Life Sciences Commons^™

Environmental Magnesium Ion Affects Global Gene Expression, Motility, Biofilm Formation And Virulence Of Vibrio Parahaemolyticus, Xue Li, Xiaobai Zhang, Miaomiao Zhang, Xi Luo, Tingting Zhang, Xianjin Liu, Renfei Lu, Yiquan Zhang

Journal Articles

No abstract provided.

The Stability Of Epigenetic Variants That Can Act As Loci Causing Phenotypic Change, Raul Faburrieta

Biology Theses

Epigenetic variations are a possible source of heritable phenotypic variation. In this study I focus on phenotypic alterations seen in epigenetic Recombinant Inbred Lines (epiRILs) of Arabidopsis thaliana. These epiRILs allow me to study the effects differentially methylated regions (DMRs) have on phenotypic variance. In a study performed in 2014 by Cortijo et al., they found that DMR’s affect flowering time and root length when grown under greenhouse conditions. In this study, I replicated the Cortijo et al. (2014) study, with some changes, to see whether the same significant eQTL regions are found. I found that, some of the eQTLs …

A Genomics Driven Induced Pluripotent Stem Cell Model Of Infant Acute Lymphoblastic Leukemia - Early Results, Meagan Vacek, Jacqelyn Nemechek, Irina Pushel, Bradley Thornton, Molly Leyda, Priyanka Prem Kumar, Midhat Farooqi, Jay L. Vivian, Erin M. Guest, John M. Perry

Research Days

While the cure rates for pediatric ALL have improved over the decades, infants with ALL (iALL) have not benefitted from these advances and continue to have a devastating prognosis. Unfortunately progress in treatment has also been slowed by inadequate research models. With this project, we address this unmet need by investigating a novel model to understand the cellular and molecular changes that occur during iALL onset and progression.

Optimizing Immunotherapies For Improved Cancer Treatment, Anne Talkington, Anthony Kearsley

Biology and Medicine Through Mathematics Conference

No abstract provided.

Identification Of Genetic Disorders Based On Phenotype And Subsequent Medical Management, Sara J. Strandlund, Jotishna Sharma, Bonnie R. Sullivan, Ashley K. Sherman, Laura A. Cross

Research Days

Many genetic disorders in the neonatal period contribute to significant morbidity and mortality. This study evaluates the indications for genetic testing based on phenotype and compares these with the diagnostic yield of symptom driven exome sequencing and chromosome microarray in the NICU. Overall, this study highlights that while there are diagnostic limitations to exome sequencing, genetic testing remains an important adjunct to clinical care.

Screen For Beneficial Genetic And Chemical Modifiers In Drosophila Models Of Als And Traumatic Brain Injury, Will Bonderer

Biological Sciences Theses and Dissertations

The underlying molecular processes of aberrant protein expression in neurodegeneration are intricate and multifaceted, with ribosome-associated quality control (RQC) emerging as a promising avenue of exploration. Ribosome-associated quality control is integral to cellular function. Its evolutionarily conserved pathway encompasses a network of mechanisms designed to ensure the fidelity of protein synthesis, folding, and degradation within the cells of all eukaryotes. The ribosome, central to protein synthesis, plays a pivotal role in this quality control network, and its malfunction can lead to the accumulation of misfolded or aberrant proteins. In the context of neurodegenerative disorders, this dysfunction can have dire consequences. …

With Love, ; An Interdisciplinary And Intersectional Look At Why Creativity Is Essential, Theo Starr Gardner

Whittier Scholars Program

My Whittier Scholars Program self-designed major, Teaching Creativity, is a mixture of Art, Literature, and Education classes. My research and praxis classes have been focused on the ‘how?’s and 'why?’s of creativity, so it felt only right that my project should be a constructivist, generative project. The project I have been working on throughout my time at Whittier, and that has just fully come to fruition on April 11th, 2024, was a solo art gallery/open mic event entitled ‘With Love,’. With Love, was conceptually inspired by the research I’ve conducted on creativity and creative arts education over the past few …

