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Open Access Publications from the University of California

Scholarly Works (32 results)

  • Article
  • Peer Reviewed
UCLA Pacific Basin Law Journal, Volume 18, Issue 2 (2000)
    Cover page: Foreign Business and Consumer Rights: A Survey of Consumer Protection Law in China
    • Thesis
    • Peer Reviewed
    UC Riverside Electronic Theses and Dissertations (2012)

    Barrow Peninsula is located on the North Slope of Alaska with much of it consisting of high latitude wetlands. Thaw lakes, an important feature of these wetlands, have been shown to be significant sources of methane to the atmosphere; however the origins of the methane remain poorly constrained. We have used lipid biomarkers to better understand biogenic methane production in lake sediments by characterizing microbial communities that may be involved in methane cycling as well as the organic matter that is available as substrates for methanogens.

    Surprisingly, we found a relatively low amount of lipids associated with methane cycling, with no detection of lipids derived from anaerobic methane oxidizing archaea, low but detectable amounts of compounds produced by Type I methanotrophic bacteria, as well as low but detectable amounts of lipids likely derived from methanogens. However, archaeol concentration, and hence methanogen abundance, did appear to correlate with TOC amounts. We also found a strong signal of in situ primary production in the form of a high 2-methylhopane index (> 10 %), reflecting cyanobacterial inputs, coupled with abundant nC22-nC26 n-alkanes and high sterane/hopane ratios which are characteristic of green algae.The elevated archaeol levels in the lake cores that displayed the greatest TOC amounts (and by extension greatest primary production) may show that future methane emission rates of these lakes may ultimately be tied to the type of organic matter deposition methylhopanes and archaeol were found in all lakes sampled and most likely were produced by aerobic methane-oxidizing proterobacteria and archaea (likely methanogens), respectively.

    Conversely, abundant 2-methylhopanes, biomarkers associated with cyanobacterial primary production when abundances of gammacerane (relative to hopanes) are low, were found in many total organic carbon (TOC) rich sections and may indicate high productivity occurring within the lake, either from planktonic or benthic cyanobacteria. Similarly, high sterane/hopane ratios were also found in all the lake sampled, particularly in Sukok Seep (SS), which may be a result of high eukaryotic productivity occurring within the lakes. This may lead to productivity occurring within the lake having a much larger control on methanogenesis than material that is washed into the lake. This may complicate methane emissions as temperatures warm, since lake nutrient availability, which affects productivity, may be an important control on methanogenesis along with changes in metabolic activity and water table position. Biomarkers of methane cycling organisms have been found in abundance in both modern and ancient marine cold seep environments and through recent phylogenetic and stable isotope work, the source assignments have become more robust. However, very little work has been done on their freshwater analogues that inhabit water-saturated environments at high-latitudes and how they may differ from their marine counterparts. The sampling of these lakes sediments allow us to see how these organism have responded to climate change in the past, indicating how they might respond to the expected high latitude warming in the future.

