Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (12 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2017)

Single nucleotide polymorphisms (SNP) in a gene sequence are markers for variety of human diseases. Their detection with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme based methods or fluorophore-labeled assays that are time consuming, need lab-scale settings, and are expensive. Electrical detection of DNA has been advancing rapidly, with to achieve high specificity, sensitivity and portability. However, existing electrical charge-based SNP detectors have insufficient specificity and accuracy limiting their effectiveness. Its actual implementation is still in infancy because of the low specificity, especially for analytically optimal and practically useful length of target DNA strands. Most of the research so far has focused on the enhancement of the sensitivity of DNA biosensors while the specificity problem has remained unresolved. The low specificity is primarily due to the non-specific binding during hybridization of probe and the target DNA. Here, we have addressed these limitations by designing a functional prototype of electrical biosensors for SNP detection. We demonstrate the use of DNA strand displacement-based probes on a graphene field effect transistor (FET) for high specificity single nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double helix DNA strands (e.g., 47 nucleotides) minimize false positive. We describe the first integrated dynamic DNA nanotechnology and 2-D material electronics, to overcome current limitations for the detection of DNA single nucleotide polymorphism (SNP). Existing SNP detection systems have poor sensitivity and specificity and lack portability and real-time wireless transmission of detected molecular signals. We have integrated two different kinds of dynamic DNA nano-devices as nucleic acid-sensing probes with electrical biosensors using graphene FET and analytical wireless communication platform. The signal was transmitted remotely using a microcontroller board and Bluetooth standard to personal electronics, including smart phones, tablets and computers. Our electrical sensor-based SNP detection technology without labeling and without apparent cross-hybridization artifacts would allow fast, sensitive and portable SNP detection with single-nucleotide resolution. Practical implementation of this enabling technology will provide cheaper, faster and portable point-of-care molecular diagnostic devices for personalized global health management. It will have wide applications in digital and implantable biosensors and high-throughput DNA genotyping with transformative implications for personalized medicine.

    Cover page: Gene-Chip Diagnostics for Personalized Global Medicine
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)

    Background

    Residency prepares trainees to deliver clinical care. It's unknown if there is adequate career preparation, particularly for academic medicine. Prior literature has shown that interest in pursuing an academic career wanes during residency. Few trainees believe residency provides them with the necessary skills to be successful in academic medicine. Formalized areas of concentration may allow for deepened experience and mentorship in a specific field and may contribute to increased scholarly productivity which has been associated with selecting an academic career. Some training programs have instituted specialized tracks to allow residents to explore and develop an academic or clinical niche. The pervasiveness and characteristics of tracks currently available are unknown. A crucial first step in understanding how to best prepare residents for future careers is to understand current practice. The objective of this study was to identify the prevalence and characteristics of specialized tracks in emergency medicine (EM) training programs in the United States of America (USA).

    Methods

    Allopathic EM training programs in the USA were identified by the Society for Academic Emergency Medicine residency catalogue. Program websites were identified through this catalogue and an internet search. Each page of a program's website was dissected to identify basic program information and descriptions of their curricula including presence and descriptions of specialized tracks. Descriptive statistics are reported.

    Results

    163 programs were identified, 156(95.7%) programs provided detailed descriptions of their curricula on their program website. 33/156(21.2%) offered dedicated tracks. Tracks were more common in four year programs (15/40;37.5%) compared to three years (18/116;15.5%). 23/33(70%) programs with tracks provided titles of their tracks and these commonly (20/23;87%) mirrored typical fellowships in EM. For programs that described the timing of tracks (15/33;45.5%), most spanned multiple years of training (12/15;80%).

    Conclusion

    The presence of specialized tracks is not widespread in EM training programs in the USA, but is more commonly seen in four year programs. The timing of tracks varied but typically spanned multiple years of training. This information is a critical first step to allow future research to understand the impact of specialized tracks and their role in EM career choice and preparation for an academic career.
      • Article
      • Peer Reviewed
      Western Journal of Emergency Medicine: Integrating Emergency Care with Population Health, Volume 19, Issue 3 (2018)

      Introduction: Career preparation in residency training is not standardized. Scholarly tracks have emerged in emergency medicine (EM) residencies to allow specialized training in an area of focus.  The characteristics of these tracks and their value and impact on resident career choice are unknown. We aim to describe the current state of scholarly tracks in residency training programs and their association with pursuit of an academic career.

      Methods: Program leaders at EM training programs completed an online survey consisting of multiple-choice items with free-text option. Additionally, participants completed a matrix of dropdown items identifying the immediately chosen post-residency position and applicable track of each member of their graduating class. Descriptive statistics were calculated and reported for multiple-choice items. We performed comparative statistics using chi-squared and Wilcoxon rank-sum tests.  Free-text responses were analyzed using a thematic approach.  

      Results: 113/157(72%) programs participated, 51 with and 62 without tracks. Tracks were more common in four-year programs (odds ratio [OR]=4.8;[2.0-11.9]) and larger programs (chi-sq, p=0.001). Perceived benefits of tracks from programs with them included advanced training (46/50; 92%), career guidance (44/50; 88%), mentorship (44/50; 88%), and preparation for an academic career (40/50; 80%). Residents often participated in a single track (37/50; 74%) usually during their later residency years. Programs with tracks were more likely to graduate residents to an academic career, OR 1.8;[1.3-2.4].

