Life Sciences Commons^™

Multivariate Models And Algorithms For Systems Biology, Lipi Rani Acharya

University of New Orleans Theses and Dissertations

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete …

Habitat Characteristics Affecting Site Occupation In Wintering Henslow’S Sparrows At Mississippi Sandhill Crane National Wildlife Refuge, Mary E. Nicholson

University of New Orleans Theses and Dissertations

Henslow’s sparrow (Ammodramus henslowii) winters in recently burned sites in pine savannas of the Southeastern United States. Previous studies have suggested that factors such as seed abundance and litter depth are important to wintering Henslow’s sparrows. My study asked how habitat variables including vegetation structure, seed abundance, and arthropod abundance predict Henslow’s sparrow site occupancy at Mississippi Sandhill Crane National Wildlife Refuge. In this study, Henslow’s sparrow more often occupied sites burned one growing season earlier than sites burned two growing seasons earlier, and did not occupy sites burned three or more growing seasons earlier. Data indicated that mass …

Evolutionary Relationships Among Duiker Antelope (Bovidae: Cephalophinae), Anne Johnston

University of New Orleans Theses and Dissertations

Duikers are a species rich subfamily of threatened African antelope whose recent origin poses a challenge to the molecular identification of taxa and estimation of their phylogeny. I test the ability of DNA barcodes to identify all taxa within this group. I then use mitochondrial and nuclear genes to estimate a multi-locus species tree and to date divergence times. DNA barcodes are unable to distinguish many sister taxa, calling into question the utility of barcodes for the regulation of duiker trade or in identification of field-collected feces. The multi-locus phylogeny provides support for the relationships among major duiker lineages and …

Bycatch Of The Lake Pontchartrain Basin Inshore Shrimp Fishery And Its Effect On Two Sea Catfish Species: The Gafftopsail Catfish (Bagre Marinus) And The Hardhead Catfish (Ariopsis Felis), Scott P. Eustis

University of New Orleans Theses and Dissertations

In Lake Pontchartrain Basin, commercial fishing in estuarine habitats impacts many non-target species collected as bycatch. I investigated the bycatch assemblages collected by commercial vessels and compared these to assemblages collected by typical fishery-independent methods. I compared assemblages using analysis of similarity (ANOSIM) and determined important species by weight and abundance using similarity percentages analyses (SIMPER). I also examined differences in size-class distributions by gear type using density kernel plots and Mann-Whitney U tests. The two gear types collected significantly different assemblages (ANOSIM R = 0.522, p = 0.001) and gear type explained more composition differences than other factors such …

Factors That Affect Harem Stability In A Feral Horse (Equus Caballus) Population On Shackleford Banks Island, Nc, Jessa Madosky

University of New Orleans Theses and Dissertations

Mammal species often live in social groups, but the factors that promote group cohesion can be difficult to analyze due to the prevalence of strong group affiliations. Feral horses maintain stable harems of one or two males and several females, and harem stability is strongly related to individual fitness. Anecdotal evidence and an early study in the non-breeding season suggest that management of the Shackleford Banks island horses with immunocontraception reduces harem stability in the population, providing an opportunity to study the factors that influence harem stability. I investigated the effects of the immunocontraceptive PZP on harem stability during the …

Computational Pipeline For Human Transcriptome Quantification Using Rna-Seq Data, Guorong Xu

University of New Orleans Theses and Dissertations

The main theme of this thesis research is concerned with developing a computational pipeline for processing Next-generation RNA sequencing (RNA-seq) data. RNA-seq experiments generate tens of millions of short reads for each DNA/RNA sample. The alignment of a large volume of short reads to a reference genome is a key step in NGS data analysis. Although storing alignment information in the Sequence Alignment/Map (SAM) or Binary SAM (BAM) format is now standard, biomedical researchers still have difficulty accessing useful information. In order to assist biomedical researchers to conveniently access essential information from NGS data files in SAM/BAM format, we have …

Identification And Characterization Of Enzymes Involved In The Biosynthesis Of Different Phycobiliproteins In Cyanobacteria, Avijit Biswas

University of New Orleans Theses and Dissertations

A multi-plasmid, co-expression system was used to recreate the biosynthetic pathway for phycobiliproteins from the cyanobacterium Synechococcus sp. PCC 7002 in E. coli. This system efficiently produced chromophorylated allophycocyanin (ApcA/ApcB), -phycocyanin, and -phycocyanin. This system was used to demonstrate that CpcS-I and CpcU proteins are both required attaching PCB to allophycocyanin subunits ApcD (AP-B) and ApcF (18). The N-terminal, AP-like domain of ApcE (LCM99) was produced in soluble form and shown to have intrinsic bilin lyase activity. In addition, this system was used to chromophorylated CpcA from Synechococystis sp. PCC 6803 with a non-cognate bilin; PEB with the aid …

Metabolism And Cryo-Sensitivity Of Domestic Cat (Felis Catus) And Cheetah (Acinonyx Jubatus) Spermatozoa, Kimberly Terrell

