Characterization of the Microcystis Bloom and Its Nitrogen Supply in San Francisco Estuary Using Stable Isotopes

Accurate estimates of freshwater flow to the San Francisco Estuary are important in successfully regulating this water body, in protecting its beneficial uses, and in accurately modeling its hydrodynamic and water-quality transport regime. For regulatory purposes, freshwater flow to the estuary is not directly measured; rather, it is estimated from a daily balance of upstream Delta inflows, exports, and in-Delta water use termed the net Delta outflow index (NDOI). Field research in the 1960s indicated that NDOI estimates are biased low in summer–fall and biased high in winter–spring as a result of conflating Delta island evapotranspiration estimates with the sum of ungauged hydrologic interactions between channels and islands referred to as net channel depletions. In this work, we employed a 50-year observed salinity record along with gauged tidal flows and an ensemble of five empirical flow-salinity (X2) models to test whether a seasonal bias in Delta outflow estimates could be inferred. We accomplished this objective by conducting statistical analyses and evaluating whether model skill could be improved through seasonal NDOI flow adjustments. Assuming that model residuals are associated with channel depletion uncertainty, our findings corroborate the 1960s research and suggest that channel depletions are biased low in winter months (i.e., NDOI is biased high) and biased high in late summer and early fall months (i.e., NDOI is biased low). The magnitude of seasonal bias, which can reach 1,000 cfs, is a small percentage of typical winter outflow but represents a significant percentage of typical summer outflow. Our findings were derived from five independently developed models, and are consistent with the physical understanding of water exchanges on the islands. This work provides motivation for improved characterization of these exchanges to improve Delta outflow estimates, particularly during drought periods when water supplies are scarce and must be carefully managed.

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Supporting Restoration Decisions through Integration of Tree-Ring and Modeling Data: Reconstructing Flow and Salinity in the San Francisco Estuary over the Past Millennium

Water ◽

10.3390/w13152139 ◽

2021 ◽

Vol 13 (15) ◽

pp. 2139

Author(s):

Paul H. Hutton ◽

David M. Meko ◽

Sujoy B. Roy

Keyword(s):

San Francisco ◽

Tree Ring ◽

San Francisco Estuary ◽

Salinity Intrusion ◽

Estuarine Ecosystem ◽

Freshwater Flow ◽

The Past ◽

Decadal Scale ◽

Tree Ring Data ◽

Past Millennium

This work presents updated reconstructions of watershed runoff to San Francisco Estuary from tree-ring data to AD 903, coupled with models relating runoff to freshwater flow to the estuary and salinity intrusion. We characterize pre-development freshwater flow and salinity conditions in the estuary over the past millennium and compare this characterization with contemporary conditions to better understand the magnitude and seasonality of changes over this time. This work shows that the instrumented flow record spans the range of runoff patterns over the past millennium (averaged over 5, 10, 20 and 100 years), and thus serves as a reasonable basis for planning-level evaluations of historical hydrologic conditions in the estuary. Over annual timescales we show that, although median freshwater flow to the estuary has not changed significantly, it has been more variable over the past century compared to pre-development flow conditions. We further show that the contemporary period is generally associated with greater spring salinity intrusion and lesser summer–fall salinity intrusion relative to the pre-development period. Thus, salinity intrusion in summer and fall months was a common occurrence under pre-development conditions and has been moderated in the contemporary period due to the operations of upstream reservoirs, which were designed to hold winter and spring runoff for release in summer and fall. This work also confirms a dramatic decadal-scale hydrologic shift in the watershed from very wet to very dry conditions during the late 19th and early 20th centuries; while not unprecedented, these shifts have been seen only a few times in the past millennium. This shift resulted in an increase in salinity intrusion in the first three decades of the 20th century, as documented through early records. Population growth and extensive watershed modification during this period exacerbated this underlying hydrologic shift. Putting this shift in the context of other anthropogenic drivers is important in understanding the historical response of the estuary and in setting salinity targets for estuarine restoration. By characterizing the long-term behavior of San Francisco Estuary, this work supports decision-making in the State of California related to flow and salinity management for restoration of the estuarine ecosystem.

