Other Biochemistry, Biophysics, and Structural Biology Commons^™

Biological Physics Student Edition 2020: Chapter 1, Philip C. Nelson

Department of Physics Papers

Chapter 1: What the Ancients Knew

The Effects Of Largazole, A Histone Deacetylase Inhibitor, On Breast Cancer Cell Viability And Metastasis, Hannah Mccowan

Honors Theses

Histone deacetylase enzymes modify epigenetic characteristics of a genome by removing acetyl groups from histone proteins in chromatin. Histone deacetylase inhibitors work by stopping this activity which can have various results in a cell including apoptosis, cell cycle arrest, differentiation, and migration. The purpose of these experiments was to see how largazole, a histone deacetylase inhibitor, affected cell viability for breast cancer and associated metastatic cell lines in both normoxic and hypoxic conditions. The experiment was completed by setting up two 96-well plates with varying concentrations of largazole and conducting a sulforhodamine viability assay. The specific cell lines used in ...

Alternative Polyadenylation Modulates Expression Of Pro-Fibrotic Proteins And Contributes To Lung Fibrosis, Junsuk Ko

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease which affects about 5 to 8 million individuals in the world. Despite the high prevalence, there is currently no cure for IPF, and the cause of this disease is still unclear. Our laboratory and collaborators have shown that nudix hydrolase 21 (NUDT21, which is also known as cleavage factor 25, CFIm25) is a key regulator of alternative polyadenylation (APA). NUDT21 depletion causes 3’UTR shortening via APA leading to enhanced mRNA stability and protein translation. This NUDT21 reduction promotes tumor growth in glioblastoma by enhancing expression of oncogenes. Cancer and IPF ...

A Study Of The Antioxidant Versus Pro-Oxidant Nature Of The Amyloid Beta Peptide And An Analysis Of The Natural Products, Isorhamnetin And Narignenin, As Antioxidants, Kaylee Holmes

Honors Theses

Alzheimer’s disease is a neurodegenerative disorder with no cure. Due to the widespread effects of this disease, abundant research efforts have gone towards finding a cure. The amyloid beta (Ab) peptide has been shown to be a potential cause of the disease due to destructive effects on tissues that it can have both by itself and through reactive oxygen species (ROS) generation. This study was performed in order to assess the structural properties of Ab₄₂monomers, fibrils and oligomers, to assess the antioxidant versus pro-oxidant behavior of the Ab peptide, and to assess the antioxidant nature of the ...

Transcriptome Analysis-Identified Long Noncoding Rna Crnde In Maintaining Endothelial Cell Proliferation, Migration, And Tube Formation, Matthew Moran, Xiao Cheng Zeng, Mohamed Sham Shihabudeen Haider Ali, Nishikant Wase, Nghi Nguyen, Weilong Yang, Chi Zhang, Concetta C. Dirusso, Xinghui Sun

Biochemistry -- Faculty Publications

Obesity is a leading risk factor for type-2 diabetes. Diabetes often leads to the dysregulation of angiogenesis, although the mechanism is not fully understood. Previously, long noncoding RNAs (lncRNAs) have been found to modulate angiogenesis. In this study, we asked how the expression levels of lncRNAs change in endothelial cells in response to excessive palmitic acid treatment, an obesitylike condition. Bioinformatics analysis revealed that 305 protein-coding transcripts were upregulated and 70 were downregulated, while 64 lncRNAs were upregulated and 46 were downregulated. Gene ontology and pathway analysis identified endoplasmic reticulum stress, HIF-1 signaling, and Toll-like receptor signaling as enriched after ...

The Genome Evolution And Domestication Of Tropical Fruit Mango, Peng Wang, Yingfeng Luo, Jianfeng Huang, Shenghan Gao, Guopeng Zhu, Zhiguo Dang, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shuangyang Wu, Edgar B. Cahoon, Beibei Bai, Zhichang Zhao, Qian Li, Junya Wei, Huarui Chen, Ruixiong Luo, Deyong Gong, Kexuan Tang, Bing Zhang, Zhangguang Ni, Guodi Huang, Songnian Hu, Yeyuan Chen

Biochemistry -- Faculty Publications

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis.

Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical ...

From Synthesis To Utilization: The Ins And Outs Of Mitochondrial Heme, Samantha A. Swenson, Courtney M. Moore, Jason R. Marcero, Amy E. Medlock, Amit R. Reddi, Oleh Khalimonchuk

Biochemistry -- Faculty Publications

Heme is a ubiquitous and essential iron containing metallo-organic cofactor required for virtually all aerobic life. Heme synthesis is initiated and completed in mitochondria, followed by certain covalent modifications and/or its delivery to apo-hemoproteins residing throughout the cell. While the biochemical aspects of heme biosynthetic reactions are well understood, the trafficking of newly synthesized heme—a highly reactive and inherently toxic compound—and its subsequent delivery to target proteins remain far from clear. In this review, we summarize current knowledge about heme biosynthesis and trafficking within and outside of the mitochondria.

Systematic Age-, Organ-, And Diet-Associated Ionome Remodeling And The Development Of Ionomic Aging Clocks, Bohan Zhang, Dmitriy I. Podolskiy, Marco Mariotti, Javier Seravalli, Vadim N. Gladyshev

Biochemistry -- Faculty Publications

Aging involves coordinated yet distinct changes in organs and systems throughout life, including changes in essential trace elements. However, how aging affects tissue element composition (ionome) and how these changes lead to dysfunction and dis-ease remain unclear. Here, we quantified changes in the ionome across eight organs and 16 age groups of mice. This global profiling revealed novel interactions between elements at the level of tissue, age, and diet, and allowed us to achieve a broader, organismal view of the aging process. We found that while the entire ionome stead-ily transitions along the young-to-old trajectory, individual organs are characterized by ...

Structural Basis Of Non-Canonical Transcriptional Regulation By The A-Bound Iron-Sulfur Protein Whib1 In M. Tuberculosis, Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang, Donald F. Becker, Limei Zhang

Biochemistry -- Faculty Publications

WhiB1 is amonomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress inM. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 A° -resolution crystal structure of the [4Fe–4S] cluster-bound (holo- )WhiB1 in complex with the C-terminal domain of the 70-family primary sigma factor A of M. tuberculosis containing the conserved region 4 (A 4). Region 4 of the 70-family primary sigma factors is commonly used ...

High-Throughput Nano-Scale Characterization Of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography, Alex J. Vecchio, Robert M. Stroud

Biochemistry -- Faculty Publications

Structural biology has revealed predicting heterologous expression levels, homogeneity, and stability of a protein from its primary structure are exceedingly difficult. Membrane proteins, in particular, present numerous challenges that make obtaining milligram quantities of quality samples problematic. For structural and functional investigation of these molecules, however, this is what is required. Fluorescence size-exclusion chromatography (F-SEC), a technique where a protein of biological interest is fused to green fluorescent protein (GFP) and monitored, circumvents many bottlenecks inherent to membrane protein structural biology. In vivo expression yields, as well as in vitro homogeneity and stability, can be rapidly evaluated utilizing nanogram quantities ...

Effects Of The Dihydrouracil Lesion On Dna Using 1h/31p 1d And 2d Solution Nmr, Benjamin M. Boyd

MSU Graduate Theses

The effects of the dihydrouracil lesion in DNA were studied using two dimensional NMR spectroscopy. The sequence used was based off of the Drew-Dickerson Dodecamer, with the cytosine in the three position replaced by a dihydrouracil. All of the nonexchangeable proton chemical shifts, with the exception of the H2, H5’, and H5’’, of the lesioned DNA were identified using NOESY spectra and then compared to the chemical shift values of the Drew Dickerson Dodecamer. The largest differences in chemical shifts were observed in the nucleotides neighboring the lesion, both within the strand and on the opposite strand. The imino exchangeable ...

Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah

Biochemistry -- Faculty Publications

Background: The ETDRS stereoscopic seven-field (7F) has been a standard imaging and grading protocol for assessment of diabetic retinopathy (DR) severity score in many clinical trials. To the best of our knowledge, the comparison between montage and stereoscopic 7F has not been reported in the literature. Therefore, the main purpose of this study is to compare agreement between montage and stereoscopic seven-field (7F) photographs in the assessment of DR severity.

Methods: Stereoscopic 7F photographs were captured from subjects with DR. Montages of monoscopic 7F images were created using Adobe Photoshop CS6 Extended©. The best quality image of each stereo pair ...

#1 - Alu-Derived Orthologous Chromosome Classification For The Primate Order, Mehul Mehra, Nitish Sood, Anav Mittal, Christopher Bates

Georgia Undergraduate Research Conference (GURC)

Orthologous chromosomes between any family of related species have been difficult thus far to obtain, often requiring substantial biochemical testing and computationally-intensive genomic analysis. By employing computational strategies on repeated non-coding DNA, numerous advantages to accurately determining orthologous chromosomes between species can be ascertained. Throughout the primate genome, the Alu repeated element covers 10% of the genome among higher order primates, spanning across each chromosome. These non-protein-coding sequences replicate themselves repeatedly, with each iteration allowed to mutate more than their protein-coding counterparts. Therefore, upon examining the genetic sequences of such “junk” DNA, increasingly specific distinctions can be made between any ...

#11 - Sequence Analysis Of Alu Repeated Elements For Primate Phylogenetic Tree Construction, Nitish Sood, Mehul Mehra, Anav Mittal, Christopher Bates

Georgia Undergraduate Research Conference (GURC)

Phylogenetic tree construction can be a particularly challenging and time-intensive process. This study employs a novel computational approach to phylogenetic tree construction, using the Alu repeating element, a SINE. Repetitive elements including Short and Long Interspersed Nuclear Elements (SINEs/LINEs) have successfully been applied as accurate tools for phylogenetic analysis, as they are predominately unidirectional and homoplasy-free. However, previous analysis of phylogenetic relationships using these repeating elements has been limited to a small number of isolated repeats among relatively few organisms.

As a highly repetitive sequence, the Alu element and its associated subfamilies can provide detailed analysis on evolutionary divergence ...

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pK_a on host-guest interactions ...

Some Of The Most Interesting Casp11 Targets Through The Eyes Of Their Authors, Andriy Kryshtafovych, John Moult, Arnaud Basle, Alex Burgin, Timonthy K. Craig, Robert A. Edwards, Deborah Fass, Marcus D. Hartmann, Mateusz Korycinski, Richard J. Lewis, Donald Lorimer, Andrei N. Lupas, Janet Newman, Thomas S. Peat, Kurt H. Piepenbrink, Janani Prahlad, Mark J. Van Raaij, Forest Rohwer, Anca M. Segall, Victor Seguritan, Eric J. Sundberg, Abhimanyu K. Singh, Mark A. Wilson, Torsten Schwede

Kurt Piepenbrink

The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features, and assess whether these features were correctly reproduced in the predictions submitted to CASP11.

Dna Uptake By Type Iv Filaments, Kurt H. Piepenbrink

Kurt Piepenbrink

Bacterial uptake of DNA through type IV filaments is an essential component of natural competence in numerous gram-positive and gram-negative species. Recent advances in the field have broadened our understanding of the structures used to take up extracellular DNA. Here, we review seminal experiments in the literature describing DNA binding by type IV pili, competence pili and the flp pili of Micrococcus luteus; collectively referred to here as type IV filaments. We compare the current state of the field on mechanisms of DNA uptake for these three appendage systems and describe the current mechanistic understanding of both DNA-binding and DNA-uptake ...

Role Of The Drosophila Beaf Protein In Chromatin Domain Insulator And Promoter Function, Mukesh Maharjan

LSU Doctoral Dissertations

Proper folding of eukaryotic genomes is required to allow correct interactions between different parts of chromosomes. Precise and timely interactions among different parts of a chromosome allow proper functioning inside a nucleus, including gene regulation, DNA replication and DNA repair. Eukaryotic regulatory elements that facilitate folding and interactions include enhancers, promoters and insulator elements. Insulator elements and their binding proteins play an important role in regulating correct chromatin structure and function. The Drosophila melanogaster special chromatin structure (scs’) is one such insulator. The Boundary Element Associated Factor (BEAF) binds to scs’. BEAF is a 32 kDa protein that has two ...

Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells ...

The Effects Of Eicosapentaenoic Acid (Epa) And Docosahexaenoic Acid (Dha) On Brown Adipogenesis In Stem Cell Culture, Darynne Dahlem

Animal Science Undergraduate Honors Theses

Polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are major maternal dietary supplements due to their positive benefits on neurological tissue growth during the first 12 weeks of gestation. Previous studies show that EPA and DHA inhibit muscle formation but promote adipogenesis. However, no research has addressed the question whether high intake of EPA and DHA affects brown fat development during gestation. The objective of this study was to measure the effect of EPA and DHA supplement on brown adipogenesis and potential pathways related to mitochondrial biosynthesis using fibroblasts as in vitro model. Using Oil-Red-O staining ...