Experimental And Computational Analysis Of Chloroplast Transit Peptide Domain Architecture And Function, 2013 University of Tennessee, Knoxville
Experimental And Computational Analysis Of Chloroplast Transit Peptide Domain Architecture And Function, Prakitchai Chotewutmontri
Doctoral Dissertations
The Majority of chloroplast proteins are nuclear-encoded and utilize an N-terminal transit peptide (TP) to target into chloroplasts via the general import pathway. Bioinformatic and proteomic analyses provide thousands of predicted TPs, which show low sequence similarity. How the common chloroplast translocon components recognize these diverse TPs is not well understood. Previous results support either sequence- or physicochemical-specific recognitions. To further address this question, a reverse sequence approach was utilized such that the reverse TP contains the same amino acid composition as wild-type TP but lack similar sequence motifs. Using both native and reverse TPs of the two well-studied precursors, …
Metagenomic Insights Into Anaerobic Metabolism Along An Arctic Peat Soil Profile, 2013 San Diego State University
Metagenomic Insights Into Anaerobic Metabolism Along An Arctic Peat Soil Profile, David A. Lipson, John M. Haggerty, Archana Srinivas, Ted K. Raab, Shashank Sathe, Elizabeth A. Dinsdale
Ted K. Raab
A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance …
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, 2013 College of Saint Benedict/Saint John's University
Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May
Biology Faculty Publications
Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …
Geometric Framework For Evaluating Rare Variant Tests Of Association, 2013 Harvard University
Geometric Framework For Evaluating Rare Variant Tests Of Association, Keli Liu, Shannon Fast, Matthew Zawistowski, Nathan L. Tintle
Faculty Work Comprehensive List
The wave of next-generation sequencing data has arrived. However, many questions still remain about how to best analyze sequence data, particularly the contribution of rare genetic variants to human disease. Numerous statistical methods have been proposed to aggregate association signals across multiple rare variant sites in an effort to increase statistical power; however, the precise relation between the tests is often not well understood. We present a geometric representation for rare variant data in which rare allele counts in case and control samples are treated as vectors in Euclidean space. The geometric framework facilitates a rigorous classification of existing rare …
Optimal Methods For Using Posterior Probabilities In Association Testing, 2013 Harvard University
Optimal Methods For Using Posterior Probabilities In Association Testing, Keli Liu, Alexander Luedtke, Nathan L. Tintle
Faculty Work Comprehensive List
Objective: The use of haplotypes to impute the genotypes of unmeasured single nucleotide variants continues to rise in popularity. Simulation results suggest that the use of the dosage as a one-dimensional summary statistic of imputation posterior probabilities may be optimal both in terms of statistical power and computational efficiency; however, little theoretical understanding is available to explain and unify these simulation results. In our analysis, we provide a theoretical foundation for the use of the dosage as a one-dimensional summary statistic of genotype posterior probabilities from any technology. Methods: We analytically evaluate the dosage, mode and the more general set …
Microarray Analysis Of Mrna Translation State In Arabidopsis Thaliana, 2013 University of Tennessee - Knoxville
Microarray Analysis Of Mrna Translation State In Arabidopsis Thaliana, Bayu Sisay Tiruneh
Masters Theses
The synthesis of proteins – translation – is one of the cellular processes that consume a great deal of energy. Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different stresses and environmental and growth signals. Similar assays have revealed how translation of specific mRNAs is perturbed by genetic mutations in eukaryotic translation initiation factors (eIFs). I performed genome-wide analyses of translation state in A. thaliana seedlings with mutant genotypes for a specific eIF (subunit h of eIF3) and the large ribosomal protein, L24 (RPL24B). Using data from prior microarray …
Bio-Separation Process Improvement Via Genomic Manipulation: Development Of Novel Strains For Use In Immobilized Metal Affinity Chromatography (Imac), 2013 University of Arkansas, Fayetteville
Bio-Separation Process Improvement Via Genomic Manipulation: Development Of Novel Strains For Use In Immobilized Metal Affinity Chromatography (Imac), Ryan Curtis Haley
Graduate Theses and Dissertations
The dissertation is comprised of three parts. Part I describes proteomic analysis of native bacterial proteins from Escherichia coli (E.coli) that bind during Immobilized Metal Affinity Chromatography (IMAC). Part II describes the value in exploiting proteome based data as a tool toward the design an E. coli expression strain that is particularly useful when Immobilized Metal Affinity Chromatography is employed as the initial capture step of a homologous protein purification process. Part III describes a methodology of chromosomal mapping of all contaminant gene products.
