Life Sciences Commons^™

Characterization Of Bacteriophages From Environmental Water Samples And The Potential Of Bacteriophages Tailspike Proteins (Tsp) In Bacteria Detection, Gayathri Upeksha Gunathilaka

Wayne State University Theses

ABSTRACT

CHARACTERIZATION OF BACTERIOPHAGES FROM ENVIRONMENTAL WATER SAMPLES AND THE POTENTIAL OF BACTERIOPHAGES TAILSPIKE PROTEINS (TSP) IN BACTERIA DETECTION

by

GAYATHRI UPEKSHA GUNATHILAKA

May 2014

Advisor: Dr. Yifan Zhang

Major: Nutrition and Food Science

Degree: Master of Science

The high abundance of phage in the environment and their specificity with the bacteria host make them an excellent tool for bacteria detection. To characterize phage specific to Salmonella and E. coli from water samples in the Southeastern Michigan and to develop a novel bacterial detection method using phage, environmental water samples were collected from rivers and waste water treatment plant (WWTP) …

Screening Of Natural Antimicrobial Agents And Antimicrobial-Resistant Bacteria Using A Soleris System, Mingyang Huang

Wayne State University Theses

ABSTRACT

SCREENING OF NATURAL ANTIMICROBIAL AGENTS AND ANTIMICROBIAL - RESISTANT BACTERIA USING A SOLERIS SYSTEM

by

MINGYANG HUANG

May 2014

Advisor: Dr. Yifan Zhang

Major: Food Science and Nutrition

Degree: Master of Science

Traditional broth micro-dilution method is a common assay of measuring Minimum Inhibitory Concentration (MIC) to determine the antimicrobial activity of an antimicrobial agent. However, this method is generally time-consuming and labor intensive. Alternatively, an automated optical method using the Soleris system was applied in this study. The system was compared to the traditional broth micro-dilution 96-well assay to test the antimicrobial activity of 11 essential oils and …

Effects Of Statin Drugs And Tocotrienol Rich Fraction Supplementation In Chronic Hemodialysis Patients And Metabolomic Profile, Eno Latifi

Wayne State University Theses

Chronic kidney disease (CKD) is known as a heterogeneous disorder which currently is on the rise and lately has been classified as a public health issues in the United State and worldwide. CKD is an irreversible and progressive disease which can lead to kidney failure, and this is depicted by the advanced stage of the disorder when it reaches the point, that is classified as end stage of renal disease (ESRD) (Stage 5 of CKD) (eGRF <15 mL/min/ 1.73 m2 working capacity), where both organs are in a total or permanent kidney failure. End-Stage renal disease patients, on hemodialysis have been associated to experience an accelerated form of atherosclerosis, which is induced by inflammation, impairment of antioxidant system and elevated oxidative stress. Since the problem effecting ESRD patients is multifactorial, the objective of this investigation is to explore and look at the effects of supplementing with vitamin E-tocotrienol rich fraction (TRF), a micronutrient which has anti-inflammatory, antioxidant, and lipid lower capabilities into tackling these comorbid conditions experienced by this population. Therefore the aims of this investigation will be to explore changes in lipid profiles, inflammatory markers, and oxidative status, as well as look at any changes in metabolomic profiles. It was hypothesized that by supplementing with TRF a vitamin E, for 16 weeks in ESRD patients undergoing hemodialysis, it may help reverse and/or improve, oxidative status, inflammatory markers, increase antioxidants status and improve lipid profiles.

The study was double-blinded, randomized, parallel, placebo-controlled design trial, of 81 adult patients undergoing chronic hemodialysis at Great Lake Dialysis Clinic, Detroit MI, where …

Approaches To Improving Detection Of Invasive Fish Species In Western Lake Erie Through Analysis Of Monitoring Efficiencies And Metrics Of Community Distribution, Joshua Alan Southern

Wayne State University Theses

Efficient monitoring programs are essential for the early detection of invasive species. The Ohio Department of Natural Resources (ODNR) monitoring program encompassing 21 years of fish survey data from western Lake Erie was evaluated using Chao biodiversity analysis to determine the efficiency and precision of collection strategies of trawl and gillnet sampling, at detecting rare or non-native species. Overall, ODNR sampling annually accounted for ~80% of extant fish species, leaving gaps in coverage where rare and invasive species may be overlooked and proliferate.Obtaining 90% efficiency would require an estimated doubling of previous sampling effort. Computer simulations calculating different proportions of …

