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Biochemistry, Biophysics, and Structural Biology Commons™
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Articles 1 - 22 of 22
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
The Role Of Rad51 In Trichomonas Vaginalis, Dominique Hall
The Role Of Rad51 In Trichomonas Vaginalis, Dominique Hall
University of the Pacific Theses and Dissertations
Drug resistance to the current treatments on the market is on the rise, therefore there is strong interest in understanding what could be causing the resistance, how resistance could be spreading through the population, and finding some possible new drug targets. One protein of interest is Radiation Sensitive Protein 51 (Rad51). It is a protein that is involved in homologous recombination as well as other processes such as DNA damage repair. While Trichomonas vaginalis traditionally has been known to replicate via binary fission, a modified form of closed mitosis, there is some evidence that meiosis, or at least some form …
Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams
Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams
Senior Theses
Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such …
Dynamic Mechanisms Of Multidrug Resistance In Human Cancers And Gram Negative Pathogens, Lauren Ammerman
Dynamic Mechanisms Of Multidrug Resistance In Human Cancers And Gram Negative Pathogens, Lauren Ammerman
Biological Sciences Theses and Dissertations
This dissertation focuses upon dynamic agents of multidrug resistance (MDR). We used a combination of in silico and in vitro techniques to investigate two membrane transporters that confer MDR – P-glycoprotein, which confers MDR in human cancers, and MtrD, which confers MDR in Neisseria gonorrhoeae. Inhibitors targeting both proteins have tremendous potential for use as co-therapeutics in the treatment of multidrug resistant cancers, or of multidrug resistant infections. However, previously identified inhibitors of P-gp have failed clinical trials due to off-target effects and associated toxicities. Furthermore, the molecular mechanism of antibiotic transport by MtrD is poorly understood, and this dearth …
Pectin And Alginate Extraction To Treat Liquid Cafo Manure, Clare Sunderman
Pectin And Alginate Extraction To Treat Liquid Cafo Manure, Clare Sunderman
Honors Projects
For this project, various extraction methods were used to extract pectin from Pastinaca Sativa and alginate from Macrocystis. These extractions were then dried and used in treating 250mL of manure along with a CaCl2 or FeCl3 coagulant. It was found that CaCl2 was not as effective as FeCl3 in coagulating manure. But the results obtained suggest that pectin and alginate obtained with a simpler extraction method is just as effective as the highly purified and refined pectin and alginate produced for the food industry, in the treatment of CAFO manure. The liquid portion of the …
Toxicity Analysis Of 2’-Deoxyguanosine-N2-6-Aminopyrene And 2’-Deoxyguanosine-N2-8-Aminopyrene In Escherichia Coli, Emily Janeiro
Toxicity Analysis Of 2’-Deoxyguanosine-N2-6-Aminopyrene And 2’-Deoxyguanosine-N2-8-Aminopyrene In Escherichia Coli, Emily Janeiro
Honors Scholar Theses
Cancer is a disease that stems from genomic errors that are not corrected properly by cellular repair mechanisms. Errors are more likely to form when organisms are subjected to DNA damage by mutagenic compounds. 1-Nitropyrene, a nitrated polycyclic aromatic hydrocarbon (nitro-PAH), has been shown to be a potent mutagen that causes cancer. Nitro-PAHs can arise from diesel exhaust products in the environment. Out of all nitro-PAHs, 1-nitropyrene is found in largest quantities in the environment. This poses a great need to study its effects biochemically in order to address its toxicity in DNA. Other nitropyrene derivatives, including 1,6-dinitropyrene and 1,8-dinitropyrene, …
Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue
Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue
Student Scholar Symposium Abstracts and Posters
The World Health Organization found that 37.9 million people were living with HIV by the end of 2018. HIV is a virus that weakens the immune system through viral replication and the destruction of CD4+ T-cells, which are white blood cells that detect infection and make antibodies. A cure for HIV has not yet been discovered. HIV-1 contains a Gag polyprotein which regulates the stages of viral replication. Previous studies suggest that the myristoyl group of a matrix protein peptide found on the Gag polyprotein, MA, forms a complex with a calcium-binding, multifunctional regulatory protein called Calmodulin (CaM). CaM …
Proteomic Analysis Of Fetal Rat Neural Stem Cells After Treatment With Hericium Erinaceus, Bright Adam Test
Proteomic Analysis Of Fetal Rat Neural Stem Cells After Treatment With Hericium Erinaceus, Bright Adam Test
University of the Pacific Theses and Dissertations
The fungus, Hericium erinaceus, has outstanding chemical properties, displaying health benefits in digestive, hepatic, and nervous tissues. Its ease of accessibility and use makes it one of the most common substances used for treatment in Eastern medicine. More and more recent research is confirming the incredible health benefits of this fungus, especially the impact that is seen on nervous tissue growth and recovery post-treatment. Such neurite outgrowth and myelin sheath regeneration could illustrate the beginning of the cure to lifelong neurodegenerative diseases such as Multiple Sclerosis. In this first-of-its-kind study, we cultured and differentiated fetal rat neural stem cells while …
Structural Characterization Of Black Widow Spider Dragline Silk Proteins Crp1 And Crp4, Mikayla Shanafelt
Structural Characterization Of Black Widow Spider Dragline Silk Proteins Crp1 And Crp4, Mikayla Shanafelt
University of the Pacific Theses and Dissertations
