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Open Access Publications from the University of California

Scholarly Works (12 results)

  • Article
  • Peer Reviewed
Research Theses and Dissertations (2010)

Cyclomarins are potent anti-inflammatory cyclic peptides originally encountered in the estuarine streptomycete, strain CNB-982, and subsequently isolated from the marine obligate actinobacterium Salinispora arenicola CNS-205 along with the truncated antibacterial diketopiperazine cyclomarazines. The cyclomarins are composed of seven amino acid residues, two of which are of unique biosynthetic interest, 2-amino-3,5-dimethylhex-4-enoic acid (ADH), which has never been reported as a constituent of any peptide, and N-(1,1-dimethyl-1-allyl)-tryptophan, which is a rare example of the prenylation of a bacterial nonribosomalpeptide. The N-prenylated tryptophan residue, along with δ-hydroxyleucine, is present in both the cyclomarins and cyclomarazines, suggesting a common biosynthetic origin.

Because of the unique structural features of ADH and N-(1,1-dimethyl-1-allyl)-tryptophan, along with the extensive tailoring of the remaining residues of cyclomarin, we initiated the interrogation of the biosynthetic machinery behind cyclomarin and cyclomarazine synthesis. We were able to determine the basic steps of cyclomarin and cyclomarazine production, along with insights into how the two unique amino acids are synthesized. Furthermore, we were able to identify the oxidative enzymes involved in tailoring both peptides. Analysis of the genome sequence of S. arenicola CNS-205 revealed the cym biosynthetic gene cluster, which is dominated by cymA, encoding for a seven module nonribosomal peptide synthetase. Downstream of cymA are the genes for N-(1,1- dimethyl-1-allyl)- tryptophan synthesis via the prenyltransferase CymD, and ADH via cymE-H. CymEF is an aldolase/dehydrogenase pair utilized for the key C-C bond forming step of ADH synthesis, along with a methyltransferase CymG, and a dehydrogenase CymH. Upstream of cymA is the Fe2+/α-ketoglutarate dependent leucine δ-oxygenase CymW, and three cytochrome P450s oxidases, CymO, CymS, and CymV. Bioinformatic analysis coupled with in vivo mutagenesis confirmed the role of Cym W along with CymS as a N-(1,1-dimethyl-1-allyl)- tryptophan β-hydroxylase, and CymV as a N-(1,1-dimethyl-2,3- epoxypropyl)-tryptophan epoxidase, and suggested the function of CymO as a phenylalanine β-hydroxylase . In addition to establishing the function of the xxiv aforementioned enzymes, we were able to generate the novel N-(1-methyl)-tryptophan and N-(1-propargyl)-tryptophan analogs of both sized peptides in the cymD deficient mutant, confirming the preference for N-alkylated tryptophan residues and the amenability of cyclomarin and cyclomarazine to derivatization via mutasynthesis.

