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University of Illinois – Urbana-Champaign
1.
Witt Dillon, Kelsey E.
A demographic and dietary history of ancient dogs in the Americas using ancient DNA.
Degree: PhD, Ecol, Evol, Conservation Biol, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/98204 
► Dogs were domesticated more than 15,000 years ago, and since then they have become an integral part of human lives. They have served as hunters,…
(more)
▼ Dogs were domesticated more than 15,000 years ago, and since then they have become an integral part of human lives. They have served as hunters, guards, and pets, and have migrated with humans to multiple continents, including the Americas and Australia. The close relationship between humans and dogs makes dogs a valuable proxy when studying human history. In this study, we use
ancient dog remains from the Americas to gain an understanding of their demographic and dietary history, as well as that of humans. Mitochondrial
DNA sequences of the hypervariable region of
ancient dogs were compared to modern and
ancient American dogs to model dog demography and compare populations to identify shared haplotypes. This study identified multiple founding haplotypes, and suggested that dogs arrived to the Americas after the initial human migration. The majority of published
ancient American dog
DNA sequences is of the hypervariable region, so this comparison gives us the opportunity to look at the largest number of dogs across the Americas. We also sequenced complete mitochondrial genomes (mitogenomes), to determine if mitogenome data could be used to confirm the hypotheses made about
ancient American dog demography using the hypervariable region. Mitogenome sequences show a higher-resolution perspective on dog diversity, and the longer sequences revealed different aspects of dog demography. We were able to support the hypotheses that suggest that dogs migrated to the Americas with humans, and that dog populations vary in genetic diversity, but were not able to support the hypotheses that
ancient and modern dogs show continuity, and that dogs arrived to the Americas later in time. We also found that
ancient dog demography mirrors
ancient Native American demography in specific regions of North America, such as the Pacific Coast and Southeast. Finally, we assessed the diet in dogs from the American Bottom using both stable isotopes and shotgun sequencing of dog coprolites, and used the findings about dog diet to infer human diet during the Late Woodland and Mississippian periods. We found that dogs (and humans) ate no maize during the Late Woodland Period, but were consuming large amounts of maize as early as 1010 AD, and maize was likely present in the American Bottom by 900 AD. Additionally, Mississippian dogs and humans supplemented their diet of maize with other foods including squash and fish. The analysis of the history of dogs has yielded a wealth of information about how dogs and humans interacted in the Americas.
Advisors/Committee Members: Malhi, Ripan S (advisor), Malhi, Ripan S (Committee Chair), Kukekova, Anna V (committee member), Roca, Alfred L (committee member), Ambrose, Stanley H (committee member), Kemp, Brian M (committee member).
Subjects/Keywords: Ancient deoxyribonucleic acid (DNA); Domestic dog; Population genetics; Demography; Mitochondrial deoxyribonucleic acid (DNA); Americas; Stable isotopes; Diet
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APA (6th Edition):
Witt Dillon, K. E. (2017). A demographic and dietary history of ancient dogs in the Americas using ancient DNA. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98204
Chicago Manual of Style (16th Edition):
Witt Dillon, Kelsey E. “A demographic and dietary history of ancient dogs in the Americas using ancient DNA.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/98204.
MLA Handbook (7th Edition):
Witt Dillon, Kelsey E. “A demographic and dietary history of ancient dogs in the Americas using ancient DNA.” 2017. Web. 03 Mar 2021.
Vancouver:
Witt Dillon KE. A demographic and dietary history of ancient dogs in the Americas using ancient DNA. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/98204.
Council of Science Editors:
Witt Dillon KE. A demographic and dietary history of ancient dogs in the Americas using ancient DNA. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98204
Victoria University of Wellington
2.
Sirisena, Katugampalage Kosala Ayantha.
Molecular characterization of bacterial diversity in New Zealand groundwater.
Degree: 2014, Victoria University of Wellington
URL: http://hdl.handle.net/10063/3525
► Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and…
(more)
▼ Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and availability of groundwater are both extensively monitored in New Zealand and globally, under State-of-the-Environment (SOE) monitoring programmes. SOE groundwater monitoring in New Zealand mainly evaluates hydrochemistry and until this thesis has largely overlooked the biotic component. Microbes including bacteria play a crucial role in ecosystem functioning by mediating biogeochemical processes in subsurface environments. Therefore, analysis of microbiological content will enable better evaluation of the health of groundwater ecosystems that is not fully reflected by chemical data alone.
This project characterizes the bacterial diversity in New Zealand groundwater at national and regional scales using molecular methods and explores the underlying factors that shape the bacterial community structure. A simple molecular profiling tool, Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine community structure at local and national scales. The results revealed considerable diversity that was driven by groundwater chemistry. Roche 454-pyrosequencing was then used to obtain a deeper insight into New Zealand groundwater ecosystems, and showed that bacterial communities have many low abundance taxa and relatively few highly abundant species. In addition, microbial diversity is mainly related to the redox potential of the groundwater. But, despite this relationship, Pseudomonas spp. were the dominant genus at many sites even those with diverse chemistries and environmental factors. The final phase of the project set the platform to test whether these Pseudomonas spp. have acquired genetic material from other species via horizontal gene transfer (HGT) enabling them to adapt into a diverse range of habitats. A whole-genome sequencing approach (Illumina MiSeq platform) was used to develop six metagenomic databases as a resource to test this hypothesis. Initial results show some evidence for HGT and further investigations are underway.
Overall, the knowledge generated across all phases of this project provides novel insights into New Zealand groundwater ecosystems and creates a scientific basis for the future inclusion of microbial status assessment criteria into regional and national groundwater monitoring programmes and related policies in New Zealand.
Advisors/Committee Members: Chambers, Geoff.
Subjects/Keywords: Microbiology; DNA; Deoxyribonucleic acid; Groundwater
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APA (6th Edition):
Sirisena, K. K. A. (2014). Molecular characterization of bacterial diversity in New Zealand groundwater. (Doctoral Dissertation). Victoria University of Wellington. Retrieved from http://hdl.handle.net/10063/3525
Chicago Manual of Style (16th Edition):
Sirisena, Katugampalage Kosala Ayantha. “Molecular characterization of bacterial diversity in New Zealand groundwater.” 2014. Doctoral Dissertation, Victoria University of Wellington. Accessed March 03, 2021.
http://hdl.handle.net/10063/3525.
MLA Handbook (7th Edition):
Sirisena, Katugampalage Kosala Ayantha. “Molecular characterization of bacterial diversity in New Zealand groundwater.” 2014. Web. 03 Mar 2021.
Vancouver:
Sirisena KKA. Molecular characterization of bacterial diversity in New Zealand groundwater. [Internet] [Doctoral dissertation]. Victoria University of Wellington; 2014. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10063/3525.
Council of Science Editors:
Sirisena KKA. Molecular characterization of bacterial diversity in New Zealand groundwater. [Doctoral Dissertation]. Victoria University of Wellington; 2014. Available from: http://hdl.handle.net/10063/3525
University of Illinois – Urbana-Champaign
3.
Tan, Li Huey.
Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity.
Degree: PhD, Chemistry, 2015, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/88262
► Nanomaterials with their unique optical, electrical and chemical properties are promising candidates for various applications ranging from catalysis to biomedicine. To realize the full potential…
(more)
▼ Nanomaterials with their unique optical, electrical and chemical properties are promising candidates for various applications ranging from catalysis to biomedicine. To realize the full potential of nanomaterials, it is important to demonstrate fine control over nanoparticle morphology, and precise spatial control of the position and orientation between multiple nanoparticles. These issues in the field of nanomaterials are challenging to address and would greatly benefit from the precision and programmability of biomaterials such as
DNA. In order to better apply
DNA to solve issues in the field of nanomaterials, it is necessary to understand the interactions between
DNA and metal nanoparticles. This thesis demonstrates the use of
DNA to offer control over nanoparticle morphology and anisotropicity. The role of
DNA in programming the growth of nanoparticles into different shapes were investigated through ex situ and in situ experiments. The optimal pH range for
DNA to guide nanoparticle growth was investigated. In addition to shape control, precise positioning and assembly of nanoparticles are also important. Anisotropic nanoparticles have been synthesized through competition of
DNA and another hydrophobic ligand on the nanoparticle. Finally, the stabilities of
DNA in the presence of nanoparticles were further investigated to understand the conditions suitable for the
DNA-nanoparticle hybrids to be used for various applications.
Advisors/Committee Members: Lu, Yi (advisor), Lu, Yi (Committee Chair), Braun, Paul V. (committee member), Cheng, Jianjun (committee member), Murphy, Catherine J. (committee member).
Subjects/Keywords: nanoparticle; shape control; Deoxyribonucleic acid (DNA); anisotropicity
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Tan, L. H. (2015). Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/88262
Chicago Manual of Style (16th Edition):
Tan, Li Huey. “Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/88262.
MLA Handbook (7th Edition):
Tan, Li Huey. “Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity.” 2015. Web. 03 Mar 2021.
Vancouver:
Tan LH. Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/88262.
Council of Science Editors:
Tan LH. Studying the interface between DNA and inorganic nanoparticles to control shape and anisotropicity. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/88262
4.
Li, Chen-Yu.
Transport properties of DNA nanostructures.
Degree: PhD, Biophysics & Computnl Biology, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/98248
► Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction…
(more)
▼ Besides the role of genetic information storage,
DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2
DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the
DNA origami. The basic principle of
DNA origami is the programmed folding of a long (tens of thousands of nucleotides)
DNA strand into a custom shape, guided by multiple specially designed short
DNA strands which connect different parts of the long
DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions.
Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the
DNA nanostructures. Recently, an atomic-level model of
DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of
DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of
DNA nanostructures and the underlying mechanism have remained relatively unexplored.
Here, several simulation studies focusing on the transport properties of
DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of
DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of
DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of
DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest
DNA channels so far were developed. The first
DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of
DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.
Advisors/Committee Members: Aksimentiev, Aleksei (advisor), Aksimentiev, Aleksei (Committee Chair), Lu, Yi (committee member), Schleife, Andre (committee member), Shukla, Diwakar (committee member).
Subjects/Keywords: Deoxyribonucleic acid (DNA) origami; Molecular dynamics simulation
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Li, C. (2017). Transport properties of DNA nanostructures. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98248
Chicago Manual of Style (16th Edition):
Li, Chen-Yu. “Transport properties of DNA nanostructures.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/98248.
MLA Handbook (7th Edition):
Li, Chen-Yu. “Transport properties of DNA nanostructures.” 2017. Web. 03 Mar 2021.
Vancouver:
Li C. Transport properties of DNA nanostructures. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/98248.
Council of Science Editors:
Li C. Transport properties of DNA nanostructures. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98248
University of Illinois – Urbana-Champaign
5.
Smith, Lucas David.
Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting.
