Biochemistry Commons^™

Mutual Information Upper Bound Of Molecular Communication Based On Cell Metabolism, Massimiliano Pierobon, Zahmeeth Sakkaff, Jennie L. Catlett, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in synthetic biology stands in the development of reliable techniques to control the engineered cells from the external environment. In this …

Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant Ovarian Cancer, Canan Schumann, Stephanie Chan, Oleh Khalimonchuk, Shannon Khal, Vitaliya Moskal, Vidhi Shah, Adam W. G. Alani, Olena Taratula, Oleh Taratula

Department of Biochemistry: Faculty Publications

We report an efficient therapeutic modality for platinum resistant ovarian cancer based on siRNAmediated suppression of a multifunctional DJ-1 protein that is responsible for the proliferation, growth, invasion, oxidative stress and overall survival of various cancers. The developed therapeutic strategy can work alone or in concert with a low dose of the first line chemotherapeutic agent cisplatin, to elicit a maximal therapeutic response. To achieve an efficient DJ-1 knockdown, we constructed the polypropylenimine dendrimer-based nanoplatform targeted to LHRH receptors overexpressed on ovarian cancer cells. The quantitative PCR and western immunoblotting analysis, revealed that the delivered DJ-1 siRNA downregulated the expression …

Engineering A Trifunctional Proline Utilization A Chimaera By Fusing A Dna-Binding Domain To A Bifunctional Puta, Benjamin W. Arentson, Erin L. Hayes, Weidong Zhu, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ¹-pyrroline-5- carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the …

Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Ed Harris

Department of Biochemistry: Faculty Publications

The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific …

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.

Selection Of A Novel Aptamer Against Vitronectin Using Capillary Electrophoresis And Next Generation Sequencing, C. H. Stuart, Kathryn R. Riley, O. Boyacioglu, D. M. Herpai, W. Debinski, S. Qasem, F. C. Marini, C. L. Colyer, W. H. Gmeiner

Chemistry & Biochemistry Faculty Works

Breast cancer (BC) results in ≃40,000 deaths each year in the United States and even among survivors treatment of the disease may have devastating consequences, including increased risk for heart disease and cognitive impairment resulting from the toxic effects of chemotherapy. Aptamer-mediated drug delivery can contribute to improved treatment outcomes through the selective delivery of chemotherapy to BC cells, provided suitable cancer-specific antigens can be identified. We report here the use of capillary electrophoresis in conjunction with next generation sequencing to develop the first vitronectin (VN) binding aptamer (VBA-01; Kd 405 nmol/l, the first aptamer to vitronectin (VN; Kd = …

Functional Roles For Post-Translational Modifications Of T-Snares In Platelets, Jinchao Zhang

Theses and Dissertations--Molecular and Cellular Biochemistry

Platelets affect vascular integrity by secreting a host of molecules that promote hemostasis and its sequela. Given its importance, it is critical to understand how platelet exocytosis is controlled. Post-translational modifications, such as phosphorylation and acylation, have been shown to affect signaling pathways and platelet function. In this dissertation, I focus on how these modifications affect the t-SNARE proteins, SNAP-23 and syntaxin-11, which are both required for platelet secretion. SNAP-23 is regulated by phosphorylation. Using a proteoliposome fusion assay, I demonstrate that purified IκB Kinase (IKK) phosphorylated SNAP-23, which increased the initial rates of SNARE-mediated liposome fusion. SNAP-23 mutants …

Substrate Specificity Of The Lipn Hydrolase From Mycobacterium Ulcerans, Stephanie Raynor

Undergraduate Honors Thesis Collection

Mycobacterium ulcerans is the causative agent of Buruli ulcer, a tropical skin disease that affects thousands of individuals annually. Recent studies have revealed that lipolytic enzymes are involved in the pathogenicity processes of mycobacterium and could be potential targets for novel antibiotics. LipN is one proposed serine hydrolase in Mycobacterium ulcerans that contains the conserved α/β hydrolase protein fold and utilizes the conserved catalytic traid of serine, histidine, and aspartate/glutamate. The physiological substrate and biological role of LipN from M. ulcerans have not yet been determined. In this study, LipN was cloned into a pET28a plasmid and overexpressed in an …

Structure And Biological Activity Of A D3g Mutation In The Human Mitochondrial Chaperonin Hsp60, Jihui Li

