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San Francisco Bay Mercury Research Coordination Meeting February 23, 2005 Presentation- Introduction to the QA Program for Mercury Studies.2005. (146.49 KB)
San Francisco Bay Nutrient Management Strategy: Detailed Modeling Workplan for FY15-FY21. San Francisco Estuary Institute: Richmond, CA.2014. (1.66 MB)
The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality. Regional Studies in Marine Science 4.2016.
The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a novel partnership between regulatory agencies and the regulated community to provide the scientific foundation to manage water quality in the largest Pacific estuary in the Americas. The RMP monitors water quality, sediment quality and bioaccumulation of priority pollutants in fish, bivalves and birds. To improve monitoring measurements or the interpretation of data, the RMP also regularly funds special studies. The success of the RMP stems from collaborative governance, clear objectives, and long-term institutional and monetary commitments. Over the past 22 years, high quality data and special studies from the RMP have guided dozens of important decisions about Bay water quality management. Moreover, the governing structure and the collaborative nature of the RMP have created an environment that allowed it to stay relevant as new issues emerged. With diverse participation, a foundation in scientific principles and a continual commitment to adaptation, the RMP is a model water quality monitoring program. This paper describes the characteristics of the RMP that have allowed it to grow and adapt over two decades and some of the ways in which it has influenced water quality management decisions for this important ecosystem.
2018 RMP Bird Egg Monitoring Sampling and Analysis Plan. SFEI Contribution No. 891. San Francisco Estuary Institute: Richmond, CA.2018. (882.63 KB)
2018 RMP Detailed Workplan and Budget. San Francisco Estuary Institute : Richmond, CA.2017. (390.05 KB)
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 844. San Francisco Estuary Institute : Richmond, CA.2017. (1.68 MB)
2017 Margins Sediment Cruise Plan. SFEI Contribution No. 847. San Francisco Estuary Institute : Richmond, CA.2017. (919.33 KB)
Summary of Workshop on Monitoring for Acidification Threats in West Coast Estuaries: A San Francisco Bay Case Study.2017. (2.04 MB)
Recommendations for a Modeling Framework to Answer Nutrient Management Questions in the Sacramento-San Joaquin Delta. Central Valley Regional Water Quality Control Board: Rancho Cordova, CA.2016. (542.21 KB)
Status & Trends Monitoring Design: 2018 Update. San Francisco Estuary Institute : Richmond, CA.2018. (1.13 MB)
2018 Bay RMP Multi-Year Plan. SFEI Contribution No. 860. San Francisco Estuary Institute : Richmond, CA.2018. (3.88 MB)
Charter: Regional Monitoring Program for Water Quality in San Francisco Bay. SFEI Contribution No. 750. San Francisco Estuary Institute: Richmond, Calif.2015. (554.31 KB)
The overarching goal of the RMP is to collect data and communicate information about water quality in San Francisco Bay in support of management decisions. The RMP was created in 1993 through Regional Board Resolution No. 92-043 that directed the Executive Officer to implement a Regional Monitoring Plan in collaboration with permitted dischargers pursuant to California Water Code, Sections 13267, 13383, 13268, and 13385. The goal was to replace individual receiving water monitoring requirements for dischargers with a comprehensive Regional Monitoring Program.
The Program is guided by a Memorandum of Understanding (MOU) between the Regional Board and SFEI, first approved in 1996 and amended at various times since (see Appendix C of this Charter). Section VIII of the MOU states the roles and responsibilities of the Regional Board and SFEI in the implementation of the Program. Participating dischargers pay fees to the Program to comply with discharge permit requirements. The cost allocation schedule for Participants is described in Appendix B. The RMP provides an open forum for a wide range of Participant Groups and other Interested Parties to discuss contaminant issues, prioritize science needs, and monitor potential impacts of discharges on the Bay.
In support of the overarching goal described above, the following guiding principles define the intentions and expectations of RMP Participants. Implementation of the RMP will:
- Develop sound scientific information on water quality in the Bay;
- Prioritize funding decisions through collaborative discussions;
- Conduct decision-making in a transparent manner that consistently represents the diversity of RMP Participant interests;
- Utilize external science advisors for guidance and peer review;
- Maintain and make publicly available the data collected by the Program;
- Enhance public awareness and support by regularly communicating the status and trends of water quality in the Bay; and
- Coordinate with other monitoring and scientific studies in the Bay-Delta region to ensure efficiency.
Relative sensitivities of toxicity test protocols with the amphipods Eohaustorius estuarius and Ampelisca abdita. Ecotoxicology and Environmental Safety 69 (1), 24-31.2007.
General guidelines for using the sediment quality triad. Mar. Poll. Bull 34, 368-372 . SFEI Contribution No. 198.1997.
Sediment Quality Assessments in the San Francisco Estuary. SFEI Contribution No. 574. San Francisco Estuary Institute: Oakland, Ca.2008. (2.52 MB)
Low levels of agreement among experts using best professional judgment to assess benthic condition in the San Francisco Estuary and Delta. Ecological Indicators 12 (1), 167-173 . SFEI Contribution No. 636.2011. (177.24 KB)
Atlas of Sediment Contamination, Toxicity, and Benthic Assemblages in San Francisco Bay. SFEI Contribution No. 38. San Francisco Estuary Institute: Richmond, CA.1999.
Estimated Sediment Contaminant Concentrations Associated with Biological Impacts at San Diego Bay Cleanup Sites. SFEI Contribution No. 584. San Francisco Estuary Institute: Oakland, Ca.2009. (1.25 MB)
Research Recommendations for the San Francisco Estuary: Understanding the Ecosystem. SFEI Contribution No. 181. San Francisco Estuary Institue: Richmond, Ca. p 49.1994.
Biological Effects of Anthropogenic Contaminants in the San Francisco Estuary. Environmental Research 105, 156-174 . SFEI Contribution No. 495.2007. (528.14 KB)
Bioaccumulation of contaminants by bivalve molluscs in the vicinity of municipal wastewater discharges to San Francisco Bay: Wet season results, 1991/1992. SFEI Contribution No. 170. Aquatic Habitat Institute: Richmond, CA.1992.
Understanding Microplastic Levels, Pathways, and Transport in the San Francisco Bay Region. SFEI Contribution No. 950. San Francisco Estuary Institute: Richmond, CA.2019. (4.95 MB) (66.14 MB)
Microplastics (particles less than 5 mm) are ubiquitous and persistent pollutants in the ocean and a pervasive and preventable threat to the health of marine ecosystems. Microplastics come in a wide variety of shapes, sizes, and plastic types, each with unique physical and chemical properties and toxicological impacts. Understanding the magnitude of the microplastics problem and determining the highest priorities for mitigation require accurate measures of microplastic occurrence in the environment and identification of likely sources.
To develop critical baseline data and inform solutions, the San Francisco Estuary Institute and the 5 Gyres Institute have completed the first comprehensive regional study of microplastic pollution in a major estuary. This project supported multiple scientific components to develop improved knowledge about and characterization of microparticles and microplastics in San Francisco Bay and adjacent National Marine Sanctuaries, with the following objectives:
- Contribute to the development and standardization of sample collection and analysis methodology for microplastic transportation research.
- Determine a baseline for future monitoring of microplastics in San Francisco Bay surface water, sediment, and fish, and in ocean waters outside the Golden Gate.
- Characterize pathways by which microplastics enter the Bay, including urban stormwater and treated wastewater effluent.
- Investigate the contribution of Bay microplastics to the adjacent National Marine Sanctuaries through computer simulations.
- Communicate findings to regional stakeholders and the general public through meetings and educational materials.
- Facilitate evaluation of policy options for San Francisco Bay, with recommendations on source reduction.
This document presents the findings of this three-year project. A companion document, "San Francisco Bay Microplastics Project: Science-Supported Solutions and Policy Recommendations," has been developed by 5 Gyres using the findings of this study (Box and Cummins, 2019).
Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. 2017 Revision. SFEI Contribution No. 815. San Francisco Estuary Institute: Richmond, CA.2017. (5.51 MB)
Polybrominated Diphenyl Ethers (PBDEs) in San Francisco Bay: A Summary of Occurrence and Trends. SFEI Contribution No. 713. San Francisco Estuary Institute: Richmond, CA. p 62.2014. (2 MB)
Occurrence and Sources of Pesticides to Urban Wastewater and the Environment. In Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. Pesticides in Surface Water: Monitoring, Modeling, Risk Assessment, and Management. American Chemical Society: Washington, DC. pp 63-88.2019.
