Life Sciences Commons^™

Microfluidic Devices With Integrated Sample Preparation For Improved Analysis Of Protein Biomarkers, Pamela Nsang Nge

Theses and Dissertations

Biomarkers present a non-invasive means of detecting cancer because they can be obtained from body fluids. They can also be used for prognosis and assessing response to treatment. To limit interferences it is essential to pretreat biological samples before analysis. Sample preparation methods include extraction of analyte from an unsuitable matrix, purification, concentration or dilution and labeling. The many advantages offered by microfluidics include portability, speed, automation and integration. Because of the difficulties encountered in integrating this step in microfluidic devices most sample preparation methods are often carried out off-chip. In the fabrication of micro-total analysis systems it is important …

Multifactorial Patterns Of Gene Expression In Colonic Epithelial Cells Predict Disease Phenotypes In Experimental Colitis, Aubrey Leigh Frantz, Maria E. C. Bruno, Eric William Rogier, Halide Tuna, Donald A. Cohen, Subbarao Bondada, Ralph Lakshman Chelvarajan, J. Anthony Brandon, C. Darrell Jennings, Charlotte S. Kaetzel

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background— The pathogenesis of inflammatory bowel disease (IBD) is complex and the need to identify molecular biomarkers is critical. Epithelial cells play a central role in maintaining intestinal homeostasis. We previously identified five “signature” biomarkers in colonic epithelial cells (CEC) that are predictive of disease phenotype in Crohn's disease. Here we investigate the ability of CEC biomarkers to define the mechanism and severity of intestinal inflammation.

Methods— We analyzed the expression of RelA, A20, pIgR, tumor necrosis factor (TNF), and macrophage inflammatory protein (MIP)-2 in CEC of mice with dextran sodium sulfate (DSS) acute colitis or T-cell-mediated chronic colitis. …

Blast Brain Injury Elevates Catecholamine Biosynthesis In The Nucleus Tractus Solitaries And Oxidative Stress In The Hypothalamus In Rats, Nihal Tumer, Stanislav Svetlov, Nataliya Kirichenko, Melissa Whidden, Benedek Erdos, Victor Prima, Alexandra Sherman, Firas H. Kobeissy, Robert Yezierski, Charles Vierck, Kevin Wang

Kinesiology Faculty Publications

Introduction: Traumatic Brain Injury (TBI) produces major health problems impacting the lives of both military and civilian personnel. TBI disrupts autonomic function but the nature of this disruption is unknown. Following blast brain injury, we assessed selective biochemical markers for autonomic function in adult male Sprague Dawley rats. Methods: Rats were subjected to head-directed overpressure blast injury (OBI) of 358 kPa magnitude at the target. At the same time for sham controls, rats were anesthetized as the previous group but instead of OBI were exposed just to noise being placed at ~ 2 m distance from the shock tube nozzle. …

Statistical Methods For Proteomic Biomarker Discovery Based On Feature Extraction Or Functional Modeling Approaches, Jeffrey S. Morris

Jeffrey S. Morris

In recent years, developments in molecular biotechnology have led to the increased promise of detecting and validating biomarkers, or molecular markers that relate to various biological or medical outcomes. Proteomics, the direct study of proteins in biological samples, plays an important role in the biomarker discovery process. These technologies produce complex, high dimensional functional and image data that present many analytical challenges that must be addressed properly for effective comparative proteomics studies that can yield potential biomarkers. Specific challenges include experimental design, preprocessing, feature extraction, and statistical analysis accounting for the inherent multiple testing issues. This paper reviews various computational …

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple platforms …

Biomarkers Of Petroleum Contamination In The Digestive Gland Of Perna Viridis (L.), Xivanand Narayan Verlecar, Karmabeer Jena, Somshekher Raghoba Desai, Priya Brata Das, Gagan Bihari Nityananda Chainy

