Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

Workshop on climate change and salmon production, Vancouver, March 26-27, 1998: technical report

The Workshop on Climate Change and Salmon Production was held in Vancouver, Canada, 26-27 March 1998. The Workshop was organized and sponsored by the North Pacific Anadromous Fish Commission (NPAFC). Each Party to the Commission designated one scientist to the Workshop Steering Committee. Each member of the Steering Committee chaired one half-day session of the Workshop. All necessary arrangements were made by the NPAFC Secretariat in cooperation with the Steering Committee and the Canadian Party to the Commission. (PDF contains 60 pages) Over 70 scientists, industry representatives and fisheries officials attended the Workshop. There were 20 presentations of scientific papers followed by the discussion sessions. Extended abstracts are included in this Technical Report, which also contains opening address by the Chairman of the Steering Committee and short review of the Workshop by the Coordinator. The material presented in the Technical Report has not been peer reviewed and does not necessarily reflect the views of either the NPAFC or the Parties. The material has been edited by the technical editor for clarity and publication purposes only. Items in this Report should not be cited except as personal communication and with the author's permission.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Isotopic proxies for microbial and environmental change : insights hydrogen isotopes and the Ediacaran Khufai Formation

Microbes have profoundly influenced the Earth’s environments through time. Records of these interactions come primarily from the development and implementation of proxies that relate known modern processes to chemical signatures in the sedimentary record. This thesis is presented in two parts, focusing first on novel proxy development in the modern and second on interpretation of past environments using well-established methods. Part 1, presented in two chapters, builds on previous observations that different microbial metabolisms produce vastly different lipid hydrogen isotopic compositions. Chapter 1 evaluates the potential environmental expression of metabolism-based fractionation differences by exploiting the natural microbial community gradients in hydrothermal springs. We find a very large range in isotopic composition that can be demonstrably linked to the microbial source(s) of the fatty acids at each sample site. In Chapter 2, anaerobic culturing techniques are used to evaluate the hydrogen isotopic fractionations produced by anaerobic microbial metabolisms. Although the observed fractionation patterns are similar to those reported for aerobic cultures for some organisms, others show large differences. Part 2 changes focus from the modern to the ancient and uses classical stratigraphic methods combined with isotope stratigraphy to interpret microbial and environmental changes during the latest Precambrian Era. Chapter 3 presents a detailed characterization of the facies, parasequence development, and stratigraphic architecture of the Ediacaran Khufai Formation. Chapter 4 presents measurements of carbon, oxygen, and sulfur isotopic ratios in stratigraphic context. Large oscillations in the isotopic composition of sulfate constrain the size of the marine sulfate reservoir and suggest incorporation of an enriched isotopic source. Because this data was measured in stratigraphic context, we can assert with confidence that these isotopic shifts are not related to stratigraphic surfaces or facies type but instead reflect the evolution of the ocean through time. This data integrates into the chemostratigraphic global record and contributes to the emerging picture of changing marine chemistry during the latest Precambrian Era.

Coastal brownfields and adaptation to climate change: Discussions on potential hazards from contaminated groundwater displacement due to saltwater incursion

Toxic-waste associated with coastal brownfield sites can pose serious risks to human and environmental health. In light of anticipated sea-level rise (SLR) due to global climate change, coastal brownfields require heightened attention. The primary intent of this study is to pose questions and encourage discussion of this problem among policy makers. Impacts from SLR on coastal zones are examined within a brownfield policy framework and, current coastal brownfield policy discussions with respect to SLR are also examined. (PDF contains 4 pages)

Assessing societal vulnerability of U.S. Pacific Northwest communities to storm induced coastal change

Progressive increases in storm intensities and extreme wave heights have been documented along the U.S. West Coast. Paired with global sea level rise and the potential for an increase in El Niño occurrences, these trends have substantial implications for the vulnerability of coastal communities to natural coastal hazards. Community vulnerability to hazards is characterized by the exposure, sensitivity, and adaptive capacity of human-environmental systems that influence potential impacts. To demonstrate how societal vulnerability to coastal hazards varies with both physical and social factors, we compared community exposure and sensitivity to storm-induced coastal change scenarios in Tillamook (Oregon) and Pacific (Washington) Counties. While both are backed by low-lying coastal dunes, communities in these two counties have experienced different shoreline change histories and have chosen to use the adjacent land in different ways. Therefore, community vulnerability varies significantly between the two counties. Identifying the reasons for this variability can help land-use managers make decisions to increase community resilience and reduce vulnerability in spite of a changing climate. (PDF contains 4 pages)

