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Open Access Publications from the University of California

Scholarly Works (12 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2012)

Coding of information in the peripheral olfactory system and resulting olfactory dependent behavior is thought to depend primarily on two fundamental factors: the interaction of individual odors with different subsets of the odor receptor (Or) repertoire, and the mode of signaling that an individual receptor-odor interaction elicits, activation or inhibition. In order to better understand these processes, we design and implement a structure-based virtual screening approach that identifies common structural features that are highly correlated with odor activity for individual receptors. We then apply these features to rapidly screen for putative ligands in silico from a large untested odor space (>240,000 putative volatiles) for the majority of odor receptors in the Drosophila antenna, allowing for analysis of odor coding for the majority of receptors for the first time. Functional experiments support a high success rate (~71%) for the screen and we validate numerous new activators and inhibitors for the receptors. Following our initial application in Drosophila, we extend our approach to predict activating and inhibiting odors for a large number of important pest and disease vector species including 50 Anopheles gambiae Ors (65% validated accuracy), the CO2 receptors of multiple species (48% validated accuracy), 9 newly identified Citrus Psyllid ORNs, and a large number of functionally distinct mammalian receptors. We next extended our in silico screening approach to identify shared structural features important for a behavioral response for DEET-like repellents which the molecular target has not yet been identified, identify ~150 natural compounds as candidate repellents. We select 4 candidates, 3 approved as safe for human food use, and demonstrate that they are strong olfactory and gustatory repellents to both mosquitoes and Drosophila. As only a small region of odor space has been explored, there remains potential to uncover previously unidentified patterns of odor coding. Through a combination of in silico and electrophysiology screens, we identify odors with ultra-prolonged termination kinetics that are delayed for several minutes, resulting in a memory trace that affects subsequent odor detection. Finally, we successfully perform structure- based virtual screen, identifying potential inhibitors of an important Tuberculosis drug target EthR.

    Cover page: Computational Analysis of Receptor-Odor Interactions and Prediction of Behavior-Modifying Chemical Space
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2013)
    Coding of information in the peripheral olfactory system depends on two fundamental : interaction of individual odors with subsets of the odorant receptor repertoire and mode of signaling that an individual receptor-odor interaction elicits, activation or inhibition. We develop a cheminformatics pipeline that predicts receptor-odorant interactions from a large collection of chemical structures (>240,000) for receptors that have been tested to a smaller panel of odorants (∼100). Using a computational approach, we first identify shared structural features from known ligands of individual receptors. We then use these features to screen in silico new candidate ligands from >240,000 potential volatiles for several Odorant receptors (Ors) in the Drosophila antenna. Functional experiments from 9 Ors support a high success rate (∼71%) for the screen, resulting in identification of numerous new activators and inhibitors. Such computational prediction of receptor-odor interactions has the potential to enable systems level analysis of olfactory receptor repertoires in organisms. DOI:http://dx.doi.org/10.7554/eLife.01120.001.
      Cover page: Expanding the olfactory code by in silico decoding of odor-receptor chemical space
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2016)
      Odorants activate receptors in the peripheral olfactory neurons, which sends information to higher brain centers where behavioral valence is determined. Movement and airflow continuously change what odor plumes an animal encounters and little is known about the effect one plume has on the detection of another. Using the simple Drosophila melanogaster larval model to study this relationship we identify an unexpected phenomenon: response to an attractant can be selectively blocked by previous exposure to some odorants that activates the same receptor. At a mechanistic level, we find that exposure to this type of odorant causes prolonged tonic responses from a receptor (Or42b), which can block subsequent detection of a strong activator of that same receptor. We identify naturally occurring odorants with prolonged tonic responses for other odorant receptors (Ors) as well, suggesting that termination-kinetics is a factor for olfactory coding mechanisms. This mechanism has implications for odor-coding in any system and for designing applications to modify odor-driven behaviors.
        Cover page: Short-term memory trace mediated by termination kinetics of olfactory receptor
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2013)
        There are major impediments to finding improved DEET alternatives because the receptors causing olfactory repellency are unknown, and new chemicals require exorbitant costs to determine safety for human use. Here we identify DEET-sensitive neurons in a pit-like structure in the Drosophila melanogaster antenna called the sacculus. They express a highly conserved receptor, Ir40a, and flies in which these neurons are silenced or Ir40a is knocked down lose avoidance to DEET. We used a computational structure-activity screen of >400,000 compounds that identified >100 natural compounds as candidate repellents. We tested several and found that most activate Ir40a(+) neurons and are repellents for Drosophila. These compounds are also strong repellents for mosquitoes. The candidates contain chemicals that do not dissolve plastic, are affordable and smell mildly like grapes, with three considered safe in human foods. Our findings pave the way to discover new generations of repellents that will help fight deadly insect-borne diseases worldwide.
          Cover page: Odour receptors and neurons for DEET and new insect repellents
          • Article
          • Peer Reviewed
          UC Riverside Previously Published Works (2013)
          Female mosquitoes that transmit deadly diseases locate human hosts by detecting exhaled CO2 and skin odor. The identities of olfactory neurons and receptors required for attraction to skin odor remain a mystery. Here, we show that the CO2-sensitive olfactory neuron is also a sensitive detector of human skin odorants in both Aedes aegypti and Anopheles gambiae. We demonstrate that activity of this neuron is important for attraction to skin odor, establishing it as a key target for intervention. We screen ~0.5 million compounds in silico and identify several CO2 receptor ligands, including an antagonist that reduces attraction to skin and an agonist that lures mosquitoes to traps as effectively as CO2. Analysis of the CO2 receptor ligand space provides a foundation for understanding mosquito host-seeking behavior and identifies odors that are potentially safe, pleasant, and affordable for use in a new generation of mosquito control strategies worldwide.
            Cover page: Targeting a Dual Detector of Skin and CO2 to Modify Mosquito Host Seeking
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2013)