Turkish Journal of Biology

Oxidative stress responses were evaluated in the digestive gland tissue of Perna viridis exposed to water-accommodated fractions (WAFs) of petrol and diesel at 0.5% and 5% concentrations over 5-, 10-, and 15-day periods. Increased lipid peroxidation, protein carbonyl, DNA integrity, and hydrogen peroxide in WAF-exposed specimens are indicative of oxidative damage due to dissolved petroleum extracts. A consistent increase in superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, glutathione-S-transferase, reduced glutathione, and ascorbic acid in WAF-exposed specimens signify the importance of antioxidants in protecting the cell against the oxidative damage arising from petroleum contamination. The responses of field specimens collected from …

Australian Healthy Eating Index Is Associated With Homocysteine, Vitamin B12 And Folate Biomarkers, Ali Sadeghpour, Jo Russell, Vicki Flood, Paul Mitchell

Faculty of Health and Behavioural Sciences - Papers (Archive)

No abstract provided.

Development Of Biomarkers For Endocrine Disrupting Compounds In The Fathead Minnow, Pimephales Promelas, Tara Frare

Undergraduate Review

Organic waste compounds (OWC’s) are an environmental concern that can have adverse effects on humans, animals, and the environment. Ethinyl estradiol (EE2) is one common OWC and is an active ingredient in oral birth control pills. The presence of EE2 in aquatic environments and drinking water can be linked to decreased fertility and altered physiology in fish. I am developing Q-PCR biomarkers to detect changes in fish at low concentrations before adverse effects occur at higher concentrations. RNA was extracted from twenty fathead minnows that had not been exposed to OWC’s and will be used to synthesize cDNA. Thus far …

In Vitro Inhibitory Activity Of Black Seed Oil And Potassium Chloride Against The Biomarkers Of Triple Negative Breast Cancer, Tamaratina Jombai

LSU Master's Theses

Breast cancer is the leading cause of death among women and is highly heterogeneous in nature. One very aggressive subtype of this disease is Triple Negative Breast Cancer. Triple Negative Breast Cancer (TNBC), is a very aggressive disease characterized by the lack of expression of estrogen receptors (ER), progesterone receptors (PR) and human epidermal growth factor receptor-2 (HER-2). TNBC patients account for approximately 15% of total breast cancer patients. This breast cancer subtype is characterized by high mortality rate, and is typically associated with poor prognosis. Current clinical methods have proven to have low success rates against TNBC, it is …

Integrated Affinity Column Capillary Electrophoresis Microdevices For Biomarker Analysis, Weichun Yang

Theses and Dissertations

In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify target …

Validation Of Fingertip Whole Blood Against Common Blood Biomarkers Of Omega-3 Status In A Dose-Response Intervention, C E. Sparkes, A J. Sinclair, R A. Gibson, P L. Else, B J. Meyer

Faculty of Health and Behavioural Sciences - Papers (Archive)

No abstract provided.

A Meta-Analysis Of Biomarkers Associated With The Overtraining Syndrome, Alissa Donaldson, Frank B. Wyatt, Elise Brown, Tyler Fagan

International Journal of Exercise Science: Conference Proceedings

Overtraining (OT) syndrome has been investigated extensively with little agreement as to reliable markers for detection. A meta-analytic review is a procedure designed to compile studies in an area with hopes of reaching a consensus view. PURPOSE: The purpose of this meta-analysis was to provide summary quantitative findings of biomarkers (i.e., blood) associated with the overtraining syndrome. METHODS: A meta-analytic research design was utilized to investigate selected studies allowing for a coding process to record data. Thirteen studies met inclusion/exclusion criteria. Biomarkers included samples taken with subjects in normal (N) condition and during OT. These biomarkers were the following: glutamine …

The Future (Or Lack Of Future) Of Personalized Prescription In Psychiatry, Jose De Leon

Psychiatry Faculty Publications

Rapid technological advances in genetics have created conceptual chaos regarding the genetics of drug response. Terms for differing concepts are used interchangeably: pharmacogenetics with pharmacogenomics, personalized medicine with personalized prescription. Biomarker has many definitions. The author prefers the concept of personalized prescription and uses it with implications beyond pharmacogenetics by considering all scientific information valid for prescribing medication. Genetics may not be crucial for all drugs. In this comprehensive view, clinicians must consider genetic, environmental and personal variables when prescribing medication and incorporate some basic pharmacological principles: (1) safety and efficacy, (2) pharmacokinetics and pharmacodynamics, (3) therapeutic window and prescriber's …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