Municipal wastewater has not been extensively examined as a pathway by which pesticides contaminate surface water, particularly relative to the well-recognized pathways of agricultural and urban runoff. A state-of-the-science review of the occurrence and fate of current-use pesticides in wastewater, both before and after treatment, indicates this pathway is significant and should not be overlooked. A comprehensive conceptual model is presented to establish all relevant pesticide-use patterns with the potential for both direct and indirect down-the-drain transport. Review of available studies from the United States indicates 42 pesticides in current use. While pesticides and pesticide degradates have been identified in wastewater, many more have never been examined in this matrix. Conventional wastewater treatment technologies are generally ineffective at removing pesticides from wastewater, with high removal efficiency only observed in the case of highly hydrophobic compounds, such as pyrethroids. Aquatic life reference values can be exceeded in undiluted effluents. For example, seven compounds, including three pyrethroids, carbaryl, fipronil and its sulfone degradate, and imidacloprid, were detected in treated wastewater effluent at levels exceeding U.S. Environmental Protection Agency (US EPA) aquatic life benchmarks for chronic exposure to invertebrates. Pesticides passing through wastewater treatment plants (WWTPs) merit prioritization for additional study to identify sources and appropriate pollution-prevention strategies. Two case studies, diazinon and chlorpyrifos in household pesticide products, and fipronil and imidacloprid in pet flea control products, highlight the importance of identifying neglected sources of environmental contamination via the wastewater pathway. Additional monitoring and modeling studies are needed to inform source control and prevention of undesirable alternative solutions.
Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. 2015 Update. Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. SFEI Contribution No. 761. San Francisco Estuary Institute: Richmond, CA.2015. (870.96 KB)
About this Update
The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) has been investigating contaminants of emerging concern (CECs) since 2001. CECs can be broadly defined as synthetic or naturally occurring chemicals that are not regulated or commonly monitored in the environment but have the potential to enter the environment and cause adverse ecological or human health impacts.
The RMP Emerging Contaminants Workgroup (ECWG), established in 2006, includes representatives from RMP stakeholder groups, regional scientists, and an advisory panel of expert researchers that work together to address the workgroup's guiding management question – Which CECs have the potential to adversely impact beneficial uses in San Francisco Bay? The overarching goal of the ECWG is to develop cost-effective strategies to identify and monitor CECs to minimize impacts to the Bay.
To this end, the RMP published a CEC Strategy document in 2013 (Sutton et al. 2013). The strategy is a living document that guides RMP special studies on CECs, assuring continued focus on the issues of highest priority to the health of the Bay. A key focus of the strategy is a tiered risk and management action framework that guides future monitoring proposals. The strategy also features a multi-year plan indicating potential future research priorities.
This 2015 CEC strategy update features revised designations of CECs in the tiered risk and management action framework based on monitoring and research conducted since 2013. Brief summaries of relevant RMP findings are provided. In addition, a proposed multi-year plan for future RMP Special Studies on CECs is outlined. A full revision of the CEC strategy is anticipated in 2016.
Microplastic Monitoring and Science Strategy for San Francisco Bay. SFEI Contribution No. 798. San Francisco Estuary Institute: Richmond, Calif.2017. (17.38 MB)
Microplastic Contamination in San Francisco Bay - Fact Sheet. 2015, Revised 2016. SFEI Contribution No. 770.2016. (4.05 MB)
Characterization of brominated, chlorinated, and phosphate flame retardants in San Francisco Bay, an urban estuary. Science of the Total Environment 652, 212-223 . SFEI Contribution No. 859.2019.
Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely wide-ranging characterization of flame retardants was conducted, including polybrominated diphenyl ethers (PBDEs) and 52 additional brominated, chlorinated, or phosphate analytes, in water, sediment, bivalves, and harbor seal blubber of San Francisco Bay, a highly urbanized estuary once considered a hot spot for PBDE contamination. Among brominated flame retardants, PBDEs remained the dominant contaminants in all matrices, though declines have been observed over the last decade following their phase-out. Hexabromocyclododecane (HBCD) and other hydrophobic, brominated flame retardants were commonly detected at lower levels than PBDEs in sediment and tissue matrices. Dechlorane Plus (DP) and related chlorinated compounds were also detected at lower levels or not at all across all matrices. In contrast, phosphate flame retardants were widely detected in Bay water samples, with highest median concentrations in the order TCPP > TPhP > TBEP > TDCPP > TCEP. Concentrations in Bay water were often higher than in other estuarine and marine environments. Phosphate flame retardants were also widely detected in sediment, in the order TEHP > TCrP > TPhP > TDCPP > TBEP. Several were present in bivalves, with levels of TDCPP comparable to PBDEs. Only four phosphate flame retardants were detected in harbor seal blubber: TCPP, TDCPP, TCEP, and TPhP. Periodic, multi-matrix screening is recommended to track contaminant trends impacted by changes to flammability standards and manufacturing practices, with a particular focus on contaminants like TDCPP and TPhP that were found at levels comparable to thresholds for aquatic toxicity.
Microplastic contamination in the San Francisco Bay, California, USA. Marine Pollution Bulletin 109 . SFEI Contribution No. 769.2016.
Despite widespread detection of microplastic pollution in marine environments, data describing microplastic abundance in urban estuaries and microplastic discharge via treated municipal wastewater are limited. This study presents information on abundance, distribution, and composition of microplastic at nine sites in San Francisco Bay, California, USA. Also presented are characterizations of microplastic in final effluent from eight wastewater treatment plants, employing varying treatment technologies, that discharge to the Bay. With an average microplastic abundance of 700,000 particles/km2, Bay surface water appears to have higher microplastic levels than other urban waterbodies sampled in North America. Moreover, treated wastewater from facilities that discharge into the Bay contains considerable microplastic contamination. Facilities employing tertiary filtration did not show lower levels of contamination than those using secondary treatment. As textile-derived fibers were more abundant in wastewater, higher levels of fragments in surface water suggest additional pathways of microplastic pollution, such as stormwater runoff.
A Broad Scan of Bay Contaminants. San Francisco Estuary Institute: Richmond, CA.2015. (1.34 MB)
Declines in Polybrominated Diphenyl Ether Contamination of San Francisco Bay following Production Phase-Outs and Bans. Environmental Science and Technology 49 (2), 777-784 . SFEI Contribution No. 742.2015.
The RMP Emerging Contaminants Program - Fact Sheet. SFEI Contribution No. 778.2016. (249.12 KB)
Contaminants of Emerging Concern in San Francisco Bay: A Strategy for Future Investigations. San Francisco Estuary Institute: Richmond, CA.2013. (5.01 MB)
Selenium in White Sturgeon Tissues: 2015 Sturgeon Derby. SFEI Contribution No. 834.2017. (1.85 MB)
Contaminant Concentrations in Sport Fish from San Francisco Bay, 2014. SFEI Contribution No. 806.2017. (1.42 MB)
Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study. SFEI Contribution No. 897. San Francisco Estuary Institute: Richmond, CA.2019. (1.17 MB)
This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) tissues collected during the 2015-2017 Sturgeon Derby events in North San Francisco Bay. The goal of this study was to investigate the distribution of selenium among sturgeon tissues to inform the toxicological and regulatory interpretation of selenium measured in non-lethally collected tissues, including muscle plugs and fin rays. This technical report provides documentation of the study and presents its major findings.
RMP Field Sampling Report 2016. SFEI Contribution No. 826. San Francisco Estuary Institute: Richmond, CA.2017. (1.08 MB)
Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017. SFEI Contribution No. 929. San Francisco Estuary Institute : Richmond, CA.2018. (2.24 MB)
Selenium in White Sturgeon from North San Francisco Bay: The 2015-2017 Sturgeon Derby Study - (Coming Soon). SFEI Contribution No. 897. San Francisco Estuary Institute : Richmond, CA.2018.
Non-Targeted Analysis of Water-Soluble Compounds Highlights Overlooked Contaminants and Pathways (Coming Soon). SFEI Contribution No. 905. San Francisco Estuary Institute: Richmond, CA.2018.
Old Science, New Science: Incorporating Traditional Ecological Knowledge into Contemporary Management, 3.2002. (817.47 KB)
Estimation of Means, Totals, and Distribution Functions from Probability Survey Data. SFEI Contribution No. 110. San Francisco Estuary Institute: Oakland, CA.2002. (907.38 KB)
Recommended Methods for Outlier Detection and Calculations of Tolerance Intervals and Percentiles – Application to RMP data for Mercury-, PCBs-, and PAH-contaminated Sediments. SFEI: Oakland.2011. (1.01 MB)
Long term bioaccumulation monitoring with transplanted bivalves in San Francisco Bay. Marine Pollution Bulletin 38, 170-181 . SFEI Contribution No. 32.1999.