Degree: MS, Biology, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/98221
► The focus of my graduate research is on the development of simplified and ultrasensitive methods for quantifying low abundance biomarkers with the ultimate goal of…
(more)
▼ The focus of my graduate research is on the development of simplified and ultrasensitive methods for quantifying low abundance biomarkers with the ultimate goal of developing robust tools for advancing disease diagnosis. In recent years there has been an immense expansion in the identification of sensitive and specific indicators of disease. As our understanding of these biochemical parameters continues to advance, the ability to quantify low abundance biomarkers from small samples sizes has become increasingly important to continue expanding the range of available disease indicators. Further, as medical diagnostics continues to transition to point-of-care testing, the development of simplified protocols capable of producing rapid results has been a main element limiting the development of portable devices. Together, each of these factors will play a critical role in the analysis of clinical samples for the purpose of providing more robust diagnostic and prognostic information to patients suffering from diseases ranging from infectious disease to cancer, metabolic, autoimmune, and gastrointestinal disorders. This thesis focuses on two independent projects which aim to address these limitations through the design of improved methods for the quantification of microRNA (miRNA) and protein in biological fluids.
The first of my projects relates to the ultrasensitive detection of miRNA, one of the most exciting emerging classes of biomarkers. In recent years, miRNA in blood circulating have been identified as robust indicators of a variety of diseases. Despite extensive research into the potential impact of miRNAs as clinical indicators, state of the art methods remain dependent on incredibly complex and time consuming techniques. Together, these limitations have been main factors extending research timelines and precluding the development of POC assays. Main factors contributing to the complexity of existing tests include the dependence on reverse transcriptase,
DNA ligase, and PCR steps, each of which necessitate time consuming reagent handling as well as 1-2 h incubations.
To addresses these issues, my research has focused on the development of an efficient RNA amplification technique which uses enzymatic chemical labeling to generate densely labeled double stranded products that are then labeled with fluorescent probes. Individual molecules are then directly counted using total internal reflection fluorescence microscopy, as opposed to conventional indirect methods using the polymerase chain reaction (PCR). This technology provides a fundamental framework for the development of an ultrasensitive miRNA detection method which allows for the absolute and direct quantification of miRNAs in clinical samples. This thesis demonstrates enzymatic labeling of miRNA with fluorescent probes as well as the optimization of surface attachment and probe labeling methods. Ultimately this research concludes with the successful detection of labeled miRNA, establishing a framework for advancing the sensitivity of this method…
Advisors/Committee Members: Smith, Andrew M (advisor).
Subjects/Keywords: Micro-ribonucleic acid (miRNA); Deoxyribonucleic acid (DNA); Synthesis; Microscopy; Single molecule imaging; Fluorophore; Circulating biomarker; Deoxyribonucleic acid (DNA) synthesis; Quantum dot
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Smith, L. D. (2017). Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/98221
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Smith, Lucas David. “Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting.” 2017. Thesis, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/98221.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Smith, Lucas David. “Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting.” 2017. Web. 03 Mar 2021.
Vancouver:
Smith LD. Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/98221.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Smith LD. Ultrasensitive quantification of circulating disease biomarkers through enzymatic labeling and single molecule counting. [Thesis]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/98221
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Bridgeport
6.
Cano, Julian.
Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
.
Degree: 2013, University of Bridgeport
URL: https://scholarworks.bridgeport.edu/xmlui/handle/123456789/1394
► For the past decade, Prostate specific antigen levels have been the diagnostic method to diagnose Prostate cancer. Testing PSA gene levels by themselves are not…
(more)
▼ For the past decade, Prostate specific antigen levels have been the diagnostic method to diagnose Prostate cancer. Testing PSA gene levels by themselves are not enough to diagnose prostate cancer. In fact, one can argue that DNA hypermethylation, histones methylation and hypoacetylation genes are better markers to diagnose prostate cancer. These markers are the most common somatic alterations present in prostate cancer. Furthermore, evidence suggests that epigenetic mechanisms, such as DNA hypermethylation, histones methylation and hypoacetylation affect gene expression in patients with prostate cancer. One can argue that one of the first hallmarks of epigenetic alterations in DNA hypermethylation is the addition of a methyl group to the 5’-carbon of cytosine in the Cytosine-phosphate-Guanine (CpG) sequences catalyzed by DNA methyltransferase. Furthermore, such epigenetics aberration modified the humoral response, cell cycle control, tumor invasion/tumor architecture, DNA damage repair, signal transduction and inflammation response genes. The objective of Naturopathic medicine is to identify and prevent the Epigenetics aberrations in DNA and histones genes in the genome sequence. Furthermore, a potential treatment can be a combination of DNA methyltransferase and Histones deacetylation inhibitors for patients with prostate cancer by using nutrition and botanical medicine.
Subjects/Keywords: Epigenetics;
Deoxyribonucleic acid (DNA) hypermethylation;
Histones methylation;
Histones acetylation;
Prostate cancer;
Polyphenols;
Naturopathy;
Deoxyribonucleic acid (DNA)
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APA ·
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APA (6th Edition):
Cano, J. (2013). Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
. (Thesis). University of Bridgeport. Retrieved from https://scholarworks.bridgeport.edu/xmlui/handle/123456789/1394
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Cano, Julian. “Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
.” 2013. Thesis, University of Bridgeport. Accessed March 03, 2021.
https://scholarworks.bridgeport.edu/xmlui/handle/123456789/1394.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cano, Julian. “Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
.” 2013. Web. 03 Mar 2021.
Vancouver:
Cano J. Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
. [Internet] [Thesis]. University of Bridgeport; 2013. [cited 2021 Mar 03].
Available from: https://scholarworks.bridgeport.edu/xmlui/handle/123456789/1394.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cano J. Epigenetcs and Naturopathic Medicine: Their Role in Prostate Cancer
. [Thesis]. University of Bridgeport; 2013. Available from: https://scholarworks.bridgeport.edu/xmlui/handle/123456789/1394
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Pretoria
7.
[No author].
Analysis and standardization of marker genotype data
for DNA fingerprinting applications
.
Degree: 2011, University of Pretoria
URL: http://upetd.up.ac.za/thesis/available/etd-10212011-171754/
► Genetic polymorphisms can be seen as the occurrence of more than one form of a DNA- or protein sequence at a single locus in a…
(more)
▼ Genetic polymorphisms can be seen as the occurrence
of more than one form of a
DNA- or protein sequence at a single
locus in a group of organisms, where these different forms occur
more frequently than can be attributed to mutation alone. The
combination of genetic polymorphisms present in the genome of a
particular individual is referred to as its genotype. A wide range
of genotyping techniques have been developed to detect and
visualize genetic polymorphisms. One such technique examines highly
polymorphic repetitive
DNA regions called microsatellites, also
called “short tandem repeats” (STRs) and sometimes “simple sequence
repeats” (SSRs) or “simple-sequence length polymorphisms” (SSLPs).
A microsatellite region consists of a
DNA sequence of identical
units of usually 2-6 base pairs strung together to produce highly
variable numbers of tandem repeats among individuals of a
population. Microsatellite genotyping is a popular choice for many
types of studies including individual identification, paternity
testing, germplasm evaluation, genome mapping and diversity studies
and can be used in many commercial, academic, social, and
agricultural applications. There are, however, many obstacles in
effectively managing and analysing microsatellite genotype data.
Currently, researchers are struggling to effectively manage and
analyse rapidly growing volumes of genotyping data. Management
problems range from simply the lack of a secure, easily accessible
central data repository to more complex issues like the merging and
standardization of data from multiple sources into combined
datasets. Due to these issues, genetic fingerprinting applications
such as identity matching and relatedness studies can be
challenging when data from different experiments or laboratories
have to be combined into a central database. The main aim of this
M.Sc study in Bioinformatics was to develop a bioinformatics
resource for the management and analysis of genetic fingerprinting
data from microsatellite marker genotyping studies, and to apply
the software to the analysis of microsatellite marker data from
ramets of Pinus patula clones with the purpose of analysing clonal
identity in pine breeding programmes. The software resource
developed here is called GenoSonic. It is a web application that
provides users with a secure, easily accessible space where
genotyping project data can be managed and analysed as a team.
Users can upload and download large amounts of marker genotype
data. Once uploaded to the system,
DNA fingerprint data needs to be
standardised before it can be used in further analyses. To do this,
a two-step approach was implemented in GenoSonic. The first step is
to assign standardized allele sizes to all of the input allele
sizes of the microsatellite fingerprints automatically using a
novel automated binning algorithm called CSMerge-1, which was
designed specifically to bin data from multiple experiments. The
second step is to manually verify the results from the automated
binning function and add the verified data to a standardized…
Advisors/Committee Members: Myburg, Alexander Andrew (advisor), Joubert, Fourie (advisor).
Subjects/Keywords: Genetic polymorphisms;
Deoxyribonucleic acid (DNA);
Fingerprinting applications;
Genotype data;
UCTD
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❌
APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
author], [. (2011). Analysis and standardization of marker genotype data
for DNA fingerprinting applications
. (Masters Thesis). University of Pretoria. Retrieved from http://upetd.up.ac.za/thesis/available/etd-10212011-171754/
Chicago Manual of Style (16th Edition):
author], [No. “Analysis and standardization of marker genotype data
for DNA fingerprinting applications
.” 2011. Masters Thesis, University of Pretoria. Accessed March 03, 2021.
http://upetd.up.ac.za/thesis/available/etd-10212011-171754/.
MLA Handbook (7th Edition):
author], [No. “Analysis and standardization of marker genotype data
for DNA fingerprinting applications
.” 2011. Web. 03 Mar 2021.
Vancouver:
author] [. Analysis and standardization of marker genotype data
for DNA fingerprinting applications
. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Mar 03].
Available from: http://upetd.up.ac.za/thesis/available/etd-10212011-171754/.
Council of Science Editors:
author] [. Analysis and standardization of marker genotype data
for DNA fingerprinting applications
. [Masters Thesis]. University of Pretoria; 2011. Available from: http://upetd.up.ac.za/thesis/available/etd-10212011-171754/
University of Pretoria
8.
Schriek, Cornelis
Arnold.
Analysis and
standardization of marker genotype data for DNA fingerprinting
applications.
Degree: Biochemistry, 2011, University of Pretoria
URL: http://hdl.handle.net/2263/28908
► Genetic polymorphisms can be seen as the occurrence of more than one form of a DNA- or protein sequence at a single locus in a…
(more)
▼ Genetic polymorphisms can be seen as the occurrence of
more than one form of a
DNA- or protein sequence at a single locus
in a group of organisms, where these different forms occur more
frequently than can be attributed to mutation alone. The
combination of genetic polymorphisms present in the genome of a
particular individual is referred to as its genotype. A wide range
of genotyping techniques have been developed to detect and
visualize genetic polymorphisms. One such technique examines highly
polymorphic repetitive
DNA regions called microsatellites, also
called “short tandem repeats” (STRs) and sometimes “simple sequence
repeats” (SSRs) or “simple-sequence length polymorphisms” (SSLPs).
A microsatellite region consists of a
DNA sequence of identical
units of usually 2-6 base pairs strung together to produce highly
variable numbers of tandem repeats among individuals of a
population. Microsatellite genotyping is a popular choice for many
types of studies including individual identification, paternity
testing, germplasm evaluation, genome mapping and diversity studies
and can be used in many commercial, academic, social, and
agricultural applications. There are, however, many obstacles in
effectively managing and analysing microsatellite genotype data.
