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Open Access Publications from the University of California

Scholarly Works (34 results)

  • Article
  • Peer Reviewed
UC Santa Barbara Previously Published Works (2005)

Biological reserves are intended to protect species, communities, and ecosystems in human-dominated landscapes. However, existing protected areas represent only relatively small, geographically biased samples of species and habitats. Climate change and habitat loss can exacerbate these biases and the net result is a small, skewed subset of historic environmental conditions. We developed a general model to improve the representation of environmental conditions across the range of at-risk species or any other elements targeted for conservation. We implemented the model as an integer linear-programming problem to select additional areas to complement existing reserves and create new portfolios that are bioclimatically representative across a range of climatic scenarios. We demonstrated the use of the model for a small dataset including two hydrologic variables across the range of five species of fairy shrimp (Anostraca) in the Central Valley ecoregion of California, USA under three climate scenarios. The bioclimatic representation model identified solutions that meet biodiversity representation goals and substantially improve bioclimatic representation at minimal additional cost in terms of total land selected for a conservation portfolio. Additional constraints rewarding bioclimatic representation under two conflicting climate scenarios resulted in only a small decrease in the performance of solutions with respect to current climate. We conclude that this model provides a general tool for improving bioclimatic representation, and results from the Central Valley case study suggest an encouraging, testable hypothesis that climatically robust bioclimatic representation can be achieved at negligible marginal costs.

    Cover page: Selection of bioclimatically representative biological reserve systems under climate change
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (1994)
    The development of techniques to cultivate human primary melanocytes in vitro has provided the technical foundation for understanding the biology of this cell. Human melanocytes require various growth factors and agents for proliferation in vitro. These compounds activate two major signal transduction pathways: a calcium- and phospholipid-dependent (protein kinase C or PKC) pathway and a cyclic AMP (cAMP)-dependent (protein kinase A or PKA) pathway. Alterations in these signal transduction pathways coupled with changes in specific genes (protooncogenes, growth factors, and tumor suppressor genes) have been observed in human melanoma cells compared with normal melanocytes. Our own work indicates that loss in the expression of the PKC beta II isotype is a common, if not universal, alteration that occurs early in human melanocyte transformation. In this review, we concentrate on alterations in the signal transduction pathways in human melanocytes and melanoma cells and delineate how an understanding of these changes may allow us to understand the molecular mechanisms involved in human melanocyte transformation.
      Cover page: Alterations in Gene Expression and Signal Transductions in Human Melanocytes and Melanoma CellsCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Santa Barbara Previously Published Works (2007)

      Fog deposition is an important water source for endemic conifer species during the annual summer drought along the California coast ( and in other coastal and montane areas). We present a new design for a passive fog collector that is useful both for characterizing fog regimes ( timing and quantity of deposition) and for collecting fog water for subsequent isotopic analysis. The new collector both mimics vegetation collection efficiency and minimizes isotopic fractionation under a range of fog conditions. Low construction cost and collector durability allow widely distributed installation and greater insight into spatially heterogeneous fog patterns. We installed 21 fog collectors throughout a stand of Bishop pines ( Pinus muricata D. Don) on Santa Cruz Island. In general, there was greater fog deposition with increasing elevation and decreasing frequency farther inland. Within these broad patterns, there was large spatial and temporal variability in fog deposition. Monthly samples of fog and rain waters reveal differences in stable isotope composition ( delta O-18 and delta D) large enough to serve as tracers of different water sources moving through the ecosystem.

