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Open Access Publications from the University of California

Scholarly Works (17 results)

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

Alzheimer’s disease (AD) is characterized by extensive cell death and accumulation of misfolded proteins in the brain, which consist of amyloid beta (Aβ) plaques and hyperphosphorylated tau neurofibrillary tangles (NFTs). We sought to determine the effects of endoplasmic reticulum (ER) stress on classical AD characteristics in neurons and neural stem cells (NSCs). We used isogenic human induced pluripotent stem cell (hiPSC)-derived neurons and NSCs that were genetically modified with the presenilin 1 exon 9 deletion (PS1-ΔE9) mutation. We found that after two days, tunicamycin induced cell death in the PS1-ΔE9 neurons, but not wild type neurons; treatment for five days with thapsigargin, however, induced more cell death in wild type neurons than PS1-∆E9 neurons.

While previous studies have suggested connections between ER stress, Aβ, and phosphorylated tau (P-tau), results have remained controversial. To measure the effects of ER stress on Aβ42/Aβ40 and P-tau/T-tau (total tau) ratios, we treated neurons with tunicamycin or thapsigargin for two or five days. We observed no change in Aβ42/Aβ40 ratio with tunicamycin or thapsigargin, but observed a dose- and time-dependent reduction in overall Aβ42 and Aβ40 levels. P-tau/T-tau ratio was decreased in PS1-∆E9, but not wild type neurons in response to both tunicamycin and thapsigargin at 2 days. However, after 5 days of treatment we observed reduced P-tau/T-tau ratio in response to tunicamycin only in wild type and PS1-∆E9 neurons. The results presented in this study show that the PS1-∆E9 mutation sensitizes and confers resistance to neurons in response to different ER stressors, and suggest that ER stress may rescue AD phenotypes.

    Cover page: The impact of the unfolded protein response on human neurons carrying the familial Alzheimer's disease PSEN1-deltaE9 mutation
    • Thesis
    • Peer Reviewed
    UCLA Electronic Theses and Dissertations (2018)

    This thesis is devoted to improving the spectroscopic performance of the gallium antimonide (GaSb)/aluminum arsenide antimonide (AlAsSb) energy-sensitive detector. The heterostructure device is realized by integrating the GaSb absorber and the AlAsSb digital-alloy, combined with a field-control layer to optimize the electric field profile. This work attempts to enhance the energy resolving ability of the detector by lowering its surface leakage current, which is the dominant dark current source and limits the signal to noise ratio (SNR) of the detection system. To achieve the proposed goal, a layer of aluminum oxide (Al2O3) is deposited on the detector surface by ALD (Atomic Layer Deposition), which suppresses the formation of surface leakage path by interface chemistry between Al2O3 and the native oxides (e.g. Ga2O3 and Sb2O3). Well-improved dark current levels are measured in the Al2O3-passivated device, and the spectroscopic performance also indicates reduced electronic noise.

      Cover page: Improvement in Spectroscopic Performance of Gallium Antimonide/Aluminum Arsenide Antimonide Heterostructure Energy-sensitive Detectors by Aluminum Oxide Surface Passivation
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2012)
      Most of the natural variation in wheat vernalization response is determined by allelic differences in the MADS-box transcription factor VERNALIZATION1 (VRN1). Extended exposures to low temperatures during the winter (vernalization) induce VRN1 expression and promote the transition of the apical meristem to the reproductive phase. In contrast to its Arabidopsis homolog (APETALA1), which is mainly expressed in the apical meristem, VRN1 is also expressed at high levels in the leaves, but its function in this tissue is not well understood. Using tetraploid wheat lines with truncation mutations in the two homoeologous copies of VRN1 (henceforth vrn1-null mutants), we demonstrate that a central role of VRN1 in the leaves is to maintain low transcript levels of the VRN2 flowering repressor after vernalization. Transcript levels of VRN2 were gradually down-regulated during vernalization in both mutant and wild-type genotypes, but were up-regulated after vernalization only in the vrn1-null mutants. The up-regulation of VRN2 delayed flowering by repressing the transcription of FT, a flowering-integrator gene that encodes a mobile protein that is transported from the leaves to the apical meristem to induce flowering. The role of VRN2 in the delayed flowering of the vrn1-null mutant was confirmed using double vrn1-vrn2-null mutants, which flowered two months earlier than the vrn1-null mutants. Both mutants produced normal flowers and seeds demonstrating that VRN1 is not essential for wheat flowering, which contradicts current flowering models. This result does not diminish the importance of VRN1 in the seasonal regulation of wheat flowering. The up-regulation of VRN1 during winter is required to maintain low transcript levels of VRN2, accelerate the induction of FT in the leaves, and regulate a timely flowering in the spring. Our results also demonstrate the existence of redundant wheat flowering genes that may provide new targets for engineering wheat varieties better adapted to changing environments.
        Cover page: Wheat TILLING Mutants Show That the Vernalization Gene VRN1 Down-Regulates the Flowering Repressor VRN2 in Leaves but Is Not Essential for Flowering
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2016)