Antimicrobial Activity Of Essential Oil Emulsions And Possible Synergistic Effect On Food Borne Pathogens, Varun Tahlan

Wayne State University Theses

The objective of this study was to evaluate the antimicrobial activity of essential oil emulsions against food borne pathogenic bacteria and determine potential applications. The oils used for this study were cinnamon, oregano, clove, thyme, rosemary, sage, bergamot, nutmeg, lemon grass and bay. Oil in water emulsions were prepared using Tween 80 as an emulsifying agent, with a stock oil concentration in the emulsions of 20,000 ppm. Essential oil emulsions were individually screened against E. coli (ATCC 25922), E. coli (ATCC 700927), L. monocytogens (ATCC 19115), L. innocua (ATCC 33090) and S. Typhimurium (ATCC 19585) using the broth micro dilution …

Comparitive Study On Antioxidant Properties Of Dendrobium Officinale (Tiepishihu), Wenjun Zhu

Wayne State University Theses

For ages, Chinese herbs, such as Dendrobium Officinale (DO), have been used in Asian regions for treating various illnesses due to the high medicinal value. In this study, the DO plant Acetone and Ethanolic extracts possibly containing antioxidants were tested using different methodologies for comparison and determination of specific antioxidant capacity. The total phenolic content assay expressed as Gallic Acid Equivalent showed 9.43±;0.23 mg GAE /g of extract. Further analysis using DPPH· assay indicated that antioxidants presented in the sample were able to significantly scavenge 37% and 44% radicals at the concentrations of 25mg/ml and 50mg/mL respectively, after a period …

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 …

The Impact Of Down Syndrome And Folate Depletion On Genomic Stabilizing Pathways Of Lymphoblastoid Cells, Khadijah Ibrahim Alnabbat

Wayne State University Theses

Understanding the role of nutrition plays in Down syndrome (DS) could help in the development and implementation of strategies that help overcome the negative consequences phenotypes of Down syndrome. Conserving genome integrity is crucial for cells to survive, and thus understanding how genetic defects induce damage to genomic DNA and impair subsequent repair of this damage is important. Evidence accumulated points to increased DNA damage and mutation accumulation associated with a decline in DNA repair capacity, Base Excision Repair (BER) in particular. Thus, the successful clinical management of DS resides in understanding the metabolic imbalance provoked by overexpression of genes …

The Movement Of Escherichia Coli And Enterococci Among Beach Sand, Lyngbya Wollei, And The Water Column: Implications For Human Health, Krystal Ann Bakkila

Wayne State University Theses

Occurrence of the filamentous cyanobacteria Lyngbya wollei has become an increasing concern in the Great Lakes region. Prior to the early 1900's, L. wollei had been occasionally documented in the Great Lakes region, but in the last decade it has been observed with increasing frequency. In the Great Lakes L. wollei has been proliferating, fragmenting, and accumulating ashore, where it decays forming thick detrital mats harboring potentially harmful bacteria such as Escherichia coli and enterococci. While the filamentous green algae species Cladophora glomerata has been well studied in this region, very little research has been done on the cyanobacteria L. …

Compare Effects Of Diets Made With Different Saturated Fatty Acids On Body Weight Regulation And Metabolism In Wister Rats, Dilruba Fatema

Wayne State University Theses

Animal fats are known to cause elevated blood total and low-density- lipoprotein (LDL) cholesterol levels in humans and animals. This study was designed to investigate the effects of both the quality (coconut oil and a modified beef tallow with reduced saturated fatty acid content) and quantity (low and high) of dietary fat in body weight regulation and alteration of blood cholesterol levels in an animal model. Forty two male Wister rats were randomly divided into 4 groups: Control Low Fat (CLF, n=10), Control High Fat (CHF, n=10), Modified Low Fat (MLF, n=11), and Modified High Fat (MLF, n=11). They were …

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 …

Species - Dependent Cardiac And Motor Responses To Cholinergic Stimulation In Daphnia Pulex And Daphnia Magna, Bryan James Hannan