    Cover page: Biosynthesis and Engineering of Cyclomarin and Cyclomarazine: Prenylated, Non-Ribosomal Cyclic Peptides of Marine Actinobacterial Origin
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2010)
    Cyclomarins are potent anti-inflammatory cyclic peptides originally encountered in the estuarine streptomycete, strain CNB-982, and subsequently isolated from the marine obligate actinobacterium Salinispora arenicola CNS-205 along with the truncated antibacterial diketopiperazine cyclomarazines. The cyclomarins are composed of seven amino acid residues, two of which are of unique biosynthetic interest, 2-amino-3,5-dimethylhex-4-enoic acid (ADH), which has never been reported as a constituent of any peptide, and N-(1,1-dimethyl-1-allyl)- tryptophan, which is a rare example of the prenylation of a bacterial non-ribosomal peptide. The N-prenylated tryptophan residue, along with [delta]-hydroxyleucine, is present in both the cyclomarins and cyclomarazines, suggesting a common biosynthetic origin. Because of the unique structural features of ADH and N-(1,1-dimethyl-1-allyl)- tryptophan, along with the extensive tailoring of the remaining residues of cyclomarin, we initiated the interrogation of the biosynthetic machinery behind cyclomarin and cyclomarazine synthesis. We were able to determine the basic steps of cyclomarin and cyclomarazine production, along with insights into how the two unique amino acids are synthesized. Furthermore, we were able to identify the oxidative enzymes involved in tailoring both peptides. Analysis of the genome sequence of S. arenicola CNS-205 revealed the cym biosynthetic gene cluster, which is dominated by cymA, encoding for a seven module non- ribosomal peptide synthetase. Downstream of cymA are the genes for N-(1,1-dimethyl-1-allyl)- tryptophan synthesis via the prenyltransferase CymD, and ADH via cymE-H. CymEF is an aldolase/dehydrogenase pair utilized for the key C-C bond forming step of ADH synthesis, along with a methyltransferase CymG, and a dehydrogenase CymH. Upstream of cymA is the Fe²⁺/[alpha]-ketoglutarate dependent leucine [delta]-oxygenase CymW, and three cytochrome P450s oxidases, CymO, CymS, and CymV. Bioinformatic analysis coupled with in vivo mutagenesis confirmed the role of Cym W along with CymS as a N-(1,1-dimethyl-1-allyl)- tryptophan [beta]-hydroxylase, and CymV as a N-(1,1- dimethyl-2,3-epoxypropyl)-tryptophan epoxidase, and suggested the function of CymO as a phenylalanine [beta]- hydroxylase . In addition to establishing the function of the aforementioned enzymes, we were able to generate the novel N-(1-methyl)-tryptophan and N-(1-propargyl)- tryptophan analogs of both sized peptides in the cymD deficient mutant, confirming the preference for N- alkylated tryptophan residues and the amenability of cyclomarin and cyclomarazine to derivatization via mutasynthesis
      Cover page: Biosynthesis and engineering of cyclomarin and cyclomarazine : prenylated, non- ribosomal cyclic peptides of marine actinobacterial origin
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2022)
      Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought.
        Cover page: Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance.
        • Article
        • Peer Reviewed
        San Francisco Estuary and Watershed Science, Volume 21, Issue 2 (2023)
        Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented (2018, 2020). In augmented years, we detected higher total zooplankton abundance and altered community composition in Suisun Bay and Suisun Marsh. Increased freshwater in these regions was associated with higher abundance of Pseudodiaptomus forbesi, a preferred prey of Delta Smelt, while species associated with higher salinities—Acartiella sinensis and Tortanus dextrilobatus—were less abundant. Thus, autumn flow augmentations can influence foraging habitat and prey availability for Delta Smelt, underscoring the complex responses of estuarine zooplankton communities to changes in response to flow and salinity regimes. This study is management- relevant because it shows that important Delta Smelt prey items increase in downstream regions when X2 is lower. Whether that results in a response in Delta Smelt abundance remains to be seen.
          Cover page: Flow Augmentations Modify an Estuarine Prey FieldCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2021)

          Background

          The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species' vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE.

          Methods

          Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt.

          Results

          Overall, otolith size varied linearly with fish size (from 10-60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0-30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such experimental assessments across multiple developmental stages are key steps toward assessing confidence in otolith-derived metrics that are often used to assess the dynamics of wild fish populations.
            Cover page: Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish
            • Article
            • Peer Reviewed
            San Francisco Estuary and Watershed Science, Volume 22, Issue 2 (2024)
            The Delta Smelt is a largely zooplank­tivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites, were the most prevalent contaminants detected in 2017 and 2018, and a variety of contaminants associated with the rice harvest were detected in 2019. No acute toxicity was observed during any exposure, but we observed negative effects in the livers of Delta Smelt exposed to agricultural water from the Toe Drain and Cache Slough during a 2019 pulse flow action, which coincided with elevated detections and concentrations of organic pesticides. Other noteworthy sub-lethal effects, likely occurring in response to contaminant mixtures, included severe gill lesions in Delta Smelt exposed to Decker Island water in 2019. In the drier year of 2018, lesions were generally mild or absent. Thus, the trade-offs between increased habitat availability and contaminant loading may provide one explanation for why Delta Smelt abundance does not consistently respond positively to outflow.
            • 2 supplemental PDFs
            Cover page: Sub-Lethal Responses of Delta Smelt to Contaminants Under Different Flow ConditionsCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2019)
            A captive breeding programme was developed in 2008 for delta smelt Hypomesus transpacificus in reaction to dramatic population decline over several decades. We took 526 sub-adult captive-reared delta smelt and cultured them for 200 days without providing artificial food or water quality management to assess their performance once released in the wild. The results indicated captive-reared sub-adult delta smelt could survive in a semi-natural environment with uncontrolled water quality and naturally produced wild prey through spawning and into their post spawning phase.
              Cover page: A pilot study of the performance of captive‐reared delta smelt Hypomesus transpacificus in a semi‐natural environment
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2022)
              Condition indices are key predictors of health and fitness in wild fish populations. Variation in body condition, therefore, can be used to identify stressful conditions that may impact endangered species, such as California’s endemic Delta Smelt (Hypomesus transpacificus McAllister, 1963). Here, we examined spatiotemporal variation in the condition indices of > 1600 Delta Smelt collected over nine years (2011–2019), a period characterized by tremendous variability in hydrodynamic and water quality conditions. The population exhibited low hepatosomatic index (HSI) and condition factor (CF) during September/October/November (fall), and both condition indices declined over the nine-year study during fall. HSI was positively correlated with indicators of pelagic productivity (e.g., Chlorophyll a, zooplankton biomass, and proximity to tidal wetlands), whereas CF was negatively correlated with temperature, peaking at a relatively cool 10–13 °C. In sum, seasonal and interannual variation in body condition corresponded most strongly with pelagic productivity and water temperature, with little correlation to freshwater outflow. Management actions that increase pelagic productivity, restore and freshen productive wetlands during late summer-fall, and reduce water temperatures overall are likely to benefit condition indices and, therefore, fitness of the Delta Smelt population.
                Cover page: Patterns and predictors of condition indices in a critically endangered fish
                • Article
                • Peer Reviewed
                San Francisco Estuary and Watershed Science, Volume 16, Issue 3 (2018)