        Key message

        The combination of three non-functional alleles of the flowering repressor VRN2 results in a spring growth habit in wheat. In temperate cereals with a winter growth habit, a prolonged exposure to low temperatures (vernalization) accelerates flowering. Before vernalization, the VRN2 locus plays a central role in maintaining flowering repression. Non-functional VRN2 alleles result in spring growth habit and are frequent in diploid wheat and barley. However, in hexaploid wheat, the effect of these non-functional VRN2 alleles is masked by gene redundancy. In this study, we developed a triple VRN2 mutant (synthetic vrn2-null) in hexaploid wheat by combining the non-functional VRN-A2 allele present in most polyploid wheats with a VRN-B2 deletion from tetraploid wheat, and a non-functional VRN-D2 allele from Aegilops tauschii (Ae. tauschii) (the donor of hexaploid wheat D genome). Non-vernalized vrn2-null plants flowered 118 days (P < 2.8E-07) earlier than the winter control, and showed a limited vernalization response. The functional VRN-B2 allele is expressed at higher levels than the functional VRN-D2 allele and showed a stronger repressive effect under partial vernalization (4 °C for 4 weeks), and also in non-vernalized plants carrying only a functional VRN-B2 or VRN-D2 in heterozygous state. These results suggest that different combinations of VRN-B2 and VRN-D2 alleles can be a used to modulate the vernalization response in regions with mild winters. Spring vrn2-null mutants have been selected repeatedly in diploid wheat and barley, suggesting that they may have an adaptative value and that may be useful in hexaploid wheat. Spring wheat breeders can use these new alleles to improve wheat adaptation to different or changing environments.
          Cover page: Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2018)
          In the original version of this article, PCR fragments and digestion product sizes for the VRN-B2 and VRN-D2 markers were not accurate. The corrected sizes are detailed below.
            Cover page: Correction to: Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2016)

            Background

            In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intensity or quality of light. Phytochromes are dimeric photoreceptors that absorb light maximally in the red and far-red wavelengths and induce large-scale transcriptional changes in response to variation in light quality. In wheat, PHYC is required for early flowering under long days. However, it is currently unknown whether this function requires the presence of PHYB. In this study, we characterized the role of PHYB in wheat development and used RNA-seq to analyze and compare the transcriptomes of phyB-null and phyC-null TILLING mutants.

            Results

            Under long-day photoperiods, phyB-null plants exhibit a severe delay in flowering comparable to the delay observed in phyC-null plants. These results demonstrate that both genes are required for the induction of wheat flowering under long days. Using replicated RNA-seq studies we identified 82 genes that are significantly up or down regulated in both the phyB-null and phyC-null mutant relative to their respective wild-type controls. Among these genes are several well-characterized positive regulators of flowering, including PPD1, FT1 and VRN1. Eight-fold more genes were differentially regulated only in the phyB-null mutant (2202) than only in the phyC-null mutant (261). The PHYB-regulated genes were enriched in components of the auxin, gibberellin and brassinosteroid biosynthesis and signaling pathways, and in transcription factors with putative roles in regulating vegetative development and shade-avoidance responses. Several genes involved in abiotic stress tolerance pathways were also found to be regulated by PHYB.

            Conclusions

            PHYB and PHYC are both required for the photoperiodic induction of wheat flowering, whereas PHYB alone regulates a large number of genes involved in hormone biosynthesis and signaling, shade-avoidance response, and abiotic stress tolerance. Our analysis provides a comprehensive overview of the PHYB- and PHYC-mediated transcriptional changes during light signaling, and an initial step towards the dissection of this regulatory gene network in wheat. This further dissection will be required to explore the individual phytochrome-mediated developmental responses and to evaluate their potential to improve wheat adaptation to changing environments.
              Cover page: RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2019)
              The spikelet is the basic unit of the grass inflorescence. In this study, we show that wheat MADS-box genes VRN1, FUL2 and FUL3 play critical and redundant roles in spikelet and spike development, and also affect flowering time and plant height. In the vrn1ful2ful3-null triple mutant, the inflorescence meristem formed a normal double-ridge structure, but then the lateral meristems generated vegetative tillers subtended by leaves instead of spikelets. These results suggest an essential role of these three genes in the fate of the upper spikelet ridge and the suppression of the lower leaf ridge. Inflorescence meristems of vrn1ful2ful3-null and vrn1ful2-null remained indeterminate and single vrn1-null and ful2-null mutants showed delayed formation of the terminal spikelet and increased number of spikelets per spike. Moreover, the ful2-null mutant showed more florets per spikelet, which together with a higher number of spikelets, resulted in a significant increase in the number of grains per spike in the field. Our results suggest that a better understanding of the mechanisms underlying wheat spikelet and spike development can inform future strategies to improve grain yield in wheat.
                Cover page: Wheat VRN1, FUL2 and FUL3 play critical and redundant roles in spikelet development and spike determinacy
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2014)
                Wheat vernalization requirement is mainly controlled by the VRN1, VRN2, VRN3, and VRN4 genes. The first three have been cloned and have homoeologs in all three genomes. VRN4 has been found only in the D genome (VRN-D4) and has not been cloned. We constructed a high-density genetic map of the VRN-D4 region and mapped VRN-D4 within a 0.09 cM interval in the centromeric region of chromosome 5D. Using telocentric 5D chromosomes generated from the VRN-D4 donor Triple Dirk F, we determined that VRN-D4 is located on the short arm. The VRN-D4 candidate region is colinear with a 2.24 Mb region on Brachypodium distachyon chromosome 4, which includes 127 predicted genes. Ten of these genes have predicted roles in development but we detected no functional polymorphisms associated to VRN-D4. Two recombination events separated VRN-D4 from TaVIL-D1, the wheat homolog of Arabidopsis vernalization gene VIL1, confirming that this gene is not a candidate for VRN-D4. We detected significant interactions between VRN-D4 and other four genes controlling vernalization requirement (Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3), which confirmed that VRN-D4 is part of the vernalization pathway and that it is either upstream or is part of the regulatory feedback loop involving VRN1, VRN2 and VRN3 genes. The precise mapping of VRN-D4 and the characterization of its interactions with other vernalization genes provide valuable information for the utilization of VRN-D4 in wheat improvement and for our current efforts to clone this vernalization gene.
                  Cover page: Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2023)
                  Vasoactive intestinal peptide (VIP) interneurons in sensory cortex modulate sensory responses based on global exploratory behavior and arousal state, but their function during non-exploratory, goal-directed behavior is not well understood. In particular, whether VIP cells are activated by sensory cues, reward-seeking actions, or directly by reinforcement is unclear. We trained mice on a Go/NoGo whisker touch detection task that included a delay period and other features designed to separate sensory-evoked, action-related, and reward-related neural activity. Mice had to lick in response to a whisker stimulus to receive a variable-sized reward. Using two-photon calcium imaging, we measured ΔF/F responses of L2/3 VIP neurons in whisker somatosensory cortex (S1) during behavior. In both expert and novice mice, VIP cells were strongly activated by whisker stimuli and goal-directed actions (licking), but not by reinforcement. VIP cells showed somatotopic whisker tuning that was spatially organized relative to anatomical columns in S1, unlike lick-related signals which were spatially widespread. In expert mice, lick-related VIP responses were suppressed, not enhanced, when a reward was delivered, and the amount of suppression increased with reward size. This reward-related suppression was not seen in novice mice, where reward delivery was not yoked to licking. These results indicate that besides arousal and global state variables, VIP cells are activated by local sensory features and goal-directed actions, but not directly by reinforcement. Instead, our results are consistent with a role for VIP cells in encoding the expectation of reward associated with motor actions.
                    Cover page: VIP interneurons in sensory cortex encode sensory and action signals but not direct reward signals.
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2020)
                    Collagen is the most abundant protein in animals. Its dysregulation contributes to aging and many human disorders, including pathological tissue fibrosis in major organs. How premature collagen proteins in the endoplasmic reticulum (ER) assemble and route for secretion remains molecularly undefined. From an RNA interference screen, we identified an uncharacterized Caenorhabditis elegans gene tmem-131, deficiency of which impairs collagen production and activates ER stress response. We find that amino termini of human TMEM131 contain bacterial PapD chaperone-like domains, which recruit premature collagen monomers for proper assembly and secretion. Carboxy termini of TMEM131 interact with TRAPPC8, a component of the TRAPP tethering complex, to drive collagen cargo trafficking from ER to the Golgi. We provide evidence that previously undescribed roles of TMEM131 in collagen recruitment and secretion are evolutionarily conserved in C. elegans, Drosophila, and humans.
                      Cover page: Broadly conserved roles of TMEM131 family proteins in intracellular collagen assembly and secretory cargo trafficking
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