Selection During Reproduction In Mimulus Guttatus, Desmond C. Willson, Karla De Lima Berg, Mitch Cruzan

Student Research Symposium

A lack of genomic studies examining gametophytic selection and selective embryo abortion—which occur during the reproduction of angiosperms—leaves questions regarding the adaptive and evolutionary effects of these processes. Analyzing deviations from Mendelian segregation offers an avenue for identifying loci targeted by GS and SEA, and their contributions to purging of genetic load. However, other selective processes such as meiotic drive and cytonuclear interactions, as well as pollen and ovule abortion, can cause distortion. To distinguish the effects of GS and SEA from other causes of distortion, we will perform reciprocal crosses between highly homozygous and highly heterozygous individuals of Mimulus …

Improved Genome Maintenance And Dna Replication In The Anoxia Tolerant Annual Killifish, Riley A. Roth-Carter

Student Research Symposium

Timely and faithful replication of the genome is a requirement for cell survival and proliferation, with errors in this process leading to cancers and cell death. DNA replication during exposure to stressful conditions can lead to increased mutational burden, with collapsed replication forks causing mutations leading to cancers due to loss of repair capabilities during these exposures. Learning how stressful DNA replication takes places can lead to a better understanding of how resistant cancers survive similar conditions, like hypoxic tumor microenvironment, direct irradiation, and DNA damaging chemotherapeutics. Using an extremophile model, Austrofundulus limnaeus, which can survive these genotoxic stressors could …

Guide Rna Design And Delivery For Crispr/Cas9 Editing In Annual Killifish, Keria N. Moritsugu-Vandehey, Isabel Henkes, Yekaterina Chmykh, Amie Romney, Jason Podrabsky

Student Research Symposium

The CRISPR-Cas9 genome editing tool has shown to be successful in knocking out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has been demonstrated in many species of fish, but this technology has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus would lead to the development of fish without the ability to produce melanin, the black/brown pigment molecule. Early embryos (1-cell stage) were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target …

The Trnaval Half: A Strong Endogenous Toll-Like Receptor 7 Ligand With A 5′-Terminal Universal Sequence Signature, Kamlesh Ganesh Pawar, Takuya Kawamura, Yohei Kirino

Computational Medicine Center Faculty Papers

Toll-like receptors (TLRs) are crucial components of the innate immune system. Endosomal TLR7 recognizes single-stranded RNAs, yet its endogenous ssRNA ligands are not fully understood. We previously showed that extracellular (ex-) 5'-half molecules of tRNA^HisGUG (the 5'-tRNA^HisGUG half) in extracellular vesicles (EVs) of human macrophages activate TLR7 when delivered into endosomes of recipient macrophages. Here, we fully explored immunostimulatory ex-5'-tRNA half molecules and identified the 5'-tRNA^ValCAC/AAC half, the most abundant tRNA-derived RNA in macrophage EVs, as another 5'-tRNA half molecule with strong TLR7 activation capacity. Levels of the ex-5'-tRNA^ValCAC/AAC half were highly up-regulated in macrophage EVs …

