Biochemistry Commons^™

Genomic Signatures For Paclitaxel And Gemcitabine Resistance In Breast Cancer Derived By Machine Learning., Stephanie N Dorman, Katherina Baranova, Joan H M Knoll, Brad L Urquhart, Gabriella Mariani, Maria Luisa Carcangiu, Peter K Rogan

Biochemistry Publications

Increasingly, the effectiveness of adjuvant chemotherapy agents for breast cancer has been related to changes in the genomic profile of tumors. We investigated correspondence between growth inhibitory concentrations of paclitaxel and gemcitabine (GI50) and gene copy number, mutation, and expression first in breast cancer cell lines and then in patients. Genes encoding direct targets of these drugs, metabolizing enzymes, transporters, and those previously associated with chemoresistance to paclitaxel (n = 31 genes) or gemcitabine (n = 18) were analyzed. A multi-factorial, principal component analysis (MFA) indicated expression was the strongest indicator of sensitivity for paclitaxel, and copy number and expression …

Development Of Gamma-Modified Atp Analogs To Study Kinase-Catalyzed Phosphorylations, Ahmed Eid Fouda

Wayne State University Dissertations

Kinase-catalyzed protein phosphorylation is one of the most important post-translational modifications that controls cascades of biochemical reactions. Irregularities in phosphorylation result in many diseases, such as diabetes mellitus, Parkinsons, and cancer. The development of new methods to monitor kinase-catalyzed phosphorylation is needed to decipher details of normal and diseased cell signaling. The Pflum lab recently developed several -modified ATP analogs to study kinase catalyzed phosphorylation reactions. The -modified ATP analogs have different tags, such as biotin for substrate labeling or aryl-azide for kinase substrates identification. Unfortunately, use of -modified ATP analogs was limited to in vitro studies due to the …

Nitrogenase Femoco Investigated By Spatially Resolved Anomalous Dispersion Refinement, Thomas Spatzal, Julia Schlesier, Eva-Maria Burger, Daniel Sippel, Limei Zhang, Susana L.A. Andrade, Douglas C. Rees, Oliver Einsle

Department of Biochemistry: Faculty Publications

The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S 1⁄4 3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the …

A Critical Role Of Cxcr2 Pdz Motif-Mediated Interactions In Endothelial Progenitor Cell Homing And Angiogenesis, Yuning Hou

Wayne State University Dissertations

Bone marrow-derived endothelial progenitor cells (EPCs) participate in postnatal vascularization in response to growth factors, cytokines, and chemokines. Chemokine receptor CXCR2 and its cognate ligands are reported to mediate EPC recruitment and angiogenesis. CXCR2 possesses a consensus PSD-95/DlgA/ZO-1 (PDZ) motif at its carboxyl terminus. The PDZ motif has been reported to regulate cellular signaling and functions. Here we investigated the potential role of the PDZ motif in CXCR2-mediated EPC motility and angiogenesis. We have found that introducing exogenous CXCR2 C-terminus significantly attenuated in vitro EPC migration and angiogenic activities in response to CXCR2 ligands, as well as in vivo EPC …

The Development Of Peptide Ligands To Target H69 Rrna, Danielle Nicole Dremann

Wayne State University Dissertations

ABSTRACT

THE DEVELOPMENT OF PEPTIDE LIGANDS TO TARGET H69

by

DANIELLE NICOLE DREMANN

December 2015

Advisor: Prof. Christine S. Chow

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

In the development of peptide ligands to target H69, SPPS and ESI MS was used to determine if 1) peptides could bind to modified H69 and 2) if increased affinity for the target RNA could be enhanced with modification. An alanine and arginine scan was synthesized and tested for this determination. Selected peptides were then tested using biophysical techniques such as circular dichroism and isothermal titration calorimetry. An assay was also designed to …

Bacterial Forensics: Revolutionizing Biochemical Analysis, Caitlin Cain

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Eva Childrey is a junior forensic science and chemistry double major working in Dr. Eh- rhardt’s research laboratory at VCU. The main goal of the research conducted in this laboratory is to explore the lipid profiles of different bacterial species.