Evaluating Salivary Alpha-Amylase As A Biomarker Fro Stress, Denise L. Alfano

Seton Hall University Dissertations and Theses (ETDs)

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Ontology Driven Semantic Provenance For Heterogeneous Bionomics Experimental Data, Satya S. Sahoo, Michael L. Raymer, Cory Andrew Henson, Amit P. Sheth, William S. York

Kno.e.sis Publications

Scientific experimental data generated by all the bionomic technologies is characterized by heterogeneity in its representation formats, constituents, and generation processes and, therefore, also in its usage. Using the proteomics domain we demonstrate the important role of provenance information o manage, interpret and analyze experimental data. We present a novel approach that employs an ontology as a knowledge model to automatically create semantic provenance information for high-throughput mass spectrometry (MS) data in the glycoproteomics domain. The Semantic Provenance Annotation of Data in protEomics (SPADE) implementation is based on the ProPreO ontology, a large-process ontology ( ~500 classes, 40 named relationships …

Evaluation Of Cortisol And Dhea As Biomarkers For Stress, Jennifer A. Smith

Seton Hall University Dissertations and Theses (ETDs)

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Maldi Mass Spectrometry Imaging For The Discovery Of Prostate Carcinoma Biomarkers, Lisa Harris Cazares

Theses and Dissertations in Biomedical Sciences

The elucidation of new biological markers of prostate cancer (PCa) should aid in the detection, and prognosis of this disease. Diagnostic decision making by pathologists in prostate cancer is highly dependent on tissue morphology. The ability to localize disease-specific molecular changes in tissue would help improve this critical pathology decision making process. Direct profiling of proteins in tissue sections using MALDI imaging mass spectrometry (MALDI-IMS) has the power to link molecular detail to morphological and pathological changes, enhancing the ability to identify candidates for new specific biomarkers. However, critical questions remain regarding the integration of this technique with clinical decision …

Gene Response Profiles For Daphnia Pulex Exposed To The Environmental Stressor Cadmium Reveals Novel Crustacean Metallothioneins, Joseph R. Shaw, John K. Colbourne, Jennifer C. Davey, Stephen P. Glaholt, Thomas H. Hampton, Celia Y. Chen, Carol L. Folt, Joshua W. Hamilton

Dartmouth Scholarship

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

Secular Trends In The Association Of Socio-Economic Position With Self-Reported Dietary Attributes And Biomarkers In The Us Population: National Health And Nutrition Examination Survey (Nhanes) 1971–1975 To Nhanes 1999–2002, Ashima K. Kant, Barry I. Graubard

Publications and Research

Objective: Recent reports suggest persistence of health disparities related to socioeconomic position (SEP). To understand if diet may be a contributor to these trends, we examined secular trends in the association of diet and indicators of SEP from 1971–1975 to 1999–2002.

Design: We used data from the National Health and Nutrition Examination Surveys (NHANES) I (1971–1975), II (1976–1980), III (1988–1994) and 1999–2002 to examine the independent associations of poverty income ratio (PIR) and education with diet and biomarkers of diet and disease in 25–74-year-olds (n ¼ 36 600). We used logistic and linear regression methods to adjust for multiple covariates …

Characterization Of Volatile Organic Compounds In Bovine Breath Using Solid-Phase Microextraction And Gas Chromatography-Mass Spectrometry, Jacek A. Koziel, Jarett P. Spinhirne, Norbert K. Chirase

Jacek A. Koziel

A face mask sampling device, DVB/Carboxen/PDMS 50/30 µ m solid phase microextraction (SPME) fibers, and a gas chromatograph with a mass spectrometer detector (GC-MS) were used for sampling and analysis of volatile organic compounds (VOCs) in bovine breath. Breath of 3 morbid steers with respiratory tract infections and 3 healthy steers were sampled 7 times in 19 days for 15 min at each sampling. A total of 21 VOCs were detected, many of them for the first time in cattle breath. Preliminary statistical analyses using Chi-square Test on the frequency of detection of each VOC in each group was performed. …