Genetics and Genomics Commons^™

Conserved Structural Domains In Foxd4l1, A Neural Forkhead Box Transcription Factor, Are Required To Repress Or Activate Target Genes, Steven L. Klein, Karen M. Neilson, John Orban, Sergey Yaklichkin, Jennifer Hoffbauer, Kathy Mood, Ira O. Daar, Sally Ann Moody

Anatomy and Regenerative Biology Faculty Publications

FoxD4L1 is a forkhead transcription factor that expands the neural ectoderm by down-regulating genes that promote the onset of neural differentiation and up-regulating genes that maintain proliferative neural precursors in an immature state. We previously demonstrated that binding of Grg4 to an Eh-1 motif enhances the ability of FoxD4L1 to down-regulate target neural genes but does not account for all of its repressive activity. Herein we analyzed the protein sequence for additional interaction motifs and secondary structure. Eight conserved motifs were identified in the C-terminal region of fish and frog proteins. Extending the analysis to mammals identified a high scoring …

Contributions Of Apolipoprotein E And Environmental Factors In Alzheimer’S Disease, Kelly C. Mcmullen

Senior Honors Theses

Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder, which currently affects nearly 5.5 million people in the United States alone. Clinical features often exhibited in AD include memory loss, unusual behavior, personality changes, and impaired cognitive function. The primary molecular hallmarks of AD include deposits of senile plaques and neurofibrillary tangles in brain tissue. A myriad of risk factors are associated with the disease, but this review will focus on Apolipoprotein E polymorphisms and certain environmental factors. Understanding the role of Apolipoprotein E in AD pathology may aid in the development of certain drug therapies and possible cures for AD. …

The Advertisement Calls And Distribution Of Two Sympatric Species Of Chiasmocleis (Méhely 1904) (Anura, Microhylidae, Gastrophryninae) From The Atlantic Forest, Mauricio C. Florani, Caio Vinicus De Mira Mendes, Iuri Ribeiro Dias, Danilo Silva Ruas, João Fillipe Riva Tonini, Rafael O. De Sá

Biology Faculty Publications

The advertisement calls of Chiasmocleis cordeiroi and C. crucis are described for populations from the municipalities of Igrapiúna and Camacan, respectively, state of Bahia, Brazil. Both calls consist of multipulsed notes produced in series. Differences between the two calls are: dominant frequency, higher in C. cordeiroi (range 4500–4898 Hz; C. crucis range 4069–4435 Hz); note rate, higher in C. cordeiroi (range 6.20–7.46 s/note; C. crucis range 5.17–5.59 s/note); pulse rate, higher in C. cordeiroi (151.82–194.83 s/note; C. crucis range 125.30– 142.12 s/note); and the structure of the modulation patterns of the notes. Moreover, the advertisement calls of C. crucis and …

Functional Annotation And Comparative Analysis Of A Zygopteran Transcriptome, Alexander G. Shanku, Mark A. Mcpeek, Andrew D. Kern

Dartmouth Scholarship

In this paper we present a de novo assembly of the transcriptome of the damselfly (Enallagma hageni) through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera, in the order Odonata, and Odonata organisms form the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mitochondrial DNA or ribosomal nuclear DNA. This Enallagma transcriptome contained 31,661 contigs that were assembled and translated into 14,813 individual open reading frames. Using these data, we constructed an extensive dataset of 634 orthologous nuclear protein-encoding …

Patterns Of Gene Expression From Human Costal Cartilage In Relation To The Chest Wall Deformity Pectus Carinatum, Janna E. Grubbs

Biological Sciences Theses & Dissertations

Cartilage deformities within the human chest wall, specifically pectus excavatum (PE) and pectus carinatum (PC) are common (1/400-1/1000) and yet, despite their clinical significance, are some of the least studied disorders pertaining to cartilage [1]. The costal cartilage connecting "false ribs" 8-10 to the sternum is often abnormally grown and can lead to formation of a severely sunken "funnel" chest (PE) or push outwards to form a "pigeon" chest (PC). Both conditions can have impact on the diaphragm, heart, lungs, and psychological function. An established ratio of PE and PC in males to females is 4:1, indicating a sex-linked male …

Assortative Mating In Ixodes Scapularis (Acari: Ixodidae) Ticks? And Ixodes Scapularis Infest Male Deer More Often Than Female Deer At Savannah River Site, (Aiken, Sc), Jenny Dickson

