Biochemistry, Biophysics, and Structural Biology Commons^™

Tagtools: New Toolkit Analyzing High Resolution Biologging Data In R, Yuqian Wang, Oghenesuvwe Ogedegbe, Stacy L. De Ruiter

Summer Research

Bio-logging studies with high-resolution movement-sensors offer opportunities to observe animal behavior in unprecedented detail, but analysis of the resulting data is often complex, and there is a need for freely available, easy-to-use, flexible, welldocumented software tools to facilitate analysis and interpretation. We introduce a new open-source tool kit for processing data from tags with highresolution movement sensors.

Examples of Tags: DTAG, CATS, Acousonde, DailyDiary, etc.

Dna Damage Response Activates The Electron Transport Chain And Oxidative Metabolism By Two Parallel Mechanisms, Shreya Nagar

Theses and Dissertations

The DNA damage response (DDR) is an evolutionarily conserved process essential for cell survival. Major part of DDR is coordinated by DNA damage checkpoint (DDC). In addition to DDC, eukaryotic cells also have DNA replication checkpoint (DRC) that is distinct from the DDC and specifically signals slowly progressing or arrested replication forks. DDR involves stalling or arrest of the cell cycle, initiation of DNA repair, and altered regulation of transcription, translation, and the ubiquitin-proteasome system. DDR also triggers transcription shut-off of histone genes. One of the key outcomes of DDC/DRC activation is the increased synthesis of the deoxyribonucleoside triphosphates (dNTPs), …

Chemical Disinfection In Rural Ecuador, Lachlan Beebe, Chad Tatko, Julie Wildschut

Summer Research

The Clean Water Institute, in conjunction with Calvin University seeks to address issues with water availability in developing countries, particularly as it relates to quality of the water. The research done this summer was to investigate the potential implementations of improvements for clean water in rural Ecuador. These improvements manifested themselves in two distinct initiatives: The first initiative was to investigate the implementation of a passive chlorinator in a small Ecuadorean community. This involved literature review to decide a chlorinator to pursue, followed by extensive testing to validate the efficacy of the chlorinator under a variety of conditions. The second …

Temperature Effects On Conductivity Of Phospholipid Bilayers, Dylan Mount, Sebastian Grabill, Loren Haarsma

Summer Research

Phospholipids molecules contain a fatty acid tail and a head made of a phosphate group (Fig.1) and serve as the building blocks of cellular membranes. The tails are hydrophobic, meaning they are weakly attracted to water, while the head group is hydrophilic, which is strongly attracted to water. Lipids in water will spontaneously form into bilayers with the tails towards the center (Fig.2) and the heads pointing towards the water on either side. This is how the lipid bilayers are formed to separate a cell's interior from exterior. Biological cells contain mixtures of many lipids and other molecules. In our …

Molecular Regulation Of The Salicylic Acid Hormone Pathway In Plants Under Changing Environmental Conditions, Christina A. M. Rossi, Eric J. R. Marchetta, Jong Hum Kim, Christian Castroverde

Biology Faculty Publications

Salicylic acid (SA) is a central plant hormone mediating immunity, growth, and development. Recently, studies have highlighted the sensitivity of the SA pathway to changing climatic factors and the plant microbiome. Here we summarize organizing principles and themes in the regulation of SA biosynthesis, signaling, and metabolism by changing abiotic/biotic environments, focusing on molecular nodes governing SA pathway vulnerability or resilience. We especially highlight advances in the thermosensitive mechanisms underpinning SA-mediated immunity, including differential regulation of key transcription factors (e.g., CAMTAs, CBP60g, SARD1, bHLH059), selective protein–protein interactions of the SA receptor NPR1, and dynamic phase separation of the recently identified …

Developing Red Fluorescent Zn2+ Sensors And Characterizing Zn2+ Homeostasis In Mucolipidosis Type Iv Disease, Anna M. Dischler

Electronic Theses and Dissertations

Zinc (Zn²⁺) is a divalent, redox-inert metal that plays a vital role in many cellular processes either by acting as a catalytic cofactor or a labile signaling molecule in the cytoplasm. Cytosolic Zn²⁺ levels are tightly regulated to stay within a narrow window of concentrations, but fluctuations in Zn²⁺ signals have been detected in a variety of cells. We developed a genetically encoded, single red fluorescent protein (RFP) based Zn²⁺ sensor, RZnP1, that can be used alongside green-wavelength sensors for the simultaneous detection of different signaling molecules within the same cells or among different subcellular …

Alterations In C:N Ratio To Understand Plant Metabolic Pathways In Response To Pressure From Goat Grazing In The Invasive Species: Rhamnus Cathartica, Vivian Marchan

