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Title: Discovery of novel molecular targets in cancer using bioinformatics.
Creator: De Young, Maurice Phillip, V., Florida Atlantic University, Narayanan, Ramaswamy
Abstract/Description: The Cancer Genome Anatomy Project (CGAP) database of the National Cancer Institute contains thousands of expressed sequences, both known and novel, derived from diverse sets of normal, precancerous, and tumor cDNA libraries. This offers the possibility of using this database as a rational starting point for bioinformatics-based cancer gene discovery. Using the Digital Differential Display tool of the CGAP database, a hypothesis-driven gene discovery approach was undertaken to analyze...
Show moreThe Cancer Genome Anatomy Project (CGAP) database of the National Cancer Institute contains thousands of expressed sequences, both known and novel, derived from diverse sets of normal, precancerous, and tumor cDNA libraries. This offers the possibility of using this database as a rational starting point for bioinformatics-based cancer gene discovery. Using the Digital Differential Display tool of the CGAP database, a hypothesis-driven gene discovery approach was undertaken to analyze differential expression of various solid tumor types. Two hundred known genes and five hundred novel sequences were discovered to be differentially expressed, and a comprehensive database was established to facilitate identification of cancer diagnostic and therapeutic targets. To validate the use of bioinformatics in discovering genes with organ- and tumor-selectivity, novel ESTs predicted to be colon tumor-specific were analyzed further for expression specificity. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) analysis using matched sets of colon normal- and tumor-derived cDNAs identified one EST to be specifically expressed in the majority of colon tumors and normal small intestine. Due to this apparent specificity, the gene was termed Colon Carcinoma Related Gene (CCRG). Based on protein sequence analysis, CCRG belongs to a novel class of secreted factors. Another gene identified in this study showed homology to Single Minded 2 gene (SIM2). Involvement between SIM2 and cancer has not yet been reported. Isoform-specific expression of SIM2 short-form (SIM2-s) was seen in colon, pancreas, and prostate carcinomas but not in most normal tissues. Using a large collection of paraffin sections from colon, pancreas, and prostate tumor and normal tissues, elevated protein expression was seen in tumors compared to normal tissue specimens, demonstrating the diagnostic potential of SIM2-s. Antisense inhibition of SIM2-s expression in colon and pancreatic cancer cell lines caused inhibition of gene expression, growth inhibition, and apoptosis. Administration of SIM2-s antisense in nude mice caused inhibition of colon tumor growth without pronounced gross toxicity. Using GeneChipRTM technology, a gene expression profile indicative of apoptosis was observed in the colon cancer model. CCRG and SIM2-s offer both a diagnostic and therapeutic potential in select cancers and validate the use of bioinformatics approaches in the gene discovery paradigm.
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Date Issued: 2003
PURL: http://purl.flvc.org/fau/fd/FADT12053
Subject Headings: Bioinformatics, Gene expression, Oncogenes
Format: Document (PDF)

Title: Selective destruction of transformed cells by reovirus: Cellular targets and active reovirus proteins analysis.
Creator: Alter, Sarah., Florida Atlantic University, Roner, Michael R.
Abstract/Description: It is known that Reovirus selectively destroys transformed cells, but the complex mechanism is not completely understood at this time. In this study, gene expression was examined by comparing Reovirus-infected SV-40 transformed human embryonic fibroblasts, with mock-infected cells. Among the 40 genes shown to be altered, 38 genes were up regulated, and 2 genes were down regulated. Out of the 40 genes having differential gene expression, 8 were significantly over induced. 3 of these were DNA...
Show moreIt is known that Reovirus selectively destroys transformed cells, but the complex mechanism is not completely understood at this time. In this study, gene expression was examined by comparing Reovirus-infected SV-40 transformed human embryonic fibroblasts, with mock-infected cells. Among the 40 genes shown to be altered, 38 genes were up regulated, and 2 genes were down regulated. Out of the 40 genes having differential gene expression, 8 were significantly over induced. 3 of these were DNA binding transcription factors. Activation of transcription factors following Reovirus infection suggests that gene expression is essential in Reovirus induced transformed cell killing. Another 3 genes were found to be tumor suppressor proteins and oncogenes expressed downstream of the Ras pathway. The over expression of these was shown to induce apoptosis induced cell killing by Reovirus. Finally, 2 of the 8 significantly up regulated genes cause cell cycle progression inhibition. The cell cycle arrest then leads to cell death.
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Date Issued: 2002
PURL: http://purl.flvc.org/fcla/dt/12966
Subject Headings: Reoviruses, Gene expression
Format: Document (PDF)