Wetlands of the Southern California Coast: Historical Extent and Change Over Time. SFEI Contribution No. 720. Southern California Coastal watershed Research Project (SCCWRP), San Francisco Estuary Institute (SFEI), CSU Northridge Center for Geographical Studies: Costa Mesa, Richmond, Northridge.2014. (5.96 MB)
Detection of Organophosphate Flame Retardants in Furniture Foam and U.S. House Dust. Environmental Science and Technology 7490–7495 . SFEI Contribution No. 591.2009. (255.57 KB)
Alternate and New Brominated Flame Retardants Detected in US House Dust. Environmental Science & Technology.2008. (372.68 KB)
Characterization of the brominated chemicals in a PentaBDE replacement mixture and their detection in biosolids collected from two San Francisco Bay Area Waste water treatment plants.2008. (2.01 MB)
Alameda Creek Watershed Historical Ecology Study. San Francisco Estuary Institute: Richmond, CA.2013. (335.05 MB) (163.08 MB)
East Contra Costa Historical Ecology Study. SFEI Contribution No. 648. SFEI: Oakland.2011. (17.71 MB) (123.69 MB) (149.82 MB) (193.36 MB)
Summary Report: Green Sturgeon, Longfin Smelt, and Dredging Operations in the San Francisco Estuary. SFEI Contribution No. 598. San Francisco Estuary Institute: Oakland, Ca.2009. (4.1 MB)
Test Application of a High Resolution 3-dimensional Hydrodynamic Model (SUNTANS) to San Francisco Bay. San Francisco Estuary Institute: Oakland, CA.2011. (5.49 MB)
Re-Oaking Silicon Valley: Building Vibrant Cities with Nature. SFEI Contribution No. 825. San Francisco Estuary Institute: Richmond, CA.2017. (65.64 MB) (31.88 MB)
In this report, we investigate how re-integrating components of oak woodlands into developed landscapes — "re-oaking" — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically-resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.
Making Nature's City. SFEI Contribution No. 947. San Francisco Estuary Institute: Richmond, CA.2019. (10.41 MB) (33.4 MB)
A Pilot Study of the Effects of Contaminants on surfperch (Cymatogaster aggregata) in the San Francisco Bay Estuary. San Francisco Estuary Institute.2007. (1.62 MB)
Watching Our Watersheds: Santa Clara Valley Past, Google Earth KMZ files: Santa Clara Valley historical points of interest, stream courses and habitats.2012. (10.61 MB)
Effects of salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper. Aquatic Toxicology 175.2016.
Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.
Towards an Optimal Sampling Design for the RMP. SFEI Contribution No. 6. San Francisco Estuary Institute: Richmond, CA.1994.
DOD Sediment Criteria Project Ambient Analysis Draft Interim Report. SFEI Contribution No. 9. San Francisco Regional Water Quality Control Board: Oakland, CA.1996.
Mercury Effects, Sources, and Control Measures. SFEI Contribution No. 20. San Francisco Estuary Institute: Richmond, CA.1996. (89.59 KB)
The UC Davis Biosentinel Mercury Program: Using Small Fish to Monitor Fine-scale Patterns of Methylmercury Contamination in the Watershed. SFEI Contribution No. 552. San Francisco Estuary Institute.2008. (3.21 MB)
2019 RMP Contaminant Concentrations in San Francisco Bay Sportfish Cruise Report. SFEI Contribution No. 968. Marine Pollution Studies Laboratory, Moss Landing Marine Laboratories: Moss Landing, CA.2019. (12.28 MB)
This report contains information on the spring and summer field sampling efforts conducted by the Marine Pollution Studies Laboratory at Moss Landing Marine Labs (MPSL-MLML). The purpose of this field effort was to collect sportfish for an eighth season of data (in support of 1994, 1997, 2000, 2003, 2006, 2009, and 2014 surveys) in the ongoing study of Contamination in San Francisco Bay Sportfish. The work was contracted through the San Francisco Estuary Institute (SFEI) for the Regional Monitoring Program (RMP) for Water Quality.
Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup:Tier 1 Risk Assessment of California Department of Boating and Waterways Aquatic Herbicide Use in the Sacramento-San Joaquin River Delta. SFEI Contribution No. 436. San Francisco Estuary Institute.2006. (459.4 KB)
Aquatics Herbicides: Overview of Usage, Fate and Transport, Potential Environmental Risk, and Future Recommendations for the Sacramento-San Joaquin Delta and Central Valley. SFEI Contribution No. 414. San Francisco Estuary Institute.2005. (633.6 KB)
Aquatic Pesticides Monitoring Program Monitoring Project Final Report. SFEI Contribution No. 392. San Francisco Estuary Institute: Oakland, CA.2005. (905.48 KB)
Aquatic Pesticides Monitoring Program Phase 1 (2002) Project Report. SFEI Contribution No. 103.2003.
Aquatic Pesticides Monitoring Program Phase 2 (2003) Monitoring Project Report. SFEI Contribution No. 108. San Francisco Estuary Institute: Oakland, CA.2004. (1.06 MB)
Aquatic Pesticides Monitoring Program Phase 3 (2004) Monitoring Project Report. SFEI Contribution No. 391. San Francisco Estuary Institute: Oakland, CA.2004. (1.15 MB)
Aquatic Pesticide Monitoring Program Literature Review. SFEI Contribution No. 71. San Francisco Estuary Institute: Oakland, CA.2003. (5.45 MB)
Data Collection Protocol Sedimentation- Erosion Tables (SET's). SFEI Contribution No. 244. University of San Francisco, Wetlands and Water Resources: San Francisco, CASan Rafael, CA.2002.
2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute : Richmond, CA.2018. (466.59 KB)
2018 RMP Bivalve Retrieval Cruise Plan. SFEI Contribution No. 893. San Francisco Estuary Institute: Richmond, CA.2018. (466.59 KB)
2018 RMP Bivalve Deployment Cruise Plan. SFEI Contribution No. 892. San Francisco Estuary Institute: Richmond, CA.2018. (268.38 KB)
Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.2018. (1.43 MB)


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Christian Brannstrom
Associate Dean for Academic Affairs, College of Geosciences
Dr. Brannstrom's research focuses on social and political aspects of renewable energy and unconventional fossil fuels in Texas. He also studies geographical dimensions of wind-power expansion in Brazil, where he has partnered with geographers at the Universidade Federal do Ceará. He regularly hosts visiting scholars interested in theoretical and empirical dimensions of environmental governance. His work has been supported by the National Science Foundation, the National Geographic Society, Texas Sea Grant, the TAMU Glasscock Center for Humanities Research, and Brazilian funding agencies.
Dr. Brannstrom's research on geographical dimensions of energy in Texas supports his teaching of Geography 309 (Energy) through two course field trips that introduce undergraduates to several aspects of the value chain of wind power in Sweetwater, Texas, and to the post-November 2014 energy debates in Denton, Texas. His work with Brazilian geographers at the Universidade Federal do Ceará on wind power aims to foster socially and political sustainable ways to implement wind power while co-training Brazilian graduate students in new methods and new literatures.
