Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics

Theses/Dissertations

Discipline
Institution
Publication Year
Publication

Articles 1 - 30 of 103

Full-Text Articles in Life Sciences

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus Aug 2019

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus

University of New Orleans Theses and Dissertations

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement ...


Wavelet Analysis Of Short Globular Homologous Proteins In Mesophile And Thermophile Prokaryotes, John B. Linehan Jun 2019

Wavelet Analysis Of Short Globular Homologous Proteins In Mesophile And Thermophile Prokaryotes, John B. Linehan

College of Science and Health Theses and Dissertations

This study looked to identify features related to thermal stability and function in the amino acid chains of short globular proteins from mesophile and thermophile species, within the constraint that the protein fold to perform a speci_c function. To do so 540 homologous pairs of proteins were studied. The amino acid chains were con-verted to hydrophobicity signals by assigning a hydropathy score to each residue in the polypeptide. The hydrophobicity signals were passed through a wavelet packet transform and the resulting spectra analyzed. Bootstrapping was used to gener-ate a control data set to determine if the true ordering of amino ...


Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar May 2019

Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar

UT GSBS Dissertations and Theses (Open Access)

Lung cancer, of which non-small cell lung cancer (NSCLC) is the most common form, is the second most prevalent cancer and the leading cause of cancer-related deaths. NSCLCs primarily comprise adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC). Advances in early detection and prevention have been limited by the lack of early-stage biomarkers and targets. A comprehensive molecular characterization of premalignant lesions and tumor-adjacent normal tissue can aid in better understanding NSCLC pathogenesis. However, these investigations are further challenged by limited tissue availability and low cellular fractions of detectable somatic mutations.

Therefore, there is a dearth of knowledge about the pathogenesis ...


Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr Jan 2019

Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr

Theses and Dissertations

PrediXcan is a recent software for the imputation of gene expression from genotype data alone. Using an overlapping set of transcriptome datasets from postmortem brain tissues of donors with alcohol use disorder and neurotypical controls, which were generated by two different platforms (e.g., Arraystar and Affymetrix), and an additional unrelated transcriptome dataset from lung tissue, we sought to evaluate PrediXcan’s ability to impute gene expression and identify differentially expressed genes. From the Arraystar platform, 1.3% of matched genes between the measured and imputed expression had a Pearson correlation ≥ 0.5. Our attempt to replicate this finding using ...


Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee Jan 2019

Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee

Graduate Theses and Dissertations

With every newly sequenced species we discover hundreds of novel protein coding genes. Many of these "orphan" genes have been experimentally proven to have dramatic functions in development, sexual dimorphism, pathogen resistance, and social traits like symbiosis. Whereas in the past, researchers viewed genes as the product of continuous variation acting on ancient material, we now know that novel genes may arise de novo from non-genic sequence. Thus evolutionary experimentation is not limited to tweaking existing genes or their regulatory patterns. Any orphan genes that arose in the distant past, should appear today as lineage-specific genes (or gene families). The ...


Exploring Strategies To Integrate Disparate Bioinformatics Datasets, Charbel Bader Fakhry Jan 2019

Exploring Strategies To Integrate Disparate Bioinformatics Datasets, Charbel Bader Fakhry

Walden Dissertations and Doctoral Studies

Distinct bioinformatics datasets make it challenging for bioinformatics specialists to locate the required datasets and unify their format for result extraction. The purpose of this single case study was to explore strategies to integrate distinct bioinformatics datasets. The technology acceptance model was used as the conceptual framework to understand the perceived usefulness and ease of use of integrating bioinformatics datasets. The population of this study included bioinformatics specialists of a research institution in Lebanon that has strategies to integrate distinct bioinformatics datasets. The data collection process included interviews with 6 bioinformatics specialists and reviewing 27 organizational documents relating to integrating ...


Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly Aug 2018

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation ...


