Molecular Biology and Biochemistry - Theses, Dissertations, and other Required Graduate Degree Essays

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Sex determination in the genus Salmo

Author: 
Date created: 
2010-12-09
Abstract: 

Salmonids share a strictly genetic mechanism for sex determination with males being the heterogametic sex. FISH analysis using BACs containing sexlinked microsatellite markers in Atlantic salmon identified chromosome 2 as its sex chromosome. The same sized chromosome 2 pairs in both sexes suggesting that the sex chromosome in Atlantic salmon is not highly differentiated. Combining information from sex determination pathways in different phyla, I created a list of 14 candidate sex determining genes. Candidate gene mapping identified all gene locations. However, their positions rule them out as the master regulatory gene. Comparative genomic analysis shows that the closest related species brown trout sex linkage group (LG) is syntenic to Atlantic salmon autosomal LG 8. FISH analysis revealed the brown trout sex chromosomes as a pair of small submetacentric chromosomes. Although they are closely related, I predict that Atlantic salmon and brown trout are likely to have different sex determining genes.

Document type: 
Thesis
File(s): 
Senior supervisor: 
William S. Davidson
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Light-controlled regulation of eukaryotic gene expression using a diffusible effector

Author: 
Date created: 
2010-07-28
Abstract: 

This project focuses on the design of a small synthetic, trans-acting noncoding RNA to directly regulate gene expression by light irradiation in a eukaryotic system at the mRNA level. This trans-acting noncoding RNA is designed to incorporate an in vitro-selected small ligand-binding domain, called an aptamer domain. This aptamer domain selectively binds to one but not the other of the two isomers of a dihydropyrene photo-switch compound. Such an aptamer sequence allowed us to design an allosteric riboregulator, a RNA molecule with a regulatory function whose mode of activity depends on its photo-switch ligand binding to the aptamer domain, which in turn is influenced by light irradiation at an appropriate wavelength. This light-controlled riboregulator is referred to as an antiswitch. This antiswitch is specifically designed to control the expression of Green Fluorescent protein (GFP) in vivo in Saccharomyces cerevisiae as a model organism.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. Dipankar Sen
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Characterization of nematode DAF-19 and human RFX6 transcription factors

Author: 
Date created: 
2010-07-16
Abstract: 

Regulatory factor X (RFX) transcription factors play an important role in regulating expression of ciliary genes associated with ciliopathies. However, the annotation of RFX genes may be incomplete and their function is not well understood. Here I describe two novel tissue-specific RFX genes in humans: RFX6 and RFX7. To study RFX genes in the model organism Caenorhabditis elegans, I undertook examining the expression of all four known isoforms of daf-19, the only RFX gene in C. elegans, by using Mos1 mediated Single Copy transgene Insertion (MosSCI) method. I discovered that both daf-19c and daf-19d isoforms are expressed in ciliated neurons and that their promoters are modular. In particular, daf-19c is expressed in all ciliated neurons while daf-19d in all but labial neurons. My analysis helped select suitable promoters for driving expression of RFX6 in ciliated neurons of C. elegans for testing its function in cilia.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. Jack Chen
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Determining the correlation between structure and function for the Drosophila insulin receptor substrate chico

Date created: 
2010-08-09
Abstract: 

The Drosophila gene chico codes for the homolog of the vertebrate insulin receptor substrate (IRS) family of proteins. CHICO is phosphorylated by an activated insulin receptor and signals to several downstream signalling pathways through various predicted binding domains. To investigate how the structure of CHICO contributes to its function, an ethyl methanesulfonate (EMS) screen was performed to generate novel chico alleles. One novel allele, chico13063, was recovered out of 22,072 lines screened. This allele displayed numerous chico phenotypes including: reduced body size, weight, wing size, and developmental time delay. These phenotypes were stronger in the chico13063 allele than the null allele, chico1 and the deficiency, Df(2L)flp 147E. The chico13063 coding region was sequenced and no genetic lesions were found, suggesting the mutation is in the regulatory region. Future work would be to sequence putative regulatory regions of chico and examine the expression levels of CHICO in the chico13063 mutant.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Esther Verheyen
Eve Stringham
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Molecular identification and phenotypic characterization of let-65 (mars-1) in Caenorhabditis elegans.