            Background

            The prevention of human papillomavirus (HPV)-induced anal cancer in high-risk populations such as human immunodeficiency virus (HIV)-infected men who have sex with men (MSM) remains an urgent priority, given rising incidence rates despite widespread antiretroviral therapy use.

            Methods

            HPV genotypes and anal disease prevalence, by cytology and histopathologic findings, were evaluated among 363 HIV-infected MSM. We modeled fractions of high-grade anal intraepithelial neoplasia (HGAIN) attributable to individual carcinogenic HPV genotypes and estimated the range of the proportion of HGAIN cases potentially preventable by prophylactic HPV vaccines.

            Results

            HPV16 was the most common genotype overall (26.4% of cases) and among HGAIN cases (55%). Prevalence of multiple (≥ 2) carcinogenic HPV genotypes increased from 30.9% in cases of AIN grade <1 to 76.3% in cases of AIN grade 3 (P(trend) < .001). The fractions of HGAIN cases attributable to carcinogenic HPV16/18 targeted by currently licensed bivalent and quadrivalent HPV vaccines ranged from 12% to 61.5%, and the fractions attributable to carcinogenic HPV16/18/31/33/45/52/58 targeted by an investigational nonavalent HPV vaccine ranged from 39% to 89.4%.

            Conclusions

            Our analytical framework allows estimation of HGAIN cases attributable to individual HPV genotypes in the context of multiple concurrent HPV infections, which are very common among HIV-infected MSM. Our results suggest that licensed and investigational HPV prophylactic vaccines have the potential to prevent a substantial proportion of HGAIN cases in this population.
              Cover page: Human Papillomavirus Genotype Attribution and Estimation of Preventable Fraction of Anal Intraepithelial Neoplasia Cases Among HIV-Infected Men Who Have Sex With Men
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2013)

              Background

              The prevention of human papillomavirus (HPV)-induced anal cancer in high-risk populations such as human immunodeficiency virus (HIV)-infected men who have sex with men (MSM) remains an urgent priority, given rising incidence rates despite widespread antiretroviral therapy use.

              Methods

              HPV genotypes and anal disease prevalence, by cytology and histopathologic findings, were evaluated among 363 HIV-infected MSM. We modeled fractions of high-grade anal intraepithelial neoplasia (HGAIN) attributable to individual carcinogenic HPV genotypes and estimated the range of the proportion of HGAIN cases potentially preventable by prophylactic HPV vaccines.

              Results

              HPV16 was the most common genotype overall (26.4% of cases) and among HGAIN cases (55%). Prevalence of multiple (≥ 2) carcinogenic HPV genotypes increased from 30.9% in cases of AIN grade <1 to 76.3% in cases of AIN grade 3 (P(trend) < .001). The fractions of HGAIN cases attributable to carcinogenic HPV16/18 targeted by currently licensed bivalent and quadrivalent HPV vaccines ranged from 12% to 61.5%, and the fractions attributable to carcinogenic HPV16/18/31/33/45/52/58 targeted by an investigational nonavalent HPV vaccine ranged from 39% to 89.4%.

              Conclusions

              Our analytical framework allows estimation of HGAIN cases attributable to individual HPV genotypes in the context of multiple concurrent HPV infections, which are very common among HIV-infected MSM. Our results suggest that licensed and investigational HPV prophylactic vaccines have the potential to prevent a substantial proportion of HGAIN cases in this population.
                Cover page: Human papillomavirus genotype attribution and estimation of preventable fraction of anal intraepithelial neoplasia cases among HIV-infected men who have sex with men.
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2014)
                Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (P(trend) < 0.001), HPV18 (P(trend) = 0.07), and other carcinogenic types (P(trend) < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV.
                  Cover page: Analytic and clinical performance of cobas HPV testing in anal specimens from HIV-positive men who have sex with men.
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2014)
                  Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (P(trend) < 0.001), HPV18 (P(trend) = 0.07), and other carcinogenic types (P(trend) < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV.
                    Cover page: Analytic and Clinical Performance of cobas HPV Testing in Anal Specimens from HIV-Positive Men Who Have Sex with Men
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2014)

                    Purpose

                    The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1.

                    Methods

                    Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data.

                    Results

                    All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele.

                    Conclusion

                    NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.
                      Cover page: Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum–associated degradation pathway
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