The objective of Part I was to identify all E. coli proteins that bind to Co(II), …
Genome-Wide Profiling Unveils Criticial Functions Of P53 In Human Embryonic Stem Cells, 2013 The University of Texas Graduate School of Biomedical Sciences at Houston
Genome-Wide Profiling Unveils Criticial Functions Of P53 In Human Embryonic Stem Cells, Kadir C. Akdemir
Dissertations & Theses (Open Access)
Embryonic stem cells (ESCs) possess two unique characteristics: infinite self-renewal and the potential to differentiate into almost every cell type (pluripotency). Recently, global expression analyses of metastatic breast and lung cancers revealed an ESC-like expression program or signature, specifically for cancers that are mutant for p53 function. Surprisingly, although p53 is widely recognized as the guardian of the genome, due to its roles in cell cycle checkpoints, programmed cell death or senescence, relatively little is known about p53 functions in normal cells, especially in ESCs. My hypothesis is that p53 has specific transcription regulatory functions in human ESCs (hESCs) that …
The Natural And Orthogonal Interaction (Noia) Models For Quantitative Traits (Qts) And Complex Diseases, 2013 The University of Texas Graduate School of Biomedical Sciences at Houston
The Natural And Orthogonal Interaction (Noia) Models For Quantitative Traits (Qts) And Complex Diseases, Feifei Xiao
Dissertations & Theses (Open Access)
My dissertation focuses on developing methods for gene-gene/environment interactions and imprinting effect detections for human complex diseases and quantitative traits. It includes three sections: (1) generalizing the Natural and Orthogonal interaction (NOIA) model for the coding technique originally developed for gene-gene (GxG) interaction and also to reduced models; (2) developing a novel statistical approach that allows for modeling gene-environment (GxE) interactions influencing disease risk, and (3) developing a statistical approach for modeling genetic variants displaying parent-of-origin effects (POEs), such as imprinting.
In the past decade, genetic researchers have identified a large number of causal variants for human genetic diseases and …
The Role Of Oswrky71 And Its Interacting Proteins In Seed Germination And Early Growth Of Cereal Grains, 2013 University of Nevada, Las Vegas
The Role Of Oswrky71 And Its Interacting Proteins In Seed Germination And Early Growth Of Cereal Grains, Margaret Ja Shin
UNLV Theses, Dissertations, Professional Papers, and Capstones
During seed germination and early seedling growth, complex molecular and physiological events occur in rice (Oryza sativa) and other cereal grains. As the seed transitions to vegetative tissue, it responds to both favorable and unfavorable environmental conditions and is vulnerable to attack by predation and disease. Although seeds are relatively small and tender in size, extensive and sophisticated molecular networks enables the immobile seed to grow, survive and adapt in its environment. One of the networks I am interested in is in the crosstalk between the gibberellin (GA) and abscisic acid (ABA) signaling pathways. These pathways are interesting because they …
Predicting Complex Phenotype-Genotype Relationships In Grasses: A Systems Genetics Approach, 2013 Clemson University
Predicting Complex Phenotype-Genotype Relationships In Grasses: A Systems Genetics Approach, Stephen Ficklin
All Dissertations
It is becoming increasingly urgent to identify and understand the mechanisms underlying complex traits. Expected increases in the human population coupled with climate change make this especially urgent for grasses in the Poaceae family because these serve as major staples of the human and livestock diets worldwide. In particular, Oryza sativa (rice), Triticum spp. (wheat), Zea mays (maize), and Saccharum spp. (sugarcane) are among the top agricultural commodities. Molecular marker tools such as linkage-based Quantitative Trait Loci (QTL) mapping, Genome-Wide Association Studies (GWAS), Multiple Marker Assisted Selection (MMAS), and Genome Selection (GS) techniques offer promise for understanding the mechanisms behind …
Development Of Novel Methods To Minimize The Impact Of Sequencing Errors In The Next-Generation Sequencing Data Analysis, 2013 The University of Texas Graduate School of Biomedical Sciences at Houston
Development Of Novel Methods To Minimize The Impact Of Sequencing Errors In The Next-Generation Sequencing Data Analysis, Xiaofeng Zheng
Dissertations & Theses (Open Access)
Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. .