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Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00125-2 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Preeti Anand ◽

Jay Prakash Pandey ◽

Dev Mani Pandey

Keyword(s):

San Francisco ◽

Tertiary Structure ◽

Polyacrylamide Gel Electrophoresis ◽

Sodium Dodecyl ◽

Evolutionary Genetics ◽

Imaging Analysis ◽

Silk Cocoon ◽

Natural Color ◽

Sds Page

Abstract Background Cocoonase is a proteolytic enzyme that helps in dissolving the silk cocoon shell and exit of silk moth. Chemicals like anhydrous Na2CO3, Marseille soap, soda, ethylene diamine and tartaric acid-based degumming of silk cocoon shell have been in practice. During this process, solubility of sericin protein increased resulting in the release of sericin from the fibroin protein of the silk. However, this process diminishes natural color and softness of the silk. Cocoonase enzyme digests the sericin protein of silk at the anterior portion of the cocoon without disturbing the silk fibroin. However, no thorough characterization of cocoonase and sericin protein as well as imaging analysis of chemical- and enzyme-treated silk sheets has been carried out so far. Therefore, present study aimed for detailed characterization of cocoonase and sericin proteins, phylogenetic analysis, secondary and tertiary structure prediction, and computational validation as well as their interaction with other proteins. Further, identification of tasar silkworm (Antheraea mylitta) pupa stage for cocoonase collection, its purification and effect on silk sheet degumming, scanning electron microscope (SEM)-based comparison of chemical- and enzyme-treated cocoon sheets, and its optical coherence tomography (OCT)-based imaging analysis have been investigated. Various computational tools like Molecular Evolutionary Genetics Analysis (MEGA) X and Figtree, Iterative Threading Assembly Refinement (I-TASSER), self-optimized predicted method with alignment (SOPMA), PROCHECK, University of California, San Francisco (UCSF) Chimera, and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) were used for characterization of cocoonase and sericin proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein purification using Sephadex G 25-column, degumming of cocoon sheet using cocoonase enzyme and chemical Na2CO3, and SEM and OCT analysis of degummed cocoon sheet were performed. Results Predicted normalized B-factors of cocoonase and sericin with respect to α and β regions showed that these regions are structurally more stable in cocoonase while less stable in sericin. Conserved domain analysis revealed that B. mori cocoonase contains a trypsin-like serine protease with active site range 45 to 180 query sequences while substrate binding site from 175 to 200 query sequences. SDS-PAGE analysis of cocoonase indicated its molecular weight of 25–26 kDa. Na2CO3 treatment showed more degumming effect (i.e., cocoon sheet weight loss) as compared to degumming with cocoonase. However, cocoonase-treated silk cocoon sheet holds the natural color of tasar silk, smoothness, and luster compared with the cocoon sheet treated with Na2CO3. SEM-based analysis showed the noticeable variation on the surface of silk fiber treated with cocoonase and Na2CO3. OCT analysis also exemplified the variations in the cross-sectional view of the cocoonase and Na2CO3-treated silk sheets. Conclusions Present study enlightens on the detailed characteristics of cocoonase and sericin proteins, comparative degumming activity, and image analysis of cocoonase enzyme and Na2CO3 chemical-treated silk sheets. Obtained findings illustrated about use of cocoonase enzyme in the degumming of silk cocoon at larger scale that will be a boon to the silk industry.

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Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

Estuaries and Coasts ◽

10.1007/s12237-020-00880-4 ◽

2021 ◽

Author(s):

Nicole M. Aha ◽

Peter B. Moyle ◽

Nann A. Fangue ◽

Andrew L. Rypel ◽

John R. Durand

Keyword(s):

San Francisco ◽

Growth Rates ◽

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Nursery Habitat ◽

San Francisco Estuary ◽

Rice Fields ◽

Fish Growth ◽

Juvenile Chinook Salmon ◽

Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

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