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Open Access Publications from the University of California

Scholarly Works (20 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2014)

Background

Debate surrounds the accuracy of U.S. government's estimates of job-related injuries and illnesses in agriculture. Whereas studies have attempted to estimate the undercount for all industries combined, none have specifically addressed agriculture.

Methods

Data were drawn from the U.S. government's premier sources for workplace injuries and illnesses and employment: the Bureau of Labor Statistics databanks for the Survey of Occupational Injuries and Illnesses (SOII), the Quarterly Census of Employment and Wages, and the Current Population Survey. Estimates were constructed using transparent assumptions; for example, that the rate (cases-per-employee) of injuries and illnesses on small farms was the same as on large farms (an assumption we altered in sensitivity analysis).

Results

We estimated 74,932 injuries and illnesses for crop farms and 68,504 for animal farms, totaling 143,436 cases in 2011. We estimated that SOII missed 73.7% of crop farm cases and 81.9% of animal farm cases for an average of 77.6% for all agriculture. Sensitivity analyses suggested that the percent missed ranged from 61.5% to 88.3% for all agriculture.

Conclusions

We estimate considerable undercounting of nonfatal injuries and illnesses in agriculture and believe the undercounting is larger than any other industry. Reasons include: SOII's explicit exclusion of employees on small farms and of farmers and family members and Quarterly Census of Employment and Wages's undercounts of employment. Undercounting limits our ability to identify and address occupational health problems in agriculture, affecting both workers and society.
    Cover page: An estimate of the U.S. government's undercount of nonfatal occupational injuries and illnesses in agriculture
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2024)
    Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.
      Cover page: Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations.
      • Article
      • Peer Reviewed
      The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

      Arabidopsis was used as a model plant to study the molecular regulation mechanism of iron uptake in strategy I plants and two new iron-regulated bHLH proteins (AtbHLH38 and AtbHLH39) have been identified. They showed interaction with FIT, a central regulatory gene involved in regulation iron uptake in Arabidopsis, by yeast-two-hybridization. Expression of FIT/AtbHLH38 or FIT/AtbHLH39 in yeast cells was able to activate GUS expression driven by AtFRO2 (ferric chelate reductase) and AtIRT1 (ferrous transporter) promoters. Overexpression of both FIT and either AtbHLH38 or AtbHLH39 converted the expression of the iron uptake genes AtFRO2 and AtIRT1 from induced to constitutively, and the overexpression plants accumulated more iron in their shoots than the wild type and exhibited more tolerance against iron deficiency. The results indicate that transcription of the iron uptake genes AtFRO2 and AtIRT1 in Arabidopsis is directly regulated by a complex of FIT/AtbHLH38 or FIT/AtbHLH39.

        Cover page: AtbHLH38 and AtbHLH39 interact with FIT, functioning in control of iron uptake in Arabidopsis
        • Article
        • Peer Reviewed
        The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

        Iron (Fe) is an essential mineral for plant growth and development. It plays crucial roles in many fundamental processes in cells, such as respiration, photosynthesis. In plant cells, iron is compartmentalized into different organelles, such as chloroplasts, mitochondria and vacuoles for its synthetic functions or storage. Chloroplast, a photosynthetic apparatus, represents one of the organelles possessing the most iron-enriched biochemical reaction systems (photosystem I, photosystem II, cytochrome b6-f complex and ferredoxin) in the plant cell. However, little is to known about the iron metabolism in this organelle.

        The ATP-dependent Clp protease is widely distributed in bacteria, cyanobacteria, mitochondria and chloroplasts and plays an important role in protein import to chloroplast (literature). In plants, the ATP-dependent Clp protease in chloroplasts is encoded by a nucleus gene ClpC. It is imported into chloroplast and functions in control of chlorophyll b synthesis (Nakagawara et al., 2007). Here, we show that CipC is involved in the iron homeostasis in mesophyll cells. Lesion of ClpC caused leaf chlorosis and growth inhibition, and this phenotype can be rescued by supplying iron. Expression profile analysis showed that the lesion of ClpC significantly increased the expression of AtFRO8 in the leaf, indicating that ClpC might be indirectly involved in the control of the expression of AtFRO8, consequently effect on iron homeostasis in chloroplasts.