Wayne State University Theses

The role of acetylcholine (ACh) in regulating the activity of the heart and `feeding current' driven by the beating thoracic appendages of Daphnia pulex and Daphnia magna was evaluated using acetylcholinesterase inhibitors (AChE-I) and muscarinic receptor agonists. Single animals, tethered to a stainless steel pin, were tested in a watertight aquatic chamber that allowed free movement of appendages and swimming antennae. Heart contraction rate and the rate of thoracic appendage beating were quantified optically by measuring fluctuating changes in light-intensity caused by movement. Physostigmine, neostigmine, oxotremorine, pilocarpine as well as nicotine were used to study ACh and AChE. Atropine was …

Bacteriophage Isolated From The Environment And E. Coli Of Meat Origin As A Reservoir Of Antibiotic Resistance, Manisha Polur

Wayne State University Theses

ABSTRACT

BACTERIOPHAGE ISOLATED FROM THE ENVIRONMENT AND E. COLI OF MEAT ORIGIN AS A RESERVOIR OF ANTIBIOTIC RESISTANCE

by

MANISHA POLUR

April 2014

Advisor: Dr. Yifan Zhang

Major: Nutrition and Food Science

Degree: Master of Science

This study was aimed to determine the extent of antibiotic resistance reservoir in bacteriophage. Bacteriophages were isolated and purified from waste water treatment plants, Detroit river, Belle Isle, Urban Garden soils and examined for the presence of beta-lactam antibiotic resistance genes. Thirty E. coli isolates from retail meat were analyzed for the presence of beta-lactam antibiotic resistance genes. 95% of E. coli them carried …

The Effects Of Phragmites Australis Litter On Seed Emergence In The Erie-Huron Corridor, Michigan, Travis White

Wayne State University Theses

The invasive reed, Phragmites australis, is widespread within the Great Lakes region, and is often blamed for habitat degradation. Once established, it creates dense litter mats that may persist following remediation efforts of living stock removal. We investigated the effects of P. australis and Typha angustifolia, narrow-leaf cattail, litter on seedling emergence from the native seed bank by harvesting soils from five Great Lakes coastal marshes densely populated by either Phragmites or Typha and exposing them to Phramities or Typha litter in treatments of varying litter depths. Seedling emergences were quantified for six weeks. Soils from Phragmites dominated sites had …

The Rna Newton Polytope And Learnability Of Energy Parameters, Elmirasadat Forouzmand

Wayne State University Theses

Computational RNA secondary structure prediction has been a topic of much research interest for several decades now. Despite all the progress made in the field, even the state-of-the-art algorithms do not provide satisfying results, and the accuracy of output is limited for all the existent tools. Very complex energy models, different parameter estimation methods, and recent machine learning approaches had not been the answer for this problem. We believe that the first step to achieve results with high quality is to use the energy model with the potential for predicting accurate output. Hence, it is necessary to have a systematic …

Saudi Arabian Students In Detroit Use Natural Health Products More So Than Other University Students In Detroit, Samiah Naji Alqahtani

Wayne State University Theses

Natural Health Products (NHP), are defined as products that derive from organisms and may include supplements and herbal/traditional remedies. Prior research indicates that females use NHP more than males. We have unpublished data to show that students use NHP for health maintenance with significantly different use of NHP by Native/Aboriginal students vs. other students. Less is known about Saudi students. We hypothesize that: (1) There are gender differences in NHP used; and (2) There are geo-ethnic differences in NHP used. We also determine the predictor variables that influence NHP use by students. Students from Wayne State University (n=560; 193 …

Development And Evaluation Of Plga-S-S-Peg Micelles Coencapsulating Curcumin Difluorinated And Paclitaxel For Synergistic Therapeutic Efficacy, Lakshmi Deepika Cheemalakonda

Wayne State University Theses

ABSTRACT

DEVELOPMENT AND EVALUATION OF PLGA-S-S-PEG MICELLES COENCAPSULATING CURCUMIN DIFLUORINATED AND PACLITAXEL FOR SYNERGISTIC THERAPEUTIC EFFICACY

by

LAKSHMI DEEPIKA CHEEMALAKONDA

August 2014

Advisor: Dr. Joshua Reineke Major: Pharmaceutical Sciences Degree: Master of Science

