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Articles 1 - 25 of 25
Full-Text Articles in Genetics
A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes
A Machine Learning Model Of Perturb-Seq Data For Use In Space Flight Gene Expression Profile Analysis, Liam F. Johnson, James Casaletto, Lauren Sanders, Sylvain Costes
Graduate Industrial Research Symposium
The genetic perturbations caused by spaceflight on biological systems tend to have a system-wide effect which is often difficult to deconvolute it into individual signals with specific points of origin. Single cell multi-omic data can provide a profile of the perturbational effects, but does not necessarily indicate the initial point of interference within the network. The objective of this project is to take advantage of large scale and genome-wide perturbational datasets by using them to train a tuned machine learning model that is capable of predicting the effects of unseen perturbations in new data. Perturb-Seq datasets are large libraries of …
Exploring The Evolution Of Callose Synthase In Green Plants, Giovanna Durante
Exploring The Evolution Of Callose Synthase In Green Plants, Giovanna Durante
The Journal of Purdue Undergraduate Research
No abstract provided.
Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase
Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase
Graduate Industrial Research Symposium
Genetic frameshifts are a mutation in which
a nucleotide skip leads to a shift in the
reading frame. In viruses, these frameshifts
can be programmed using a slippery
sequence to bypass the stop codon
associated with the initial protein. This
allows for variable control of protein
expression. In bacteriophages, translational
frameshifts have been identified but only a
few have been proven experimentally. Using
experimental data and comparative
genomics, non-traditional slippery
sequences can be identified as assisting in
controlling the protein coding throughout
viruses. Novel slippery sequences can aid in
the understanding of protein expression in
biological environments and further the …
Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran
Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran
The Summer Undergraduate Research Fellowship (SURF) Symposium
Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being …
Genetic Study Of Carotenoids In Maize Grain (Zea Mays L.), Oscar Rafael Espejel Venado
Genetic Study Of Carotenoids In Maize Grain (Zea Mays L.), Oscar Rafael Espejel Venado
Open Access Theses
Pro-Vitamin A (proVA) carotenoids, which are converted into retinol (Vitamin A) in the human body, have been the subject of human nutrition studies and are a target for biofortification of staple crops. Historically, β-carotene has been the principal target for enhancing levels of proVA, yet there is recent interest in enhancing the proVA carotenoid β-cryptoxanthin. Studies have shown that β-cryptoxanthin has excellent bioavailability, and its use in maize may be nearly as effective as β-carotene in providing retinol. The primary aim of this study was to gain a better understanding of the genetic control of levels of β-cryptoxanthin, conversion of …
Improving And Elucidating Factors Regulating Black Walnut (Juglans Nigra L.) Clonal Propagation, Micah E. Stevens
Improving And Elucidating Factors Regulating Black Walnut (Juglans Nigra L.) Clonal Propagation, Micah E. Stevens
Open Access Dissertations
Black walnut (Juglans nigra L.) is a fine hardwood tree species native to the central hardwood region of the United States. High-quality black walnut timber is highly desirable. Traded in both regional and global markets, it has been used for veneer, and the manufacture of high-end products such as cabinets, furniture, and gunstocks. As a result of its high economic value, black walnut has been commercially cultivated for many years, and breeding programs have generated superior timber genotypes with improved marketable traits. Once elite genotypes were developed, it was quickly recognized that black walnut was recalcitrant to clonal propagation …
Performance Benchmarks For Scholarly Metrics Associated With Fisheries And Wildlife Faculty, Robert K. Swihart, Mekala Sundaram, Tomas O. Höök, James Andrew Dewoody, Kenneth F. Kellner
Performance Benchmarks For Scholarly Metrics Associated With Fisheries And Wildlife Faculty, Robert K. Swihart, Mekala Sundaram, Tomas O. Höök, James Andrew Dewoody, Kenneth F. Kellner
Department of Forestry & Natural Resources Faculty Publications
Research productivity and impact are often considered in professional evaluations of academics, and performance metrics based on publications and citations increasingly are used in such evaluations. To promote evidence-based and informed use of these metrics, we collected publication and citation data for 437 tenure-track faculty members at 33 research-extensive universities in the United States belonging to the National Association of University Fisheries and Wildlife Programs. For each faculty member, we computed 8 commonly used performance metrics based on numbers of publications and citations, and recorded covariates including academic age (time since Ph.D.), sex, percentage of appointment devoted to research, and …
