Other Genetics and Genomics Commons^™

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381

Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.

Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of …

The Potential Of Epigenetics Research To Transform Conceptions Of Phenotype Development, David S. Moore

Pitzer Faculty Publications and Research

Epigenetics remains an exciting subdiscipline of biology, generating discoveries and insights about development. Because epigenetic phenomena can draw attention to the dynamic, interactional, and probabilistic nature of phenotype development, epigenetics research could hasten the demise of both nature-nurture debates and reductionist, genetically determinist perspectives on phenotype development. However, new data alone will not inevitably transform conceptualizations of phenotype origins, because it remains possible to assimilate epigenetic phenomena into traditional conceptual frameworks; epigenetic discoveries could even strengthen biologically determinist conclusions if traditional conceptualizations are retained. Although epigenetics will not force conceptual transformation, epigenetics research encourages the dismissal of the nature-nurture dichotomy …

K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler

Graduate Student Theses, Dissertations, & Professional Papers

Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …

Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

A Population Genetic Investigation Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi) On Eglin Air Force Base, Alexander S. Wendt

College of Graduate Studies: Theses & Dissertations

The reticulated flatwoods salamander (RFS) is an endangered salamander with a unique life history. One of the largest known, best studied refuges for RFS is found on Eglin Air Force Base, and these RFS have been sampled and managed extensively since 2010. My thesis seeks to better understand RFS by using genetic techniques to address several unknowns, including: 1) determining the population structuring of RFS and the manageable units for species conservation, 2) estimating the size and status of populations, 3) understanding dispersal of RFS and factors that influence this, 4) exploring the breeding biology and recruitment patterns of RFS …

Punctuated Evolution Within A Eurythermic Genus (Mesenchytraeus) Of Segmented Worms: Genetic Modification Of The Glacier Ice Worm F1f0 Atp Synthase, Shirley A. Lang

Graduate School of Biomedical Sciences Theses and Dissertations

Segmented worms (Annelida) are among the most successful animal inhabitants of extreme environments worldwide. An unusual group of Mesenchytraeus worms endemic to the Pacific Northwest of North America occupy geographically proximal ecozones ranging from low elevation temperate rainforests to high altitude glaciers. Along this altitudinal transect, Mesenchytraeus representatives from disparate habitat types were collected and subjected to deep mitochondrial and nuclear phylogenetic analyses. Evidence presented here employing modern bioinformatic analyses (i.e., maximum likelihood, Bayesian inference, multi-species coalescent) supports a Mesenchytraeus “explosion” in the upper Miocene (5-10 million years ago) that gave rise to ice, snow and terrestrial worms, derived from …

Exploring Molecular Mechanisms Of Paradoxical Activation In The Braf Kinase Dimers: Atomistic Simulations Of Conformational Dynamics And Modeling Of Allosteric Communication Networks And Signaling Pathways, Amanda Tse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We …

Sheep Updates 2016, Mick Keogh, David Cornish, Michael Chilvers, Gerry Hinkley, Danielle England, Rosemary Bartle, Brad Wooldridge, Norm Santich, John Young, Ashley Herbert, Jamie Heinrich, Graeme Howie, Bruce Mullan

Sheep Updates

This session covers eleven papers from different authors:

1. Forward, Dr Bruce Mullan, Director Sheep Industry Development, Department of Agriculture and Food Western Australia

2. The Australian sheep industry in 2025, Mick Keogh, Australian Farm Institute

3. Decision making in a risky environment, David Cornish, Cornish Consulting

4. Business Transitioning, Michael Chilvers, Nile Tasmania

5. Advisory Boards in WA Agriculture - making life 'easier' for everyone, Gerry Hinkley, Producer, Tincurrin and Danielle England, Aginnovate

6. Principles of Successful Family Business Succession Strategies, Rosemary Bartle, Succession Planning Facilitator, Rabobank

7. Diversifying the Feedbase...is the …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca²⁺ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we …

The Role Of Daf-19 In Non-Ciliated Neurons: How Is Neural Development Regulated By Different Daf-19 Isoforms?, Zabdiel Ek Vazquez