Genetic Variants For Head Size Share Genes And Pathways With Cancer, Maria J Knol, Raymond A Poot, Tavia E Evans, Claudia L Satizabal, Aniket Mishra, Muralidharan Sargurupremraj, Sandra Van Der Auwera, Marie-Gabrielle Duperron, Xueqiu Jian, Isabel C Hostettler, Dianne H K Van Dam-Nolen, Sander Lamballais, Mikolaj A Pawlak, Cora E Lewis, Amaia Carrion-Castillo, Theo G M Van Erp, Céline S Reinbold, Jean Shin, Markus Scholz, Asta K Håberg, Anders Kämpe, Gloria H Y Li, Reut Avinun, Joshua R Atkins, Fang-Chi Hsu, Alyssa R Amod, Max Lam, Ami Tsuchida, Mariël W A Teunissen, Nil Aygün, Yash Patel, Dan Liang, Alexa S Beiser, Frauke Beyer, Joshua C Bis, Daniel Bos, R Nick Bryan, Robin Bülow, Svenja Caspers, Gwenaëlle Catheline, Charlotte A M Cecil, Shareefa Dalvie, Jean-François Dartigues, Charles Decarli, Maria Enlund-Cerullo, Judith M Ford, Barbara Franke, Barry I Freedman, Nele Friedrich, Melissa J Green, Simon Haworth, Catherine Helmer, Per Hoffmann, Georg Homuth, M Kamran Ikram, Clifford R Jack, Neda Jahanshad, Christiane Jockwitz, Yoichiro Kamatani, Annchen R Knodt, Shuo Li, Keane Lim, W T Longstreth, Fabio Macciardi, Outi Mäkitie, Bernard Mazoyer, Sarah E Medland, Susumu Miyamoto, Susanne Moebus, Thomas H Mosley, Ryan Muetzel, Thomas W Mühleisen, Manabu Nagata, Soichiro Nakahara, Nicholette D Palmer, Zdenka Pausova, Adrian Preda, Yann Quidé, William R Reay, Gennady V Roshchupkin, Reinhold Schmidt, Pamela J Schreiner, Kazuya Setoh, Chin Yang Shapland, Stephen Sidney, Beate St Pourcain, Jason L Stein, Yasuharu Tabara, Alexander Teumer, Anne Uhlmann, Aad Van Der Lugt, Meike W Vernooij, David J Werring, B Gwen Windham, A Veronica Witte, Katharina Wittfeld, Qiong Yang, Kazumichi Yoshida, Han G Brunner, Quentin Le Grand, Kang Sim, Dan J Stein, Donald W Bowden, Murray J Cairns, Ahmad R Hariri, Ching-Lung Cheung, Sture Andersson, Arno Villringer, Tomas Paus, Sven Cichon, Vince D Calhoun, Fabrice Crivello, Lenore J Launer, Tonya White, Peter J Koudstaal, Henry Houlden, Myriam Fornage, Fumihiko Matsuda, Hans J Grabe, M Arfan Ikram, Stéphanie Debette, Paul M Thompson, Sudha Seshadri, Hieab H H Adams

Journal Articles

The size of the human head is highly heritable, but genetic drivers of its variation within the general population remain unmapped. We perform a genome-wide association study on head size (N = 80,890) and identify 67 genetic loci, of which 50 are novel. Neuroimaging studies show that 17 variants affect specific brain areas, but most have widespread effects. Gene set enrichment is observed for various cancers and the p53, Wnt, and ErbB signaling pathways. Genes harboring lead variants are enriched for macrocephaly syndrome genes (37-fold) and high-fidelity cancer genes (9-fold), which is not seen for human height variants. Head size …

Rnai “Flexon” Approach To Gonad Gene Knockdown In C. Elegans, Sofia Suzanne Douglas

Undergraduate Theses

All living things require some form of genetic regulation so that gene products are correctly produced and maintained. One significant form of post-transcriptional gene expression is RNA silencing, a biological mechanism in which double stranded RNA molecules inhibit gene expression by blocking translation of targeted mRNA molecules. Due to its extensive applications in biotechnology, it’s been adapted as an experimental technique referred to as RNAi. This technique is temporary, transient, and easy to use. A new form of RNAi, referred to as the “Flexon” technique, is a novel approach that provides a method for post-transcriptional gene regulation that allows for …

Integrated Transcriptomics And Histopathology Approach Identifies A Subset Of Rejected Donor Livers With Potential Suitability For Transplantation, Ankita Srivastava, Alexandra Manchel, John Waters, Manju Ambelil, Benjamin K. Barnhart, Jan B. Hoek, Ashesh P. Shah, Rajanikanth Vadigepalli

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Liver transplantation is an effective treatment for liver failure. There is a large unmet demand, even as not all donated livers are transplanted. The clinical selection criteria for donor livers based on histopathological evaluation and liver function tests are variable. We integrated transcriptomics and histopathology to characterize donor liver biopsies obtained at the time of organ recovery. We performed RNA sequencing as well as manual and artificial intelligence-based histopathology (10 accepted and 21 rejected for transplantation).

