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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 2020 University of Mississippi

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 ...


Faculty Spotlight—Dr. Phil Danielson, Hannah Stanley, William Moody 2020 University of Denver

Faculty Spotlight—Dr. Phil Danielson, Hannah Stanley, William Moody

DU Undergraduate Research Journal Archive

Interview with Dr. Phil Danielson


Aminoacyl-Trna Synthetases, Miguel Angel Rubio Gomez, Michael Ibba 2020 The Ohio State University

Aminoacyl-Trna Synthetases, Miguel Angel Rubio Gomez, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key ...


Chemoenzymatic Study Of Coa-Linked Rna In Bacteria, Krishna Sapkota 2020 The University of Southern Mississippi

Chemoenzymatic Study Of Coa-Linked Rna In Bacteria, Krishna Sapkota

Dissertations

The ability of RNA to store genetic information and to catalyze biochemical transformations led to the speculation of the existence of RNA world before the evolution of contemporary ribonucleoprotein (RNP) world. Recent discovery of RNA molecules containing metabolic cofactors including coenzyme A and its various thioesters at their 5’ end further supported the RNA world hypothesis as these CoA-linked RNA molecules could be the molecular fossils with very ancient origin. As both RNA and Coenzyme A are believed to have co-existed since last universal common ancestor (LUCA) or even before, the CoA-RNA conjugates in current biology may reveal fundamental molecular ...


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 2020 University of Nebraska - Lincoln

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 ...


Compounds For Increasing Lipid Synthesis And Storage, Concetta C. DiRusso, Nishikant Wase 2020 University of Nebraska - Lincoln

Compounds For Increasing Lipid Synthesis And Storage, Concetta C. Dirusso, Nishikant Wase

Biochemistry -- Faculty Publications

This invention relates to methods for increasing lipid production in cells. Methods of producing biofuel from cells and preparing mutraceuticals comprising lipids produced according to a method provided herein are also provided.


Targeting Trna-Synthetase Interactions Towards Novel Therapeutic Discovery Against Eukaryotic Pathogens, Paul Kelly, Fatemeh Hadi-Nezhad, Dennis Y. Liu, Travis J. Lawrence, Roger G. Linington, Michael Ibba, David H. Ardell 2020 The Ohio State University

Targeting Trna-Synthetase Interactions Towards Novel Therapeutic Discovery Against Eukaryotic Pathogens, Paul Kelly, Fatemeh Hadi-Nezhad, Dennis Y. Liu, Travis J. Lawrence, Roger G. Linington, Michael Ibba, David H. Ardell

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including ...


Covalent Labeling-Mass Spectrometry For Characterizing Protein-Ligand Complexes, TIANYING LIU 2020 University of Massachusetts Amherst

Covalent Labeling-Mass Spectrometry For Characterizing Protein-Ligand Complexes, Tianying Liu

Doctoral Dissertations

This dissertation focuses on applying covalent labeling (CL) and mass spectrometry (MS) for characterizing protein-ligand complexes. Understanding protein-ligand interactions has both fundamental and applied significance. Covalent labeling is a protein surface modification technique that selectively modifies solvent-exposed amino acid side chains of proteins. A covalent bond is formed between the functional groups of labeling reagent and protein’s side chain. One of the key factors that affects CL reactivity is a side chain’s solvent accessibility. Ligand binding protects residues on the protein surface from being labeled, and residues involved in ligand binding can be indicated via decreases in labeling ...


Mutational Analysis And Domain Characterization Of The Apolipoprotein L-1 Ion Channel, Charles M. Schaub 2020 The Graduate Center, City University of New York

Mutational Analysis And Domain Characterization Of The Apolipoprotein L-1 Ion Channel, Charles M. Schaub

Dissertations, Theses, and Capstone Projects

The human innate immunity factor Apolipoprotein L-1 (APOL1) protects against Trypanosoma brucei brucei infection. Recent studies have shown recombinant APOL1 (rAPOL1) inserts into planar lipid bilayers at an acidic pH 5.6 and forms a cation-selective channel, which opens upon subsequent neutralization, pH 7.2. This corresponds with the pH changes APOL1 would encounter during endosome recycling, suggesting that APOL1 forms a pH-gated ion channel in the plasma membrane of the parasite, leading to uncontrolled ion flux and osmotic imbalance. However, structural and domain characteristics of the APOL1 channel are poorly understood, despite potential similarities to diphtheria and colicin toxins ...


Deconstructing Bioluminescence: From Molecular Detail To In Vivo Imaging., Spencer T. Adams Jr. 2020 University of Massachusetts Medical School

Deconstructing Bioluminescence: From Molecular Detail To In Vivo Imaging., Spencer T. Adams Jr.

GSBS Dissertations and Theses

Bioluminescence is the chemical production of light that results when a luciferase enzyme catalyzes the luminogenic oxidation of a small-molecule luciferin substrate. The numerous luciferases and luciferins nature has evolved can be used to illuminate biological processes, from in vitro assays to imaging processes in live animals. However, we can improve the utility of bioluminescence through modification of these enzymes and substrates. My thesis work focuses on developing reporters that expand the bioluminescent toolkit and improving our understanding of how bioluminescence works on a molecular level.

The first part of my thesis focuses on characterizing luciferases and luciferins that improve ...


Faculty Spotlight—Dr. Robert Dores, Anit Tyagi, William Moody 2020 University of Denver

Faculty Spotlight—Dr. Robert Dores, Anit Tyagi, William Moody

DU Undergraduate Research Journal Archive

Robert Dores Interview

Edited by Will Moody


Genome Biology Of The Paleotetraploid Perennial Biomass Crop Miscanthus, Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu, Katarzyna Glowacka, Kankshita Swaminathan, Daniel S. Rokhsar, 35 additional co-authors 2020 University of California, Berkeley

Genome Biology Of The Paleotetraploid Perennial Biomass Crop Miscanthus, Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu, Katarzyna Glowacka, Kankshita Swaminathan, Daniel S. Rokhsar, 35 Additional Co-Authors

Biochemistry -- Faculty Publications

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M ...