Cultivating Ecosystems: Microbial Communities In Recirculating Aquaculture Systems, Ryan Bartelme Aug 2018

Cultivating Ecosystems: Microbial Communities In Recirculating Aquaculture Systems, Ryan Bartelme

Theses and Dissertations

Intensive cultivation of fish is necessary to meet future global market demands. Recirculating aquaculture systems (RAS) enable dense growth of fish, while occupying less space than traditional aquaculture farms. However, RAS often experience complications and high fish mortalities due to disease and improper waste management. In properly functioning systems, the microorganisms associated with fish (gut, scales) as well as those found in the system environment (water, component surfaces) remove waste and maintain fish health by discouraging growth of opportunistic pathogens. Previous RAS microbiome studies are small in scope, utilize coarse methods, and contain limited long-term spatial or temporal data. With ...


Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle Aug 2018

Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle

Electronic Theses and Dissertations

Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences ...


A Study Of Scalability And Cost-Effectiveness Of Large-Scale Scientific Applications Over Heterogeneous Computing Environment, Arghya K. Das Jun 2018

A Study Of Scalability And Cost-Effectiveness Of Large-Scale Scientific Applications Over Heterogeneous Computing Environment, Arghya K. Das

LSU Doctoral Dissertations

Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing and transfer. Consequently, scientists are in dire need of robust high performance computing (HPC) solutions that can scale with terabytes of data.

In this thesis, I address the challenges in three major aspects of scientific big data processing as follows: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures ...


A Systems Chemical Biology Approach For Dissecting Differential Molecular Mechanisms Of Action Of Clinical Kinase Inhibitors In Lung Cancer, Natalia Junqueira Sumi Jun 2018

A Systems Chemical Biology Approach For Dissecting Differential Molecular Mechanisms Of Action Of Clinical Kinase Inhibitors In Lung Cancer, Natalia Junqueira Sumi

Graduate Theses and Dissertations

Lung cancer is the second most common cancer type and is associated with high mortality rates. The survival rate for lung cancer patients has increased slowly in the last decade mainly as the result of the development of novel targeted and immune therapies. However, non-small cell lung cancer patients lacking known or actionable driver mutations and small cell lung cancer patients with recurrent disease are still in urgent need of new therapies. Drug repurposing is an efficient way to identify new therapies since it uses clinically relevant small molecule drugs. Determination of off-targets of small molecules is a novel approach ...


Genomewide Evaluation Of Cis-Elements And Cognate Transcription Factors In Nicotiana Attenuata Predicts 27 Unique Transcription Factor-Binding Site Pairs, Ashton Omdahl May 2018

Genomewide Evaluation Of Cis-Elements And Cognate Transcription Factors In Nicotiana Attenuata Predicts 27 Unique Transcription Factor-Binding Site Pairs, Ashton Omdahl

Undergraduate Honors Theses

Nicotiana attenuata has been widely studied for its ecological plant-herbivore relationships and response to environmental stress. The jasmonate signaling pathway regulated by jasmonate ZIM-domiain (JAZ) repressor proteins that modulate defense response levels has been of particular focus in this research. While our understanding of the genes associated with defense response and their regulation continues to expand, the transcriptional regulation of these genes is largely uncharacterized. In an effort to provide insight into these relationships, we performed genomewide analysis of transcript level data in order to predict transcription factors (TFs), their respective binding sites (TFBS), and the genes they regulate. We ...


A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen, James B. Herrick May 2018

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen, James B. Herrick

Senior Honors Projects, 2010-current

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also conduct ...


Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, Kevin Loftus May 2018

Evolution Of Bordetella Pertussis Genome May Play A Role In The Increased Rate Of Whooping Cough Cases In The United States, Kevin Loftus

Senior Honors Projects, 2010-current

Bordetella pertussis is the bacterium responsible for pertussis, a disease commonly referred to as whooping cough. Recently, pertussis has made a resurgence in the U.S. despite high-vaccination coverage. Possible causes of the increased number of pertussis cases include genetic evolution of B. pertussis, increased awareness of the disease, better laboratory diagnostics, and the switch from a whole-cellular (wP) vaccine to an acellular vaccine (aP) in the 1990s. Fortunately, just as B. pertussis is evolving, so is the arsenal of technologies used to understand and combat this pathogenic bacterium. Whole genome sequencing is one technology that helps researchers better understand ...


Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu Feb 2018

Identification Of Novel Genetic Variations For Amyotrophic Lateral Sclerosis (Als), Guang Xu

GSBS Dissertations and Theses

A list of genes have been identified to carry mutations causing familial ALS such as SOD1, TARDBP, C9orf72. But for sporadic ALS, which is 90% of all ALS cases, the underlying genetic variants are still largely unknown. There are multiple genome-wide association study (GWAS) for sporadic ALS, but usually a large number nominated SNP can hardly be replicated in larger cohort analysis. Also majority of GWAS SNP lie within noncoding region of genome, imposing a huge challenge to study their biological role in ALS pathology. With the rapid development of next-generation sequencing technology, we are able to sequence exome and ...


Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste Jan 2018

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome ...


Role Of Miniature Inverted-Repeat Transposable Elements In Genome Evolution Of Potamopyrgus Antipodarum, Emily Lyon Jan 2018

Role Of Miniature Inverted-Repeat Transposable Elements In Genome Evolution Of Potamopyrgus Antipodarum, Emily Lyon

Honors Theses at the University of Iowa

Transposable elements are genomic parasites that move within the genome and can cause gene and genome evolution. Transposable elements make up significant portions of many eukaryotic genomes but have been little studied in animals. This research study focuses on characterizing and identifying a type of transposable element, called miniature inverted-repeat transposable elements (MITEs) within the Potamopyrgus antipodarum genome. MITEs are particularly small transposable elements which can occur in thousands of copies within a genome. This research is conducted using the genome of P. antipodarum, a species of mud snail that is native to New Zealand. This genome is currently being ...


Scalable Feature Selection And Extraction With Applications In Kinase Polypharmacology, Derek Jones Jan 2018

Scalable Feature Selection And Extraction With Applications In Kinase Polypharmacology, Derek Jones

Theses and Dissertations--Computer Science

In order to reduce the time associated with and the costs of drug discovery, machine learning is being used to automate much of the work in this process. However the size and complex nature of molecular data makes the application of machine learning especially challenging. Much work must go into the process of engineering features that are then used to train machine learning models, costing considerable amounts of time and requiring the knowledge of domain experts to be most effective. The purpose of this work is to demonstrate data driven approaches to perform the feature selection and extraction steps in ...


The Use Of Bioinformatics And Current Genome Editing Tools In Investigating Zebrafish Rb1-Deficient Brain Tumors, Jeffrey Allen Haltom Jan 2018

The Use Of Bioinformatics And Current Genome Editing Tools In Investigating Zebrafish Rb1-Deficient Brain Tumors, Jeffrey Allen Haltom

Graduate Theses and Dissertations

This dissertation focuses on the analysis of RNA-Seq data in the context of cancer, ultimately leading to the identification of candidate genes to target for downstream analysis of their role in cell transformation and oncogenesis. Chapter 1 is a review of the current research being done with retinoblastoma deficient cancer, and the current bioinformatics solutions available for the analysis of high throughput sequence data, which will aid in molecular classification of tumor entities and in the identification of candidate genes to target for downstream analysis. Chapter 2 describes transcriptome analysis of a zebrafish RB1-primitive neuroectodermal tumor model as well as ...


An Interdisciplinary Approach To The Target Elucidation Of Novel Antibiotic 31g12, Larissa A. Walker Jan 2018

An Interdisciplinary Approach To The Target Elucidation Of Novel Antibiotic 31g12, Larissa A. Walker

Graduate Student Theses, Dissertations, & Professional Papers

Staphylococcus aureus is a Gram-positive bacterial pathogen responsible for nosocomial and community-acquired infections that can quickly acquire antibiotic resistance. We have identified a novel triazole antimicrobial 31G12 based on the natural product core of nonactin isolated from the fermentation of Streptomyces griseus, that is active against many Gram-positive bacteria as well as antibiotic resistant methicillin-resistant S. aureus and vancomycin-resistant Enterococcus. The synthesis and characterization indicate that 31G12 exists as a mixture of two rotamers at room temperature and displays bacteriostatic activity against S. aureus with moderate mammalian cell toxicity. We have currently identified potential protein targets of 31G12 in S ...