Open Access Theses & Dissertations

Proteins are essential components in all cellular activities, including signal transduction, gene expression regulation, immune response, structural support and many others. Following their synThesis on the ribosome, proteins need to fold into their precise three-dimensional structure to obtain functionality. If they fold incorrectly they are prone to aggregation and cause a wide range of neurodegenerative diseases. Some proteins are capable of folding without assistance but others need help from protein complexes known as chaperonins. Chaperonins are a family of proteins that assemble into barrel-shaped cages the create a protected chamber for misfolded proteins to refold into their biologically active state. …

Quantitative Comparison Of A Nanoengineered Alumina Coated Cnt Arrays To Sio2 Coated Cnts And Solution Based Delivery System, Shree Aier

Maseeh Summer Undergraduate Research Experience

To meet the growing need for nanoengineered biocompatible materials to serve as drug delivery platforms, in this research, carbon nanotube arrays were fabricated by chemical vapor deposition, followed by an alumina coating by the high yielding, tightly controlled atomic layer deposition. This nanoengineered vertically aligned alumina nanowire array serves as a platform for delivering antigens, which act as cancer adjuvants. The physicochemical characteristics of the nanowires (NWs) can significantly influence the delivery of a biomolecule to immune cells. To investigate the material characteristics, the delivery efficiency of the antigen using NWs was quantitatively assessed by flow cytometry. Further, the mechanism …

Label-Free Quantitative Proteomics Reveals A Novel Sgta/Peroxiredoxin I Complex That Regulates Androgen Receptor Activity, Yenni Alejandra Garcia

Open Access Theses & Dissertations

The dynamic Hsp70-90 chaperone machinery along with its cochaperone partners are well-characterized for their ability to fold, assemble, and regulate steroid hormone receptors (SHRs). Human small glutamine rich tetratricopeptide repeat (TPR) containing protein alpha (SGTA) is a recently identified protein that has a characteristic Hsp90-binding TPR domain and is a key participant in the androgen, glucocorticoid, and progesterone receptor signaling pathway. In addition, SGTA plays a role in cellular processes such as cell cycle progression and apoptosis. We have demonstrated that SGTA binds directly to both Hsp70 (kd = 6 μM) and Hsp90 (kd = 11 μM). In a cell-free …

A Review Of Natural And Engineered Enzymes Involved In Bioethanol Production, Ines Cuesta Urena

Graduate Student Theses, Dissertations, & Professional Papers

Alternative petroleum-derived fuels, such as biofuels, is another form to decrease the dependence of non-renewable energy. The most promising alternative energy is cellulosic ethanol because of the abundance of cellulose and the overall lack of concern for the food-versus-fuel dilemma.

In order to produce ethanol from cellulosic materials, pretreatment is required to “open” the lignocellulosic matrix and make cellulose more susceptible to enzymatic degradation. Enzymatic hydrolysis of lignocellulose is an important area of research due to the absence of negative effects in downstream processes in comparison with acid hydrolysis. Both natural enzymes and engineered enzymes can be used in the …

Functional Effects Of Calcium Regulation Of Thin Filaments At Single Particle Resolution, Christopher Solis-Ocampo

Electronic Theses and Dissertations

Heart disease is the leading cause of death in the United States. Understanding heart function at the molecular level is critical for developing of more effective treatments. In the cardiac muscle, the thin filament is composed by troponin (Tn), tropomyosin (Tm), and F-actin. It provides Ca2+-dependent regulation of contraction by modulating myosin attachment and force generation in a cooperative scheme. However, this mechanism remains unclear. To understand thin filament activation, we studied the binding and functional properties of Tn and Tm to F-actin at single particle resolution by employing fluorescence image colocalization, in vitro motility assays, and Förster resonance energy …

Role Of Apoptotic Hepatocytes In Hcv Dissemination: Regulation By Acetaldehyde, Murali Ganesan, Sathish Kumar Natarajan, Jinjin Zhang, Justin L. Mott, Larisa I. Poluektova, Benita L. Mcvicker, Kusum K. Kharbanda, Dean J. Tuma, Natalie A. Osna

Department of Biochemistry: Faculty Publications

Alcohol consumption exacerbates hepatitis C virus (HCV) pathogenesis and promotes disease progression, although the mechanisms are not quite clear. We have previously observed that acetaldehyde (Ach) continuously produced by the acetaldehyde-generating system (AGS), temporarily enhanced HCV RNA levels, followed by a decrease to normal or lower levels, which corresponded to apoptosis induction. Here, we studied whether Ach-induced apoptosis caused depletion of HCV-infected cells and what role apoptotic bodies (AB) play in HCV-alcohol crosstalk. In liver cells exposed to AGS, we observed the induction of miR-122 and miR-34a. As miR-34a has been associated with apoptotic signaling and miR-122 with HCV replication, …