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Title: Utilization of Genomic Tools to Enhance the Commercial Aquaculture of the Florida Pompano Trachinotus carolinus.
Creator: King, Laura Elizabeth, Wills, Paul S., Florida Atlantic University, Department of Biological Sciences, Charles E. Schmidt College of Science
Abstract/Description: The goal of this project is to gain access to valuable genetic information that will be utilized to create a genetics-based selective breeding program. This selective breeding program will be implemented to produce and maintain a healthy and diverse breeding stock of the Florida Pompano Trachinotus carolinus. The Florida Pompano is a popular food fish found in abundance off Florida's east and west coasts. There has been interest in the aquaculture of this species for decades with minimal...
Show moreThe goal of this project is to gain access to valuable genetic information that will be utilized to create a genetics-based selective breeding program. This selective breeding program will be implemented to produce and maintain a healthy and diverse breeding stock of the Florida Pompano Trachinotus carolinus. The Florida Pompano is a popular food fish found in abundance off Florida's east and west coasts. There has been interest in the aquaculture of this species for decades with minimal success. With recent improvements in aquaculture systems and nutrition, now is the time to bring this fish to commercialization. The main research objectives of this study are to create a bioinformatics workflow to generate a draft whole-genome of the Florida Pompano, identify variation sites within this genome, and run a comparative analysis with two closely related Trachinotus species, Permit T. falcatus and Palometa T. goodei. These two species were chosen because they are found in the same environment as the Florida Pompano but grow to substantially different sizes. To sequence and assemble the whole genome of the Florida Pompano, a hybrid method was applied using long and short-read sequencing technologies. The draft genome was found to be 733.5 Mb in length with a total of 26,891 protein-coding genes. Sites of variation within this assembled genome were identified using a 2b-RAD sequencing method on 62 individuals collected off Florida’s east and gulf coasts.
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Date Issued: 2023
PURL: http://purl.flvc.org/fau/fd/FA00014181
Subject Headings: Florida pompano, Aquaculture, Genomics
Format: Document (PDF)

Title: Characterization of a novel close-to-root papillomavirus from aFlorida manatee by using multiply primed rolling-circle amplification: Trichechus manatus latirostrispapillomavirus type 1.
Creator: Rector, A., Bossart, Gregory D., Ghim, Shin-je, Sundberg, J. P., Jenson, A. Bennett, Van Ranst, M., Harbor Branch Oceanographic Institute
Date Issued: 2004
PURL: http://purl.flvc.org/fau/fd/FA00007037
Subject Headings: Manatees--Florida, Papillomavirus, Genomes
Format: Document (PDF)

Title: Temporal and spatial variation of shellmicrostructure of Polymesoda Caroliniana (Bivalvia: Heterodonta).
Creator: Tiu, Antonieto Tan, Harbor Branch Oceanographic Institute
Date Issued: 1989
PURL: http://purl.flvc.org/fau/fd/FA00007186
Subject Headings: Bivalves, Shells, Microstructure, Genome, Variation (Biology)
Format: Document (PDF)

Title: Bioinformatic analysis of viral genomic sequences and concepts of genome-specific national vaccine design.
Creator: Chatterjee, Sharmistha P., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: This research is concerned with analyzing a set of viral genomes to elucidate the underlying characteristics and determine the information-theoretic aspects of the genomic signatures. The goal of this study thereof, is tailored to address the following: (i) Reviewing various methods available to deduce the features and characteristics of genomic sequences of organisms in general, and particularly focusing on the genomes pertinent to viruses; (ii) applying the concepts of information...
Show moreThis research is concerned with analyzing a set of viral genomes to elucidate the underlying characteristics and determine the information-theoretic aspects of the genomic signatures. The goal of this study thereof, is tailored to address the following: (i) Reviewing various methods available to deduce the features and characteristics of genomic sequences of organisms in general, and particularly focusing on the genomes pertinent to viruses; (ii) applying the concepts of information-theoretics (entropy principles) to analyze genomic sequences; (iii) envisaging various aspects of biothermodynamic energetics so as to determine the framework and architecture that decide the stability and patterns of the subsequences in a genome; (iv) evaluating the genomic details using spectral-domain techniques; (v) studying fuzzy considerations to ascertain the overlapping details in genomic sequences; (vi) determining the common subsequences among various strains of a virus by logistically regressing the data obtained via entropic, energetics and spectral-domain exercises; (vii) differentiating informational profiles of coding and non-coding regions in a DNA sequence to locate aberrant (cryptic) attributes evolved as a result of mutational changes and (viii) finding the signatures of CDS of genomes of viral strains toward rationally conceiving plausible designs of vaccines. Commensurate with the topics indicated above, necessary simulations are proposed and computational exercises are performed (with MatLabTM R2009b and other software as needed). Extensive data gathered from open-literature are used thereof and, simulation results are verified. Lastly, results are discussed, inferences are made and open-questions are identified for future research.
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Date Issued: 2013
PURL: http://purl.flvc.org/FAU/3360772
Subject Headings: Genetic engineering, Bioinformatics, Genomics, DNA microarrays, Proteomics
Format: Document (PDF)

Title: Discovery and visualization of co-regulated genes relevant to target diseases.
Creator: Lad, Vaibhan., College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description: In this thesis, we propose to discover co-regulated genes using microarray expression data, as well as providing visualization functionalities for domain experts to study relationships among discovered co-regulated genes. To discover co-regulated genes, we first use existing gene selection methods to select a small portion of genes which are relevant to the target diseases, on which we build an ordered similarity matrix by using nearest neighbor based similarity assessment criteria. We then...
Show moreIn this thesis, we propose to discover co-regulated genes using microarray expression data, as well as providing visualization functionalities for domain experts to study relationships among discovered co-regulated genes. To discover co-regulated genes, we first use existing gene selection methods to select a small portion of genes which are relevant to the target diseases, on which we build an ordered similarity matrix by using nearest neighbor based similarity assessment criteria. We then apply a threshold based clustering algorithm named Spectral Clustering to the matrix to obtain a number of clusters. The genes which are clustered together in one cluster represent a group of co-regulated genes and to visualize them, we use Java Swings as the tool and develop a visualization platform which provides functionalities for domain experts to study relationships between different groups of co-regulated genes; study internal structures within each group of genes, and investigate details of each individual gene and of course for gene function prediction. Results are analyzed based on microarray expression datasets collected from brain tumor, lung cancers and leukemia samples.
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Date Issued: 2010
PURL: http://purl.flvc.org/FAU/2976447
Subject Headings: Genomics, Gene mapping, Cell transformation, Cellular signal transduction
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: Statistical physics inspired methods to assign statistical significance in bioinformatics and proteomics: From sequence comparison to mass spectrometry based peptide sequencing.
Creator: Alves, Gelio, Florida Atlantic University, Yu, Yi-Kuo
Abstract/Description: After the sequencing of many complete genomes, we are in a post-genomic era in which the most important task has changed from gathering genetic information to organizing the mass of data as well as under standing how components interact with each other. The former is usually undertaking using bioinformatics methods, while the latter task is generally termed proteomics. Success in both parts demands correct statistical significance assignments for results found. In my dissertation. I study two...
Show moreAfter the sequencing of many complete genomes, we are in a post-genomic era in which the most important task has changed from gathering genetic information to organizing the mass of data as well as under standing how components interact with each other. The former is usually undertaking using bioinformatics methods, while the latter task is generally termed proteomics. Success in both parts demands correct statistical significance assignments for results found. In my dissertation. I study two concrete examples: global sequence alignment statistics and peptide sequencing/identification using mass spectrometry. High-performance liquid chromatography coupled to a mass spectrometer (HPLC/MS/MS), enabling peptide identifications and thus protein identifications, has become the tool of choice in large-scale proteomics experiments. Peptide identification is usually done by database searches methods. The lack of robust statistical significance assignment among current methods motivated the development of a novel de novo algorithm, RAId, whose score statistics then provide statistical significance for high scoring peptides found in our custom, enzyme-digested peptide library. The ease of incorporating post-translation modifications is another important feature of RAId. To organize the massive protein/DNA data accumulated, biologists often cluster proteins according to their similarity via tools such as sequence alignment. Homologous proteins share similar domains. To assess the similarity of two domains usually requires alignment from head to toe, ie. a global alignment. A good alignment score statistics with an appropriate null model enable us to distinguish the biologically meaningful similarity from chance similarity. There has been much progress in local alignment statistics, which characterize score statistics when alignments tend to appear as a short segment of the whole sequence. For global alignment, which is useful in domain alignment, there is still much room for exploration/improvement. Here we present a variant of the direct polymer problem in random media (DPRM) to study the score distribution of global alignment. We have demonstrate that upon proper transformation the score statistics can be characterized by Tracy-Widom distributions, which correspond to the distributions for the largest eigenvalue of various ensembles of random matrices.
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Date Issued: 2006
PURL: http://purl.flvc.org/fcla/dt/12194
Subject Headings: Molecular biology--Data processing, Bioinformatics, Proteomics, Genomics
Format: Document (PDF)

Title: Manipulation of normal cells to produce a cancer-like mitotic phenotype.
Creator: Luffman, Christina., Harriet L. Wilkes Honors College
Abstract/Description: Most tumors contain multiple karyotypes due to genomic instability gained through chromosomal segregational defects. The variability of genomic changes within a population makes it difficult to study specific processes without the existence of confounding mutations. My project is to create a model system for observation of mitotic defects, specifically multipolar spindles, in a normal cell line, where the genome is intact. Induction of centrosome amplification is required for formation of...
Show moreMost tumors contain multiple karyotypes due to genomic instability gained through chromosomal segregational defects. The variability of genomic changes within a population makes it difficult to study specific processes without the existence of confounding mutations. My project is to create a model system for observation of mitotic defects, specifically multipolar spindles, in a normal cell line, where the genome is intact. Induction of centrosome amplification is required for formation of multipolar spindles. Treatments with colcemid showed a 10% increase in abnormal centrosome numbers over control. However, treatment with hydroxyurea and transfection of hMPSl showed little increase. Extra centrosomes are insufficient to drive multipolarity, therefore, I am using siRNA-mediated knockdown of Nek2 or HSET to decluster the extra centrosomes. Successful declustering will preferably show an increase in multipolar frequency, allowing us to study the formation and resolution of these structres to better understand how they contribute to aneuploidy and tumor progression.
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Date Issued: 2009
PURL: http://purl.flvc.org/FAU/3325079
Subject Headings: Cell division, Karyokinesis, Cancer, Genetic aspects, Genomics, Cellular signal transduction, Centrosomes
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: DNA fingerprints of human oral microbiome: a first step towards early diagnosis of oral diseases.
Creator: Chakraborty, Shreyasee, Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: This study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non...
Show moreThis study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non-smokers and periodontal disease subjects were evident suggesting the presence of potential indicators of health and poor oral health. Taxon diversity was higher in smokers including members of the genera Rothia, Synechococcus, Neisseria, Thiomargarita and Pyrobaculum but highest in periodontal disease. The two techniques successfully aligned the subjects within appropriate categories (based on their oral microbial genetic patterns)confirming their diagnostic suitability.
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Date Issued: 2014
PURL: http://purl.flvc.org/fau/fd/FA00004184, http://purl.flvc.org/fau/fd/FA00004184
Subject Headings: Molecular microbiology., Mouth--Microbiology., Bacterial genetics., Cellular signal transduction., Microbial genomics.
Format: Document (PDF)

Title: ACCURATE DETECTION OF SELECTIVE SWEEPS WITH TRANSFER LEARNING.
Creator: Sigler, Priya, DeGiorgio, Michael, Florida Atlantic University, Department of Computer and Electrical Engineering and Computer Science, College of Engineering and Computer Science
Abstract/Description: Positive natural selection leaves detectable, distinctive patterns in the genome in the form of a selective sweep. Identifying areas of the genome that have undergone selective sweeps is an area of high interest as it enables understanding of species and population evolution. Previous work has accomplished this by evaluating patterns within summary statistics computed across the genome and through application of machine learning techniques to raw population genomic data. When using raw...
Show morePositive natural selection leaves detectable, distinctive patterns in the genome in the form of a selective sweep. Identifying areas of the genome that have undergone selective sweeps is an area of high interest as it enables understanding of species and population evolution. Previous work has accomplished this by evaluating patterns within summary statistics computed across the genome and through application of machine learning techniques to raw population genomic data. When using raw population genomic data, convolutional neural networks have most recently been employed as they can handle large input arrays and maintain correlations among elements. Yet, such models often require massive amounts of training data and can be computationally expensive to train for a given problem. Instead, transfer learning has recently been used in the image analysis literature to improve machine learning models by learning the important features of images from large unrelated datasets beforehand, and then refining these models through subsequent application on smaller and more relevant datasets. We combine transfer learning with convolutional neural networks to improve classification of selective sweeps from raw population genomic data. We show that the combination of transfer learning with convolutional neural networks allows for accurate classification of selective sweeps.
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Date Issued: 2021
PURL: http://purl.flvc.org/fau/fd/FA00013785
Subject Headings: Transfer learning (Machine learning), Neural networks (Computer science), Natural selection, Genomes
Format: Document (PDF)

Title: Influence of sex hormones and genetic predisposition in dry eye in Sjèogren's syndrome: a new clue to the immunopathogenesis of dry eye disease.
Creator: Mostafa, Safinaz, Charles E. Schmidt College of Medicine, Department of Biological Sciences
Abstract/Description: Sjèogren's syndrome (S) is a chronic autoimmune disease characterized by ocular and oral dryness and primarily affects post menopausal women. In the present study we investigated the time course of lymphocytic infiltration, apoptosis, caspase-3 activity and different cytokines levels in the lacrimal glands of both genetically predisposed and control mice to elucidate immunopathological mechanism leading to dry eye. The results of our experiments showed that ovariectomy accelerated...
Show moreSjèogren's syndrome (S) is a chronic autoimmune disease characterized by ocular and oral dryness and primarily affects post menopausal women. In the present study we investigated the time course of lymphocytic infiltration, apoptosis, caspase-3 activity and different cytokines levels in the lacrimal glands of both genetically predisposed and control mice to elucidate immunopathological mechanism leading to dry eye. The results of our experiments showed that ovariectomy accelerated pathological findings of SS by increasing lympocytic infiltration, cytokine production, lacrimal gland cell death and cleaved caspase-3 activity, and these effects were more pronounced and persistent in the genetically predisposed mouse model of SS. In addition, we observed that lymphocytic infiltration occurred earlier compared to apoptosis which may perpetuate immune mediated destruction of lacrimal epithelial cells. Furthermore, treatment with physioloigical doses of 17-B Estradiol (E2) or DIhydrotestosterone (DHT) prevented all these pathological events observed after ovariectomy.
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Date Issued: 2011
PURL: http://purl.flvc.org/FAU/3353086
Subject Headings: Dry eye syndromes, Immunological aspects, Sjèogren's syndrome, Immunological aspects, Disease susceptibility, Human genome, Medical genetics
Format: Document (PDF)

Title: Bioinformatics mining of the dark matter proteome for cancer targets discovery.
Creator: Delgado, Ana Paula, Narayanan, Ramaswamy, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description: Mining the human genome for therapeutic target(s) discovery promises novel outcome. Over half of the proteins in the human genome however, remain uncharacterized. These proteins offer a potential for new target(s) discovery for diverse diseases. Additional targets for cancer diagnosis and therapy are urgently needed to help move away from the cytotoxic era to a targeted therapy approach. Bioinformatics and proteomics approaches can be used to characterize novel sequences in the genome...
Show moreMining the human genome for therapeutic target(s) discovery promises novel outcome. Over half of the proteins in the human genome however, remain uncharacterized. These proteins offer a potential for new target(s) discovery for diverse diseases. Additional targets for cancer diagnosis and therapy are urgently needed to help move away from the cytotoxic era to a targeted therapy approach. Bioinformatics and proteomics approaches can be used to characterize novel sequences in the genome database to infer putative function. The hypothesis that the amino acid motifs and proteins domains of the uncharacterized proteins can be used as a starting point to predict putative function of these proteins provided the framework for the research discussed in this dissertation.
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Date Issued: 2015
PURL: http://purl.flvc.org/fau/fd/FA00004361, http://purl.flvc.org/fau/fd/FA00004361
Subject Headings: Bioinformatics, Cancer -- Genetic aspects, Drug development -- Data processing, Genomics, Medical informatics, Proteomes -- Data processing, Tumors -- Immunological aspects
Format: Document (PDF)

FAU Theses and Dissertations (10)	+ -
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Honors Student Theses (1)	+ -

Genomics (7)	+ -
Bioinformatics (4)	+ -
Cellular signal transduction (2)	+ -
Gene expression (2)	+ -
Genomes (2)	+ -

Proteomics (2)	+ -
Aquaculture (1)	+ -
Bacterial genetics. (1)	+ -
Bivalves (1)	+ -
CRISPR-associated protein 9 (1)	+ -
CRISPR/Cas9 (1)	+ -
Cancer (1)	+ -
Cancer -- Genetic aspects (1)	+ -
Cell division (1)	+ -
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Cellular signal transduction. (1)	+ -
Centrosomes (1)	+ -
Colon (Anatomy)--Cancer (1)	+ -
DNA microarrays (1)	+ -
Disease susceptibility (1)	+ -
Drug development -- Data processing (1)	+ -
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thesis (1)	+ -

Florida Atlantic University (7)	+ -
Department of Biological Sciences (6)	+ -
Charles E. Schmidt College of Science (5)	+ -
College of Engineering and Computer Science (3)	+ -
Department of Computer and Electrical Engineering and Computer Science (3)	+ -

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