Students' Perception Of Educational Environment At Aga Khan University Medical College, Karachi, Pakistan, Rehana Rehman, Kulsoom Ghias, Syeda Sadia Fatima, Mehwish Hussain, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To assess educational environment in Aga Khan University Medical College (AKUMC) by Dundee Ready Educational Environmental Measure (DREEM) scale.
Methods: A cross-sectional survey of students at the AKUMC with simple random sampling was carried out from June 2014 till March 2015. Responses in five subscales were used to calculate DREEM scores.
Results: The average DREEM score was 125.77±16.8 with a reliability of 91.3%. With regards to subscales, on the 12-item students' perceptions of learning (PoL) subscale, the maximum score was 48; 11 items of students' perceptions of teachers (PoT) had a maximum score of 44; students' academic self-perceptions (ASP) …

Regulation Of Cytochrome C Functions By Phosphorylation, Gargi Mahapatra

Wayne State University Dissertations

The long term goal of my thesis research is to understand how tissue-specific

phosphorylations on the small mitochondrial protein, cytochrome c (Cytc), regulate its

functions, under both physiologically healthy and stressed conditions, and to identify the

cell signaling pathways targeting Cytc. Cytc is a functionally diverse protein that carries

electrons in the electron transport chain and plays a critical role in cellular apoptosis, two

diverse pathways that maintain cellular health that are active under diverse conditions.

Since Cytc plays a pivotal role in both these highly divergent pathways, regulation of the

protein is very important—phosphorylation of the protein under physiological …

Studies Towards Broadening The Substrate Profile And Regulation Of Histone Deacetylase 1, Dhanusha Ashanthi Nalawansha

Wayne State University Dissertations

Aberrant expression of histone deacetylase 1 (HDAC1) is implicated in multiple diseases, including cancer. As a consequence, HDAC1 has emerged as an important therapeutic target for drug development. HDAC1 regulates key cellular processes, such as cell proliferation, apoptosis, and cell survival, by deacetylating both histone and non-histone substrates. Due to the lack of simple tools to identify physiological substrates of HDAC1, the full spectrum of HDAC1 activities in the cell remains unclear. Here, we employed a substrate trapping strategy to identify cellular substrates of HDAC1. Using this approach, we identified mitosis-related protein Eg5 as a substrate. HDAC1 colocalizes with Eg5 …

The Unusual Substrate Specificity Of A Virulence Associated Serine Hydrolase From The Highly Toxic Bacterium, Francisella Tularensis, Alexander M. Farberg, Whitney K. Hart, R. Jeremy Johnson

Scholarship and Professional Work - LAS

Francisella tularensis is the causative agent of the highly, infectious disease, tularemia. Amongst the genes identified as essential to the virulence of F. tularensis was the proposed serine hydrolase FTT0941c. Herein, we purified FTT0941c to homogeneity and then characterized the folded stability, enzymatic activity, and substrate specificity of FTT0941c. Based on phylogenetic analysis, FTT0941c was classified within a divergent Francisella subbranch of the bacterial hormone sensitive lipase (HSL) superfamily, but with the conserved sequence motifs of a bacterial serine hydrolase. FTT0941c showed broad hydrolase activity against diverse libraries of ester substrates, including significant hydrolytic activity across alkyl ester substrates from …

Thermodynamics And Kinetics Of The Three-Way Junction Of Phi29 Motor Prna And Its Assembly Into Nanoparticles For Therapeutic Delivery To Prostate Cancer, Daniel W. Binzel

Theses and Dissertations--Pharmacy

The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles, but has been limited by particle instability. Previously, it was found the three-way junction (3WJ) of the Phi29 DNA packaging motor pRNA was found to be ultra-stable and assemble in solution without the presence of metal ions. The three-way junction is composed of three short oligo RNA strands and proven to be thermodynamically stable. Here the assembly mechanism, thermodynamic and enzymatic stabilities, and kinetics are examined in order to understand the stability behind this unique motif. Thermodynamic and kinetics studies found that the pRNA 3WJ formed out of …

