Biochemistry, Biophysics, and Structural Biology Commons^™

Loss Of Non-Motor Kinesin Kif26a Causes Congenital Brain Malformations Via Dysregulated Neuronal Migration And Axonal Growth As Well As Apoptosis, Xuyu Qian, Ellen M Degennaro, Maya Talukdar, Shyam K Akula, Abbe Lai, Diane D Shao, Dilenny Gonzalez, Jack H Marciano, Richard S Smith, Norma K Hylton, Edward Yang, J Fernando Bazan, Lee Barrett, Rebecca C Yeh, R Sean Hill, Samantha G Beck, Aoi Otani, Jolly Angad, Tadahiro Mitani, Jennifer E Posey, Davut Pehlivan, Daniel Calame, Hatip Aydin, Osman Yesilbas, Kendall C Parks, Emanuela Argilli, Eleina England, Kiho Im, Ajay Taranath, Hamish S Scott, Christopher P Barnett, Peer Arts, Elliott H Sherr, James R Lupski, Christopher A Walsh

Faculty, Staff and Students Publications

Kinesins are canonical molecular motors but can also function as modulators of intracellular signaling. KIF26A, an unconventional kinesin that lacks motor activity, inhibits growth-factor-receptor-bound protein 2 (GRB2)- and focal adhesion kinase (FAK)-dependent signal transduction, but its functions in the brain have not been characterized. We report a patient cohort with biallelic loss-of-function variants in KIF26A, exhibiting a spectrum of congenital brain malformations. In the developing brain, KIF26A is preferentially expressed during early- and mid-gestation in excitatory neurons. Combining mice and human iPSC-derived organoid models, we discovered that loss of KIF26A causes excitatory neuron-specific defects in radial migration, localization, dendritic and …

Inhibiting Glutamine Utilization Creates A Synthetic Lethality For Suppression Of Atp Citrate Lyase In Kras-Driven Cancer Cells, Ahmet Hatipoglu, Deepak Menon, Talia Levy, Maria A. Frias, David A. Foster

Publications and Research

Metabolic reprogramming is now considered a hallmark of cancer cells. KRas-driven cancer cells use glutaminolysis to generate the tricarboxylic acid cycle intermediate α -ketoglutarate via a transamination reaction between glutamate and oxaloacetate. We reported previously that exogenously supplied unsaturated fatty acids could be used to synthesize phosphatidic acid–a lipid second messenger that activates both mammalian target of rapamycin (mTOR) complex 1 (mTORC1) and mTOR complex 2 (mTORC2). A key target of mTORC2 is Akt–a kinase that promotes survival and regulates cell metabolism. We report here that mono- unsaturated oleic acid stimulates the phosphoryla tion of ATP citrate lyase (ACLY) at …

Whole Genome Sequencing Of Moraxella Bovis Strains From North America Reveals Two Genotypes With Different Genetic Determinants, Emily L. Wynn, Matthew M. Hille, John Dustin Loy, Gennie Schuller, Kristen L. Kuhn, Aaron M. Dickey, James L. Bono, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and …

Genetic Inhibition Of Nuclear Factor Of Activated T-Cell C2 Prevents Atrial Fibrillation In Crem Transgenic Mice, Li Ni, Satadru K Lahiri, Jiali Nie, Xiaolu Pan, Issam Abu-Taha, Julia O Reynolds, Hannah M Campbell, Haihao Wang, Markus Kamler, Wilhelm Schmitz, Frank Ulrich Müller, Na Li, Xiang Wei, Dao Wen Wang, Dobromir Dobrev, Xander H T Wehrens

Faculty, Staff and Students Publications

AIMS: Abnormal intracellular calcium (Ca2+) handling contributes to the progressive nature of atrial fibrillation (AF), the most common sustained cardiac arrhythmia. Evidence in mouse models suggests that activation of the nuclear factor of activated T-cell (NFAT) signalling pathway contributes to atrial remodelling. Our aim was to determine the role of NFATc2 in AF in humans and mouse models.

METHODS AND RESULTS: Expression levels of NFATc1-c4 isoforms were assessed by quantitative reverse transcription-polymerase chain reaction in right atrial appendages from patients with chronic AF (cAF). NFATc1 and NFATc2 mRNA levels were elevated in cAF patients compared with those in normal sinus …

Control Of Ribosomal Rna Synthesis By Hematopoietic Transcription Factors, Charles Antony, Subin S George, Justin Blum, Patrick Somers, Chelsea L Thorsheim, Dexter J Wu-Corts, Yuxi Ai, Long Gao, Kaosheng Lv, Michel G Tremblay, Tom Moss, Kai Tan, Jeremy E Wilusz, Austen R D Ganley, Maxim Pimkin, Vikram R Paralkar