      Cover page: A Lipid Biomarker Investigation of Organic Matter Sources and Methane Cycling in Alaskan Thaw Lake Sediments
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2000)
      The 3′-termini of maize mitochondrial RNAs were characterized by ligation of an anchor oligonucleotide, reverse transcription and amplification. DNA sequence analysis of cDNA clones for tRNASer and 18S rRNA confirmed the expected 3′-terminal nucleotides and demonstrated the accuracy and fidelity of the protocol. Analysis of cDNAs for rps12, cox2 and atp9 indicated that non-genomically encoded nucleotides were present at the 3′-terminus. rps12 cDNAs exhibited the highest degree of modification, with 94% of 35 cDNA clones analyzed containing one to four non-genomically encoded C or A residues; 83% of these cDNAs terminated with the trinucleotide CCA. DNA sequence and transcript mapping analyses demonstrated that four positions exhibited modified 3′-termini within a small region of the 3′ flank of rps12 transcripts. These transcript termini represented low abundance, truncated forms of rps12 mRNAs which may be intermediates in degradation. cox2 mRNAs are also modified at a truncated position. Sixty percent of the cox2 cDNAs were modified with 1–5 nt that most frequently included A and C residues, but also included a few G and T residues. Non-genomically encoded nucleotides were detected in 27% of the atp9 cDNAs as a single C or A residue.
        Cover page: Addition of non-genomically encoded nucleotides to the 3?-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCACreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        Proceedings of the Annual Meeting of the Cognitive Science Society, Volume 34 (2012)
          Cover page: The effect of metabolic loading on statistical learning
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2015)
          Effects of infrared heaters on snow accumulation, snowmelt, and snow–atmosphere energy exchange were examined at Niwot Ridge, Colorado (CO) and compared to a naturally warmer, but otherwise similar subalpine site in the Valles Caldera National Preserve, New Mexico (NM). Observed snow accumulation was 30% lower on average and snow melted out 16 days earlier in the heated plots compared to the controls. Soil temperature during snowmelt was 3°C greater on average and soil moisture was 4% lower on average in heated plots compared to controls. In NM, snow accumulation was 23% lower, snow melted 23 days earlier, soil temperature was 0.6°C greater, and soil moisture was 13% lower on average relative to CO controls. In order to estimate differences in energy and mass balance fluxes at the snow–atmosphere interface in control versus warmer plots, the 1-D, physically based snowmelt model, SNOWPACK, was used. Model results indicated that heaters alter radiative, turbulent and mass fluxes by amounts comparable to the differences between CO and NM fluxes. The proportion of the energy flux associated with latent heat exchange during snowmelt was 9–27% of the total energy flux in heated models and 19–22% of NM models compared to 3–7% in control models. Thus, sublimation loss to the atmosphere was greater in both experimentally and naturally warmer cases relative to the control case. We conclude that IR heaters can provide alterations to the timing and magnitude of snow accumulation and snowmelt consistent with conditions observed at a warmer analog site and with climate and hydrology model projections. Impacts of IR heating on energy partitioning and sublimation should be considered when designing manipulations of the snowpack, as reductions in snowmelt water may alter biological or ecological processes.
            Cover page: Snowpack-climate manipulation using infrared heaters in subalpine forests of the Southern Rocky Mountains, USA
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2014)
            This study compares stream nitrate (NO3-) concentrations to spatially distributed snowmelt in two alpine catchments, the Green Lakes Valley, Colorado (GLV4) and Tokopah Basin, California (TOK). A snow water equivalent reconstruction model and Landsat 5 and 7 snow cover data were used to estimate daily snowmelt at 30 m spatial resolution in order to derive indices of new snowmelt areas (NSAs). Estimates of NSA were then used to explain the NO3- flushing behavior for each basin over a 12 year period (1996-2007). To identify the optimal method for defining NSAs and elucidate mechanisms underlying catchment NO3- flushing, we conducted a series of regression analyses using multiple thresholds of snowmelt based on temporal and volumetric metrics. NSA indices defined by volume of snowmelt (e.g., snowmelt ≤ 30 cm) rather than snowmelt duration (e.g., snowmelt ≤ 9 days) were the best predictors of stream NO3- concentrations. The NSA indices were better correlated with stream NO3- concentration in TOK (average R2= 0.68) versus GLV4 (average R2= 0.44). Positive relationships between NSA and stream NO3- concentration were observed in TOK with peak stream NO3- concentration occurring on the rising limb of snowmelt. Positive and negative relationships between NSA and stream NO3- concentration were found in GLV4 with peak stream NO3- concentration occurring as NSA expands. Consistent with previous works, the contrasting NO3- flushing behavior suggests that streamflow in TOK was primarily influenced by overland flow and shallow subsurface flow, whereas GLV4 appeared to be more strongly influenced by deeper subsurface flow paths.
              Cover page: Relationships between stream nitrate concentration and spatially distributed snowmelt in high‐elevation catchments of the western U.S.
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2009)
              Fluxes of CO2 during the snow-covered season contribute to annual carbon budgets, but our understanding of the mechanisms controlling the seasonal pattern and magnitude of carbon emissions in seasonally snow-covered areas is still developing. In a subalpine meadow on Niwot Ridge, Colorado, soil CO2 fluxes were quantified with the gradient method through the snowpack in winter 2006 and 2007 and with chamber measurements during summer 2007. The CO2 fluxes of 0.71 μmol m−2 s−1 in 2006 and 0.86 μmol m−2 s−1 in 2007 are among the highest reported for snow-covered ecosystems in the literature. These fluxes resulted in 156 and 189 g C m−2 emitted over the winter, ~30% of the annual soil CO2 efflux at this site. In general, the CO2 flux increased during the winter as soil moisture increased. A conceptual model was developed with distinct snow cover zones to describe this as well as the three other reported temporal patterns in CO2 flux from seasonally snow-covered soils. As snow depth and duration increase, the factor controlling the CO2 flux shifts from freeze–thaw cycles (zone I) to soil temperature (zone II) to soil moisture (zone III) to carbon availability (zone IV). The temporal pattern in CO2 flux in each zone changes from periodic pulses of CO2 during thaw events (zone I), to CO2 fluxes reaching a minimum when soil temperatures are lowest in mid-winter (zone II), to CO2 fluxes increasing gradually as soil moisture increases (zone III), to CO2 fluxes decreasing as available carbon is consumed. This model predicts that interannual variability in snow cover or directional shifts in climate may result in dramatically different seasonal patterns of CO2 flux from seasonally snow-covered soils.
                Cover page: Process-level controls on CO2 fluxes from a seasonally snow-covered subalpine meadow soil, Niwot Ridge, Colorado
                • Article
                • Peer Reviewed
                UC Merced Previously Published Works (2000)
                We investigated the hydrologic, geochemical, and biogeochemical controls on stream chemical composition on the Green Lakes Valley and Andrews Creek watersheds using the alpine hydrochemical model (AHM). Both sites had comparable data sets from 1994 and 1996, including high-resolution spatial data and high-frequency time series of hydrology, geochemistry, and meteorology. The model of each watershed consisted of three terrestrial subunits (soil, talus, and rock), with the routing between the subunits determined by spatial land cover data. Using 1994 data for model calibration and 1996 data for evaluation, AHM captured the dominant processes and successfully simulated daily stream chemical composition on both watersheds. These results confirm our procedure of using spatial and site-specific field and laboratory data to generate an initial catchment model and then calibrating the model to calculate effective parameters for unmeasured processes. A net source of nitrogen was identified in the Andrews Creek watershed during the spring snowmelt period, whereas nitrogen was immobilized in the Green Lakes Valley. This difference was most likely due to the larger and more dominant area of talus in the Andrews Creek watershed. Our results also indicate that routing of snowmelt through either soil or talus material is sufficient for retention of H+ and release of base cations but that N retention is more important on areas mapped as soil. Owing to the larger ionic pulse and larger fraction of surface runoff the Green Lakes Valley was more sensitive to a doubling of wet deposition chemistry than the Andrews Creek watershed.
                  • Article
                  • Peer Reviewed
                  UC Merced Previously Published Works (1995)
                  The fluxes and transformations of nitrogen (N) were investigated from 1985 through 1987 at the Emerald Lake watershed (ELW), a 120 ha high-elevation catchment located in the southern Sierra Nevada, California, USA. Up to 90% of annual wet deposition of N was stored in the seasonal snowpack; NO3- and NH4+ were released from storage in the form of an ionic pulse, where the first fraction of meltwater draining from the snowpack had concentrations of NO3- and NH4+ as high as 28 μeq L-1 compared to bulk concentrations of <5 μeq L-1 in the snowpack. The soil reservoir of organic N (81 keq ha-1) was about ten times the N storage in litter and biomass (12 keq ha-1). Assimilation of N by vegetation was balanced by the release of N from soil mineralization, nitrification, and litter decay. Mineralization and nitrification processes produced 1.1 keq ha-1 yr-1 of inorganic N, about 3 1/2 times the loading of N from wet and dry deposition. Less than 1% of the NH4+ in wet and dry deposition was exported from the basin as NH4+. Biological assimilation was primarily responsible for retention of NH4+ in the basin, releasing one mode of H+ for every mole of NH4+ retained and neutralizing about 25% of the annual acid neutralizing capacity produced by mineral weathering in the basin. Nitrate concentrations in stream waters reached an annual peak during the first part of snowmelt runoff, with maximum concentrations in stream water of 20 μeq L-1, more than 4 times the volume-weighted mean annual concentrations of NO3- in wet deposition. This annual peak in stream water NO3- was consistent with the release of NO3- from the snowpack in the form of an ionic pulse; however soil processes occurring underneath the winter snowpack were another potential source of this NO3-. Concentrations of stream water NO3- during the summer growing season were always near or below detection limits (0.5 μeq L-1). © 1995 Kluwer Academic Publishers.
                    • Article
                    • Peer Reviewed
                    UC Irvine Previously Published Works (2009)

                    Background

                    Taste bud cells transmit information regarding the contents of food from taste receptors embedded in apical microvilli to gustatory nerve fibers innervating basolateral membranes. In particular, taste cells depolarize, activate voltage-gated sodium channels, and fire action potentials in response to tastants. Initial cell depolarization is attributable to sodium influx through TRPM5 in sweet, bitter, and umami cells and an undetermined cation influx through an ion channel in sour cells expressing PKD2L1, a candidate sour taste receptor. The molecular identity of the voltage-gated sodium channels that sense depolarizing signals and subsequently initiate action potentials coding taste information to gustatory nerve fibers is unknown.

                    Results

                    We describe the molecular and histological expression profiles of cation channels involved in electrical signal transmission from apical to basolateral membrane domains. TRPM5 was positioned immediately beneath tight junctions to receive calcium signals originating from sweet, bitter, and umami receptor activation, while PKD2L1 was positioned at the taste pore. Using mouse taste bud and lingual epithelial cells collected by laser capture microdissection, SCN2A, SCN3A, and SCN9A voltage-gated sodium channel transcripts were expressed in taste tissue. SCN2A, SCN3A, and SCN9A were expressed beneath tight junctions in subsets of taste cells. SCN3A and SCN9A were expressed in TRPM5 cells, while SCN2A was expressed in TRPM5 and PKD2L1 cells. HCN4, a gene previously implicated in sour taste, was expressed in PKD2L1 cells and localized to cell processes beneath the taste pore.

                    Conclusion

                    SCN2A, SCN3A and SCN9A voltage-gated sodium channels are positioned to sense initial depolarizing signals stemming from taste receptor activation and initiate taste cell action potentials. SCN2A, SCN3A and SCN9A gene products likely account for the tetrodotoxin-sensitive sodium currents in taste receptor cells.
                      Cover page: Voltage-gated sodium channels in taste bud cellsCreative Commons 'BY' version 4.0 license
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