Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Big data (2)
- Bioinformatics (2)
- Extremophyte (2)
- RNA-seq (2)
- Salt stress (2)
-
- Systems biology (2)
- 3C (1)
- 4C (1)
- Abiotic stress (1)
- Ahr (1)
- Alternative splicing (1)
- Alu (1)
- Anabaena (1)
- Antiviral defense (1)
- ApbC (1)
- BEAF (1)
- Behavior (1)
- Blockchain (1)
- Brucella (1)
- Brucellosis (1)
- C.elegans (1)
- Carbon fixation (1)
- Cell Wall (1)
- Cichlid (1)
- Comparative genomics (1)
- DIET (1)
- DNA (1)
- Differential gene expression (1)
- Disorderdness of transcripts (1)
- Distributed systems (1)
Articles 1 - 19 of 19
Full-Text Articles in Life Sciences
Differences In Plant Hormone Responses Between Arabidopsis Thaliana And Schrenkiella Parvula Facing Lithium Toxicities, Jifeng Li
LSU Doctoral Dissertations
Investigating stress responses in plants is central to plant development studies and crop research. Identifying mechanisms of plant abiotic stress tolerance and adaptation will be keys to relieve the conflict between an increasing global population and declining agronomic land. Studies on extremophytes and their genetic responses to environmental stress are a way to help understand how and why these extremophile plants can develop well under extreme environments including high salinity and heavy metal toxicity. The studies herein first focus on comparative responses at the genetic level to lithium toxicity between Arabidopsis thaliana and Schrenkiella parvula. Based on elemental quantification …
The Impacts Of Immune Challenges On Fish Behavior And Physiology, Teisha King
The Impacts Of Immune Challenges On Fish Behavior And Physiology, Teisha King
LSU Doctoral Dissertations
For species living in dominance hierarchies, social rank dictates access to resources and often contributes to reproductive success. To ensure survival, individuals constantly evaluate trade- offs between crucial biological systems, like the reproductive and immune systems, depending on their social rank and physiological state. Little is known about how social species balance interactions between immune system function, fluctuations in social status and reproductive fitness, and the performance of behaviors necessary for maintaining social status when sick, particularly in fishes, the largest and most diverse group of vertebrates. My dissertation research uses a whole animal approach to examine how physiological profiles …
Spatiotemporal Transcriptome Diversity And Responses To Salinity Tolerance In The Extremophyte Schrenkiella Parvula, Chathura Wijesinghege
Spatiotemporal Transcriptome Diversity And Responses To Salinity Tolerance In The Extremophyte Schrenkiella Parvula, Chathura Wijesinghege
LSU Doctoral Dissertations
Schrenkiella parvula is an extremophyte model related to the most widely studied plant model, Arabidopsis thaliana and Brassica crops in the mustard family (Brassicaceae). It can thrive in highly saline environments where the soil is enriched in Na+, K+, Li+, borates, and chlorides. Understanding how this extremophyte can survive high salinity with genomic adaptations can provide insight into developing stress resilient crops in the future. Gene expression of S. parvula in response to salt has been investigated using shoot and root tissue from mature vegetative-phase plants. However, prior studies have not examined the transcript …
Comparative Genomics And Virulence Studies Of Streptomyces Soil Rot And Scab Pathogen Species, Natasha Soares
Comparative Genomics And Virulence Studies Of Streptomyces Soil Rot And Scab Pathogen Species, Natasha Soares
LSU Doctoral Dissertations
Comparative genomic analyses were performed to gain insights into the organization and content of the genome of Streptomyces ipomoeae, the soil rot pathogen that infects sweetpotatoes. Unlike Streptomyces scab pathogens, the thaxtomin phytotoxin gene cluster (txt) in S. ipomoeae does not appear to reside within a genomic island and has diverged from its scab pathogen counterparts. Increased usage of the rare TTA codon, particularly for the txt cluster, suggests greater translational control by the bldA tRNA in S. ipomoeae. Orthologous gene searches and secondary metabolite profiling yielded ortholog groups and metabolite gene clusters that were exclusive …
The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle
The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle
LSU Doctoral Dissertations
Brucella spp. are a bacterium that cause brucellosis, a zoonotic disease, which is commonly seen in cattle, sheep, goats, swine, and canines. Brucellosis is a problem worldwide, although it is eradicated in some countries (Garin-Bastuji et al. 1998). The reason for designing recombinant DNA (rDNA) vaccines opposed to utilizing the live-attenuated vaccines on the market is that they cannot be given to pregnant animals without potentially causing abortion, while an rDNA vaccine should be safe for pregnant animals since it does not contain viable bacteria. Also, there are no serological tests that can accurately distinguish between an animal vaccinated …
