Biochemistry Commons^™

Mechanisms Of Age-Related Inflammation And Cancer : The Synergistic Effect Of Oxidants And Calcium, Donald A. Mccarthy

Legacy Theses & Dissertations (2009 - 2024)

The accumulation of senescent cells during the process of aging has been implicated as causal in numerous age-related pathologies. Senescent cells adopt a secretory phenotype consisting of many factors including matrix remodeling enzymes, growth factors, cytokines, and chemokines. Their secretory nature is the primary reason that they are associated with disease, but it remains unclear why they become so inflammatory. Using primary human fibroblasts cultured to senescence, we mechanistically determined why senescent cells are such potent inducers of inflammation. Our findings indicate that the early production of the cytokine Interleukin 1-α (IL-1α) is central to this transition. We found that …

Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson

Legacy Theses & Dissertations (2009 - 2024)

RNA folding is the process whereby a single stranded RNA molecule assumes its three-dimensional functional conformation. Along with the protein folding problem, the RNA folding problem remains as one of the great unsolved problems in biophysics. Generally RNA folding occurs in a hierarchical manner whereby the sequence of an RNA (primary structure) determines which regions will form helical segments (secondary structure) before further rearrangement and base pairing of secondary structure motifs (tertiary structure). Due to the intimate connection between structure and function within molecular biology, increased familiarity with the thermodynamic and kinetic factors that govern RNA folding will permit the …

Mechanistic Studies Of C- And Y-Family Dna Polymerases, Indrajit Lahiri

Legacy Theses & Dissertations (2009 - 2024)

DISSERTATION ABSTRACT

Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova

Legacy Theses & Dissertations (2009 - 2024)

The efficient and accurate diagnosis at the early stages of dementia is a key moment for effective treatment and productive research to find a new ways to combat the disease. It is especially true for Alzheimer's disease (AD) for which there is no effective cure, but several treatments are known to allow slowing down the degenerative processes. Alzheimer's disease (AD) displays only non-specific clinical symptoms of mental decline for decades after the initiation and is very challenging to differentiate even at the later stages when it becomes very aggressive. Despite the great need, current diagnostic tests are unable to diagnose …

A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender

Legacy Theses & Dissertations (2009 - 2024)

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus belonging to the lentivirus genus of the orthoretrovirinae family. HIV-1 is widely known for causing acquired immunodeficiency syndrome (AIDS) in humans and being responsible for 1.8 million deaths due to AIDS associated illnesses in 201016.

Quantification Of Free Sialic Acid In Human Plasma Through A Robust Quinoxalinone Derivatization And Lc–Ms/Ms Using Isotope-Labeled Standard Calibration, Dan Wang, Xiang Zhou, Lin Wang, Sihe Wang, Xue-Long Sun

Chemistry Faculty Publications

We report an accurate quantification of free sialic acid (SA) in human plasma using LC–MS/MS method with isotope-labeled standard calibration (ILSC) and robust derivatization. Specifically, derivatization of SA with a stable and inexpensive 3,4-diaminotoluene (DAT) provides a stable product of SA with high MS response, proving a convenient and cost-effective LC–MS/MS analysis of free SA. In addition, the use of ¹³C₃-SA as calibration standard ensured the accuracy for the measurement. This assay used ultra high performance liquid chromatography (UHPLC) for separation of native/labeled SA and IS from matrix interference, and employed mass spectrometry in multiple reaction monitoring …

Identification And Characterization Of Human Plasma Prekallikrein-Prolylcarboxypeptidase Interaction Sites, Jingjing Wang

Electronic Theses and Dissertations

Prolylcarboxypeptidase isoform1 (PRCP1, also known as angiotensinase C, PCP, PRCP, PrCP) is a widely distributed serine protease found throughout the human body. PRCP1 removes the C-terminal amino acid which is next to a proline residue of a peptide. Through this activity, PRCP1 is postulated to play distinct biological roles including the regulation of vascular homeostasis, the induction of inflammation and the adjustment of metabolism. Compelling evidence indicates that human PRCP1 activates plasma prekallikrein (PK) to kallikrein on endothelial cells. However, the mechanism of this activation is yet unknown. The formation of kallikrein leads to the generation of proinflammatory factors and …

Comparative Phenolic Content And Antioxidant Activities Of Blueberry (Vaccinium Corymbosum) Afected By In Vitro Digestion, Sonia Gharbi

Wayne State University Theses

Abstract

COMPARATIVE PHENOLIC CONTENT AND ANTIOXIDANT ACTIVITIES OF BLUEBERRY (VACCINIUM CORYMBOSUM) AFECTED BY IN VITRO DIGESTION