Title: Characterization of the spinster gene ortholog C13C4.5 in Caenorhabditis elegans.
Creator: Zahornacky, Darrin., Harriet L. Wilkes Honors College
Abstract/Description: The dauer larva is an alternate larval stage which allows the nematode C. elegans to survive environmestress during development. Dauer formation requires autophagy, a cellular process responsible for degrading and recycling cytoplasmic components. I investigated the role of a spinster orthiolog, C13C4.5, by examining the effects of C13C4.5 loss-of-function and by generating a transgenic strain which expressed a C13C4.5::GFP fusion protein. Under normal conditions C13C4.5::GFP is expressed...
Show moreThe dauer larva is an alternate larval stage which allows the nematode C. elegans to survive environmestress during development. Dauer formation requires autophagy, a cellular process responsible for degrading and recycling cytoplasmic components. I investigated the role of a spinster orthiolog, C13C4.5, by examining the effects of C13C4.5 loss-of-function and by generating a transgenic strain which expressed a C13C4.5::GFP fusion protein. Under normal conditions C13C4.5::GFP is expressed diffusely in the intestine, but under autophagy-promoting conditions the expression pattern becomes more punctate. This is consistent with localization of C13C4.5 to autophagolysomoes during autophagy, as has been shown for spinster in D. melanogaster. Loss of C13C4.5 function in a dauer-constitutive mutant resulted in a reduction in the proportion of animals entering into the dauer stage. Together these data suggest that C13C4.5 is involved in dauer formation and the autophagy pathway.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3359320
Subject Headings: Gene expression, Apoptosis, Caenorhabditis elegans, Proteins, Analysis
Format: Document (PDF)

Title: Analysis of gene expression profiles from normal and chronic lymphocytic leukemia white blood cells.
Creator: Chapp, Robert James., Florida Atlantic University, Hartmann, James X.
Abstract/Description: This project used a bioinformatics approach to identify the genetic differential expression of chronic lymphocytic leukemia (CLL) white blood cells as compared to normal white blood cells. Several public access databases and data mining tools were used to collect these data. The data collected was validated by independent bioinformatics databases and the methodology was supported by previously published "gene chip" differential expression data. This research identifies a pattern of...
Show moreThis project used a bioinformatics approach to identify the genetic differential expression of chronic lymphocytic leukemia (CLL) white blood cells as compared to normal white blood cells. Several public access databases and data mining tools were used to collect these data. The data collected was validated by independent bioinformatics databases and the methodology was supported by previously published "gene chip" differential expression data. This research identifies a pattern of differential gene expression specific to CLL white blood cells that can be used for the early diagnosis of CLL. The study also identifies the probable genetic origin for the low expression of tyrosine kinase and IgM immunoglobulin observed in CLL B-cells. Also presented are genes associated with chromosomal regions previously reported as deleted in a high percentage of CLL cases. These data can be used in further research and for the treatment of CLL.
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Date Issued: 2003
PURL: http://purl.flvc.org/fcla/dt/13024
Subject Headings: Lymphocytic leukemia, Gene expression, Bioinformatics, Leucocytes
Format: Document (PDF)

Title: Targeted Gene Knock-out Via Promoter Tagging in Tomato (Lycopersicon Esculentum) and Tobacco (Nicotiana Tabacum).
Creator: Kazy, Alia, Zhang, Xing-Hai, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Many different ways to create mutants have been established. This research demonstrates yet another variation of the promoter tagging technique that allows for a single step selection of the putative transgenic plants that have a mutation in constitutively expressed genes. While tomato transformants have not yet been convincingly confirmed, tobacco transformation resulted in seven transgenic lines showing resistance to high concentrations of kanamycin. Two transgenic lines were further...
Show moreMany different ways to create mutants have been established. This research demonstrates yet another variation of the promoter tagging technique that allows for a single step selection of the putative transgenic plants that have a mutation in constitutively expressed genes. While tomato transformants have not yet been convincingly confirmed, tobacco transformation resulted in seven transgenic lines showing resistance to high concentrations of kanamycin. Two transgenic lines were further investigated and three putative promoters isolated. Transient expression analysis of leaves transformed by particle bombardment with vectors carrying beta-glucuronidase gene driven by these putative promoters suggests two of them to be functional. Further investigation is needed to confirm the expression in the stably transformed plants as well as cloning of the genes downstream of the functional promoters and research of their functions.
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Date Issued: 2007
PURL: http://purl.flvc.org/fau/fd/FA00000779
Subject Headings: Gene mapping--Methodology, Gene mapping--Data processing, Gene expression, Microbial genetics, Computational biology
Format: Document (PDF)