University of New Orleans Theses and Dissertations

Teratospermia (ejaculation of ≥ 60% structurally abnormal spermatozoa) is prevalent among felids facing extinction risk, including the cheetah. This trait also occurs in certain domestic cat populations, providing a valuable research model. Multiple components of sperm function are disrupted in teratospermic cats, and even structurally normal spermatozoa from these ejaculates may be functionally compromised. Teratospermic ejaculates are highly sensitive to damage during cryopreservation, limiting the success of genome resource banking programs for species conservation. Although both teratospermia and cryopreservation are linked to disruptions in multiple energy-dependent sperm processes, the metabolism of these cells has not been investigated. This project explored …

Nuclear Scaffold Attachment Sites Within Encode Regions Associate With Actively Transcribed Genes, Christopher M. Taylor, Mignon A. Keaton, Ryan M. Layer, Anindya Dutta

Computer Science Faculty Publications

The human genome must be packaged and organized in a functional manner
for the regulation of DNA replication and transcription. The nuclear
scaffold/matrix, consisting of structural and functional nuclear
proteins, remains after extraction of nuclei and anchors loops of DNA.
In the search for cis-elements functioning as chromatin domain
boundaries, we identified 453 nuclear scaffold attachment sites
purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across
30 Mb of the human genome studied by the ENCODE pilot project. The
scaffold attachment sites mapped predominately near expressed genes and
localized near transcription start sites and the ends of genes but not
to …

Population Proteomics: Quantitative Variation Within And Among Populations In Cardiac Protein Expression, Bernard Rees

Biological Sciences Faculty Publications

Population analysis of gene expression is typically achieved by quantifying levels of mRNA; however, gene expression is also a function of protein translation and turnover. Therefore, a complete understanding of population variation in gene expression requires quantitative knowledge of protein expression within and among natural populations. We used two dimensional fluorescence difference gel electrophoresis (2D-DIGE) to quantitatively compare expression of heart ventricle proteins among 18 individuals in three populations of the teleost fish Fundulus. Among populations, expressions between orthologous proteins and mRNAs were generally positively correlated. Additionally, similar to the pattern of cardiac mRNA expression for the same populations, we …

Oxygen Limitation And Tissue Metabolic Potential Of The African Fish Barbus Neumayeri: Roles Of Native Habitat And Acclimatization, Bernard Rees

Biological Sciences Faculty Publications

Oxygen availability in aquatic habitats is a major environmental factor influencing the ecology, behaviour, and physiology of fishes. This study evaluates the contribution of source population and hypoxic acclimatization of the African fish, Barbus neumayeri, in determining growth and tissue metabolic enzyme activities. Individuals were collected from two sites differing dramatically in concentration of dissolved oxygen (DO), Rwembaita Swamp (annual average DO 1.35 mgO₂ L^-1) and Inlet Stream West (annual average DO 5.58 mgO₂ L^-1) in Kibale National Park, Uganda, and reciprocally transplanted using a cage experiment in the field, allowing us to …

Biosynthesis Of Cyanobacterial Phycobiliproteins In Escherichia Coli: Chromophorylation Efficiency And Specificity Of All Bilin Lyases From Synechococcus Sp. Strain Pcc 7002, Wendy M. Schluchter

Biological Sciences Faculty Publications

No abstract provided.

Effects Of Modified Phycobilin Biosynthesis In The Cyanobacterium Synechococcus Sp. Strain Pcc 7002, Wendy M. Schluchter

Biological Sciences Faculty Publications

No abstract provided.

Attachment Of Non-Cognate Chromophores To Cpca Of Synechocystis Sp. Strain Pcc 6803 Expressed In E. Coli, Wendy M. Schluchter

Biological Sciences Faculty Publications

No abstract provided.

Geographic Variation In The Effects Of Heat Exposure On Maximum Sprint Speed And Hsp70 Abundance In Populations Of The Western Fence Lizard, Scelopolus Occidentalis, D M. Mcmillan, D J. Irschick, Bernard B. Rees

Biological Sciences Faculty Publications

We examined whether western fence lizards Sceloporus occidentalis

occurring in thermally divergent environments display differential

responses to high temperature in locomotor performance

and heat-shock protein (Hsp) expression. We measured

maximum sprint speed in S. occidentalis from four populations

at paired latitudes and elevations before and after exposure to

an experimental heat treatment and then quantified hind-limb

muscle Hsp70 expression. Lizards collected from northern or

high-elevation collection sites suffered a greater reduction in

sprint speed after heat exposure than lizards collected from

southern or low-elevation sites. In addition, lizards from northern

collection sites also exhibited an increase in Hsp70 expression

after …

Oxygen Limitation And Tissue Metabolic Potential Of The African Fish Barbus Neumayeri: Roles Of Native Habitat And Acclimatization, Martinez M. L, Raynard E. L, Bernard B. Rees, Chapman L. J

Biological Sciences Faculty Publications

Background: Oxygen availability in aquatic habitats is a major environmental factor influencing the ecology, behaviour, and physiology of fishes. This study evaluates the contribution of source population and hypoxic acclimatization of the African fish, Barbus neumayeri, in determining growth and tissue metabolic enzyme activities. Individuals were collected from two sites differing dramatically in concentration of dissolved oxygen (DO), Rwembaita Swamp (annual average DO 1.35 mgO2 L-1) and Inlet Stream West (annual average DO 5.58 mgO2 L-1) in Kibale National Park, Uganda, and reciprocally transplanted using a cage experiment in the field, allowing us to maintain individuals under natural conditions of …