Selected Publications
Gorayeb, A., C. Brannstrom, A. J. A. Meireles, J. S. Mendes (2018) "Wind power gone bad: Critiquing wind power planning processes in northeastern Brazil," Energy Research and Social Science 40: 82-88 DOI: 10.1016/j.erss.2017.11.027
Murphy, T., C. Brannstrom, M. Fry, M. Ewers (2018), "Economic development stakeholder perspectives on boomtown dynamics in the Eagle Ford, Texas," Geographical Review 108(1): 24-44 DOI: 10.1111/gere.12226
Fry, M., C. Brannstrom, M. Sakinejad (2017) "Suburbanization and shale gas wells: Patterns, planning perspectives, and reverse setback policies," Landscape and Urban Planning 168: 9-21 DOI: 10.1016/j.landurbplan.2017.08.005
Frate, C. A., C. Brannstrom (2017) "Stakeholder subjectivities regarding barriers and drivers to the introduction of utility-scale solar photovoltaic power in Brazil," Energy Policy 111: 346-352 DOI: 10.1016/j.enpol.2017.09.048
Fry, M., C. Brannstrom (2017) "Emergent patterns and processes in urban hydrocarbon governance," Energy Policy 111: 383-393 DOI:10.1016/j.enpol.2017.09.042
Murphy, T., C. Brannstrom, M. Fry (2017) "Ownership and spatial distribution of Eagle Ford mineral wealth in Live Oak County, Texas," Professional Geographer 69(4): 616-628 DOI: 10.1080/00330124.2017.1298451
Brannstrom, C., et al. (2017) "Is Brazilian wind power development sustainable? Insights from a review of conflicts in Ceará state," Renewable and Sustainable Energy Reviews 67: 62-71 http://dx.doi.org/10.1016/j.rser.2016.08.047
Broadstone, S. and C. Brannstrom (2017) "Growing food is work: The labour challenges of urban agriculture in Houston, Texas," in Global Urban Agriculture: Convergence of Theory and Practice between North and South, ed. A. M. G. A. WinklerPrins (Boston: CABI), pp. 66-78
Brannstrom, C., and M. Fry (2017) "New geographies of the Texas energy revolution," in The Routledge Research Companion to Energy Geographies, eds. Bouzarovski, S., M. Pasqualetti, V. Castán Broto (New York: Routledge), pp. 17-31
Brannstrom, C. (2016) "The discovery of Hispanic child labor in the Lower Rio Grande Valley: A life-geography approach," Annals of the American Association of Geographers 106(3): 705-721 doi: 10.1080/24694452.2015.1131142
Brannstrom, C. and J. Vadjunec (eds.), Land Change Science, Political Ecology, and Sustainability: Synergies and Divergences (Abingdon: Earthscan from Routledge, 2013)
Ph.D. Geography, University of Wisconsin-Madison (1998)
Distinguished Achievement Award (Teaching), Texas A&M University and Association of Former Students (2017)
Outstanding Service to CLAG, Conference of Latin Americanist Geographers (2017)
Bush Excellence Award for Faculty in International Teaching, Texas A&M University (2016)
Distinguished Achievement Award College Level (teaching), College of Geosciences and Association of Former Students, Texas A&M University (2013)
Additional Information
Graduate Students
- Thomas Loder, PhD Student (Chair)
- Ryan Dicce, PhD Student (Chair)

subset: commoncrawl


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|Direct observations of transition dynamics from macro- to micro-phase separation in asymmetric lipid bilayers induced by externally added glycolipids
In general, phase separation in binary liquid mixtures completes by relaxation below the transition temperature. However, it is also well known that the competition between local attractive and long-ranged repulsive interactions between two phases leads to stable micro-phase separation. The coarsening dynamics from a homogeneous phase to macro- or micro-phase has been extensively investigated in binary mixture systems of polymeric and/or low-molecular-weight molecules. In contrast, the dynamics from macro- to micro-phase separation remains poorly understood because no appropriate experiments and models exist for investigating this phenomenon (figure a). In this letter, We present the first direct observations of morphological transitions from macro- to micro-phase separation using micrometer-sized asymmetric lipid vesicles exposed to externally added glycolipids (GM1:monosialotetrahexosylganglioside). The transition occurs via an intermediate stripe morphology state. During the transition, monodisperse micro-domains emerge through repeated scission events of the stripe domains (figure b,c). By numerically analyzing the bending elastic model and the time-dependent Ginzburg-Landau equation (figure b), we gained insights into the mechanism of the novel transitions, which is apparently governed by the local spontaneous curvature induced by the local asymmetric composition. Our findings could provide important mechanistic clues for new material designs and for understanding the dynamics of the heterogeneities existing in cell membranes.
|"Direct observations of transition dynamics from macro- to micro-phase separation in asymmetric lipid bilayers induced by externally added glycolipids" Shunsuke F. Shimobayashi, Masatoshi Ichikawa and Takashi Taniguchi, Europhysics Letters, 113, 56005 (2016).
|Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface
Active force generation in living organisms, which is mainly involved in actin cytoskeleton and myosin molecular motors, plays a crucial role in various biological processes. Although the contractile properties of actomyosin have been extensively investigated, their dynamic contribution to a deformable membrane remains unclear because of the cellular complexities and the difficulties associated with in vitro reconstitution. Here, by overcoming these experimental difficulties, we demonstrate the dynamic deformation of a reconstituted lipid interface coupled with self-organized structure of contractile actomyosin. Therein, the lipid interface repeatedly oscillates without any remarkable periods. The oscillatory deformation of the interface is caused by the aster-like three-dimensional hierarchical structure of actomyosin inside the droplet, which is revealed that the oscillation occurs stochastically as a Poisson process.
|"Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface", Y. Nishigami, H. Ito, S. Sonobe and M. Ichikawa, Sci. Rep., 6, 18964 (2016).
|Coupling between pore formation and phase separation in charged lipid membranes
We investigated the effect of charge on the membrane morphology of giant unilamellar vesicles (GUVs) composed of various mixtures containing charged lipids. We observed the membrane morphologies by fluorescent and confocal laser microscopy in lipid mixtures consisting of a neutral unsaturated lipid (DOPC), a neutral saturated lipid (DPPC), a charged unsaturated lipid (DOPG(∁E), a charged saturated lipid (DPPG(∁E), and cholesterol (Chol). In binary mixtures of neutral DOPC-DPPC and charged DOPC-DPPG(∁E, spherical vesicles were formed. On the other hand, pore formation was often observed with GUVs consisting of DOPG(∁E and DPPC. In a DPPC-DPPG(∁E-Chol ternary mixture, pore-formed vesicles were also frequently observed. The percentage of pore-formed vesicles increased with the DPPG(∁E concentration. Moreover, when the head group charges of charged lipids were screened by the addition of salt, pore-formed vesicles were suppressed in both the binary and ternary charged lipid mixtures. We discuss the mechanisms of pore formation in charged lipid mixtures and the relationship between phase separation and the membrane morphology. Finally, we reproduce the results seen in experimental systems by using coarse-grained molecular dynamics simulations.
|"Coupling between pore formation and phase separation in charged lipid membranes", H. Himeno, H. Ito, Y. Higuchi, T. Hamada, N. Shimokawa, and M. Takagi, Phys. Rev. E, 92, 062713 (2015).
|Wrinkling of a spherical lipid interface induced by actomyosin cortex
Actomyosin actively generates contractile forces that provide the plasma membrane with the deformation stresses essential to carry out biological processes. Although the contractile property of purified actomyosin has been extensively studied, to understand the physical contribution of the actiomyosin contractile force on a deformable membrane is still a challenging problem and of great interest in the field of biophysics. Here, we reconstituted a model system with a cell-sized deformable interface that exhibits anomalous curvature dependent wrinkling caused by actomyosin cortex underneath the spherical closed interface. Through the shape analysis of the wrinkling deformation, we found that the dominant contributor on the wrinkled shape changes from bending elasticity to stretching elasticity of the reconstituted cortex by increasing the droplet curvature radius of the order of the cell-size, i.e., tens of micrometer. The observed curvature dependence was explained by the theoretical description of the cortex elasticity and contractility. Our present results provide a fundamental insight on the deformation of a curved membrane induced by the actomyosin cortex.
|"Wrinkling of a spherical lipid interface induced by actomyosin cortex", H. Ito, Y. Nishigami, S. Sonobe, and M. Ichikawa, Phys. Rev. E, 92, 062711 (2015).
|Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions
We report a centrifugal microfluidic method, droplet-shooting and size-filtration (DSSF), for the production of cell-sized liposomes with controlled lipid compositions. This involves the generation of large and small droplets from the tip of a glass capillary and the selective transfer of small droplets through an oil-water interface, thus resulting in the generation of cell-sized liposomes. We demonstrate control of the microdomain formation as well as the formation of asymmetric lipid bilayer liposomes of uniform size by the control of lipid composition. The DSSF method involves simple microfluidics and is easy to use. In addition, only a small volume (0.5 E mL) of sample solution is required for the formation of hundreds of cell-sized liposomes. We believe that this method can be applied to generate cell-sized liposomes for a wide variety of uses, such as the construction of artificial cell-like systems.
|"Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions", M. Morita, H. Onoe, M. Yanagisawa, H. Ito, M. Ichikawa, K. Fujiwara, H. Saito, and M. Takinoue, ChemBioChem, 16, 2029 (2015).
|Molecular behavior of DNA in a cell-sized compartment coated by lipids
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space. Globular DNA showed a cell-size-dependent unfolding transition after adsorption on the membrane. Furthermore, when DNA interacted with a two-phase membrane surface, DNA selectively adsorbed on the membrane phase, such as an ordered or disordered phase, depending on its conformation. We discuss the mechanism of these trends by considering the free energy of DNA together with a polyamine in the solution. The free energy of our model was consistent with the present experimental data. The cooperative interaction of DNA and polyamines with a membrane surface leads to the size-dependent behavior of molecular systems in a small space. These findings may contribute to a better understanding of the physical mechanism of molecular events and reactions inside a cell.
|"Molecular behavior of DNA in a cell-sized compartment coated by lipids", Tsutomu Hamada, Rie Fujimoto, Shunsuke F. Shimobayashi, Masatoshi Ichikawa and Masahiro Takagi, Physical Review E, 91(6), 062717 (2015).