Impacts of climate change of seaports: A survey of knowledge, perceptions, and planning efforts among port administrators

Port authorities from around the world were surveyed to ascertain how administrators feel climate change might impact their operations, what level of change would be problematic, and how they plan to adapt to new conditions. The survey was distributed to 350 major ports through two leading international port organizations, the International Association of Ports and Harbors and the American Association of Port Authorities. (PDF contains 4 pages)

Stormwater runoff - modeling impacts of urbanization and climate change

Development pressure throughout the coastal areas of the United States continues to build, particularly in the southeast (Allen and Lu 2003, Crossett et al. 2004). It is well known that development alters watershed hydrology: as land becomes covered with surfaces impervious to rain, water is redirected from groundwater recharge and evapotranspiration to stormwater runoff, and as the area of impervious cover increases, so does the volume and rate of runoff (Schueler 1994, Corbett et al. 1997). Pollutants accumulate on impervious surfaces, and the increased runoff with urbanization is a leading cause of nonpoint source pollution (USEPA 2002). Sediment, chemicals, bacteria, viruses, and other pollutants are carried into receiving water bodies, resulting in degraded water quality (Holland et al. 2004, Sanger et al. 2008). (PDF contains 5 pages)

National perspectives on climate change adaptation: A panel discussion of climate change adaptation efforts in diverse coastal regions of the United States

Climate change has rapidly emerged as a significant threat to coastal areas around the world. While uncertainty regarding distribution, intensity, and timescale inhibits our ability to accurately forecast potential impacts, it is widely accepted that changes in global climate will result in a variety of significant environmental, social, and economic impacts. Coastal areas are particularly vulnerable to the effects of climate change and the implications of sea-level rise, and coastal communities must develop the capacity to adapt to climate change in order to protect people, property, and the environment along our nation’s coasts. The U.S. coastal zone is highly complex and variable, consisting of several regions that are characterized by unique geographic, economic, social and environmental factors. The degree of risk and vulnerability associated with climate change can vary greatly depending on the exposure and sensitivity of coastal resources within a given area. The ability of coastal communities to effectively adapt to climate change will depend greatly on their ability to develop and implement feasible strategies that address unique local and regional factors. A wide variety of resources are available to assist coastal states in developing their approach to climate change adaptation. However, given the complex and variable nature of the U.S. coastline, it is unlikely that a single set of guidelines can adequately address the full range of adaptation needs at the local and regional levels. This panel seeks to address some of the unique local and regional issues facing coastal communities throughout the U.S. including anticipated physical, social, economic and environmental impacts, existing resources and guidelines for climate change adaptation, current approaches to climate change adaptation planning, and challenges and opportunities for developing adaptation strategies. (PDF contains 4 pages)

Climate change adaptation and planning: An example from Kailua Beach, Oahu, Hawaii

The University of Hawaii Sea Grant College Program (UHSG) in partnership with the Hawaii Department of Land and Natural Resources (DLNR), Office of Conservation and Coastal Lands (OCCL) is developing a beach and dune management plan for Kailua Beach on the eastern shoreline of Oahu. The objective of the plan is to develop a comprehensive beach management and land use development plan for Kailua Beach that reflects the state of scientific understanding of beach processes in Kailua Bay and abutting shoreline areas and is intended to provide long-term recommendations to adapting to climate change including potential coastal hazards such as sea level rise. The development of the plan has lead to wider recognition of the significance of projected sea level rise to the region and provides the rational behind some of the land use conservation strategies. The plan takes on a critical light given global predictions for continued, possibly accelerated, sea-level rise and the ongoing focus of intense development along the Hawaiian shoreline. Hawaii’s coastal resource managers are faced with the daunting prospect of managing the effects of erosion while simultaneously monitoring and regulating high-risk coastal development that often impacts the shoreline. The beach and dune preservation plan is the first step in a more comprehensive effort prepare for and adapt to sea level rise and ensure the preservation of the beach and dune ecosystem for the benefit of present and future generations. The Kailua Beach and Dune Management plan is intended to be the first in a series of regional plans in Hawaii to address climate change adaptation through land use planning. (PDF contains 3 pages)

Adaptation of coastal communities in the Philippines to the impacts climate change