Investigating And Expanding The Functionality Of Rna Catalysts: Studies Of The Hepatitis Delta Virus, The Hammerhead, And The Aminoacyl-Trna Synthetase-Like Ribozymes, Ji Chen

Open Access Dissertations

Ribozymes, just like protein enzymes, catalyze diverse chemical reactions. The first goal of this dissertation is to understand the mechanism of ribozyme-mediated phosphodiester cleavage reaction. Biochemical assays and X-ray crystallography were used for probing the active site of two small self-cleaving ribozymes, the hepatitis delta virus (HDV) ribozyme and the hammerhead ribozyme. Results presented here suggest that divalent metal ions play critical roles in the catalytic mechanisms of both the HDV and the hammerhead ribozymes. In the HDV ribozyme, the result is consistent with an active site Mg2+ being directly involved in catalysis. In the hammerhead ribozyme, however, Mg2+ ions …

Assessment Of Ovarian Reserve: Anti-Mullerian Hormone Versus Follicle Stimulating Hormone, Zehra Jamil, Syeda Sadia Fatima, Zahra Cheema, Safia Baig, Roha Ahmed Choudhary

Department of Biological & Biomedical Sciences

Background: This study aimed to evaluate the strength of anti-Mullerian hormone (AMH) and follicle stimulating hormone (FSH) in reflecting the antral follicle count (AFC) in infertile females.
Materials and methods: This cross-sectional study was conducted on 160 females, visiting infertility clinic for assisted reproduction. Serum samples collected on the 3rd day of the cycle were assayed for FSH, luteinizing hormone, and AMH while AFC was assessed via transvaginal ultrasound. The study cohort was segregated into three groups based on AFC.
Results: Chronological age and FSH was significantly high in females with very low AFC (P < 0.01 and 0.009, respectively), yet they failed to discriminate patients with normal and higher follicle count (P = 0.65 and 0.84). Conversely, AMH reported highly significant difference between very low AFC and with those having either normal AFC (P = 0.002) or higher AFC (P = 0.001). Moreover, a significant difference in AMH was observed between normal and higher AFC group (P = 0.04).
Conclusion: Compared to female's age …

Kcnq1 Rs2237895 Polymorphism Is Associated With Gestational Diabetes In Pakistani Women, Syeda Sadia Fatima, Bushra Chaudhry, Taseer Ahmed Khan, Saad Farooq

Department of Biological & Biomedical Sciences

Background and Objective: Genetic studies on gestational diabetes (GDM) are relatively scarce; moreover, limited data is available for KCNQ1 polymorphism in Pakistani pregnant women. We aimed to determine the frequency of KCNQ1 rs2237895 in GDM and normal pregnant controls and its association with GDM-related phenotypes.
Methods: A total of 637 pregnant females (429 controls and 208 cases) in their second trimester were classified according to the International Association of the Diabetes and Pregnancy Study criteria in this study. Their blood samples were genotyped for KCNQ1 SNP rs2237895 using PCR-RFLP method and sequencing. Fasting and two hour-post glucose load blood levels, …

Anti Mullerian Hormone: Ovarian Response Indicator In Young Patients Receiving Long Gnrh Agonist Protocol For Ovarian Stimulation, Zehra Jamil, Syeda Sadia Fatima, Rehana Rehman, Faiza Alam, Sara Arif

