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Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush 2020 University of Mississippi

Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush

Honors Theses

Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry is a powerful technique for the analysis of protein topography as it generates covalent mass labels that can survive downstream sample handling, and it is sensitive to the solvent accessibility of amino acid sidechains. Of the multiple platforms for HRPF, fast photochemical oxidation of proteins (FPOP) utilizes a pulsed 248 nm KrF excimer laser to label proteins by photolyzing hydrogen peroxide. FPOP is the most widely used HRPF platform because it labels proteins faster than unfolding can occur. Variations in FPOP sample conditions make it difficult to compare results between experiments ...


Titus Thesis Figures.Docx, Titus Hou 2020 University of Iowa

Titus Thesis Figures.Docx, Titus Hou

Titus Hou

No abstract provided.


Titus Thesis.Docx, Titus Hou 2020 University of Iowa

Titus Thesis.Docx, Titus Hou

Titus Hou

No abstract provided.


Cloning And Expression Of Hydra Innexin 2, A Gap Junction Protein Required For Coordinated Contraction Of The Body Column, Ashley O'Brien 2020 Buffalo State College

Cloning And Expression Of Hydra Innexin 2, A Gap Junction Protein Required For Coordinated Contraction Of The Body Column, Ashley O'Brien

Biology Theses

In invertebrates gap junctions are formed by the innexin family of proteins. Remarkably, the genome of Hydra magnipapillata contains 17 innexin genes. This study focused on Hydra innexin-2 (h-Inx2) which is expressed in nerve cells and plays a role in contraction of the body column. The gene sequence of H-Inx2 was obtained from the National Center for Biotechnology Information (NCBI), the gene was synthesized externally and transferred to a vector suitable for expression in Xenopus oocytes (pcDNA3.1 CT-GFP TOPO). The TOPO CT-GFP vector includes a priming site for RNA polymerase which allows in vitro preparation of RNA. Another advantage ...


Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey 2020 State University of New York College at Buffalo - Buffalo State College

Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey

Biology Theses

At least five beta-type connexins are expressed in various layers of the skin (Cx26, Cx30, Cx30.3, Cx31, and Cx32) and all include a glycine residue at position 12. Glycine12 (G12) is located about halfway through the cytoplasmic amino terminus and has been the focus of several studies related to connexin diseases and gap junction channel structure. The importance of this residue is evident in the severity and diversity of diseases associated with amino acid substitutions at G12 including hereditary forms of skin disease, deafness and neuropathy. This study uses bioinformatic analysis in combination with mutational analysis and electrophysiology to ...


Pedagogical Approaches To Enhance Q2s Conversion Teaching And Learning: Application Of The Acue Effective Practice Framework To Upper Division Biochemistry, Jason Burke 2020 California State University, San Bernardino

Pedagogical Approaches To Enhance Q2s Conversion Teaching And Learning: Application Of The Acue Effective Practice Framework To Upper Division Biochemistry, Jason Burke

Q2S Enhancing Pedagogy

The Effective Practice Framework course by the Association of College and University Educators (ACUE), and offered through the CSUSB Teaching Resource Center (TRC), was applied to the upper division biochemistry course series (CHEM 436A and 437A) in preparation for the Q2S conversion. This essay includes five reflections on the application of enhanced pedagogical approaches curated from a total of twenty-five. The enhanced pedagogies covered in the course are: designing and effective course and class; establishing a productive learning environment; using active learning techniques; promoting higher-order thinking; and assessing to inform instruction and promote learning. The reflections that follow have been ...


470— Quantifying The Shape Of A Plant (Brassica Rapa) During Growth Under Different Light Intensities Using Fractal Geometry, Matthew Cotroneo 2020 SUNY Geneseo

470— Quantifying The Shape Of A Plant (Brassica Rapa) During Growth Under Different Light Intensities Using Fractal Geometry, Matthew Cotroneo

GREAT Day

Over time plants not only increase in size but also change their shape. Quantifying this change in shape, however, is challenging. Fractal dimension, a measure of how these plants fill space, can provide a wholistic understanding of plant shape and how that shape changes as the plants react to their environments. I used a high-resolution, three-dimensional scanner to estimate the shape of Brassica rapa plants during growth under three different light intensities: low (40 Einsteins), medium (75 Einsteins) and high (100 Einsteins). From these data, each plant's above-ground shape was quantified using fractal geometry. The fractal dimension (D) of ...


The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta 2020 University of Nebraska - Lincoln

The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta

Theses and Dissertations in Biochemistry

Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood.

Here we use X-ray crystallography, computer simulations, site directed mutagenesis and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in the enzyme, isocyanide hydratase (ICH), affects the protein ...