Spider dragline silk is a biomaterial with outstanding material properties, possessing high-tensile strength and toughness. In nature, dragline silk serves a central role during spider locomotion and web construction. Today, scientists are racing to elucidate the molecular machinery governing silk extrusion, attempting to translate this knowledge into a mimicry process in the laboratory to create synthetic fibers for a wide range of different applications. During extrusion, it has been established that biochemical and mechanical forces govern spidroin folding, aggregation, and assembly. In black widow spiders, at least 7 different proteins have been identified as constituents of dragline silk fibers. These …
Proteasome Storage Granules Protect Proteasomes From Autophagic Degradation Upon Carbon Starvation, Richard S. Marshall, Richard D. Vierstra
Proteasome Storage Granules Protect Proteasomes From Autophagic Degradation Upon Carbon Starvation, Richard S. Marshall, Richard D. Vierstra
Biology Faculty Publications & Presentations
26S proteasome abundance is tightly regulated at multiple levels, including the elimination of excess or inactive particles by autophagy. In yeast, this proteaphagy occurs upon nitrogen starvation but not carbon starvation, which instead stimulates the rapid sequestration of proteasomes into cytoplasmic puncta termed proteasome storage granules (PSGs). Here, we show that PSGs help protect proteasomes from autophagic degradation. Both the core protease and regulatory particle sub-complexes are sequestered separately into PSGs via pathways dependent on the accessory proteins Blm10 and Spg5, respectively. Modulating PSG formation, either by perturbing cellular energy status or pH, or by genetically eliminating factors required for …
Approaching Undergraduate Research With Students Who Are Deaf And Hard-Of-Hearing, Austin U. Gehret, Jessica W. Trussell, Lea V. Michel
Approaching Undergraduate Research With Students Who Are Deaf And Hard-Of-Hearing, Austin U. Gehret, Jessica W. Trussell, Lea V. Michel
Journal of Science Education for Students with Disabilities
An undergraduate research experience can provide a unique opportunity for students to learn and grow as scientists; when positive, this experience is often transformative and motivates students to pursue science, technology, engineering and mathematics (STEM) graduate degrees or careers. Conversely, negative research experiences can sour a student’s opinion of research, propagate misconceptions of graduate school, and lead to attrition from STEM fields. Negative research experiences can be equally devastating for faculty mentors and may result in reluctance to mentor future research students. Using a mentoring approach that has traditionally translated to positive research experiences for hearing students may not be …
The Function Of Renalase, Brett Allen Beaupre
The Function Of Renalase, Brett Allen Beaupre
Theses and Dissertations
Renalase was originally reported to be an enzyme secreted into the blood by the kidney to lower blood pressure and slow heart rate. Despite multiple reports claiming to confirm this activity in vivo there has been considerable discord in regards to the reaction catalyzed by renalase. The structural topology of renalase resembles that of known flavoprotein oxidases, monooxygenases and demethylases, but the conserved active site residues are unique to renalase. It has been reported that the catalytic function of renalase is to oxidize circulating catecholamines, however in vitro studies have failed to demonstrate a catalytic activity in the presence of …
Dihydrosterculate In Tobacco Transformed With Bacterial Cyclopropane Fatty Acid Synthase, Katherine Schmid
Dihydrosterculate In Tobacco Transformed With Bacterial Cyclopropane Fatty Acid Synthase, Katherine Schmid
Katherine Schmid
Many gram negative bacteria accumulate cyclopropane fatty acids (CPFAs) in their membranes during stationary phase. In plants, on the other hand, CPFAs are best known as constituents of certain seed oils. CPFAs make up around 40% of Litchi chinensis seed oil [1] and a significant proportion of oils from other Sapindales. In order Malvales, small amounts of CPFA typically accompany cyclopropene fatty acids in seed oils, although up to 5% CPFA has been observed in the polar lipid fraction from Malvaceous roots [2]. Genetic engineering of oilseeds for unusual fatty acid production requires that the introduced fatty acids accumulate in …
Effects Of Cyclopropenoid Fatty Acids On Fungal Growth And Lipid Composition, Katherine Schmid, Glenn Patterson
Effects Of Cyclopropenoid Fatty Acids On Fungal Growth And Lipid Composition, Katherine Schmid, Glenn Patterson
Katherine Schmid
Cyclopropenoid fatty acids (CPE) isolated fromSterculia foetida oil by urea clathration and reverse phase high performance liquid chromatography (HPLC) were introduced into fungal cultures. Stearate levels in phospholipids and triacylglycerols fromUstilago maydis sporidia rose considerably in response to 30 μM CPE. In addition, CPE themselves were incorporated into glycerolipid fractions. Sterol composition was unaffected. Changes in lipid composition were accompanied by inhibition of dry weight accumulation and sporidial number. Treated sporidia showed irregular wall deposition and a branched morphology. Oleate alleviated CPE effects on growth and morphology. Hyphal extension byRhizoctonia solani was inhibited somewhat by 30 μM sterculate, whileFusarium oxysporum …
Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman
Gene Expression Studies For The Analysis Of Domoic Acid Production In The Marine Diatom Pseudo-Nitzschia Multiseries, Katie Boissonneault, Brooks M. Henningsen, Stephen S. Bates, Deborah L. Robertson, Sean Milton, Jerry Pelletier, Deborah A. Hogan, David E. Housman
Dartmouth Scholarship
Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.