        Cover page: Evaluating patterns of fog water deposition and isotopic composition on the California Channel Islands
        • Article
        • Peer Reviewed
        UC Santa Barbara Previously Published Works (2005)

        Numerous models have been put forth to help with the growing demand for the establishment of biodiversity reserves. One site selection model that has been used in several recent studies is SITES [S.J. Andelman, I. Ball, F.W. Davis and D.M. Stoms, SITES V 1.0: an analytical toolbox for designing ecoregional conservation portfolios, Unpublished manual prepared for the nature conservancy, 1999, 1-43. (available at http://www.biogeog.ucsb.edu /projects/tnc/toolbox.html)]. SITES includes two heuristic solvers: based on Greedy and Simulated Annealing. We discuss the formulation of the SITES model, present a new formulation for that problem, and solve a number of test problems optimally using off-the-shelf software. We compared our optimal results with the SITES Simulated Annealing heuristic and found that SITES frequently returns significantly suboptimal solutions. Our results add further support to the argument, started by Underhill [L.G. Underhill, Optimal and suboptimal reserve selection algorithms, Biol. Conserv. 70 (1994) 85-87], continuing through Rodrigues and Gaston [A.S.L. Rodrigues and K.J. Gaston, Optimization in reserve selection procedures - why not?, Biol. Conserv. 107 (2002) 123-129], for greater integration of optimal methods in the reserve design/selection literature.