By

SONIA GHARBI

May 2014

Adviser: Dr. Kevin Zhou

Major: Nutrition and Food Science

Degree: Master of Science

The biological properties of antioxidants depend on their release from the food matrix during the digestion process. Blueberry contains a wide range of phenolic compounds which are of great significance due to their antioxidant activity. In vitro digestion is a rapid and inexpensive method used to determine the availability of nutrients involved in the absorption studies with humans. Total phenolic content and antioxidant activity of Vaccinium …

In Vitro Characterization Of Serine 47 Phosphorylated Cytochrome C, Ashwathy Mary Varughese

Wayne State University Theses

Cytochrome c is a 12.4kDa ubiquitously expressed protein known to be involved in many physiological processes of the cell such as respiration and apoptosis. The goal of our lab is to increase our knowledge of the regulation of cytochrome c in these opposite activities, and our working model posits that cytochrome c is decisively regulated by phosphorylation. When phosphorylated, cytochrome c leads to an "optimal" functioning in the electron transport chain by lowering electron flux, preventing harmful high mitochondrial membrane potentials and thus ROS production under healthy conditions. However, under cellular stress cytochrome c might be dephosphorylated favoring high mitochondrial …

Biophysical Studies Of Mutant H69 Rna Constructs, Daya Nidhi Kharel

Wayne State University Theses

The importance of helix 69 (H69) of the large ribosomal subunit is emphasized by its location in the ribosome and key contacts with protein factors and tRNAs during different steps of protein synthesis. The presence of three highly conserved pseudouridine modifications in H69 has a significant impact on modulation of the ribosome conformations. Specific nucleotides of H69 may be necessary for the function of this helix-loop RNA, as some mutations are deleterious to bacterial growth. In this study, we investigated the effects of single nucleotide mutations in a 19-nucleotide H69 construct with and without pseudouridines on the RNA stability and …

Effect Of Long Term Rapamycin Treatment On Mtor Signalling Network In Colon And Liver Of C57bl/6 Mice, John Sorge

Wayne State University Theses

Many studies have investigated the effects of rapamycin on aging and cancer. However, the effects of long-term rapamycin supplementation on a cancer model have not been performed. This is the first study that investigates the effects of long-term supplementation of rapamycin in a cancer model. ACF analysis of colon tissues in mice showed no significant difference between controls and those supplemented with rapamycin. Factors such as energy balance, cellular environment, PI3K/Akt/mTOR pathway, and more have been assessed in this study. The duration of rapamycin supplementation seems to play an important role in the protection against cancer. Ultimately, this study suggests …

Genetic And Biochemical Studies Of Human Apobec3h Enzyme, Thisari Sachithra Aluthgama Guruge

Wayne State University Theses

The AID/APOBEC enzymes are DNA/RNA cytosine deaminases with important functions in innate and adaptive immunity. APOBEC3 enzymes play a crucial role in restricting the replication of exogenous retroviruses such HIV-1 and endogenous retrotransposition events. In particular, APOBEC3 enzymes have evolved in humans by gene duplication to compose seven members. APOBEC3H is highly diverse in its allelic sequence and the distribution is population-specific. It has evolved under strong positive selection over millions of years. To study the catalytic mechanism, structure, function and the underlying cause of its high diversity, a high resolution crystal or NMR structure is required are not yet …

Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo

Mechanical & Aerospace Engineering Faculty Publications

Shape is an intrinsic marker of cell cycle, an important factor for identifying a bioparticle, and also a useful indicator of cell state for disease diagnostics. Therefore, shape can be a specific marker in label-free particle and cell separation for various chemical and biological applications. We demonstrate in this work a continuous-flow electrical sorting of spherical and peanut-shaped particles of similar volumes in an asymmetric double-spiral microchannel. It exploits curvature-induced dielectrophoresis to focus particles to a tight stream in the first spiral without any sheath flow and subsequently displace them to shape-dependent flow paths in the second spiral without any …

Biochemical Characterization Of Four Distinct Proteins, Gustavo A. Avila

Open Access Theses & Dissertations

Proteins are ubiquitous in all living organisms, executing the majority of cellular functions in distinct ways. Understanding a protein's role necessitates investigating its structure and function, which are closely related. My research couples these two aspects by delving into the biochemical and structural characterization of proteins in four distinct systems, all playing central roles in numerous significant disease progressions. These four original research endeavors were all targeted for structural studies with a unifying relationship to establish our new structural biochemistry lab. These four systems are: (1) Gam1, an early adenovirus protein globally inhibiting host SUMOylation; (2) Anthrax toxin complexed with …

Investigating Structure And Protein-Protein Interactions Of Key Post-Type Ii Pks Tailoring Enzymes, Theresa E. Downey