Department of Biological & Biomedical Sciences

Objective: Anti Mullerian hormone (AMH) is gaining place as ovarian marker, chiefly in infertility assistance. We explored its correlation with oocytes retrieval after long GnRH agonist protocol for stimulation, in younger and older infertile population.
Methods: This retrospective analysis compiled data of 166 females, receiving ICSI treatment from June 2014 to March 2015. Serum FSH, LH, Estadiol, AMH and antral follicle count were assessed. Outcomes were measured as good (5 to 19 oocytes) and bad responders.
Results: Higher discriminatory power of AMH (AUROC; 0.771; p < 0.05) was seen in comparison to FSH (0.692; p < 0.05) and AFC (0.690; p < 0.01). AMH reported strongest association with oocyte retrieved (odds ratio of 15.06). Subgroup analysis reported 68.6 % risk of bad response with AMH levels of less than 1.37ng/ml. This association was observed more significant in young infertile patients <35 year of age (r=0.245; p=0.012) versus older population >35 year (r=0.169; p>0.05).
Conclusion: Our study reaffirms that serum AMH correlates well with …

Use Of Follicular Output Rate To Predict Intracytoplasmic Sperm Injection Outcome, Rehana Rehman, Rozina Mustafa, Mukhtiar Baig, Sara Arif, Muhammad Faisal Hashmi

Department of Biological & Biomedical Sciences

Background: The measurement of follicular output rate (FORT) has been proposed as a good indicator for evaluating follicular response to the exogenous recombinant folliclestimulating hormone (rFSH). This places FORT as a promising qualitative marker for ovarian function. The objective of the study was to determine FORT as a predictor of oocyte competence, embryo quality and clinical pregnancy after intracytoplasmic sperm injection (ICSI).
Materials and Methods: This prospective study was carried out on a group of infer- tile females (n=282) at Islamabad Clinic Serving Infertile Couples, Islamabad, Pakistan, from June 2010 till August 2013. Downregulated females were stimulated in injection gonadotropins …

Anti-Mullerian Hormone: Above And Beyond Conventional Ovarian Reserve Markers, Zehra Jamil, Syeda Sadia Fatima, Khalid Ahmed, Rabia Malik

Department of Biological & Biomedical Sciences

Management of ovarian dysfunctions requires accurate estimation of ovarian reserve (OR). Therefore, reproductive hormones and antral follicle count (AFC) are assessed to indicate OR. Serum anti-Mullerian hormone (AMH) is a unique biomarker that has a critical role in folliculogenesis as well as steroidogenesis within ovaries. Secretion from preantral and early antral follicles renders AMH as the earliest marker to show OR decline. In this review we discuss the dynamics of circulating AMH that remarkably vary with sex and age. As it emerges as a marker of gonadal development and reproductive disorders, here we summarize the role of AMH in female …

A New Model Of Master Of Philosophy In Physiological Sciences, H R. Ahmad, F M. Arain, N A. Khan

Department of Biological & Biomedical Sciences

The objectives of Master of Philosophy (MPhil) in Physiological Sciences are: 1) to describe the new ways in which anatomy, biochemistry and physiology on one hand, and microbiology, pathology and pharmacology on other hand meet their functional requirements through multidisciplinary integrated concepts; 2) to elucidate relationships between cell biology, molecular biology and molecular genetics by connecting dots of how cell functions are driven by molecules and being controlled by genes. This forms the basis of cell, molecular and genetics [CMG] module upon which 7 multidisciplinary modules of Physiological Sciences follow; 3) these 24 credit hours provide the physiological basis for …

How To Write A Doctoral Thesis, H R. Ahmad

Department of Biological & Biomedical Sciences

No abstract provided.

Studies Into The Allosteric Regulation Of Adp-Glucose Pyrophosphorylases, Benjamin Luke Hill

Dissertations

The synthesis of glycogen in bacteria and starch in plants is allosterically controlled by the production of ADP-glucose by ADP-glucose pyrophosphorylase. Using computational studies, site directed mutagenesis, and kinetic characterization, and protein crystallography we found a critical region for transmitting the allosteric signal in the Escherichia coli and A. tumefaciens ADP-glucose pyrophosphorylase. Molecular dynamics simulations and structural comparisons with other ADP-glucose pyrophosphorylases provided information to hypothesize communication pathways that link allosteric and active sites, and this was tested by site-directed mutagenesis and kinetic characterization of the mutant enzymes. In addition, the application of x-ray crystallography enabled the pinpointing of the …