Focus: A Graph Approach For Data-Mining And Domain-Specific Assembly Of Next Generation Sequencing Data, Julia Sommer Dec 2017

Focus: A Graph Approach For Data-Mining And Domain-Specific Assembly Of Next Generation Sequencing Data, Julia Sommer

Theses & Dissertations

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the ...


Identification Of Prognostic Cancer Biomarkers Through The Application Of Rna-Seq Technologies And Bioinformatics, Nathan Wong Dec 2017

Identification Of Prognostic Cancer Biomarkers Through The Application Of Rna-Seq Technologies And Bioinformatics, Nathan Wong

Engineering and Applied Science Theses & Dissertations

MicroRNAs (miRNAs) are short single-stranded RNAs that function as the guide sequence of the post-transcriptional regulatory process known as the RNA-induced silencing complex (RISC), which targets mRNA sequences for degradation through complementary binding to the guide miRNA. Changes in miRNA expression have been reported as correlated with numerous biological processes, including embryonic development, cellular differentiation, and disease manifestation. In the latter case, dysregulation has been observed in response to infection by human papillomavirus (HPV), which has also been established as both oncogenic in cervical cancers and oropharyngeal cancers and favorable for overall patient survival after tumor formation. The identification of ...


Computational Identification Of Noncoding Driver Mutations Based On Impact On Rna Processing, Kevin Zhu Dec 2017

Computational Identification Of Noncoding Driver Mutations Based On Impact On Rna Processing, Kevin Zhu

UT GSBS Dissertations and Theses (Open Access)

Despite the prevalence of mutations in the noncoding regions of the DNA, their effects on cancer development remain largely uninvestigated. This is especially evident when compared to coding mutations, which have been relatively well-studied and, in certain cases, been identified as driver mutations for cancer. Recent studies, however, have identified noncoding mutations that frequently appear in certain types of cancer, which may be evidence that those mutations are important to cancer development. Nonetheless, the role of noncoding mutations in cancer remains unclear. A potential vector for understanding this mechanism is through observing the relation between noncoding mutations and functional RNA ...


Error Correction And De Novo Genome Assembly Of Dna Sequencing Data, Michael Z. Molnar Nov 2017

Error Correction And De Novo Genome Assembly Of Dna Sequencing Data, Michael Z. Molnar

Electronic Thesis and Dissertation Repository

The ability to obtain the genetic code of any species has caused a revolution in biological sciences. Current technologies are capable of sequencing short pieces of DNA with very high quality. These short pieces of DNA determint the sequence of bases in the genome of any species. This information is key in understanding many of the aspects of how life functions.

The accuracy of sequencing is extremely important since the differences between individuals of the same species are caused by very few changes. All sequencing technologies make errors, and before the data can be used for downstream applications it is ...


Biased Genetic Screen Identifies Novel Genes Involved In Antiviral Defense, Tianyun Long Nov 2017

Biased Genetic Screen Identifies Novel Genes Involved In Antiviral Defense, Tianyun Long

LSU Doctoral Dissertations

ABSTRACT

RNA interference (RNAi) mediates potent antiviral response across kingdoms. In Caenorhabditis elegans nematodes, antiviral RNAi requires a virus sensor that is conserved in mammals and is amplified by secondary small interfering RNAs that are produced in a Dicer-independent manner.

To better understand worm antiviral RNAi, I carried out a biased genetic screen, aiming to identify novel antiviral RNAi genes. To speed up the gene discovery process, the reporter worms used for this genetic screen were engineered to contain extra copies of 4 known antiviral RNAi genes. Therefore, genetic alleles derived from these 4 genes will be automatically rejected during ...


Bioinformatics And Next Generation Sequencing: Applications Of Arthropod Genomes, Zaichao Zhang Sep 2017

Bioinformatics And Next Generation Sequencing: Applications Of Arthropod Genomes, Zaichao Zhang

Electronic Thesis and Dissertation Repository

Over the past decade, the Next Generation Sequencing (NGS) technology has been broadly applied in many areas such as genomics, medical diagnosis, biotechnology, virology, biological systematics, forensic biology, and anthropology. Taken together, it has offered us brilliant insights into life sciences. Most of the work presented in this thesis describes NGS applications on genome assembly, genome annotation, and comparative genomics, using arthropods as case studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic signature variations and indicative of pest adaptations; (2) we sequenced, assembled and annotated five ...


Machine Learning Based Protein Sequence To (Un)Structure Mapping And Interaction Prediction, Sumaiya Iqbal Aug 2017

Machine Learning Based Protein Sequence To (Un)Structure Mapping And Interaction Prediction, Sumaiya Iqbal

University of New Orleans Theses and Dissertations

Proteins are the fundamental macromolecules within a cell that carry out most of the biological functions. The computational study of protein structure and its functions, using machine learning and data analytics, is elemental in advancing the life-science research due to the fast-growing biological data and the extensive complexities involved in their analyses towards discovering meaningful insights. Mapping of protein’s primary sequence is not only limited to its structure, we extend that to its disordered component known as Intrinsically Disordered Proteins or Regions in proteins (IDPs/IDRs), and hence the involved dynamics, which help us explain complex interaction within a ...


An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao Jul 2017

An Integrated Bioinformatic/Experimental Approach For Discovering Novel Type Ii Polyketides Encoded In Actinobacterial Genomes, Wubin Gao

Chemistry ETDs

Discovery of new natural products (NPs) is critical both for diseases treatment and crops protection. Numerous NP biosynthetic gene clusters (BGCs) in sequenced microbial genomes allow identification of new NPs through genome mining. Developing an integrated bioinformatic/experimental approach for discovering novel type II polyketides (PK-IIs) facilitates investigation of this family of NPs in an efficient, systematic way. Here, we developed an approach to analyze ketosynthase α/β (KSα/β) gene sequences to predict PK-II core structures, allowing us to target novel PK-II BGCs either from isolated genomic DNA or genomes from the NCBI databank, and to isolate novel PK-IIs ...


Repeaterator: A Tool For Visualizing Dna Repeat Motifs In Actinobacteriophage Genomes, Grant A. Rybnicky May 2017

Repeaterator: A Tool For Visualizing Dna Repeat Motifs In Actinobacteriophage Genomes, Grant A. Rybnicky

Senior Honors Projects, 2010-current

Horizontal gene transfer plays a large role in microbial genetic diversity. Bacteriophages can mediate diversity within their hosts through transduction, the uptake and dispersal of microbial host DNA between bacterial hosts. However, bacteriophages themselves experience horizontal gene transfer through mobile genetic elements and recombination. Unlike their hosts, bacteriophages cannot easily be mapped onto a phylogenic tree as they do not all possess a common trait like the 16s RNA gene. However, their genomes are typically small enough to be analyzed usingThere are tools to compare bacteriophages such as Gepard and Phamerator that compare nucleotide identity across bacteriophage entire genomes. However ...


The Microbial Ecology Of Bacterial Lignocellulosic Degradation In The Ocean, Hannah Laing Yee Woo May 2017

The Microbial Ecology Of Bacterial Lignocellulosic Degradation In The Ocean, Hannah Laing Yee Woo

Doctoral Dissertations

The overarching theme of my dissertation is to study the role of bacteria in lignocellulose degradation. In recent years, more research has investigated the biodegradability of lignocellulose for biofuel production. The components of the lignocellulosic plant cell wall are considered intrinsically recalcitrant due to their structure. However, we hypothesize that these components are not intrinsically recalcitrant but their biodegradation is contingent on the environmental conditions, particularly the bacterial diversity. We believe bacteria will become especially important in lignocellulose degradation in conditions that are unfavorable for white-rot fungi. Therefore, we investigated the potential for lignin degradation by bacteria in the ocean ...