RESULTS: We identified two transcriptomically distinct rejected subsets (termed rejected-1 and rejected-2), where rejected-2 exhibited a near-complete transcriptomic overlap with the accepted livers, …

Characterizing The Role Of Pa5189 Of Pseudomonas Aeruginosa In Deletion And Overexpression Mutants, Seh Na Mellick

Theses/Capstones/Creative Projects

In the context of rising multidrug resistance in biofilm-forming pathogens like Pseudomonas aeruginosa, this study investigates the role of the understudied transcription factor PA5189 in antibiotic resistance and biofilm formation. PA5189 deletion and overexpression mutants were created in a parent P. aeruginosa strain using pEX18Tc-based recombinant suicide vectors, with genotypic verification of putative triparental conjugants achieved through restriction digestion and PCR. The study revealed that PA5189 overexpression significantly increases resistance to commonly used broad spectrum antibiotics such as ciprofloxacin and imipenem. Additionally, differential expression of PA5189 was found to notably affect biofilm formation, with variations contingent on the nutrient …

Towards Understanding The Function Of An Ets-Like Gene In Nematostella Vectensis: Generation Of A Knockout Mutant Line And A Transgenic Reporter Line, Emily Bullock

Biological Sciences Undergraduate Honors Theses

Due to their unique phylogenic position as sister to Bilateria, Cnidaria are often credited with the utility of allowing for reconstruction of ancestral biology based on characteristics shared with bilaterians and other animals. This factor makes investigation into the nervous systems of cnidarians critical in understanding early neural evolution. Wamides, a class of neuropeptides, have been shown to play a regulatory role in life cycle transitions across many different species. The cnidarian specific Wamide neuropeptide, GLWamide, has previously been identified to play an accelerator role in the metamorphic timing of a specific species of sea anemone, Nematostella vectensis. However, …

Key Variants Via The Alzheimer's Disease Sequencing Project Whole Genome Sequence Data, Yanbing Wang, Chloé Sarnowski, Honghuang Lin, Achilleas N Pitsillides, Nancy L Heard-Costa, Seung Hoan Choi, Dongyu Wang, Joshua C Bis, Elizabeth E Blue, Eric Boerwinkle, Philip L De Jager, Myriam Fornage, Ellen M Wijsman, Sudha Seshadri, Josée Dupuis, Gina M Peloso, Anita L Destefano

Journal Articles

INTRODUCTION: Genome-wide association studies (GWAS) have identified loci associated with Alzheimer's disease (AD) but did not identify specific causal genes or variants within those loci. Analysis of whole genome sequence (WGS) data, which interrogates the entire genome and captures rare variations, may identify causal variants within GWAS loci.

METHODS: We performed single common variant association analysis and rare variant aggregate analyses in the pooled population (N cases = 2184, N controls = 2383) and targeted analyses in subpopulations using WGS data from the Alzheimer's Disease Sequencing Project (ADSP). The analyses were restricted to variants within 100 kb of 83 previously …

Survey Of The Bolctes From Fish River Nature Preserve, Noah T. Nelson

Honors Theses

Boletes are a special kind of mushroom inside of the Kingdom Fungi that are distinguished from other mushrooms by their uniquely pored hymenium, as opposed to gills. Many boletes are ectomycorrhizal, meaning they are mutualists with vascular plants, and thus beneficial to the overall health of the terrestrial ecosystem. Some are well-known for their edibility and are of economic importance. In the United States 59 genus-level clades comprising 290 operational taxonomic units have been reported. The southeastern US and Gulf Coast regions however are less researched and recorded for their mushroom ecology. In Alabama, only 56 bolete species have been …