Title: The many faces of gene expression profiling: transcriptome analyses applied towardselucidating marine organismal interactions and metabolism.
Creator: Lopez, Jose V., Mouzon, B., McCarthy, Peter J., Kerr, Russell G.
Date Issued: 2009
PURL: http://purl.flvc.org/fau/fd/FA00007286
Subject Headings: Gene expression, Transcriptome, Molecular biotechnology, Marine ecology, Marine organisms
Format: Document (PDF)

Title: Functional genomics of a novel colon carcinoma-related gene (CCRG).
Creator: Damania, Hema D., Florida Atlantic University, Narayanan, Ramaswamy, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description: Recently Dr. Narayanan's laboratory, utilizing bioinformatics approaches, identified a novel gene which may play a role in colon cancer. This gene in view of its expression specificity was termed Colon Carcinoma Related Gene (CCRG). The CCRG belongs to a novel class of secreted molecules with a unique cysteine rich motif. The function of CCRG however, remains unknown. The basis of this project revolved around establishing the putative function (functional genomics) of CCRG. The rationale for...
Show moreRecently Dr. Narayanan's laboratory, utilizing bioinformatics approaches, identified a novel gene which may play a role in colon cancer. This gene in view of its expression specificity was termed Colon Carcinoma Related Gene (CCRG). The CCRG belongs to a novel class of secreted molecules with a unique cysteine rich motif. The function of CCRG however, remains unknown. The basis of this project revolved around establishing the putative function (functional genomics) of CCRG. The rationale for the project was to test a hypothesis that CCRG may offer a growth advantage to cancer cells. The availability of diverse tumor-derived cell lines, which were CCRG negative offered a possibility to study the consequence of enforced expression of CCRG. A breast carcinoma cell line was transfected with an exogenous CCRG expression vector and the stable clones were characterized. The stable transfectants of CCRG showed enhanced growth and a partial abrogation of serum growth factor(s) requirement. These results provide a framework for future experiments to further elucidate the function of CCRG.
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Date Issued: 2002
PURL: http://purl.flvc.org/fcla/dt/12965
Subject Headings: Colon (Anatomy)--Cancer, Genomics, Bioinformatics, Gene expression
Format: Document (PDF)

Title: THE RELATIONSHIP OF GENE EXPRESSION, STRESS, DEPRESSION, AND THE SOCIAL DETERMINANTS OF HEALTH DURING PREGNANCY.
Creator: Brennen, Marlene Brown, Tappen, Ruth, Florida Atlantic University, Christine E. Lynn College of Nursing, Christine E. Lynn College of Nursing
Abstract/Description: The purpose of this study was to explore differences in perceived stress, glucocorticoid receptor (GR), and the expression of histone acetylation (HAT) of the corticotropin-releasing hormone (CRH) gene between non-Hispanic Black and non-Hispanic White women in their 2nd trimester of pregnancy. Black women are 2–3 times more likely to experience preterm birth (PTB) and maternal mortality than White women (Hoyert, 2022; Martin et al., 2019). Researchers have reported chronic stress associated...
Show moreThe purpose of this study was to explore differences in perceived stress, glucocorticoid receptor (GR), and the expression of histone acetylation (HAT) of the corticotropin-releasing hormone (CRH) gene between non-Hispanic Black and non-Hispanic White women in their 2nd trimester of pregnancy. Black women are 2–3 times more likely to experience preterm birth (PTB) and maternal mortality than White women (Hoyert, 2022; Martin et al., 2019). Researchers have reported chronic stress associated with factors such as experiencing discrimination, financial hardship, and abuse may induce dysregulation of the stress hormones (Kramer et al., 2013; Shapiro-Mendoza et al., 2016). Likewise, the stress hormones glucocorticoid and CRH dysregulation have been linked to early labor, preeclampsia, and maternal death (Kramer et al., 2013; Shapiro-Mendoza et al., 2016; Yu et al., 2013). Additionally, social status, gender, education, and income are recognized as social determinants of health. This study used an observational, cross-sectional design to analyze the differences in perceived stress, depression, GR, and HAT of the CRH gene between a group of Black and White pregnant women in their 2nd trimester of pregnancy. This study analyzed perceived stress, depression, and peripheral blood monocytes cells (PMBC) using secondary, deidentified data from pregnant women. The Perceived Stress Scale was used to measure stress, the profile in Mood Depression Scale measured depression, a chromatin immunoprecipitation (ChIP) to quantitative Polymerase chain reaction (qPCR) analysis was used to measure GR and HAT of the CRH gene. The data were analyzed using correlation and analysis of covariance (ANCOVA) to examine relationships and the differences between groups.
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Date Issued: 2023
PURL: http://purl.flvc.org/fau/fd/FA00014286
Subject Headings: Social Determinants of Health, Gene expression, Pregnancy--Health aspects
Format: Document (PDF)