Axonal Transport And Life Cycle Of Mitochondria In Parkinson's Disease Model, Hyun Sung
Axonal Transport And Life Cycle Of Mitochondria In Parkinson's Disease Model, Hyun Sung
Open Access Dissertations
In neurons, normal distribution and selective removal of mitochondria are essential for preserving compartmentalized cellular function. Parkin, an E3 ubiquitin ligase associated with familial Parkinson’s disease, has been implicated in mitochondrial dynamics and removal. However, it is not clear how Parkin plays a role in mitochondrial turnover in vivo, and whether the mature neurons possess a compartmentalized Parkin-dependent mitochondrial life cycle. Using the live Drosophila nervous system, here, I investigate the involvement of Parkin in mitochondrial dynamics; organelle distribution, morphology and removal. Parkin deficient animals displayed less number of axonal mitochondria without disturbing organelle motility behaviors, morphology and metabolic state. …
Using The Intact Method To Study Pickle In Individual Cell Types, Jacqueline L. Phipps, Daniela N. Martir, Ben Carter, Joe Ogas
Using The Intact Method To Study Pickle In Individual Cell Types, Jacqueline L. Phipps, Daniela N. Martir, Ben Carter, Joe Ogas
The Summer Undergraduate Research Fellowship (SURF) Symposium
Cell differentiation is an essential part of development in multicellular organisms. Cells with identical genomic DNA are able to differentiate into a variety of tissues due to selective expression and repression of genes. This tissue-specific gene expression is enabled in part by proteins called chromatin remodelers, which can move, remove, or restructure histone proteins to restrict or allow physical access to genomic DNA. PICKLE (PKL) is a member of the CHD family of ATP-dependent chromatin remodelers that promotes cellular identity in the plant model organism Arabidopsis thaliana. PKL promotes cell identity by silencing embryonic genes during seed germination by promoting …
Captive Breeding Protocols And Their Impact On Genetic Diversity In White-Footed Mice (Peromyscus Leucopus): Implications For Threatened And Endangered Species, Maureen C. Lamb, Janna R. Willoughby, J. Andrew Dewoody
Captive Breeding Protocols And Their Impact On Genetic Diversity In White-Footed Mice (Peromyscus Leucopus): Implications For Threatened And Endangered Species, Maureen C. Lamb, Janna R. Willoughby, J. Andrew Dewoody
The Summer Undergraduate Research Fellowship (SURF) Symposium
Captive breeding protocols used in zoos often are aimed at increasing population sizes and retaining genetic diversity of endangered species. However, captive breeding causes genetic adaptation to captivity that can lead to an overall decrease in genetic diversity and reduce chances of a successful reintroduction to the wild. In this study, we assess how 3 different breeding protocols—random mating, preferential breeding of individuals with the lowest mean kinship scores, and selection for docility—affect the variability of mitochondrial DNA in white-footed mice (Peromyscus leucopus). We used mice that were captured from the wild but were mated for up to …
Genetic, Agronomic And Compositional Characterization Of Brown Midrib Sweet Sorghum Lignocellulosic Biomass For Ethanol Production, Luis A. Rivera Burgos
Genetic, Agronomic And Compositional Characterization Of Brown Midrib Sweet Sorghum Lignocellulosic Biomass For Ethanol Production, Luis A. Rivera Burgos
Open Access Dissertations
Sorghum is a promising bioenergy crop due to its unique phenotypic and genotypic attributes. Quality (low lignin and high stem sugar concentration) and quantity (biomass yield, plant height, plant maturity, etc.) biomass traits are key contributors to ethanol yield and production. In this study, a 236 sorghum recombinant inbred line (RIL) population was subjected to genetic, agronomic and compositional characterization for ethanol yield and production. We found that the sweet mutation enhances biomass quantity traits in the RILs which translates to higher ethanol production and biomass quality which improves ethanol yield. The variance components showed from moderate to high heritability …
Using Large Snp Datasets To Understand The Genetic Mechanisms Of Complex Traits In Arabidopsis Thaliana, Elisabeth S. Harrison
Using Large Snp Datasets To Understand The Genetic Mechanisms Of Complex Traits In Arabidopsis Thaliana, Elisabeth S. Harrison
Open Access Theses
Arabidopsis thaliana, as a model species, has been widely genotyped and sequenced. Many studies have been done to understand the kinship and population structure of the species. This data and information is beneficial for understanding the genetic mechanisms of complex traits. In this thesis, we first used genotyped data for 5,967 accessions to study the occurrence of tetraploidy in the species. We found that tetraploidy is a transient character state, and the species is a diploid species. Secondly, we used 211K and 1.6M SNPs for 440 accessions to run genome-wide analyses (GWA) for four traits: glufosinate tolerance, hybrid incompatibilities, seed …
Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang
Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang
Open Access Dissertations
DNA methylation is a key epigenetic mark for transcriptional gene silencing in many eukaryotes. DNA methylation status can be dynamically controlled by methylation and active demethylation processes. Compared to the well-known mechanisms of DNA methylation, the mechanisms of DNA demethylation and its regulation are poorly understood. In order to better understand the DNA demethylation pathway, we developed two genetic screening systems in Arabidopsis to identify new components involved in the DNA demethylation. In the first system, which is based on 35S promoter driven SUC2 (sucrose transporter 2) transgene, a mutant (91-1) was isolated and map-based cloning identified the …
Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad
Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad
Open Access Dissertations
Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …
Regulation Of Mor By Different Abiotic Stresses In Arabidopsis Thaliana, Luke Stepan, Rucha Karve, Anjali Iyer-Pascuzzi
Regulation Of Mor By Different Abiotic Stresses In Arabidopsis Thaliana, Luke Stepan, Rucha Karve, Anjali Iyer-Pascuzzi
The Summer Undergraduate Research Fellowship (SURF) Symposium
The climate is changing and as a consequence the environment is becoming hotter and drier. How different plants will react to these changes is unknown. Identification of genes involved in stress tolerance can help predict plant-environment interactions and lead to stress tolerant plants. The MOR gene (Modulator Of Root ROS, ROS = Reactive Oxygen Species) in the model plant Arabidopsis thaliana encodes a transcription factor that may regulate stress responses, as mor mutants are drought tolerant. We hypothesized that MOR expression changes in response to different abiotic stress stimuli. We tested MOR expression in response to salt (NaCl), abscisic acid …
Development Of Transgenic North American White Ash (Fraxinus Americana) Expressing A Bacillus Thuringiensis Protein For Management Of The Emerald Ash Borer, Eric A. Dean, Paula M. Pijut Phd., Micah E. Stevens
Development Of Transgenic North American White Ash (Fraxinus Americana) Expressing A Bacillus Thuringiensis Protein For Management Of The Emerald Ash Borer, Eric A. Dean, Paula M. Pijut Phd., Micah E. Stevens
The Summer Undergraduate Research Fellowship (SURF) Symposium
White ash (WA), Fraxinus americana, is an integral part of the hardwood forest ecosystem. Economically, WA provides wood for important products such as baseball bats, tool handles, and hardwood flooring. Ecologically WA provides cover and mast to support wildlife. The emerald ash borer (EAB) is a significant threat to all ash species because of a lack of native resistance in North American ash trees, its rapid spread, and the ineffectiveness and expense of control measures. EAB is a non-native beetle that consumes tree vascular tissue while in the larval stage. The development of an Agrobacterium-mediated transformation protocol may …
Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park
Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park
Open Access Theses
Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …
Naturalized Offspring From An 85-Year-Old Chinese Chestnut (Castanea Mollissima) Planting: Stand Dynamics And Genetic Relationships, Amy Christel Miller
Naturalized Offspring From An 85-Year-Old Chinese Chestnut (Castanea Mollissima) Planting: Stand Dynamics And Genetic Relationships, Amy Christel Miller
Open Access Theses
Chestnuts, members of the genus Castanea , family Fagaceae, are valuable worldwide, and all species have noteworthy ecological, economic, and cultural importance in their native ranges. Historically, American chestnut (Castanea dentata (Marshall) Borkh.) was an abundant tree species in eastern North America until its decimation in the early 20 th century by chestnut blight, caused by the fungus Cryphonectria parasitica . To regain the benefits of this prized species in North America, efforts are ongoing to produce and introduce blight-resistant hybrids of C. dentata and the blight-resistant Chinese chestnut ( C. mollissima Blume). It is important that the C. …
Identification Of Set1 Target Genes, William Beyer, Scott D. Briggs
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 …
Forward Genetic Screen Of Trichomes For Discovery Of Cytoskeleton-Based Mutants, Adam M. Fessenden, Samuel Belteton, Daniel B. Szymanski
Forward Genetic Screen Of Trichomes For Discovery Of Cytoskeleton-Based Mutants, Adam M. Fessenden, Samuel Belteton, Daniel B. Szymanski
The Summer Undergraduate Research Fellowship (SURF) Symposium
