Biochemistry, Biophysics, and Structural Biology Commons^™

Vinyl Chloride Accident Unleashes A Toxic Legacy, Chengjun Li, Peng Gao, Riqing Yu, Huan Zhong, Mengjie Wu, Su Shiung Lam, Christian Sonne

Biology Faculty Publications and Presentations

A railroad accident on February 3, 2023, led to the release and combustion of 115,580 gallons, equivalent to over 437,000 L, of vinyl chloride monomer (VCM) in East Palestine, Ohio [1]. This monomer is used in polyvinyl chloride (PVC) production, and its burning produces additional toxins such as hydrochloric acid and lethal phosgene, known as a notorious chemical weapon during World War I

Expanding The Conservation Genomics Toolbox: Incorporating Structural Variants To Enhance Genomic Studies For Species Of Conservation Concern, Stephanie J. Galla

Biology Faculty Publications and Presentations

Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics …

Authentication Of A Novel Antibody To Zebrafish Collagen Type Xi Alpha 1 Chain (Col11a1a), Jonathon C. Reeck, Makenna J. Hardy, Xinzhu Pu, Cynthia Keller-Peck, Julia Thom Oxford

Biology Faculty Publications and Presentations

Objective: Extracellular matrix proteins play important roles in embryonic development and antibodies that specifically detect these proteins are essential to understanding their function. The zebrafish embryo is a popular model for vertebrate development but suffers from a dearth of authenticated antibody reagents for research. Here, we describe a novel antibody designed to detect the minor fibrillar collagen chain Col11a1a in zebrafish (AB strain).

Results: The Col11a1a antibody was raised in rabbit against a peptide comprising a unique sequence within the zebrafish Col11a1a gene product. The antibody was affinity-purified and characterized by ELISA. The antibody is effective for immunoblot and immunohistochemistry …

Complete Mitochondrial Genome Sequence Of The Gulf Coast Tick (Amblyomma Maculatum), Amanda E. Brenner, Rahul Raghavan

Biology Faculty Publications and Presentations

The complete circularized mitochondrial genome sequence of Amblyomma maculatum is 14,803 bp long. It encodes 13 protein coding genes, 2 rRNA genes, 22 tRNA genes, 2 tick box motifs, and 2 control regions. The gene arrangement and content are consistent with those of previously reported Metastriata tick mitochondrial genomes.

Data Management Tools To Measure The Impact Of Core Facilities, Diane B. Smith, Tracy L. Yarnell, Barbara J. Jibben, Linda E. Liou, Carolyn J. Hovde, Julia Thom Oxford

Biology Faculty Publications and Presentations

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges …

Honeybees Fail To Discriminate Floral Scents In A Complex Learning Task After Consuming A Neonicotinoid Pesticide, Julie A. Mustard, Annie Gott, Jennifer Scott, Nancy L. Chavarria, Geraldine A. Wright

Biology Faculty Publications and Presentations

Neonicotinoids are pesticides used to protect crops but with known secondary influences at sublethal doses on bees. Honeybees use their sense of smell to identify the queen and nestmates, to signal danger and to distinguish flowers during foraging. Few behavioural studies to date have examined how neonicotinoid pesticides affect the ability of bees to distinguish odours. Here, we use a differential learning task to test how neonicotinoid exposure affects learning, memory, and olfactory perception in foraging-age honeybees. Bees fed with thiamethoxam could not perform differential learning and could not distinguish odours during short and long-term memory tests. Our data indicate …

Evaluation Of The Efficacy Of A Cholera Toxin-Based Staphylococcus Aureus Vaccine Against Bovine Intramammary Challenge, Hussain A. Alabdullah, Elise Overgaard, Danielle Scarbrough, Janet E. Williams, Omid Mohammad Mousa, Gary Dunn, Laura Bond, Mark A. Mcguire, Juliette K. Tinker

Biology Faculty Publications and Presentations

Staphylococcus aureus (S. aureus) is a primary agent of bovine mastitis and a source of significant economic loss for the dairy industry. We previously reported antigen-specific immune induction in the milk and serum of dairy cows following vaccination with a cholera toxin A₂ and B subunit (CTA₂/B) based vaccine containing the iron-regulated surface determinant A (IsdA) and clumping factor A (ClfA) antigens of S. aureus (IsdA + ClfA-CTA₂/B). The goal of the current study was to assess the efficacy of this vaccine to protect against S. aureus infection after intramammary challenge. Six mid-lactation …