      Conclusion: This study describes the current characteristics and perceptions of scholarly tracks in EM residencies. Scholarly tracks are associated with an academic position immediately following residency. The results of this study may inform the development and use of scholarly tracks in residency training programs.

      • 1 supplemental PDF
      Cover page: Scholarly Tracks in Emergency Medicine Residency Programs Are Associated with Increased Choice of Academic CareerCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2020)

      Background & aims

      Biotin is a water-soluble vitamin that is indispensable for human health. Biotin deficiency can cause failure-to-thrive, immunodeficiency, alopecia, dermatitis, and conjunctivitis. We previously reported that biotin deficiency also can lead to severe colitis in mice, which is completely reversed with supplementation. Our aim in this study was to determine if high-dose biotin supplementation can provide a therapeutic benefit in a preclinical model for inflammatory bowel disease (IBD) and to identify the molecular mechanism by which this occurs.

      Methods

      Mice were challenged with dextran sodium sulfate to induce colitis and were treated with 1 mmol/L biotin to induce or maintain remission. Clinical response was monitored by the Disease Activity Index and fecal calprotectin levels. The colon tissue was investigated for histology, length, as well as expression of inflammatory cytokines (interleukin 6, tumor necrosis factor-α, interleukin 1β), intestinal permeability, tight junctions (zonula occludens-1 and claudin-2), and the transcription factor nuclear factor-κB (NF-κB).

      Results

      Biotin therapy led to delayed onset and severity of colitis as well as accelerated healing. There was improvement in the Disease Activity Index, fecal calprotectin levels, colon length, and histology. In addition, biotin-treated mice had reduced expression of inflammatory cytokines, reduced intestinal permeability, and reduced activation of NF-κB.

      Conclusions

      Oral supplementation with biotin provides benefit for maintenance and induction of remission in the dextran sodium sulfate preclinical model for IBD. Biotin does this by reducing the activation of NF-κB, which prevents the production of inflammatory cytokines and helps maintain the integrity of the intestinal barrier. Clinically, the NF-κB pathway is important in the development of IBD and this finding suggests that biotin may have therapeutic potential for patients with IBD.
        Cover page: Biotin Supplementation Ameliorates Murine Colitis by Preventing NF-κB Activation
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2016)
        Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.
          Cover page: Highly specific SNP detection using 2D graphene electronics and DNA strand displacement.
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2023)
          Biotin is an essential vitamin and critical cofactor in several metabolic pathways, and its deficiency has been linked to several disorders including inflammatory bowel disease (IBD). We previously reported that biotin deficiency (BD) in mice, whether modeled through intestine-specific deletion of biotin transporter (SMVT-icKO) or through a biotin-deficient diet, resulted in intestinal inflammation consistent with an IBD-like phenotype. To assess whether the gut microbiome is associated with these BD-induced changes, we collected stool and intestinal samples from both of these mouse models and utilized them for 16S rRNA gene sequencing. We find that both diet-mediated and deletion-mediated BD result in the expansion of opportunistic microbes including Klebsiella, Enterobacter, and Helicobacter, at the expense of mucus-resident microbes including Akkermansia. Additionally, microbiome dysbiosis resulting from diet-mediated BD precedes the onset of the IBD-like phenotypic changes. Lastly, through the use of predictive metagenomics, we report that the resulting BD-linked microbiome perturbations exhibit increased biotin biosynthesis in addition to several other perturbed metabolic pathways. Altogether, these results demonstrate that biotin deficiency results in a specific microbiome composition, which may favor microbes capable of biotin synthesis and which may contribute to intestinal inflammation.
            Cover page: Biotin Deficiency Induces Intestinal Dysbiosis Associated with an Inflammatory Bowel Disease-like Phenotype
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2016)
            Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.
              Cover page: Highly specific SNP detection using 2D graphene electronics and DNA strand displacement
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2014)
              Current work in tuning DNA kinetics has focused on changing toehold lengths and DNA concentrations. However, kinetics can also be improved by enhancing the completion probability of the strand displacement process. Here, we execute this strategy by creating a toehold DNA motor device with the inclusion of a synthetic nucleotide, inosine, at selected sites. Furthermore, we found that the energetic bias can be tuned such that the device can stay in a stable partially displaced state. This work demonstrates the utility of energetic biases to change DNA strand displacement kinetics and introduces a complementary strategy to the existing designs.
                Cover page: Energetically Biased DNA Motor Containing a Thermodynamically Stable Partial Strand Displacement State
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2018)
                Electronic DNA-biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA-biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real-time wireless data transmission. DNA-tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA-tweezers probe with high-quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000-fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand-displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point-of-care molecular health status monitoring and diagnostic devices.
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2018)
                  Electronic DNA-biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA-biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real-time wireless data transmission. DNA-tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA-tweezers probe with high-quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000-fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand-displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point-of-care molecular health status monitoring and diagnostic devices.
                    Cover page: DNA Nanotweezers and Graphene Transistor Enable Label‐Free Genotyping
                    Top