Clostridium Perfringens Adhesion Through Type Iv Pili, Alexander Meyer, Josephine Liess, Kurt Piepenbrink 2020 University of Nebraska-Lincoln

Clostridium Perfringens Adhesion Through Type Iv Pili, Alexander Meyer, Josephine Liess, Kurt Piepenbrink

UCARE Research Products

Bacteria infect host cells through several mechanisms, one of which is a surface protein called a type IV pilus. Type IV pili are thin, hair-like protein fibers on the bacterial surface capable of being extended and retracted from a bacterial cell; they are used for functions including motility, biofilm formation, and adherence to host cells. Clostridium perfringens is a Gram-positive bacterium best known as a food pathogen that is believed to use type IV pili for host cell adherence. These pili are poorly characterized and understanding how C. perfringens uses type IV pili will provide a model for how these ...


Cryoem Structure Of Ctbp2 Confirms Tetrameric Architecture, Anne M. Jecrois, M. Michael Dcona, Xiaovan Deng, Dipankar Bandyopadhyay, Steven R. Grossman, Celia A. Schiffer, William E. Royer 2020 University of Massachusetts Medical School

Cryoem Structure Of Ctbp2 Confirms Tetrameric Architecture, Anne M. Jecrois, M. Michael Dcona, Xiaovan Deng, Dipankar Bandyopadhyay, Steven R. Grossman, Celia A. Schiffer, William E. Royer

University of Massachusetts Medical School Faculty Publications

C-terminal binding proteins 1 and 2 (CtBP1 and CtBP2) are transcriptional regulators that activate or repress many genes involved in cellular development, apoptosis and metastasis. CtBP proteins are activated under hypoxic conditions where NAD(H) levels tend to be higher. NADH-dependent activation of CtBP2 has direct implication in multiple types of cancers and poor patient prognosis. Previous studies have proposed dimeric CtBP as the relevant oligomeric state, however our studies with multi-angle light scattering have shown that the primary effect of NADH binding is to promote the assembly of two CtBP dimers into tetramers. Here, we present the cryoEM structures ...


Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He 2020 Old Dominion University

Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He

College of Sciences Posters

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a ...


Avoiding Drug Resistance By Substrate Envelope-Guided Design: Toward Potent And Robust Hcv Ns3/4a Protease Inhibitors, Ashley N. Matthew, Jacqueto Zephyr, Nageswara Rao Desaboini, Mina Henes, Wasih Kamran, Klajdi Kosovrasti, Adam Hedger, Gordon J. Lockbaum, Jennifer Timm, Akbar Ali, Nese Kurt Yilmaz, Celia A. Schiffer 2020 University of Massachusetts Medical School

Avoiding Drug Resistance By Substrate Envelope-Guided Design: Toward Potent And Robust Hcv Ns3/4a Protease Inhibitors, Ashley N. Matthew, Jacqueto Zephyr, Nageswara Rao Desaboini, Mina Henes, Wasih Kamran, Klajdi Kosovrasti, Adam Hedger, Gordon J. Lockbaum, Jennifer Timm, Akbar Ali, Nese Kurt Yilmaz, Celia A. Schiffer

University of Massachusetts Medical School Faculty Publications

Hepatitis C virus (HCV) infects millions of people worldwide, causing chronic liver disease that can lead to cirrhosis, hepatocellular carcinoma, and liver transplant. In the last several years, the advent of direct-acting antivirals, including NS3/4A protease inhibitors (PIs), has remarkably improved treatment outcomes of HCV-infected patients. However, selection of resistance-associated substitutions and polymorphisms among genotypes can lead to drug resistance and in some cases treatment failure. A proactive strategy to combat resistance is to constrain PIs within evolutionarily conserved regions in the protease active site. Designing PIs using the substrate envelope is a rational strategy to decrease the susceptibility ...


Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker 2020 University of Massachusetts Medical School

Detecting Chromatin Interactions Along And Between Sister Chromatids With Sisterc, Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, Job Dekker

University of Massachusetts Medical School Faculty Publications

Accurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during S-phase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst ...


Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao 2020 University of Texas at El Paso

Hiv-1 Did Not Contribute To The 2019-Ncov Genome, Chuan Xiao, Xiaojun Li, Shuying Liu, Yongming Sang, Shou-Jiang Gao, Feng Gao

Coronavirus COVID-19 Publications by UMMS Authors

When a new pathogen that causes a global epidemic in humans, one key question is where it comes from. This is especially important for a zoonotic infectious disease that jumps from animals to humans. Knowing the origin of such a pathogen is critical to develop means to block further transmission and to develop vaccines. Discovery of the origin of a newly human pathogen is a sophisticated process that requires extensive and vigorous scientific validations and generally takes many years, such as the cases for HIV-1, SARS and MERS. Unfortunately, before the natural sources of new pathogens are clearly defined, conspiracy ...