Archaeosine Modification Of Archaeal Trna - A Role In Structural Stabilization, Ben Turner, Brett W. Burkhart, Katrin Weidenbach, Robert Ross, Patrick A. Limbach, Ruth A. Schmitz, Valérie De Crécy-Lagard, Kenneth M. Stedman, Thomas J. Santangelo, Dirk Iwata-Reuyl

Biology Faculty Publications and Presentations

Archaeosine (G+) is a structurally complex modified nucleoside found quasi-universally in the tRNA of Archaea and located at position 15 in the dihydrouridine loop, a site not modified in any tRNA outside of the Archaea. G+ is characterized by an unusual 7-deazaguanosine core structure with a formamidine group at the 7-position. The location of G+ at position 15, coupled with its novel molecular structure, led to a hypothesis that G+ stabilizes tRNA tertiary structure through several distinct mechanisms. To test whether G+ contributes to tRNA stability and define the biological role of G+, we investigated the consequences of introducing targeted …

Cullin-3 Dependent Deregulation Of Actn1 Represents A New Pathogenic Mechanism In Nemaline Myopathy, Jordan Blondelle, Kavya Tallapaka, Jane T. Seto, Majid Ghassemian, Madison Clark, Jenni M. Laitila, Adam Bournazos, Jeffrey Singer, Stephan Lange

Biology Faculty Publications and Presentations

Nemaline myopathy is a congenital neuromuscular disorder characterized by muscle weakness, fiber atrophy, and presence of nemaline bodies within myofibers. However, understanding of the underlying pathomechanisms is lacking. Recently, mutations in KBTBD13, KLHL40, and KLHL41, three substrate adaptors for the E3 ubiquitin ligase Cullin-3, have been associated with early-onset nemaline myopathies. We hypothesized that deregulation of Cullin-3 and its muscle protein substrates may be responsible for disease development. Using Cullin-3–knockout mice, we identified accumulation of non-muscle α-actinins (ACTN1 and ACTN4) in muscles of these mice, which we also observed in patients with mutations in KBTBD13. Our …

Small Noncoding Rna Profiles Along Alternative Developmental Trajectories In An Annual Killifish, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryonic development of Austrofundulus limnaeus can occur along two phenotypic trajectories that are physiologically and biochemically distinct. Phenotype appears to be influenced by maternal provisioning based on the observation that young females produce predominately non-diapausing embryos and older females produce mostly diapausing embryos. Embryonic incubation temperature can override this pattern and alter trajectory. We hypothesized that temperature-induced phenotypic plasticity may be regulated by post-transcriptional modification via noncoding RNAs. As a first step to exploring this possibility, RNA-seq was used to generate transcriptomic profiles of small noncoding RNAs in embryos developing along the two alternative trajectories. We find distinct profiles of …

Cell Cycle Arrest Associated With Anoxia-Induced Quiescence, Anoxic Preconditioning, And Embryonic Diapause In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Camie Lynn Meller, Robert Meller, Roger P. Simon, Kristin M. Culpepper, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryos of the annual killifish Austrofundulus limnaeus can enter into dormancy associated with diapause and anoxia-induced quiescence. Dormant embryos are composed primarily of cells arrested in the G1/G0 phase of the cell cycle based on flow cytometry analysis of DNA content. In fact, most cells in developing embryos contain only a diploid complement of DNA, with very few cells found in the S, G2, or M phases of the cell cycle. Diapause II embryos appear to be in a G0-like state with low levels of cyclin D1 and p53. However, the active form of pAKT is high during diapause II. …

Isolation Of A Ubiquitous Obligate Thermoacidophilic Archaeon From Deep-Sea Hydrothermal Vents, Anna-Louise Reysenbach, Yitai Liu, Amy B. Banta, Terry J. Beveridge, Julie D. Kirshtein, Stefan Schouten, Margaret K. Tivey, Karen L. Von Damm, Mary A. Voytek

Biology Faculty Publications and Presentations

Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide–sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem. It has been proposed that fluid pH in the actively venting sulphide structures is generally low (pH < 4.5), yet no extreme thermoacidophile has been isolated from vent deposits. Culture-independent surveys based on ribosomal RNA genes from deep-sea hydrothermal deposits have identified a widespread euryarchaeotal lineage, DHVE2 (deep-sea hydrothermal vent euryarchaeotic 2) Despite the ubiquity and apparent deep-sea endemism of DHVE2, cultivation of this group has been unsuccessful and thus its metabolism remains a mystery. Here we report the isolation and cultivation of a member of the DHVE2 group, which is an obligate thermoacidophilic sulphur- or iron-reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 55 and 75 °C. In addition, we demonstrate that this isolate constitutes up to 15% of the archaeal population, providing evidence that thermoacidophiles may be key players in the sulphur and iron cycling at deep-sea vents.