                An extreme decline in Delta Smelt (Hypomesus transpacificus) abundance has led to a number of management actions to support this endangered species, including the development and refinement of culture techniques and the creation of a refuge population. The wild Delta Smelt population has diminished to the point that many in the scientific community believe population supplementation using cultured fish needs to be experimentally evaluated as a possible management tool. Concerns about supplementation include the effectiveness of this action, and its potential to divert attention and funding from other needed management actions such as habitat restoration. Here, we describe the outcomes of a 2-day workshop that described the current refuge population, and identified key issues for potential future use of cultured Delta Smelt for research and management. Expanded use of cultured Delta Smelt is controversial and requires consideration for complexities that include legal constraints and permitting requirements. Developing policies that allow for in situ experiments using cultured Delta Smelt appears to be a precursor for advancing policies that might allow supplementation actions. Releases of cultured fish, either experimentally or as a management action, clearly need to be conducted within an adaptive management program that is integrated with other strategies, including habitat restoration. We describe a general framework for evaluating the potential risks of supplementation and include suggestions for how to reduce risks and uncertainty. Overall, we conclude there is sufficient baseline information about Delta Smelt and the existing culture program to proceed with targeted field research that utilizes cultured fish. Finally, given the dire status of this species, we conclude that rapid progress toward the development of a viable and testable supplementation program must be a priority for Delta Smelt conservation.

                  Cover page: Considerations for the Use of Captive-Reared Delta Smelt for Species Recovery and ResearchCreative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2020)
                  There is an extensive literature establishing, validating, and quantifying a wide range of responses of fishes to fasting. Our study complements this work by comparing fed and unfed treatments of hatchery-raised Delta Smelt (Hypomesus transpacificus)-an imperiled fish that is endemic to the San Francisco Estuary and its tributaries in California, USA-across a diverse suite of endpoints over a two-month time series. The experiment was conducted at 15.9°C, and individuals were sampled at 12 time points as starvation became increasingly severe. We found that hepatosomatic index and condition factor were relatively sensitive to starvation, becoming significantly depressed at Day 4 and 7, respectively. Histological analysis of liver showed elevated cytoplasmic inclusion bodies at Day 7, followed by increased glycogen depletion, single cell necrosis, and hydropic vacuolar degeneration at Day 14, 21, and 28, respectively. Of four antioxidants measured, glutathione decreased at Day 4, superoxide dismutase increased at Day 14, catalase increased at Day 56, and glutathione peroxidase was not affected by starvation. The net result was a ~2-fold increase in lipid peroxidation (malondialdehyde) in fasted fish that was highly inconsistent through time. RNA to DNA ratio and triglycerides in muscle were relatively insensitive to starvation, only consistently decreasing with fasting after mortality began increasing in the 'No Feeding' treatment, at Day 21. Together, these results suggest that Delta Smelt mobilize hepatic energy stores far more rapidly than lipids in muscle when subjected to fasting, leading to rapid atrophy of liver and the development of cytoplasmic inclusion bodies-possibly autophagosomes-in hepatocytes.
                    Cover page: The health and condition responses of Delta Smelt to fasting: A time series experiment.
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