          Cover page: ClpC, A ATP-Dependent Chloroplast Protease (Clp), Is Involved In Iron Metabolism in Arabidopsis
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2015)
          The strychnine-sensitive glycine receptor (GlyR) mediates inhibitory synaptic transmission in the spinal cord and brainstem and is linked to neurological disorders, including autism and hyperekplexia. Understanding of molecular mechanisms and pharmacology of glycine receptors has been hindered by a lack of high-resolution structures. Here we report electron cryo-microscopy structures of the zebrafish α1 GlyR with strychnine, glycine, or glycine and ivermectin (glycine/ivermectin). Strychnine arrests the receptor in an antagonist-bound closed ion channel state, glycine stabilizes the receptor in an agonist-bound open channel state, and the glycine/ivermectin complex adopts a potentially desensitized or partially open state. Relative to the glycine-bound state, strychnine expands the agonist-binding pocket via outward movement of the C loop, promotes rearrangement of the extracellular and transmembrane domain 'wrist' interface, and leads to rotation of the transmembrane domain towards the pore axis, occluding the ion conduction pathway. These structures illuminate the GlyR mechanism and define a rubric to interpret structures of Cys-loop receptors.
            Cover page: Glycine receptor mechanism elucidated by electron cryo-microscopy
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2017)
            Multifunctional black-silicon (b-Si) integrated on the surface of an implantable intraocular pressure sensor significantly improves sensor performance and reliability in six-month in vivo studies. The antireflective properties of b-Si triples the signal-to-noise ratio and increases the optical readout distance to a clinically viable 12 cm. Tissue growth and inflammation response on the sensor is suppressed demonstrating desirable anti-biofouling properties.
              Cover page: Biocompatible Multifunctional Black‐Silicon for Implantable Intraocular Sensor
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2017)
              Optimized glaucoma therapy requires frequent monitoring and timely lowering of elevated intraocular pressure (IOP). A recently developed microscale IOP-monitoring implant, when illuminated with broadband light, reflects a pressure-dependent optical spectrum that is captured and converted to measure IOP. However, its accuracy is limited by background noise and the difficulty of modeling non-linear shifts of the spectra with respect to pressure changes. Using an end-to-end calibration system to train an artificial neural network (ANN) for signal demodulation we improved the speed and accuracy of pressure measurements obtained with an optically probed IOP-monitoring implant and make it suitable for real-time in vivo IOP monitoring. The ANN converts captured optical spectra into corresponding IOP levels. We achieved an IOP-measurement accuracy of ±0.1 mmHg at a measurement rate of 100 Hz, which represents a ten-fold improvement from previously reported values. This technique allowed real-time tracking of artificially induced sub-1 s transient IOP elevations and minor fluctuations induced by the respiratory motion of the rabbits during in vivo monitoring. All in vivo sensor readings paralleled those obtained concurrently using a commercial tonometer and showed consistency within ±2 mmHg. Real-time processing is highly useful for IOP monitoring in clinical settings and home environments and improves the overall practicality of the optical IOP-monitoring approach.
                Cover page: Real-Time In Vivo Intraocular Pressure Monitoring Using an Optomechanical Implant and an Artificial Neural Network
                • Article
                • Peer Reviewed
                UC Riverside Previously Published Works (2024)
                Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
                  Cover page: Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization.
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2019)
                  Our understanding of ocular hemodynamics and its role in ophthalmic disease progression remains unclear due to the shortcomings of precise and on-demand biomedical sensing technologies. Here, we report high-resolution in vivo assessment of ocular hemodynamics using a Fabry-Pérot cavity-based micro-optical sensor and a portable optical detector. The designed optical system is capable of measuring both static intraocular pressure and dynamic ocular pulsation profiles in parallel. Through a dynamic intensity variation analysis method which improves sensing resolution by 3-4 folds, our system is able to extract systolic/diastolic phases from a single ocular pulsation profile. Using a portable detector, we performed in vivo studies on rabbits and verified that ophthalmic parameters obtained from our optical system closely match with traditional techniques such as tonometry, electrocardiography, and photo-plethysmography.
                    Cover page: Fabry–Pérot Optical Sensor and Portable Detector for Monitoring High-Resolution Ocular Hemodynamics
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2017)
                    Intraocular pressure (IOP) is a key clinical parameter in glaucoma management. However, despite the potential utility of daily measurements of IOP in the context of disease management, the necessary tools are currently lacking, and IOP is typically measured only a few times a year. Here we report on a microscale implantable sensor that could provide convenient, accurate, on-demand IOP monitoring in the home environment. When excited by broadband near-infrared (NIR) light from a tungsten bulb, the sensor's optical cavity reflects a pressure-dependent resonance signature that can be converted to IOP. NIR light is minimally absorbed by tissue and is not perceived visually. The sensor's nanodot-enhanced cavity allows for a 3-5 cm readout distance with an average accuracy of 0.29 mm Hg over the range of 0-40 mm Hg. Sensors were mounted onto intraocular lenses or silicone haptics and secured inside the anterior chamber in New Zealand white rabbits. Implanted sensors provided continuous in vivo tracking of short-term transient IOP elevations and provided continuous measurements of IOP for up to 4.5 months.
                      Cover page: A microscale optical implant for continuous in vivo monitoring of intraocular pressure
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