Title: Identification of MicroRNA biomarkers for cancer by combining multiple feature selection techniques.
Creator: Kotlarchyk, Alex J., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: MicroRNAs (miRNAs) may serve as diagnostic and predictive biomarkers for cancer. The aim of this study was to identify novel cancer biomarkers from miRNA datasets, in addition to those already known. Three published miRNA cancer datasets (liver, breast, and brain) were evaluated, and the performance of the entire feature set was compared to the performance of individual feature filters, an ensemble of those filters, and a support vector machine (SVM) wrapper. In addition to confirming many...
Show moreMicroRNAs (miRNAs) may serve as diagnostic and predictive biomarkers for cancer. The aim of this study was to identify novel cancer biomarkers from miRNA datasets, in addition to those already known. Three published miRNA cancer datasets (liver, breast, and brain) were evaluated, and the performance of the entire feature set was compared to the performance of individual feature filters, an ensemble of those filters, and a support vector machine (SVM) wrapper. In addition to confirming many known biomarkers, the main contribution of this study is that seven miRNAs have been newly identified by our ensemble methodology as possible important biomarkers for hepatocellular carcinoma or breast cancer, pending wet lab confirmation. These biomarkers were identified from miRNA expression datasets by combining multiple feature selection techniques (i.e., creating an ensemble) or by the SVM-wrapper, and then classified by different learners. Generally speaking, creating a subset of features by selecting only the highest ranking features (miRNAs) improved upon results generated when using all the miRNAs, and the ensemble and SVM-wrapper approaches outperformed individual feature selection methods. Finally, an algorithm to determine the number of top-ranked features to include in the creation of feature subsets was developed. This algorithm takes into account the performance improvement gained by adding additional features compared to the cost of adding those features.
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Date Issued: 2011
PURL: http://purl.flvc.org/FAU/3332260
Subject Headings: Gene silencing, Biochemical markers, Cancer, Diagnosis, Data processing, Cancer, Diagnosis, Research, Gene expression, Tumor markers, Diagnostic use
Format: Document (PDF)

Title: Temporal analysis of gene expression in a field population of the Scleractinian coral Montastraea faveolata.
Creator: Edge,Sara E., Morgan, Michael B., Snell, Terry W., Harbor Branch Oceanographic Institute
Date Issued: 2008-02-22
PURL: http://purl.flvc.org/FCLA/DT/1745597
Subject Headings: Coral reef biology, Coral reef ecology, Coral reef ecology --Florida --Florida Keys, Gene Expression
Format: Document (PDF)

Title: Understanding the role of transgenic catalase in T-cell development in murine-based studies.
Creator: Smith, Richard M., Harriet L. Wilkes Honors College
Abstract/Description: The thymus provides a unique microenvironment that facilitates T lymphocytes differentiation and maturation. However, the thymus atrophies after puberty which leads to an overall expression of metabolism gene pathways and low gene expression of certain peroxide scavenger enzymes such as catalase in thymic stromal compartments. From this data, we postulate that thymic stromal cells are highly susceptible to oxidative damage. We utilized a transgenic mice model overexpressing human catalase...
Show moreThe thymus provides a unique microenvironment that facilitates T lymphocytes differentiation and maturation. However, the thymus atrophies after puberty which leads to an overall expression of metabolism gene pathways and low gene expression of certain peroxide scavenger enzymes such as catalase in thymic stromal compartments. From this data, we postulate that thymic stromal cells are highly susceptible to oxidative damage. We utilized a transgenic mice model overexpressing human catalase targeted to the mitochondria (mCat) to test our hypothesis that gerater oxidative protection should lower the degree of thymus atrophy. Our experiment focused on a direct comparison of organ weights (thymus, kidney, lymph nodes, spleen and heart), cellularity and histology between transgenic and wildtype mice. We found that mCat had selective increases in thymus size.
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Date Issued: 2012
PURL: http://purl.flvc.org/FAU/3359325
Subject Headings: T cells, Differentiation, Developmental genetics, Gene expression, Human cell culture, Thymus, Physiology
Format: Document (PDF)

Title: Analysis of SLKED gene expression in CRISPR/Cas9-mediated gene knockouts in Tomato (Micro-Tom).
Creator: Vichyavichien, Paveena, Zhang, Xing-Hai, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas) protein system, CRISPR/Cas9, uses single-guide RNA to guide Cas9 to the target site for genome editing. In this study, the CRISPR/Cas9 system was used to knockout KED in tomato (Solanum lycopersicum). KED was first identified while screening the wounded tobacco (Nicotiana tabacum) leaves. We found that alignment of the protein sequence of SlKED (Solanum lycopersicum KED) and NtKED (Nicotiana tabacum KED)...
Show moreClustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas) protein system, CRISPR/Cas9, uses single-guide RNA to guide Cas9 to the target site for genome editing. In this study, the CRISPR/Cas9 system was used to knockout KED in tomato (Solanum lycopersicum). KED was first identified while screening the wounded tobacco (Nicotiana tabacum) leaves. We found that alignment of the protein sequence of SlKED (Solanum lycopersicum KED) and NtKED (Nicotiana tabacum KED) showed 55.1% identity. To investigate, we generated SlKED knockout tomato plants with a single base pair deletion, a five base pair deletion and a three base pair deletion with a single base pair insertion. We performed wounding assays and analyzed gene expression and found that the wounded SlKED knockout plant showed no gene induction. Furthermore, the biological assay results revealed that the tobacco hornworm (Manduca sexta) gained more mass when fed on the SlKED knockout plant. Our studies show that the KED gene plays a role in wound-induced mechanism and suggested it may involve in the plant defense system against biological stress and insect feeding.
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Date Issued: 2019
PURL: http://purl.flvc.org/fau/fd/FA00013275
Subject Headings: Genome editing, Gene expression, CRISPR/Cas9, CRISPR-associated protein 9
Format: Document (PDF)

Title: A Novel Role of the Ankyrin-Binding Motif of L1-Type CAM Neuroglian in Nuclear Import and Transcriptional Regulation of Myc.
Creator: Kakad, Priyanka P., Godenschwege, Tanja A., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: L1-type cell adhesion molecule (L1CAM) plays an essential role in the development of nervous system and is also highly relevant for the progression of diseases such as Alzheimer’s disease, stroke and cancers, some of the leading causes of human mortality. In addition to its canonical role as a plasma membrane protein organizing the cytoskeleton, recent in vitro studies have revealed that transmembrane as well as cytosolic fragments of proteolytically cleaved vertebrate L1CAM translocate to...
Show moreL1-type cell adhesion molecule (L1CAM) plays an essential role in the development of nervous system and is also highly relevant for the progression of diseases such as Alzheimer’s disease, stroke and cancers, some of the leading causes of human mortality. In addition to its canonical role as a plasma membrane protein organizing the cytoskeleton, recent in vitro studies have revealed that transmembrane as well as cytosolic fragments of proteolytically cleaved vertebrate L1CAM translocate to the nucleus and regulate expression of genes involved in DNA post-replication repair, cell cycle control, migration and differentiation. However, little is known about the in vivo function of L1CAM in the adult nervous system. This dissertation research focuses on studying in vivo nuclear translocation and function of L1CAM. Using the Drosophila model system, we first show that the sole Drosophila L1CAM homolog, Neuroglian (Nrg), is proteolytically cleaved by Alzheimer’s associated secretases, similar to L1CAM, and is also translocated to the nucleus in the adult nervous system. Subsequently, we have shown that the deletion of highly conserved Ankyrin binding domain or FIGQY motif disrupts nuclear import. Further experiments have revealed that the nuclear translocation of Nrg is in fact regulated by the phosphorylation of the FIGQY motif. Importantly, our studies also show transgenic expression of full-length Nrg or the intracellular domain of Nrg resulted in increased myc expression, which is associated with increased sensitivity to oxidative stress and reduced life span. On the other hand, deletion of the FIGQY motif or mutations preventing its phosphorylation led to decrease in myc expression. In summary, we have identified a novel role for the highly conserved Ankyrin binding domain in nuclear translocation and transcriptional regulation of the Drosophila myc oncogene, which is of high relevance to neurodegenerative diseases and cancer associated with oxidative stress.
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Date Issued: 2018
PURL: http://purl.flvc.org/fau/fd/FA00013076
Subject Headings: Cell adhesion molecules., Myc proteins., Transcription, Genetic., Transcription factors, Gene expression., Ankyrins., Translocation, Genetic.
Format: Document (PDF)

Title: Biological Computation: the development of a genomic analysis pipeline to identify cellular genes modulated by the transcription / splicing factor srsf1.
Creator: Clark, Evan, Asghar, Waseem, Florida Atlantic University, College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: SRSF1 is a widely expressed mammalian protein with multiple functions in the regulation of gene expression through processes including transcription, mRNA splicing, and translation. Although much is known of SRSF1 role in alternative splicing of specific genes little is known about its functions as a transcription factor and its global effect on cellular gene expression. We utilized a RNA sequencing (RNA-¬‐Seq) approach to determine the impact of SRSF1 in on cellular gene expression and...
Show moreSRSF1 is a widely expressed mammalian protein with multiple functions in the regulation of gene expression through processes including transcription, mRNA splicing, and translation. Although much is known of SRSF1 role in alternative splicing of specific genes little is known about its functions as a transcription factor and its global effect on cellular gene expression. We utilized a RNA sequencing (RNA-¬‐Seq) approach to determine the impact of SRSF1 in on cellular gene expression and analyzed both the short term (12 hours) and long term (48 hours) effects of SRSF1 expression in a human cell line. Furthermore, we analyzed and compared the effect of the expression of a naturally occurring deletion mutant of SRSF1 (RRM12) to the full-¬‐length protein. Our analysis reveals that shortly after SRSF1 is over-¬‐expressed the transcription of several histone coding genes is down-¬‐regulated, allowing for a more relaxed chromatin state and efficient transcription by RNA Polymerase II. This effect is reversed at 48 hours. At the same time key genes for the immune pathways are activated, more notably Tumor Necrosis Factor-¬‐Alpha (TNF-¬‐α), suggesting a role for SRSF1 in T cell functions.
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Date Issued: 2017
PURL: http://purl.flvc.org/fau/fd/FA00004858, http://purl.flvc.org/fau/fd/FA00004858
Subject Headings: Gene expression., Computational biology., Markov processes., Bioinformatics., Genetic engineering., Molecular biology.
Format: Document (PDF)

Title: Characterization of SNAG-zinc finger protein (ZFP) transcription factors.
Creator: Chiang, Cindy Chung-Yue., Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Transcriptional regulation is an important area of research due to the fact that it leads to gene expression. Transcription factors associated with the regulation can either be activators or repressors of target genes, acting directly or with the aid of other factors. A majority of transcriptional repressors are zinc finger proteins (ZFPs) which bind to specific DNA sequences. The Snail/Gfi (SNAG) domain family, with members such as Slug, Smuc, Snail, and Scratch, are transcriptional...
Show moreTranscriptional regulation is an important area of research due to the fact that it leads to gene expression. Transcription factors associated with the regulation can either be activators or repressors of target genes, acting directly or with the aid of other factors. A majority of transcriptional repressors are zinc finger proteins (ZFPs) which bind to specific DNA sequences. The Snail/Gfi (SNAG) domain family, with members such as Slug, Smuc, Snail, and Scratch, are transcriptional repressors shown to play a role in various diseases such as cancer. The SNAG transcription factors contain a conserved SNAG repression domain and DNA binding domain zinc fingers. The specific DNA sequences to which each SNAG-ZFP binds, as well as a general consensus -TGCACCTGTCCGA, have been determined. Also, putative protein-protein interactions in which the Slug domain participates has been identified via binding assays. All these results contribute to better understanding of SNAG-ZFP functions.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/186676
Subject Headings: Zinc-finger proteins, Synthesis, Metalloproteins, Synthesis, Genetic transcription, Regulation, Cellular signal transduction, Gene expression
Format: Document (PDF)

Title: Characterization of Group B Sox genes in the development of Drosophila nervous system.
Creator: Singh, Shweta, Dawson-Scully, Ken, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Sox proteins all contain a single ~70 amino acid High Mobility Group (HMG) DNA-binding domain with strong homology to that of Sry, the mammalian testisdetermining factor. In Drosophila melanogaster, there are four closely related members of the B group, Dichaete (D), Sox Neuro (Sox N), Sox 21a, and Sox 21b that each exhibit ~90% sequence identity within the HMG domain.The previous study has shown that Dichaete plays a major role in embryonic nervous system development and is expressed in...
Show moreSox proteins all contain a single ~70 amino acid High Mobility Group (HMG) DNA-binding domain with strong homology to that of Sry, the mammalian testisdetermining factor. In Drosophila melanogaster, there are four closely related members of the B group, Dichaete (D), Sox Neuro (Sox N), Sox 21a, and Sox 21b that each exhibit ~90% sequence identity within the HMG domain.The previous study has shown that Dichaete plays a major role in embryonic nervous system development and is expressed in several clusters of neurons in the brain, including intermingled olfactory LNs and central-complex neurons strongly expressed in local interneuron of the olfactory system. However, little is known about the possible expression and functions of the related group B Sox genes in the larval and adult brain. In particular, it is unclear if Sox N may function along with Dichaete in controlling the development or physiology of the adult olfactory system. Our data suggests Sox N potential role in the elaboration of the olfactory circuit formation.
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Date Issued: 2017
PURL: http://purl.flvc.org/fau/fd/FA00004907, http://purl.flvc.org/fau/fd/FA00004907
Subject Headings: Drosophila melanogaster--Physiology., Transcription factors., Gene expression., Genetic transcription., Cell cycle., Neural stem cells.
Format: Document (PDF)

Title: Chronic variable stress affects hippocampal neurotrophic factor gene expression in the novelty-seeking phenotype: epigenetic regulation.
Creator: Oztan, Ozge., Charles E. Schmidt College of Medicine
Abstract/Description: Experimentally naive rats exhibit varying degrees of novelty exploration. Some rats display high rates of locomotor reactivity to novelty (high responders; HR), and others display low rates (low responders; LR). The novelty-seeking phenotype (LRHR) is introduced as a model of stress responsiveness. In this thesis I examined effects of chronic variable physical and social stress or control handling on the levels of various neurotrophins in the hippocampus, and changes in mossy fibre terminal...
Show moreExperimentally naive rats exhibit varying degrees of novelty exploration. Some rats display high rates of locomotor reactivity to novelty (high responders; HR), and others display low rates (low responders; LR). The novelty-seeking phenotype (LRHR) is introduced as a model of stress responsiveness. In this thesis I examined effects of chronic variable physical and social stress or control handling on the levels of various neurotrophins in the hippocampus, and changes in mossy fibre terminal fields in LRHR rats. A positive correlation is seen between histone deacetylase 2 and brain-derived neurotrophic factor (BDNF) levels both of which are oppositely regulated in LRHR CA3 fields in response to chronic social stress. Increase in BDNF levels in CA3 field accompanied increase in supra-pyramidal mossy fibre terminal field size (SP-MF) in HRs, and decrease in BDNF levels accompanied decrease in SP-MF volume in LRs. Epigenetic regulation of neurotrophic support underlying these structural changes is discussed.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/215290
Subject Headings: Rats as laboratory animals, Cellular signal transduction, Gene expression, Hippocampus (Brain), Physiology, Neural transmission, Genetic regulation
Format: Document (PDF)

Title: Effects of stressors on differential gene expression and secondary metabolites by Axinella corrugata.
Creator: Grima, Jennifer., Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Sponges are an important source of bioactive marine natural products, or secondary metabolites. The common Caribbean reef sponge, Axinella corrugata, produces an antitumor and antibacterial chemical, stevensine. This study determined whether environmental stressors, such as elevated temperature and exposure to Amphibalanus amphitrite larvae, affect the production of stevensine by A.corrugata and if the stressors caused A.corrugata to exhibit differential gene expression. Temperature stress...
Show moreSponges are an important source of bioactive marine natural products, or secondary metabolites. The common Caribbean reef sponge, Axinella corrugata, produces an antitumor and antibacterial chemical, stevensine. This study determined whether environmental stressors, such as elevated temperature and exposure to Amphibalanus amphitrite larvae, affect the production of stevensine by A.corrugata and if the stressors caused A.corrugata to exhibit differential gene expression. Temperature stress resulted in no significant change in the production of stevensine; only two genes were significantly differentially expressed, including hsp70. Larval stressed resulted in increased production of stevensine and significant differential gene expression (more than seventy genes). This study suggests that A.corrugata may be resilient to elevations in temperature and that one of stevensine's roles in nature is as an antifoulant.
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Date Issued: 2013
PURL: http://purl.flvc.org/fcla/dt/3360781
Subject Headings: Axinellida, Sponges, Marine pharmacology, Adaptation (Biology), Gene expression, Genetic regulation, Stress (Physiology), Ecophysiology
Format: Document (PDF)

Title: Effects of gene selection and data sampling on prediction of breast cancer treatments.
Creator: Heredia, Brian, Khoshgoftaar, Taghi M., Florida Atlantic University, College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: In recent years more and more researchers have begun to use data mining and machine learning tools to analyze gene microarray data. In this thesis we have collected a selection of datasets revolving around prediction of patient response in the specific area of breast cancer treatment. The datasets collected in this paper are all obtained from gene chips, which have become the industry standard in measurement of gene expression. In this thesis we will discuss the methods and procedures used in...
Show moreIn recent years more and more researchers have begun to use data mining and machine learning tools to analyze gene microarray data. In this thesis we have collected a selection of datasets revolving around prediction of patient response in the specific area of breast cancer treatment. The datasets collected in this paper are all obtained from gene chips, which have become the industry standard in measurement of gene expression. In this thesis we will discuss the methods and procedures used in the studies to analyze the datasets and their effects on treatment prediction with a particular interest in the selection of genes for predicting patient response. We will also analyze the datasets on our own in a uniform manner to determine the validity of these datasets in terms of learning potential and provide strategies for future work which explore how to best identify gene signatures.
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Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00004292, http://purl.flvc.org/fau/fd/FA00004292
Subject Headings: Antineoplastic agents -- Development, Breast -- Cancer -- Treatment, Cancer -- Genetic aspects, DNA mircroarrays, Estimation theory, Gene expression
Format: Document (PDF)

Title: Gene selection for sample sets with biased distribution.
Creator: Kamal, Abu Hena Mustafa., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: Microarray expression data which contains the expression levels of a large number of simultaneously observed genes have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for many tasks such as building prediction models from the microarray expression data or gene regulatory network discovery. Traditional gene selection methods, however, fail to take the class distribution into the...
Show moreMicroarray expression data which contains the expression levels of a large number of simultaneously observed genes have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for many tasks such as building prediction models from the microarray expression data or gene regulatory network discovery. Traditional gene selection methods, however, fail to take the class distribution into the selection process. In biomedical science, it is very common to have microarray expression data which is severely biased with one class of examples (e.g., diseased samples) significantly less than other classes (e.g., normal samples). These sample sets with biased distributions require special attention from researchers for identification of genes responsible for a particular disease. In this thesis, we propose three filtering techniques, Higher Weight ReliefF, ReliefF with Differential Minority Repeat and ReliefF with Balanced Minority Repeat to identify genes responsible for fatal diseases from biased microarray expression data. Our solutions are evaluated on five well-known microarray datasets, Colon, Central Nervous System, DLBCL Tumor, Lymphoma and ECML Pancreas. Experimental comparisons with the traditional ReliefF filtering method demonstrate the effectiveness of the proposed methods in selecting informative genes from microarray expression data with biased sample distributions.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/186330
Subject Headings: Gene expression, Research, Methodology, Medical informatics, Apoptosis, Molecular aspects, DNA microarrays, Research
Format: Document (PDF)

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