Ignite the Spark Outstanding Undergraduate Research and Scholarship

The high fecundity and high germination rates of Rhamus cathartica serves the species to out-compete regional plant native species. Its high abundance in deciduous forest ecosystems forces species that are unable to utilize R. cathartica as a food source to migrate to areas of lower density, further contributing to the decline in regional biodiversity. Bare soil conditions left as the result of the high concentration of Nitrogen in senesced leaves and leaf litter, cause further amplification of the migration of non-plant species to areas of lower R. cathartica density. Nitrogen is essential to primary and secondary metabolism, thus minimizing the …

Post-Translational Modification Of Proteins Via Ambient Air Pollutants And Endogenous Reactive Species, Rachel Lauren Davey

Electronic Theses and Dissertations

Proteins can react with reactive oxygen species (ROS) and reactive nitrogen species (RNS) to form post-translational modifications (PTMs), which can affect protein structure and function. The formation of 3-nitrotyrosine (NTyr) and dityrosine (DiTyr) upon reaction of proteins with ROS/RNS are two common PTMs studied due to their stability and irreversibility, as well as their ability to enhance the allergenicity of pollen allergens upon formation. Many common techniques used to study the formation of these PTMs can reliably detect the PTMs but can only provide semi-quantitative information due to many assumptions and limitations. In Chapter 2 we present an analysis of …

Identifying The Role Of Phospholipase D1 And Phosphatidic Acid In Exocytosis, Broderick L. Bills

Electronic Theses and Dissertations

Exocytosis is an essential process for intercellular communication in eukaryotic cells. This process involves significant changes in membrane curvature, and lipids and curvature-sensing proteins can assist these processes. One protein in particular, phospholipase D1 (PLD1), and its product, the lipid phosphatidic acid (PA), are involved in multiple exocytic processes. However, PLD1 and PA’s role in this process has remained unclear. In this work, PLD1 and the production of PA were visualized during exocytosis, and PA localization to regions of membrane curvature was established. Together, these results support the hypothesis that PLD1 production of PA stabilizes negative curvature during membrane fusion. …

Investigating The Binding Of G-Quadruplex Dna To Lispro And Bovine Insulin, Sarah E. Bultje, Luke D. Witvliet, Kumar Sinniah

Summer Research

Type 1 Diabetes (T1D) is a disease characterized by the inability to produce insulin. Susceptibility to T1D is complex, involving both genetic and environmental factors. o One of the genetic components involved in insulin gene expression, and suspected T1D susceptibility, is the insulin-linked polymorphic region (ILPR). The ILPR element is located on chromosome 11p15 in the proximal promoter region, 363 base pairs upstream from the gene transcription site. o Other researchers (using fluorescence spectroscopy) and we (using ITC) have demonstrated that insulin binds to G-Quadruplex DNA with µM affinity. Since the DNA sequences in the ILPR form G-Quadruplexes and are …

Interferon Gamma Signaling In Ovarian Cancer Cells, Bijaya Gaire

Theses and Dissertations

Interferon gamma (IFNγ) is a pleiotropic cytokine that can have, depending on the cellular and molecular context, both anti-tumor and pro-tumorigenic functions. IFNγ expression can be induced in cancer cells in response to radiation therapy or immune checkpoint blockade used in cancer treatment. We have previously shown that IFNγ induces expression of the Bcl3 proto-oncogene in ovarian cancer (OC) cells, resulting in their increased proliferation and migration, but the mechanisms are unknown. Here, I demonstrate that the IFNγ-induced Bcl3 expression is dependent on JAK1 and STAT1 signaling, and on p65 NFkB. Furthermore, my data show that the IFNγ-induced Bcl3 expression …

Comparing Insect Biodiversity Between Curb-Cut Rain Gardens And Residential Lawns, Dave Warners, Naomi Dykstra, Julia Klooster

Summer Research

Global insect biodiversity is at a major decline. The drop in population can largely be attributed to a loss of natural habitat through conversion into urban and agricultural land. Insects are important parts of food webs and many play an important role in pollination, control of weeds, control of agricultural pests, and the decomposition of wood and leaves.

Role Of Integrins In Hiv Infection Of Resting Cd4+ T Cells Stimulated By Intestinal Endothelial Cells, Anding Shen, Sarah Logan, Tim Kim, Zihan Zhang

Summer Research

Eradicating HIV remains a formidable challenge due to the persistence of latent reservoirs within resting CD4+ T cells. Intestinal endothelial cells (IECs) have been shown to promote HIV infection and latent reservoir formation in resting CD4+ T cells. Our research investigates the role of integrins and their ligands, specifically ICAM, VCAM, and MAdCAM, in resting T cells and their impact on productive and latent HIV infection. Findings reveal that VCAM stimulation was the most effective in promoting productive HIV infection. MAdCAM and ICAM had minimal effect. Cytokine IL-6 consistently displayed synergy with all CAMs, amplifying effects on productive HIV infection. …

Selective Reduction Of Nitriles In The Presence Of Aromatic Nitro Groups, Esther Seoha Yoo, Dr. Michael Barbachyn

Summer Research

• Identify reliable aprotic reaction conditions for selective reduction of a nitrile in the presence of a nitro group. •
• Examine a range of nitrobenzonitriles and nitrophenyl acetonitriles to determine the scope of the methodology.