Elucidation Of The Overexpression Of Taf2 In Eukaryotic Cells, Morgan Osborn

Honors Theses

Through several studies, Taf2 has been found to be upregulated in various cancer cells. However, the mechanism through which this increased expression of Taf2 occurs remains unknown. As evolutionarily conserved ubiquitin-proteasome system (UPS) maintains protein homeostasis for normal cellular function, we hypothesized that stability of Taf2 may be regulated by this UPS and this UPS may be dysregulated in cancer cells causing overexpression of Taf2. To test our hypothesis, we assessed the role of the UPS in the regulation of the stability of Taf2 by 26S proteasome-mediated degradation. To do so, we performed molecular experiments mainly through two steps: 1st …

Exploring Genomic Convergence For Adaptations To Freezing Environments In Polar Fish, Ethan Talley

Biological Sciences Undergraduate Honors Theses

Convergent evolution provides valuable insights into how natural selection shapes species traits. Genomic analysis of lineages that display convergent traits has the potential to identify candidate genes for environmental adaptations across the scope of entire genomes. One remarkable example of convergent evolution is the independent development of antifreeze proteins (AFPs) in phylogenetically distant polar fish lineages. While AFPs themselves are relatively well studied, the full genomic context of adaptation to freezing conditions in these fish lineages remains largely unexplored. Leveraging the whole genome sequences previously assembled in our lab, along with other high-quality genomes available in GenBank, I examined the …

West Coast Rock Lobster Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed by the Department of Primary Industries and Regional Development (DPIRD, the Department) to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act …

Examining Population Structure Of Cismontane And Desert Populations Of Zebra-Tailed Lizards (Callisaurus Draconoides) Using Mitochondrial And Nuclear Intron Dna., Lauren Nicole Morrison

Electronic Theses, Projects, and Dissertations

Callisaurus draconoides, also known as the Zebra-Tailed lizard, belongs to the family Phrynosomatidae family (Pianka, et al. 1972). C. draconoides is a widespread desert lizard found western North America. In California, this species can be found in the Mojave and Colorado Deserts. There are currently several populations that reside in the San Bernardino basin on the cismontane side of the Transverse and Peninsular ranges. These mountain ranges have the potential to have isolated the cismontane populations from their typical desert ranges. In addition, geological passes have the potential to serve as migration corridor between the Deserts and cismontane regions. The …

Uncovering Novel Small Regulatory Rna In Protostome, Sweta Khanal

Dissertations

Small RNAs play pivotal roles in post-transcriptional gene regulation across diverse phylum of protostomes. In this study, we investigate the functional significance of atypical miRNAs, mirtron miR-1017 in Drosophila. Through ectopic expression in neuronal cells, we demonstrate that miR-1017 extends lifespan by targeting its host transcript, acetylcholine receptor Dα2, and influencing its splicing. This novel trans-regulatory function suggests a mechanism for mirtron evolution, highlighting the interplay between splicing and post-transcriptional regulation. Additionally, we profile small RNA populations in the polychaete developmental model Capitella teleta, shedding light on the small RNA landscape in annelid worms. Our analysis reveals a rich …

An Investigation Of Information Structures In Dna, Joel Mohrmann

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

The information-containing nature of the DNA molecule has been long known and observed. One technique for quantifying the relationships existing within the information contained in DNA sequences is an entity from information theory known as the average mutual information (AMI) profile. This investigation sought to use principally the AMI profile along with a few other metrics to explore the structure of the information contained in DNA sequences.

Treating DNA sequences as an information source, several computational methods were employed to model their information structure. Maximum likelihood and maximum a posteriori estimators were used to predict missing bases in DNA sequences. …

Single Cell Pharmacodynamic Modeling Of Cancer Cell Lines, Arnab Mutsuddy

All Dissertations

Cancer is one of the leading causes of disease related death worldwide. Since the discovery of the genomic origins of cancer, targeted therapy has been developed towards specific mutations implicated for oncogenic transformation. However, current standard-of-care for mapping cancer patients to efficacious drug combination is often inadequate. The pathophysiology of tumor progression relies on the dysregulation of biomolecular pathways of which the topology and the dynamics challenge prognosis. Moreover, the overall genomic instability involved in disease states and the resulting inter-patient as well as intra-tumoral heterogeneity challenge rationalization of therapy and clinical decision-making. It highlights the need for the use …

Characterization Of Ato Family Transporters In The Fungal Pathogen Cryptococcus Neoformans, Will Betsill

All Theses

Fungal pathogens are a significant threat to public health as they are becoming increasingly common and more resistant to treatment. Cryptococcus neoformans contributes greatly to this threat annually by causing an estimated 278,000 cases of cryptococcal meningitis resulting in approximately 181,000 deaths globally according to the CDC. C. neoformans is ubiquitous across most of the globe and can be found in such places as in trees or soil. Exposure to this fungus is especially dangerous to individuals who are immunocompromised or immunosuppressed. In these cases, inhalation of spores can lead to infection in the lungs. Once in the lungs, C. …

The Role Of B Cell Activation State And Sex In Aryl Hydrocarbon Receptor Mediated Induction Of Chemokine Receptor 9 And Alpha4beta7 Expression In Vitro, Logan Bauerle

Master's Theses

Defense of mucosal tissues from microbial infection and allergy is reliant on continual production of antibodies. The aryl hydrocarbon receptor (AhR) is known to regulate B cell development and is associated with suppression of systemic humoral immunity. Recent attention has been paid to the role of the AhR in altering expression of cell adhesion molecules (CAMs). B cells express CAMs and chemokine receptors to migrate around the body for localized secretion of antibodies. AhR agonists promote B cell migration to the small intestine through upregulation of chemokine receptor 9 (CCR9) and integrin α₄β₇. Both the AhR …

The Impact Of A Pgym Variant On Myophosphorylase Deficiency In Red Angus Composite Cattle And Changes In The Skeletal Muscle Transcriptome Due To The Intramuscular Administration Of Lidocaine In Wether Lambs, Mackenzie Christin Batt

School of Biological Sciences: Dissertations, Theses, and Student Research

Project 1 focused on eight calves in a Nebraska herd (composite Simmental, Red Angus, Gelbvieh) that displayed exercise intolerance during forced activity. Available sire pedigrees contained a paternal ancestor within 2-4 generations in all affected calves. Pedigrees of the calves’ dams were unavailable, however, the cows were ranch-raised and retained from prior breeding seasons, where bulls used for breeding occasionally had a common ancestor. Therefore, it was hypothesized that a de novo autosomal recessive variant was causative of exercise intolerance in these calves. A genome-wide association analysis followed by whole-genome sequencing led to the identification of a variant in the …

Trna Anticodon Cleavage By Target-Activated Crispr-Cas13a Effector, Ishita Jain, Matvey Kolesnik, Konstantin Kuznedelov, Leonid Minakhin, Natalia Morozova, Anna Shiriaeva, Alexandr Kirillov, Sofia Medvedeva, Alexei Livenskyi, Laura Kazieva, Kira S Makarova, Eugene V Koonin, Sergei Borukhov, Konstantin Severinov, Ekaterina Semenova

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Type VI CRISPR-Cas systems are among the few CRISPR varieties that target exclusively RNA. The CRISPR RNA–guided, sequence-specific binding of target RNAs, such as phage transcripts, activates the type VI effector, Cas13. Once activated, Cas13 causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from the phage spread. We show here that the principal form of collateral RNA degradation elicited by Leptotrichia shahii Cas13a expressed in Escherichia coli cells is the cleavage of anticodons in a subset of transfer RNAs (tRNAs) with uridine-rich anticodons. This tRNA cleavage is accompanied by inhibition of protein synthesis, thus …

How Dna Reveals God’S Design, Alan L. Gillen

Faculty Publications and Presentations

Codes are big in today’s world: QR codes, barcodes, computer codes, cell phone codes, and more. Specific information is needed to identify, diagnose, and inform. DNA is the code for life: microbes, plants, parasites, animals, and man. DNA Day is April 25 because it was this day in history (April 25, 1953) when James Watson and Francis Crick described DNA as the double helix and the code for life. Although we consider DNA the genetic blueprint for life, it has only been known for 80 years. On February 1, 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty wrote a revolutionary …