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Design considerations in high-throughput automation for biotechnology protocols
Title
Design considerations in high-throughput automation for biotechnology protocols.
Creator
Cardona, Aura, Roth, Zvi S., Florida Atlantic University, College of Engineering and Computer Science, Department of Computer and Electrical Engineering and Computer Science
Abstract/Description
In this dissertation a computer-aided automation design methodology for biotechnology applications is proposed that leads to several design guidelines. Because of the biological nature of the samples that propagate in the automation line, a very specific set of environmental and maximum allowed shelf time conditions have to be followed to obtain good yield. In addition all biotechnology protocols require precise sequence of steps, the samples are scarce and the reagents are costly, so no...
Show moreIn this dissertation a computer-aided automation design methodology for biotechnology applications is proposed that leads to several design guidelines. Because of the biological nature of the samples that propagate in the automation line, a very specific set of environmental and maximum allowed shelf time conditions have to be followed to obtain good yield. In addition all biotechnology protocols require precise sequence of steps, the samples are scarce and the reagents are costly, so no waste can be afforded.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00004272, http://purl.flvc.org/fau/fd/FA00004272
Subject Headings
Biotechnological process control, Biotechnological process monitoring, Molecular biology -- Automation, Molecular biology -- Technique, Molecular cloning -- Technique, Pharmacognosy
Format
Document (PDF)
Anatomy and reproductive biology of two Western Atlantic species of Vitrinellidae, with a case of protandrous hermaphroditism in the Rissoacea
Title
Anatomy and reproductive biology of two Western Atlantic species of Vitrinellidae, with a case of protandrous hermaphroditism in the Rissoacea.
Creator
Bieler, R., Mikkelsen, Paula M., Harbor Branch Oceanographic Institute
Date Issued
1988
PURL
http://purl.flvc.org/FCLA/DT/3351935
Subject Headings
Vitrinellidae, Reproductive biology, Anatomy, Hermaphroditism, Sex Determination Processes
Format
Document (PDF)
Biological and geological processes at the shelf edge investigated with submersibles
Title
Biological and geological processes at the shelf edge investigated with submersibles.
Creator
Reed, John K., Hoskin, Charles M.
Date Issued
1987
PURL
http://purl.flvc.org/fau/fd/FA00007289
Subject Headings
Continental shelf--United States, Submersibles, Geology, Biological Processes, Oculinidae
Format
Document (PDF)
Statistical physics inspired methods to assign statistical significance in bioinformatics and proteomics: From sequence comparison to mass spectrometry based peptide sequencing
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)
Biological Computation: the development of a genomic analysis pipeline to identify cellular genes modulated by the transcription / splicing factor srsf1
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)
Targeted Gene Knock-out Via Promoter Tagging in Tomato (Lycopersicon Esculentum) and Tobacco (Nicotiana Tabacum).
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)
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics
Title
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics.
Creator
Liebovitch, Larry S., Figueiroa, Josed N., Nogueira, Romildo A., Varanda, Wamberto A.
Date Issued
2000-10-07
PURL
http://purl.flvc.org/FAU/165249
Subject Headings
Ion channels-Mathematical models, Memory, Chemical kinetics, Calcium channels, Fractals, Markov processes, Leydig cells, Molecular biology--Statistical methods
Format
Document (PDF)
A generalized stochastic birth/death population model based on Indian RiverLagoon dolphins
Title
A generalized stochastic birth/death population model based on Indian RiverLagoon dolphins.
Creator
Stonger, Jon, Noonburg, Erik G., Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
For over a decade, researchers at Harbor Branch Oceanographic Institute (HBOI) have conducted surveys of the bottlenose dolphin (Tursiops truncatus) population of Indian River Lagoon (IRL) in Florida. I have constructed a 4-stage population model using the statistical program R. The model is used to conduct a viability analysis by analyzing the relationship between birth, calf and adult survival rates. The power analysis compares survey frequency to expected confidence intervals in estimating...
Show moreFor over a decade, researchers at Harbor Branch Oceanographic Institute (HBOI) have conducted surveys of the bottlenose dolphin (Tursiops truncatus) population of Indian River Lagoon (IRL) in Florida. I have constructed a 4-stage population model using the statistical program R. The model is used to conduct a viability analysis by analyzing the relationship between birth, calf and adult survival rates. The power analysis compares survey frequency to expected confidence intervals in estimating abundance. The sensitivity analysis shows that the population is most sensitive to changes in adult survival, followed by birth rate and calf survival. The model shows a strong chance of viability over a 50 year time span. The population is vulnerable to long periods of decline if birth, calf or adult survival rates fall below certain thresholds. Overall, the model simulates the future impacts of demographic change, providing a tool for conservation efforts.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00004163, http://purl.flvc.org/fau/fd/FA00004163
Subject Headings
Animal populations -- Estimates, Bottlenose dolphin -- Florida -- Indian River Lagoon -- Geographical distribution, Indian River (Fla : Lagoon), Marine mammal populations -- Estimates -- Florida -- Mathematical models, Population biology, Stochastic processes
Format
Document (PDF)