Understanding plant cell development and what genes influence cell growth can lead to breakthroughs in beneficial areas such as bioremediation, agricultural production, and biofuels. However, information on many of the genes that control plant cell growth is either unknown or severely limited. Further research to fully comprehend the genetic pathways within the cells will enable the genetic engineering of plants to further benefit society. One approach is the combined use of a forward genetic screen, sophisticated growth analysis, and gene identification. Using Arabidopsis thaliana trichomes, leaf hairs, as a model system, the mutagenized population of thousands of plants was screened …
Saccharomyces Cerevisiae Cdc7 Homology In Drosophila Melanogaster, Marcus R. Hosler, Robert E. Stephenson, Vikki M. Weake
Saccharomyces Cerevisiae Cdc7 Homology In Drosophila Melanogaster, Marcus R. Hosler, Robert E. Stephenson, Vikki M. Weake
The Summer Undergraduate Research Fellowship (SURF) Symposium
Saccharomyces cerevisiae Dbf4(Dumbbell former 4) and Cdc7(Cell Division Cycle 7) form a complex that phosphorylates Mcm2 (Minichromosome maintenance 2) to initiate DNA replication. Cdc7 is a target for cancer research because there is a Cdc7 ortholog in humans that is necessary for DNA replication and cell survival. Our goal is to characterise a putative Cdc7 homolog in Drosophila melanogaster (dCdc7). We have previously shown that expression of the known Drosophila Dbf4 ortholog, Chiffon, and dCdc7 can rescue yeast cells deficient in active Cdc7. Our hypothesis is that the dCdc7 is activated by Chiffon to phosphorylate MCM2. To test this hypothesis, …
Notchless Interacts With Multiple Signaling Pathways During Mouse Peri-Implantation Development, Chiao-Ling Lo
Notchless Interacts With Multiple Signaling Pathways During Mouse Peri-Implantation Development, Chiao-Ling Lo
Open Access Dissertations
During peri-implantation, the embryo transitions from a suspension environment in the fallopian tubes to an adherent system within the uterus. Successful transition requires maternal and fetal signaling cascades that establish maternal-fetal boundaries. Failure is common, as ~ 25% of all human pregnancies terminate during these steps. A large-scale mutation study in mice produced two mutants (l11Jus1 and l11Jus4) that are excellent models of this transition. l11Jus1 and l11Jus4 contain missense mutations in the Notchless homolog 1 (Drosophila) (Nle1) gene. NLE1 is thought to signal via the canonical NOTCH pathway in vertebrates. Although in invertebrates and lower vertebrates, NOTCH signaling directs …
Natural Genetic Variation Affecting Calcium Homeostasis, Rebecca Anna Replogle
Natural Genetic Variation Affecting Calcium Homeostasis, Rebecca Anna Replogle
Open Access Dissertations
Calcium (Ca) is essential for multiple functions within the body including skeletal health. The level of Ca in the serum is tightly regulated. During periods of habitual low Ca intake, the body senses a decrease in serum Ca and increases renal conversion of 25 hydroxyvitamin D (25(OH)D) to 1,25 dihydroxyvitamin D (1,25(OH)2D). 1,25(OH)2D acts through the vitamin D receptor (VDR) to increase intestinal Ca absorption, renal Ca reabsorption and skeletal Ca resorption. Efficient intestinal Ca absorption, especially during periods of low Ca intake, is critical for protecting bone mass. Ca absorption and its primary regulator, 1,25(OH)2D, are affected by both …
The Genetic Architecture Of Juvenile Migration In Rainbow Trout (Oncorhynchus Mykiss), Benjamin Charles Hecht
The Genetic Architecture Of Juvenile Migration In Rainbow Trout (Oncorhynchus Mykiss), Benjamin Charles Hecht
Open Access Dissertations
Animal migrations play a critical role in the health and balance of ecological systems and in the evolution and diversification of species, and this is perhaps best displayed amongst salmonid fishes (salmon, trout, and char) who exhibit variation in the propensity to migrate both within and among species. Rainbow and steelhead trout (Oncorhynchus mykiss), members of the salmonid family of fishes, capture this variation throughout their native range. Some populations and ecotypes will remain resident in freshwater habitats throughout their life history; while others have the ability to embark on tremendous marine migrations. Those that migrate undergo a suite of …
Understanding Osmoregulation And Immunity In Heteromyid Rodents Through Insights Gained From Rna-Seq, Nicholas John Marra
Understanding Osmoregulation And Immunity In Heteromyid Rodents Through Insights Gained From Rna-Seq, Nicholas John Marra
Open Access Dissertations
Understanding the genetic basis of adaptation is one of the central questions of evolutionary genetics. In the face of selective pressure, individuals with adaptive phenotypes survive and pass on their beneficial alleles that conferred this fitness advantage. Over sufficient time scales and under strong selection, differences accumulate between taxa in the form of physical and/or behavioral traits that have been shaped differently. By looking at the transcriptomes of related taxa we can identify sequence and regulatory differences that represent molecular signatures of these different selection regimes. When we study these differences between taxa that have evolved under opposing selective forces …