|Direct measurement of DNA-mediated adhesion between lipid bilayers
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous artificial materials have been synthesised by functionalising the outer surface of compliant Brownian units, for example emulsion droplets and lipid vesicles, with selective linkers, in particular short DNA sequences. This development extended the range of applicability of DNA as a selective glue, originally applied to solid nano and colloidal particles. On very deformable lipid vesicles, the coupling between statistical effects of multivalent interactions and mechanical deformation of the membranes gives rise to complex emergent behaviours, as we recently contributed to demonstrate [Parolini et al., Nature Communications, 2015, 6, 5948]. Several aspects of the complex phenomenology observed in these systems still lack a quantitative experimental characterisation and fundamental understanding. Here we focus on the DNA-mediated multivalent interactions of a single liposome adhering to a flat supported bilayer. This simplified geometry enables the estimate of the membrane tension induced by the DNA-mediated adhesive forces acting on the liposome. Our experimental investigation is completed by morphological measurements and the characterisation of the DNA-melting transition, probed by in-situ Förster Resonant Energy Transfer spectroscopy. Experimental results are compared with the predictions of an analytical theory that couples the deformation of the vesicle to a full description of the statistical mechanics of mobile linkers. With at most one fitting parameter, our theory is capable of semi-quantitatively matching experimental data, confirming the quality of the underlying assumptions.
| Reference
|"Direct measurement of DNA-mediated adhesion between lipid bilayers", Shunsuke F. Shimobayashi, B. M. Mognetti, L. Parolini, D. Orsi, P. Cicuta and L. Di Michele, Physical Chemistry Chemical Physics , 17(24),15615-15628 (2015).
|Quantification of the influence of endotoxins on the mechanics of adult and neonatal red blood cells
We physically modeled the influence of endotoxin-induced sepsis symptoms on human red blood cells (RBCs) by quantifying the impact of endotoxins on the cell mechanics by the analysis of Fourier-transformed mean square amplitude of shape fluctuation, called flicker spectroscopy. With the aid of a microfluidic diffusion chamber, we noninvasively determined principal mechanical parameters of human RBCs in the absence and presence of endotoxins for individual RBCs for the first time. Because of the elongation of saccharide chain length of endotoxins, we found an increase in the morphological transition from discocytes to echinocytes, and monotonic changes in the mechanical parameters. Since septic shocks often cause lethal risks of neonates, we measured the mechanical parameters of neonatal RBCs, and compared them to those of adult RBCs. The quantitative comparison reveals that neonatal RBCs are more susceptible to the effect of endotoxins than adult RBCs. Furthermore, coincubation with the antiseptic peptide P19-2.5 (Aspidasept) with endotoxin results in a slight suppression of the impact of the endotoxin. The strategy proposed in our study can potentially be applied for the quantitative diagnosis of RBCs based on mechanical readouts.
| Reference
|"Quantification of the influence of endotoxins on the mechanics of adult and neonatal red blood cells", H. Ito, N. Kuss, Bastian E. Rapp, Masatoshi Ichikawa, Thomas Gutsmann, Klaus Brandenburg, Johannes M. B. Poeschl, and Motomu Tanaka, J. Phys. Chem. B, 119, 7837 (2015).
|Emergence of DNA-Encapsulating Liposomes from a DNA–Lipid Blend Film
Spontaneous generation of DNA-enclosing liposomes from a DNA–lipid blend film is investigated. The special properties of the lipid vesicles, namely, micrometer size, unilamellarity, and dense polymer encapsulation acquired by the dehydration–rehydration process, are physicochemically revealed. We found that the formation of giant unilamellar vesicles encapsulating DNAs are governed by micropatterns of the films, such as dots and network patterns. From the results, we proposed a plausible physical mechanism for the dehydration–rehydration process, making it possible to optimize the encapsulation of any agent.
5 times speed, 81.6square
| Reference
| "Emergence
of DNA-Encapsulating Liposomes from a
DNA–Lipid Blend Film", Shunsuke F. Shimobayashi, and Masatoshi Ichikawa
The Journal of Physical Chemistry B, 118 (36),
10688-10694 (2014).
|Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface
Recently, the transfer method has been shown to be useful for preparing cell-sized phospholipid bilayer vesicles, within which desired substances at desired concentrations can be encapsulated, with a desired asymmetric lipid composition. Here, we investigated the transfer process of water-in-oil (W/O) droplets coated by phospholipid monolayers across an oil/water interface by both experimental observation and theoretical modeling. Real-time experimental observation of the transfer revealed that the transfer process is characterized by three kinetic regimes: a precontact process (approaching regime), an early fast process (entering regime), and a late slow process (relaxation regime). In addition, bigger droplets require much more time to transfer than smaller droplets. We propose a theoretical model to interpret this kinetic process. Our theoretical model reproduces the essential aspects of the transfer kinetics, including its size-dependence.
| Reference
| "Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface", H. Ito, T. Yamanaka, S. Kato, T. Hamada, M. Takagi, M. Ichikawa, and K. Yoshikawa, Soft Matter, 9, 9539-9547 (2013).
|Emergence of a thread-like pattern with charged phospholipids on an oil/water interface
The spontaneous formation of a thread-like pattern with negatively charged lipids on an oil/water interface is reported. An analysis of the time-dependent change at the interface observed by fluores- cence microscopy revealed that the thread-like pattern is generated through a two-step mechanism. First, inverted lipid micelles in the bulk-oil phase gradually diffuse onto the oil/water interface. Next, the micelles are adsorbed on the interface and self-assemble to form the thread-like pattern. The essential characteristics of this pattern formation are theoretically reproduced by a simple Monte Carlo simulation that takes into account the kinetics in the coalescence of charged micelles on a 2D interface.
| "Emergence of a thread-like pattern with charged phospholipids on an oil/water interface", H. Ito, M. Yanagisawa, M. Ichikawa, and
K. Yoshikawa, J. Chem. Phys. , 136, 204903 (2012).
|Oscillation and collective conveyance of water-in-oil droplets by microfluidic bolus flow
Microfluidic techniques have been extensively developed to realize micro-total analysis systems in a small chip. For microanalysis, electro-magnetic forces have generally been utilized for the trapping of objects, but hydrodynamics has been little explored despite its relevance to pattern formation. Here, we report that water-in-oil (W/O) droplets can be transported in the grid of an array of other large W/O droplets. As each droplet approaches an interspace of the large droplet array, while exhibiting persistent back-and-forth motion, it is conveyed at a velocity equal to the droplet array. We confirm the appearance of closed streamlines in a numerical simulation, suggesting that a vortex-like stream is involved in trapping the droplet. Furthermore, more than one droplet is also conveyed as an ordered cluster with dynamic reposition.
| "Oscillation and collective conveyance of water-in-oil droplets by microfluidic bolus flow", T. Ohmura, M. Ichikawa, K. Kamei, and Y.T. Maeda, Applied Physics Letters, 107, 074102 (2015).
|Novel Micro-scale DC Motor: Noise Induces Regular Rhythmic Motion
We demonstrated that a micro scale water droplet shows regular oscillatory motion under DC voltage of several volts. Interestingly, we also found that external noise stabilizes the periodic motion. In our earlier studies (PRE 74,046301 (2006) and APL 96,104105(2010)), it has been reported that oscillatory motion of a droplet is generated under DC voltage on the order of 100V without any switching device. Here, we show that one-order smaller DC voltage induces oscillatory motion and it is stable against noise. Such significant development in this study on the micro droplet motion suggests the possibility to construct a new Nano-scale motor driven by DC less than a volt, working under Brownian noise, in a near future; mimicking the essence of molecular motor in living system.
| "Micro back-and-forth motion under DC electronic
Field E T. Kurimura, M. Takinoue, K. Yoshikawa and M. Ichikawa, Physical
Review E, 88, 042918/1-5 (2013).
|Spontaneous mode-selection in the self-propelled motion of a solid/liquid composite driven by interfacial instability
Spontaneous motion of a solid/liquid composite induced by a chemical Marangoni effect, where an oil droplet attached to a solid soap is placed on a water phase, was investigated. The composite exhibits various characteristic motions, such as revolution (orbital motion) and translational motion. The results showed that the mode of this spontaneous motion switches with a change in the size of the solid scrap. The essential features of this mode-switching were reproduced by ordinary differential equations by considering nonlinear friction with proper symmetry.
| "Spontaneous
mode-selection in the self-propelled motion of a solid/liquid composite
driven by interfacial instability", F. Takabatake, N. Magome, M.