Theses and Dissertations--Pharmacy

Type II polyketide synthase (PKS) produced natural products have proven to be an excellent source of pharmacologically relevant molecules due to their rich biological activities and chemical scaffolds. Type II-PKS manufactured polyketides share similar polycyclic aromatic backbones leaving their diversity to stem from various chemical additions and alterations facilitated by post-PKS tailoring enzymes. Evidence suggests that post-PKS tailoring enzymes form complexes in order to facilitate the highly orchestrated process of biosynthesis. Thus, protein-protein interactions between these enzymes must play crucial roles in their structures and functions. Despite the importance of these interactions little has been done to study them. In …

Simultaneous Bactericidal And Osteogenic Effect Of Nanoparticulate Calcium Phosphate Powders Loaded With Clindamycin On Osteoblasts Infected With Staphylococcus Aureus, Vuk Uskoković, Tejal A. Dasai

Pharmacy Faculty Articles and Research

S aureus internalized by bone cells and shielded from the immune system provides a reservoir of bacteria in recurring osteomyelitis. Its targeting by the antibiotic therapy may thus be more relevant for treating chronic bone infection than eliminating only the pathogens colonizing the bone matrix. Assessed was the combined osteogenic and antibacterial effect of clindamycinloaded calcium phosphate nanoparticles of different monophasic compositions on co-cultures comprising osteoblasts infected with S aureus. Antibiotic-carrying particles were internalized by osteoblasts and minimized the concentration of intracellular bacteria. In vitro treatments of the infected cells, however, could not prevent cell necrosis due to the …

Β-Lactam Estrogen Receptor Antagonists And A Dual-Targeting Estrogen Receptor/Tubulin Ligand, Niamh O'Boyle, Jade K. Pollock, Miriam Carr, Andrew Js Knox, Seema M. Nathwani, Shu Wang, Laura Caboni, Daniela M. Zisterer, Mary Meegan

Articles

Twelve novel β-lactams were synthesised and their antiproliferative effects and binding affinity for the predominant isoforms of the estrogen receptor (ER), ERα and ERβ, were determined. β-Lactams 23 and 26 had the strongest binding affinities for ERα (IC₅₀ values: 40 and 8 nM respectively) and ERβ (IC₅₀ values: 19 and 15 nM). β-Lactam 26 was the most potent in antiproliferative assays using MCF-7 breast cancer cells, and further biochemical analysis showed that it caused accumulation of cells in G₂/M phase (mitotic blockade) and depolymerisation of tubulin in MCF-7 cells. Compound 26 also induced apoptosis and downregulation …

A Conservative Isoleucine To Leucine Mutation Of Klentaq1 Dna Polymerase 1 Induces Conformational Change For Cold-Sensitive Phenotype, Emma Caroline Materne

Honors Theses

Polymerase Chain Reaction (PCR) typically employs the Taq or Klentaq1 DNA polymerase from Thermus aquaticus to elongate short sequences of DNA during DNA amplification. Both Taq and Klentaq1 retain activity at room temperature. During assembly of PCR at room temperature, the activity of Taq and Klentaq1 can result in spurious products due to elongation of primers bound to non-target sequences. A mutation of isoleucine to leucine at position 707 of Klentaq1 results in slowing of the enzyme at room temperature without compromising the fidelity of the enzyme. To understand how a mutation over 20Å from the active site can affect …

The Benefits Of Breastfeeding, Avery Kordus

Senior Honors Theses

Breastfeeding research is plentiful, and the majority of the literature shows that breast milk is the superior form of infant nutrition except in the rare circumstances of infant metabolic disorders, maternal drug use, or positive HIV status. In comparison to formula, breast milk provides improved cognition, development, behavior, bonding, nutrition, digestion, immunity, and long-term health with fewer diseases and conditions in infants. Mothers are benefited by breastfeeding through bonding, faster weight loss, and reduction in certain cancers and conditions. Breast milk contains the proper amount of carbohydrates, fats, proteins, vitamins, and minerals, and is also specialized for each infant and …

One-Pot Heteroconjugate Addition-Diels-Alder Reactions And Acetate-Catalyzed Aldol Reactions Of Α-Silyl Nitriles, Carly Mueller

Honors Theses

1. A one-pot three-step Diels–Alder reaction sequence of ethyl propiolate and thiols can be performed to produce high yields of complex bicyclic products. A KOt-Bu-catalyzed thioconjugate addition of thiols to enoates, oxidation of the generated thioenoate by mCPBA, and Li-catalyzed Diels–Alder addition of cyclopentadiene occur in situ, without any purification of intermediates.
2. Stereoselectivity of the Diels–Alder product was examined by utilizing a chiral sulfone substrate. It was determined that these substrates were unable to provide significant stereochemical control.
3. Silylation of 3-phenylpropionitrile is achieved at the α-position with trimethylsilyl trifluoromethanesulfonate and trialkylamine base. Catalyzed by tetrabutylammonium acetate (2.5 mol%), …