Genetics and Genomics Commons^™

Common Garden Experiment Reveals Altered Nutritional Values And Dna Methylation Profiles In Micropropagated Three Elite Ghanaian Sweet Potato Genotypes, Belinda Akomeah, Marian D. Quain, Sunita A. Ramesh, Lakshay Anand, Carlos M. Rodríguez López

Horticulture Faculty Publications

Micronutrient deficiency is the cause of multiple diseases in developing countries. Staple crop biofortification is an efficient means to combat such deficiencies in the diets of local consumers. Biofortified lines of sweet potato (Ipomoea batata L. Lam) with enhanced beta-carotene content have been developed in Ghana to alleviate Vitamin A Deficiency. These genotypes are propagated using meristem micropropagation to ensure the generation of virus-free propagules. In vitro culture exposes micropropagated plants to conditions that can lead to the accumulation of somaclonal variation with the potential to generate unwanted aberrant phenotypes. However, the effect of micropropagation induced somaclonal variation on …

Developing Technologically Advanced Research In Low- And Middle-Income Countries, Isa Abdulkadir, Tina Slusher, Fidelia Bode-Thomas, Sean Riordan, Jean-Baptiste Lepichon, Laila Hassan, Shehu Abdullahi, Akinyemi Ofakunrin, Stephen Oguche, Steven Shapiro, William Ogala

Posters

This poster presents a collaboration between a group of scientists in Nigeria and the USA in developing a genomic research project and the solutions adopted in tackling the ethical implications and partnership equity and ownership of such a project.

Phylogeny Of The Australian Solanum Dioicum Group Using Seven Nuclear Genes: Testing Symon’S Fruit And Seed Dispersal Hypotheses., Christopher T. Martine, Ingrid E. Jordon-Thaden, Angela J. Mcdonnell, Jason T. Cantley, Daniel S. Hayes, Morgan D. Roche, Emma S. Frawley, Ian S. Gilman, David C. Tank

Faculty Journal Articles

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed …

Transcriptional Regulation Factors Of The Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 (Slc25a13): Usf1 As Basal Factor And Foxa2 As Activator In Liver Cells, Paolo Convertini, Simona Todisco, Francesco De Santis, Ilaria Pappalardo, Dominga Iacobazzi, Maria Antonietta Castiglione Morelli, Yvonne N. Fondufe-Mittendorf, Giuseppe Martelli, Ferdinando Palmieri, Vittoria Infantino

Molecular and Cellular Biochemistry Faculty Publications

Mitochondrial carriers catalyse the translocation of numerous metabolites across the inner mitochondrial membrane, playing a key role in different cell functions. For this reason, mitochondrial carrier gene expression needs tight regulation. The human SLC25A13 gene, encoding for the mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), catalyses the electrogenic exchange of aspartate for glutamate plus a proton, thus taking part in many metabolic processes including the malate-aspartate shuttle. By the luciferase (LUC) activity of promoter deletion constructs we identified the putative promoter region, comprising the proximal promoter (−442 bp/−19 bp), as well as an enhancer region (−968 bp/−768 bp). Furthermore, with different …

Deletion Of Uls1 Confers Damage Tolerance In Sgs1 Mutants Through A Top3-Dependent D-Loop Mediated Fork Restart Pathway, M. Rebecca Glineburg, Eleanor Johns, F. Brad Johnson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Homologous recombination (HR)-based repair during DNA replication can apparently utilize several partially overlapping repair pathways in response to any given lesion. A key player in HR repair is the Sgs1-Top3-Rmi1 (STR) complex, which is critical for resolving X-shaped recombination intermediates formed following bypass of methyl methanesulfonate (MMS)-induced damage. STR mutants are also sensitive to the ribonucleotide reductase inhibitor, hydroxyurea (HU), but unlike MMS treatment, HU treatment is not accompanied by X-structure accumulation, and it is thus unclear how STR functions in this context. Here we provide evidence that HU-induced fork stalling enlists Top3 prior to recombination intermediate formation. The resistance …

