Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Genetics (14)
- Physical Sciences and Mathematics (11)
- Biochemistry, Biophysics, and Structural Biology (9)
- Computational Biology (9)
- Bioinformatics (8)
-
- Mathematics (7)
- Molecular Biology (7)
- Applied Mathematics (6)
- Cell and Developmental Biology (6)
- Genomics (6)
- Cell Biology (5)
- Biochemistry (4)
- Ecology and Evolutionary Biology (4)
- Discrete Mathematics and Combinatorics (3)
- Dynamical Systems (3)
- Ordinary Differential Equations and Applied Dynamics (3)
- Statistics and Probability (3)
- Biology (2)
- Evolution (2)
- Molecular Genetics (2)
- Neuroscience and Neurobiology (2)
- Other Applied Mathematics (2)
- Other Ecology and Evolutionary Biology (2)
- Other Genetics and Genomics (2)
- Population Biology (2)
- Agriculture (1)
- Bioresource and Agricultural Engineering (1)
- Biostatistics (1)
- Keyword
-
- CRISPR (2)
- Pennycress (2)
- Seed meal (2)
- Aminoacyl-tRNA synthetase (aaRS) (1)
- Arabidopsis (1)
-
- Archaea (1)
- Beta distribution (1)
- Biodiesel (1)
- Biofuel (1)
- Bistability (1)
- Boolean Networks (1)
- CRISPR-Cas9 (1)
- Cell Wall (1)
- Cell to cell variation (1)
- Drosophila melanogaster (1)
- EMSA (1)
- Finite Dynamical Systems (1)
- Gamma tubulin (1)
- Gene Editing (1)
- Gene Regulatory Networks (1)
- Gene regulatory networks (1)
- Genes (1)
- Genome Defense (1)
- Genome editing (1)
- Germ Layer Formation (1)
- Glucosinolate (1)
- Homeotic genes (1)
- Homologous Chromosomes (1)
- Homology Searching (1)
- Hypocotyl (1)
- Publication Year
- Publication
- Publication Type
Articles 1 - 30 of 30
Full-Text Articles in Genetics and Genomics
Model-Free Identification Of Relevant Variables From Response Data, Alan Veliz-Cuba, David Murrugarra
Model-Free Identification Of Relevant Variables From Response Data, Alan Veliz-Cuba, David Murrugarra
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Reducing Seed Coat Fiber Content And Pod Shatter, And Engineering Medium Chain Fatty Acids-Containing Oil, In The Oilseed Crop Pennycress ( Thlaspi Arvense L. ), Maliheh Esfahanian
Reducing Seed Coat Fiber Content And Pod Shatter, And Engineering Medium Chain Fatty Acids-Containing Oil, In The Oilseed Crop Pennycress ( Thlaspi Arvense L. ), Maliheh Esfahanian
Theses and Dissertations
The overall goal of this thesis was to genetically improve agronomic traits of pennycress (Thlaspi arvense L.; Field Pennycress) and demonstrate the production of value-added designer seed oils to domesticate pennycress and enable its establishment as a new winter annual oilseed/meal/cover crop to be grown in temperate regions of the world. In the U.S. Midwest, pennycress can be double cropped on existing farmland during the time between corn harvest and subsequent planting of soybeans the following spring. Pennycress has the potential to produce 2,000 lbs/acre seeds, which at 33% by weight oil content and 20% protein, would yield 85 gallons/acre …
A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz
A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz
Theses and Dissertations
An ancient and ubiquitous set of enzymes known as the aminoacyl-tRNA synthetases are required for the viability of all organisms. The aminoacyl-tRNA synthetases catalyze the attachment of amino acids onto tRNA molecules. The aminoacylated, or charged, tRNA is then transported and utilized at the ribosome for the synthesis of proteins. The genome of the hyperthermophilic microorganism Sulfolobus islandicus (S. islandicus) harbors a unique leucyl-tRNA synthetase paralog, LeuRS-I, of unknown function. While its duplicate, LeuRS-F, carries out all the classical functions of LeuRS-family enzymes, LeuRS-I fails to charge leucine onto tRNALeu, despite its ability to activate this amino acid and bind …
The Effect Of Fcgammariia Polymorphisms On Dengue Outbreak Severity, Leah Darwin, Richard V. Clarke
The Effect Of Fcgammariia Polymorphisms On Dengue Outbreak Severity, Leah Darwin, Richard V. Clarke
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Genetic Polymorphism Of Bitter Taste Perception In Tempe, Arizona And Its Association With Nutritional Status, Daniel Woodley, Benjamin Cabrera
Genetic Polymorphism Of Bitter Taste Perception In Tempe, Arizona And Its Association With Nutritional Status, Daniel Woodley, Benjamin Cabrera
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
An Investigation Of Gene Regulatory Network State Space Variability, Sara Faye Liesman
An Investigation Of Gene Regulatory Network State Space Variability, Sara Faye Liesman
Theses and Dissertations
Genes are segments of DNA that provide a blueprint for cells and organisms to effectively control processes and regulations within individuals. There have been many attempts to quantify these processes, as a greater understanding of how genes operate could have large impacts on both personalized and precision medicine. Gene interactions are of particular interest, however, current biological methods can not easily reveal the details of these interactions. Therefore, we infer networks of interactions from gene expression data which we call a gene regulatory network, or GRN. Due to the robust behavior of genes and the inherent variability within interactions, models …
Elucidating The Role Of The High Aliphatic Glucosinolate ( Hag ) Genes In Pennycress ( Thlaspi Arvense L. ) Glucosinolate Production, Dalton Williams