Conformational Changes In The Ebola Virus Membrane Fusion Machine Induced By Ph, Ca2+, And Receptor Binding, Dibyendu Kumar Das, Uriel Bulow, William E. Diehl, Natasha D. Durham, Fernando Senjobe, Kartik Chandran, Jeremy Luban, James B. Munro 2020 Tufts University

Conformational Changes In The Ebola Virus Membrane Fusion Machine Induced By Ph, Ca2+, And Receptor Binding, Dibyendu Kumar Das, Uriel Bulow, William E. Diehl, Natasha D. Durham, Fernando Senjobe, Kartik Chandran, Jeremy Luban, James B. Munro

Open Access Articles

The Ebola virus (EBOV) envelope glycoprotein (GP) is a membrane fusion machine required for virus entry into cells. Following endocytosis of EBOV, the GP1 domain is cleaved by cellular cathepsins in acidic endosomes, removing the glycan cap and exposing a binding site for the Niemann-Pick C1 (NPC1) receptor. NPC1 binding to cleaved GP1 is required for entry. How this interaction translates to GP2 domain-mediated fusion of viral and endosomal membranes is not known. Here, using a bulk fluorescence dequenching assay and single-molecule Forster resonance energy transfer (smFRET)-imaging, we found that acidic pH, Ca2+, and NPC1 binding synergistically induce conformational ...


Skp, Cullin, F-Box (Scf)-Met30 And Scf-Cdc4-Mediated Proteolysis Of Cenp-A Prevents Mislocalization Of Cenp-A For Chromosomal Stability In Budding Yeast, Wei-Chun Au, Richard E. Baker, Munira A. Basrai 2020 National Institutes of Health

Skp, Cullin, F-Box (Scf)-Met30 And Scf-Cdc4-Mediated Proteolysis Of Cenp-A Prevents Mislocalization Of Cenp-A For Chromosomal Stability In Budding Yeast, Wei-Chun Au, Richard E. Baker, Munira A. Basrai

Open Access Articles

Restricting the localization of the histone H3 variant CENP-A (Cse4 in yeast, CID in flies) to centromeres is essential for faithful chromosome segregation. Mislocalization of CENP-A leads to chromosomal instability (CIN) in yeast, fly and human cells. Overexpression and mislocalization of CENP-A has been observed in many cancers and this correlates with increased invasiveness and poor prognosis. Yet genes that regulate CENP-A levels and localization under physiological conditions have not been defined. In this study we used a genome-wide genetic screen to identify essential genes required for Cse4 homeostasis to prevent its mislocalization for chromosomal stability. We show that two ...


Structural Study Of The Complex Between Dna Polymerase Iota And Ub-Pcna, Harrison Taylor 2020 The University of Western Ontario

Structural Study Of The Complex Between Dna Polymerase Iota And Ub-Pcna, Harrison Taylor

Electronic Thesis and Dissertation Repository

DNA polymerase iota (polι) is a member of the Y-family, polymerases which are key components in translesion synthesis (TLS). As part of the DNA damage response, TLS allows cells to bypass damaged template DNA. Each member of the Y-family is capable of accurately replicating across from certain lesions. All Y-family polymerases are recruited by ubiquitination of the DNA sliding clamp, PCNA, by direct interaction with PCNA and ubiquitin. The mechanism of polymerase choice is not well understood, nor are the interactions between Ub-PCNA and the TLS polymerases. We studied the structure of the complex between the interacting region of polι ...


A Thermophilic Phage Uses A Small Terminase Protein With A Fixed Helix-Turn-Helix Geometry, Janelle A. Hayes, Brendan J. Hilbert, Christl Gaubitz, Nicholas P. Stone, Brian A. Kelch 2020 University of Massachusetts Medical School

A Thermophilic Phage Uses A Small Terminase Protein With A Fixed Helix-Turn-Helix Geometry, Janelle A. Hayes, Brendan J. Hilbert, Christl Gaubitz, Nicholas P. Stone, Brian A. Kelch

Open Access Articles

Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here, we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerS(P76-26) oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerS(P76-26) revealed that it forms a ring ...


Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan McNamara 2020 The University of Akron

Non-Invasive Method For Leptin Supplementation In Zebrafish (Danio Rerio), Regan Mcnamara

Williams Honors College, Honors Research Projects

I tested the hypothesis that recombinant leptin protein can be introduced to zebrafish in vivo through non-invasive soaking in a solution containing the protein. One way to study various molecules’ effects in vivo is through intraperitoneal or intracerebroventricular injections during the embryonic or larval stage, which is invasive, difficult to administer, and can have a high mortality rate. 48 hours post fertilization (hpf) zebrafish were soaked in a His-tagged recombinant leptin protein solution at 10 nM and 100 nM concentrations (produced by Genscript). After soaking, zebrafish larvae were washed extensively to remove all recombinant protein on their exterior before homogenization ...


The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans PhD 2020 West Virginia University

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry ...


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