Solid tumors like pancreatic tumor has unique property of forming a dense desmoplastic layer around the tumor cells making it difficult for the drug to transport across this layer. Multi drug resistance is also one of the major limitation of chemotherapy. Therefore the aim of this project was to make PLGA-SS-PEG micelles encapsulating CDF and paclitaxel for synergistic cancer therapy. CDF was found to have 16-fold better …

Effect Of Folate Deficiency On Mtor Signaling Network On The Liver Of Wild Type Mice, Essra Moussawi

Wayne State University Theses

Through various studies of dietary nutrients on the affects of the physiological and molecular pathways are a key study in understanding the interaction between dietary nutrients and the human genome that may severely impact the development of various cancers. A primary approach is observing the dietary nutrients, that we consume and how it plays a role in the cellular pathway of our bodies through experimental methods. Folate deficiency (FD) has shown, through studies, to play a role anti-cancer progression. Our goal was to observe the autophagy related proteins in the mTOR signaling pathway as it was suggested that mTOR may …

The Phenotypic Analysis Of The Knockdown Of The Sin3a Complex Components And Their Role In Recruitment And Cell Proliferation, Kelly Ann Laity

Wayne State University Theses

The SIN3A-RPD3 complex components have previously been identified in Drosophila melanogaster. The role of these components in SIN3A function and recruitment was not known. Polytene chromosome analysis following RNAi knockdown was performed to determine if any of the complex members affect the ability of SIN3A to bind to chromatin. The complex components effect on cell proliferation was also examined through clonal analysis of imaginal wing discs. The results of this work implicate a role of several members of the SIN3A complex for proper recruitment and localization to chromatin. All of the SIN3A complex members had some varying effect on cell …

De Novo Co-Assembly Of Bacterial Genomes From Multiple Single Cells, Narjes Sadat Movahedi Tabrizi

Wayne State University Theses

Recent progress in DNA amplication techniques, particularly multiple displacement amplication (MDA), has made it possible to sequence and assemble bacterial genomes from a single cell. However, the quality of single cell genome assembly has not yet reached the quality of normal multicell genome assembly due to the coverage bias and errors caused by MDA. Using a template of more than one cell for MDA or combining separate MDA products has been shown to improve the result of genome assembly from few single cells, but providing identical single cells, as a necessary step for these approaches, is a challenge. As a …

Rates And Modes Of Sequence Evolution In Various Lineages Within Chenopodiaceae, James Andrew Naeger

Wayne State University Theses

Sexual dimorphism in domesticated spinach, Spinacia oleracea, is thought to be determined by differential expression of floral organ identity genes. We examined the floral organ morphologies of seven species in the Chenopodiaceae, including two wild species of spinach, in order to gain insight into the evolution of floral reproductive strategy in this clade. The species within the Anserineae demonstrate extensive evolution in floral morphology and reproductive strategy, and Spinacia is unique for having been domesticated rather recently and for being dioecious. We found C. album to be hermaphroditic, C. foliosum and M. nuttalliana to be gynomonoecious, while C. bonus-henricus …

Site-Directed Mutagenesis Of Conserved Amino Acids Residues In N5-Carboxyaminoimidazole Ribonucleotide Mutase: Converting N5-Cair Mutase Into Aminoimidazole Ribonnucleotide Carboxylase & Developing A High-Throughput Screening Assay For The Discovery Of N5-Carboxyaminoimidazole Ribonucleotide Mutase, Zhiwen Shi

Wayne State University Theses

The de novo purine biosynthesis pathway plays a critical role in providing new purines to the cell. Previous studies have shown differences between the human and bacterial pathways which suggests that pathway may be a potential target for antibiotic drug discovery. Three critical enzymes are involved in the pathway divergence. In the bacterial pathway, N5-CAIR synthetase (PurK) first converts AIR to N5-CAIR, which is then transformed into CAIR catalyzed by the enzyme N5-CAIR mutase (Class I PurE). In the human pathway, AIR carboxylase (Class II PurE) catalyzes the direct conversion of AIR to CAIR. Class I and Class II PurEs …

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 …

Functional Studies Of 5-Carboxyaminoimidazole Ribonucleotide Synthetase And Mutase From Thermotoga Maritima, Mingyang Zhao