Faculty, Staff and Students Publications

Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA …

Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …

Activity Of The Lactate Dehydrogenase Inhibitor Oxamic Acid Against The Fermentative Bacterium Streptococcus Mitis/Oralis: Bactericidal Effects And Prevention Of Daptomycin Resistance In Vitro And In An Ex Vivo Model, Razieh Kebriaei, Arnold S. Bayer, Christian K. Lapitan, Michael J. Rybak, Greg A. Somerville, Nagendra N. Mishra

School of Veterinary and Biomedical Sciences: Faculty Publications

Streptococcus mitis/oralis is a fermentative bacterium that relies on lactate dehydrogenase to balance its redox poise and keep glycolysis active. Metabolomic analysis of an in vitro– derived daptomycin-resistant (DAP-R) S. mitis/oralis strain (351-D10) revealed differences in glucose catabolism relative to its DAP-susceptible (DAP-S) parental strain, 351. Metabolic changes associated with the transition to this DAP-R phenotype suggested that inhibiting glycolysis could alter DAP susceptibility. In addition, the strong reliance of S. mitis/oralis on glycolysis for energy and biosynthetic intermediates suggested that inhibiting glycolysis would adversely affect growth and biomass accumulation. To test these hypotheses, we used the lactate dehydrogenase inhibitor …

Ngly1 Deficiency Affects Glycosaminoglycan Biosynthesis And Wnt Signaling Pathway In Mice, Amy Batten

PANDION: The Osprey Journal of Research and Ideas

Individuals affected by NGLY1 Deficiency cannot properly deglycosylate and recycle certain proteins. Even though less than 100 people worldwide have been diagnosed with this rare autosomal recessive condition, thousands are affected by similar glycosylation disorders. Common phenotypic manifestations of NGLY1 Deficiency include severe neural and intellectual delay, impaired muscle and liver function, and seizures that may become intractable. Very little is currently known about the various mechanisms through which NGLY1 deficiency affects the body and this has led to a lack of viable treatment options for those afflicted. This experiment uses a loss-of-function (LOF) mouse model of NGLY1 Deficiency homologous …

3,6-Dimethoxyxanthone From 2,2’,4,4’- Tetrahydroxy-Benzophenone Via Microwave-Assisted Annulation, Sarah E. Knisely, Faith R. Rosario, Salem F. Gebeyehu, Paige E. Heiple, Robert E. Lee Sr

Journal of the South Carolina Academy of Science

Xanthones are tricyclic aromatic compounds that have multiple pharmacological uses due to their anti-tumor, antioxidant, anti-inflammatory, anti-bacterial, and potentially chemopreventive properties. The target of this research was to optimize a two-step synthesis of 3,6-dimethoxyxanthone (3) from 2,2’,4,4’-tetrahydroxy-benzophenone (1) via microwave-assisted (200 °C, 30-40 min., 150 W) sodium acetate-catalyzed annulation. The product, 3,6-dihydroxyxanthone (2), was then methylated to (3) using dimethyl sulfate (DMS) and sodium carbonate in acetone at reflux. The product yields were 93% (>99% purity) for (2) and 94% (>99% purity) for (3). Characterization was accomplished using ¹H NMR, FTIR, melting point, TLC, HPLC, and GCMS. …

Ez Clear For Simple, Rapid, And Robust Mouse Whole Organ Clearing, Chih-Wei Hsu, Juan Cerda, Jason M Kirk, Williamson D Turner, Tara L Rasmussen, Carlos P Flores Suarez, Mary E Dickinson, Joshua D Wythe

Faculty, Staff and Students Publications

Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevent the widespread adoption of these methods. Here, we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hr in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, samples …

Direct Measurement Of Stokes–Einstein Diffusion Of Cowpea Mosaic Virus With 19 Μs-Resolved Xpcs, Kacper Switalski, Jingyu Fang, Luxi Li, Miaoqi Chu, Erik Sarnello, Pete Jemian, Tao Li, Qian Wang, Qingteng Zhang

Faculty Publications

Brownian motion of Cowpea mosaic virus (CPMV) in water was measured using small-angle X-ray photon correlation spectroscopy (SA-XPCS) at 19.2 mu s time resolution. It was found that the decorrelation time tau(Q) = 1/DQ(2) up to Q = 0.091 nm(-1). The hydrodynamic radius R-H determined from XPCS using Stokes-Einstein diffusion D = kT/(6 pi eta R-H) is 43% larger than the geometric radius R-0 determined from SAXS in the 0.007 M K3PO4 buffer solution, whereas it is 80% larger for CPMV in 0.5 M NaCl and 104% larger in 0.5 M (NH4)(2)SO4, a possible effect of aggregation as well as …

Polyamine Enzymes As Potential Targets For Cancer Therapeutics To Mitigate Diabetic Triple Negative Breast Cancer Advancement, Hadassha Tofilau