Elucidating The Role Of The High Aliphatic Glucosinolate ( Hag ) Genes In Pennycress ( Thlaspi Arvense L. ) Glucosinolate Production, Dalton Williams
Theses and Dissertations
Pennycress (Thlaspi arvense L.) is a Brassica species being developed into an oilseed-producing winter cash cover crop. Similar to its relatives, rapeseed (Brassica napus L.) and camelina (Camelina sativa L.), pennycress seeds produce high levels of oil and protein (~34% oil and ~19% protein dry weight). For pennycress to be economically viable and environmentally sustainable as a crop, both the oil and seed meal must be utilized. Pennycress like other Brassicaceae, produces high levels of glucosinolates in the seed coat. Glucosinolates taste bitter and can be metabolized by the enzyme, myrosinase, into toxic isothiocyanates, nitriles, and epithionitriles. Seed meal containing …
Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun
Sdrap: An Annotation Pipeline For Highly Scrambled Genomes, Jasper Braun
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Network Structure And Dynamics Of Biological Systems, Deena R. Schmidt
Network Structure And Dynamics Of Biological Systems, Deena R. Schmidt
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Loop Homology Of Bi-Secondary Structures, Andrei Bura
Loop Homology Of Bi-Secondary Structures, Andrei Bura
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Quantifying Pollen Traits To Build A Mathematical Model Of Pollen Competition - A Biologist's Perspective, Rob Swanson, Alex Capaldi
Quantifying Pollen Traits To Build A Mathematical Model Of Pollen Competition - A Biologist's Perspective, Rob Swanson, Alex Capaldi
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka
Topology And Dynamics Of Gene Regulatory Networks: A Meta-Analysis, Claus Kadelka
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Stochastic Difference Model For Evolutional Dynamics Of Large Antigen Repertoires In African Trypanosomes, Fan Yu
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Developing Pennycress ( Thlaspi Arvense ) As A Biodiesel Feedstock Crop And Plant Model System, Michaela Mcginn
Developing Pennycress ( Thlaspi Arvense ) As A Biodiesel Feedstock Crop And Plant Model System, Michaela Mcginn
Theses and Dissertations
Thlapsi arvense L. (pennycress) is currently being developed as a profitable oilseed-producing winter annual cover crop with extreme cold tolerance and a rapid life cycle that can be grown on fallow farmland throughout the U.S. Midwest Corn Belt, controlling soil erosion and nutrient runoff while serving as an additional source of income for the American farmer without displacing food crops. The research comprising this dissertation demonstrates that pennycress can serve as a user-friendly model system highly similar to Arabidopsis thaliana, and is well-suited for both laboratory and field experimentation, being readily employable in existing growth facilities. After 10 generations of …
Bioinformatic Analysis Of The Evolution And Function Of Parasitoid Wasp Venom, Nathan T. Mortimer
Bioinformatic Analysis Of The Evolution And Function Of Parasitoid Wasp Venom, Nathan T. Mortimer
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
G-Onramp: Create Genome Browsers That Enable Undergraduate Students To Participate In Collaborative Genome Annotations, Wilson Leung, Yating Liu, Luke Sargent, Jeremy Goecks, Sarah C.R. Elgin
G-Onramp: Create Genome Browsers That Enable Undergraduate Students To Participate In Collaborative Genome Annotations, Wilson Leung, Yating Liu, Luke Sargent, Jeremy Goecks, Sarah C.R. Elgin
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Chromosome Conformation In Context, James Taylor
Chromosome Conformation In Context, James Taylor
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Kacsoh, Giovanni Bosco
A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Kacsoh, Giovanni Bosco
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Cage: A Tool For Identifying Genes With Correlated Spatiotemporal Expression, Basheer Becerra
Cage: A Tool For Identifying Genes With Correlated Spatiotemporal Expression, Basheer Becerra
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson
Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Study Of Antidepressant Molecular Structure Leading To Safer Dosing, Meera Garg
Study Of Antidepressant Molecular Structure Leading To Safer Dosing, Meera Garg
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Elucidating The Molecular Parameters And Mechanism Of Homology Searching During Meiosis In Neurospora Crassa, Nicholas Adam Rhoades
Elucidating The Molecular Parameters And Mechanism Of Homology Searching During Meiosis In Neurospora Crassa, Nicholas Adam Rhoades
Theses and Dissertations
Integration of foreign DNA into a host genome is often detrimental to the host organism, as the DNA is often of viral or transposon origin. Many organisms have established DNA surveillance and genome integrity mechanisms to defend against these harmful DNA insertions. Neurospora crassa, a filamentous fungus belonging to the Ascomycota group, has several DNA defense mechanisms to combat foreign DNA integration to its genome. One such mechanism is Meiotic Silencing of Unpaired DNA (MSUD). During meiosis, this remarkable system can detect unpaired genes on homologous chromosomes during sexual reproduction and silence their expression throughout meiosis. In order for the …
General Equations For Natural Selection Under Complete Dominance, Kasthuri Kannan, Adriana Heguy
General Equations For Natural Selection Under Complete Dominance, Kasthuri Kannan, Adriana Heguy
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Exploring The Space Of Rna Secondary Structures, Heather C. Smith
Exploring The Space Of Rna Secondary Structures, Heather C. Smith
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager
Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager
Spora: A Journal of Biomathematics
The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by discussing our …
Investigating The Roles And Interactions Of Sad-6 Within The Parameters Of Meiotic Silencing By Unpaired Dna ( Msud )., Zachary J. Smith
Investigating The Roles And Interactions Of Sad-6 Within The Parameters Of Meiotic Silencing By Unpaired Dna ( Msud )., Zachary J. Smith
Theses and Dissertations
Meiotic silencing by unpaired DNA (MSUD) is a process observed in the model organism Neurospora crassa. During this process unpaired DNA between homologous chromosomes is detected and silenced, resulting in the suppression of unpaired genes. The effects of MSUD can be seen using phenotypic markers such as the Roundspore gene and evidence supports the existence of a physical search for unpaired DNA. However, the mechanism for detecting unpaired DNA remains uncertain. Previously, we have shown evidence that a Rad54-like protein, SAD-6 is required for the efficient completion of MSUD and may be necessary for the detection of unpaired DNA. Currently, …
Cell Wall Mutants In Arabidopsis Thaliana, Christy Jane Moore
Cell Wall Mutants In Arabidopsis Thaliana, Christy Jane Moore
Theses and Dissertations
Plant cell walls are versatile structures, playing important roles in communication, defense, organization and support. The importance of each of these functions varies by cell type, with specialized cells often utilizing one or two functions more than others. Trichomes, or leaf hairs, and hypocotyl cells for instance, exhibit distinct cell wall characteristics. Trichomes have developed very thick cell walls with several raised structures, known as papillae, on their surfaces. It is believed that these cells function in defense against predators, making it difficult to crawl on the leaf surface, and in protection against ultra violet radiation, through refraction of light …
Investigating The Initial Detection Stage Of Meiotic Silencing By Unpaired Dna In The Model Organism Neurospora Crassa, Pegan A. Sauls
Investigating The Initial Detection Stage Of Meiotic Silencing By Unpaired Dna In The Model Organism Neurospora Crassa, Pegan A. Sauls
Theses and Dissertations
In an attempt to neutralize transposable elements or retrovirus invasions Neurospora crassa will rely on one of its many genome defense mechanism, Meiotic Silencing by Unpaired DNA (MSUD). MSUD works in a two-step process that first detects unpaired sequences between homologous chromosomes followed by downstream silenced expression of the sequence. The ultimate silencing stage of MSUD is widely accepted to operate through an RNAi-like system. However, the mechanics of the detection step of MSUD remains elusive. The research presented attempts to elaborate on how the initial stage of MSUD occurs and its specifics. First, a genetic approach is utilized to …
Genetic Analysis Of Ton2 Dependent Processes In Microtubule Organization In Arabidopsis Thaliana, Samantha Nicole Atkinson
Genetic Analysis Of Ton2 Dependent Processes In Microtubule Organization In Arabidopsis Thaliana, Samantha Nicole Atkinson
Theses and Dissertations
Microtubules carry out many functions within the cell. They're used during mitosis and meiosis to move chromosomes to opposite sides of the cell so that cell division can occur. They're also used as structural support for the cell and are involved in establishing the cell shape. Microtubules are also able to reorient from a longitudinal orientation to a transverse orientation in response to gibberellic acid and auxin (two hormones that are involved in cell elongation). The mechanism for how this reorientation occurs is unknown. The TONNEAU2 (TON2) protein is necessary for proper microtubule organization. We looked at how TON2 affects …
Abd-A Regulation By The Iab-8 Noncoding Rna, Maheshwar Gummalla, Robert K. Maeda, Javier J. Castro Alvarez, Henrik Gyurkovics, Kevin A. Edwards, Swetha Singari, Welcome Bender
Abd-A Regulation By The Iab-8 Noncoding Rna, Maheshwar Gummalla, Robert K. Maeda, Javier J. Castro Alvarez, Henrik Gyurkovics, Kevin A. Edwards, Swetha Singari, Welcome Bender
Faculty Publications – Biological Sciences
The homeotic genes in Drosophila melanogaster are aligned on the chromosome in the order of the body segments that they affect. The genes affecting the more posterior segments repress the more anterior genes. This posterior dominance rule must be qualified in the case of abdominal-A (abd-A) repression by Abdominal-B (Abd-B). Animals lacking Abd-B show ectopic expression of abd-A in the epidermis of the eighth abdominal segment, but not in the central nervous system. Repression in these neuronal cells is accomplished by a 92 kb noncoding RNA. This "iab-8 RNA" produces a micro RNA to repress abd-A, but also has a …