Wayne State University Theses

De novo purine biosynthesis is divergent depending upon the organism. In bacteria, yeasts and plants, 5-aminoimidazole ribonucleotide (AIR) is converted to 4-carboxyaminoimidazole ribonucleotide (CAIR) by N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) synthetase (PurK) and N5-CAIR mutase (Class I PurE). In animals, AIR is converted into CAIR by AIR carboxylase (Class II PurE). The distinction makes PurK and Class I PurE good targets in design of antimicrobial drugs. N5-CAIR is chemically unstable with t1/2 of about 0.9 minutes at pH 7.8 and 37 °C. If the production of N5-CAIR is not regulated relative to its conversion to CAIR, ATP utilization can rapidly become non-stoichiometric. …

Proteomic Discovery Of Protein Phosphatase 1 Catalytic Subunit Protein Interaction Partners In Human Skeletal Muscle, Zhao Yang

Wayne State University Theses

Protein Phosphatase 1 (PP1), a member of Serine/ Threonine Phosphatase family, targets its dephosphorylation activity on serine and threonine residues. As the catalytic subunit of PP1, PP1c can achieve its substrate specificity only by binding with PP1 regulatory subunits. Previous researches have shown that PP1c can involve in multiple functional regulation by associating with various interaction partners. Since serine/ threonine phosphorylation on the Insulin receptor substrate-1 (IRS1) may direct inactivation and degradation of IRS1, this phosphorylation activity is believed to be a source of Insulin Resistance. PP1 is hypothesized to dephosphorylate serine/ threonine site on IRS1, which may rescue the …

The Nh2-Hypervariable Region Modulates The Binding Affinity Of Troponin T For Tropomyosin, Chinthaka Kaushalya Amarasinghe

Wayne State University Theses

The troponin complex plays a central role in the allosteric function of sarcomeric thin filaments by enacting conformational changes during the Ca2+-regulated contraction and relaxation of striated muscle. The troponin subunit T (TnT) has two binding sites for tropomyosin (Tm) and is responsible for anchoring the troponin complex to the thin filament. Although the C-terminal and middle regions of the TnT polypeptide chain are highly conserved among the three muscle type isoforms, the hypervariable N-terminal region has evolutionarily diverged significantly among isoforms. Previous studies have shown that the N-terminal variable region fine-tunes Ca2+ regulation of muscle contractility via modulation of …

Comparative Study Of The Prevalence Of Psk41 In Heterogenous Vancomycin-Intermediate Staphylococcus Aureus Isolates Against Non- Heterogenous Vancomycin-Intermediate Staphylococcus Aureus Isolates And The Prevalence By Patient Severity, Poorva Mukund Divekar

Wayne State University Theses

COMPARATIVE STUDY OF THE PREVALENCE OF PSK41 IN HETEROGENOUS VANCOMYCIN-INTERMEDIATE STAPHYLOCOCCUS AUREUS ISOLATES AGAINST NON- HETEROGENOUS VANCOMYCIN-INTERMEDIATE STAPHYLOCOCCUS AUREUS ISOLATES AND THE PREVALENCE BY PATIENT SEVERITY

by

POORVA DIVEKAR

December 2014

Advisor: Dr. Emily T. Martin

Major: Pharmaceutical Sciences

Degree: Master of Science

Earlier studies have reported that pSK41 plays an important role in the transfer of vancomycin resistance from Vancomycin-resistant Enterococci (VRE) to S. aureus. This transfer leads to the development of Vancomycin-resistant S. aureus (VRSA). Thirteen VRSA cases have been reported in the United States since 2002. To determine and compare the prevalence of pSK41 in hVISA isolates …

Synthesis And Characterization Of Brain Penetrant Prodrug Of Neuroprotective D264: Potential Disease Modifying Treatment Agent For Parkinson's Disease, Fahd Shamoon Dholkawala

Wayne State University Theses

Parkinson's disease (PD) is a complex neurodegenerative disorder with progressive loss of dopamanergic neurons in the substantia nigra region of the brain and accumulation of intracytoplasmic inclusions called `Lewy bodies'. PD is characterized by tremors, rigidity, slowness of movement, bradykinesia and postural imbalances. Although the etiology of PD is not well understood, it is well established that oxidative stress, mitochondrial dysfunction, alpha-synuclein aggregation play a central role in the pathogenesis of PD. Current treatment methods are based on symptomatic relief without addressing the underlying pathophysiological factors responsible for the disease. It is important to develop therapies which can address these …