College of Graduate Studies: Theses & Dissertations

In this study we explored the hypothesis that the mitochondrial genetic diversity observed in Ixodes Scapularis ticks in the Southeastern United States is maintained through assortative mating. The study of 319 couples of ticks collected in copula from deer at the Savannah River Site (Aiken, SC) showed that ticks assigned to mitochondrial (12SrDNA and d-loop genes) phylogenetic monophyletic clades do not chose their mating partner based on genetic similarity or genetic diversity. The genetic composition of couples did not differ significantly from random choice. Our data indicate that if genetic diversity is maintained in this tick population, this cannot be …

Variation In Egg Components: A Study Of Maternal Investment And Resource Partitioning In The Nesting Loggerhead Sea Turtle; Estimating Genic Variation And Mapping Genetic Lineage Of A Rare Captive Helodermatid Population: Heloderma Horridum Charlesbogerti, Ketan V. Patel

College of Graduate Studies: Theses & Dissertations

Loggerhead sea turtles have the highest egg yields of any oviparous non-avian reptiles. Blood urea nitrogen levels increased as the season progressed while total blood albumen and total protein levels decreased. Wet egg mass (H = 1.7719 df = 2 p = 0.0375*) and albumen mass (H = 6.0507 df = 2 p = 0.0485*) significantly decreased across the nesting season however, wet yolk did not. Analysis of dried egg components showed that dry yolk and albumen did not differ across the nesting season. In addition on no seasonal change in dried egg components, hatchling size was conserved across the …

Sugar Promotes Vegetative Phase Change In Arabidopsis Thaliana By Repressing The Expression Of Mir156a And Mir156c, Li Yang, Mingli Xu, Yeonjong Koo, Jia He, R. Scott Poethig

Faculty Publications

Nutrients shape the growth, maturation, and aging of plants and animals. In plants, the juvenile to adult transition (vegetative phase change) is initiated by a decrease in miR156. In Arabidopsis, we found that exogenous sugar decreased the abundance of miR156, whereas reduced photosynthesis increased the level of this miRNA. This effect was correlated with a change in the timing of vegetative phase change, and was primarily attributable to a change in the expression of two genes, MIR156A and MIR156C, which were found to play dominant roles in this transition. The glucose-induced repression of miR156 was dependent on the …

Bed Bugs Evolved Unique Adaptive Strategy To Resist Pyrethroid Insecticides, Fang Zhu, Hemant Gujar, Jennifer R. Gordon, Kenneth F. Haynes, Michael F. Potter, Subba R. Palli

Entomology Faculty Publications

Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reaching the target sites on nerve cells, where an additional layer of resistance (kdr) is possible. This strategy evolved in bed bugs is based on their unique morphological, physiological and behavioral characteristics …

Reproductive Isolation In The Elegans-Group Of Caenorhabditis, Scott Everet Baird, Sara Rose Seibert

Biological Sciences Faculty Publications

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus Caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of Caenorhabditis is poised to become an important experimental …

Functional Analysis Of The Aspergillus Nidulans Kinome, Colin P. De Souza, Shahr B. Hashmi, Aysha H. Osmani, Peter Andrews, Carol S. Ringelberg, Jay C. Dunlap, Stephen A. Osmani

Dartmouth Scholarship

The filamentous fungi are an ecologically important group of organisms which also have important industrial applications but devastating effects as pathogens and agents of food spoilage. Protein kinases have been implicated in the regulation of virtually all biological processes but how they regulate filamentous fungal specific processes is not understood. The filamentous fungus Aspergillus nidulans has long been utilized as a powerful molecular genetic system and recent technical advances have made systematic approaches to study large gene sets possible. To enhance A. nidulans functional genomics we have created gene deletion constructs for 9851 genes representing 93.3% of the encoding genome. …

Sequencing And De Novo Transcriptome Assembly Of Brachypodium Sylvaticum (Poaceae), Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, Pankaj Jaiswal

Biology Faculty Publications and Presentations

Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum . The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium …

The Telomere And Telomerase Activity, Kerrie Conwell

The Review: A Journal of Undergraduate Student Research

In lieu of an abstract, below is the article's first paragraph.