Currently, researchers are struggling to effectively manage and
analyse rapidly growing volumes of genotyping data. Management
problems range from simply the lack of a secure, easily accessible
central data repository to more complex issues like the merging and
standardization of data from multiple sources into combined
datasets. Due to these issues, genetic fingerprinting applications
such as identity matching and relatedness studies can be
challenging when data from different experiments or laboratories
have to be combined into a central database. The main aim of this
M.Sc study in Bioinformatics was to develop a bioinformatics
resource for the management and analysis of genetic fingerprinting
data from microsatellite marker genotyping studies, and to apply
the software to the analysis of microsatellite marker data from
ramets of Pinus patula clones with the purpose of analysing clonal
identity in pine breeding programmes. The software resource
developed here is called GenoSonic. It is a web application that
provides users with a secure, easily accessible space where
genotyping project data can be managed and analysed as a team.
Users can upload and download large amounts of marker genotype
data. Once uploaded to the system,
DNA fingerprint data needs to be
standardised before it can be used in further analyses. To do this,
a two-step approach was implemented in GenoSonic. The first step is
to assign standardized allele sizes to all of the input allele
sizes of the microsatellite fingerprints automatically using a
novel automated binning algorithm called CSMerge-1, which was
designed specifically to bin data from multiple experiments. The
second step is to manually verify the results from the automated
binning function and add the verified data to a standardized…
Advisors/Committee Members: Myburg, Alexander Andrew (advisor), Joubert, Fourie (coadvisor).
Subjects/Keywords: Genetic
polymorphisms;
Deoxyribonucleic acid (DNA); Fingerprinting
applications; Genotype
data;
UCTD
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APA (6th Edition):
Schriek, C. (2011). Analysis and
standardization of marker genotype data for DNA fingerprinting
applications. (Masters Thesis). University of Pretoria. Retrieved from http://hdl.handle.net/2263/28908
Chicago Manual of Style (16th Edition):
Schriek, Cornelis. “Analysis and
standardization of marker genotype data for DNA fingerprinting
applications.” 2011. Masters Thesis, University of Pretoria. Accessed March 03, 2021.
http://hdl.handle.net/2263/28908.
MLA Handbook (7th Edition):
Schriek, Cornelis. “Analysis and
standardization of marker genotype data for DNA fingerprinting
applications.” 2011. Web. 03 Mar 2021.
Vancouver:
Schriek C. Analysis and
standardization of marker genotype data for DNA fingerprinting
applications. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2263/28908.
Council of Science Editors:
Schriek C. Analysis and
standardization of marker genotype data for DNA fingerprinting
applications. [Masters Thesis]. University of Pretoria; 2011. Available from: http://hdl.handle.net/2263/28908
University of Illinois – Urbana-Champaign
9.
Kim, Grace.
Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility.
Degree: MS, 0408, 2015, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/73080
► The ends of human telomeric DNA consist of single-stranded overhangs of tandem TTAGGG repeats (ssTEL) that can form into a G-quadruplex (GQ). This guanine-rich sequence…
(more)
▼ The ends of human telomeric
DNA consist of single-stranded overhangs of tandem TTAGGG repeats (ssTEL) that can form into a G-quadruplex (GQ). This guanine-rich sequence is prone to 8-oxoguanine (8OG) damage, which is one of the most common oxidative
DNA lesions that can compromise telomere integrity. Here, we use single molecule Förster Resonance Energy Transfer (smFRET) to characterize the effect of 8OG on the structural dynamics and accessibility of ssTEL. We show that the stable GQ folding observed in ssTEL is disrupted by a single 8OG, generating dynamic conformational fluctuations of the
DNA. Such structural dynamics induced by 8OG contributes to increased passive binding of complementary
DNA oligonucleotides, as well as faster and more effective active binding of the protection of telomeres 1 (POT1) shelterin protein, suggesting enhanced accessibility of telomeric
DNA to interacting molecules. The increased dynamics and accessibility caused by 8OG is comparable to the effect of a base substitution from G to C at the same position, which abolishes the Hoogsteen basepairing required for GQ folding. Our results suggest that a single 8OG can lead to destabilization of GQ folding, which may allow loading of telomeric proteins, including those involved in telomere length maintenance.
Advisors/Committee Members: Myong, Su-A (advisor).
Subjects/Keywords: Oxidative stress; 8-oxo-guanine; Quadruplex; Deoxyribonucleic Acid (DNA); Telomere; Accessibility
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kim, G. (2015). Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/73080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Kim, Grace. “Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility.” 2015. Thesis, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/73080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kim, Grace. “Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility.” 2015. Web. 03 Mar 2021.
Vancouver:
Kim G. Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/73080.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kim G. Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility. [Thesis]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/73080
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Urbana-Champaign
10.
Zhao, Yang.
Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications.
Degree: MS, 1200, 2012, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/29457
► This thesis discusses the use of carbon nanotube field effect transistors as sensors for DNA. It proposes a band-gap modulation as the underlying physical mechanism…
(more)
▼ This thesis discusses the use of carbon nanotube field effect transistors as sensors for
DNA. It proposes a band-gap modulation as the underlying physical mechanism by which detection occurs. Previous works have established that either Schottky – barrier modulation or electro – static gating are the most significant mechanisms, depending on the particular device. By analyzing field effect mobilities it can be seen that the band-gap modulation effect shows up in every device and can be a reliable means by which detection of hybridized
DNA molecules can occur.
Advisors/Committee Members: Liu, Gang Logan (advisor).
Subjects/Keywords: Carbon nanotubes; Deoxyribonucleic acid (DNA); bio-sensing; mobility
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APA (6th Edition):
Zhao, Y. (2012). Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29457
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Zhao, Yang. “Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications.” 2012. Thesis, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/29457.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhao, Yang. “Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications.” 2012. Web. 03 Mar 2021.
Vancouver:
Zhao Y. Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/29457.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhao Y. Analysis of physical mechanisms for the detection of DNA in carbon nanotube field effect transistors for bio-sensing applications. [Thesis]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29457
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Urbana-Champaign
11.
Tabatabaei Yazdi, Seyed Mohammadhossein.
DNA–based data storage system.
Degree: PhD, Electrical & Computer Engr, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/99359
► Despite the many advances in traditional data recording techniques, the surge of Big Data platforms and energy conservation issues has imposed new challenges to the…
(more)
▼ Despite the many advances in traditional data recording techniques, the surge of Big Data platforms and energy conservation issues has imposed new challenges to the storage community in terms of identifying extremely high volume, non-volatile and durable recording media. The potential for using macromolecules for ultra-dense storage was recognized as early as 1959 when Richard Feynman outlined his vision for nanotechnology in a lecture, “There is plenty of room at the bottom”. Among known macromolecules,
DNA is unique insofar as it lends itself to implementations of non-volatile recording media of outstanding integrity and extremely high storage capacity.
The basic system implementation steps for
DNA-based data storage systems include synthesizing
DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders.
In this work we advance the field of macromolecular data storage in three directions. First, we introduce the notion of weakly mutually uncorrelated (WMU) sequences. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. For this purpose, WMU sequences used for primer design in DNAbased data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefixsynchronized and cyclic codes.
Second, we describe the first
DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on the newly developed WMU coding techniques and accompanying
DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in
DNA corresponding to three of these schools. The results suggest that
DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.
Third, we demonstrate for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. Every solution for
DNA-based data storage systems so far has exclusively focused on Illumina sequencing devices, but such sequencers are…
Advisors/Committee Members: Milenkovic, Olgica (advisor), Milenkovic, Olgica (Committee Chair), Veeravalli, Venugopal Varadachari (committee member), Singer, Andy (committee member), Duursma, Iwan M (committee member), Ma, Jian (committee member).
Subjects/Keywords: Data storage; Deoxyribonucleic acid (DNA)-based data storage system
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Tabatabaei Yazdi, S. M. (2017). DNA–based data storage system. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/99359
Chicago Manual of Style (16th Edition):
Tabatabaei Yazdi, Seyed Mohammadhossein. “DNA–based data storage system.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/99359.
MLA Handbook (7th Edition):
Tabatabaei Yazdi, Seyed Mohammadhossein. “DNA–based data storage system.” 2017. Web. 03 Mar 2021.
Vancouver:
Tabatabaei Yazdi SM. DNA–based data storage system. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/99359.
Council of Science Editors:
Tabatabaei Yazdi SM. DNA–based data storage system. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/99359
University of Illinois – Urbana-Champaign
12.
Serrano, Julio Francisco.
Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA.
Degree: PhD, Chemistry, 2017, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/99509
► Mismatched base pairs are ubiquitous in more than 30 hereditary disorders whose origin can be traced to unstable repeating sequences in genomic DNA. For instance,…
(more)
▼ Mismatched base pairs are ubiquitous in more than 30 hereditary disorders whose origin can be traced to unstable repeating sequences in genomic
DNA. For instance, non-Watson– Crick T–T mismatch base pairs flanked by G–C base pairs appear in myotonic dystrophy type 1 (DM1), which is caused by the expansion of CTG trinucleotide repeats (TNR) in the 3’- untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. Extensive efforts have made it possible to elucidate its pathogenesis and mechanism of action. In this regard, numerous compounds have been developed that target the toxic repeating CUG RNA transcript (r(CUG)exp) and inhibit its sequestration of key pre-mRNA splicing proteins, such as MBNL1. Indeed, since we reported our first ligand JFA in 2009, our group has been at the forefront in discovering ligands that specifically bind U–U mismatches and can potentially be used as therapeutics. More recently, we have started to focus our efforts to discover molecules that target the parent CTG expanded repeats (d(CTG)exp) in hopes to develop a more promising therapeutic. A brief overview of targeting
DNA,
DNA mismatches, DM1 and our ligands is given in Chapter 1.
A previous anisotropy screen in our lab of ligands that inhibit the MBNL1–r(CUG)exp complex identified a novel lead pyrroloquinazoline compound. However, as we will see in Chapter 2, further investigation revealed that it was selective for T–T mismatches. Interestingly, we noted that mode of binding toward CTG mismatched sites appeared to be cooperative. Due to its limited water solubility, we attempted to develop further derivatives. We took into consideration these observations to develop and improve our acridine-base ligands in the last chapter.
To further improve the affinity and selectivity of our acridine-based ligands, we proceeded to develop a series of enforced stacked intercalators. Our first approach involved utilizing a larger mismatch-recognition diaminopurine unit, as the described in the first part of Chapter 3. However, although selective for T–T and C–C mismatches, its nonspecific binding was not improved. Finally, we employed a macrocyclic design, and developed a small library of macrocycles. We showed that these ligands selectively bind to CTG trinucleotide repeats in
DNA with negligible nonspecific binding to duplex
DNA. In addition, they were about twice as effective and selective in inhibiting transcription than the control. Lastly, we discovered that the macrocyclic structure design of our ligands did not necessarily correlate with a reduction in their cytotoxicity in HeLa cells, as we had previously hypothesized. The synthesis, biophysical studies, and in vitro activity of these macrocyclic ligands are described in the second part of Chapter 3.
Advisors/Committee Members: Zimmerman, Steven C. (advisor), Zimmerman, Steven C. (Committee Chair), Mitchell, Douglas A. (committee member), van der Donk, Wilfred A. (committee member), Huang, Raven H. (committee member).
Subjects/Keywords: Macrocycle bisintercalator; Deoxyribonucleic acid (DNA) targeting; Small molecules
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Serrano, J. F. (2017). Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/99509
Chicago Manual of Style (16th Edition):
Serrano, Julio Francisco. “Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA.” 2017. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/99509.
MLA Handbook (7th Edition):
Serrano, Julio Francisco. “Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA.” 2017. Web. 03 Mar 2021.
Vancouver:
Serrano JF. Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/99509.
Council of Science Editors:
Serrano JF. Development of enforced stacked intercalators that target trinucleotide repeat mismatches in DNA. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2017. Available from: http://hdl.handle.net/2142/99509
Texas Tech University
13.
Hirsch, Rachael.
Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation.
Degree: TTUHSC – Cell and Molecular Biology, 2006, Texas Tech University
URL: http://hdl.handle.net/2346/19437
► Complete and accurate DNA replication is essential for proper cell division and thus the genetic integrity of all organisms. Several mechanisms regulate the process of…
(more)
▼ Complete and accurate
DNA replication is essential for proper cell division and thus the genetic integrity of all organisms. Several mechanisms regulate the process of
DNA replication particularly during the initiation stage. Initiation must be carefully regulated to ensure that each segment of the
DNA is replicated at the appropriate time, and only once per cell cycle. Cells achieve this by having a distinct stage that occurs prior to S-phase when replication origins become licensed for replication. At the onset of S-phase, replication forks are initiated only at these licensed origins. Licensing corresponds to the ordered assembly of multiprotein complexes celled pre-replication complexes (pre-RCs) onto the
DNA at replication origins. These complexes are composed of Orc, Cdc6, Cdt1, and Mcm proteins. Once assembled the pre-RCs are activated at the appropriate time to trigger
DNA replication. Two major kinases are known to participate in this activation, Cdk2/Cyclin E and Cdc7/Dbf4, though their mechanism of action is unknown. How these kinases regulate the initiation of replication is an important question underlying the regulation of the cell cycle and the maintenance of genomic integrity in all organisms.
My study focuses on determining the role of the Cdc7 kinase in
DNA replication initiation using an in vitro cell free system derived from Xenopus laevis eggs. Cdc7 kinase activity is reportedly dependent on a regulatory binding partner, called Dbf4. Members of our laboratory identified two potential Dbf4-related proteins in Xenopus laevis, XDbf4 and XDrf1. Since multiple Dbf4-related proteins within the same species had previously been reported in other organisms, I hypothesized that both of these proteins could interact with Xenopus Cdc7 to form active kinases that function during early embryonic
DNA replication.
In this study I show that both XDbf4 and XDrf1 physically interact with XCdc7 in interphase egg extracts to form two separate active kinase complexes. Furthermore I suggest that these two complexes are developmentally regulated indicating the possibility that they could function during different stages of early Xenopus development. Interestingly my data indicate that only the XCdc7/Drf1 complex is required for efficient early embryonic
DNA replication. Furthermore, this complex seems to function specifically at the point of pre-RC activation, and not during pre-RC assembly. I also examined the mechanisms that could contribute to the regulation of the XCdc7 kinase. Cell-cycle mediated phosphorylation of the XCdc7 complex did not appear to affect its kinase activity. However, pre-phosphorylation of its XMcm2 substrate by Cdk did enhance its phosohorylation by XCdc7. Therefore, this could indicate a direct relationship between S-phase Cdks and the Cdc7 kinase. In addition to these studies, I also analyzed the potential involvement of the XCdc7 kinases in replication checkpoints that ensure that the cell cycle does not proceed without proper
DNA replication. My studies indicated that these two…
Advisors/Committee Members: Coue, Martine (Committee Chair), Schneider, Brandt (committee member), MacDonald, Clinton C. (committee member), Hutson, Jim (committee member), Whelly, Sandra M. (committee member).
Subjects/Keywords: Deoxyribonucleic acid (DNA) replication
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APA ·
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MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Hirsch, R. (2006). Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/19437
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hirsch, Rachael. “Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation.” 2006. Thesis, Texas Tech University. Accessed March 03, 2021.
http://hdl.handle.net/2346/19437.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hirsch, Rachael. “Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation.” 2006. Web. 03 Mar 2021.
Vancouver:
Hirsch R. Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation. [Internet] [Thesis]. Texas Tech University; 2006. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2346/19437.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hirsch R. Characterization of XCdc7/Dbf4 and Cdc7/Drf1 in DNA replication initiation. [Thesis]. Texas Tech University; 2006. Available from: http://hdl.handle.net/2346/19437
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Texas Tech University
14.
London, Darin M.
The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae).
Degree: Biology, 1999, Texas Tech University
URL: http://hdl.handle.net/2346/13447
► Proctolaelaps regalis DeLeon (Acari: Ascidae) is a species of free-living, omnivorous mites recently implicated as a potential vector in a horizontal gene transfer event between…
(more)
▼ Proctolaelaps regalis DeLeon (Acari: Ascidae) is a species of free-living, omnivorous mites recently implicated as a potential vector in a horizontal gene transfer event between Drosophila willistoni and D. melanogaster. In this research, I investigated behaviors of the mite impacting its potential to acquire, maintain within the mite population, and transfer genes between flies. The potential of the mite to acquire and transfer genes is related to its propensity to prey upon the fly, but also to the population size and density of mites and flies within their habitat. Thus, aggregation and social behaviors exhibited by mites should influence their potential to acquire and transfer genes, and to maintain genes within the population. Mites were observed clustering in groups within the colony and depositing eggs in clusters. Mites were also observed to prefer fly growth medium previously conditioned to conspecific mites in culture over fresh medium, suggesting the presence of an aggregation pheromone. To investigate the propensity of the mites to prey upon D. melanogaster, and the search behavior response of mites to conspecific eggs and conspecific-conditioned growth medium, I used a paired-sample design in which individual mites were sequentially exposed to a control environment and seven potential resources. Each mite's behavior was recorded to determine its response. Mites were assessed for general attraction to the treatment in relation to their behavior in the control environment. Mites were also assessed for shifts in their search path pattern in response to the treatments. Mites were observed in small colonies for behaviors not addressed in the research design. The behavior of the mite was not influenced by the life-history stages of D. melanogaster. Mites were attracted to conspecific eggs, and strongly attracted to the conditioned growth medium. Mites exhibited potential social interactions within the colony, including intimate contacts between individual mites. They also exhibited aggressive behaviors and egg cannibalism. The lack of attraction to flies could decrease the mite's potential to acquire and transmit the gene. However, the mites may prey upon flies opportunistically, or switch to predation under periods of habitat decline. This would limit predation to certain times, but would not necessarily reduce the mite's potential as a vector.
Subjects/Keywords: Drosophila; Deoxyribonucleic acid (DNA); Mites
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APA ·
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Export
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Manager
APA (6th Edition):
London, D. M. (1999). The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae). (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/13447
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
London, Darin M. “The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae).” 1999. Thesis, Texas Tech University. Accessed March 03, 2021.
http://hdl.handle.net/2346/13447.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
London, Darin M. “The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae).” 1999. Web. 03 Mar 2021.
Vancouver:
London DM. The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae). [Internet] [Thesis]. Texas Tech University; 1999. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2346/13447.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
London DM. The feeding and reproductive behavior of Proctolaelaps regalis (Gamasina: Ascidae). [Thesis]. Texas Tech University; 1999. Available from: http://hdl.handle.net/2346/13447
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Urbana-Champaign
15.
Madabhusi Ragunathan, Kaushik.
Single molecule fret study on the mechanism of RecA mediated strand exchange.
Degree: PhD, 0319, 2012, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/32044
► RecA plays a critical role during double strand break repair via homologous recombination. During the strand exchange reaction, RecA forms a helical filament on single…
(more)
▼ RecA plays a critical role during double strand break repair via homologous recombination. During the strand exchange reaction, RecA forms a helical filament on single stranded (ss)
DNA that searches for homology and exchanges complementary base pairs with a homologous double strand (ds)
DNA to form a new heteroduplex. The study of strand exchange in ensemble assays is limited by the diffusion limited homology search process which masks the subsequent strand exchange reaction. We developed a single molecule fluorescence assay with a few basepair and milliseconds resolution which can separate initial docking from the subsequent propagation of joint molecule formation. Our data suggests that propagation occurs in 3 bp increments with destabilization of the incoming dsDNA and concomitant pairing with the reference ssDNA. Our model for strand exchange links structural models of RecA to its catalytic function.
Next, we investigated the mechanism of RecA mediated homology search. Using tools with high spatiotemporal resolution to observe the encounter complex between the RecA filament and dsDNA, we present evidence in support of the “sliding model” wherein a RecA filament diffuses on a dsDNA track. Our results suggest that the sliding of the dsDNA relative to the RecA filament can explain the rapid changes in FRET which we have observed upon the docking of non-homologous dsDNA to the RecA filament. We further show that homology can be identified during such sliding. Sliding is thermally driven and occurs in the absence of ATP hydrolysis. Furthermore, homology recognition and basepairing can involve as few as 6 bp of complementarity. Our observation presents an example of how a multi-protein complex bound to
DNA can serve as a vehicle enabling homology search processes via 1-D sliding.
Finally, we demonstrate how an extension of the two color FRET assay to measure four colors simultaneously allows us to measure the correlation of reaction completion between the two ends of a single synaptic complex. We expect that this method will enable a multi dimensional analysis of independent reaction coordinates with broad applications in measuring the correlated dynamics of more complex biological systems
Advisors/Committee Members: Ha, Taekjip (advisor), Ha, Taekjip (Committee Chair), Nair, Satish K. (committee member), Spies, Maria (committee member), Chemla, Yann R. (committee member).
Subjects/Keywords: DNA repair; recombination; single molecule; Fluorescence resonance energy transfer (FRET); fluorescence; Deoxyribonucleic acid (DNA)
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APA (6th Edition):
Madabhusi Ragunathan, K. (2012). Single molecule fret study on the mechanism of RecA mediated strand exchange. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/32044
Chicago Manual of Style (16th Edition):
Madabhusi Ragunathan, Kaushik. “Single molecule fret study on the mechanism of RecA mediated strand exchange.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/32044.
MLA Handbook (7th Edition):
Madabhusi Ragunathan, Kaushik. “Single molecule fret study on the mechanism of RecA mediated strand exchange.” 2012. Web. 03 Mar 2021.
Vancouver:
Madabhusi Ragunathan K. Single molecule fret study on the mechanism of RecA mediated strand exchange. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/32044.
Council of Science Editors:
Madabhusi Ragunathan K. Single molecule fret study on the mechanism of RecA mediated strand exchange. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/32044
University of Illinois – Urbana-Champaign
16.
Hsiao, Kuei-Yang.
A histone H4 code regulates 53BP1-mediated responses to DNA damage.
Degree: PhD, 0325, 2012, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/29532
► Individual histone post-translational modifications have been implicated in regulating many cellular events. Modifications can occur at high densities in the N-terminal tail domains of core…
(more)
▼ Individual histone post-translational modifications have been implicated in regulating many cellular events. Modifications can occur at high densities in the N-terminal tail domains of core histones, enabling the possibility that combinations of modifications regulate chromatin processes differently than modifications occurring individually. However, surprisingly little is known about the nature and functions of multi-site histone modification. This study investigates functional interactions between acetylation of lysine 16 (K16ac) and methylation of lysine 20 (K20me), two modifications that frequently occur together on molecules of histone H4 (H4). Methylation state-specific binding of the P53-binding protein 1 (53BP1) to dimethyl K20 H4 (K20me2) and the formation of 53BP1 nuclear foci near double strand breaks are early events in
DNA damage responses (DDR) that provide a platform for the assembly of downstream effectors. Since global levels of K20me2 are relatively stable and are established independently of
DNA damage, we propose that reversible changes in the levels of K16ac co-modification act like a dynamic switch to modulate DDR responses mediated by K20me2. Analyses of the interaction of the K20me2 binding domain of 53BP1 with H4 peptides in vitro reveal that K16ac co-modification attenuates specific recognition of K20me1/2 (mono- and di-methylation) by 53BP1. The possibility that K16ac and K20me2 interact functionally in vivo is demonstrated by my finding that K16 deacetylation accompanies the induction of H2A.X phosphorylation, a well-known marker for DDR, following
DNA damage by either UV irradiation, hydroxyurea or bleocin treatment. Moreover, the effects of expressing K16 mutants of H4 and inhibition of histone deacetylases on 53BP1 foci formation induced by
DNA damage support the hypothesis that K16ac co-modification negatively regulates the formation of 53BP1 foci. The functional significance of these interactions is underscored by the finding that K16 hyperacetylation also hindered 53BP1-mediated nonhomologous end-joining as demonstrated by treatment of HDACi and overexpression of a H4 mutant mimicking acetylation at K16.
DNA damage-induced deacetylation was associated with transcriptional repression, but was not linked to chromatin decondensation. Deregulated DDR mechanisms are frequently involved in the development and progression of cancer, and interruption of the DDR is used in chemotherapeutic treatments against cancer. Further investigation of the role of H4 modifications in DDR will enhance our understanding of how genome integrity is maintained in normal cells and may provide insights crucial for developing new cancer therapies.
Advisors/Committee Members: Mizzen, Craig A. (advisor), Bagchi, Milan K. (committee member), Kemper, Byron W. (committee member), Nardulli, Ann M. (committee member), Spies, Maria (committee member).
Subjects/Keywords: DNA damage; P53-binding protein 1 (53BP1); histone H4; methylation; acetylation; deacetylation; Deoxyribonucleic acid (DNA)
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MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Hsiao, K. (2012). A histone H4 code regulates 53BP1-mediated responses to DNA damage. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29532
Chicago Manual of Style (16th Edition):
Hsiao, Kuei-Yang. “A histone H4 code regulates 53BP1-mediated responses to DNA damage.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/29532.
MLA Handbook (7th Edition):
Hsiao, Kuei-Yang. “A histone H4 code regulates 53BP1-mediated responses to DNA damage.” 2012. Web. 03 Mar 2021.
Vancouver:
Hsiao K. A histone H4 code regulates 53BP1-mediated responses to DNA damage. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/29532.
Council of Science Editors:
Hsiao K. A histone H4 code regulates 53BP1-mediated responses to DNA damage. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29532
University of Illinois – Urbana-Champaign
17.
He, Ying.
Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays.
Degree: PhD, 0130, 2012, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/29571
► Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+…
(more)
▼ Fluorescence resonance energy transfer (FRET) is used to monitor the metal ion dependent conformational change of the UO22+ specific DNAzyme 39E. Inactive metal ions, Mg2+ and Zn2+ are found capable of inducing folding between two pairs of stems while the active ions UO22+ and Pb2+ are not able to bring about the folding in any pairs of the stems. By correlating the enzymatic cleavage results, the Mg2+ and Zn2+ induced folding exerts a counter-productive effect
on the activities. This result contradicts with the normal productive role that Mg2+ plays in the activation of ribozyme functions. At reduced ionic strength, even UO22+ and Pb2+ can induce folding due to the nonspecific electrostatic interaction from their divalent metal ion nature. And the progression of Mg2+ and Na+ concentration leads to an inactive-active-inactive transition in
the DNAzyme function. Single molecule FRET is also used to obtain kinetics for low UO22+
concentration at reduced imaging buffer strength. Together with the biochemical characterization
for the catalytic cores and optimal working conditions, a thorough understanding of this
DNAzyme 39E is obtained, which might be helpful in the design of sensitive and selective
DNAzymes.
FRET is also used to gain step-wise kinetic information of adenosine aptamer structure-switching sensor. The kinetic information for individual steps (folding and releasing) obtained by
monitoring FRET process between fluorophores labeled at several positions of the aptamer
structure switching sensor provides direct evidence for sequential occurrences, as predicted by the structure switching principle. The information obtained here will facilitate sensors designed based
on the structure-switching principle.
Electrohydrodynamic jet (E-jet) printing is applied to the protein microarray field. With the development of multi-nozzle printing system, both single-protein array and multiple-protein
arrays are successfully demonstrated. Several proteins, such as streptavidin, Green fluorescence protein (GFP), mCherry (a red fluorescence protein), et.al, have been printed, proving E-jet printing is generally applicable to many types of proteins. The printed streptavidin maintains its
binding character with biotin, showing the printed streptavidin is still structurally intact and
functionally active. What???s more, this printing technology has also been employed to immunology application. Immunoglobulin (Ig) G from several animal species are printed by E-jet printing, and their binding specificities to corresponding secondary antibody, anti IgG, are maintained. To prove this technique suitable for more practical applications, an inch-sized array with well controlled feature details has been completely in a short period of time. Overall, this technique will be a promising candidate for future protein microarray fabrication method.
Advisors/Committee Members: Lu, Yi (advisor), Rogers, John A. (committee member), Braun, Paul V. (committee member), Ha, Taekjip (committee member), Cheng, Jianjun (committee member).
Subjects/Keywords: Functional DNA; Fluorescence resonance energy transfer (FRET); Protein microarray; Deoxyribonucleic acid (DNA)
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
He, Y. (2012). Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29571
Chicago Manual of Style (16th Edition):
He, Ying. “Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/29571.
MLA Handbook (7th Edition):
He, Ying. “Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays.” 2012. Web. 03 Mar 2021.
Vancouver:
He Y. Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/29571.
Council of Science Editors:
He Y. Fluorescence resonance energy transfer study of the global folding of functional DNAs and electrohydrodynamic printing of protein arrays. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29571
University of Illinois – Urbana-Champaign
18.
Barati Farimani, Amir.
Nanopores for detecting and sensing biological molecules.
Degree: PhD, Mechanical Engineering, 2015, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/89267
► In spite of significant advances in the detection, separation and counting of single biological molecules (DNA, proteins, aminoacids, etc.) with solid-state nanopores, atomically-resolved scanning and…
(more)
▼ In spite of significant advances in the detection, separation and counting of single biological molecules (
DNA, proteins, aminoacids, etc.) with solid-state nanopores, atomically-resolved scanning and detection of these molecules remains a significant challenge. In most nanopore-based
DNA sequencing and single molecule detection techniques, ionic current blockade and blockade duration are the primary signatures associated with reading and scanning. Although these techniques are good enough for single molecule detection, they are not sophisticated enough to analyze and detect single
DNA bases, fine structures, homologues and mutagenesis. Aside from the detection difficulties, low signal to noise ratio (SNR), fast speed of translocation, and lack of a cross-check signal are the biggest challenges of current nanopore technology. In this study, we explored different nanopore architectures and materials to find solutions to these current challenges. Using extensive atomistic simulations, we showed that a single layer molybdenum Disulfide (MoS2) nanopore is attractive pore for single base
DNA detection with high SNR and multi-level conductance. We introduced and simulated MscL (Mechano-Sensitive Channel of Large Conductance) as an alternative to traditional biological nanopores (Alpha-Hemolysin, MspA) since it provides a flexible nanopore with adaptability to
DNA base types. Induced tension in MscL is shown to be different and distinguishable for each
DNA base type. The speed of
DNA translocation is also decreased by one order of magnitude in MscL, providing a better detection resolution compared to its counterpart, e.g. MspA. Next, we explored
DNA origami-graphene hybrid nanopore for
DNA detection. We found that the dwell time of each base type in the hybrid pore is different and distinguishable compared to pristine graphene nanopore. The specific interaction (hydrogen bonds) between the complimentary bases at the edge of the pore and the translocating
DNA bases give rise to distinguishable dwell time for each
DNA. In addition to
DNA sequencing studies, we also investigated the recognition of natively folded proteins using graphene nanopore. We specifically focused on the detection of Immunoglobin G subclasses since the separation and the detection of different subclasses of IgG is the signature of many diseases. These four subclasses differ only in their hinge regions and are 95% homologues. We showed that the one atom thick graphene is highly capable of distinguishing between the subclasses by using ionic current and water flux signals.
Advisors/Committee Members: Aluru, Narayan R (advisor), Aluru, Narayan R (Committee Chair), Jakobsson, Eric (committee member), Tajkhorshid, Emad (committee member), Lyding, Joseph W (committee member).
Subjects/Keywords: Nanopore; Deoxyribonucleic acid (DNA); Detection; Protein; DNA origami; molybdenum Disulfide (MoS2); Graphene
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APA ·
Chicago ·
MLA ·
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Export
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APA (6th Edition):
Barati Farimani, A. (2015). Nanopores for detecting and sensing biological molecules. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/89267
Chicago Manual of Style (16th Edition):
Barati Farimani, Amir. “Nanopores for detecting and sensing biological molecules.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/89267.
MLA Handbook (7th Edition):
Barati Farimani, Amir. “Nanopores for detecting and sensing biological molecules.” 2015. Web. 03 Mar 2021.
Vancouver:
Barati Farimani A. Nanopores for detecting and sensing biological molecules. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/89267.
Council of Science Editors:
Barati Farimani A. Nanopores for detecting and sensing biological molecules. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/89267
Texas Tech University
19.
Baker, Cheryl H.
The role of positions 99 and 127 in cAMP-mediated activation of CRP.
Degree: Chemistry, 1999, Texas Tech University
URL: http://hdl.handle.net/2346/19257
► The cycHc 3':5'-adenosine monophosphate (cAMP) receptor protein (CRP) of Escherichia coli hinds cycHc nucleotides. When complexed with cAMP, CRP binds to specific DNA sequences located…
(more)
▼ The cycHc 3':5'-adenosine monophosphate (cAMP) receptor protein (CRP) of Escherichia coli hinds cycHc nucleotides. When complexed with cAMP, CRP binds to specific DNA sequences located upstream of a number of promoters leading to the formation of active transcription complexes composed of CRP, cAMP, DNA, and RNA polymerase (RNAP). Molecular dynamics (MD) simulations were performed on CRP:(cAMP)2 structure. Analysis of amino acid residue proximities to cAMP in the MD-CRP:(cAMP)2 complex confirmed that known protein/Ugand contacts were maintained during the simidation and revealed the repositioning of tyrosine at position 99 (Y99) to interact with cAMP. To determine the vahdity of the MDpredicted Y99:cAMP interaction the crp gene was mutated to replace the Y99 codon with either an alanine (A) or a phenylalanine (F) codon. The mutant genes were expressed and characterized in vivo. Cells that contained wildtype (WT), alanine (Y99A), or phenylalanine (Y99F) CRP expressed pgalactosidase only when cultured in the presence of cAMP. Those cultures that contained Y99A or Y99F CRP showed cAMP-dependent inhibition of cell growth. In vitro studies showed that purified WT, Y99A and Y99F CRP found sequentially two molecules of cAMP, exhibited negative cooperativity in cAMP binding and activated the lactose promoter (lacP)in the presence of cAMP. These data, when coupled with the characteristics of cAMPS(Rp)binding to and effect on WT CRP, are consistent with a Y99:R82:cAMP interaction observed for the CRP:(cAMP)2 complex.
In addition to the Y99 studies, the DNA binding and lacP activation characteristics of mutant forms of CRP (cysteine [C], glycine [G], isoleucine [I] or serine [S] for threonine [T]) at position 127 were investigated. The results demonstrated that allosteric changes important for cAMP-mediated CRP DNA binding is differentially affected by amino acid substitution at position 127. However, cAMP-dependent interaction of CRP with RNAP observed regardless of the amino acid at position 127. This study further investigates the characteristics of these mutants with respect to lacP DNAand cAMP-binding. The results lead to the conclusion that threonine 127 plays an important role in transduction of the signal from the CRP cyclic nucleotide binding pocket that promotes proper orientation of the DNAbinding helices and only a minor, if any, role in the functional exposure of the CRP RNAP interaction domain.
Subjects/Keywords: Molecular dynamics; Deoxyribonucleic acid (DNA)-protein interactions; Deoxyribonucleic acid (DNA)-ligand interactions
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APA ·
Chicago ·
MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Baker, C. H. (1999). The role of positions 99 and 127 in cAMP-mediated activation of CRP. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/19257
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Baker, Cheryl H. “The role of positions 99 and 127 in cAMP-mediated activation of CRP.” 1999. Thesis, Texas Tech University. Accessed March 03, 2021.
http://hdl.handle.net/2346/19257.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Baker, Cheryl H. “The role of positions 99 and 127 in cAMP-mediated activation of CRP.” 1999. Web. 03 Mar 2021.
Vancouver:
Baker CH. The role of positions 99 and 127 in cAMP-mediated activation of CRP. [Internet] [Thesis]. Texas Tech University; 1999. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2346/19257.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Baker CH. The role of positions 99 and 127 in cAMP-mediated activation of CRP. [Thesis]. Texas Tech University; 1999. Available from: http://hdl.handle.net/2346/19257
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
20.
Powell, Madison S.
The organization and abundance of repetitive DNA sequences among great apes and humans.
Degree: Zoology, 1995, Texas Tech University
URL: http://hdl.handle.net/2346/13768
► Most studies of the human genome are focused upon coding DNA sequences which provide the structural genes and enzymatic machinery necessary for life. However, repetitive…
(more)
▼ Most studies of the human genome are focused upon coding DNA sequences which provide the structural genes and enzymatic machinery necessary for life. However, repetitive DNA sequences constitute a substantial portion of eukaryotic genomes. Formerly referred to as "junk" DNA, their importance is just now being realized as many of these repetitive sequences have been implicated in human disease, chromosomal structure, and gene regulation. Our view of human genome organization and human evolution is incomplete, without an understanding of how repetitive DNA has evolved to its present abundance and distribution. To address this problem genomic libraries were constructed from DNA samples of a human (Homo sapiens) and representatives from each of the four extant great apes; gorilla (Gorilla gorilla) chimpanzee (Pan troglodvtes)bonobo Pan paniscus). and orangutan (Pongo pvgmaeus). The libraries were screened with radiolabeled, synthetic oligonucleotides for the presence of the major classes of repetitive DNAs found in humans. These repetitive classes included tandemly repeated microsatellites, a minisatellite. and satellite DNAs as well as dispersed repetitive sequences represented by a LINE-1 element, a SINE, and a human retrotransposon, THE1. Addressing genome organization with this technique has proven useful because it provided a minimal estimate of human repetitive element copy number similar to the estimates obtained in previous studies through examination of genomic and chromosome 16 specific DNA libraries. However, the abundance of some repetitive probes varied considerably among the ape libraries, indicating variation in repetitive element copy number can be substantial among closely related species. The technique also indicated non-random associations between selected repetitive sequences and supported a previously erected hypothesis that a-satellite DNA and Alu sequences are negatively associated.
Subjects/Keywords: Deoxyribonucleic acid (DNA); Apes; Recombinant Deoxyribonucleic acid (DNA)
…cytosine triphosphate
DM
myotonic dystrophy
DNA
deoxyribonucleic acid
ECN
estimated copy… …molecular weight
DNA isolated from fibroblast cell lines
25
Partial digestion of high molecular… …weight
human genomic DNA with Sau3A1
26
Scanned image of the autoradiograph showing
half of… …Autoradiograph of Pan troglodvtes
library clones hybridized with the
satellite III DNA probe
11… …Autoradiograph of Pan paniscus
library clones hybridized with the
satellite II DNA probe
78…
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Powell, M. S. (1995). The organization and abundance of repetitive DNA sequences among great apes and humans. (Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/13768
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Powell, Madison S. “The organization and abundance of repetitive DNA sequences among great apes and humans.” 1995. Thesis, Texas Tech University. Accessed March 03, 2021.
http://hdl.handle.net/2346/13768.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Powell, Madison S. “The organization and abundance of repetitive DNA sequences among great apes and humans.” 1995. Web. 03 Mar 2021.
Vancouver:
Powell MS. The organization and abundance of repetitive DNA sequences among great apes and humans. [Internet] [Thesis]. Texas Tech University; 1995. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2346/13768.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Powell MS. The organization and abundance of repetitive DNA sequences among great apes and humans. [Thesis]. Texas Tech University; 1995. Available from: http://hdl.handle.net/2346/13768
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Pretoria
21.
Bosman, Anna-Mari.
Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
.
Degree: 2011, University of Pretoria
URL: http://upetd.up.ac.za/thesis/available/etd-01032011-141014/
► Feline babesiosis, first described in domestic cats in South Africa in 1937, is regarded to be of great importance in the coastal regions although isolated…
(more)
▼ Feline babesiosis, first described in domestic cats
in South Africa in 1937, is regarded to be of great importance in
the coastal regions although isolated cases also occur on the
eastern highlands of Mpumalanga Province. Babesia felis (described
from domestic cats) and B. leo (described from lions) are the two
best characterised Babesia species in felids. These two parasites
are morphologically similar when examined under a light microscope,
but are serologically and genetically distinct. In this study the
prevalence of these two Babesia species in various wild and
domestic felid species was determined. A total of 358 samples were
tested using the reverse line blot hybridization (RLB) assay. This
assay makes it possible to simultaneously detect and differentiate
between blood parasites using
DNA probes. The RLB consists of three
basic steps, the first being amplification of the variable region
(V4) in the 18S rRNA gene using genus-specific primers where one is
labelled with biotin. This is followed by a blotting step, where
the amplicons are hybridized to oligonucleotides bound to a
nitrocellulose membrane. The third and last step is the detection
of the hybridized amplicons by using chemiluminescence reagents.
This assay is a screening tool utilizing the variable (V4) region
in the 18S rRNA gene to detect and differentiate between blood
parasites. A new B. felis-specific
DNA probe was developed to use
in the RLB assay. Results demonstrated that these two parasites not
only occur in the felid species from which they have been
described, but also in other felid species. Babesia microti was
also detected in various felid species, while B. rossi was detected
in 1 of the lion samples. Two hundred and twelve samples tested
positive for Babesia spp., of which only 54.24% of the samples
reacted with the genus-specific probe. This indicates the presence
of a novel Babesia or Theileria species or variant of a
species.
Advisors/Committee Members: Penzhorn, Barend Louis (advisor), Venter, Estelle Hildegard (advisor).
Subjects/Keywords: Babesia felis;
South Africa;
Domestic cats;
Deoxyribonucleic acid;
Babesia species;
UCTD;
DNA
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Bosman, A. (2011). Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
. (Masters Thesis). University of Pretoria. Retrieved from http://upetd.up.ac.za/thesis/available/etd-01032011-141014/
Chicago Manual of Style (16th Edition):
Bosman, Anna-Mari. “Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
.” 2011. Masters Thesis, University of Pretoria. Accessed March 03, 2021.
http://upetd.up.ac.za/thesis/available/etd-01032011-141014/.
MLA Handbook (7th Edition):
Bosman, Anna-Mari. “Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
.” 2011. Web. 03 Mar 2021.
Vancouver:
Bosman A. Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Mar 03].
Available from: http://upetd.up.ac.za/thesis/available/etd-01032011-141014/.
Council of Science Editors:
Bosman A. Detection of Babesia species in domestic and wild
Southern African felids by means of DNA probes
. [Masters Thesis]. University of Pretoria; 2011. Available from: http://upetd.up.ac.za/thesis/available/etd-01032011-141014/
University of Pretoria
22.
Bosman, Anna-Mari.
Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes.
Degree: Veterinary Tropical
Diseases, 2011, University of Pretoria
URL: http://hdl.handle.net/2263/23149
► Feline babesiosis, first described in domestic cats in South Africa in 1937, is regarded to be of great importance in the coastal regions although isolated…
(more)
▼ Feline babesiosis, first described in domestic cats in
South Africa in 1937, is regarded to be of great importance in the
coastal regions although isolated cases also occur on the eastern
highlands of Mpumalanga Province. Babesia felis (described from
domestic cats) and B. leo (described from lions) are the two best
characterised Babesia species in felids. These two parasites are
morphologically similar when examined under a light microscope, but
are serologically and genetically distinct. In this study the
prevalence of these two Babesia species in various wild and
domestic felid species was determined. A total of 358 samples were
tested using the reverse line blot hybridization (RLB) assay. This
assay makes it possible to simultaneously detect and differentiate
between blood parasites using
DNA probes. The RLB consists of three
basic steps, the first being amplification of the variable region
(V4) in the 18S rRNA gene using genus-specific primers where one is
labelled with biotin. This is followed by a blotting step, where
the amplicons are hybridized to oligonucleotides bound to a
nitrocellulose membrane. The third and last step is the detection
of the hybridized amplicons by using chemiluminescence reagents.
This assay is a screening tool utilizing the variable (V4) region
in the 18S rRNA gene to detect and differentiate between blood
parasites. A new B. felis-specific
DNA probe was developed to use
in the RLB assay. Results demonstrated that these two parasites not
only occur in the felid species from which they have been
described, but also in other felid species. Babesia microti was
also detected in various felid species, while B. rossi was detected
in 1 of the lion samples. Two hundred and twelve samples tested
positive for Babesia spp., of which only 54.24% of the samples
reacted with the genus-specific probe. This indicates the presence
of a novel Babesia or Theileria species or variant of a
species.
Advisors/Committee Members: Penzhorn, Barend Louis (advisor), Venter, Estelle Hildegard (coadvisor).
Subjects/Keywords: Babesia
felis; South Africa
(SA); Domestic
cats;
Deoxyribonucleic acid (DNA); Babesia
species;
UCTD
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APA (6th Edition):
Bosman, A. (2011). Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes. (Masters Thesis). University of Pretoria. Retrieved from http://hdl.handle.net/2263/23149
Chicago Manual of Style (16th Edition):
Bosman, Anna-Mari. “Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes.” 2011. Masters Thesis, University of Pretoria. Accessed March 03, 2021.
http://hdl.handle.net/2263/23149.
MLA Handbook (7th Edition):
Bosman, Anna-Mari. “Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes.” 2011. Web. 03 Mar 2021.
Vancouver:
Bosman A. Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes. [Internet] [Masters thesis]. University of Pretoria; 2011. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2263/23149.
Council of Science Editors:
Bosman A. Detection of
Babesia species in domestic and wild Southern African felids by
means of DNA probes. [Masters Thesis]. University of Pretoria; 2011. Available from: http://hdl.handle.net/2263/23149
North-West University
23.
Peters, Dimetrie Leslie.
Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
.
Degree: 2011, North-West University
URL: http://hdl.handle.net/10394/6929
► The diagnostic value of extracellular occurring DNA (eoDNA) is limited by our lack of understanding its biological function. eoDNA exists in a number of forms,…
(more)
▼ The diagnostic value of extracellular occurring DNA (eoDNA) is limited by our lack of
understanding its biological function. eoDNA exists in a number of forms, namely vesicle
bound DNA, histone/DNA complexes or nucleosomes and virtosomes. These forms of DNA
can also be categorized under the terms circulating DNA, cell free DNA, free DNA and
extracellular DNA. The DNA can be released by means of form–specific mechanisms and
seem to be governed by cell cycle phases and apoptosis. Active release is supported by
evidence of energy dependant release mechanisms and various immunological– and
messenger functions. Sequencing has shown that eoDNA sequences present in the nucleome
reflects traits and distribution of genome sequences and are regulated by ways of release
and/or clearance. eoDNA enables the horizontal transfer of gene sequences from one cell to
another, over various distances. The ability of eoDNA to partake in horizontal gene transfer
makes it an important facet in the field of epigenetic variation. Clinical implementation of
eoDNA diagnostics requires that all of the subgroups of eoDNA be properly investigated. It
is suggested that eoDNA is the result of the metabolic fraction of DNA that is released by the
cell. Various observations indicate that eoDNA may also be incorporated into the genome of
a cell, from where it may affect cell function. Therefore horizontal gene transfer in higher
organisms is a real possibility. In this study, variations and increases in eoDNA levels over
time correlate with stressors that are subjected to 143B human osteosarcoma cells. It seems
viable to assume that a stressor is met by a change in the molecular machinery of a cell,
required to neutralise the onset of metabolic instability. This may be done by amplification of
necessary cistrons, producing metabolic DNA, that may then be observed after its release as
eoDNA. The presence of hydrolysing enzymes gives an updated real time picture of the state
of eoDNA. The eogenics hypothesis emanating from this study, suggests that amplification
and horizontal transfer of cistrons affect tissue and organ function over long periods of time,
in order for an organism to evolve one or more a specialized genomes.
Subjects/Keywords: Circulating;
Extracellular;
Nucleic Acids;
Deoxyribonucleic acid (DNA);
Horizontal Gene Transfer;
Virtosome;
Blood Nucleome
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APA (6th Edition):
Peters, D. L. (2011). Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
. (Thesis). North-West University. Retrieved from http://hdl.handle.net/10394/6929
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Peters, Dimetrie Leslie. “Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
.” 2011. Thesis, North-West University. Accessed March 03, 2021.
http://hdl.handle.net/10394/6929.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Peters, Dimetrie Leslie. “Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
.” 2011. Web. 03 Mar 2021.
Vancouver:
Peters DL. Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
. [Internet] [Thesis]. North-West University; 2011. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/10394/6929.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Peters DL. Evaluation of eukaryotic cultured cells as a model to study extracellular DNA / D.L. Peters
. [Thesis]. North-West University; 2011. Available from: http://hdl.handle.net/10394/6929
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Urbana-Champaign
24.
Vafabakhsh, Reza.
Single molecule fluorescence studies of biomolecular interactions.
Degree: PhD, 0240, 2013, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/44466
► Single molecule fluorescent techniques have become standard approaches to study protein-DNA interactions. However, these techniques have largely been confined by limitations in assays to studying…
(more)
▼ Single molecule fluorescent techniques have become standard approaches to study protein-
DNA interactions. However, these techniques have largely been confined by limitations in assays to studying the interaction between simple
DNA substrates and a single protein. During my PhD I developed several novel assays to study a long-standing controversial biophysics question (flexibility of short dsDNA), genome packaging in viruses (Influenza and T4) and dynamics of challenging protein complexes (membrane proteins).
The classical view of
DNA posits that
DNA must be stiff below the persistence length (<150 base pair) but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free, assay for studying the cyclization of single
DNA molecules in real time. The looping rate for short
DNA molecules has remarkably weak length dependence between 67 and 106 bps, deviating significantly from the worm-like chain model. We propose that many biologically significant protein-
DNA interactions that involve looping and bending of
DNA below 100 bp likely use this intrinsic bendability of
DNA.
One of the critical aspects of a virus life cycle is packaging of the viral genome. Different viruses have devised intelligent mechanisms to perform this task. I studied packaging mechanism in Bacteriophage T4 and Influenza. Influenza A virus possesses a segmented genome of eight, single-stranded RNAs. However, the exact copy number of each viral RNA segment per individual virus particles has been controversial for the past 50 years. To address this question we combined single molecule TIRF microscopy and multi-color fluorescent in situ hybridization (FISH) to study the composition of viral RNAs at single-virus particle resolution. Our results showed that a high percentage of virus particles package a single copy of each segment of viral RNAs. Our findings support a model that the packaging of influenza genome is a selective and robust process.
Finally we developed a single molecule fluorescence assay to study initiation and re-initiation of dsDNA packaging in the T4 bacteriophage. Using this assay we quantified the details of T4 “packasome” assembly. Also, we showed that the T4 packaging machine can package multiple
DNA into the same head in burst-like fashion.
Advisors/Committee Members: Ha, Taekjip (advisor), Goldenfeld, Nigel D. (Committee Chair), Ha, Taekjip (committee member), Stack, John D. (committee member), Chemla, Yann R. (committee member).
Subjects/Keywords: Single molecule; Fluorescence Resonance Energy Transfer (FRET); Deoxyribonucleic Acid (DNA); Influenza; bacteriophage T4 packaging
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APA ·
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MLA ·
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Export
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Manager
APA (6th Edition):
Vafabakhsh, R. (2013). Single molecule fluorescence studies of biomolecular interactions. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/44466
Chicago Manual of Style (16th Edition):
Vafabakhsh, Reza. “Single molecule fluorescence studies of biomolecular interactions.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/44466.
MLA Handbook (7th Edition):
Vafabakhsh, Reza. “Single molecule fluorescence studies of biomolecular interactions.” 2013. Web. 03 Mar 2021.
Vancouver:
Vafabakhsh R. Single molecule fluorescence studies of biomolecular interactions. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/44466.
Council of Science Editors:
Vafabakhsh R. Single molecule fluorescence studies of biomolecular interactions. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/44466
University of Illinois – Urbana-Champaign
25.
Brown, Darius.
Ultrasensitive DNA aptasensors based on exponential amplification reaction.
Degree: MS, 0335, 2014, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/46916
► This is a comprehensive project for the development of a general method to enhance the sensitivity of DNA aptasensors by coupling them with an isothermal…
(more)
▼ This is a comprehensive project for the development of a general method to enhance the sensitivity of
DNA aptasensors by coupling them with an isothermal
DNA amplification technique known as exponential amplification reaction (EXPAR). The method involves two steps: (1) first, the target-induced structure-switching of
DNA aptamers causes the release of trigger oligonucleotides from the aptamers immobilized on a surface; (2) then, the released trigger oligonucleotides are amplified by the EXPAR technique for ultrasensitive detection. It is shown that the detection limit of a cocaine aptasensor is improved from 5 micromolar in assays without amplification to 0.8-1micromolar when EXPAR is applied, providing a 5-fold enhancement. The flexibility in designing the sequences of the trigger oligonucleotides enables the method generally applicable to other aptasensor systems such as thrombin aptamers. By EXPAR, the method has also achieved 10-fold enhancement in sensitivity from 4nM to 400 pM for thrombin detection, in comparison with similar assays without EXPAR.
Advisors/Committee Members: Lu, Yi (advisor).
Subjects/Keywords: Aptasensor; Cocaine; Thrombin; Exponential amplification reaction (EXPAR); Magnetic Beads; Deoxyribonucleic acid (DNA)
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APA ·
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CSE |
Export
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Manager
APA (6th Edition):
Brown, D. (2014). Ultrasensitive DNA aptasensors based on exponential amplification reaction. (Thesis). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46916
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Brown, Darius. “Ultrasensitive DNA aptasensors based on exponential amplification reaction.” 2014. Thesis, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/46916.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Brown, Darius. “Ultrasensitive DNA aptasensors based on exponential amplification reaction.” 2014. Web. 03 Mar 2021.
Vancouver:
Brown D. Ultrasensitive DNA aptasensors based on exponential amplification reaction. [Internet] [Thesis]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/46916.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Brown D. Ultrasensitive DNA aptasensors based on exponential amplification reaction. [Thesis]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46916
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Illinois – Urbana-Champaign
26.
Girdhar, Anuj.
Quantum transport in graphene nanotransistors.
Degree: PhD, Physics, 2015, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/78634
► Over the past decade, interest in using graphene in condensed-matter physics and materials science applications has exploded, owing to its unique electrical properties. Narrow strips…
(more)
▼ Over the past decade, interest in using graphene in condensed-matter physics and materials science applications has exploded, owing to its unique electrical properties. Narrow strips of graphene, called graphene nanoribbons, also display exotic behavior. A nanoribbon’s edge geometry determines its electronic transport properties, and the rich behavior
of conductance of nanoribbons in response to external potentials makes them ideal for use within transistors.
In this thesis, we work towards creating an accurate model of graphene nanoribbon transistors, and we asses two possible applications which exploit their amazing potential. We begin by outlining the basic theoretical and computational framework for the model developed in this work. We then demonstrate the capability of graphene nanoribbon transistors, with nanopores, to electronically detect, characterize, and manipulate translocating
DNA
strands. Specifically, we explore the tunability of such devices, by examining the role of lattice geometry, such as a quantum point contact constriction, on their performance. We perform a demonstration of the ability to detect the passage of double and single-stranded
DNA, through molecular dynamics simulations. The transistors presented are capable of sensing the helical shape of double-stranded
DNA molecules, the unraveling of a
DNA helix into a planar-zipper form, and the passage of individual nucleotides of a single strand of
DNA
through the nanopore. We outline a preliminary analysis on the proper design of a multilayer transistor stack to control both the electronic properties of the conducting membrane, as well as the motion of the
DNA. Lastly, we present another type of nanoribbon device,
an all-carbon spintronic transistor for use in cascaded logic circuits. A thorough analysis of the transport properties of zigzag nanoribbon transistors in magnetic fields, in addition to the design and construction of logic gate circuits containing these spintronic transistors, is presented.
Advisors/Committee Members: Leburton, Jean-Pierre (advisor), Mason, Nadya (Committee Chair), Schulten, Klaus J. (committee member), Bashir, Rashid (committee member).
Subjects/Keywords: graphene; quantum; transport; nanoribbon; Deoxyribonucleic Acid (DNA); sequencing; transistor; nanopore; sensing; genome; monolayer; gate
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Export
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Manager
APA (6th Edition):
Girdhar, A. (2015). Quantum transport in graphene nanotransistors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/78634
Chicago Manual of Style (16th Edition):
Girdhar, Anuj. “Quantum transport in graphene nanotransistors.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/78634.
MLA Handbook (7th Edition):
Girdhar, Anuj. “Quantum transport in graphene nanotransistors.” 2015. Web. 03 Mar 2021.
Vancouver:
Girdhar A. Quantum transport in graphene nanotransistors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/78634.
Council of Science Editors:
Girdhar A. Quantum transport in graphene nanotransistors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/78634
University of Kansas
28.
LeGresley-Rush, Sarah Elizabeth.
Mathematical Methods for studying DNA and Protein Interactions.
Degree: PhD, Physics & Astronomy, 2017, University of Kansas
URL: http://hdl.handle.net/1808/26015
► Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may…
(more)
▼ Deoxyribnucleic
Acid (
DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may be as high as 100,000 per cell per day. Because of the devastating effects that
DNA damage can have,
DNA repair mechanisms are of great interest yet are not completely understood. To gain a better understanding of possible
DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between
DNA and proteins. I developed a damaged
DNA model to estimate the probabilities of damaged
DNA being located at specific positions. Experiments were then performed that suggested that the damaged
DNA may be repositioned. These experimental results were consistent with the model's prediction that damaged
DNA has preferred locations. To study how proteins might be moving along the
DNA, I studied the use of the uniform motion “n-step” model. The n-step model has been used to determine the kinetics parameters (e.g. rates at which a protein moves along the
DNA, how much energy is required to move a protein along a specified amount of
DNA, etc.) of proteins moving along the
DNA. Monte Carlo methods were used to simulate proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the
DNA. Estimates for the kinetics parameters in the n-step model were found by fitting of the Monte Carlo simulation data. Analysis indicated that non-uniform motion of the protein may lead to over or underestimation of the kinetic parameters of this n-step model.
Advisors/Committee Members: Fischer, Christopher J. (advisor), Anthony-Twarog, Barbara J. (cmtemember), Murray, Michael J. (cmtemember), Shi, Jack J. (cmtemember), Stetler, Dean A. (cmtemember).
Subjects/Keywords: Physics; Biophysics; deoxyribonucleic acid (DNA); kinetics; motor proteins; nucleosome; nucleosome breathing; translocation
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APA ·
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Export
to Zotero / EndNote / Reference
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APA (6th Edition):
LeGresley-Rush, S. E. (2017). Mathematical Methods for studying DNA and Protein Interactions. (Doctoral Dissertation). University of Kansas. Retrieved from http://hdl.handle.net/1808/26015
Chicago Manual of Style (16th Edition):
LeGresley-Rush, Sarah Elizabeth. “Mathematical Methods for studying DNA and Protein Interactions.” 2017. Doctoral Dissertation, University of Kansas. Accessed March 03, 2021.
http://hdl.handle.net/1808/26015.
MLA Handbook (7th Edition):
LeGresley-Rush, Sarah Elizabeth. “Mathematical Methods for studying DNA and Protein Interactions.” 2017. Web. 03 Mar 2021.
Vancouver:
LeGresley-Rush SE. Mathematical Methods for studying DNA and Protein Interactions. [Internet] [Doctoral dissertation]. University of Kansas; 2017. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/1808/26015.
Council of Science Editors:
LeGresley-Rush SE. Mathematical Methods for studying DNA and Protein Interactions. [Doctoral Dissertation]. University of Kansas; 2017. Available from: http://hdl.handle.net/1808/26015
University of Texas – Austin
29.
Ikkanda, Brian Aki.
Assembly of complimentary naphthyl units in nucleotidomimetic foldamers.
Degree: PhD, Chemistry, 2016, University of Texas – Austin
URL: http://hdl.handle.net/2152/68382
► The large and complex architectures found in biomolecules not only are an amazing feat of molecular construction, but they also function to carry out all…
(more)
▼ The large and complex architectures found in biomolecules not only are an amazing feat of molecular construction, but they also function to carry out all the processes necessary to sustain a living organism. For the organic chemist and biochemist that wish to mimic, improve or modify the structure and function of such natural molecular architectures, an understanding of non-covalent interactions in solution is necessary. In order to probe the particular inter- and intramolecular interactions involved in constructing higher order molecular architectures, the study of foldamers, small synthetic oligomers that adopt well-defined conformations in solution, has emerged.
Our lab has been studying the particular interaction between complementary aromatic units, 1,4,5,8-naphthalenetetracarboxylic
acid diimide (NDI) and 1,5-dialkoxynaphthalene (DAN) and their ability to drive the construction of aromatic foldamers in aqueous environments. Utilizing flexible peptide linked units of DAN and NDI, our lab has constructed a variety of unique folding assemblies. From the very first aromatic foldamer that folds into a pleated secondary structure in water to a heteroduplex system assembling oligo-DAN and oligo-NDI units in an intertwined fashion, the use of these complementary aromatic units has proven its versatility in foldamer assembly.
Generally, this dissertation describes studies of the first NDI and DAN
deoxyribonucleic acid oligonucleotides. While our previous foldamer assemblies utilized peptide linkers to string together DAN and NDI units, the work described herein draws inspiration from the sugar-phosphate backbone of
DNA to assemble aromatic units.
Chapter 2 describes the design and synthesis of 4,4’-dimethoxytrityl protected DAN and NDI phosphoramidites that can subsequently be incorporated into strands of natural
DNA oligonucleotides using automated solid phase oligonucleotide synthesis. Chapter 3 investigates the insertion of a 3 base pair region of varying sequences of DAN and NDI into a 12-mer
DNA oligonucleotide to explore the effect of DAN and NDI on duplex structure and stability. Chapter 4 describes the stability and structure of a 9-mer
DNA oligonucleotide that incorporates two NDI-DAN-NDI triplet sequences either inserted into the interior of the duplex or appended at the terminal positions of the duplex. The NDI-DAN-NDI triplets appended to the terminal positions led to a profound increase in duplex stability (in comparison to internal positions), significantly beyond that seen with analogous sequences of G-C base pairs.
Advisors/Committee Members: Iverson, Brent L. (advisor), Willson, Carlton G (committee member), Anslyn, Eric V (committee member), Keatinge-Clay, Adrian T (committee member), Kerwin, Sean M (committee member).
Subjects/Keywords: Aromatic; DNA; Deoxyribonucleic acid; DAN; NDI; Foldamer; Organic chemistry; Bioorganic chemistry; Chemical biology
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APA ·
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MLA ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ikkanda, B. A. (2016). Assembly of complimentary naphthyl units in nucleotidomimetic foldamers. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/68382
Chicago Manual of Style (16th Edition):
Ikkanda, Brian Aki. “Assembly of complimentary naphthyl units in nucleotidomimetic foldamers.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed March 03, 2021.
http://hdl.handle.net/2152/68382.
MLA Handbook (7th Edition):
Ikkanda, Brian Aki. “Assembly of complimentary naphthyl units in nucleotidomimetic foldamers.” 2016. Web. 03 Mar 2021.
Vancouver:
Ikkanda BA. Assembly of complimentary naphthyl units in nucleotidomimetic foldamers. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2152/68382.
Council of Science Editors:
Ikkanda BA. Assembly of complimentary naphthyl units in nucleotidomimetic foldamers. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/68382
University of Illinois – Urbana-Champaign
30.
Suksombat, Sukrit.
Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase.
Degree: PhD, Physics, 2015, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/78654
► DNA inside a cell is continuously damaged through multiple mechanisms including environmental exposure to radiation, chemical agents, or UV light. Certain products of the cell's…
(more)
▼ DNA inside a cell is continuously damaged through multiple mechanisms including environmental exposure to radiation, chemical agents, or UV light. Certain products of the cell's own metabolism, such as reactive oxygen species, can also damage the
DNA. In the worst-case scenario, this damage results in double-stranded
DNA (dsDNA) breaks. Double-stranded
DNA breaks are lethal, and difficult to repair, with potential complications from genome rearrangement. To prevent this genetic instability, a cell can utilize a homologous chromosome as a template to accurately repair DSBs. This process is called homologous recombination.
Homologous recombination begins when an enzyme complex binds to a blunt end of a dsDNA break. The complex unzips the dsDNA through its helicase activity, and simultaneously cleaves the newly-generated 5' end of the ssDNA. This process leaves the remaining ssDNA strand exposed to the surrounding environment and prone to nucleolytic and chemical attacks. Cells have evolved single-stranded
DNA binding (SSB) proteins to wrap and protect this ssDNA. In E. coli, SSB is known to wrap ssDNA in a variety of binding configurations, or modes. Three different binding modes, (SSB)65, (SSB)56, and (SSB)35, which wraps 65, 56, and 35 nucleotides (nt) respectively, have been observed in vitro Previous studies have suggested that SSB binding in different modes may exhibit different levels of binding cooperativity. SSBs in the (SSB)65 binding mode form isolated clusters (limited cooperativity), while SSBs in the (SSB)35 binding mode form long filaments (unlimited cooperativity). These different levels of binding cooperativity have been proposed to be used selectively in different
DNA metabolic processes, including
DNA replication, recombination, and repair.
In homologous recombination, recombinase RecA must bind and form nucleoprotein filaments on the ssDNA, in direct competition with SSB. Prior studies have shown that RecA is capable of forming filaments on ssDNA wrapped by SSBs in the (SSB)65 binding mode, but filament formation on ssDNA wrapped by SSBs in the (SSB)35 binding mode is inhibited. Recent single-molecule studies have been conducted to investigate this competitive process, but the detailed mechanisms remain unclear.
Here, we use high-resolution optical tweezers with simultaneous fluorescence microscopy to observe directly the activity of ssDNA-SSB, ssDNA-RecA, and ssDNA-SSB-RecA complexes under tension, and characterize their mechanical properties. The instrument allows us to simultaneously probe and visualize the interactions of RecA and SSB with ssDNA in real time and with nanometer resolution.
We confirm that individuals SSBs bind and compact ssDNA in discrete modes. Under low tension (1-3 pN), a single SSB wraps ssDNA in the (SSB)65 or (SSB)56 binding mode. At higher tension (4-8 pN), SSB exhibits transient wrapping-unwrapping, switching between the (SSB)56, (SSB)35, and (SSB)17 wrapping modes. When multiple SSBs are present on the ssDNA, the SSBs form isolated clusters in those solution…
Advisors/Committee Members: Chemla, Yann R. (advisor), Ha, Taekjip (Committee Chair), Aksimentiev, Aleksei (committee member), Myong, Su-A (committee member).
Subjects/Keywords: Optical Tweezers; Single-stranded DNA Binding Protein; Single-stranded DNA binding (SSB); RecA; Deoxyribonucleic Acid (DNA); Single-Molecule; Optical Traps
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Suksombat, S. (2015). Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/78654
Chicago Manual of Style (16th Edition):
Suksombat, Sukrit. “Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 03, 2021.
http://hdl.handle.net/2142/78654.
MLA Handbook (7th Edition):
Suksombat, Sukrit. “Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase.” 2015. Web. 03 Mar 2021.
Vancouver:
Suksombat S. Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 03].
Available from: http://hdl.handle.net/2142/78654.
Council of Science Editors:
Suksombat S. Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/78654
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