Rediscovering The Axolotl As A Model For Thyroid Hormone Dependent Development, Anne Crowner, Shivam Khatri, Dana Blichmann, S. Randal Voss

Neuroscience Faculty Publications

The Mexican axolotl (Ambystoma mexicanum) is an important model organism in biomedical research. Much current attention is focused on the axolotl's amazing ability to regenerate tissues and whole organs after injury. However, not forgotten is the axolotl's equally amazing ability to thwart aspects of tissue maturation and retain juvenile morphology into the adult phase of life. Unlike close tiger salamander relatives that undergo a thyroid hormone regulated metamorphosis, the axolotl does not typically undergo a metamorphosis. Instead, the axolotl exhibits a paedomorphic mode of development that enables a completely aquatic life cycle. The evolution of paedomorphosis allowed axolotls …

Improved Draft Genome Sequence Of Bacillus Sp. Strain Yf23, Which Has Plant Growth-Promoting Activity, Ye Xia, Seth Debolt, Qin Ma, Adam Mcdermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides

Horticulture Faculty Publications

We report here the improved draft genome sequence of Bacillus sp. strain YF23, a bacterium originally isolated from switchgrass (Panicum virgatum) plants and shown to exhibit plant growth-promoting activity. The genome comprised 5.82 Mbp, containing 5,933 genes, with 193 as RNA genes, and a GC content of 35.10%.

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point …

Small Molecule Kras Agonist For Mutant Kras Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, Xingming Deng

Articles, Abstracts, and Reports

BACKGROUND: Lung cancer patients with KRAS mutation(s) have a poor prognosis due in part to the development of resistance to currently available therapeutic interventions. Development of a new class of anticancer agents that directly targets KRAS may provide a more attractive option for the treatment of KRAS-mutant lung cancer.

RESULTS: Here we identified a small molecule KRAS agonist, KRA-533, that binds the GTP/GDP-binding pocket of KRAS. In vitro GDP/GTP exchange assay reveals that KRA-533 activates KRAS by preventing the cleavage of GTP into GDP, leading to the accumulation of GTP-KRAS, an active form of KRAS. Treatment of human lung cancer …

Gene Lifestyle Interactions With Relation To Obesity, Cardiometabolic, And Cardiovascular Traits Among South Asians, Shafqat Ahmad, Syeda Sadia Fatima, Gull Rukh, Caren E. Smith

Department of Biological & Biomedical Sciences

The rapid rise of obesity, type 2 diabetes mellitus (T2DM) and cardiovascular disease (CVD) during the last few decades among South Asians has been largely attributed to a major shift in lifestyles including physical inactivity, unhealthy dietary patterns, and an overall pattern of sedentary lifestyle. Genetic predisposition to these cardiometabolic risk factors may have interacted with these obesogenic environments in determining the higher cardiometabolic disease prevalence. Based on the premise that gene-environment interactions cause obesity and cardiometabolic diseases, we systematically searched the literature and considered the knowledge gaps that future studies might fulfill. We identified only seven published studies that …

Oxygen And Hydrogen Isotopes In Human Hair And Tap Water: Modeling Relationships In A Modern Mexican Population, Chelsey A. Juarez, Robin Ramey, David T. Flaherty, Belinda Akpa

Human Biology Open Access Pre-Prints

This study investigates the relationship between O and H isotopes in samples of Mexican hair and drinking water. The purpose of this study was twofold. First, we wanted to quantify the relationship between isotopes in Mexican hair and tap water to understand the impact of water stress and differing socioeconomic status on accurate predictions of drinking water. Second, we wanted to determine whether currently existing semi mechanistic models could accurately represent the relationship between hair and tap water. For this study, we used a subset of paired (N = 62) human hair and (N = 76) tap water samples. Isotope …

Age-At-Death Estimation For Modern Populations In Mexico And Puerto Rico Through The Use Of 3d Laser Scans Of The Pubic Symphysis, Cristina Figueroa Soto, Bridget F.B. Algee-Hewitt, Guillermo Bravo Morante, Dennis E. Slice, Dawnie W. Steadman