Metabolic Feedback Inhibition Influences Metabolite Secretion By The Human Gut Symbiont Bacteroides Thetaiotaomicron, Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan 2020 University of Nebraska-Lincoln

Metabolic Feedback Inhibition Influences Metabolite Secretion By The Human Gut Symbiont Bacteroides Thetaiotaomicron, Jennie L. Catlett, Jonathan Catazaro, Mikaela Cashman, Sean Carr, Robert Powers, Myra B. Cohen, Nicole R. Buan

Biochemistry -- Faculty Publications

Microbial metabolism and trophic interactions between microbes give rise to complex multispecies communities in microbe-host systems. Bacteroides thetaiotaomicron (B. theta) is a human gut symbiont thought to play an important role in maintaining host health. Untargeted nuclear magnetic resonance metabolomics revealed B. theta secretes specific organic acids and amino acids in defined minimal medium. Physiological concentrations of acetate and formate found in the human intestinal tract were shown to cause dose-dependent changes in secretion of metabolites known to play roles in host nutrition and pathogenesis. While secretion fluxes varied, biomass yield was unchanged, suggesting feedback inhibition does not affect metabolic ...


Automated Inference Of Boolean Models From Molecular Interaction Maps Using Casq, Sara Sadat Aghamiri, Vidisha Singh, Aurelien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis 2020 Universite Paris-Saclay

Automated Inference Of Boolean Models From Molecular Interaction Maps Using Casq, Sara Sadat Aghamiri, Vidisha Singh, Aurelien Naldi, Tomáš Helikar, Sylvain Soliman, Anna Niarakis

Biochemistry -- Faculty Publications

Motivation: Molecular interaction maps have emerged as a meaningful way of representing biological mechanisms in a comprehensive and systematic manner. However, their static nature provides limited insights to the emerging behaviour of the described biological system under different conditions. Computational modelling provides the means to study dynamic properties through in silico simulations and perturbations. We aim to bridge the gap be- tween static and dynamic representations of biological systems with CaSQ, a software tool that infers Boolean rules based on the topology and semantics of molecular interaction maps built with CellDesigner.

Results: We developed CaSQ by defining conversion rules and ...


Sbml Level 3: An Extensible Format For The Exchange And Reuse Of Biological Models, Sarah M. Keating, Dagmar Waltemath, Tomáš Helikar, Michael Hucka, 50 additional co-authors 2020 California Institute of Technology

Sbml Level 3: An Extensible Format For The Exchange And Reuse Of Biological Models, Sarah M. Keating, Dagmar Waltemath, Tomáš Helikar, Michael Hucka, 50 Additional Co-Authors

Biochemistry -- Faculty Publications

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraintbased models, reaction-diffusion models, logical network models, and rule-based models. The format leverages ...


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 2020 Chinese Academy of Tropical Agricultural Sciences & Ministry of Agriculture Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China

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 2020 University of Nebraska - Lincoln

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.


Insights From The Inclusive Environments And Metrics In Biology Education And Research Network: Our Experience Organizing Inclusive Biology Education Research Events, Rebecca A. Campbell-Montalvo, Natalia Caporale, Gary S. McDowell, Candice Idlebird, Katie M. Wiens, Kimberly M. Jackson, Jana D. Marcette, Michael E. Moore 2020 University of Connecticut

Insights From The Inclusive Environments And Metrics In Biology Education And Research Network: Our Experience Organizing Inclusive Biology Education Research Events, Rebecca A. Campbell-Montalvo, Natalia Caporale, Gary S. Mcdowell, Candice Idlebird, Katie M. Wiens, Kimberly M. Jackson, Jana D. Marcette, Michael E. Moore

Biochemistry -- Faculty Publications

In contrast to efforts focusing on improving inclusion in STEM classrooms from kindergarten through un-dergraduate (K–16), efforts to improve inclusion in scientific meetings and conferences, important hubs of STEM culture, are more recent. Markers of inclusion that are sometimes overlooked at these events can include the composition of panels, how workshops are run, the affordability of conferences, and various other mechanisms that maintain pre-existing hierarchies and norms that limit the participation of early-career researchers and individuals of minoritized cultural, linguistic, and economic backgrounds. The Inclusive Environments and Metrics in Biology Education and Research (iEMBER) network coordinates efforts of researchers ...


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 2020 Brigham and Women's Hospital and Harvard Medical School

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 ...


Connecting Theory To Practice: Using Self-Determination Theory To Better Understand Inclusion In Stem, Michael E. Moore, Dulce M. Vega, Katie M. Wiens, Natalia Caporale 2020 University of Nebraska-Lincoln

Connecting Theory To Practice: Using Self-Determination Theory To Better Understand Inclusion In Stem, Michael E. Moore, Dulce M. Vega, Katie M. Wiens, Natalia Caporale

Biochemistry -- Faculty Publications

In the United States, persistence for women and ethnic minorities in science, technology, engineering, and math (STEM) careers is strongly impacted by affective factors such as science identity, agency, and sense of belonging. Policies aimed at increasing the diversity of the national STEM student population and workforce have recently focused on fostering inclusive learning environments that can positively impact the experi-ences of underrepresented minorities (URMs) in STEM, thus increasing their retention. While research on inclusion in STEM in higher education is relatively new, inclusion research has a rich history in several other disciplines. These fields have developed theoretical frameworks and ...


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