Regulation Of P53 By Trpm6 And Trpm7, Thomas Whitbread

Theses and Dissertations

TRPM6 and TRPM7 are two divalent metal cation channels that also possess a serine/threonine kinase domain. They both play critical roles in cellular and organismal metal homeostasis, and are necessary for proper embryonic development and human health. They may function independently in homomeric units, or act together as heterotetramers that display unique characteristics compared to the homomeric channels. These channel-kinases have increasingly been linked to cancer, displaying altered expression levels in a variety of human cancers and contributing to disease progression. Prior work has shown that TRPM6 and TRPM7 can participate in cancer-related signaling pathways. Here, the potential for TRPM6 …

Comparing The Performance Of A Targeted Pull-Down Assay To Shotgun Sequencing For Improving Respiratory Infectious Disease Surveillance, Monica R. Christian

Browse all Theses and Dissertations

Current surveillance focuses on well characterized pathogens such as influenza. Since 2000, there have been multiple outbreaks of respiratory disease. These outbreaks have demonstrated the need for robust and collaborative global efforts to identify, monitor, and contain novel respiratory viruses. This study aims to improve the ability of public health agencies to monitor and respond to respiratory disease outbreaks. Using five respiratory pathogens, this study compares a molecular capture technology from Twist Biosciences to the shotgun sequencing approach of whole transcriptome amplification (WTA, Qiagen) with the goal of determining which method is most effective using cost, usability, and sequencing quality …

Investigating Peptide Folding Of Tryptophan Zippers, Chad Tatko, Jessica Bedow, Kachel Bedow, Maddy Hoogstra, Douglas Vander Griend

Summer Research

Protein folding has been a subject of interest in the research community for its wide array o f applications in academia and medicine. By understanding how the interaction of localized amino acids in different environmental factors affect the global folding of peptides, one can anticipate synthesis of proteins or manipulation of exis ting pro teins to have more desirable functions. For this investigation, tryptophan zippers (monomeric β-hairpin peptides) were synthesized, titrated in differing pH, and analyzed by NMR

Purification Of Anginex: An Inhibitor Of Tumor Metastasis Using Rdrd Tag, Suraj Kolluru

Inquiry: The University of Arkansas Undergraduate Research Journal

Anginex is a cytokine-like β-sheet forming peptide of 33 amino acids with potent anti-angiogenic activity.Anginex is essential in inhibiting abnormal processes caused by angiogenesis, such as tumor growth and blood vessel formation. However, Anginex has limitations, including poor stability, short half-life, complicated synthesis, and low purity. Rubredoxin dimer (RdRd) is used as a protein tag to improve stability and detection of Anginex during purification for the first time. A plasmid was designed to contain the RdRd-Anginex fusion protein. RdRd-Anginex plasmid was transformed and expressed in E. coli BL21star cells. The results show RdRd-Anginex has been purified using a Nickel Sepharose …

Easy Nanostring Ncounter Data Analysis With The Nanotube, Caleb Class, Caiden J. Lukan, Christopher A. Bristow, Kim-Anh Do

Scholarship and Professional Work – COPHS

Summary: The NanoTube is an open-source pipeline that simplifies the processing, quality control, normalization and analysis of NanoString nCounter gene expression data. It is implemented in an extensible R library, which performs a variety of gene expression analysis techniques and contains additional functions for integration with other R libraries performing advanced NanoString analysis techniques. Additionally, the NanoTube web application is available as a simple tool for researchers without programming expertise.

Availability and implementation: The NanoTube R package is available on Bioconductor under the GPL-3 license (https://www.bioconductor.org/packages/NanoTube/). The R-Shiny application can be downloaded at https://github.com/calebclass/Shiny-NanoTube, or a simplified version of this …

Novel Application Of Graphene Oxide In Conjunction With Dna Binding Dcas9 For Detecting Antibiotic Resistance Genes, Langley Williams

Mahurin Honors College Capstone Experience/Thesis Projects

The frequent emergence of antibiotic resistance genes poses a stumbling block to prompt treatment of pathogen-originating diseases and therefore spurs the demand for a simple, rapid diagnostic device that can outcompete the time and cost of traditional methods such as PCR and cell culturing. The proposed method for detecting pathogenic DNA utilizes the binding properties of deactivated CRISPR-associated protein9 (dCas9) complexed with fluorescein-labeled single-guide RNA (sgRNA) and the fluorescence quenching properties previously demonstrated in graphene oxide (GO). For our assay, we designed sgRNAs to target specific 20 nucleotide sequences extracted from the tetracycline resistance (tetM) gene sequence and covalently modified …