An Ethnobotanical Approach To Finding Antimicrobial Compounds In Wooly Blue Curls (Trichostema Lanatum) Using A Kirby-Bauer Disc Diffusion Assay, Matthew C. Fleming, P. Matthew Joyner
An Ethnobotanical Approach To Finding Antimicrobial Compounds In Wooly Blue Curls (Trichostema Lanatum) Using A Kirby-Bauer Disc Diffusion Assay, Matthew C. Fleming, P. Matthew Joyner
Featured Research
Plants can be an important source of creativity and production of new drugs. In this study, extracts of wooly blue curls (Trichostema lanatum) were made using DMSO and tested for antimicrobial activity on a panel of bacteria commonly found in separate ecological niches. Wooly blue curls (WBC) was chosen due to its being recorded as a strong disinfectant by the Chumash people. It was found that WBC does exhibit antimicrobial activity against gram positive bacteria and not against gram negative bacteria. However, gram negative bacteria with reduced drug efflux function became susceptible to the WBC extract.
Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham
Development And Application Of Mass Spectrometry-Based Proteomics To Generate And Navigate The Proteomes Of The Genus Populus, Paul Edward Abraham
Doctoral Dissertations
Historically, there has been tremendous synergy between biology and analytical technology, such that one drives the development of the other. Over the past two decades, their interrelatedness has catalyzed entirely new experimental approaches and unlocked new types of biological questions, as exemplified by the advancements of the field of mass spectrometry (MS)-based proteomics. MS-based proteomics, which provides a more complete measurement of all the proteins in a cell, has revolutionized a variety of scientific fields, ranging from characterizing proteins expressed by a microorganism to tracking cancer-related biomarkers. Though MS technology has advanced significantly, the analysis of complicated proteomes, such as …
Organization And Characterization Of Nuclear Receptor Af1 Domain, Angela Frantz
Organization And Characterization Of Nuclear Receptor Af1 Domain, Angela Frantz
Chancellor’s Honors Program Projects
No abstract provided.
Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang
Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang
Chemistry Faculty Publications
The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by the lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We have developed a novel MR imaging probe targeting to HER2, a biomarker for various cancer types and a drug target for anti-cancer therapies. This multimodal HER20targeted MR imaging probe integrates a de novo designed protein contrast agent with a high affinity HER2 affibody and a near IR fluorescent dye. Our probe can differentially monitor tumors with different expression levels of HER2 in both human cell lines and xenograft mice …
10th Annual Senior Research Symposium Of The Department Of Biological Sciences, Chemistry And Biochemistry, Messiah College
10th Annual Senior Research Symposium Of The Department Of Biological Sciences, Chemistry And Biochemistry, Messiah College
School of Science, Engineering & Health (SEH) Symposium
No abstract provided.
Species Boundaries And Evolutionary Lineages In The Blue Green Damselfishes Chromis Viridis And Chromis Atripectoralis (Pomacentridae), Philadelphia University
Species Boundaries And Evolutionary Lineages In The Blue Green Damselfishes Chromis Viridis And Chromis Atripectoralis (Pomacentridae), Philadelphia University
Philadelphia University, Jordan
No abstract provided.
In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng
In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng
Honors Scholar Theses
The major histocompatibility complex (MHC) is a gene family responsible for many critical functions of the immune system in most vertebrates. The MHC consists of three classes differentiated by their structure and function, and MHC class I encodes antigen binding proteins as well as chaperone and accessory proteins such as tapasin. The purpose of this project is to reconstitute several human MHC class I molecules in their peptide-filled and peptide-deficient forms, and to purify these proteins for biochemical study. The expressed proteins include wild type and mutant variants of the fusion protein human leukocyte antigen HLA-B*0801-fos, and human beta-2-microglobulin (β2m). …
Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal
Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal
Department of Biological & Biomedical Sciences
No abstract provided.