          Cover page: The SITES reserve selection system: A critical review
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)
          Many bacteria and other microbes achieve locomotion via flagella, which are organelles that function as a swimming motor. Depending on the environment, flagellar motility can serve a variety of beneficial functions and confer a fitness advantage. For example, within a mammalian host, flagellar motility can provide bacteria the ability to resist clearance by flow, facilitate access to host epithelial cells, and enable travel to nutrient niches. From the host's perspective, the mobility that flagella impart to bacteria can be associated with harmful activities that can disrupt homeostasis, such as invasion of epithelial cells, translocation across epithelial barriers, and biofilm formation, which ultimately can decrease a host's reproductive fitness from a perspective of natural selection. Thus, over an evolutionary timescale, the host developed a repertoire of innate and adaptive immune countermeasures that target and mitigate this microbial threat. These countermeasures are wide-ranging and include structural components of the mucosa that maintain spatial segregation of bacteria from the epithelium, mechanisms of molecular recognition and inducible responses to flagellin, and secreted effector molecules of the innate and adaptive immune systems that directly inhibit flagellar motility. While much of our understanding of the dynamics of host-microbe interaction regarding flagella is derived from studies of enteric bacterial pathogens where flagella are a recognized virulence factor, newer studies have delved into host interaction with flagellated members of the commensal microbiota during homeostasis. Even though many aspects of flagellar motility may seem innocuous, the host's redundant efforts to stop bacteria in their tracks highlights the importance of this host-microbe interaction.
            Cover page: Flagella at the Host-Microbe Interface: Key Functions Intersect With Redundant Responses
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2009)
            Plant invasions have tremendous potential to alter food webs by changing basal resources. Recent studies document how plant invasions may contribute to increased arthropod abundances in detritus-based food webs. An obvious mechanism for this phenomenon—a bottom-up effect resulting from elevated levels of detritus from the invasive plant litter—has not been explicitly studied. We examined the effects of an annual grass invasion on ground arthropod assemblages in the coastal sage scrub (CSS) of southern California. Bottom-up food web theory predicts that the addition of detritus would increase generalist-feeding arthropods at all trophic levels; accordingly, we expected increases in fungi, Collembola, and common predators such as mites and spiders. For the common ant taxa, habitat alteration may also be important for predicting responses. Thus we expected that Forelius mccooki and Pheidole vistana, the most common ant species, would decline because of changes in soil temperature (F. mccooki) and habitat structure (P. vistana) associated with litter. We studied trends observationally and conducted a 3-year experiment in which we manipulated litter quantity. In contrast to other published studies, most detritus-based arthropod taxa declined in areas of high grass invasion, and, within trophic levels, responses often varied idiosyncratically. For the two most common taxa, a native ant (F. mccooki), and predatory mites in the Anystidae, we experimentally linked declines in abundance to increased levels of invasive grass litter. Such declines, especially those exhibited by the most common ant taxa, could have cascading effects on the CSS ecosystem, where ants are numerically dominant and thus may have broad influences on food web and ecosystem properties. Our results highlight that accurately predicting arthropod responses to invasive plant litter requires careful consideration of the structural and food resources provided by detritus to each particular food web.
              Cover page: Complex responses to invasive grass litter by ground arthropods in a Mediterranean scrub ecosystem
              • Article
              • Peer Reviewed
              LBL Publications (2022)
              The mechanical and dynamic properties of developing networks near the gel point are susceptible to the distribution of clusters coexisting with percolating networks. The distribution of cluster numbers follows a broad power law, wrapped by a cutoff function that rapidly decays at a characteristic size. The form of the cutoff function has been speculated based on known results from lattice percolation and, in certain cases, solved. We obtained this cutoff function from simulated dynamic clusters of polymeric precursor chains using a hybrid Monte Carlo algorithm. The results obtained from three different precursor chain lengths are consistent with each other and are consistent with the expectation from lattice percolation.
                Cover page: Distribution Cutoff for Clusters near the Gel PointCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (1991)
                Analysis of the regulation of c-jun, jun-B, and c-fos RNA transcript expression was performed in human primary melanocytes and metastatic melanoma cell strains. The medium requirements for human melanocyte in vitro growth are phorbol esters, agents that elevate intracellular cAMP levels, hormones, and growth factors. Cellular jun, jun-B, and c-fos gene expression are known to be affected by growth promoting agents. In primary melanocytes, the expression of c-jun, jun-B, and c-fos RNA transcripts was dependent on the growth-promoting agents present in the medium. Uniformly high c-jun, jun-B, and c-fos RNA transcript levels were observed in melanocytes cultivated in complete medium. Higher levels of c-jun RNA transcripts and low levels of c-fos RNA transcripts were observed in melanocytes cultivated in plain medium. In contrast, a range of c-jun, jun-B, and c-fos RNA transcript levels was detected in metastatic melanoma cell strains cultivated in medium with or without serum. In general, an increase in jun-B and c-fos RNA transcript expression and a decrease in c-jun RNA transcript expression was observed in metastatic melanomas compared to neonatal melanocytes. These data suggest a potential role for c-jun, jun-B, and c-fos genes in the transformation of melanocytes to malignant melanoma.
                  Cover page: Expression of c-jun, jun-B, and c-fos Proto-Oncogenes in Human Primary Melanocytes and Metastatic MelanomasCreative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2009)
                  Fog drip is a crucial water source for plants in many ecosystems, including a number of global biodiversity hotspots. In California, dozens of rare, drought-sensitive plant species are endemic to coastal areas where the dominant summer moisture source is fog. Low clouds that provide water to these semi-arid ecosystems through fog drip can also sharply reduce evaporative water losses by providing shade. We quantified the relative hydrological importance of cloud shading vs. fog drip. We then examined how both factors influence the range dynamics of an apparently fog-dependent plant species spanning a small-scale cloud gradient. The study area is on Santa Cruz Island off the coast of southern California. It is near the southern range limit of bishop pine (Pinus muricata D. Don), a tree endemic to the coasts of California and Baja, Mexico. We measured climate across a pine stand along a 7 km, coastal-inland elevation transect. Short-term (1-5 years) monitoring and remote sensing data revealed strong climatic gradients driven primarily by cloud cover. Long-term (102 years) effects of these gradients were estimated using a water balance model. We found that shade from persistent low clouds near the coast reduced annual drought stress by 22-40% compared with clearer conditions further inland. Fog drip at higher elevations provided sufficient extra water to reduce annual drought stress by 20-36%. Sites located at both high elevation and nearer the coast were subject to both effects. Together, these effects reduced average annual drought stress by 56% and dramatically reduced the frequency of severe drought over the last century. At lower elevation (without appreciable fog drip) and also near the inland edge of the stand (with less cloud shading) severe droughts episodically kill most pine recruits, thereby limiting the local range of this species. Persistent cloud shading can influence hydrology as much as fog drip in cloud-affected ecosystems. Understanding the patterns of both cloud shading and fog drip and their respective impacts on ecosystem water budgets is necessary to fully understand past species range shifts and to anticipate future climate change-induced range shifts in fog-dependent ecosystems.
                    • Article
                    LBL Publications (2010)
                      Cover page: Site Determination and Magnetism of Mn Doping in Protein Encapsulated Iron Oxide Nanoparticles
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