In the past few years, a new area of genetics has emerged that has scientists in many other fields intrigued. The discovery of telomeres, the end segments on our chromosomes, and the enzyme that controls them, has evoked an interest in professionals from a wide range of specialties. Articles on the subject have appeared in journals of cell and molecular biology, microbiology, genetics, gerontology, and have even surfaced in the popular media. There is already a wealth of information to be found on the topic, yet there is many …

Sire Evaluation For Milking Duration, James Macedo

Dairy Science

The objective of this study was to utilize electronically recorded data from on-farm milk recording systems and herd management software to determine if a sire has a genetic influence on his daughter’s milking duration. Measurements of milking duration from three dairy facilities were taken between January 27, 2013 and January 31, 2013. These measurements supplied 25,070 observations, corresponding to 9,418 cows and 895 sires. These data were evaluated with a SAS alongside a herd-mate comparison. The statistical analysis demonstrated that a sire does have a genetic influence on the milking duration of his progeny. The Van Beek Brothers and Dairyland …

Attitudes And Beliefs Regarding Participation In Genomic Research Studies: Insights From Argentines Affected With Neural Tube Defects (Ntd), Ariel C. Armony

Center for Latin American Studies Publications

Over the last several years, the field of genetics and genomics has grown exponentially in comparison to other areas of medicine. The study of genomic medicine, however, goes beyond the reach of traditional genetics research and investigates the interaction between environmental factors and the genetic code. In this regard, the success of genomic studies depends on the participation of diverse populations; Latin American groups, however, are generally underrepresented in such studies. This research project, conducted via a focus group of Argentines residing in Buenos Aires, seeks to explore personal knowledge, attitudes, beliefs, and perceptions in one area of Latin America …

Detection And Quantification Of Methylation In Dna Using Solid-State Nanopores., Jiwook Shim, Gwendolyn I Humphreys, Bala Murali Venkatesan, Jan Marie Munz, Xueqing Zou, Chaitanya Sathe, Klaus Schulten, Farhad Kosari, Ann M Nardulli, George Vasmatzis, Rashid Bashir

College of Science & Mathematics Departmental Research

Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated in the presence of only a single bound protein, thereby giving a resolution of a single …

Adenosine Triphosphate (Atp) Is A Candidate Signaling Molecule In The Mitochondria-To-Nucleus Retrograde Response Pathway, Feng Zhang, Tammy Pracheil, Janet Thornton, Zhengchang Liu

Biological Sciences Faculty Publications

Intracellular communication from the mitochondria to the nucleus is achieved via the retrograde response. In budding yeast, the retrograde response, also known as the RTG pathway, is regulated positively by Rtg1, Rtg2, Rtg3 and Grr1 and negatively by Mks1, Lst8 and two 14-3-3 proteins, Bmh1/2. Activation of retrograde signaling leads to activation of Rtg1/3, two basic helix-loop-helix leucine zipper transcription factors. Rtg1/3 activation requires Rtg2, a cytoplasmic protein with an N-terminal adenosine triphosphate (ATP) binding domain belonging to the actin/Hsp70/sugar kinase superfamily. The critical regulatory step of the retrograde response is the interaction between Rtg2 and Mks1. Rtg2 binds to …

Assessing The Impact Of Differential Genotyping Errors On Rare Variant Tests Of Association, Morgan Mayer-Jochimsen, Shannon Fast, Nathan L. Tintle

Faculty Work Comprehensive List

Genotyping errors are well-known to impact the power and type I error rate in single marker tests of association. Genotyping errors that happen according to the same process in cases and controls are known as non-differential genotyping errors, whereas genotyping errors that occur with different processes in the cases and controls are known as differential genotype errors. For single marker tests, non-differential genotyping errors reduce power, while differential genotyping errors increase the type I error rate. However, little is known about the behavior of the new generation of rare variant tests of association in the presence of genotyping errors. In …

Genome-Wide Association Analyses Of Sow Reproduction And Lifetime Productivity, Daniel Ciobanu

Department of Animal Science: Faculty Publications

Concurrent with increased prolificacy, high sow death losses and replacement rates are serious economic and welfare issues facing producers. Reproductive failure is the most frequent reason for culling sows. Lifetime productivity is characterized by moderate heritability and high phenotypic variance and, as a result, substantial genetic variation is expected to exist in most populations. Traditional selection for sow reproductive longevity results is ineffective due to low heritability and late expression of the trait. The primary goal of this research project was to identify DNA markers associated with reproductive and sow lifetime productivity that can be used in nucleus herds to …

Landscape Genetics Of Leaf-Toed Geckos In The Tropical Dry Forest Of Northern Mexico, Christopher Blair, Victor H. Jimenez-Arcos, Fausto R. Mendez De La Cruz, Robert W. Murphy

Publications and Research

Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites …