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A rapid colorimetric microassay to detect agonists/antagonists of protein kinase C based on adherence of EL-4.IL-2 cells
Title
A rapid colorimetric microassay to detect agonists/antagonists of protein kinase C based on adherence of EL-4.IL-2 cells.
Creator
Longley, Ross E., Harmody, Dedra K., Harbor Branch Oceanographic Institute
Date Issued
1991
PURL
http://purl.flvc.org/FCLA/DT/3351944
Subject Headings
Protein kinase C, Colorimetric analysis, Diglycerides
Format
Document (PDF)
Characterization of the spinster gene ortholog C13C4.5 in Caenorhabditis elegans
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)
TOPOLOGICAL DATA ANALYSIS FOR DATA SCIENCE: THE DELAUNAY-RIPS COMPLEX, TRIANGULATION STABILITIES, AND PROTEIN STABILITY PREDICTIONS
Title
TOPOLOGICAL DATA ANALYSIS FOR DATA SCIENCE: THE DELAUNAY-RIPS COMPLEX, TRIANGULATION STABILITIES, AND PROTEIN STABILITY PREDICTIONS.
Creator
Mishra, Amish, Motta, Francis, Florida Atlantic University, Department of Mathematical Sciences, Charles E. Schmidt College of Science
Abstract/Description
Topological Data Analysis (TDA) is a relatively new field of research that utilizes topological notions to extract discriminating features from data. Within TDA, persistent homology (PH) is a robust method to compute multi-dimensional geometric and topological features of a dataset. Because these features are often stable under certain perturbations of the underlying data, are often discriminating, and can be used for visualization of structure in high-dimensional data and in statistical and...
Show moreTopological Data Analysis (TDA) is a relatively new field of research that utilizes topological notions to extract discriminating features from data. Within TDA, persistent homology (PH) is a robust method to compute multi-dimensional geometric and topological features of a dataset. Because these features are often stable under certain perturbations of the underlying data, are often discriminating, and can be used for visualization of structure in high-dimensional data and in statistical and machine learning modeling, PH has attracted the interest of researchers across scientific disciplines and in many industry applications. However, computational costs may present challenges to effectively using PH in certain data contexts, and theoretical stability results may not hold in practice. In this dissertation, we develop an algorithm that can reduce the computation burden of computing persistent homology on point cloud data. Naming it Delaunay-Rips (DR), we define, implement, and empirically test this computationally tractable simplicial complex construction for computing persistent homology of Euclidean point cloud data. We demonstrate the practical robustness of DR for persistent homology in comparison with other simplical complexes in machine learning applications such as predicting sleep state from patient heart rate. To justify the theoretical stability of DR, we prove the stability of the Delaunay triangulation of a pointcloud P under perturbations of the points of P. Specifically, we impose a notion of genericity on the points of P to ensure stability. In the final chapter, we contribute to the field of computational biology by taking a data-driven approach to learn topological features of designed proteins from their persistence diagrams. We find correlations between the learned topological features and biochemical features to investigate how protein structure relates to features identified by subject-matter experts. We train several machine learning models to assess the performance of incorporating topological features into training with biochemical features. Using cover-tree differencing via entropy reduction (CDER), we identify distinguishing regions of the persistence diagrams of stable/unstable proteins. More notably, we find statistically significant improvement in classification performance (in terms of average precision score) for certain designed secondary structure topologies.
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Date Issued
2023
PURL
http://purl.flvc.org/fau/fd/FA00014311
Subject Headings
Data Science, Data Analysis, Topology--Data processing, Protein Stability
Format
Document (PDF)
Development of Methods for Separation and Characterization of Proteins from Gorgonian Sources
Title
Development of Methods for Separation and Characterization of Proteins from Gorgonian Sources.
Creator
Jett, Steven W., Florida Atlantic University, Kerr, Russell G., Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
Research into the chemical constituents of marine organisms is a relatively new and growing field, given that much of the marine environment has only in the last half century become accessible. Despite the strides that have been made in ocean exploration, the marine biome has still been only barely explored. Much of the impetus for the isolation and identification of chemical entities from marine organisms has been related to their potential as medicines. For a number of reasons, including...
Show moreResearch into the chemical constituents of marine organisms is a relatively new and growing field, given that much of the marine environment has only in the last half century become accessible. Despite the strides that have been made in ocean exploration, the marine biome has still been only barely explored. Much of the impetus for the isolation and identification of chemical entities from marine organisms has been related to their potential as medicines. For a number of reasons, including synthetic efficiency, this has meant that many marine compounds isolated and studied have been small molecules. In recent years, large strides have been made in techniques for the isolation and identification of biological macromolecules, especially proteins. The understanding of these molecules, and their relationship to the biochemical processes of the marine organisms from which they have been isolated, is important not only because of the potential for this information to help in the synthesis of medicines, but because it may help in the recognition of processes that affect the very viability of marine organisms increasingly exposed to anthropogenic threats to their environment. This work consists of four related studies involving the development of methods for the separation and identification of proteins from a number or gorgon ian species. Chromatographic and gel based methods were used to isolate an elisabethatriene synthase (ELS) which shows promise as a biotechnological tool for the production or pseudopterosins. A number of gorgonians were screened for the presence of proteins that might have antimicrobial properties, and several organisms were identified that might be of interest in this context. Two-dimensional gel electrophoresis methods were then developed to allow the construction of gel maps for the azooxanthellate gorgonian Leptogorgia minimata and the xoozanthellae gorgonian Pseudopterogorgia e/isahethae, the separated proteins were digested and analyzed by LC/MSMS. and the information generated was used to examine the proteome of the organism for functional and phylogenetic relationships. Finally, the gorgonian EuniceafiShow less
Date Issued
2007
PURL
http://purl.flvc.org/fau/fd/FA00000862
Subject Headings
Marine biology, Pharmaceutical biotechnology, Proteins--Analysis, Gene expression--Research--Methodology, Biomolecules--Analysis
Format
Document (PDF)
Characterization of RNase in Mycoplasma genitalium and study of its possible role in tRNA processing
Title
Characterization of RNase in Mycoplasma genitalium and study of its possible role in tRNA processing.
Creator
Lalonde, Maureen S., Florida Atlantic University, Li, Zhongwei, Charles E. Schmidt College of Medicine, Department of Biomedical Science
Abstract/Description
Exoribonucleases degrade RNA and are important in RNA metabolism and gene expression. Mycoplasma genitalium, a bacterium with the smallest genome known, has only one identified exoribonuclease, RNase R (MgR). In this work RNA degradation properties of purified MgR were examined. As observed in Escherichia coli RNase R (EcR) studies, MgR degrades poly(A), rRNA, and oligoribonucleotides in 3'--->5' direction, though its substrate specificity and optimal activity requirements vary. Interestingly...
Show moreExoribonucleases degrade RNA and are important in RNA metabolism and gene expression. Mycoplasma genitalium, a bacterium with the smallest genome known, has only one identified exoribonuclease, RNase R (MgR). In this work RNA degradation properties of purified MgR were examined. As observed in Escherichia coli RNase R (EcR) studies, MgR degrades poly(A), rRNA, and oligoribonucleotides in 3'--->5' direction, though its substrate specificity and optimal activity requirements vary. Interestingly, MgR is sensitive to 2-O-methylation stopping downstream of such modifications in native rRNA and synthetic oligoribonucleotides. MgR removes the 3' trailer sequence from a tRNA precursor of M. genitalium and generates products equal to the mature tRNA, demonstrating a role of MgR in tRNA maturation. The 3' terminal CCA sequence and the acceptor stem of tRNA play a role in determining the formation of such products by MgR. These results suggest multiple functions of RNase R in RNA metabolism in Mycoplasma.
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Date Issued
2006
PURL
http://purl.flvc.org/fcla/dt/13317
Subject Headings
Gene expression, RNA-protein interactions, Cellular control mechanisms, Ribonucleases--Analysis, Cell membranes
Format
Document (PDF)
Assay development for lysyl hydroxylase
Title
Assay development for lysyl hydroxylase.
Creator
Patel, Deepak A., Florida Atlantic University, Fields, Gregg B.
Abstract/Description
Hydroxylysine is produced as a posttranslational modification mainly in collagens, the most abundant protein in mammals. Lysyl hydroxylase (LH) is the enzyme that catalyzes the formation of hydroxylysyl residues in collagen by hydroxylation of -X-Lys-Gly- sequences, for which it requires Fe 2+, 2-oxoglutarate, O2 and ascorbate. In order to study the hydroxylation reaction catalysed by LH, we have synthesized 4 different peptides [for example, GFP*GLP*GAKGE (P*=hydroxyproline) and the...
Show moreHydroxylysine is produced as a posttranslational modification mainly in collagens, the most abundant protein in mammals. Lysyl hydroxylase (LH) is the enzyme that catalyzes the formation of hydroxylysyl residues in collagen by hydroxylation of -X-Lys-Gly- sequences, for which it requires Fe 2+, 2-oxoglutarate, O2 and ascorbate. In order to study the hydroxylation reaction catalysed by LH, we have synthesized 4 different peptides [for example, GFP*GLP*GAKGE (P*=hydroxyproline) and the corresponding hydroxylated (hydroxylysine-containing) peptide] using Fmoc solid-phase methodology. Peptides have been characterized by HPLC, MALDI-TOF mass spectrometry and CD spectroscopy. A new method for efficient separation of lysine- from hydroxylysine-containing peptides by HPLC has been developed in both organic phase (1-anthroylnitrile as derivatizating reagent) and aqueous phase (dansyl chloride as derivatizating reagent). These reagents have been used to derivatize peptides prior to HPLC analysis. The products (di- and tetra-substituted lysine- and hydroxylysine-containing peptides) have been fully separated by HPLC and their structure confirmed by MALDI-TOF MS analysis. Efficient separation of derivatized peptides will allow for the convenient and rapid measurement of LH activity by HPLC methods.
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Date Issued
2006
PURL
http://purl.flvc.org/fcla/dt/13384
Subject Headings
Biological transport, Proteins--Metabolism, Peptides--Analysis, Coenzymes, Bioorganic chemistry
Format
Document (PDF)
Using ATR-IR spectroscopy to study the conformation of cell-penetrating peptides
Title
Using ATR-IR spectroscopy to study the conformation of cell-penetrating peptides.
Creator
Fontoura, Luiza, Rezler, Evonne
Date Issued
2012-04-06
PURL
http://purl.flvc.org/fcla/dt/3351389
Subject Headings
Cell-Penetrating Peptides, Antennapedia Homeodomain Protein, Homeodomain Proteins --chemistry, Spectroscopy, Fourier Transform Infrared --methods, Spectrum Analysis, Amides --chemistry, Carrier Progeins
Format
Document (PDF)
Relationships between the global structure of genetic networks and mRNA levels measured by cDNA microarrays
Title
Relationships between the global structure of genetic networks and mRNA levels measured by cDNA microarrays.
Creator
Liebovitch, Larry S., Shehadeh, Lina A., Jirsa, Viktor K.
Date Issued
2006-05-16
PURL
http://purl.flvc.org/fau/165446
Subject Headings
DNA microarrays, DNA--genetics, Gene Expression Regulation, DNA- protein interactions, Genetic regulation, Messenger RNA--Analysis
Format
Document (PDF)