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Open Access Publications from the University of California

Scholarly Works (11 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2025)

Access to safe and affordable drinking water remains a persistent global challenge, particularly for underdeveloped and remote regions. Local groundwater is often served as the only primary and reliable source of drinking water for communities in remote or under-resourced regions. However, groundwater supplies may be impaired due to the presence of various naturally occurring contaminants such as nitrates, arsenic, and boron. Groundwater contamination and elevated total dissolved solids (TDS) concentrations can also result from anthropogenic activities such as agricultural runoff and septic system leaching or from natural geophysical processes such as saltwater intrusion.

Elevated concentrations of nitrate and salinity in drinking water have been linked to an increased risk of certain cancers, and cardiovascular diseases respectively. In the U.S., the Environmental Protection Agency (EPA) has established a maximum contaminant level (MCL) of 10 mg/L for nitrate as nitrogen and a secondary contaminant level (SMCL) of 500 mg/L for TDS as critical thresholds for protecting public health and water quality. Recently, the flexible reverse osmosis (FLERO) system, a configuration of conventional reverse osmosis (RO) water treatment developed and operated by the University of California, Los Angeles (UCLA) Water Technology Research (WaTeR) Center, was demonstrated to be effective for water treatment and desalination. However, there remains a need to assess its performance, affordability, and long-term viability for wellhead treatment in small, remote, disadvantaged communities (DACs). Accordingly, a technoeconomic assessment (TEA) was conducted based on operational and financial data from three deployed RO-based distributed wellhead water treatment and desalination (DWTD) systems to evaluate their performance, reliability, and affordability as a viable approach for producing safe drinking water in DACs. The TEA was structured into three phases: (i) characterization of the study communities and DWTD systems, (ii) evaluation of system performance, and (iii) analysis of site-specific capital and operational costs. First, community demographics, infrastructure upgrades, and DWTD systems was conducted to contextualize system performance and cost. Second, water production, treatment efficiency, and energy consumption for each site was analyzed based on acquired high-resolution operational data. Finally, the capital, operational, and maintenance expenditures were determined to calculate the levelized cost of treated water (LCoW) for each DWTD system. The local water supplies of the three study DACs, located in Salinas Valley, California, were contaminated with nitrate at levels ( 12–87 mg/L as NO_3^--N) above the California MCL of 10 mg/L as NO_3^--N, and had elevated water salinity (~600–1,600 mg/L total dissolved solids(TDS)) above the SMCL of 500 mg/L TDS. Reliable DWTD operation provided treated water quality, with respect to nitrate and salinity, in the range of 0.5–6.3 mg/L mg/L as NO_3^--N and 57–161 mg/L TDS, respectively, which were well below the respective MCL and SMCL. The levelized cost of water treatment was determined to be in the range of ~$2/m3 - $2.9/m3 which aligns with typical residential water costs in California and in the study region, and monthly residential water cost ($39-$74/residential unit/month) was also within the range in California. The study showcased the DWTD approach as a viable and potentially scalable solution for upgrading the impaired local potable water supply of communities lacking centralized water delivery infrastructure. However, streamlined permitting processes and standardized regulatory frameworks are critical to promoting wider adoption and maximizing the socio-economic benefits of the DWTD approach. Moreover, DACs are likely to require government subsidies to cover the capital expenditures of DWTD systems in addition to upgrade of site infrastructure.

    Cover page: Technoeconomic Assessment of Membrane-Based Distributed Wellhead Water Treatment and Desalination Systems
    • Thesis
    • Peer Reviewed
    UC Santa Cruz Electronic Theses and Dissertations (2018)

    ABSTRACT

    LOS CLAROSCUROS DEL CAFÉ: SOCIOECOLOGICAL COMPLEXITIES IN THE COFFEE-BIODIVERSITY NEXUS IN SOUTHERN MEXICO

    María Estelí Jiménez Soto

    Coffee is one of the most demanded commodities worldwide, supporting the livelihoods of 25 million families. Coffee has been traditionally cultivated within biodiversity hotspots, making these ideal places for biodiversity conservation. Research has pointed out that biodiverse coffee systems support biodiversity and ecosystem functions. However, less is known about the specific ecological mechanisms supporting higher biodiversity and abundance of natural enemies of coffee pests in complex agroecosystems. Resource heterogeneity could be an important factor for arthropod communities; yet, this is still an ongoing scientific exploration in coffee systems. A second area of attention in coffee studies comprises human perceptions of the associated biodiversity in coffee agroecosystems. Most studies highlight the importance of biodiverse coffee smallholdings in delivering food security and contribute to livelihoods of peasant households. However, farm workers are a marginalized sector within the coffee production chain, and much less work has examined the lived-experience of farm workers in coffee agroecosystems. I disentangle the socio-ecological complexities of coffee plantations through three disciplines: agroecology, political ecology, and multi-species ecologies. I examine coffee plantations as spaces constructed by the actions of human and non-human entities, the ecological meanings and narratives constructed from our scientific endeavors, market forces, and peoples’ everyday lived experiences. My research takes place in the Soconusco region in Mexico, a well-known coffee-producing region in the country. The methodologies I use include observations, field and laboratory experiments, ethnographic research, and participant observation in the coffee plantation system. In my work, I demonstrate how ecological mechanisms and abiotic factors drive species diversity and interactions in shaded-coffee plantations, focusing primarily on ants, an important group of natural enemies in coffee systems. I show that diversity of nesting resources drive species coexistence through niche partitioning. I demonstrate that the availability of nectar resources influence colony reproduction. I show that the availability of connectivity resources at the local scale relate to biological pest control of the coffee berry borer, the most important insect coffee pest worldwide. Finally, I present the contradictions and social struggles that arise when conservation narratives meet the everyday-lived-experience of farmworkers in organic shade-grown coffee plantations in Southeast Mexico.