Date created: 
2010-07-26
Abstract: 

let-65 was first identified in a screen for lethal mutations in C. elegans’unc-22 region. I have demonstrated the molecular identity of let-65 to be F58B3.5 (mars-1), which encodes a methionyl tRNA synthetase (MARS-1). To develop a deeper insight into MARS-1 activity, I experimentally confirmed, from its sub-cellular localization, that it is a cytoplasmic enzyme. I also attempted to determine the sub-cellular localization of every known C. elegans amino-acyl tRNA synthetase using computational methods and, in collaboration with WormBase, renamed the genes appropriately. In addition, I studied let-65 transcription regulation by analyzing its 5’ promoter containing region. Haplo-insufficiency phenotypes manifest as a consequence of reduction in copy number of genes that encode proteins involved in translation. I have investigated this in C. elegans. I used two alleles of each of let-65 (mars-1) and let-336 (rps-27) and examined putative haplo-insufficiency phenotypes for both these genes.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. David L. Baillie
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

Identification, evolution and expression of three olfactory gene families in Atlantic salmon (Salmo salar)

Date created: 
2011-11-30
Abstract: 

It has been hypothesized that salmonids use olfactory cues to return to their natal rivers and streams. However, the key components of the molecular pathway involved in imprinting and homing are still unknown. If odorants are involved in salmon homing migration then olfactory receptors should play a critical role in the dissipation of information from the environment to the fish. To understand the molecular basis for imprinting and homing in Atlantic salmon (Salmo salar), it is important to identify and characterize the olfactory receptors in the Atlantic salmon genome. Aquatic chemical cues are received through the salmon nares and into the nasal cavity that contains a single olfactory organ, olfactory rosette. The olfactory rosette contains sensory neurons, which are thought to express only one olfactory receptor. In this study, three major superfamilies of fish olfactory receptors (MOR, ora and OlfC) were examined. To identify the olfactory genes in Atlantic salmon several genomic and bioinformatic techniques were used. First, an Atlantic salmon bacterial artificial chromosome (BAC) library was screened with probes designed from previously identified fish olfactory receptor sequences. Then a selected number of hybridization positive BACs containing olfactory receptors were shotgun cloned and sequenced. From these BAC sequences, two ora genes and 55 OlfC genes were identified in Atlantic salmon. The second technique used to identify olfactory receptors in Atlantic salmon was a bioinformatic approach that involved screening a 3-fold Atlantic salmon genome sequence for olfactory receptors. Using this approach, 24 MOR and the remaining five ora genes were identified, as well as another 24 partial genes or pseudogenes. As a first step to understand how olfactory receptors are involved in imprinting and homing, a suite of olfactory receptors were selected to examine the expression profiles of these genes across different life stages and life histories of wild Atlantic salmon from Newfoundland, Canada. Seven differentially expressed OlfC genes were identified in juvenile anadromous salmon compared to returning adult salmon. From this research, I hypothesize that OlfC genes may play an important role in the imprinting of home stream water olfactory cues in anadromous Atlantic salmon.

Document type: 
Thesis
File(s): 
Senior supervisor: 
William Davidson
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) Ph.D.

Generation and Analysis of Suppressors of Caenorhabditis Elegans Unc-2 Alleles

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2004
Document type: 
Thesis
File(s): 
Senior supervisor: 
David L. Baillie
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.

HSP90 and NO/cGMP in the development of ascidians and echinoids

Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2002
Document type: 
Thesis
File(s): 
Senior supervisor: 
Bruce P. Brandhorst
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Dissertation) Ph.D.

Molecular basis of Bardet-Biedl syndrome with particular reference to the Newfoundland families

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2004
Document type: 
Thesis
File(s): 
Senior supervisor: 
William S. Davidson
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Dissertation) Ph.D.

Computational detection of transcriptional regulators of protein complexes in apoptosis

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2004
Document type: 
Thesis
File(s): 
Senior supervisor: 
Frederic Pio
Department: 
Science: Department of Molecular Biology and Biochemistry
Thesis type: 
(Thesis) M.Sc.