To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing …
Compound Identification Using Penalized Linear Regression., 2013 University of Louisville
Compound Identification Using Penalized Linear Regression., Ruiqi Liu
Electronic Theses and Dissertations
In this study, we propose a new method for compound identification using penalized linear regression. Compound identification is often achieved by matching the experimental mass spectra to the mass spectra stored in a reference library based on mass spectral similarity. In the context of the linear regression, the response variable is an experimental mass spectrum (i.e., query) and all the compounds in the reference library are the independent variables. However, the number of compounds in the reference library is much larger than the range of m/z values so that the data become high dimensional data with suffering from singularity. For …
Radiomics Of Nsclc: Quantitative Ct Image Feature Characterization And Tumor Shrinkage Prediction, 2013 The University of Texas Graduate School of Biomedical Sciences at Houston
Radiomics Of Nsclc: Quantitative Ct Image Feature Characterization And Tumor Shrinkage Prediction, Luke Hunter
Dissertations & Theses (Open Access)
Radiomics is the high-throughput extraction and analysis of quantitative image features. For non-small cell lung cancer (NSCLC) patients, radiomics can be applied to standard of care computed tomography (CT) images to improve tumor diagnosis, staging, and response assessment.
The first objective of this work was to show that CT image features extracted from pre-treatment NSCLC tumors could be used to predict tumor shrinkage in response to therapy. This is important since tumor shrinkage is an important cancer treatment endpoint that is correlated with probability of disease progression and overall survival. Accurate prediction of tumor shrinkage could also lead to individually …
Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, 2013 University of Vigo
Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
Tracy Heath
Bioinformatics Approach To Probe Protein-Protein Interactions: Understanding The Role Of Interfacial Solvent In The Binding Sites Of Protein-Protein Complexes;Network Based Predictions And Analysis Of Human Proteins That Play Critical Roles In Hiv Pathogenesis., 2013 Virginia Commonwealth University
Bioinformatics Approach To Probe Protein-Protein Interactions: Understanding The Role Of Interfacial Solvent In The Binding Sites Of Protein-Protein Complexes;Network Based Predictions And Analysis Of Human Proteins That Play Critical Roles In Hiv Pathogenesis., Mesay Habtemariam
Theses and Dissertations
The thesis work contains two projects under the same umbrella. The first project is to provide a detailed analysis on the behavior of interfacial water molecules at protein-protein complexes, in this case focusing on homodimeric complexes, and to investigate their effect with respect to different residue types. For that reason the homodimeric data-set, which includes high-resolution (≤ 2.30 Å) X-ray crystal structures of 252 (140 Biological & 112 Non-biological) protein complexes was chosen to explore fundamental differences between interfaces that Nature has “engineered” vs. compared to interfaces found under man-made conditions. The data set was comprised of 5391 water molecules …
A Semantic Situation Awareness Framework For Indoor Cyber-Physical Systems, 2013 Wright State University - Main Campus
A Semantic Situation Awareness Framework For Indoor Cyber-Physical Systems, Pratikkumar Desai
Kno.e.sis Publications
Recently, the domain of cyber-physical systems (CPSs) has emerged as a successor to the traditional embedded systems and the wireless sensor networks. The relatively new cyber-physical domain offers tight integration of control, communication and computation components to develop advanced web based application in various heterogeneous domains such as health care, disaster management, automation and environment monitoring. The applications of indoor CPSs include remote patient monitoring, smart home, etc. with focus on situation awareness via event identification from context information. The principal challenges associated with the development of situation awareness applications include uncertainty in contextual data, incomplete domain knowledge, interoperability between …
A Mobile Genetic Element With Unknown Function Found In Distantly Related Viruses, 2013 Norwegian Veterinary Institute
A Mobile Genetic Element With Unknown Function Found In Distantly Related Viruses, Torstein Tengs Dr.
Dr. Torstein Tengs
BACKGROUND
The genetic element s2m seems to represent one of very few examples of mobile genetic elements in viruses. The function remains obscure and a scattered taxonomical distribution has been reported by numerous groups.
METHODS
We have searched GenBank in order to identify all viral accessions that have s2m(-like) sequence motifs. Rigorous phylogenetic analyses and constrained tree topology testing were also performed in order to investigate the apparently mobile nature of s2m.
RESULTS
The stem-loop s2m structure can be found in four families of + ssRNA viruses; Astroviridae, Caliciviridae, Picornaviridae and Coronaviridae. In all of these virus families, with the …
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., 2013 The University of Western Ontario
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., Abu Sadat Md. Sayem
Electronic Thesis and Dissertation Repository
Representing DNA sequences graphically and evaluating, as well as displaying, species’ relationships have been considered to be an important aspect of molecular biology research. A novel approach is proposed in this thesis that combines three methods: a) Chaos Game Representation (CGR), to portray quantitative characteristics of a DNA sequence as a black-and -white image, b) Structural Similarity (SSIM) index, an image comparison method, to compute pair-wise distances between these images, and c) Multidimensional Scaling (MDS), to visually display each sequence as a point in a two-dimensional Euclidean space. The proposed method produces a visual representation called Genome Distance Map (GDM) …
A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, 2013 Loyola University Chicago
A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer
Computer Science: Faculty Publications and Other Works
RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …