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University of California – Riverside
1.
Dong, Xuefeng.
Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins.
Degree: Bioengineering, 2017, University of California – Riverside
URL: http://www.escholarship.org/uc/item/8w89461r 
► Förster resonance energy transfer (FRET) is a technology that analyzes protein-protein interactions using fluorescent proteins tags, such as cyanoprotein (CyPet) and yellow fluorescent protein (YPet).…
(more)
▼ Förster resonance energy transfer (FRET) is a technology that analyzes protein-protein interactions using fluorescent proteins tags, such as cyanoprotein (CyPet) and yellow fluorescent protein (YPet). In our lab, we developed a mature quantitative FRET technology to measure protein-protein interactions, especially the interactions of some proteins which be involved in cancer induction and regulation process. Cancer is a disease that when cells and tissues on any part of the body without control. These cells can continue to grow without limitation, invade nearby tissues, and interfere with organ functions. There is one important mechanism involved in cancer induction process which is SUMOylation pathway. SUMOylation pathway has been extensively studied for a long time but the accurate components of SUMOylation are still not very clear. There are lots of induction factors of cancer, one of them has been found recently is influenza virus. Influenza, an infectious disease caused by an influenza virus which can kill many people every year and spread in various methods .It has three different types which are Type A, Type B, and Type C. H1N1 virus is a subtype influenza A virus. It including 8 RNA segments coding for 12 proteins. According to recent reports, some of H1N1 virus proteins can be SUMOylated so that it makes H1N1 has a high investigation value. There are some other proteins can be potential SUMO targets that contribute to cancer induction such as PD-1 and PD-L1.Programmed cell death protein1 (PD-1 or CD279), is known as a very important cell surface receptor of T- cell and plays an important role in the immune reaction mechanisms, such as it can suppress T-cell immune activities. Programmed death-ligand1 (PD-L1 or CD274 or B7-H1) plays an important role in immune system too. In this study, I applied our FRET technology to measure SUMOylation reactions of some H1N1 proteins and do quantitative Kd determination of PD-1/PD-L1. Through with construct design, gene clone, transformation and protein purification to get proteins with high purity. Then I measured Kd and SUMOylation reactions with these proteins. As results, I got the Kd of YPet-NP and CyPet-Ubc9, PD-1 extra-cellular domain and PD-L1 extra-cellular domain. And I found that NP virus protein which is one of H1N1 proteins can be SUMOylated. These results can contribute to protein-protein interaction studies of H1N1 virus and potential drug target detection of PD-1 and PD-L1 pathway.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Dong, X. (2017). Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/8w89461r
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):
Dong, Xuefeng. “Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins.” 2017. Thesis, University of California – Riverside. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/8w89461r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Dong, Xuefeng. “Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins.” 2017. Web. 04 Mar 2021.
Vancouver:
Dong X. Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins. [Internet] [Thesis]. University of California – Riverside; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/8w89461r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Dong X. Optimize Bacterial Protein Expression System for Quantitative FRET Assays of Influenza Virus and Immune Check Point Proteins. [Thesis]. University of California – Riverside; 2017. Available from: http://www.escholarship.org/uc/item/8w89461r
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
2.
Sinha, Mridu Bhashini.
Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach.
Degree: Bioengineering, 2017, University of California – San Diego
URL: http://www.escholarship.org/uc/item/1sm3w42b
► The greatest risk of childhood deaths occurs in the first few weeks of life. Two of the major concerns, birth asphyxia, and sepsis are responsible…
(more)
▼ The greatest risk of childhood deaths occurs in the first few weeks of life. Two of the major concerns, birth asphyxia, and sepsis are responsible for the loss of over 2.5 million infants in this vulnerable period. Worse, the survivors are at a high risk for long-term morbidity. This doctoral research work focuses on developing screening tools to influence timely clinical decision-making for targeted treatment for such high risk-infants. First, we developed a web-based decision support tool to encourage timely initiation of therapeutic hypothermia, the only available therapy for infants at risk for brain injury due to birth asphyxia. This tool provides access to widely accepted clinical guidelines and strategies in a simplified way which can be easy to follow and access in clinical settings. Such a clinical decision support tool can obviate some of the time and effort needed for rigorous training and refresher sessions for providers at low acuity, low volume birthing centers. Second, we developed a platform for rapid, reliable and automated identification of bloodborne pathogens responsible for neonatal sepsis using DNA melting analysis directly after digital PCR amplification. Specifically, we designed a high resolution digital melt platform with precise thermal control to accomplish reliable, high-throughput heat ramping of microfluidic chip digital PCR reactions. We characterized the sources of variability to minimize run to run variations with the system using synthetic DNA oligos. We also demonstrate the use of novel rate-dependent melt signatures for enhancing automated melt genotyping. Further, we developed software for analysis to classify melt curves and identify novel pathogens. Our hope is that in future, this platform can translate into a near-point of care, cost-effective technology for screening for sepsis.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Sinha, M. B. (2017). Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/1sm3w42b
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):
Sinha, Mridu Bhashini. “Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach.” 2017. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/1sm3w42b.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sinha, Mridu Bhashini. “Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach.” 2017. Web. 04 Mar 2021.
Vancouver:
Sinha MB. Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach. [Internet] [Thesis]. University of California – San Diego; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/1sm3w42b.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sinha MB. Improving Clinical Practices in the Neonatal Intensive Care Unit: A Bioengineering Approach. [Thesis]. University of California – San Diego; 2017. Available from: http://www.escholarship.org/uc/item/1sm3w42b
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
3.
Zhou, Zixu.
Cell-free RNA Sequencing from Microliters of Unprocessed Serum.
Degree: Bioengineering, 2017, University of California – San Diego
URL: http://www.escholarship.org/uc/item/4750b8bx
► Though numerous treatments for breast cancer have been developed, recurrence still exists, biomarkers and risk assessment tools are thus desired by the field. Cell-free RNA…
(more)
▼ Though numerous treatments for breast cancer have been developed, recurrence still exists, biomarkers and risk assessment tools are thus desired by the field. Cell-free RNA in blood or serum is now receiving more and more interest as a pool of biomarkers and RNA sequencing was believed to be a powerful tool for its analysis. However, development of the field was hindered by large volume of serum required for RNA extraction. In this study, by circumventing RNA extraction and with the inspiration from single-cell RNA sequencing, we developed a technology being able to construct RNA sequencing libraries in large scale with microliters of direct unprocessed serum input. Optimizations for sequencing and mapping qualities, library complexity and library construction efficiency were conducted by varying serum input volume, adding custom sequencing primer and applying liquid handling instrument epMotion 5075. The optimized strategy “construct 96 different libraries in one single automated batch with 7ul serum input” was proposed accordingly. A huge diversity of genes could be found in serum with this technology. The developed technology was then applied to 96 breast cancer patients’ serums for its performance and potential in clinical cases. Based on the sequencing data: 465, 601 and 1259 genes were identified by three methods respectively to behave differently in recurrence and non-recurrence patients; The two populations could be separated by principle component analysis with all three sets of genes mentioned above; Preliminary recurrence risk assessment was conducted successfully with the classifier random forest.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Zhou, Z. (2017). Cell-free RNA Sequencing from Microliters of Unprocessed Serum. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/4750b8bx
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):
Zhou, Zixu. “Cell-free RNA Sequencing from Microliters of Unprocessed Serum.” 2017. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/4750b8bx.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Zhou, Zixu. “Cell-free RNA Sequencing from Microliters of Unprocessed Serum.” 2017. Web. 04 Mar 2021.
Vancouver:
Zhou Z. Cell-free RNA Sequencing from Microliters of Unprocessed Serum. [Internet] [Thesis]. University of California – San Diego; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/4750b8bx.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Zhou Z. Cell-free RNA Sequencing from Microliters of Unprocessed Serum. [Thesis]. University of California – San Diego; 2017. Available from: http://www.escholarship.org/uc/item/4750b8bx
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Riverside
4.
Hariharan, Chitra.
Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways.
Degree: Bioengineering, 2017, University of California – Riverside
URL: http://www.escholarship.org/uc/item/7pf7v6gq
► Cell death is a major process in a biological cell that occurs during development, homeostasis and immune regulation in multicellular organisms. Dysregulation of cell death…
(more)
▼ Cell death is a major process in a biological cell that occurs during development, homeostasis and immune regulation in multicellular organisms. Dysregulation of cell death pathway has been implicated in many diseases. Principle cell death pathways includeapoptosis, autophagy, necrosis, mitotic catastrophe etc. Knowledge of cell death pathways and the reason the cell chooses to die one way or the other, are key factors to understand the disease, the way it affects the cellular system and subsequent drug discovery.This study is focused on developing genetically encoded Förster Resonance Energy Transfer (FRET) based biosensors to identify apoptosis and autophagy pathways in vitro. FRET is an energy transfer phenomenon which occurs between two spectrum-overlapping fluorophores that are in close proximity. The design of the sensor is based on enzyme substrate dynamics and consists of a reporter gene fused between fluorescent proteins. Additionally, FRET based protease assay has been used to determine the kinetics of Atg4A, an enzyme involved in autophagy. The kinetic parameters km, kcat, kcat /km were derived using real time detection method. To take this forward, the sensor will be transfected in H460 lung cancer cell line to identify the type of death the cell chooses on treatment with sumoylation inhibitors that were previously developed in the lab. MTS assay was conducted to establish the supremacy of sumoylation inhibitors over other commercially available drugs. In conclusion, the biosensor developed in this study is highly sensitive in detecting apoptosis and autophagy and can be used to derive quantitative data using FRET technology. It can be used both in vitro and in mammalian cells and can differentiate between apoptosis and autophagy. The results of this study can help to expand biomedical knowledge by illuminating the mechanisms of different cell death pathways. This will pave way for simple and non-invasive ways to modulate cell death pathways for therapeutic intervention in the future.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Hariharan, C. (2017). Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways. (Thesis). University of California – Riverside. Retrieved from http://www.escholarship.org/uc/item/7pf7v6gq
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):
Hariharan, Chitra. “Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways.” 2017. Thesis, University of California – Riverside. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/7pf7v6gq.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hariharan, Chitra. “Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways.” 2017. Web. 04 Mar 2021.
Vancouver:
Hariharan C. Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways. [Internet] [Thesis]. University of California – Riverside; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/7pf7v6gq.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hariharan C. Development of Highly Sensitive FRET Based Biosensor to Detect Cell Death Pathways. [Thesis]. University of California – Riverside; 2017. Available from: http://www.escholarship.org/uc/item/7pf7v6gq
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
UCLA
5.
Shaw, Jaime.
Free-Breathing, Non-ECG, T1 Mapping in the Heart.
Degree: Bioengineering, 2017, UCLA
URL: http://www.escholarship.org/uc/item/9b3514g6
► Cardiovascular diseases are the leading cause of death in the United States, translating to a high cost burden on the healthcare system. Noninvasive imaging can…
(more)
▼ Cardiovascular diseases are the leading cause of death in the United States, translating to a high cost burden on the healthcare system. Noninvasive imaging can play a significant role in the diagnosis and triaging of cardiovascular diseases. Cardiac MRI is a noninvasive imaging technique becoming more prevalent due to its advantage of providing excellent soft-tissue contrast and high spatial resolution without the use of ionizing radiation; however, major challenges exist including respiratory and cardiac motion. One emerging application of cardiac MRI is myocardial tissue characterization using quantitative mapping techniques. Current mapping techniques rely on electrocardiogram (ECG)-gating which assumes normal sinus rhythm, as well as breath-holds or respiratory monitoring which preclude some patients from scans or prolong scan time. Quantification of spin-lattice relaxation times (or T1 mapping) of the myocardium has been shown to enable detection of diffuse myocardial fibrosis, a key feature in the progression of many cardiac diseases. The main focus of this dissertation is to remove the limitations of ECGs and respiratory monitoring from cardiac MRI to enable free-breathing, non-ECG T1 mapping. The first objective of this dissertation was to develop a two-dimensional, free-breathing, non-ECG, continuous T1 mapping technique and validate it in imaging phantoms using a gold-standard technique. We compare the T1 and extracellular volume (ECV) values to a conventional breath-hold, ECG-gated, T1 mapping technique in healthy subjects. The repeatability and accuracy of the technique were assessed for different length scans. The second objective was to demonstrate the feasibility of quantifying T1 values throughout the cardiac cycle and to assess cardiac function simultaneously with a method free of ECG and prospective respiratory monitoring. The third objective of this dissertation was to develop a three-dimensional free-breathing, non-ECG T1 mapping technique capable of providing T1 and ECV maps with full coverage of the left ventricle.This dissertation lays the groundwork for quantitative cardiac MRI with no reliance on prospective respiratory monitoring or ECGs. The removal of these limitations makes cardiac MRI accessible to all types of patients and provides a comfortable scan environment with no breath-holding. This dissertation represents a move toward a “push-button” cardiac MRI paradigm, wherein one scan with minimal setup can provide information comparable to a complex standard-of-care cardiac MRI scan.
Subjects/Keywords: Bioengineering
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APA ·
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Manager
APA (6th Edition):
Shaw, J. (2017). Free-Breathing, Non-ECG, T1 Mapping in the Heart. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/9b3514g6
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):
Shaw, Jaime. “Free-Breathing, Non-ECG, T1 Mapping in the Heart.” 2017. Thesis, UCLA. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/9b3514g6.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Shaw, Jaime. “Free-Breathing, Non-ECG, T1 Mapping in the Heart.” 2017. Web. 04 Mar 2021.
Vancouver:
Shaw J. Free-Breathing, Non-ECG, T1 Mapping in the Heart. [Internet] [Thesis]. UCLA; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/9b3514g6.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Shaw J. Free-Breathing, Non-ECG, T1 Mapping in the Heart. [Thesis]. UCLA; 2017. Available from: http://www.escholarship.org/uc/item/9b3514g6
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California, San Diego
6.
Wei, Chun-Shu.
Towards Brain Decoding for Real-World Drowsiness Detection.
Degree: 2018, University of California, San Diego
URL: http://pqdtopen.proquest.com/#viewpdf?dispub=10641645
► A brain-computer interface (BCI) allows human to communicate with a computer by thoughts. Recent advances in brain decoding have shown the capability of BCIs…
(more)
▼ A brain-computer interface (BCI) allows human to communicate with a computer by thoughts. Recent advances in brain decoding have shown the capability of BCIs in monitoring physiological and cognitive state of the brain, including drowsiness. Since drowsy driving has been an urgent issue in vehicle safety that causes numerous deaths and injuries, BCIs based on non-invasive electroencephalogram (EEG) are developed to monitor drivers’ drowsiness continuously and instantaneously. Nonetheless, on the pathway of transitioning laboratory-oriented BCI into real-world applications, there are major challenges that limit the usability and convenience for drowsiness detection (DD). To completely understand the association between human EEG and drowsiness, this study employed a large-scale dataset collected from simulated driving experiments with a lane-keeping task and EEG recordings. A DD-BCI that acquires EEG from only non-hair-bearing (NHB) areas was proposed to maximize the comfort and convenience. The performance of the NHB DD-BCI was validated and compared with that using whole-scalp EEG, showing no significant difference in the accuracy of alert/drowsy classification. In addition, a subject-transfer framework that leverages large-scale existing data from other subjects was proposed to reduce the calibration time of a DD-BCI. Alert baseline data were involved to enhance the efficiency of subject-to-subject model transfer. The subject-transfer approach significantly reduced the calibration time of the DD-BCI, exhibiting the potential in facilitating plug-and-play brain decoding for real-world BCI applications. Overall, this thesis presents the contributions to developing a DD-BCI for real-world use with maximal usability and convenience. The methodologies and findings could further catalyze the exploration of real-world BCIs in more applications.
Subjects/Keywords: Bioengineering
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APA ·
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wei, C. (2018). Towards Brain Decoding for Real-World Drowsiness Detection. (Thesis). University of California, San Diego. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=10641645
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):
Wei, Chun-Shu. “Towards Brain Decoding for Real-World Drowsiness Detection.” 2018. Thesis, University of California, San Diego. Accessed March 04, 2021.
http://pqdtopen.proquest.com/#viewpdf?dispub=10641645.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wei, Chun-Shu. “Towards Brain Decoding for Real-World Drowsiness Detection.” 2018. Web. 04 Mar 2021.
Vancouver:
Wei C. Towards Brain Decoding for Real-World Drowsiness Detection. [Internet] [Thesis]. University of California, San Diego; 2018. [cited 2021 Mar 04].
Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10641645.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wei C. Towards Brain Decoding for Real-World Drowsiness Detection. [Thesis]. University of California, San Diego; 2018. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=10641645
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
7.
Salazar, Michael.
Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/5d84f0xg
► Antibiotic-resistant Staphylococcus aureus is one of the most common causes of bacterial infections in humans and is responsible for a wide range of infections in…
(more)
▼ Antibiotic-resistant Staphylococcus aureus is one of the most common causes of bacterial infections in humans and is responsible for a wide range of infections in healthcare and community settings. Methicillin-resistant S. aureus, in particular, has proven to be resistant to β-lactams and many other classes of antibiotics. The standard for evaluation of antibiotic efficacy involves testing on cation-adjusted Mueller Hinton broth or CA-MHB. However, this is not reflective of the human host environment. Changes in media conditions and environment have led to differences in antibiotic efficacy outcomes and have major implications in treatment. To further elucidate differential antibiotic resistance mechanisms, adaptive laboratory evolution was utilized to generate strains of the S. aureus clinical isolate, USA300 TCH1516, under an increasing antibiotic pressure of nafcillin in CA-MHB as well as Roswell Park Memorial Institute medium (RPMI). Evolutionary paths for strains were characterized at the physiological and genetic level utilizing whole genome sequencing to understand the genetic and metabolic basis of antibiotic resistance. Improvements in growth rate were observed for media adaptation to RPMI but not CA-MHB. Improved fitness in stressful conditions were identified and linked to mutated copies of apt. Key reproducibly occurring mutations were compared between the two environments after exposure to nafcillin showing mutations in common regions within the vraRST operon, a regulator of cell wall metabolism genes, and in mgt, a nonessential transglycosylase. Unique susceptible phenotypes to gentamicin and azithromycin were identified after tolerance to nafcillin. Mutated genes yybT and ybbP, codY, and oatA related to regulation of nucleotide and branched chain amino acid metabolism as well as peptidoglycan biosynthesis and modification were identified for tolerance to nafcillin in RPMI only. Mutations were subsequently compared across literature and presented here.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Salazar, M. (2018). Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/5d84f0xg
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):
Salazar, Michael. “Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/5d84f0xg.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Salazar, Michael. “Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus.” 2018. Web. 04 Mar 2021.
Vancouver:
Salazar M. Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/5d84f0xg.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Salazar M. Determining Media Dependent Mechanisms of Antibiotic Resistance in Laboratory Evolved Staphylococcus aureus. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/5d84f0xg
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
8.
Weng, Liam Lingyan.
Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/4d69s42q
► Staphylococcus aureus is a gram-positive pathogenic bacterium that has colonized an estimated one-third of the human population and such infections can often become fatal. The…
(more)
▼ Staphylococcus aureus is a gram-positive pathogenic bacterium that has colonized an estimated one-third of the human population and such infections can often become fatal. The adaptive mechanisms of S. aureus, however, still remain obscure partially due to a lack of knowledge in its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes through genome-scale modeling and bioinformatics approaches. However, there is a need for a validated chemically defined minimal medium to further investigate the requirements of the cell. Identifying the nutritional requirements will provide mechanistic insights into the functional states of the cell and its pathogenicity. In this work, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated, modified, and validated to enable growth of three S. aureus strains, and enable systems analyses of this important pathogen. The formulated SMM was utilized in an adaptive laboratory evolution (ALE) experiment to further probe the ideal capabilities of the targeted strains and uncover mechanisms underlying the optimized states. The evolved strains were phenotypically characterized for their physiological characteristics and antimicrobial susceptibility. The genome of each strain was sequenced to examine the genetic basis for the observed phenotypes. The resulting SMM and the evolved strains will serve as important reagents for studying the resistance phenotypes of S. aureus.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Weng, L. L. (2018). Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/4d69s42q
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):
Weng, Liam Lingyan. “Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/4d69s42q.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Weng, Liam Lingyan. “Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus.” 2018. Web. 04 Mar 2021.
Vancouver:
Weng LL. Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/4d69s42q.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Weng LL. Investigating a Defined Minimal Medium for Systems Analyses of MDR Staphylococcus aureus. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/4d69s42q
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
9.
Sandberg, Troy.
Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/23f4m0md
► Evolution underlies the entirety of Earth’s biodiversity, as all species diverged from the last universal common ancestor billions of years ago. Although able to effect…
(more)
▼ Evolution underlies the entirety of Earth’s biodiversity, as all species diverged from the last universal common ancestor billions of years ago. Although able to effect incredible changes over long periods, the need for multiple generations of mutation and competition renders evolution nearly imperceptible, at the timescale of human observation, for all but the most quickly reproducing organisms. Thus microbial adaptation, given microbes’ rapid generation time and enormous population sizes, is perhaps most pressing to understand. This unavoidable evolutionary process facilitates the rise and spread of antibiotic resistance, and frequently countervails attempts to genetically engineer organisms for human purposes.The bacterium Escherichia coli, easily the most highly studied microbe to date, is an ideal model by which to investigate evolution. With both clinical and biotechnological relevance, a thorough understanding of the adaptive principles governing E. coli evolution is of great importance. In this dissertation I seek to probe the adaptive capabilities of E. coli using custom robotics systems that function as ‘evolution machines.’ Enabled by this automation, adaptive walks along the fitness landscape can be tracked in real-time with experimental throughput, data quality, and environmental control impossible to replicate manually.I subject E. coli to stressful perturbations and analyze the mechanisms by which it evolves to restore robust growth, using data types such as phenotypic characterization, whole genome sequencing, and transcriptomics. I demonstrate the remarkable adaptive flexibility of E. coli as it readily evolves to tolerate elevated temperatures, altered isotopic composition, rapidly fluctuating growth environments, and even replacement of important native genes with foreign DNA. Overall, these studies establish condition-specific evolutionary responses, general mechanisms for growth rate improvement, and guiding principles for the successful use of laboratory evolution experiments as a tool for biological discovery and engineering.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Sandberg, T. (2018). Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/23f4m0md
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):
Sandberg, Troy. “Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/23f4m0md.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sandberg, Troy. “Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations.” 2018. Web. 04 Mar 2021.
Vancouver:
Sandberg T. Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/23f4m0md.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sandberg T. Exploring the Adaptive Capabilities of Escherichia coli: Perturbations from a Typical Life Cycle and Resulting Evolutionary Compensations. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/23f4m0md
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
UCLA
10.
Chen, Junjie.
DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration.
Degree: Bioengineering, 2018, UCLA
URL: http://www.escholarship.org/uc/item/5wm1t02t
► Current methods of cardiac functional assessment such as ejection fraction (EF), strain imaging, and ventricular inflow diastology have known limitations. We developed and applied a…
(more)
▼ Current methods of cardiac functional assessment such as ejection fraction (EF), strain imaging, and ventricular inflow diastology have known limitations. We developed and applied a semi-automated, open-source software tool (DIAMOND) for quantitative assessment of segmental cardiac function with applicability to physiological and chemotherapy-induced cardiomyopathy conditions. Zebrafish embryos were imaged in vivo using a light-sheet fluorescence microscopy system, and the 4-D heart synchronized to address cardiac motion. Following re-orientation and isotropic resampling along the true ventricular short axis, resampled data were saved in different matrices. The ventricle was then divided based on a virtual centerline into 8 segments. To conform to the complexity of cardiac structures and deformation, we artificially created a group of rectangular parallelepipeds for 3-D rigid registration and derivation of a transformation matrix (Tm). Tm was utilized to align the diastolic myocardium to the systolic coordinate system, thereby maintaining their relative position. Therefore, DIAMOND allowed measurement of the 3-D displacement of segmental myocardial mass centroids in the same coordinate system. Following treatment of transgenic zebrafish lines with doxorubicin and by chemically and genetically manipulating the Notch signaling pathway, we demonstrate that global EF and focal DIAMOND displacement provide complementary information, with basal segments adjacent to the atrioventricular canal displaying the highest 3-D displacement, contributing the most to EF, and being the most susceptible to chemotherapy-induced cardiac injury. By utilizing a Tp1 Notch reporter line, FUCCI transgenic line, and DIAMOND, we established a temporal sequence of Dox-induced injury, Notch activation, cardiomyocyte proliferation, trabeculation restoration, and cardiac function normalization within two days post doxorubicin treatment. In conclusion, DIAMOND provides a novel approach for focal cardiac mechanics assessment to localize, track, and quantify segmental myocardial function in response to doxorubicin-induced cardiac injury and Notch signaling-medicated myocardial regeneration.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Chen, J. (2018). DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/5wm1t02t
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):
Chen, Junjie. “DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration.” 2018. Thesis, UCLA. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/5wm1t02t.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Chen, Junjie. “DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration.” 2018. Web. 04 Mar 2021.
Vancouver:
Chen J. DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration. [Internet] [Thesis]. UCLA; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/5wm1t02t.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Chen J. DIAMOND (Displacement Analysis of Myocardial Mechanical Deformation) to Uncover Segmental Susceptibility to Doxorubicin-Induced Cardiac Injury and Regeneration. [Thesis]. UCLA; 2018. Available from: http://www.escholarship.org/uc/item/5wm1t02t
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
11.
Nayak, Priya.
Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/0750h65j
► Skeletal muscle is the most abundant tissue in the body, comprising up to 40% of the total mass. In addition to its most salient role…
(more)
▼ Skeletal muscle is the most abundant tissue in the body, comprising up to 40% of the total mass. In addition to its most salient role in locomotion, it also plays a central role in metabolic homeostasis. Therefore, injury-, age- and disease-related compromise of skeletal muscle can be extremely detrimental to overall health and quality of life. As such, the development of regenerative therapies for skeletal muscle that contribute to in vivo repair, as well as in vitro strategies that can hasten the development of personalized drug treatment, could be of vital importance. Human induced pluripotent stem cells (hiPSCs) are a powerful tool that can meet both these challenges; they are patient-specific, can give rise to derivatives of all three germ layers, including myogenic progenitors, and are scalable since pluripotent cells readily self-renew in vitro. However, the robust, transgene free myogenic differentiation of hiPSCs remains a hurdle. In this dissertation, I address these challenges by identifying key time-varying signaling, transcriptional, and epigenetic-related mechanisms that lead to enhanced in vitro myogenesis by comparing the longitudinal transcriptomic profiles of multiple hiPSC lines. Furthermore, I show that targeted genetic perturbation at the outset of differentiation may bias lineage specification to the paraxial mesoderm fate. Finally, through the selective expansion and terminal differentiation of hiPSC-derived myogenic progenitor cell populations, we show that they form functional 3D microtissues in an in vitro skeletal muscle-on-a-chip platform, as well as give rise to dystophin positive fibers in vivo in a murine model of muscular dystrophy.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Nayak, P. (2018). Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/0750h65j
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):
Nayak, Priya. “Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/0750h65j.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Nayak, Priya. “Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo.” 2018. Web. 04 Mar 2021.
Vancouver:
Nayak P. Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/0750h65j.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Nayak P. Elucidation of mechanisms of in vitro myogenesis of human induced pluripotent stem cells with functional validation in vitro and in vivo. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/0750h65j
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Cornell University
12.
Taherkhani, Peyman.
Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events.
Degree: PhD, Biological and Environmental Engineering, 2018, Cornell University
URL: http://hdl.handle.net/1813/59403
► Transport of a taste stimulus from a beverage to the taste pores was computationally modeled in different anatomy scales: tongue's anterodorsal surface, circumvallate papillae and…
(more)
▼ Transport of a taste stimulus from a beverage to the taste pores was computationally modeled in different anatomy scales: tongue's anterodorsal surface, circumvallate papillae and whole oral cavity in three dimensions. The models are based on the fundamental governing equations of transport phenomena. The stimulus delivery details were based on the experiments in literature or the sensory experiments run by the author. The fluid flow and stimulus transport were simulated based on the details of each anatomy. Realistic topology of a tongue’s surface, including lingual papilla histology, and the realistic anatomy of the oral cavity of a human
subject were considered. For anterior surface of the tongue, results show that the uneven surface of the tongue has considerable influence on the persistence of supra-threshold stimulus concentration near taste pores. Time-concentration profiles were developed for various locations along the tongue’s surface. These profiles showed strong association with measured time-intensity (TI) profiles from literature, specifically, the rising phase, total duration and slopes. The computed concentration profiles can be used to better understand the course of events occurring during taste stimulation, which in turn will provide a better understanding of the relationship between a stimulus bulk concentration and its perceived intensity. For circumvallate papilla, the histological details such as secretion from von-Ebner gland into the cleft and a thin layer of saliva covering the papilla are included in the model. The experimental results show a relatively long intensity reaction time. The time-concentration profile of the tastant within the cleft shows that the secretion from von-Ebner gland contributes to the longer reaction time. Also, the comparison between the intensity and concentration profiles suggests that adaptation to taste takes place despite rising concentrations near taste buds. For the model on the whole oral cavity, the results show that the time-concentration profile near tongue is different than the time-concentration profile introduced upon stimulus delivery. Also, the computed concentration is studied against the intensity recorded under the same conditions. The results show a close association between the time-concentration profile near the tongue's surface and the time-intensity profile. The framework upon which the model is developed can be used for various consumption conditions, contributing to a quantitative understating of the relation between tastant concentration and taste intensity.
Advisors/Committee Members: Datta, Ashim K. (chair), Stroock, Abraham Duncan (committee member), Dando, Robin (committee member).
Subjects/Keywords: Bioengineering
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Taherkhani, P. (2018). Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/59403
Chicago Manual of Style (16th Edition):
Taherkhani, Peyman. “Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events.” 2018. Doctoral Dissertation, Cornell University. Accessed March 04, 2021.
http://hdl.handle.net/1813/59403.
MLA Handbook (7th Edition):
Taherkhani, Peyman. “Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events.” 2018. Web. 04 Mar 2021.
Vancouver:
Taherkhani P. Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events. [Internet] [Doctoral dissertation]. Cornell University; 2018. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/1813/59403.
Council of Science Editors:
Taherkhani P. Relating Tastant Concentration to Perceived Taste Intensity: A Mechanistic Understanding of pre-Transduction Events. [Doctoral Dissertation]. Cornell University; 2018. Available from: http://hdl.handle.net/1813/59403
University of California – San Diego
13.
Gong, Ya.
Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/2680p8rt
► Histone proteins in chromatin undergo various modifications that have profound impacts on many cellular processes, including cell cycle control, cancer, senescence, X-inactivation, cell fate decisions,…
(more)
▼ Histone proteins in chromatin undergo various modifications that have profound impacts on many cellular processes, including cell cycle control, cancer, senescence, X-inactivation, cell fate decisions, and stem cell differentiation. These histone marks do not occur isolated, but often occur mutually exclusive or concurrently. Despite the extensive research ongoing, a large part of the regulation of histone marks remained elusive due to the lack of powerful and efficient methods. Here, we present a method of constructing an epigenetic fluorescence energy resonance transfer (FRET) biosensor by tuning variables including the linker length and orientations between the fluorescent proteins in the case of a H3K27me3 FRET biosensor. It reveals that shortening the linker connecting the fluorescent protein pairs and binding partners could indeed increase the FRET change between the bound and unbound states in the biosensor. This key concept can be generally applied to optimize various different FRET biosensors, especially histone epigenetic FRET biosensors with binding domains that have relatively low binding affinities.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Gong, Y. (2018). Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/2680p8rt
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):
Gong, Ya. “Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/2680p8rt.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Gong, Ya. “Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors.” 2018. Web. 04 Mar 2021.
Vancouver:
Gong Y. Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/2680p8rt.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Gong Y. Designing Principles for Epigenetic Fluorescence Resonance Energy Transfer Biosensors. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/2680p8rt
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
14.
Richards, Andrew.
Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/4zk292pm
► DNA copy number variations (CNVs) have previously been reported in human cortical neurons from non-diseased patients, but these alterations do not appear to be consistent…
(more)
▼ DNA copy number variations (CNVs) have previously been reported in human cortical neurons from non-diseased patients, but these alterations do not appear to be consistent from cell to cell and appear to be rare among neurons overall. Interestingly, Alzheimer’s disease patients appear to have a higher prevalence of CNVs than non-diseased, although the biological significance of this observation is still largely unknown. Single-cell whole-genome next-generation sequencing holds promise to investigate these variations and the regions in which they occur in an unbiased manner. Unlike recent advances in single-cell RNA-seq, however, library preparation for single-cell DNA-seq suffers from extremely limited throughput. Furthermore, it is difficult to assess the significance of individual variations from whole-genome sequencing alone, particularly when control samples from non-diseased patients also show some variation at lower frequency. A potential solution is a multi-omics approach, in which information is collected about multiple species of biomolecules simultaneously from each sample, which taken together aid the interpretation of individual observations with respect to biological significance.This dissertation describes the design and development of a technology to physically separate DNA and RNA and to prepare sequencing libraries from each in parallel from limited starting samples without splitting, which we called Gel-seq. Thirty-two paired DNA and RNA sequencing libraries were successfully prepared from a variety of human and mouse cells lines and from mouse liver tissue using Gel-seq. Sample types could be clearly distinguished from each other based on either genomic copy number or transcriptomic profiles. This dissertation also describes the design and development of a technology to prepare a thousand single-cell whole-genome sequencing libraries in a single run. A proof-of-concept was performed with 87 cells from human and mouse lines. Copy number profiles agreed with bulk, and 96% and 92% of human and mouse cells, respectively, clustered correctly within their cell line based on copy number profile alone. These technologies will help to enable the unbiased characterization of genomic alterations not only in neurodegenerative disorders, but potentially also in other conditions associated with mosaic genomic backgrounds, such as cancer, microbiome disorders, or infectious diseases.
Subjects/Keywords: Bioengineering
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APA ·
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Export
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APA (6th Edition):
Richards, A. (2018). Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/4zk292pm
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):
Richards, Andrew. “Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/4zk292pm.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Richards, Andrew. “Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains.” 2018. Web. 04 Mar 2021.
Vancouver:
Richards A. Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/4zk292pm.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Richards A. Characterizing Genomic Mosaicism in Single Neurons from Adult Human Brains. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/4zk292pm
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
15.
Wang, Xin.
Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy.
Degree: Bioengineering, 2019, University of California – San Diego
URL: http://www.escholarship.org/uc/item/9bj2f21j
► While chimeric antigen receptor (CAR) therapy has emerged as a promising method for cancer therapy by engineering autologous T cells to redirect them to the…
(more)
▼ While chimeric antigen receptor (CAR) therapy has emerged as a promising method for cancer therapy by engineering autologous T cells to redirect them to the specific tumor-associate antigen and kill the tumor cells, these engineered T cells also have “on-target, off-tumor” toxicity, which can harm normal tissues and can be life-threatening. The non-specific activity inspires us to control CAR expression with high spatiotemporal precisions. Therefore, we present the design of heat inducible CAR, which can upregulate CAR expression after heat stimulation. The thesis introduces the study of heat inducible anti-prostate specific membrane antigen (PSMA) CAR T cells, which has been proved to be able to sense heat and produce CARs for the targeting of prostate cancer cells and triggering activation of T cells. The study can serve as a foundation for broader application in solid tumor therapy.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Wang, X. (2019). Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/9bj2f21j
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):
Wang, Xin. “Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy.” 2019. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/9bj2f21j.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Xin. “Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy.” 2019. Web. 04 Mar 2021.
Vancouver:
Wang X. Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy. [Internet] [Thesis]. University of California – San Diego; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/9bj2f21j.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang X. Heat Inducible Chimeric Antigen Receptor (CAR) T Cell for Prostate Cancer Therapy. [Thesis]. University of California – San Diego; 2019. Available from: http://www.escholarship.org/uc/item/9bj2f21j
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Irvine
16.
Mejia, Louis.
Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing.
Degree: Biomedical Engineering, 2019, University of California – Irvine
URL: http://www.escholarship.org/uc/item/0ks7c3qt
► Despite progress of the modern biomedical revolution, efficient personalized cancer cures remain largely elusive due to the vast amount of potential biomarkers to identify. This…
(more)
▼ Despite progress of the modern biomedical revolution, efficient personalized cancer cures remain largely elusive due to the vast amount of potential biomarkers to identify. This diverse pool of receptors is a product of a complex ecosystem of distinct key cell types within a tumor which may help promote proliferation. This intra-tumor heterogeneity has necessitated development of methods to identify key cell type receptors, such as molecular probes that target biomarkers. Probes harboring fluorescent species are among the most successful and couple distinct-spectra fluorescent species to a targeting protein, such as an antibody. However, existing probe libraries are limited to only 10 simultaneous detection channels, severely reducing the amount of ascertainable molecular information. Fluorescence lifetime imaging microscopy (FLIM) has been proposed as an expansion to conventional fluorescence imaging by adding an additional dimension of channels to analyze, but has been limited by the complexities of curve fitting decay half-lives. Recently, the phasor approach to FLIM provided an elegant means to analyze species mixtures on a phasor plot. Here, we demonstrate the construction of a lifetime probe library encapsulating a controlled loading ratio of fluorescent species and analyzed with the phasor approach to FLIM. Using a reverse microemulsion synthesis method, organic dyes, dark quenchers, and quantum dots have been incorporated into probe cores to unlock a variety of distinct phasor positions within a single spectral window. Probe surfaces may be modified with polyethylene glycol chains to help prevent in-vitro protein adsorption and a functional loss of targeting specificity. Bioorthogonal click chemistry linkers may be conjugated onto chain termini to allow highly specific coupling to analogous premodified antibodies via rapid in-vitro two-step targeting of tumor biomarkers, or through the formation of immunoconjugates for direct targeting. Subsequently, the presence of key receptors may be inferred using the phasor approach. With the success of our preliminary probes, multiplexed targeting assays will follow. Ultimately, we intend to use our lifetime probe library in clinical settings to efficiently characterize tumors via simultaneous detection of up to 80 pre-selected personalized biomarkers.
Subjects/Keywords: Bioengineering
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Manager
APA (6th Edition):
Mejia, L. (2019). Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/0ks7c3qt
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):
Mejia, Louis. “Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing.” 2019. Thesis, University of California – Irvine. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/0ks7c3qt.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Mejia, Louis. “Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing.” 2019. Web. 04 Mar 2021.
Vancouver:
Mejia L. Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing. [Internet] [Thesis]. University of California – Irvine; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/0ks7c3qt.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Mejia L. Constructing a Fluorescence Lifetime Nanoprobe Library to Advance Lifetime-Based Multiplexing. [Thesis]. University of California – Irvine; 2019. Available from: http://www.escholarship.org/uc/item/0ks7c3qt
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
UCLA
17.
Le, Nguyen Khoi.
Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification.
Degree: Bioengineering, 2019, UCLA
URL: http://www.escholarship.org/uc/item/9hr4w0r9
► Infectious diseases remain a public health concern worldwide. They severely impact resource-poor areas, where the top 10 causes of deaths include diarrhoeal diseases, HIV/AIDS, and…
(more)
▼ Infectious diseases remain a public health concern worldwide. They severely impact resource-poor areas, where the top 10 causes of deaths include diarrhoeal diseases, HIV/AIDS, and tuberculosis. One gold-standard detection method for these infectious agents is nucleic acid amplification with the polymerase chain reaction (PCR). Unfortunately, its requirements for laboratory trained personnel and equipment prevent it from becoming a useful diagnostic tool at the point of care. To eliminate the need for a thermocycler, isothermal DNA amplification techniques were developed, but they cannot stand alone as complete diagnostic tools. They still require an extensive DNA preparation step prior to amplification. In addition, before it can be brought to an end-user, the entire detection scheme from sample preparation to end detection needs to be incorporated on a platform, with all of the reagents stored.This thesis tackles the first aim by describing the development of an integrated method to extract, purify, and amplify DNA in one step using a micellar aqueous two-phase system (ATPS) with thermophilic helicase-dependent amplification (tHDA). This one-pot system was able to detect a target sequence from whole bacteria samples with cell concentrations as low as 102 colony forming units/mL. This is the first known application of an ATPS to isothermal DNA amplification. For the second aim, this thesis describes the work that has been done so far as part of the initial step to the development of a fully-integrated nucleic acid testing device using a microfluidic platform. To avoid relying on the cleanroom for fabrication and external pumps for fluid flow in the chips, vacuum-driven chips were made from 3D-printed master molds for the first time. In addition, to our knowledge, we demonstrated the first dehydration of a full reaction set up for the recombinase polymerase amplification (RPA), including all of the enzymes and the primers but not the reaction activator magnesium acetate. The promising results will serve as a good starting point for our work in developing stand-alone diagnostic devices that can be used at the point of care and allow for a fully automated sample-to-result testing procedure.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Le, N. K. (2019). Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/9hr4w0r9
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):
Le, Nguyen Khoi. “Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification.” 2019. Thesis, UCLA. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/9hr4w0r9.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Le, Nguyen Khoi. “Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification.” 2019. Web. 04 Mar 2021.
Vancouver:
Le NK. Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification. [Internet] [Thesis]. UCLA; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/9hr4w0r9.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Le NK. Developing Different Formats for Combining Aqueous Two-Phase Systems with Isothermal DNA Amplification. [Thesis]. UCLA; 2019. Available from: http://www.escholarship.org/uc/item/9hr4w0r9
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
18.
Mercado, Amiel.
Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts.
Degree: Bioengineering, 2019, University of California – San Diego
URL: http://www.escholarship.org/uc/item/6890k9zw
► There is general consensus that immune cells such as macrophages within injured tissue influence remodeling and fibrosis. At the cellular level, this has been attributed…
(more)
▼ There is general consensus that immune cells such as macrophages within injured tissue influence remodeling and fibrosis. At the cellular level, this has been attributed to the communication between macrophages and fibroblasts. However, precisely how these communication is mediated at the molecular level remains unknown. We hypothesized fibroblasts are influenced by type I interferon signaling, either directly or indirectly via macrophages, which is a determining factor in the induction of adverse cardiac remodeling. In this study, differential gene expression analysis at a single cell level was done between wild type and knockout mice after myocardial infarction. It was found that a subset population of macrophages produce IRF3-dependent type I Interferon genes. Further, in fibroblasts, it was found matrix metalloproteinases is dominantly expressed in wild type. Given these results, this study proposes that the overexpression of matrix metalloproteinases in fibroblasts is linked to the production of the IRF3-dependent type I interferon genes in macrophages.
Subjects/Keywords: Bioengineering
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APA ·
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CSE |
Export
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APA (6th Edition):
Mercado, A. (2019). Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/6890k9zw
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):
Mercado, Amiel. “Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts.” 2019. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/6890k9zw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Mercado, Amiel. “Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts.” 2019. Web. 04 Mar 2021.
Vancouver:
Mercado A. Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts. [Internet] [Thesis]. University of California – San Diego; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/6890k9zw.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Mercado A. Single-Cell Sequencing Reveals an IRF3-dependent Immune and Remodeling Response in Wild Type Macrophages and Fibroblasts. [Thesis]. University of California – San Diego; 2019. Available from: http://www.escholarship.org/uc/item/6890k9zw
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Harvard University
19.
Khormaee, Sariah.
Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction.
Degree: Doctor of Medicine, 2014, Harvard University
URL: http://etds.lib.harvard.edu/hms/admin/view/59
;
http://nrs.harvard.edu/urn-3:HUL.InstRepos:12407617
► Short interfering RNA (siRNA) is a class of nucleotide drugs with a profound potential to improve patient health through its ability to silence the expression…
(more)
▼ Short interfering RNA (siRNA) is a class of nucleotide drugs with a profound potential to improve patient health through its ability to silence the expression of specific genes at the post-transcriptional level. However, the clinical application of siRNA therapeutics remains hindered by a lack of efficient delivery systems that deposit siRNA into the cytoplasm of cells, a step necessary for siRNA’s silencing effect. Much research has focused on the development of siRNA delivery agents to overcome this challenge. There are no standard pre-clinical models for testing of siRNA delivery agents, and investigators have chosen to evaluate efficacy in a variety of systems including in vitro tissue culture and animal models. These systems have vastly different cellular microenvironments which may modulate cellular behavior and affect the response of cells to siRNA, thus altering the apparent efficacy of siRNA delivery agents. The substrate on which cells adhere is one aspect of the microenvironment that has been previously shown to alter cellular behavior. In this work, we tested the hypothesis that changing the properties of cellular adhesion substrates can change the apparent efficacy of a siRNA delivery agent. Specifically, we used a commonly employed in vitro cationic lipid siRNA delivery vector and evaluated siRNA silencing efficacy in U251 cells seeded on alginate hydrogel surfaces. These surfaces were synthesized to have systematic variation in integrin ligand arginine-glycine-aspartate (RGD) density and elastic modulus. We found that an eightfold increase in RGD content of the alginate grown substrate increased siRNA knockdown efficacy from 25 ± 12% to 52 ± 10%, with constant concentrations of siRNA and delivery agent. We found no difference in siRNA mediated knockdown efficacy over the elastic modulus range tested (53-133 kPa). These results indicate that the cell-adhesion substrate interaction can modulate siRNA protein silencing efficacy, a finding important for evaluation of siRNA therapeutics in the in vitro setting.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Khormaee, S. (2014). Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction. (Doctoral Dissertation). Harvard University. Retrieved from http://etds.lib.harvard.edu/hms/admin/view/59 ; http://nrs.harvard.edu/urn-3:HUL.InstRepos:12407617
Chicago Manual of Style (16th Edition):
Khormaee, Sariah. “Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction.” 2014. Doctoral Dissertation, Harvard University. Accessed March 04, 2021.
http://etds.lib.harvard.edu/hms/admin/view/59 ; http://nrs.harvard.edu/urn-3:HUL.InstRepos:12407617.
MLA Handbook (7th Edition):
Khormaee, Sariah. “Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction.” 2014. Web. 04 Mar 2021.
Vancouver:
Khormaee S. Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction. [Internet] [Doctoral dissertation]. Harvard University; 2014. [cited 2021 Mar 04].
Available from: http://etds.lib.harvard.edu/hms/admin/view/59 ; http://nrs.harvard.edu/urn-3:HUL.InstRepos:12407617.
Council of Science Editors:
Khormaee S. Optimizing siRNA Efficacy through Alteration in the Target Cell-Adhesion Substrate Interaction. [Doctoral Dissertation]. Harvard University; 2014. Available from: http://etds.lib.harvard.edu/hms/admin/view/59 ; http://nrs.harvard.edu/urn-3:HUL.InstRepos:12407617
20.
Lin, Jung-ming G.
Microfluidic Device Development for Analyzing Single Glioblastoma Cells.
Degree: Biological & Agricultural Engineering, 2017, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/3bn054m0
► Glioblastoma remains a deadly disease due to the diffuse infiltration of single tumorcells into the surrounding tissue. Even with the current treatment regimens of surgery,radiation,…
(more)
▼ Glioblastoma remains a deadly disease due to the diffuse infiltration of single tumorcells into the surrounding tissue. Even with the current treatment regimens of surgery,radiation, and chemotherapy, the median survival time is approximately one year. Likemany solid tumors, glioblastoma is extremely heterogeneous with respect to multiplephenotypes such as invasive capacity, therapeutic resistance, and tumorigenicity. Thisheterogeneity complicates our understanding of glioblastoma and consequently, ourability to treat this disease. Unfortunately, standard population-based assays can maskthe properties of rare subpopulations within a tumor and therefore, obscure ourunderstanding of these subpopulations. As a result, without tools that allow for singlecell analysis, we are unable to interrogate how different subpopulation phenotypes mayserve as indicators of glioblastoma tumor growth and progression.In this dissertation, we sought to develop and optimize new microfluidic tools to analyzesingle glioblastoma cells for a range of phenotypes: viscoelasticity, motility, andinvasion. First, we developed a cross-slot based platform and a correspondinganalytical model that enables the determination of cellular viscoelastic properties(stiffness and fluidity) in a high-throughput manner. Using this platform, we quantifiedthe viscoelastic properties of 3T3 fibroblasts and glioblastoma tumor initiating cells(TICs) and observed the expected changes in the cellular elastic modulus in responseto agents that soften or stiffen the cytoskeleton. Second, we developed a microfluidicdevice and workflows that integrates measurements of invasive motility and targetedprotein expression with single cell resolution, which we named SCAMPR (Single CellAnalysis of Motility and Proteotype). Using this platform, we identified two proteins,Nestin and EphA2, which positively correlates with TIC invasive motility.In summary, this dissertation focuses on the development of microfluidic platforms forsingle cell analysis. Our developed platforms provide a method in which to interrogatesingle cells in a high throughput manner and to identify novel relationships betweenvaried cellular phenotypes. These insights are crucial for the identification of both raresubpopulations within a given tumor and patient-specific protein markers that describethese subpopulations.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Lin, J. G. (2017). Microfluidic Device Development for Analyzing Single Glioblastoma Cells. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/3bn054m0
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):
Lin, Jung-ming G. “Microfluidic Device Development for Analyzing Single Glioblastoma Cells.” 2017. Thesis, University of California – Berkeley. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/3bn054m0.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lin, Jung-ming G. “Microfluidic Device Development for Analyzing Single Glioblastoma Cells.” 2017. Web. 04 Mar 2021.
Vancouver:
Lin JG. Microfluidic Device Development for Analyzing Single Glioblastoma Cells. [Internet] [Thesis]. University of California – Berkeley; 2017. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/3bn054m0.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lin JG. Microfluidic Device Development for Analyzing Single Glioblastoma Cells. [Thesis]. University of California – Berkeley; 2017. Available from: http://www.escholarship.org/uc/item/3bn054m0
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
21.
Golkar Narenji, Alaleh.
Photonic Transfer in DNA Nano Construct.
Degree: Bioengineering, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/3pb5s1mm
► A significant amount of work has been done to improve design and fabrication of DNA constructs with photonic and electronic transfer properties. In this thesis,…
(more)
▼ A significant amount of work has been done to improve design and fabrication of DNA constructs with photonic and electronic transfer properties. In this thesis, we evaluated the prior work for both electronic and photonic transfer. While DNA constructs with first-order fluorescent resonant energy transfer (FRET) properties have proven useful, incorporation of higher-order FRET and electronic properties into DNA has not yet led to any viable applications. In this thesis, we generated 35 base pairs long double-stranded (ds) DNA structures with different arrangements of five TAMRA donor dyes and a single TexasRed acceptor. In these constructs the distance of the distal donor dyes to the acceptor is greater than 1.7 nm or five base pairs (which is beyond the optimal FRET distance). The average FRET efficiency of these double stranded systems based on the donor intensity change and the acceptor-to-donor ratio of intensity change was 66% and 26%, respectively. Addition of surfactants and metal cations reduced quenching and enhanced the FRET efficiency of these DNA structures. After adding the surfactant and metal cations, the average FRET efficiency of these ds-systems based on the donor intensity change and the acceptor-to-donor ratio of intensity change was 89% and 75%, respectively.We also reviewed the conductivity properties of DNA and how it is influenced by temperature, UV illumination and GC content. Results from literature indicate that temperature significantly changes DNA conductivity. Moreover, the UV exposure experiments indicate a decrease in DNA conductivity due to damage of GC base pairs and the phosphate group. We also investigated the effect of nucleotide content on DNA conductivity and we showed that the higher GC content results in higher conductivity.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Golkar Narenji, A. (2018). Photonic Transfer in DNA Nano Construct. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/3pb5s1mm
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):
Golkar Narenji, Alaleh. “Photonic Transfer in DNA Nano Construct.” 2018. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/3pb5s1mm.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Golkar Narenji, Alaleh. “Photonic Transfer in DNA Nano Construct.” 2018. Web. 04 Mar 2021.
Vancouver:
Golkar Narenji A. Photonic Transfer in DNA Nano Construct. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/3pb5s1mm.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Golkar Narenji A. Photonic Transfer in DNA Nano Construct. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/3pb5s1mm
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Clemson University
22.
Pollard, David.
Histological Evaluation of the Effects of Diabetes on Renal Vasculature.
Degree: 2019, Clemson University
URL: http://pqdtopen.proquest.com/#viewpdf?dispub=13422945
► Diabetes mellitus currently affects 8.3% of the world’s population, roughly 387 million people as of 2014, with numbers rising steadily. Diabetes is a major…
(more)
▼ Diabetes mellitus currently affects 8.3% of the world’s population, roughly 387 million people as of 2014, with numbers rising steadily. Diabetes is a major risk factor for vascular pathology, affecting the vascular wall at the cellular and extracellular level. The field of tissue engineering has proven to have great potential in treating cardiovascular disease and kidney failure. In order to develop tissue-engineered replacements resistant to the alterations induced by a diabetic environment, the modifications of the native tissues are important to be elucidated. Cardiovascular remodeling is due to elevated levels of fatty deposits along the vessel wall, hyperglycemia and chronic inflammation. The major vascular matrix components, such as collagen and elastin, interact irreversibly with the elevated levels of blood glucose and lipids via oxidation and crosslinking processes resulting in the formation of advanced glycation end products and vascular stiffening. Adventitial fibroblasts, the “first-responder” to vascular injury, are involved in normal maintenance of blood vessels, contributing to repair and remodeling. Adventitial fibroblasts play an active role in the arterial response to injury, cytokines and stretch, which stimulate their activation and differentiation into myofibroblasts. Diabetes is also the most common cause of chronic renal disorders and end stage renal disease. Diabetes results in a wide range of alterations in renal tissue such as glomerular sclerotic lesions, hypertrophy of glomeruli, tubulointerstitial fibrosis, increased expression of myofibroblasts and inflammation that contribute to kidney dysfunction and diabetic nephropathy. The aim of this study was to show the histological changes of renal tissue associated with diabetes with an emphasis on remodeling of the renal vasculature. Kidney samples were explanted at a time point 3 months from diabetic and non-diabetic rats and were histologically analyzed for indications of pathological remodeling. The sample cross sections were stained and analyzed for early signs of diabetic nephropathy including glomerulus deterioration, vessel wall remodeling, and vascular cell dyfunction. This was done using hematoxylin & eosin, Masson’s trichrome, periodic acid schiff and various immunostainings for α-SMA, CD146, CD68, von Willebrand factor and collagen type IV. Dense perivascular collagen deposition could be seen under diabetic conditions. Increased macrophage infiltration was observed in diabetics as well as increased pericyte and endothelial cell expression suggesting upregulation of angiogenesis and increased remodeling and repair within the kidney. Myofibroblast activity, the main contributing cell to organ fibrosis, was upregulated in diabetics showing early signs of kidney fibrosis—a common outcome in diabetic nephropathy. In conclusion, determining the modifications induced by diabetes at a vascular cell and extracellular level could lead to finding optimal…
Subjects/Keywords: Bioengineering
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pollard, D. (2019). Histological Evaluation of the Effects of Diabetes on Renal Vasculature. (Thesis). Clemson University. Retrieved from http://pqdtopen.proquest.com/#viewpdf?dispub=13422945
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):
Pollard, David. “Histological Evaluation of the Effects of Diabetes on Renal Vasculature.” 2019. Thesis, Clemson University. Accessed March 04, 2021.
http://pqdtopen.proquest.com/#viewpdf?dispub=13422945.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pollard, David. “Histological Evaluation of the Effects of Diabetes on Renal Vasculature.” 2019. Web. 04 Mar 2021.
Vancouver:
Pollard D. Histological Evaluation of the Effects of Diabetes on Renal Vasculature. [Internet] [Thesis]. Clemson University; 2019. [cited 2021 Mar 04].
Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=13422945.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pollard D. Histological Evaluation of the Effects of Diabetes on Renal Vasculature. [Thesis]. Clemson University; 2019. Available from: http://pqdtopen.proquest.com/#viewpdf?dispub=13422945
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
UCLA
23.
Cheung, Shin Ting Sherine Frieda.
Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems.
Degree: Bioengineering, 2019, UCLA
URL: http://www.escholarship.org/uc/item/7j39x8rc
► Infectious diseases are one of the major causes of death in developing countries. These diseases are caused by pathogenic organisms, such as bacteria, viruses, and…
(more)
▼ Infectious diseases are one of the major causes of death in developing countries. These diseases are caused by pathogenic organisms, such as bacteria, viruses, and parasites. Current gold standard methods of detection include cell culturing, the enzyme-linked immunosorbent assay (ELISA), and the polymerase chain reaction (PCR); however, these methods are often complex, have a long time-to-result, and require expensive equipment and trained personnel. Such limitations make it difficult for these standard diagnostics to be used in resource-poor settings. Unfortunately, it is also these developing countries that could currently benefit most from these early diagnosis assays. Therefore, there is a growing need for simple, sensitive, and efficient diagnostic methods. To this end, researchers have made efforts to design diagnostics with the aim to be viable at the point-of-care (POC). While there have been great advances in converting complicated laboratory-based assays into POC-friendly diagnostics, the ability to simplify the method while maintaining the diagnostic test’s effectiveness remains a primary concern. Often, low assay sensitivity as a result of poor processing of samples in complex media or low concentration of biomarkers are the main challenges.One example of a POC-friendly diagnostic is the paper-based lateral-flow immunoassay (LFA). While the advantages of the LFA are that it is low-cost, rapid, user-friendly, and does not require laboratory equipment, the main drawback of the LFA is that it is not as sensitive as traditional laboratory tests. To address this problem, our laboratory has previously utilized aqueous two-phase systems (ATPSs) to concentrate biomarkers via partitioning into one of the two phases of an ATPS prior to its application to the LFA. Using this pre-concentration step, the detection limit of the LFA was improved 10-fold.While our lab has had much success in combining ATPSs and LFA to predictably concentrate biomarkers and improve the LFA limit of detection, this thesis expands the application of ATPSs for the development of other POC diagnostic formats. Chapter 2 describes the application of an ATPS to a paper-based spot immunoassay for detection of foodborne pathogens in food samples. We designed a spot immunoassay that utilizes a UCON-potassium phosphate salt ATPS for the pre-concentration of Escherichia coli (E. coli) O157:H7. This platform was tested with samples of O157:H7 spiked in phosphate-buffered saline (PBS) and milk. The ATPS was found to improve the detection limit of the spot test, yielding detection in milk at 106 colony forming units (cfu)/mL within 30 min. In Chapter 3, we extended the application of ATPSs to nucleic acid amplification tests (NAATs) by integrating an ATPS with isothermal DNA amplification. We introduced a novel system that combines thermophilic helicase-dependent amplification (tHDA) with a Triton X-100 micellar ATPS to achieve cell lysis, lysate processing, and enhanced nucleic acid amplification in a simple, one-step process. The combined one-pot…
Subjects/Keywords: Bioengineering
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APA ·
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CSE |
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APA (6th Edition):
Cheung, S. T. S. F. (2019). Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/7j39x8rc
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):
Cheung, Shin Ting Sherine Frieda. “Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems.” 2019. Thesis, UCLA. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/7j39x8rc.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cheung, Shin Ting Sherine Frieda. “Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems.” 2019. Web. 04 Mar 2021.
Vancouver:
Cheung STSF. Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems. [Internet] [Thesis]. UCLA; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/7j39x8rc.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cheung STSF. Development of Point-of-Care Diagnostic Technologies Utilizing Aqueous Two-Phase Systems. [Thesis]. UCLA; 2019. Available from: http://www.escholarship.org/uc/item/7j39x8rc
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
UCLA
24.
Kim, Soyon.
Design of a Biomimetic Hydrogel System for Tissue Engineering Application.
Degree: Bioengineering, 2019, UCLA
URL: http://www.escholarship.org/uc/item/9fb316h2
► A hydrogel platform using visible light inducible methacrylated glycol chitosan and riboflavin, an aqueous initiator from natural vitamins is biocompatible and supports proliferation of the…
(more)
▼ A hydrogel platform using visible light inducible methacrylated glycol chitosan and riboflavin, an aqueous initiator from natural vitamins is biocompatible and supports proliferation of the encapsulated cells. However, the hydrogel platform has limited cell-matrix interaction, relatively slow degradation, and poor ability to deliver growth factors, which may hinder tissue regeneration. Therefore, the objective of this research is to design a hydrogel system which mimics native extracellular microenvironments, provides tunable degradation, and stabilizes bioactivity of growth factors. The first study explores if the incorporation of native extracellular matrix components in chitosan hydrogel can promote cell-matrix interaction. The hydrogel is functionalized with cell adhesive motifs and cartilaginous or bony matrix. The modified hydrogels increase chondrogenic or osteogenic differentiation of the encapsulated cells by enhancing cell-matrix interaction. This work suggests a hydrogel platform with a specific microenvironment tailored to promote cell differentiation. Tuning hydrogel degradation enables effective and successful tissue regeneration by modulating cellular behaviors and matrix formation. A new degradable hydrogel system is developed based on a unique enzyme-substrate complex, lysozyme-chitosan. Incorporation of lysozyme accelerates hydrogel degradation in a dose dependent manner. This study proposes a novel strategy of incorporating an exogenous enzyme specific to the hydrogel which can control degradation kinetics in a cell-independent manner. Bacterial infection during surgical processes leads to serious complications and continuously results in unsuccessful wound repair. A lysozyme-chitosan conjugate not only allows tunable degradation, but also exhibits antimicrobial properties. The lysozyme modified hydrogels successfully inhibit bacterial growth and delay its proliferation. This work verifies an advanced hydrogel platform with dual functions, tunable degradability and anti-infection.Although heparin is widely used in controlled release system due to its strong binding ability and protective effect for growth factors such as bone morphogenetic protein-2 (BMP-2), it suffers from natural variability, difficulty in modification, and unknown physiological roles. Heparin mimetic sulfonated molecules can do a similar role of heparin by protecting BMP-2 against therapeutically relevant stressors and enhancing its bioactivity. This work demonstrates a new hydrogel system to improve clinical efficacy of BMP-2 and other heparin-binding growth factors. These findings suggest great potentials of material-based therapeutics for tissue engineering application.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Kim, S. (2019). Design of a Biomimetic Hydrogel System for Tissue Engineering Application. (Thesis). UCLA. Retrieved from http://www.escholarship.org/uc/item/9fb316h2
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, Soyon. “Design of a Biomimetic Hydrogel System for Tissue Engineering Application.” 2019. Thesis, UCLA. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/9fb316h2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kim, Soyon. “Design of a Biomimetic Hydrogel System for Tissue Engineering Application.” 2019. Web. 04 Mar 2021.
Vancouver:
Kim S. Design of a Biomimetic Hydrogel System for Tissue Engineering Application. [Internet] [Thesis]. UCLA; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/9fb316h2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kim S. Design of a Biomimetic Hydrogel System for Tissue Engineering Application. [Thesis]. UCLA; 2019. Available from: http://www.escholarship.org/uc/item/9fb316h2
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – San Diego
25.
Cai, Wei.
A single-cell assay and a biosample enrichment method for analyzing single cell secretion.
Degree: Materials Science and Engineering, 2019, University of California – San Diego
URL: http://www.escholarship.org/uc/item/35b927zj
► One of the key challenges of biology is to understand how individual cells process information and respond to perturbations. However, most of the existing single…
(more)
▼ One of the key challenges of biology is to understand how individual cells process information and respond to perturbations. However, most of the existing single cell analysis methods can only provide a glimpse of cell properties at specific time points and are unable to provide cell secretion and protein analysis at the single cell resolution. This thesis offers the description of a single-cell assay as well as a CO2-induced enrichment method for the analysis of single cells secretions.The single-cell assay introduced in this thesis enables the accommodation of different cellular types, allows for easy and efficient single cell loading and culturing, and is suitable for studying the efforts of in-vitro environmental factors in combination with drug screening. One salient feature of the assay is the non-invasive collection and survey of single cell secretions at different time points, producing unprecedented insight of single cell behaviors based on the biomarker signals from individual cells under given perturbations. In addition, the open-well design of the assay allows for simple collection of cells with standard tools such as pico-pipette for downstream processes in relating the single-cell secretions with gene analysis. Above all, the acquired information is quantitative. For example, measured by the number of exosomes each single cell secretes for a given time period, exosomal miRNA carried by exosomes secreted by single cell. Therefore, this single-cell assay provides a convenient, low-cost, and robust tool for quantitative, time lapsed studies of single cell properties.Another challenge for single cell secretion analysis is the limit-of-detection (LOD) and sensitivity. Thus, sample enrichment is an important step in the work flow of biosensing for disease detection and numerous biological or clinical processes. Most current techniques require devices that are tailored to specific chemical or physical characteristics of the target objects to enrich or capture them from the sample. The complexity within these devices all serve to, increase cost and may even limit the enrichment factor. Here, a technique of using a CO2 laser to drive targets towards the laser spot via mass transport without requiring any device fabrication processes or special reagents was introduced. To prove the concept, single-stranded DNA (ssDNA) has been enriched by more than 100,000-fold in less than 4 minutes. The temperature and evaporation rate profile at the enriched area are measured alongside theoretical analyses and modeling to monitor and understand the physical process. The formation of aggregates comprised of streptavidin Q-dots and biotin labeled exosomes with this method was demonstrated to show the capability of biosample detection, purification, and quantification. The method is not only simple and highly efficient, but also applicable to all types of biomolecules and bioparticles. Thereby promising a simple, cost effective and efficient solution for biological sample preparation for sensing, analytics, and diagnostics.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Cai, W. (2019). A single-cell assay and a biosample enrichment method for analyzing single cell secretion. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/35b927zj
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):
Cai, Wei. “A single-cell assay and a biosample enrichment method for analyzing single cell secretion.” 2019. Thesis, University of California – San Diego. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/35b927zj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cai, Wei. “A single-cell assay and a biosample enrichment method for analyzing single cell secretion.” 2019. Web. 04 Mar 2021.
Vancouver:
Cai W. A single-cell assay and a biosample enrichment method for analyzing single cell secretion. [Internet] [Thesis]. University of California – San Diego; 2019. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/35b927zj.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cai W. A single-cell assay and a biosample enrichment method for analyzing single cell secretion. [Thesis]. University of California – San Diego; 2019. Available from: http://www.escholarship.org/uc/item/35b927zj
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Temple University
26.
Middleton, Devon.
ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD.
Degree: PhD, 2017, Temple University
URL: http://digital.library.temple.edu/u?/p245801coll10,470546
► Bioengineering
Spinal cord injury has the potential to be debilitating, particularly in the pediatric population. Identification of the exact injury level can be difficult from…
(more)
▼ Bioengineering
Spinal cord injury has the potential to be debilitating, particularly in the pediatric population. Identification of the exact injury level can be difficult from conventional structural Magnetic Resonance Imaging (MRI) scans, and younger children often have difficulty in participating in the clinical examinations that define neurologic damage. Because of limitations of existing clinical examinations and conventional imaging, more advanced quantitative imaging techniques are important for improvement in diagnostic and prognostic evaluation of spinal cord injury. A quantitative characterization of the full spinal cord injury from both a functional and structural perspective has not been performed in pediatric subjects and has potential to provide important diagnostic and prognostic information. Diffusion tensor imaging (DTI) gives a non-invasive quantification of water diffusion in the spinal cord and can provide insight into white matter integrity, while high resolution volumetric imaging can determine cord cross sectional area reflecting atrophy occurring post injury. Multiple challenges exist in analysis of pediatric spinal cord data, including physiological motion, low signal-to-noise, thermal noise and image artifact, and cumbersome measurements of cord morphology. In this work, a complete pipeline for the acquisition and analysis of both functional DTI data and high resolution structural data is designed, tested, and implemented including MR image acquisition, motion correction, diffusion tensor estimation, region of interest analysis, and semi-automated cord cross sectional area measurement. Data for both healthy subjects and subjects with spinal cord injury is collected and significant correlations are shown between DTI and cord morphology metrics. This characterization of the injured spinal cord using both structural and functional data has the potential to offer important new information for examination of spinal cord injury.
Temple University – Theses
Advisors/Committee Members: Pleshko, Nancy, Mohamed, Feroze B.;, Faro, Scott H., Ali, Sayed;.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Middleton, D. (2017). ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,470546
Chicago Manual of Style (16th Edition):
Middleton, Devon. “ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD.” 2017. Doctoral Dissertation, Temple University. Accessed March 04, 2021.
http://digital.library.temple.edu/u?/p245801coll10,470546.
MLA Handbook (7th Edition):
Middleton, Devon. “ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD.” 2017. Web. 04 Mar 2021.
Vancouver:
Middleton D. ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD. [Internet] [Doctoral dissertation]. Temple University; 2017. [cited 2021 Mar 04].
Available from: http://digital.library.temple.edu/u?/p245801coll10,470546.
Council of Science Editors:
Middleton D. ACQUISITION, PROCESSING, AND ANALYSIS OF DIFFUSION TENSOR IMAGING AND ATROPHY MRI IN THE INJURED PEDIATRIC SPINAL CORD. [Doctoral Dissertation]. Temple University; 2017. Available from: http://digital.library.temple.edu/u?/p245801coll10,470546
Boston University
27.
Huang, Shuo.
Controllability analysis and design for underactuated stochastic neurocontrol.
Degree: PhD, Biomedical Engineering, 2019, Boston University
URL: http://hdl.handle.net/2144/34932
► Neuroengineering has advanced tremendously over the past decade, but for sensory prosthetics and similar applications, it remains an extraordinary challenge to access neurons at the…
(more)
▼ Neuroengineering has advanced tremendously over the past decade, but for sensory prosthetics and similar applications, it remains an extraordinary challenge to access neurons at the single cell resolution of most sensory encoding theories. In particular, if each neuron is “tuned” to particular stimulus features, then eliciting a target percept requires activating only neurons tuned to that percept and not others. However, most available technology is underactuated, with orders of magnitude fewer independent control inputs than neural degrees of freedom, possibly limiting its effectiveness given the inherent trade-off of resolution with network size. Here I analyze controllability for
pairs of neurons receiving a common input. In particular, I extend previous work on the deterministic control problem to include stochastic membrane dynamics, treating both cases as a bifurcation problem in the noise parameter. I determine controllable regions in parameter space using a combination of mathematical analysis and numerical solution of stochastic differential and Fokker-Planck equations. I explain how boundaries between these regions change with noise level, and connect to the dynamical mechanisms by which controllability is lost. I show that in stochastic systems, in contrast to deterministic systems, expanding the allowable input space to include exponential ramps expands the parameter range over which neuron pairs are controllable. I also describe an alternative controllability definition using only mean spike times, as compared to the probability distribution of spiking within prespecified time intervals. These results could guide future
control strategies in the development of sensory neuroprosthetics and other neurocontrol application.
Advisors/Committee Members: Ritt, Jason (advisor).
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Huang, S. (2019). Controllability analysis and design for underactuated stochastic neurocontrol. (Doctoral Dissertation). Boston University. Retrieved from http://hdl.handle.net/2144/34932
Chicago Manual of Style (16th Edition):
Huang, Shuo. “Controllability analysis and design for underactuated stochastic neurocontrol.” 2019. Doctoral Dissertation, Boston University. Accessed March 04, 2021.
http://hdl.handle.net/2144/34932.
MLA Handbook (7th Edition):
Huang, Shuo. “Controllability analysis and design for underactuated stochastic neurocontrol.” 2019. Web. 04 Mar 2021.
Vancouver:
Huang S. Controllability analysis and design for underactuated stochastic neurocontrol. [Internet] [Doctoral dissertation]. Boston University; 2019. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2144/34932.
Council of Science Editors:
Huang S. Controllability analysis and design for underactuated stochastic neurocontrol. [Doctoral Dissertation]. Boston University; 2019. Available from: http://hdl.handle.net/2144/34932
University of California – San Francisco
28.
Lee, Jessie.
Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging.
Degree: Bioengineering, 2018, University of California – San Francisco
URL: http://www.escholarship.org/uc/item/3jz903mz
► Prostate cancer is the most frequently diagnosed invasive cancer and the third leading cause of cancer death in men. Traditionally, patients with localized low- or…
(more)
▼ Prostate cancer is the most frequently diagnosed invasive cancer and the third leading cause of cancer death in men. Traditionally, patients with localized low- or intermediate-risk prostate cancer were forced to decide between the passive but psychologically burdensome active surveillance and the aggressive treatment options, such as surgery or radiation. In recent years, ultrasound thermal therapy has become an alternative for such cases since it is minimally invasive and causes fewer side effects. During the two main types of thermal therapy (thermal ablation and hyperthermia), the targeted tissue is exposed to heat, which either causes immediate cell death or alters the metabolism and perfusion of the tissue, making it more susceptible to adjuvant therapies such as radiation and chemotherapy.This dissertation focuses on monitoring the response of prostate cancer to thermal ablation and hyperthermia using the technique of hyperpolarized 13C MRI, which allows for non-invasive assessment of both tissue metabolism and perfusion with a single injection of the co-polarized 13C-labeled pyruvate and urea. These biomarkers successfully delineated the ablated regions of the tissues while providing insight into the changes in metabolism and perfusion in the tissues receiving sub-lethal heat dose. To further explore the effects of hyperthermia on prostate cancer, a compact MR-compatible ultrasound hyperthermia device was fabricated to perform hyperthermia on murine prostate tumors in a 14T preclinical MRI scanner (bore diameter = 4cm) with concurrent MR thermometry. The feasibility of monitoring the metabolic and perfusion changes in prostate cancer in vivo shortly after hyperthermia has been demonstrated. Ongoing murine studies will examine the significance of the treatment response. Noninvasive monitoring of the changes in metabolism and perfusion of prostate cancer upon thermal therapy is invaluable for determining the timing and dose of adjuvant therapies.
Subjects/Keywords: Bioengineering
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APA (6th Edition):
Lee, J. (2018). Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/3jz903mz
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):
Lee, Jessie. “Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging.” 2018. Thesis, University of California – San Francisco. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/3jz903mz.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lee, Jessie. “Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging.” 2018. Web. 04 Mar 2021.
Vancouver:
Lee J. Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging. [Internet] [Thesis]. University of California – San Francisco; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/3jz903mz.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lee J. Monitoring Response of Prostate Cancer to Ultrasound Thermal Therapy by Multi-Agent Hyperpolarized 13C Magnetic Resonance Imaging. [Thesis]. University of California – San Francisco; 2018. Available from: http://www.escholarship.org/uc/item/3jz903mz
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
29.
Harrigan, Patrick Shane.
Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks.
Degree: Biological and Medical Informatics, 2018, University of California – San Francisco
URL: http://www.escholarship.org/uc/item/29k1m7m2
► The ability to self-regulate in feedback is what allows cells to operate robustly despite the uncertainties of both a changing external environment and their own…
(more)
▼ The ability to self-regulate in feedback is what allows cells to operate robustly despite the uncertainties of both a changing external environment and their own internal biochemistry. While feedbacks underlie many dramatic cellular behaviors including cell fate decisions and chemotaxis, the vast majority of feedback is responsible for more subtle changes such as quantitatively shaping the time scales and strength of a signaling response. In these cases, the traditional genetic perturbations such as gene knockout or overexpression that are commonly used to identify feedback regulators are ill-suited for investigating their function, in part because feedback is inherently dynamic. The aforementioned static perturbations cannot test hypothesis with respect to when and how much feedback is needed for normal cellular function. This is further compounded by the system level nature of feedback as these genetic perturbations to a feedback regulator can be obscured by compensatory changes occurring in the system the feedback regulates.In this work, we address these issues by developing a new method, closed loop optogenetic control (CLOC), for systematically determining the temporal requirements of feedback regulators of a signaling pathway. This method, which uses control theory to extend the classical genetic compensation framework to the study of feedback, relies on the ability to precisely and in real time control the activity of a feedback regulator. This is accomplished through the use of a custom built hardware and software infrastructure that allows for it{in silico} control of an optogenetically activated version of the feedback regulator. The platform monitors in real time the output of a pathway deleted for a feedback regulator and automatically calculates and delivers the appropriate light input needed activate the optogenetic feedback regulator and compensate for the effects of the feedback deletion. The time varying optogenetic input needed to rescue wild type signaling dynamics serves as proxy for defining the temporal requirements of a feedback regulator in the context of native pathway signaling. In chapter 2, previous work related to in silico control of intracellular processes is reviewed. In chapter 3, I introduce the idea of studying signaling pathways using non-traditional, quantitative genetic perturbations by investigating the effect of graded expression of pathway regulators on yeast mating pathway signaling. In chapter 4 I develop CLOC as a method and use it to study three negative feedback regulators of the yeast pheromone mating pathway: SST2, MSG5, and GPA1. Surprisingly, CLOC revealed distinct dynamic requirements for the expression of each of the three feedback regulators.
Subjects/Keywords: Bioengineering
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APA ·
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APA (6th Edition):
Harrigan, P. S. (2018). Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks. (Thesis). University of California – San Francisco. Retrieved from http://www.escholarship.org/uc/item/29k1m7m2
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):
Harrigan, Patrick Shane. “Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks.” 2018. Thesis, University of California – San Francisco. Accessed March 04, 2021.
http://www.escholarship.org/uc/item/29k1m7m2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Harrigan, Patrick Shane. “Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks.” 2018. Web. 04 Mar 2021.
Vancouver:
Harrigan PS. Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks. [Internet] [Thesis]. University of California – San Francisco; 2018. [cited 2021 Mar 04].
Available from: http://www.escholarship.org/uc/item/29k1m7m2.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Harrigan PS. Combining Classical Genetics with Control Theory to Study Feedback Regulation in Signaling Networks. [Thesis]. University of California – San Francisco; 2018. Available from: http://www.escholarship.org/uc/item/29k1m7m2
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Northeastern University
30.
Mensah, Solomon.
Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease.
Degree: PhD, Department of Bioengineering, 2019, Northeastern University
URL: http://hdl.handle.net/2047/D20328715
► The endothelial glycocalyx (GCX) plays a critical role in the health of the vascular system. Degradation of the GCX has been implicated in the onset…
(more)
▼ The endothelial glycocalyx (GCX) plays a critical role in the health of the vascular system. Degradation of the GCX has been implicated in the onset of diseases like atherosclerosis and cancer because it disrupts endothelial cell (EC) function that is meant to protect from atherosclerosis and cancer. Intercellular interactions are physiologically relevant activities that ensure proper EC function. Various intercellular interactions including those mediated by gap junction proteins, like connexin, for maintaining cell to cell communication, and adhesion molecules, like those mediated by E-selectin and integrins for regulating cell to cell contact between ECs and leukocytes, cancer cells, or other circulating cells. To-date, limited progress has been made to best understand the role of the GCX in intercellular interactions. Previous work demonstrated that GCX degradation disrupts EC gap junction connexin (Cx) proteins, likely blocking interendothelial communication that maintains EC and vascular tissue homeostasis to resist disease. Other reports suggest that the ability of immune cells to interact with EC could be a model for the way cancer cells interact with EC, and these interactions are modulated by the GCX. We hypothesize that the GCX controls the opening and closing of Cx containing gap junction proteins for regulating communication and also controls accessibility to receptors on the surface of the endothelium for regulating intercellular interactions. To test our hypothesis, we performed multiple EC experiments to investigate the role of GCX in intercellular interactions. To understand GCX involvement in gap junction regulation we tested the effect of different GCX conditions on the expression of Cx isotype 43 (Cx43) containing gap junctions. Expression of Cx43 at EC borders was characterized immunocytochemically, and the function of Cx-containing gap junctions were assessed by measuring interendothelial spread of gap junction permeable Lucifer Yellow dye. We further examined the activities of the gap junctions and Cx43 after applying various regeneration techniques for GCX. GCX regeneration was achieved via treatment with exogenous heparan sulfate (HS), a major component of GCX. HS was applied with or without the GCX regenerator and protector sphingosine 1- phosphate (S1P). With intact HS, 60% of EC borders expressed Cx43 and dye spread to 2.88 ± 0.09 neighboring cells. HS degradation decreased Cx43 expression to 30% and reduced dye spread to 1.87± 0.06 cells. Artificial HS recovery with exogenous HS partially restored Cx43 expression to 46% and yielded dye spread to only 1.03 ± 0.07 cells. Treatment with both HS and S1P, recovered HS and restored Cx43 to 56% with significant dye transfer to 3.96 ± 0.23 cells. This is the first evidence of GCX regeneration in a manner that effectively restores vasculoprotective EC communication. This work validates the importance of GCX in Cx activities. We also investigated the importance of GCX in concealing or uncovering receptors that mediate cancer-endothelial cell…
Subjects/Keywords:
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APA ·
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Export
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APA (6th Edition):
Mensah, S. (2019). Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease. (Doctoral Dissertation). Northeastern University. Retrieved from http://hdl.handle.net/2047/D20328715
Chicago Manual of Style (16th Edition):
Mensah, Solomon. “Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease.” 2019. Doctoral Dissertation, Northeastern University. Accessed March 04, 2021.
http://hdl.handle.net/2047/D20328715.
MLA Handbook (7th Edition):
Mensah, Solomon. “Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease.” 2019. Web. 04 Mar 2021.
Vancouver:
Mensah S. Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease. [Internet] [Doctoral dissertation]. Northeastern University; 2019. [cited 2021 Mar 04].
Available from: http://hdl.handle.net/2047/D20328715.
Council of Science Editors:
Mensah S. Endothelial Glycocalyx-mediated Intercellular Interactions: Mechanisms And Implications For Health And Disease. [Doctoral Dissertation]. Northeastern University; 2019. Available from: http://hdl.handle.net/2047/D20328715
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Open Access Theses and Dissertations