Ichikawa, and K. Yoshikawa, J. Chem. Phys., 134, 114704
|Utilizing the eikonal relationship in strategies for reentrant wave termination in excitable media
Obstacle-anchored vortices can be terminated by the application of high-frequency wave-trains in excitable media as we have shown in Isomura et al., PRE, 2008. We theoretically derived the dependency between the obstacle radius and the maximum unpinning period through reinterpretation of the well-known eikonal equation. Figure a) shows the restitution curves for three different excitabilities and the minimum velocity on obstacles with size between 0.4 and 2.0cm. The fit of the minimum velocity (dashed line) provides all information to derive the minimum unpinning period (Tmin) to unpin an obstacle bounded spiral wave. Figure b) shows the comparison of numerically and theoretically obtained minimum unpinning period for each excitability, respectively. Our theoretical result was confirmed by experiments with cardiomyocyte monolayers. This result may be useful for improving the stimulation protocol of implantable cardiac pacemakers.
| "Utilizing
the eikonal relationship in strategies for
reentrant wave termination in excitable media", M. Hörning, A. Isomura,
Z. Jia, E. Entcheva, and K. Yoshikawa, Phys. Rev. E, 81,
056202 (2010).
|Travelling wave of segregation in a highly filled rotating drum
The dynamics of a segregation pattern for a granular mixture in a highly filled rotating drum were studied. A spontaneously segregated band pattern traveled laterally, and was accompanied by the repeated creation of new bands near the center of the drum and annihilation at both of its ends. The presence of nearly stationary convection plays an essential role in causing this travelling wave. Based on direct observations of both the interior and exterior of the segregation pattern, this spatio-temporal pattern is interpreted in terms of a one-dimensional Cahn-Hilliard equation by including the effect of stationary convection.
| Reference
wave of segregation in a highly filled rotating drum", Shio
Inagaki and Kenichi Yoshikawa, Phys. Rev. Lett., 105,
118001 (2010).
|Contribution of convection to spatiotemporal stripe patterns formed by Ag and Sb coelectrodeposition
Various spatiotemporal patterns of dark and light stripes are formed on the surface of an electrode put in an electrolyte solution in a Ag and Sb coelectrodeposition system. In this study, we investigate the effect of natural convection of the solution on these spatiotemporal patterns. When the electrode is placed vertically, natural convection generally emerges in the electrolyte solution in the vicinity of the electrode surface during electrodeposition and flows upward along the electrode surface. When convective flow along the electrode surface was eliminated by placing the electrode horizontally, the configuration of the one-directional traveling waves (anisotropic shape) changed to an isotropic shape. This indicates that the formation of an anisotropic shape for one-directional traveling waves is due to upward convective flow along the electrode surface.
| Reference
|"Contribution of convection to spatiotemporal stripe
patterns formed by
Ag and Sb coelectrodeposition", Yuko Nagamine and Kenichi Yoshikawa, Chaos,
20, 023117 (2010).
|Rotary motion driven by a direct current electric field
A water-in-oil (w/o) micro-droplet exhibits a spontaneous rotary motion under a stationary direct current electric field. The rotary motion appears above a certain critical electric potential and its frequency increases with an increase in the potential. A simple theoretical model including an over-damped equation of motion and dissipation of electric charge can describe the occurrence of the rotary motion. This rotary motion of w/o microdroplet is believed to be a novel spatiotemporal order under a electrochemical nonequilibrium open system.
| "Rotary
motion driven by a direct current electric field", M. Takinoue, Y.
Atsumi, and K. Yoshikawa, Appl. Phys. Lett., 96, 104105
|Probability of double-strand breaks in genome-sized DNA by γ -ray decreases markedly as the DNA concentration increases
By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by γ-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P 1, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.
| Reference
| "Probability
of double-strand breaks in genome-sized DNA by γ -ray decreases
markedly as the DNA concentration increases"
Shunsuke F. Shimobayashi, Takafumi Iwaki, Toshiaki Mori and Kenichi
Yoshikawa, Journal of Chemical Physics, 138 (17),
174907/1-5 (2013).
|Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness
We investigated the folding transition between an elongated coil state and a compact state on a single polymer chain confined in a small space with different stiffness with the aid of Monte Carlo simulation. In a flexible polymer, the folding transition is retarded in a confined space. In contrast, the transition is promoted for a semiflexible chain, in which the discontinuity of the volume change occupied by a single chain is diminished by confinement. This unique confinement effect is interpreted in terms of conformational entropy and self-avoiding repulsive interaction.
| Reference
| "Confinement
causes opposite effects on the folding
transition of a single polymer chain depending on its stiffness", Yuji
Higuchi, Takafumi Iwaki, and Kenichi Yoshikawa, Phys. Rev. E. ,
84, 021924 (2011).
| Related papers
| "Conformational
transition of giant DNA in a confined
space surrounded by a phospholipid membrane", Ayako Kato, Eri Shindo,
Takahiro Sakaue, Akihiko Tsuji and Kenichi Yoshikawa, Biophysical
Journal, 97, 1678(2009).
| "Stepwise
Collapse of Polyelectrolyte Chains Entrapped in a Finite Space As
Predicted by Theoretical Considerations", Seiji Takagi and Kenichi
Yoshikawa, Langmuir, 15, 4143 (1999).
|Torsional effect on the wrapping transition of a semiflexible polymer around a core as a model of nucleosome
We investigated the effect of the torsional rigidity of a semiflexible chain on the wrapping transition around a spherical core, as a model of a nucleosome, the fundamental unit of chromatin. Through molecular dynamics simulation, we show that the torsional effect has a crucial effect on the chain wrapping around the core under the topological constraints. In particular, the torsional stress (i) induces the wrapping/unwrapping transition, and (ii) leads to a unique complex structure with an antagonistic wrapping direction which never appears without the topological constraints. We further examine the effect of the stretching stress for the nucleosome model in relation to the unique characteristic effect of the torsional stress on the manner of wrapping.
| Reference
effect on the wrapping transition of a
semiflexible polymer around a core as a model of nucleosome", Yuji
Higuchi, Takahiro Sakaue, and Kenichi Yoshikawa, Phys. Rev. E. ,
82, 031909 (2010).
|Protamine-induced DNA compaction but not aggregation shows effective radioprotection against double-strand breaks
Protamine, an arginine-rich protein, is essential for the compaction of sperm DNA. We performed single-molecule observations of DNA double-strand breaks caused by 60Co -ray irradiation and quantitatively evaluated the protective effect of protamine. It was shown that double-strand breaks were significantly protected for the tightly compact DNA, whereas there is no apparent decrease on the damage for loosely aggregated DNA molecules. Our findings suggest that the densely packed structure of DNA reduces the ability of radiolytic reactive oxygen species to access DNA and thus protects DNA from double-strand breaks.
| References
DNA compaction but
not aggregation shows effective radioprotection against double-strand
breaks", Mari Suzuki, Cecile Crozatier, Kenichi Yoshikawa, Toshiaki
Mori, and Yuko Yoshikawa, Chemical Physics Letters, 480,
113 (2009).
"DNA compaction plays key role in radioprotection against double-strand breaks as revealed by single-molecule observation", Yuko Yoshikawa, Toshiaki Mori, Nobuyuki Magome, Kumiko Hibino, and Kenichi Yoshikawa, Chemical Physics Letters, 456, 80 (2008).
|Chain length dependence of folding transition in a semiflexible homo-polymer chain: Appearance of a core-shell structure
The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete transition between swollen coil and compact toroid conformations, a long chain (50 Kuhn segments) exhibits an intrachain segregated state between the disordered coil and ordered toroid.
| Reference
length dependence of folding
transition in a semiflexible homo-polymer chain: Appearance of a
core-shell structure", Yuji Higuchi, Takahiro Sakaue, and Kenichi
Yoshikawa, Chemical Physics Letters, 461, 42 (2008).
|Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification
In apoptotic cells, genomic DNA molecules are fragmented into multiple fragments with lengths that are integer multiples of ca. 180-200 base pairs (bp), i.e., the size of a single nucleosome. Here we propose a simple mathematical model for interpreting this cleavage pattern of DNA. Under the condition of a purely stochastic cleavage process, we derive a time evolution of the probability distribution of the fragment length by a Poisson distribution. We examine the applicability of our model by analyzing experimental results with apoptotic cells. Our model enables us to satisfactorily interpret the experimental trends. Interestingly, this theoretical fitting of the experimental data provides kinetic information for the cleavage reaction.
| Reference
| "Cleavage
pattern of DNA caused by endonuclease: Theoretical modeling and
experimental verification", Shio Inagaki, Li Liu, Masahiro Takinoue,
and Kenichi Yoshikawa, Applied Physics Letters, 96,
063701 (2005).


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Todays episode is filled with lots of relationship advice. First up, since the sports seasons that people care about are over, we discuss this "rap beef" between Lonzo Ball and, his teammate, Kyle Kuzma. Is this really a beef? C'mon. In the 2nd half of the show, we really get into some good advice on when the relationship is over and the actions of both men and women. Rebound sex is a real thing and women want to know why it's more prevalent for a man than it is for women.
1st Half
* Lonzo Ball Beef with teammate Kyle Kuzma
* Lebron goes to the Lakers
2nd Half
* Men run out and have sex after a break up
* Men hurt too, like women hurt
* Men take action after a break up
* Women get into their feelings after a break up


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Hello Friend,
If you are like many of us, you might feel like you don't know what to do when it comes to helping your neighbor. We all know that there are many children and families and seniors in Greater Paterson that go to bed hungry or without nutritious food in their stomach every night. But how can I help? What can I do? The information on this page might be a first step in helping you think through what you and your family can do to address Hunger and Food Insecurity. We have broken it out into Three Simple Action Steps:
#1. Educate:
A first step in helping our neighbor who might be struggling with Food Insecurity or Hunger is to learn more about the problem. For your information, I have listed a few websites that you can visit. Take some time to read about and familiarize yourself with the issue.
Food insecurity
is defined as a lack of consistent access to enough food for an active, healthy life for all household members and limited or uncertain availability of nutritionally adequate foods. Food insecure homes may reflect a household's need to make trade off's between important basic needs, such as housing or medical bills, and purchasing nutritionally adequate foods
is defined as "a potential consequence of food insecurity that, because of prolonged, involuntary lack of food, results in discomfort, illness, weakness, or pain that goes beyond the usual uneasy sensation." (USDA, 2018)
Here are some stats about hunger and food insecurity in our area:
– According to a 2018 report, more than 41 million Americans struggle with hunger.*
– One in seven Americans now rely on food pantries and meal service programs.**
– The NJ Food Insecurity rate is 13% with 1,141,890 people being food insecure***
– One in four NJ residents struggle to meet their basic needs, which often forces a choice between food and other essential costs (rent, medication, etc.)****
– Passaic County NJ has 48,880 food insecure individuals.*****
The need is real, and there are many opportunities to serve our neighbors in the name of Jesus Christ. However, in our desire to help those in need, we need to be sure that we help in such a way that preserves the dignity of the individual, and also connects them with a local church community. One of the most helpful ways to reach out to our neighbors is by simply being a friend. Below are some valuable links to learn more about ways to effectively reach those in need in your community.
How to Serve the Poor – When Helping Hurts Video Link
How Star of Hope Addresses FOOD Insecurity – www.sohm.org/ meeting basic needs.
It's all about Relationship – A Friend of the Poor Link
After you have familiarized yourself with Hunger and Food Insecurity in Greater Paterson, consider sharing with others what you learned. How about using your Facebook page to share some of the Educate Food links above? Or consider speaking to your church or your Pastor about doing a seminar about Poverty and Hunger in New Jersey?
There are a number of ways that you and your family can contribute to Star of Hope to address Food Insecurity in Paterson. Consider the following opportunities:
1. Help Star of Hope provide 3-Day FOOD Packages weekly to help our neighbors. To make a monetary donation, please click here.
2. If you would like to donate food, please click here for a suggested list of food for Star of Hope's 3-day FOOD packages. Please contact Star of Hope first if you would like to drop food off at our Paterson Headquarters, 973-742-1222 ext. 21, email firstname.lastname@example.com.
3. If you would like to organize a food drive in your church school or business, we have collection bins ready that we can deliver to you and pick up after the drive. Please request information by emailing us at: firstname.lastname@example.com.
• Feeding America
• End Hunger NJ
• FRAC Food Research & Action Center
• Living Low-Income in America
* https://www.feedingamerica.org/
** https://www.cumac.org/hunger-in-nj
*** http://endhungernj.org/about-nj-hunger
**** https://www.cumac.org/hunger-in-nj
***** www.map.feedingamerica.org


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text: Home > Medical > ADHD > ADHD News 15 October 2012 Most ADHD kids appreciate meds Children with attention deficit hyperactivity disorder (ADHD) who take stimulants tend to feel the drugs help them control their behaviour and do not turn them into "robots". 0 Children with attention deficit hyperactivity disorder (ADHD) who take stimulants such as Ritalin tend to feel the drugs help them control their behaviour and do not turn them into "robots" as many sceptics assume, a study found. The research, which for the first time asked children taking ADHD drugs what they felt about their treatment and its effects, found that many said medication helped them manage their impulsivity and make better decisions. "With medication, it's not that you're a different person. You're still the same person, but you just act a little better," said Angie, an 11-year-old from the United States who took part in the study and was quoted in a report about its findings. The results are likely to further fuel the debate in the United States and Europe about whether children with ADHD, some as young as four years old, should be given stimulants. What is ADHD? ADHD is one of the most common childhood disorders in the United States, where an average 9% of children between the ages of five and 17 are diagnosed with it each year. In Britain experts estimate that between 5 and 10% of children and adolescents have ADHD. Symptoms of the disorder include difficulty staying focused, hyperactivity and problems with controlling disruptive or aggressive behaviour. "ADHD is a very emotive subject which inspires passionate debate," said Ilina Singh, a biomedical ethicist from King's College London who led the research. "Everyone seems to have an opinion about the condition, what causes it, how to deal with children with ADHD, but the voices of these children are rarely listened to." "Who better to tell us what ADHD is like and how medication affects them than the children themselves?" How the study was done Singh's study, which was funded by medical charity the Wellcome Trust, involved interviewing children from 151 families in Britain and the United States to examine some of the ethical and societal issues surrounding ADHD - in particular the use of drug treatments such as Ritalin. Ritalin, known generically as methylphenidate, is sold by the Swiss drugmaker Novartis and is widely used in developed countries to help children with ADHD concentrate better and control impulsivity. Without effective treatment, children with ADHD can be disruptive at school and fall behind, and adolescents may engage in impulsive, risky behaviour. Singh, who presented her findings in a report called "Voices" at a briefing in London, pointed to disputes surrounding prescribing stimulant drugs for children with ADHD. Some critics argue the medications "turn children into robots", she said, or say that ADHD sufferers are being "drugged into acquiescence". But according to the results of the study, such concerns are largely unfounded, Singh said. Children 'value the medication' "The assumed ethical harms of stimulant medications were largely not supported by this study," she said. "Children value medication because it puts them into a space where they can make good moral decisions." Singh added that the study's findings were "in no way a blanket endorsement of the use of stimulant-based medicines" for ADHD, but stressed they also showed that assumptions about what ADHD drugs did appeared to be "hurting children more than the drugs". Singh said all the medicated children in the study were taking either Novartis' Ritalin, or Concerta, a longer-acting version of the same drug made by Johnson & Johnson. Other common drugs used to treat ADHD include Shire's Adderall and Vyvanse, and Eli Lilly's Strattera. (Reuters, October 2012) Read more: Medication for ADHD From our sponsor Here are some further symptoms of ADHD you might recognize in your child Do you recognize some of these symptoms of ADHD in your child? Read Health24's Comments Policy Comment on this story 0 comments Comments have been closed for this article. Logout Comment 0 characters remaining Share on Facebook Loading comments... Ask the Expert ADHD Expert Dr Renata Schoeman has been in full-time private practice as a general psychiatrist (child, adolescent and adult psychiatry) since 2008, currently based in Oude Westhof (Bellville). Renata also holds appointments as senior lecturer in Leadership (USB) and as a virtual faculty member of USB Executive Development's Neuroleadership programme. She serves on the advisory boards of various pharmaceutical companies, as a director of the Psychiatric Management Group (PsychMG) and is the co-convenor of the South African Society of Psychiatrist (SASOP) special interest group for adult ADHD, and co-founder of the Goldilocks and The Bear Foundation (www.gb4adhd.co.za) She is passionate about corporate mental health awareness and uses her neuroscience background to assist leaders in equipping them to become balanced, healthy and dynamic leaders that take their own and their team's emotional, intellectual, social health and physical needs into account. Renata is academically active and enjoys research and collaborative work, has published in many peer-reviewed journals, and has presented at local and international congresses. She is regularly invited to present at conferences and to engage with the media. During her post-graduate studies, she trained at Harvard, Boston in neurocognition and neuroimaging. Her awards include, amongst others, the Young Minds in Psychiatry award from the American Psychiatric Association, the Discovery Foundation Fellowship award, a Thuthuka award from the NRF, and a MRC Fellowship. She also received the Top MBA student award and the Director's award from USB for 2015. She was a finalist for the Businesswomen's Association of South Africa's Businesswoman of the Year Award for 2016, and received the Excellence in Media Work award from SASOP during 2016. Ask a question Questions posted to ADHD Expert questions answered by the expert Q: No feeling in my toes posted on 23/01/2020 Q: 18-year-old with ADHD and a twitch posted on 11/01/2020 Q: Adult ADHD and depression posted on 22/12/2019 1 comment Q: Adult ADHD posted on 20/11/2019 Q: What is the best chemical medicine for ADHD and OCC? posted on 20/11/2019 Q: Can homeopathic medicine help a 7 yr old boy with ADD ? is there any other medicine other than Ritalin that can help with ADD ? He only struggles with concentration. posted on 20/11/2019 Q: Suspected adult ADHD symptoms posted on 20/11/2019 Q: 60mg Adderall no longer works posted on 17/11/2019 Q: ADD Away vs Turbokidz Smart Omega posted on 07/11/2019 Q: My son's behavior changed and I would like to have some advice. posted on 28/10/2019 Q: 72mg Concerta Matric Finals posted on 23/10/2019 Q: ADD - 'HERBAL MEDS' posted on 17/10/2019 Q: Teenage daughter showing symptoms. posted on 09/10/2019 Q: detrimental effects of ritalin longterm posted on 23/09/2019 Q: son did brilliant at school without hard work posted on 22/09/2019 load more × Still have a question? Get free advice from our panel of experts Your question More detail Your name (optional) The information provided does not constitute a diagnosis of your condition. You should consult a medical practitioner or other appropriate health care professional for a physical exmanication, diagnosis and formal advice. Health24 and the expert accept no responsibility or liability for any damage or personal harm you may suffer resulting from making use of this content. I agree * You must accept our condition To prevent spam please solve this simple math problem: Forum Rules


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Traveler Rating:
- Hotel (overall)
- Food
- Public areas (Pool, Lobby, Bar)
- Cleanliness/Hygiene
- Room comfort
- Atmosphere and design
- Bathroom
- Service
- Location
- Value for money
I recommend this hotel for:
- Traveling alone
- Families with young children
- Families with older children
- Romantic vacation
- Seniors
- Business
- With friends
Would stay at this
location again: Absolutely!