The Quedan and Rural Credit Guarantee Corporation (Quedancor) of the Philippine Department of Agriculture has the critical responsibility of providing and improving credit assistance to fishers, it also has the task of helping its beneficiaries meet the repayment obligations of their loans. One reason for defaults can be attributed to the devastating impact of natural calamities. Schemes in place are still insufficient to help safeguard lending programs and operations from non-repayment of loans due to production losses and damages to personal properties.(PDF contains 5 pages) Natural calamities include the uncertainties and vagaries of weather and climate that bring about typhoons, floods, and drought; earthquakes; volcanic eruption as well as pests and diseases that affect the productivity of fisheries. When natural calamities occur, small fishers are unable to pay their loans from Quedancor, moreover they have difficulty renewing their loan applications from Quedancor or accessing credit from other sources. Failure to access credit could disable them to continue venture on fishing activities and could eventually jeopardize the welfare of their entire household. The inability of creditors to pay their loans and meet their obligations also impair, to a large extent, the financial operation and viability of the lending institutions. Risk management schemes currently employed include price stabilization measures, targeted relief` to typhoons and drought victims, and crop insurance systems, to name a few. Some of these schemes are becoming very expensive to implement. Moreover, they fail to enable fishers regain sufficient resources so that they may continue production.

Preparing for and adapting to climate change impacts: Next steps for the Washington state department of National Resources Aquatic Resources Program

In response to a growing body of research on projected climate change impacts to Washington State’s coastal areas, the Washington State Department of Natural Resources’ (DNR) Aquatic Resources Program (the Program) initiated a climate change preparedness effort in 2009 via the development of a Climate Change Adaptation Strategy (the Strategy)i. The Strategy answers the question “What are the next steps that the Program can take to begin preparing for and adapting to climate change impacts in Washington’s coastal areas?” by considering how projected climate change impacts may effect: (1) Washington’s state-owned aquatic landsii, (2) the Program’s management activities, and (3) DNR’s statutorily established guidelines for managing Washington’s state-owned aquatic lands for the benefit of the public. The Program manages Washington’s state-owned aquatic lands according to the guidelines set forth in Revised Code of Washington 79-105-030, which stipulates that DNR must manage state-owned aquatic lands in a manner which provides a balance of the following public benefits: (1) Encouraging direct public uses and access; (2) Fostering water-dependent uses; (3) Ensuring environmental protection; (4) Utilizing renewable resources. (RCW 79-105-030) The law also stipulates that generating revenue in a manner consistent with these four benefits is a public benefit (RCW 79-105-030). Many of the next steps identified in the Strategy build off of recommendations provided by earlier climate change preparation and adaptation efforts in Washington State, most notably those provided by the Preparation and Adaptation Working Group, which were convened by Washington State Executive Order 70-02 in 2007, and those made in the Washington Climate Change Impacts Assessment (Climate Impacts Group, 2009). (PDF contains 4 pages)

Adapting to climate change: Combining economics and geomorphology in coastal policy

How is climate change affecting our coastal environment? How can coastal communities adapt to sea level rise and increased storm risk? These questions have garnered tremendous interest from scientists and policy makers alike, as the dynamic coastal environment is particularly vulnerable to the impacts of climate change. Over half the world population lives and works in a coastal zone less than 120 miles wide, thereby being continuously affected by the changes in the coastal environment [6]. Housing markets are directly influenced by the physical processes that govern coastal systems. Beach towns like Oak Island in North Carolina (NC) face severe erosion, and the tax assesed value of one coastal property fell by 93% in 2007 [9]. With almost ninety percent of the sandy beaches in the US facing moderate to severe erosion [8], coastal communities often intervene to stabilize the shoreline and hold back the sea in order to protect coastal property and infrastructure. Beach nourishment, which is the process of rebuilding a beach by periodically replacing an eroding section of the beach with sand dredged from another location, is a policy for erosion control in many parts of the US Atlantic and Pacific coasts [3]. Beach nourishment projects in the United States are primarily federally funded and implemented by the Army Corps of Engineers (ACE) after a benefit-cost analysis. Benefits from beach nourishment include reduction in storm damage and recreational benefits from a wider beach. Costs would include the expected cost of construction, present value of periodic maintenance, and any external cost such as the environmental cost associated with a nourishment project (NOAA). Federal appropriations for nourishment totaled $787 million from 1995 to 2002 [10]. Human interventions to stabilize shorelines and physical coastal dynamics are strongly coupled. The value of the beach, in the form of storm protection and recreation amenities, is at least partly capitalized into property values. These beach values ultimately influence the benefit-cost analysis in support of shoreline stabilization policy, which, in turn, affects the shoreline dynamics. This paper explores the policy implications of this circularity. With a better understanding of the physical-economic feedbacks, policy makers can more effectively design climate change adaptation strategies. (PDF contains 4 pages)