Biology Theses, Dissertations, and Student Creative Activity

Breast cancer (BC) is the second leading cause of death in women. Co-existence of diabetes and BC can be lethal, leading to higher mortality than BC alone. TNBC is highly refractive, heterogenous, and resistant to most chemotherapies. Polyamines play a role in cell growth and are elevated in cancer, though their role in diabetic TNBC has not been explored. We hypothesized that high glucose/diabetic conditions increase TNBC cell proliferation through modification of enzymes in the polyamine pathway and that miR-133a would decrease TNBC cell proliferation. For this study, MDA-MB-231 and MCF-10A cell lines were both treated with normal (5mM) and …

X-Linked Ubiquitin-Specific Peptidase 11 Increases Tauopathy Vulnerability In Women, Yan Yan

USF Tampa Graduate Theses and Dissertations

Women experience significantly higher tau burden and increased risk for Alzheimer’s disease (AD) than men, yet the underlying mechanism for this vulnerability has not been explained. Here, we demonstrate through in vitro and in vivo models, as well as human AD brain tissue, that X-linked ubiquitin specific peptidase 11 (USP11) augments pathological tau aggregation via tau deubiquitination initiated at lysine-281. Removal of ubiquitin provides access for enzymatic tau acetylation at lysines 281 and 274. USP11 escapes complete X-inactivation, and female mice and people both exhibit higher USP11 levels than males. Genetic elimination of usp11 in a tauopathy mouse model preferentially …

Physicochemical Analysis Of Cold Brew And Hot Brew Peaberry Coffee, Evan T. Schwarzmann, Marlena P. Washington, Niny Z. Rao

College of Life Sciences Faculty Papers

Peaberry coffee is the result of a natural mutation of coffee beans, and they make up only about 5–7% of coffee crops. A typical coffee cherry contains two seeds that are developed against each other, resulting in the distinctive half-rounded shape of coffee beans. However, failing to fertilize both ovules of one of the seeds or failure in endosperm development can cause only one of the seeds to develop, resulting in smaller, denser beans with a more domed shape. Peaberry coffees are said to be sweeter, lighter, and more flavorful since the peaberry beans receive all nutrients from the coffee …

Speciation Jigsaw Activity, Erika Crispo

Open Educational Resources

What is a species? Why are there so many species on the planet? The question of why we have different species of organisms was the key thesis of Charles Darwin’s most famous book, On the Origin of Species.While several definitions of what constitutes a species exists, the most common definition lies within thebiological species concept. This concept states that different species exist when two individuals of different sexes are unable to reproduce with one another to yield viable offspring in the wild. A major limitation of this definition is that it can only be applied to sexually reproducing organisms that …

Bisc 504: Biometry, Jason Hoeksema

GMAS Course Syllabi

No abstract provided.

Glutathione And Glutaredoxin In Redox Regulation And Cell Signaling Of The Lens, Marjorie F. Lou

School of Veterinary and Biomedical Sciences: Faculty Publications

The ocular lens has a very high content of the antioxidant glutathione (GSH) and the enzymes that can recycle its oxidized form, glutathione disulfide (GSSG), for further use. It can be synthesized in the lens and, in part, transported from the neighboring anterior aqueous humor and posterior vitreous body. GSH is known to protect the thiols of the structural lens crystallin proteins from oxidation by reactive oxygen species (ROS) so the lens can maintain its transparency for proper visual function. Age-related lens opacity or senile cataract is the major visual impairment in the general population, and its cause is closely …

The Impacts Of Framework Mutations On Steady-State Kinetics Of An Aldolase Abzyme, Charles Andrew Mettler

Master's Theses

During affinity maturation, antibodies acquire point mutations that lead to enhanced binding strength to a particular ligand while simultaneously becoming more conformationally restricted as they become increasingly complementary to their ligand’s electrostatic geometry. This property has catalytic potential in transition-state (TS) stabilization whereby kinetic barriers (i.e., the energetic gap between the substrate and its TS) are reduced and reaction rates are enhanced. This basic mechanism is thought to underlie the majority of the rate enhancement observed for enzymes. A key integration of antibody binding specificity and strength with enzymatic catalytic strategy is the development of catalytic antibodies (“abzymes”). Abzymes are …

Structural And Transient Kinetic Analysis On Mechanism-Based Inactivators Of Human Ornithine Aminotransferase, Arseniy Butrin

Dissertations

HCC, Hepatocellular carcinoma, MBI, Mechanism-based inactivator, OAT, Ornithine Aminotransferase

The Roles Of A Probiotic Exopolysaccharide In Breast Cancer, Mai Rachel Nguyen

Dissertations

breast cancer, exopolysaccharide, probiotic