Investigation Of Arabidopsis Extremophyte Relatives, Schrenkiella Parvula And Eutrema Salsugineum Reveals Different Roads Leading To Salt Stress Tolerance, Kieu-Nga Thi Tran
Investigation Of Arabidopsis Extremophyte Relatives, Schrenkiella Parvula And Eutrema Salsugineum Reveals Different Roads Leading To Salt Stress Tolerance, Kieu-Nga Thi Tran
LSU Doctoral Dissertations
How plants adapt to salt stress has been a central question in plant biology for decades. Yet we have not been able to fully understand the molecular networks and genetic mechanisms underlying this complex trait. Most of the genetic work on salinity stress has focused on understanding salt stress responses in the leading, yet a salt-sensitive model Arabidopsis thaliana. With the recent availability of genomes for wild-relatives of A. thaliana, we can now investigate how naturally salt adapted plants may have evolved modified or novel molecular networks to adapt to salt stress. Therefore, my research utilizes a comparative …
Understanding Potassium Toxicity Stress Responses Of The Extremophyte Schrenkiella Parvula Using Systems Biology Approaches, Pramod Pantha
Understanding Potassium Toxicity Stress Responses Of The Extremophyte Schrenkiella Parvula Using Systems Biology Approaches, Pramod Pantha
LSU Doctoral Dissertations
Schrenkiella parvula is an extremophyte model closely related to Arabidopsis thaliana and Brassica crops. Its natural habitat includes shores of saline lakes in the Irano-Turanian region. It has adapted to grow in soils rich in multiple salts including Na+ and K+. I have investigated the genetic basis for high K+ tolerance in plants using S. parvula as a stress tolerant model compared to the premier plant model, Arabidopsis thaliana which is highly sensitive to salt stresses using physiological, ionomic, transcriptomic, and metabolomic approaches. Under high K+ stress, root system architecture changes significantly compared to control …
Genomic Studies Of Beaf-32 In Drosophila, John Keller Mckowen Iii
Genomic Studies Of Beaf-32 In Drosophila, John Keller Mckowen Iii
LSU Doctoral Dissertations
Compared to humans, the model organism Drosophila melanogaster is particularly gene dense and encodes several insulator binding proteins (IBP) to aid in its genome organization. Our focus of research is a particular IBP, Boundary Element-Associated Factor of 32kD (BEAF). BEAF primarily binds near the promoters of constitutively active housekeeping genes. It is thought to help maintain the active state of these genes by preventing the spread of repressive chromatin. Additionally, the enhancer blocking activity of BEAF is thought to prevent aberrant activation or silencing of genes. BEAF appears to be ubiquitously expressed among cells and tissues, albeit at varying levels. …
Molecular Mechanisms Of Boron Toxicity Tolerance In Plants, Guannan Wang
Molecular Mechanisms Of Boron Toxicity Tolerance In Plants, Guannan Wang
LSU Doctoral Dissertations
Boron toxicity is a worldwide agricultural problem that limits crop productivity and quality. However, our understanding on the genetic responses and adaption mechanisms to boron toxicity in plants is very limited. To address this gap in our knowledge, I compared boron stress-sensitive model, Arabidopsis thaliana and its stress-adapted relative Schrenkiella parvula to study how plants respond and adapt to excess boron at physiological, genomic, transcriptomic, and metabolic levels.
The overall project goal involved integration of multi-omics datasets to develop genome to phenome interpretations. To achieve this, I developed a python package, GOMCL, to facilitate the extraction of biologically meaningful information …
Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount
Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount
LSU Doctoral Dissertations
Identifying the source and structure of variation in nature is crucial to understanding fundamental aspects of evolution. Despite a recent plethora of genetic and morphological data, many interesting questions about the relationships between different groups remain unresolved. My dissertation evaluates three approaches for identifying and quantifying the variation within phylogenetic datasets. Characterizing variation within datasets and across analytical methods gives insight into biologically interesting characters, unusual evolutionary processes, and areas for model improvement.