Human Biology Open Access Pre-Prints

Reliable age-at-death estimates from the adult skeleton is of fundamental importance in forensic anthropology, as it contributes to the identity parameters used in a medico-legal death investigation. However, reliable estimates are made difficult by the fact that many traditional aging methods are dependent upon a set of population-specific criteria derived from individuals of European and African descent. The absence of information on the potential differences in the aging patterns of underrepresented, especially Hispanic populations, may hinder our efforts to produce useful age-at-death estimates. In response to these concerns, this study explores the utility of currently available aging techniques, and explores …

Population Identifiability From Forensic Genetic Markers: Ancestry Variation In Latin America, Cris E. Hughes, Bridget F.B. Algee-Hewitt, Lyle Konigsberg

Human Biology Open Access Pre-Prints

The Combined DNA Index System (CODIS) loci are a standard microsatellite marker set widely used for distinguishing among individuals in forensic DNA identity testing for medico-legal casework in the United States and in other countries. In anthropological genetic research, CODIS markers have become an important tool for uses extending beyond case investigations to quantify ancestry proportions, reveals patterns of admixture and trace population histories. These investigations are especially prevalent in studies of Latin American population structure. Nevertheless, the accuracy of the ancestry estimates computed from the CODIS loci for highly admixed Latino populations has not been formally tested. Long-standing arguments …

Neanderthal And Woolly Mammoth Molecular Resemblance: Genetic Similarities Might Underlie Cold Adaptation Suite, Meidad Kislev, Ran Barkai

Human Biology Open Access Pre-Prints

With the ongoing growth of gene-based research in recent decades, the possibility of examining changes that have taken place in structures over the course of evolution has become increasingly accessible. One intriguing subject at the forefront of evolutionary research is that of how environmental pressures affect species evolution through epigenetic adaptation. In this paper we present the available molecular components of adaptation to cold environments in two extinct mammals – the woolly mammoth and the Neanderthal. These two species co-existed in similar geographic and environmental European settings during the Middle and Upper Pleistocene and both were direct descendants of African …

Rna Interference And Validation Of Reference Genes For Gene Expression Analyses Using Qpcr In Southern Pine Beetle, Dendroctonus Frontalis, Bethany R. Kyre, Thais B. Rodrigues, Lynne K. Rieske

Entomology Faculty Publications

RNA interference (RNAi) is a highly specific gene-silencing mechanism that can cause rapid insect mortality when essential genes are targeted. RNAi is being developed as a tool for integrated pest management of some crop pests. Here we focus on an aggressive forest pest that kills extensive tracts of pine forests, the southern pine beetle (SPB), Dendroctonus frontalis. We sought to identify reference genes for quantitative real-time PCR (qPCR) and validate RNAi responses in SPB by mortality and gene silencing analysis. Using an adult beetle feeding bioassay for oral ingestion of dsRNA, we measured the expression and demonstrated knockdown of …

The Sucking Louse Fauna Of Mongolian Rodents: Host Associations, Molecular Phylogenetics And Description Of Two New Species, Chase N. Robinson

Honors College Theses

This study aimed to screen Mongolian rodents for sucking lice (Insecta: Phthiraptera: Anoplura) to better understand host-parasite associations for this understudied region. Nine species, including 3 previously undescribed, from 4 genera were identified. A molecular phylogeny based on 2 mitochondrial genes of collected louse specimens is included.

