

Dissertations and Theses

No abstract provided.

Characterization Of A Novel Gef Kiaa1362, Emily Roach

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Transcriptomic Characterization Of A Synergistic Genetic Interaction During Carpel Margin Meristem Development In Arabidopsis Thaliana, April N. Wynn, Elizabeth E. Rueschhoff, Robert G. Franks

Biological Sciences Research

In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thalianaovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using …

Global Analysis Of Serine-Threonine Protein Kinase Genes In Neurospora Crassa, Gyungsoon Park, Jacqueline A. Servin, Gloria E. Turner, Lorena Altamirano

Dartmouth Scholarship

Serine/threonine (S/T) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus Neurospora crassa. In order to assess the importance of S/T kinases to Neurospora biology, we embarked on a global analysis of 86 S/T kinase genes in Neurospora. We were able to isolate viable mutants for 77 of the 86 kinase genes. Of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing a defect in more than one trait. S/T kinase knockouts were subjected to chemical screening using a panel of eight chemical treatments, with …

The Importance Of The Set2 Gene In The Virulence Of Candida Albicans, Molly Marchel

Honors Capstones

Capstone submitted as a graduation requirement for BSU Honors Program.

Determination Of Dna Methylation Levels At Specific Genomic Loci, Rebecca Garrett

Senior Honors Theses

Alzheimer's disease is a devastating disease, affecting millions. There is some familial evidence of an inheritance pattern from a genetic basis in Alzheimer's disease patients, but even with revelation of the genetic linkage and genes associated with Alzheimer's disease, the inheritance pattern is too complicated to be properly explained. It is necessary to investigate other causes of the debilitating disease. To investigate further, the epigenome was studied - the regulation of the genome by methyl group addition.

To study the epigenome of an Alzheimer's disease-like state, isoschizomer enzymes were used to cleave CC*GG regions. Comparing the cleaved DNA sequences produced …

Molecular Identification Of Novel Genes Associated With Atherosclerosis, Stephen R. Archacki

ETD Archive

No abstract provided.

Population Structure Of Island-Associated Pantropical Spotted Dolphins (Stenella Attenuata) In Hawaiian Waters, Sarah Shelby Courbis

Dissertations and Theses

Understanding gene flow, diversity, and dispersal patterns is important for predicting effects of natural events and anthropogenic activities on dolphin populations. With the very recent exceptions of false killer whales (Pseudorca crassidens), spinner dolphins (Stenella longirostris), and common bottlenose dolphins (Tursiops truncatus), Hawaiian odontocete species are managed as single stocks within the U.S. Hawaiian Exclusive Economic Zone. These exceptions are a result of recent studies that have indicated that some species have populations that show fidelity to individual islands or groups of islands, resulting in genetic differentiation, often with management implications. The first part …

Multi-Locus Evidence Of A Late Pleistocene Divergence And Sex-Biased Dispersal In The North American Wood Duck (Aix Sponsa), Christopher T. Bigley

Browse all Theses and Dissertations

The Pleistocene was characterized by fluctuations in climate causing repeated advances and retreats of glacial ice. The advancing ice sheets caused habitat fragmentation which initiated population divergence and speciation events between eastern and western avian populations within northern temperate forests. Based on mitochondrial DNA (mtDNA) control region sequences, North American Wood Duck (Aix sponsa) populations fit this model of divergence. However, mtDNA is maternally inherited, and thus may not reflect the genomic history of this species, because of male biased-dispersal, selection, or stochastic lineage sorting. To test the "Late Pleistocene divergence" hypothesis, I sequenced 11 independent nuclear introns (nuDNA) for …

The Status Of Dwarfed Populations Of Short-Horned Lizards (Phrynosoma Hernandesi) And Great Plains Toads (Anaxyrus Cognatus) In The San Luis Valley, Colorado, Megan E. Lahti

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The San Luis Valley is a large valley formation in Colorado surrounded on either side by mountain ranges exceeding 4,267 m. Within the Valley, two of the 14 amphibian and reptile species are dwarfed: the short-horned lizard (Phrynosoma hernandesi) and the Great Plains toad (Anaxyrus cognatus). Since its initial reporting in 1968 and confirmation in 1981, no research further investigating this dwarfism has been conducted. I collected morphological measurements to determine the extent and patterns of dwarfism of both species. I then investigated the genetics of both species using mitochondrial DNA to determine whether they are …