Better each time
Posted by Wilfred
I have been staying at the Metropolitan Hotel for a couple of nights each October in the last few years. I can see improvements all the time. This year in particular I noticed the room safe, a new model that is attractive and easy to use. As always the staff are always polite and helpful.
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hotel's guest and not of inisrael.com
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text: Incredible mountain retreat home secluded from the city and yet close to town. This log cabin style home features 3 bedrooms and 3 bathrooms with an oversized 2 car garage. Granite kitchen counters with raised island bar seating. Private master bath with double shower heads, private deck, large walk-in closet. Multiple decks to enjoy the surrounding views. 42.42 private acres with Buckthorn creek crossing the property, rock outcroppings, trees, RV parking, covered pavilion, space for animals


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We Are Brothers, We Are Friends (Hardcover)
Farrar, Straus and Giroux (BYR), 9780374302016, 32pp.
Publication Date: February 28, 2017
Being a big brother is a BIG job.
There's lots to show your little brother . . .
Trains . . .
Planes . . .
How to be a dinosaur.
There are games to play and adventures to be had. And if trouble comes, it's big brother to the rescue because there's no better friend than a brother.
About the Author
Eda Kaban is an illustrator of children's books, including Old MacDonald Had a Truck written by Steve Goetz. Her work can be seen in print and galleries from San Francisco to New York. She was born and raised in Turkey and currently lives in San Francisco, California, with her husband.
Praise For We Are Brothers, We Are Friends…
"Alternating between the realistic setting of the children's room and fantasy adventures, the retro, cartoon-style illustrations fill in many details of the boy's ideas. Flat, bright colors with black details for contrast create humorous, appealing images. Full bleed two-page spreads allow readers to take in scenes at an unhurried pace." —Booklist
"With simple, straightforward text addressed directly to the wide-eyed toddler, the older brother gamely lists the types of adventures they'll have, from playing trains and planes and hide-and-seek to pretending to be dinosaurs. There is not a drop of sibling rivalry or animosity here. Penfold's earnest story portrays a child who's proud to be a big brother and takes his responsibilities seriously. . .Kaban's playful cartoon art has a retro-modern vibe, with expressive facial features and cheerful energy." —School Library Journal
"Sibling rivalry? What sibling rivalry? Penfold's cheerful big brother narrator is totally cool with having a baby brother. He looks forward to 'adventures, just the two of us,' that include pretend play with 'trains, and planes, and how to be a dinosaur.' Most poignantly, he promises, 'When you cry... I will hear you first.' Kaban—whose crisp lines, bright colors, and eager-eyed characterizations bring to mind 1960s animation—builds some wonderful images from Penfold's words." —Publishers Weekly


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New Jersey Institute of Technology (NJIT) is conducting unmanned aerial systems (UAS) flights over the Atlantic Ocean to test the feasibility of safely integrating drones into the public airspace.
NJIT will also assess the research and operational capabilities of several data-collecting sensors aboard the aircraft. The aircraft will incorporate a weather sensor to gather information on atmospheric conditions, as well as devices with mapping, communications relay and high-definition video capabilities.
Michael Chumer, a research professor of information systems at NJIT and director of the Crisis Communication Center and of UAS Applied Research for the university, is the mission's research director. Pennsylvania-based flight company American Aerospace Advisors Inc. will operate the drones from the U.S. Coast Guard Training Center in Cape May, N.J.
The aircraft will travel up to one nautical mile out over the ocean at a height not to exceed 3,000 feet and will remain airborne for up to one hour. The flights were going to take place Nov. 20-21, but an Associated Press report now says they have been postponed several weeks because of technical difficulties.
NJIT says its mission, broadly defined, is to enhance the country's homeland security and emergency management capabilities. Its primary goal is to develop drone-borne weather sensors that can predict where a major storm will make landfall as many as two days before existing technology now permits.
Communications relay devices, the institute explains, are designed to function as flying cell towers capable of relaying calls and data from communities in which telecommunications equipment has been knocked out. Enhanced mapping technology would give emergency responders immediate information on damage caused by major storms such as Hurricane Sandy.
The ground-based pilot will be in communication with air traffic controllers during the flight. After the flight, the team will assess the drone's operational performance, as well as its success in gathering data, which NJIT will share with the Federal Aviation Administration (FAA) and emergency management agencies.
In May, NJIT says, it was the first New Jersey institution to receive a Certificate of Waiver/Authorization from the FAA to conduct UAS test flights into national airspace.
In the future, NJIT says, its drones will have the authorization to fly as far as 14.5 nautical miles out over the ocean, as high as 10,000 feet into the air, and for as many as 14 to 16 hours at a time.
NJIT is a partner in the Mid-Atlantic Aviation Partnership, a 40-plus-member consortium located at Virginia Tech, which was designated as one of six test sites authorized to develop procedures to ensure the safe integration of drones into national airspace.


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Mount Photo
What is the best way to choose a mount for a photo? (mount photo)
Some people will look at a photo and immediately decide upon a mount colour that goes well with the colours in the photo without thinking about the frame .
Here's a photo of a group of friends having a drink :
Upon looking at this photo you might immediately think that a black mount would look good on this photo :
I agree … a black mount on its own looks good !!
However , when it comes to framing the photo as well as mounting it, by choosing a black mount you straight away rule out 4 of iframeonline's frame choices.
For example ;
Black frame doesn't look the best !
Oak frame doesn't look the best !
Red frame doesn't look the best !
Washed Walnut frame doesn't look the best !
There's only 2 of our frames colours that suit this mount choice properly ;
Silver frame looks good
Gold frame looks good !
The standard way of looking at it is that if you have a dark mount then a light frame will match well and if you have a light
mount then a dark frame will match well .
My own personal choice to mount and frame this photo would be :
This black frame and antique white mount combination is particularly in fashion at the moment .
By choosing an antique white mount it gives you the option of any of our frame colours as they will all match this neutral colour.
It also gives you the option of picking a frame to match the decor and furniture in the room where it will eventually hang it .
In summary :
Its best not to pick a mount, then choose a frame … They need to be picked together to get a great combination of colours!
Iframe Online can offer a wealth of advice if you are unsure about framing and mounting any of your photos, just phone or email
and we'll be more than happy to help.
Telephone: 01492 588435
About The Author:
Scott Butterworth is a Guild Commended Framer with over 25 years photo framing experience.
He is a director of Iframe Online Ltd – a specialist photo framing company.
Start Photo Framing


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The ULT jumbo filter trolley is a portable air extraction and filtration system designed to filter dust particles, mould spores, solvent vapours and other pollutants from the work environment.
Every day conservators and restorers work with a multitude of solvents, paints and preservatives such as biocides that are often classified as hazardous materials. Objects to be restored can release dusts and vapours of unknown composition, which could include mould fungus spores into the air that could be inhaled, a major health risk. For this reason, occupational health guidelines demand air-borne hazardous particles be drawn off directly at the point at which they are released before they present a hazard to human health.
The JUMBO Filtertrolley 2.0 Restauro has been designed to meet the specific needs of conservators and restorers. In addition to its very good suction performance, the unit stands out for its low weight, easy handling and a low noise level. Its compact size means that the unit can easily fit in a car and can thus be transported easily and fast to different workplaces.
Extraction rate is easily variable and can be adjusted to very low levels to insure more delicate objects remain undisturbed.
The filter trolley is a portable unit which produces low noise levels and is easy to operate and maintain. Clean air exits at the base of the unit and produces no drafts.
A range of additional nozzles and hoods are available for further control over fumes and gases. See 'Recommended' tab below.
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