Network-based community detection approaches offer a powerful tool to describe variation in phylogenetic signal across the genome (i.e., gene tree variation). In Chapter 2, I investigate the …
The Effects Of Radical Containing Combustion Derived Particulate Matter In Adult Mouse Respiratory System, Jeffrey Harding
The Effects Of Radical Containing Combustion Derived Particulate Matter In Adult Mouse Respiratory System, Jeffrey Harding
LSU Doctoral Dissertations
Epidemiological data associates high levels of combustion-derived particulate matter (PM) with deleterious respiratory outcomes, but the mechanism underlying those outcomes remains elusive. It has been acknowledged by the World Health Organization that PM exposure contributes to more than 4.2 million all-cause mortalities worldwide each year. Current literature demonstrates that PM exacerbates respiratory diseases, impairs lung function, results in chronic respiratory illnesses, and is associated with increased mortality. The proposed mechanisms revolve around oxidative stress and inflammation promoting pulmonary physiological remodeling. Our data demonstrate that environmentally persistent free radicals (EPFRs) stabilized on the surface of PM are capable of inducing oxidative …
Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro
Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro
LSU Doctoral Dissertations
Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO2 into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …
Iron-Sulfur Cluster Biosynthesis In Methanogens, Cuiping Zhao
Iron-Sulfur Cluster Biosynthesis In Methanogens, Cuiping Zhao
LSU Doctoral Dissertations
Methanogens live in a syntrophic consortium with bacteria, taking advantage of the metabolic abilities of their syntrophic partners to overcome energetic barriers and break down compounds that they cannot digest by themselves. Interspecies electron transfer, which is a major type of microbial communication in syntrophic processes, improves methanogenesis and anaerobic oxidization of methane (AOM) processes involved in syntrophic consortia. These processes have a significant impact on the global carbon cycle. Most of the essential enzymes involved in methanogenesis are iron-sulfur proteins. Iron-sulfur clusters are one of the oldest and most versatile cofactors present in all domains of life. To date, …
High-Performance Computing Frameworks For Large-Scale Genome Assembly, Sayan Goswami
High-Performance Computing Frameworks For Large-Scale Genome Assembly, Sayan Goswami
LSU Doctoral Dissertations
Genome sequencing technology has witnessed tremendous progress in terms of throughput and cost per base pair, resulting in an explosion in the size of data. Typical de Bruijn graph-based assembly tools demand a lot of processing power and memory and cannot assemble big datasets unless running on a scaled-up server with terabytes of RAMs or scaled-out cluster with several dozens of nodes. In the first part of this work, we present a distributed next-generation sequence (NGS) assembler called Lazer, that achieves both scalability and memory efficiency by using partitioned de Bruijn graphs. By enhancing the memory-to-disk swapping and reducing the …
Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii
Computational Analysis Of Papionini Evolution Using Alu Insertions, Vallmer Edward Jordan Ii
LSU Doctoral Dissertations
Alu elements are primate specific retrotransposons that have remained active throughout the course of primate evolution. As a result of this sustained mobilization. Alu elements are present in greater copy number in primate genomes than any other transposable element. An average of over one million Alu elements has been identified in every sequenced haplorrhine genome to date. These characteristics qualify Alu elements as ideal characters for studying evolutionary relationship among primates.
The increasing availability of whole genome sequencing data presents novel challenges and opportunities for comparative genomic analyses. Genomic data is now publicly available for most primate species. Such an …
A Study Of Scalability And Cost-Effectiveness Of Large-Scale Scientific Applications Over Heterogeneous Computing Environment, Arghya K. Das
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 …
Analysis Of Chromatin Interactions Of Beaf-Associated Promoters Using 4c, Shraddha Shrestha
Analysis Of Chromatin Interactions Of Beaf-Associated Promoters Using 4c, Shraddha Shrestha
LSU Doctoral Dissertations
A high degree of chromosome compaction is needed to fit nearly 2 meters of DNA inside a human nucleus of around 10 µm diameter. Correct chromatin folding is crucial to facilitate important nuclear functions such as transcription, DNA replication and DNA repair. Nuclei contain a variety of proteins, many of which help regulate chromatin structure and function. The mechanisms by which these proteins work are diverse and complicated. Here, we study the chromatin interactions of Boundary Element Associated Factor (BEAF) associated sites to gain insight into eukaryotic genome organization. We used circular chromosome conformation capture (4C) technology to detect genome-wide …
The Determinants Of Nucleosome Patterns And The Impact Of Phosphate Starvation On Nucleosome Patterns And Gene Expression In Rice, Qi Zhang
LSU Doctoral Dissertations
In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and …
Biased Genetic Screen Identifies Novel Genes Involved In Antiviral Defense, Tianyun Long
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 …