Incorporating Pathway Information Into Feature Selection Towards Better Performed Gene Signatures, Suyan Tian, Chi Wang, Bing Wang

Biostatistics Faculty Publications

To analyze gene expression data with sophisticated grouping structures and to extract hidden patterns from such data, feature selection is of critical importance. It is well known that genes do not function in isolation but rather work together within various metabolic, regulatory, and signaling pathways. If the biological knowledge contained within these pathways is taken into account, the resulting method is a pathway-based algorithm. Studies have demonstrated that a pathway-based method usually outperforms its gene-based counterpart in which no biological knowledge is considered. In this article, a pathway-based feature selection is firstly divided into three major categories, namely, pathway-level selection, …

Molecular Evolutionary Trends And Feeding Ecology Diversification In The Hemiptera, Anchored By The Milkweed Bug Genome, Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Murali, John H. Werren, Chris G. C. Jacobs, Elizabeth J. Duncan, David Armisén, Barbara M. I. Vreede, Patrice Baa-Puyoulet, Chloé S. Berger, Chun-Che Chang, Hsu Chao, Mei-Ju M. Chen, Yen-Ta Chen, Christopher P. Childers, Ariel D. Chipman, Andrew G. Cridge, Antonin J. J. Crumière, Peter K. Dearden, Elise M. Didion, Subba Reddy Palli, Jayendra Nath Shukla

Entomology Faculty Publications

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.

Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but …

X-Inactivation And Epigenetics, Serena Weston

Thinking Matters Symposium Archive

To prevent abnormal development caused by expressing both X chromosomes, female mammals inactivate one of their X chromosomes using an epigenetic process called dosage compensation. This literature review examines how X chromosome inactivation (XCI) occurs during the formation and development of an embryo. This condensation of DNA is marked by histone tail modifications, DNA methylation, and the arrival of structural proteins resulting in extraordinarily stable heterochromatin. X-inactivation is regulated in cis by the X-inactivation center (Xic) that contains the Xist gene and its antisense gene, Tsix. On one X chromosome, Xist RNA is expressed and coats the center of the …

Fys: Ethics And Technology (Phil 07/Cpsc 15) Syllabus, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

There has been an accelerated shift in the influence of computing technology and the use of algorithms in our daily lives. With this technology comes serious ethical questions. Philosophers are often well-equipped to wrestle with ethical questions, but less well-equipped to wrestle with questions of technology itself. Computer scientists are well-equipped to deal with the problems and challenges of technology, but less well-equipped to deal with the ethical problems and challenges that technology can pose. In this co-taught course, we bring together the two fields to address ethical questions involving social media, data mining, self-driving cars, artificial intelligence, and other …

Genetic Diversity In The Leucoagaricus Cultivar Fungus Of Trachymyrmex Septentrionalis Fungus-Growing Ants, Lee Deininger

MCB Articles

No abstract provided.

Male Determining Gene Nix May Bring An End To Transmission Of Diseases Through Mosquitoes, Mohammed Mahdi

Thinking Matters Symposium Archive

Female mosquitoes take blood from humans to gain protein needed to produce eggs, and in the process they can transmit viruses, such as Zika, Dengue, and chikungunya, or parasites, such as malaria. Male mosquitoes do not transmit diseases. This literature review will examine what is known about how sex is determined in mosquitoes and how this can be used to manipulate the females that spread diseases to humans. Using CRISPR Cas9, the lab of Zhijian Tu removed the Nix gene from mosquito embryos; all of these were feminized. Ectopic overexpression of Nix gene product in mosquito embryos caused even genetically …

Lab Practicum For Bias In Algorithms, Ameet Soni, Krista Karbowski Thomason

Digital Humanities Curricular Development

This is a course assignment to demonstrate potential biases encoded in algorithms (this can be linked more specifically to natural language processing, machine learning, or artificial intelligence) using the Word Embedding Association Test. In lab, students will work with programs that demonstrate the usefulness of word embedding algorithms in finding relationships between words. Then, students will use an implementation of the algorithm in "Semantics derived automatically from language corpora contain human-like biases" by Caliskan et al. to detect gender and racial bias encoded in word embeddings. The assignment has students design and run an experiment using the WEAT algorithm to …

Identification And Functional Testing Of Novel Interacting Protein Partners For The Stress Sensors Wsc1p And Mid2p Of Saccharomyces Cerevisiae, Ednalise Santiago-Cartagena, Sahily González-Crespo, Vladimir Vélez, Nelson Martínez, Jamie Snider, Matthew Jessulat, Hiroyuki Aoki, Zoran Minic, Pearl Akamine, Inoushka Mejías, Luis M. Pérez, Brian C. Rymond, Mohan Babu, Igor Stagljar, José R. Rodríguez-Medina