Lawrence University Honors Projects

A degenerative disease-like phenotype, specifically reduction in synaptic protein levels in adult worms, is correlated with loss-of-function of the only RFX transcription factor gene, daf-19, in C. elegans. This gene encodes four known transcription factor isoforms, two of which are correlated with particular functions. The DAF-19C isoform activates genes responsible for cilia development, while DAF-19M is needed for cilia specification in males. A comparison of the transcriptome of daf-19 null and isogenic wild type adult worms suggests both positive and negative regulation of gene expression is correlated with the presence of DAF-19 proteins. We have assessed DAF-19 regulation …

Identification Of Qtls For Resistance Against Rhizoctonia Solani And Phoma Glycinicola In Soybeans (Glycine Max L. Merr), Herbert Sserunkuma

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

A QTL (Quantitative trait locus) is a chromosome location of a gene controlling a specific phenotypic trait. The trait maybe governed by multiple genes. Fungal pathogens are responsible for over 50% of all soybean diseases. Rhizoctonia solani Kühn causes seedling dumping off, root and hypocotyl rots and other disease in soybeans. Phoma glycinicola de Gruyter & Boerema causes Red leaf blotch disease, predominantly in Sub-Saharan Africa. There is no reported complete resistance against these fungal pathogens in soybeans. Reaction to R.solani is reportedly a quantitative trait controlled by major and minor genes. Three QTLs contributing to reaction to R. solani …

The Effects Of Epigenetics On Stress Response, Kevin Suddarth

Themis: Research Journal of Justice Studies and Forensic Science

Despite the vast amount of resources at the disposal of humanity today, the intricacies of human biology are often a mystery. The chemical and biological products of the human genome have been well studied and documented, but many of the chemical and neurological pathways are missing quite a few details. The human stress response is one of the most primal and valuable functions of this code that developed as a self- preservation mechanism (Hans, 1975) to naturally increase the odds of procreation. However, this function is prone to overload, particularly in individuals with certain epigenetic traits instilled by early life …

Beyond Dna: Epigenetics And Proteomics In Forensic Science, Diane F. Eilerts

Themis: Research Journal of Justice Studies and Forensic Science

The use of genetic evidence in criminal cases is well established and has improved the public opinion and credibility of forensic science. However, several shortcomings associated with current genetic profiling techniques exist. Scientific research aimed at increasing the overall knowledge and understanding of biological factors will lead to the development of methods capable of improving the discriminating power of DNA evidence, overcoming limitations associated with DNA evidence, or complementing current methods of DNA profiling. Increased research in the fields of epigenetics and proteomics are particularly promising and relevant to forensic science. Research suggests that epigenetic biomarkers can be used to …

Next-Generation Sequencing Of A Multi-Drug Resistance Plasmid Captured From Stream Sediment, Kevin G. Libuit

Masters Theses, 2010-2019

Plasmids in agriculturally-impacted bodies of water may play a significant role in the dissemination of antibiotic resistance. Previously, Erika Gehr, as part of her M.S. thesis work in our laboratory, captured environmental plasmids without cultivation of host bacteria from stream sediment into Escherichia coli. Individual plasmids were capable of conferring resistance to a surprising array of antibiotics including aminoglycosides and extended-spectrum β-lactams. In this study, we developed a method to sequence multi-drug resistance plasmids using both Oxford Nanopore MinION and Ion Torrent Personal Genome Machine sequencers. Plasmid pEG1-1 was sequenced on both platforms and a hybrid assembly utilizing data …

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 …

Transgenerational Epigenetic Inheritance Via Environmental Stress In Caenorhabditis Elegans, Monica A. Arroliga

Dissertations, Masters Theses, Capstones, and Culminating Projects

No abstract available

Characterization Of Induced Rnai Silencing Of Vaccinia Virus Essential Genes, Kewa Jiang

University Scholar Projects

Vaccinia virus (VACV) is a large double-stranded DNA virus and the prototypical member of the family Poxviridae and is most notable for its use as the vaccine that eradicated smallpox (variola virus). More recently, VACV has been used to develop recombinant vaccines and immunotherapies. However, many of these processes require VACV replication to be tightly controlled. RNA interference (RNAi) is a powerful tool for in vitro silencing of mRNAs that are complimentary to 19-21 base pairs (bp) of double-stranded RNA (dsRNA). This project outlines the design and preliminary analysis of two inducible RNAi silencing constructs targeting multiple VACV essential genes …