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

Life Sciences Commons

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

Articles 1 - 7 of 7

Full-Text Articles in Life Sciences

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 ...


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 ...


Diversity And Distribution Of Diatom Endosymbionts In Amphistegina Spp. (Foraminifera) Based On Molecular And Morphological Techniques, Kwasi H. Barnes Jun 2016

Diversity And Distribution Of Diatom Endosymbionts In Amphistegina Spp. (Foraminifera) Based On Molecular And Morphological Techniques, Kwasi H. Barnes

Graduate Theses and Dissertations

Diatoms associated with foraminifers of the genus Amphistegina were assessed using a combination of morphological and molecular techniques. These included: 1) microscopic identification of diatoms cultured from the host, 2) sequencing of portions of the small subunit of the ribosomal RNA gene (18S) and the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase [i.e., RubisCO] gene (rbcL) from DNA extracted directly from the Amphistegina hosts and also from diatoms cultured from these hosts, and 3) denaturing gradient gel electrophoresis (DGGE) profiles of rbcL and internal transcribed spacer 1 (ITS1) PCR amplicons from DNA extracted directly from hosts and from ...


Scalable And Reproducible Genome Analysis In The Age Of Next-Generation Genome Sequencing, Daniel Scott Standage Jan 2016

Scalable And Reproducible Genome Analysis In The Age Of Next-Generation Genome Sequencing, Daniel Scott Standage

Graduate Theses and Dissertations

Recent advances in DNA sequencing technology and a proliferation of new algorithms for assembling, annotating, and analyzing genomes have made genome-scale sequencing more accessible than ever. As a result, the last several years have seen a dramatic increase in the number of published draft genomes. Many important research problems revolve around interpretation of these draft genomes: What are the contents of a genome? How many genes are there? Are there any conspicuous losses of genes of interest? Is the genome compact, with genes clustered very tightly, or are genes separated by large intergenic spaces? Are intergenic spaces distributed evenly throughout ...


Studies On The Causes And Consequences Of Sex Determination In Turtles, Srihari Radhakrishnan Jan 2015

Studies On The Causes And Consequences Of Sex Determination In Turtles, Srihari Radhakrishnan

Graduate Theses and Dissertations

Sex determination is a crucial decision of commitment of an individual's sexual fate into either a male or a female. In vertebrates, sex determination modes span a spectrum of extremes: genotypic sex determination (GSD), where sex is genetically determined, often due to the presence of sex chromosomes and temperature-dependent sex determination (TSD), where environmental temperature during a critical period of embryonic development establishes sexual fate. The evolution of this diversity in sex determining mechanisms is one that has defied scientific explanation for decades. An ideal system to demystify this conundrum includes turtle lineages, where both TSD and GSD co-occur ...


From Sequencing To Analysis: Building A Comparative Genomics Tool For The Biologist End-User, Paul Mangiamele Jan 2014

From Sequencing To Analysis: Building A Comparative Genomics Tool For The Biologist End-User, Paul Mangiamele

Graduate Theses and Dissertations

Advancements in sequencing technology have driven an ever-growing body of genomic sequence data to new heights. Since publication of APEC O78 sequencing paper (Chapter 2) one year ago, sequencing technology has grown in leaps and bounds and has plummeted in price. The affordability of these systems and availability of sequencing services have made these technologies accessible to smaller laboratories, focusing on individual biological organisms and systems, such as our own lab with APEC. This `perfect storm' has made it feasible to sequence several of the APEC isolates in our collection. Although data generation is only the beginning, two substantial NGS ...


Genomic Landscape Of The Soybean (Glycine Max) Genome, Jenna Lynn Woody Jan 2012

Genomic Landscape Of The Soybean (Glycine Max) Genome, Jenna Lynn Woody

Graduate Theses and Dissertations

The genomic landscape of plants, while slowly being charted, is still composed primarily of unknown territory. The landscape can be related to chromatin domains, transposable element neighborhoods, gene organization, epigenetic modifications of the genome and more. Certain patterns of expression, tissue specific versus constitutive, or high expression versus low expression, are often associated with physical attributes of the gene and genome. We have known for a while that expression is not controlled solely by the promoter but is modulated by transcription factors, small RNAs, parachromatin, as well as by all of the components that make up epigenetics (Jorgensen, 2011). Characterizing ...