      Cover page: Los Claroscuros del Café: Socioecological Complexities in the Coffee-Biodiversity Nexus in Southern Mexico
      • Article
      • Peer Reviewed
      LBL Publications (2019)
      Plants frequently incorporate the monosaccharide l-fucose (Fuc; 6-deoxy-l-galactose) into glycans and glycopolymers located in diverse cellular locations. The incorporation of Fuc onto these varied glycans is carried out by fucosyltransferases (FUTs), that make up a protein superfamily with equally varied and diverse functions. The structures wherein Fuc is found have numerous proposed and validated functions, ranging from plant growth and development, cell expansion, adhesion, and signaling, to energy metabolism, among others. FUTs from several different plant species have been identified and described; however, very few of them have been extensively characterized biochemically and biologically. In this review, we summarize plant FUTs that have been biochemically characterized and biologically investigated for associated phenotypes, offering greater insight and understanding into the physiological importance of Fuc in plants and in plant cell wall structures, glycans, and proteins.
        Cover page: Plant Fucosyltransferases and the Emerging Biological Importance of Fucosylated Plant Structures
        • Peer Reviewed
        LBL Publications (2023)
          Cover page: Chapter 4 Functional genomics of Chlamydomonas reinhardtiiCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2015)

          Background

          Swarming motility and biofilm formation are opposite, but related surface-associated behaviors that allow various pathogenic bacteria to colonize and invade their hosts. In Sinorhizobium meliloti, the alfalfa endosymbiont, these bacterial processes and their relevance for host plant colonization are largely unexplored. Our previous work demonstrated distinct swarming abilities in two S. meliloti strains (Rm1021 and GR4) and revealed that both environmental cues (iron concentration) and bacterial genes (fadD, rhb, rirA) play crucial roles in the control of surface motility in this rhizobial species. In the current study, we investigate whether these factors have an impact on the ability of S. meliloti to establish biofilms and to colonize host roots.

          Results

          We found that strain GR4, which is less prone to translocate on solid surfaces than strain Rm1021, is more efficient in developing biofilms on glass and plant root surfaces. High iron conditions, known to prevent surface motility in a wild-type strain of S. meliloti, promote biofilm development in Rm1021 and GR4 strains by inducing the formation of more structured and thicker biofilms than those formed under low iron levels. Moreover, three different S. meliloti mutants (fadD, rhb, and rirA) that exhibit an altered surface translocation behavior compared with the wild-type strain, establish reduced biofilms on both glass and alfalfa root surfaces. Iron-rich conditions neither rescue the defect in biofilm formation shown by the rhb mutant, which is unable to produce the siderophore rhizobactin 1021 (Rhb1021), nor have any impact on biofilms formed by the iron-response regulator rirA mutant. On the other hand, S. meliloti FadD loss-of-function mutants do not establish normal biofilms irrespective of iron levels.

          Conclusions

          Our studies show that siderophore Rhb1021 is not only required for surface translocation, but also for biofilm formation on glass and root surfaces by strain Rm1021. In addition, we present evidence for the existence of control mechanisms that inversely regulate swarming and biofilm formation in S. meliloti, and that contribute to efficient plant root colonization. One of these mechanisms involves iron levels and the iron global regulator RirA. The other mechanism involves the participation of the fatty acid metabolism-related enzyme FadD.
            Cover page: Biofilm formation assessment in Sinorhizobium meliloti reveals interlinked control with surface motility
            • Article
            • Peer Reviewed
            Joint Genome Institute (2021)

            ABSTRACT

            Advances in bioengineering have enabled numerous bio-based commodities. Yet most traditional approaches do not extend beyond a single metabolic pathway and do not attempt to modify gene regulatory networks in order to buffer metabolic perturbations. This is despite access to near universal technologies allowing genome-scale engineering. To help overcome this limitation, we have developed a pipeline enabling analysis of Transcription Regulation Integrated with MEtabolic Regulation (TRIMER). TRIMER utilizes a Bayesian network (BN) inferred from transcriptomic data to model the transcription factor regulatory network. TRIMER then infers the probabilities of gene states that are of relevance to the metabolism of interest, and predicts metabolic fluxes resulting from deletion of transcription factors at the genome scale. Additionally, we have developed a simulation framework to mimic the TF-regulated metabolic network, capable of generating both gene expression states and metabolic fluxes, thereby providing a fair evaluation platform for benchmarking models and predictions. Here, we present this computational pipeline. We demonstrate TRIMER’s applicability to both simulated and experimental data and show that it outperforms current approaches on both data types.
              Cover page: TRIMER: Transcription Regulation Integrated with MEtabolic Regulation
              • Article
              • Peer Reviewed
              LBL Publications (2021)
              There has been extensive research in predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes arising from interactions among different biomolecules. For more accurate and robust prediction of target metabolic behavior under different conditions, not only metabolic reactions but also the genetic regulatory relationships involving transcription factors (TFs) affecting these metabolic reactions should be modeled. We have developed a modeling and simulation pipeline enabling the analysis of Transcription Regulation Integrated with Metabolic Regulation: TRIMER. TRIMER utilizes a Bayesian network (BN) inferred from transcriptomes to model the transcription factor regulatory network. TRIMER then infers the probabilities of the gene states relevant to the metabolism of interest, and predicts the metabolic fluxes and their changes that result from the deletion of one or more transcription factors at the genome scale. We demonstrate TRIMER's applicability to both simulated and experimental data and provide performance comparison with other existing approaches.
                • Article
                • Peer Reviewed
                LBL Publications (2023)
                TRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with a transcription factor-gene regulatory network (TRN), which is modeled through a Bayesian network (BN). In this article, we focus on sensitivity analysis of metabolic flux prediction for uncertainty quantification of BN structures for TRN modeling in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty given transcriptomic expression data. With that, we analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yields of interest. The obtained sensitivity analyses can guide optimal experimental design (OED) to help acquire new data that can enhance TRN modeling and achieve specific metabolic engineering objectives, including metabolite yield alterations. We have performed small- and large-scale simulated experiments, demonstrating the effectiveness of our developed sensitivity analysis strategy for BN structure learning to quantify the edge importance in terms of metabolic flux prediction uncertainty reduction and its potential to effectively guide OED.
                  Cover page: Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction.Creative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  LBL Publications (2022)
                  This protocol explains the pipeline for condition-dependent metabolite yield prediction using Transcription Regulation Integrated with MEtabolic Regulation (TRIMER). TRIMER targets metabolic engineering applications via a hybrid model integrating transcription factor (TF)-gene regulatory network (TRN) with a Bayesian network (BN) inferred from transcriptomic expression data to effectively regulate metabolic reactions. For E. coli and yeast, TRIMER achieves reliable knockout phenotype and flux predictions from the deletion of one or more TFs at the genome scale. For complete details on the use and execution of this protocol, please refer to Niu et al. (2021).
                    Cover page: Protocol for condition-dependent metabolite yield prediction using the TRIMER pipelineCreative Commons 'BY-NC-ND' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2025)
                    Techno-economic analysis of distributed wellhead water treatment and desalination (DWTD) systems was carried out based on a three-year field study in three small, disadvantaged communities (DACs) to evaluate the reliability and affordability of upgrading their impaired well water. The local water supplies of the three study DACs, located in Salinas Valley, California, were contaminated with nitrate at levels (∼ 12-87 mg/L NO3--N) above the California maximum contaminant level (MCL) of 10 mg/L NO3--N, and had elevated water salinity (∼600-1,600 mg/L total dissolved solids(TDS)) above its secondary MCL (SMCL) of 500 mg/L TDS. Well water nitrate removal and salinity reduction were accomplished via reverse osmosis (RO) based DWTD systems that operated autonomously, supported by remote monitoring and supervisory cyberinfrastructure. Reliable DWTD operation provided treated water quality, with respect to nitrate and salinity, in the range of 0.5-6.3 mg/L NO3--N and 57-161 mg/L TDS, respectively, which were well below the respective MCL and SMCL. The levelized cost of water treatment was in the range of ∼$2/m3- $2.9/m3 which aligns with typical residential water costs in California and in the study region, and monthly residential water costs ($39-$74/residential unit/month) were also within the range in California. The study showcased the DWTD approach as a viable and potentially scalable solution for upgrading impaired local potable water supply of communities lacking centralized water delivery infrastructure. However, streamlined permitting processes and standardized regulatory frameworks are critical to promoting wider adoption and maximizing the socio-economic benefits of the DWT approach. Moreover, DACs are likely to require government subsidies in order to cover the CapEx of DWTD systems in addition to upgrade of site infrastructure.
                      Cover page: Techno-economic assessment of distributed wellhead RO water treatment for nitrate removal and salinity reduction: A field study in small disadvantaged communitiesCreative Commons 'BY' version 4.0 license
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