Biology Faculty Publications

Wsc1p and Mid2p are transmembrane signaling proteins of cell wall stress in the budding yeast Saccharomyces cerevisiae. When an environmental stress compromises cell wall integrity, they activate a cell response through the Cell Wall Integrity (CWI) pathway. Studies have shown that the cytoplasmic domain of Wsc1p initiates the CWI signaling cascade by interacting with Rom2p, a Rho1-GDP-GTP exchange factor. Binding of Rom2p to the cytoplasmic tail of Wsc1p requires dephosphorylation of specific serine residues but the mechanism by which the sensor is dephosphorylated and how it subsequently interacts with Rom2p remains unclear. We hypothesize that Wsc1p and Mid2p must …

Characterization Of Iron-Sulfur Cluster Proteins From Methanococcus Maripaludis, Melody Salmanian

Honors Capstones

No abstract provided.

The Role Of Disease & Insects In Aspen Ecology, John C. Guyon Ii

Aspen Bibliography

Aspen is a keystone species in montane forests, and enhances a number of key resource values including wildlife habitat, water resources, and fire behavior. Recently, aspen forests have experienced episodes of dieback and decline across western North America (Worrall et al. 2010, Guyon and Hoffman 2011). A large proportion of the dieback and decline has been linked to drought stress or drought-prone locations (Hanna and Kulakowski 2012). However, insects and diseases are commonly found in declining aspen stands, leading to confusion about the role of insects and diseases in aspen ecology. Additionally, aspen has a reputation for being susceptible to …

How A Cell Knows Where To Divide: Oscillation Of Mind In Vivo, Colby Ferreira

Senior Honors Projects

Over two-million people in the United States are infected by antibiotic resistant bacteria each year. Of this number 23,000 die from these infections and other complications. Due to this, novel antibiotic targets are constantly being investigated. One process in prokaryotes that holds promise is cellular division. Bacterial cells grow and reproduce using a series of proteins known as the cell division machinery. This machinery enables the division of the parental cell into two identical daughter cells. The cell division machinery is similar between bacterial taxa, making it an ideal target for new classes of antibiotics. Therefore, understanding the molecular mechanisms …

Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst

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

Genome-wide association studies are used to identify genetic variants associated with a particular phenotype. GWAS has been used in a variety of taxa, from humans, to fish to plants . The present analysis is focused on two species important to the human species: maize and sorghum. A GWAS in maize was carried out on the modification of the Ga1-s allele. The Ga1 locus has long been studied as being involved in a unilateral crossing barrier . However, it has long been suspected that the locus is modified by background genetic factors . GWAS was used to observe candidates for this …

Evaluating The Social Informational Needs Of Emerging Adults With Genetic Conditions, Courtney Whitmore

Theses and Dissertations

Purpose: This study evaluated the healthcare provider’s role during the social development of emerging adults with a genetic condition. The study also identified the type of information and ways that these adolescents hope to receive information on the potential side effects or complications from engaging in risk taking behaviors and lifestyle choices.

Methods: Participants included both males and females aged 18-26 with achondroplasia, sickle cell disease, cystic fibrosis, or Marfan syndrome. Respondents were recruited to complete an anonymous online questionnaire via social media support groups or email notification.

Results: There were 103 total respondents that completed the questionnaire and met …

Streptococcus Agalactiae Strains With Chromosomal Deletions Evade Detection With Molecular Methods, Isabella A. Tickler, Fred C. Tenover, Scott Dewell, Victoria M. Le, Rachel N. Blackman, Richard V. Goering, Amy E. Rogers, Heather Piwonka, Brittney D. Jung-Hynes, Derrick J. Chen, Michael J. Loeffelholz, Devasena Gnanashanmugam, Ellen Jo Baron

Biology Faculty Publications

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culture-positive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed …