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Using public litigation records to identify priority science needs for managing public lands
Relevant science is essential for effective natural resource decision making, including on public lands managed by the United States Department of the Interior (DOI) Bureau of Land Management (BLM), that cover 1/10th of the United States. Most of the BLM’s management decisions require analyses under the National Environmental Policy Act, and the use of science in these decisions is often challenged. Using coproduction, we assembled an interagency team of scientists and resource managers to develop a method for using public litigation to identify priority science needs for the BLM. We searched publicly available case documents finalized from 2015–2019 in Wyoming, Colorado, Utah, and New Mexico within federal courts and the DOI Office of Hearings and Appeals, and identified 108 case documents that involved challenges to the BLM’s use of science. We retained 48 case documents that contained at least one challenge about the BLM’s use of science for a specific resource. We categorized all challenges in each case document according to the proposed action, affected resource, type of science challenged (data about resources, science relevant to potential impacts, methods for analyzing potential impacts, and mitigation actions), and specific nature of the challenge (e.g., challenging direct effects analysis). We identified priority science needs based on the frequency of challenges, the number of states where similar challenges occurred, whether the BLM lost the challenge, and whether the case was remanded. Top needs related to oil and gas development actions and included science about effects on air quality and climate, water, and socioeconomics; data for air quality and climate; and methods for analyzing potential impacts to cultural resources and air quality and climate. The BLM can use this information to prioritize actions (e.g., funding new research or science syntheses) to strengthen its science foundation for decision-making.
Resistance and Protective Immunity in Redfish Lake Sockeye Salmon Exposed to M Type Infectious Hematopoietic Necrosis Virus (IHNV)
Differential virulence of infectious hematopoietic necrosis virus (IHNV) isolates from the U and M phylogenetic subgroups is clearly evident in the Redfish Lake (RFL) strain of sockeye salmon Oncorhynchus nerka. In these fish, experimental immersion challenges with U isolates cause extremely high mortality and M isolates cause low or no mortality. When survivors of M virus immersion challenges were exposed to a secondary challenge with virulent U type virus they experienced high mortality, indicating that the primary M challenge did not elicit protective immunity. Delivery of a moderate dose (2 × 104 plaque-forming units [PFU]/fish) of virus by intraperitoneal injection challenge did not overcome RFL sockeye salmon resistance to M type IHNV. Injection challenge with a high dose (5 × 106 PFU/fish) of M type virus caused 10% mortality, and in this case survivors did develop protective immunity against a secondary U type virus challenge. Thus, although it is possible for M type IHNV to elicit cross-protective immunity in this disease model, it does not develop after immersion challenge despite entry, transient replication of M virus to low levels, stimulation of innate immune genes, and development of neutralizing antibodies in some fish.
Infectious haematopoietic necrosis virus genogroup-specific virulence mechanisms in sockeye salmon, Oncorhynchus nerka (Walbaum), from Redfish Lake, Idaho
Characterization of infectious haematopoietic necrosis virus (IHNV) field isolates from North America has established three main genogroups (U, M and L) that differ in host-specific virulence. In sockeye salmon, Oncorhynchus nerka, the U genogroup is highly virulent, whereas the M genogroup is nearly non-pathogenic. In this study, we sought to characterize the virus-host dynamics that contribute to genogroup-specific virulence in a captive stock of sockeye salmon from Redfish Lake in Idaho. Juvenile sockeye salmon were challenged by immersion and injection with either a representative U or M viral strain and sampled periodically until 14 days post-infection (p.i.). Fish challenged with each strain had positive viral titre by day 3, regardless of challenge route, but the fish exposed to the M genogroup virus had significantly lower virus titres than fish exposed to the U genogroup virus. Gene expression analysis by quantitative reverse transcriptase PCR was used to simultaneously assess viral load and host interferon (IFN) response in the anterior kidney. Viral load was significantly higher in the U-challenged fish relative to M-challenged fish. Both viruses induced expression of the IFN-stimulated genes (ISGs), but expression was usually significantly lower in the M-challenged group, particularly at later time points (7 and 14 days p.i.). However, ISG expression was comparable with 3 days post-immersion challenge despite a significant difference in viral load. Our data indicated that the M genogroup virus entered the host, replicated and spread in the sockeye salmon tissues, but to a lesser extent than the U genogroup. Both virus types induced a host IFN response, but the high virulence strain (U) continued to replicate in the presence of this response, whereas the low virulence strain (M) was cleared below detectable levels. We hypothesize that high virulence is associated with early in vivo replication allowing the virus to achieve a threshold level, which the host innate immune system cannot control. ?? 2009 Blackwell Publishing Ltd.
Virulence of Renibacterium salmoninarum to salmonids
Virulence of Renibacterium salmoninarum isolates representing five origins was evaluated in eight salmonid hosts; four origins were of Lake Michigan and the fifth was of the Pacific Northwest. The species type strain, ATCC (American Type Culture Collection) 33209, was also included. Each isolate was grown in a kidney disease medium (KDM2) supplemented with 1 % ATCC 33209 culture metabolite; serial 10-fold dilutions were prepared, and groups of fish were challenged by intraperitoneal injection with 0.1 mL of each dilution. A 70-d observation period followed, and bacterial kidney disease (BKD) was diagnosed by the fluorescent antibody technique. Virulence of isolates was quantified as a dose lethal to 50% of fish (LD50) for each host–isolate challenge. In the first set of experiments, 23 isolates were used to challenge groups of brook trout Salvelinus fontinalis. The mean LD50 was 1.087 x 10 6 colony-forming units per milliliter (cfu/mL; SD = 2.022 x 10 6 ), and the LD50 values ranged from 8.457 x 10 6 to 2.227 x 10 4 cfu/mL. Analysis of variance to evaluate the effect of isolate origin on virulence in brook trout revealed no significant difference ( F = 1.502; P = 0.243). Susceptibilities of the other salmonid hosts were evaluated by challenge with six isolates of R. salmoninarum representing each origin and the species type strain. For many of the host–isolate challenge combinations, time to death was highly dependent on the dilution (number of bacteria) injected. In general, the isolates MCO4M, B26, and A34 (all of Lake Michigan origin) tended to be more virulent. Also, LD50 values were dispersed throughout a wider range among the more susceptible hosts. Lake trout Salvelinus namaycush, rainbow trout Oncorhynchus mykiss, and brook trout were relatively resistant to challenge with the strains, whereas coho salmon O. kisutch, domestic Atlantic salmon Saltno salar, and chinook salmon O. tshawytscha were relatively susceptible. Another challenge evaluated the effect of washing R. salmoninarum MCO4M cells before injection into brook trout. The calculated LD50 value, 2.009 x 10 5 cfu/mL, was similar ( X 2 = 0.878; P = 0.645) to that of the unwashed cells (1.163 x 10 5 cfu/mL). Furthermore, times to death for successive dilutions were similar regardless of whether or not the cells were washed.
Users and uses of Landsat 8 satellite imagery—2014 survey results
Executive Summary In 2013, Landsat 8 began adding high quality, global, moderate-resolution imagery to the more than 40-year archive of Landsat imagery. To assess the potential effects of the availability of Landsat 8 imagery on users and their work, the U.S. Geological Survey (USGS) Land Remote Sensing Program (LRS) initiated a survey of Landsat users. The objectives of the survey were to 1. Characterize various Landsat user groups, such as United States (U.S.) and international users and Landsat 8 and non-Landsat 8 users; 2. Identify any differences among user groups in uses and preferences; 3. Measure the importance of and satisfaction with Landsat 8 attributes; 4. Assess the importance to users of the frequency of usable imagery; and 5. Determine any challenges in using Landsat 8. The online survey was sent to 51,617 Landsat users registered with USGS in May 2014. Almost 13,000 people responded to the survey for a response rate of 25 percent (n = 12,966). Current Landsat users (users who had used Landsat in their work in the year prior to the survey) composed 89 percent of the sample (n = 11,549) and past Landsat users composed 11 percent (n = 1,417). The results reported here apply to current Landsat users registered with the USGS Earth Resources Observation and Science (EROS) Center. Users from 161 countries responded to the survey. Of those, 19 percent were citizens or permanent residents of the United States and 81 percent resided in other countries. More than 70 percent of current users had used Landsat 8 in the year prior to the survey. The majority of Landsat 8 users (65 percent) were established users who used Landsat imagery regularly both before and after Landsat 8 imagery became available. The average current Landsat user was male, 36 years old, and highly educated, with 9 years of experience using satellite imagery or geographic information system (GIS) software. Landsat 8 users had, on average, two more years of experience than non-Landsat 8 users. Users were employed predominantly by academic institutions (65 percent), followed by private businesses (13 percent), Federal governments (10 percent), State and local governments (6 percent), and nonprofit organizations (6 percent). Of the Landsat imagery obtained in the past year by current users, on average 31 percent came from a Landsat 8 sensor. An equivalent amount came from the Landsat 7 ETM+ sensor (33 percent); slightly less came from Landsats 4 and 5 TM sensors (27 percent). Much less came from Landsats 1 through 5 MSS sensors (5 percent). Overall, more than a third of users’ work used Landsat imagery (38 percent). Of this work, on average, 37 percent of the work was operational. Landsat 8 users considered a greater proportion of their work operational than non-Landsat 8 users (39 percent compared with 29 percent). Environmental sciences and management were the most commonly selected primary applications (selected by 42 percent of users). Land use/land cover (23 percent) was the second most commonly selected primary application, followed by education (12 percent), agriculture (9 percent), and planning and development (6 percent). Landsat 8 users were asked to rank the importance of certain attributes in determining whether to use Landsat 8 imagery in their work. The archive was ranked most important, followed by cost, spatial resolution, extent of coverage, data quality, and frequency of revisit. Users were asked how satisfied they were with these same attributes as they currently apply to Landsat 8 imagery. On average, users were most satisfied with lack of cost, extent of coverage, data quality, and the archive, but they were satisfied with all attributes. Users were asked how often they needed Landsat imagery to meet various requirements for their primary application. The survey question specifically asked how often users needed usable imagery, which differs from how often they would like the Landsat satellites to acquire an image. Users were asked to identify their needed frequency of usable imagery for the following levels: 1. Threshold level—the minimum frequency of usable imagery needed to be of any value to their primary application. 2. Breakthrough level—the frequency of usable imagery that would result in a significant improvement for their primary application of the imagery. 3. Target level—the frequency of usable imagery that would only provide a limited additional increase in the expected performance for their primary application. To meet the threshold level, three-quarters of users needed usable imagery every 17 days or less frequently. At the breakthrough level, two-thirds of users (64 percent) needed a usable image every 5–16 days. The current constellation of two satellites (Landsat 7 and 8) is capable of meeting the threshold and breakthrough needs of most users at least some of the time, but a single satellite would be highly unlikely to do so. Two-fifths of users (40 percent) felt that usable imagery provided every 4 days or more frequently would meet their target level which the current Landsat constellation cannot provide. Landsat 8 users were significantly more likely than non-Landsat 8 users to need usable imagery more frequently to meet their target levels. Additionally, U.S. Landsat 8 users were significantly more likely than other Landsat users to need usable imagery more frequently in order meet both their breakthrough and target levels. To explore the effect of the availability of Landsat 8 imagery on Landsat imagery use in general, established users (those who had consistently used Landsat imagery both before and after Landsat 8 imagery became available) using Landsat 8 imagery were asked about changes in the amount of Landsat imagery they used. The majority of established users using Landsat 8 imagery (60 percent) reported an average increase of 51 percent in the number of scenes obtained after Landsat 8 imagery became available. Landsat 8 users were asked if they had encountered challenges in using Landsat 8 whereas non-Landsat 8 users were asked if such challenges had played a role in why they were not using Landsat 8 imagery. Although many users did not encounter challenges when using or trying to use Landsat 8 data, slightly less than 30 percent did encounter issues with processing the data to a usable point. The most common issue reported was not being able to create or have access to a surface reflectance corrected product. Other challenges were related to the file sizes of images being too large to download, store, or analyze. There were no statistically significant differences between Landsat 8 and non-Landsat 8 users in terms of challenges encountered when using or trying to use the imagery, which indicates that users were not unduly discouraged by the challenges they may have encountered. When asked about potential consequences of not using Landsat 8, more than half of the non-Landsat 8 users did not report detrimental effects on their work from not using the imagery. Of those who did report detrimental effects, decreased quality of work, decreased scope of work, and increased time spent on work were the most common.
Research to improve ShakeAlert earthquake early warning products and their utility
Earthquake early warning (EEW) is the rapid detection of an earthquake and issuance of an alert or notification to people and vulnerable systems likely to experience potentially damaging ground shaking. The level of ground shaking that is considered damaging is defined by the specific application; for example, manufacturing equipment may experience damage at a lower intensity ground shaking than would cause damage to a building. Along the West Coast of the United States, the warning times for ground shaking could range as high as tens of seconds for moderate levels of ground shaking, or potentially longer, if a lower ground-shaking threshold is used to issue alerts. However, it is not always possible to provide advance warning of ground shaking, particularly for locations close to an earthquake that are most likely to experience very strong ground shaking. EEW alerts may be useful to individuals who can use a few seconds to move to a safe zone and to electromechanical systems that can take automatic actions to reduce damage and injuries. An EEW system, ShakeAlert, has been under development in the United States since 2006. Federal and State governments, as well as the private sector, are now investing in the ShakeAlert prototype system that will, when completed, become an operational public system for the West Coast of the United States. While the current prototype is delivering alerts to test users, improvements to the accuracy, timeliness, and utility of the alerts are needed. For this reason, it is essential that the ShakeAlert system be continuously improved through targeted research, involving not only the current ShakeAlert partner organizations, but also the broader scientific, engineering, and emergencyresponse communities. To this end, this report describes the opportunities for improvement that can be addressed through research and development over the next 5 years. Our recommendations are organized into four areas: (1) understand EEW capabilities and user needs, (2) make alerts as fast and accurate as possible, (3) ensure reliability when it counts, and (4) explore the use of new instrumentation. The first challenge is to understand EEW capabilities and user needs. EEW must deliver actionable information to people and to automated systems to mitigate short- and longterm impacts of damaging ground shaking, so development of EEW must be motivated by the needs of users. Within this challenge, we must study the technical capabilities and limitations of EEW in general, and the ShakeAlert system specifically. This includes development of performance metrics that assess the timeliness and accuracy of alerts to understand the value and utility of the ShakeAlert EEW product(s) for various user groups, including different industry sectors, emergency-management agencies, and the public. Research is needed to define the alerting choices that maximize the utility of the system for users and to determine what the available communication pathways are for providing timely alert information. Additionally, we engage users to assess how alerts will be used by different sectors to mitigate losses and to inform EEW product design. Further, social-science research is needed to develop alert messaging, including what relevant prior and follow-up information are required, to ensure effective use of alerts. The second challenge is to make alerts as fast and as accurate as possible. The timeliness and accuracy of an EEW alert is important because it will set in motion a series of actions and downstream products. An EEW alert will trigger notification across emergency-alert systems and across multiple communication channels to populations in impacted regions. The EEW alert region may grow as the earthquake fault-rupture length increases, and the EEW system’s characterization of it, evolves. We must continue research into new or improved seismic and geodetic waveform-processing methods necessary to rapidly characterize the expected ground shaking and associated uncertainties. It is important to thoroughly evaluate whether new methods improve alerts through more accurate ground-motion estimates and (or) reduced latencies (that is, longer warning times). New methods could include tracking the extent of a large rupture in real time (known as finite-fault algorithms) and ground-motionbased EEW algorithms. Additionally, ground motion predictions could be optimized for each earthquake as the earthquake fault rupture progresses by using, for example, event terms to shift ground-motion curves for more (or less) energetic ruptures. The third challenge is to ensure reliability when it counts. This challenge requires us to explore approaches that assess the expected performance of ShakeAlert across the range of earthquake magnitudes, locations, and depths that may occur within the alerting region. Large, damaging earthquakes and their associated aftershock sequences matter most for hazard and for EEW, but these large-earthquake sequences occur infrequently. We expect ShakeAlert to respond robustly to these large-earthquake sequences despite potentially long periods of relative seismic quiescence in the intervening years, and in spite of inevitable communication challenges that arise during and after a large earthquake. We must develop methods to utilize the broadest available datasets to test EEW performance, including ground-motion data recorded in other parts of the world. The observational period for large, damaging earthquakes in any particular region has been short in comparison to estimated large-earthquake recurrence times. Ground-motion records for very large, damaging western United States events and major aftershock sequences do not yet exist, nor do data exist for all potential sources of noise and spurious signals that ShakeAlert must be “tuned” to reject. In addition, robust synthetic data could provide the flexibility to test a wider range of earthquake magnitude, tectonic-setting, and noise scenarios than are covered by existing observational data. Synthetic ground-motion data must be thoroughly vetted against records of smaller magnitude earthquakes to ensure that they accurately capture both the onset and the amplitude of the ground shaking. The final challenge is to explore the use of new instrumentation. The development of EEW around the world to date has focused on the use of high-quality, scientific-grade seismic and geodetic instrumentation. The use of additional types of instrumentation or information may also improve EEW products by filling gaps in sensor coverage in countries that already have dense seismic networks or enable EEW in countries without such networks. We must keep up with these developments and continuously assess their value in supplementing existing EEW systems, such as ShakeAlert, or enabling EEW where such systems do not exist. Such developments include low-cost instrumentation with microelectromechanical system (MEMS) sensors and global positioning system (GPS)/global navigation satellite system (GNSS) antennas embedded in low-cost consumer electronics, sea-floor seismometers, geodetic instrumentation deployed along the Cascadia and Alaska megathrust margins of western North America, and borehole strainmeters that are already deployed across the region.
A more representative community of ecologists
Ecologists play a crucial role in providing solutions to the challenges facing the world. For most of the history of the field, however, the science of ecology has been pursued by white men, and increasingly, by white women. This lack of diversity is untenable today, not only because it is socially unjust, but also because solving environmental problems requires diversity. Ecology as a science is an extremely rewarding and fun career choice for many, but how can the field recruit a more diverse workforce to do this important and gratifying work? Attracting and retaining future ecologists of color is the focus of this Forum. How do young people choose a career in ecology and environmental sciences? For many ecologists, environmental scientists and managers, and future natural resource professionals, an early field experience provides a crucial introduction and gateway. A sojourn at a field station, an extended field trip, or field expedition has introduced many of today’s professionals to their fields, but at the same time, a growing literature documents problematic behavior, discrimination, and other forms of harassment that have been far too frequently reported, and little attention has been given to conscious or implicit exclusion of students from diverse backgrounds. In their lead article, Bowser and Cid, two leading researchers and long-time champions of diversity in ecology, build on experience in long-running programs as well as the literature to diagnose challenges facing diverse youth, and present approaches to encourage, rather than discourage, further engagement. They describe affirmative and creative measures that foster a sense of inclusion and community among young scholars; this sense of belonging and empowerment allows many to advance to studies and careers in ecology and environmental science. In the subsequent six papers, authors explore topics either responding to, or inspired by, the lead paper. They explore alternatives to a field experience as a gateway to a career in ecology or environmental sciences through, for example, data science or the social sciences. Other comment papers describe challenges faced in the next phases of an academic career, barriers faced by specific cultural groups and the approaches, challenges, and outcomes of programs aiming to increase the diversity of the environmental STEM workforce. All responses sound a clarion call for change to hear and value different voices and perspectives to be heard and valued. These include (1) structural and cultural change to our institutions and reward structures; (2) developing and nurturing personal relationships among students and their mentors, within teams and in internships; (3) making entry to ecology inviting and making advancement in ecology free from systemic barriers; and (4) broadening our vision of ecology, and the ways we learn about the world’s ecosystems. The Ecological Society of America, the home for Ecological Applications , is committed to the diversity, equity and inclusion needed to tackle environmental challenges in unity (https://www.esa.org/esablog/2020/09/24/time-for-action-esa-initiates-a-diversity-equity-inclusion-and-justice-deij-task-force/). The world needs all available talent and perspectives to meet environmental challenges today. Ecological Applications has long published occasional papers on the profession of ecology and never ones more important or timely than these. The editorial team is proud to provide an outlet for the voices of our field, in all its current, if inadequate, diversity and honored to host the passionate and committed views of our authors.
Specificity of DNA vaccines against the U and M genogroups of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss)
Infectious hematopoietic necrosis virus (IHNV) is a fish rhabdovirus that causes significant mortality in salmonid species. In North America IHNV has three major genogroups designated U, M, and L. Host-specificity of the M and U genogroups of IHNV has been established both in the field and in experimental challenges, with M isolates being more prevalent and more virulent in rainbow trout (Oncorhynchus mykiss), and U isolates being more prevalent and highly virulent in sockeye salmon (Oncorhynchus nerka). In this study, efficacy of DNA vaccines containing either M (pM) or U (pU) virus glycoprotein genes was investigated during intra- and cross-genogroup challenges in rainbow trout. In virus challenges at 7 days post-vaccination (early antiviral response), both pM and pU were highly protective against either M or U IHNV. In challenges at 28 days post-vaccination (specific antiviral response), both pM and pU were protective against M IHNV but the homologous pM vaccine was significantly more protective than pU in one of two experiments. At this stage both pM and pU induced comparably high protection against U IHNV challenge. Correlates of protection were also investigated by assessing the expression of the interferon-stimulated gene Mx-1 and the production of neutralizing antibodies (NAbs) following pM or pU DNA vaccination. Mx-1 gene expression, measured at 4 and 7 days post-vaccination as an indicator of the host innate immune response, was found to be significantly higher after pM than pU vaccination in some cases. Neutralizing antibody was produced in response to the two vaccines, but antibody titers did not show consistent correlation with protection. The results show that the rainbow trout innate and adaptive immune responses have some ability to distinguish between the U and M genogroup IHNV, but overall the pM and pU vaccines were protective against both homologous and cross-genogroup challenges.
Projected evolution of California's San Francisco Bay-Delta-River System in a century of continuing climate change
Background Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species. Methodology/Principal Findings We linked a series of models to investigate responses of California's San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010–2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations. Conclusions/Significance Most of these environmental indicators change substantially over the 21 st century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.
Infectious pancreatic necrosis virus: transmission from infectious to susceptible rainbow trout fry
Fry of rainbow trout Oncorhynchus mykiss were exposed to serotype VR-299 of infectious pancreatic necrosis virus (IPNV) by using a standardized immersion challenge. In concurrent experiments, fish were monitored for 11 d for excretion of IPNV or monitored for 9 d for excretion and transmission of IPNV to susceptible rainbow trout fry. Immersion-challenged fish began excreting virus within 2 d after challenge. The rate of IPNV excretion per fish increased steadily from about day 4 to day 8 and then decreased. Virus concentrations in tissues of immersion-challenged fish increased exponentially. Susceptible fish became infected with IPNV within 4 d after being introduced to immersion-challenged fish (e.g., 2 d after the challenged fish began excreting virus). By 9 d, 84% of the susceptible fish were infected with IPNV.
Vaccination of rainbow trout against infectious hematopoietic necrosis (IHN) by using attenuated mutants selected by neutralizing monoclonal antibodies
A neutralizing monoclonal antibody against infectious hematopoietic necrosis virus (IHNV) was used to select neutralization-resistant mutants from isolates of virus obtained from adult steelhead Oncorhynchus mykiss returning to the Round Butte Hatchery (RB mutants) on the Deschutes River in Oregon, USA, and from rainbow trout (nonanadromous O. mykiss) at a commercial hatchery in the Hagerman Valley of Idaho, USA (193-110 mutants). Two of the mutants, RB-1 and 193-110-4, were significantly (P < 0.001) attenuated compared with parental strains. Vaccination of rainbow trout by waterborne exposure to the mutants conferred solid protection against challenge with wild-type virus. In some trials, fish vaccinated with the RB-1 mutant at 50% tissue culture infectious doses (TCID50) of 1 X 104-1 x 105 TCID50/mL or with the 193-110-4 mutant at 1 x 102-1 x 103 TCID50/mL, held for 14 d, then challenged with the homologous wild-type strain at 1 x 105 TCID50/mL showed relative percent survival of 95-100% (P < 0.005). There was no significant difference (P > 0.05) in protection among fish exposed to the RB-1 vaccine strain at a dose of 1 x 105 TCID50/mL for periods of either 1, 12, or 24 h, held for 14 d, and then challenged with the wild-type RB isolate, although the 1-h exposure seemed to be somewhat less effective. Fish were vaccinated with the RB-1 strain at 1 x 103-1 x 105 TCID50/mL for 24 h then challenged after 1, 7, 14, or 21 d with the wild-type RB isolate. No significant (P > 0.1) protection was observed at 1 d postvaccination, but the relative percent survival increased progressively at each subsequent challenge period, becoming statistically significant by day 7 (P < 0.001) and beyond. These results suggested that resistance to challenge with wild-type virus resulted from development of IHNV-specific immunity and not from viral interference or interferon induction, and they reinforce the potential of an attenuated vaccine to control this important disease.
Pathogenicity of West Nile virus and response to vaccination in sandhill cranes ( Grus canadensis ) using a killed vaccine
West Nile virus was introduced into the United States in the vicinity of New York, New York, USA in 1999. The virus has since killed large numbers of birds nationwide, especially, but not limited to, crows ( Corvus brachyrhinchos ). One sandhill crane ( Grus canadensis ) at the Bridgeport Zoo (Bridgeport, Connecticut, USA) reportedly died from West Nile virus, so sandhill cranes and endangered whooping cranes ( Grus americana ), both in the wild and in captive breeding colonies at United States Geological Service (USGS) Patuxent Wildlife Research Center (Laurel, Maryland, USA) were considered at risk. A killed vaccine in sandhill cranes was evaluated by vaccinating and then challenging these cranes with live West Nile virus. No sandhill cranes inoculated with the killed vaccine developed significant titers when compared with unvaccinated controls. No sandhill cranes inoculated with the vaccine and challenged with the virus died from West Nile virus infection. In addition, no unvaccinated challenged sandhill cranes died. However, 2 days postchallenge, vaccinated cranes had significantly less viremia (P < 0.05) than unvaccinated cranes. Seven days postchallenge vaccinated cranes had significantly less cloacal shedding of the virus (P < 0.05) than unvaccinated cranes and significantly less weight loss (P < 0.05) as compared with unvaccinated cranes. Vaccinated sandhill cranes developed significantly higher titers 14 days postchallenge and were viremic for shorter periods of time after challenge than unvaccinated individuals. Unvaccinated challenged cranes had glial cell aggregates in both the brain and brain stem areas, and this was not observed in vaccinated challenged cranes or in vaccinated unchallenged cranes.
Western water and climate change
The western United States is a region long defined by water challenges. Climate change adds to those historical challenges, but does not, for the most part, introduce entirely new challenges; rather climate change is likely to stress water supplies and resources already in many cases stretched to, or beyond, natural limits. Projections are for continued and, likely, increased warming trends across the region, with a near certainty of continuing changes in seasonality of snowmelt and streamflows, and a strong potential for attendant increases in evaporative demands. Projections of future precipitation are less conclusive, although likely the northernmost West will see precipitation increases while the southernmost West sees declines. However, most of the region lies in a broad area where some climate models project precipitation increases while others project declines, so that only increases in precipitation uncertainties can be projected with any confidence. Changes in annual and seasonal hydrographs are likely to challenge water managers, users, and attempts to protect or restore environmental flows, even where annual volumes change little. Other impacts from climate change (e.g., floods and water-quality changes) are poorly understood and will likely be location dependent. In this context, four iconic river basins offer glimpses into specific challenges that climate change may bring to the West. The Colorado River is a system in which overuse and growing demands are projected to be even more challenging than climate-change-induced flow reductions. The Rio Grande offers the best example of how climate-change-induced flow declines might sink a major system into permanent drought. The Klamath is currently projected to face the more benign precipitation future, but fisheries and irrigation management may face dire straits due to warming air temperatures, rising irrigation demands, and warming waters in a basin already hobbled by tensions between endangered fisheries and agricultural demands. Finally, California's Bay-Delta system is a remarkably localized and severe weakness at the heart of the region's trillion-dollar economy. It is threatened by the full range of potential climate-change impacts expected across the West, along with major vulnerabilities to increased flooding and rising sea levels.
Development of a subunit vaccine for infectious pancreatic necrosis virus using a baculovirus insect/larvae system
Various attempts to develop a vaccine against infectious pancreatic necrosis virus (IPNV) have not yielded consistent results. Thus, at present, no commercial vaccine is available that can be used with confidence to immunize fry of salmon and trout. We generated a cDNA clone of the large genome segment A of an IPNV Sp strain and expressed all structural protein genes in insect cells and larvae using a baculovirus expression system. Green fluorescent protein was also co-expressed as a reporter molecule. High yields of IPNV proteins were obtained and the structural proteins self assembled to form virus-like particles (VLPs). We tested the immunogenicity of the putative VLP antigen in immersion vaccine experiments (two concentrations) in rainbow trout (Oncorhynchus mykiss) fry, and by intraperitoneal immunisation of Atlantic salmon (Salmo salar) pre-smolts using an oil adjuvant formulation. Rainbow trout were challenged by immersion using either the Sp or the VR-299 strain of IPNV two or three weeks post-vaccination, while Atlantic salmon were bath challenged with Sp strain after two months, after parr-smolt transformation. In the rainbow trout fry challenged two weeks post-immunization, cumulative mortality rates three weeks post challenge were 14 % in the fry that had received the highest dose versus 8 % in the control groups. No indication of protection was seen in repeated trials using a lower dose of antigen and challenge three weeks post-immunisation. The cumulative mortality rate of intraperitoneally immunised Atlantic salmon post-smolts four weeks post challenge was lower (56 %) than in the control fish (77 %), showing a dose-response pattern.
Errors in aerial survey count data: Identifying pitfalls and solutions
Accurate estimates of animal abundance are essential for guiding effective management, and poor survey data can produce misleading inferences. Aerial surveys are an efficient survey platform, capable of collecting wildlife data across large spatial extents in short timeframes. However, these surveys can yield unreliable data if not carefully executed. Despite a long history of aerial survey use in ecological research, problems common to aerial surveys have not yet been adequately resolved. Through an extensive review of the aerial survey literature over the last 50 years, we evaluated how common problems encountered in the data (including nondetection, counting error, and species misidentification) can manifest, the potential difficulties conferred, and the history of how these challenges have been addressed. Additionally, we used a double-observer case study focused on waterbird data collected via aerial surveys and an online group (flock) counting quiz to explore the potential extent of each challenge and possible resolutions. We found that nearly three quarters of the aerial survey methodology literature focused on accounting for nondetection errors, while issues of counting error and misidentification were less commonly addressed. Through our case study, we demonstrated how these challenges can prove problematic by detailing the extent and magnitude of potential errors. Using our online quiz, we showed that aerial observers typically undercount group size and that the magnitude of counting errors increases with group size. Our results illustrate how each issue can act to bias inferences, highlighting the importance of considering individual methods for mitigating potential problems separately during survey design and analysis. We synthesized the information gained from our analyses to evaluate strategies for overcoming the challenges of using aerial survey data to estimate wildlife abundance, such as digital data collection methods, pooling species records by family, and ordinal modeling using binned data. Recognizing conditions that can lead to data collection errors and having reasonable solutions for addressing errors can allow researchers to allocate resources effectively to mitigate the most significant challenges for obtaining reliable aerial survey data.
Applied Geochemistry Special Issue on Environmental geochemistry of modern mining
Environmental geochemistry is an integral part of the mine-life cycle, particularly for modern mining. The critical importance of environmental geochemistry begins with pre-mining baseline characterization and the assessment of environmental risks related to mining, continues through active mining especially in water and waste management practices, and culminates in mine closure. The enhanced significance of environmental geochemistry to modern mining has arisen from an increased knowledge of the impacts that historical and active mining can have on the environment, and from new regulations meant to guard against these impacts. New regulations are commonly motivated by advances in the scientific understanding of the environmental impacts of past mining. The impacts can be physical, chemical, and biological in nature. The physical challenges typically fall within the purview of engineers, whereas the chemical and biological challenges typically require a multidisciplinary array of expertise including geologists, geochemists, hydrologists, microbiologists, and biologists. The modern mine-permitting process throughout most of the world now requires that potential risks be assessed prior to the start of mining. The strategies for this risk assessment include a thorough characterization of pre-mining baseline conditions and the identification of risks specifically related to the manner in which the ore will be mined and processed, how water and waste products will be managed, and what the final configuration of the post-mining landscape will be. In the Fall 2010, the Society of Economic Geologists held a short course in conjunction with the annual meeting of the Geological Society of America in Denver, Colorado (USA) to examine the environmental geochemistry of modern mining. The intent was to focus on issues that are pertinent to current and future mines, as opposed to abandoned mines, which have been the focus of numerous previous short courses. The geochemical challenges of current and future mines share similarities with abandoned mines, but differences also exist. Mining and ore processing techniques have changed; the environmental footprint of waste materials has changed; environmental protection has become a more integral part of the mine planning process; and most historical mining was done with limited regard for the environment. The 17 papers in this special issue evolved from the Society of Economic Geologists’ short course. The relevant geochemical processes encompass the source, transport, and fate of contaminants related to the life cycle of a mine. Contaminants include metals and other inorganic species derived from geologic sources such as ore and solid mine waste, and substances brought to the site for ore processing, such as cyanide to leach gold. Factors, such as mine-waste mineralogy, hydrologic setting, mine-drainage chemistry, and microbial activity, that affect the hydrochemical risks from mining are reviewed by Nordstrom et al. In another paper, Nordstrom discusses baseline characterization at mine sites in a regulatory framework, and emphasizes the influence of mineral deposits in producing naturally elevated concentrations of many trace elements in surface water and groundwater. Surface water quality in mineralized watersheds is influenced by a number of processes that act on daily (diel) cycles and can produce dramatic variations in trace element concentrations as described by Gammons et al. Pre-mining baseline characterization studies should strive to capture the magnitude of these diel variations. Desbarats et al., using a case study of mine drainage from a gold mine, illustrate how elements that commonly occur as negatively charged species (anions) in solution, such as arsenic as arsenate, behave in an opposite fashion than most metals, which occur as positively charged species (cations). Significant improvement in the understanding of factors that influence the toxicity of metals to aquatic organisms in surface water has highlighted the importance of aqueous chemistry, particularly dissolved organic carbon, as described by Smith et al. Stream sediment contamination is another important pathway for affecting aquatic organisms, as reviewed by Besser et al. Understanding and predicting environmental consequences from mining begins with knowing the mineralogy and mineral reactivity of the ore, the wastes, and of secondary minerals formed later. Jamieson et al. review the importance of mineralogical studies in mine planning and remediation. A number of types of site-specific studies are needed to identify environmental risks related to individual mines. Lapakko reviews the general framework of mine waste characterization studies that are integral to the mine planning process. Hageman et al. present a comparative study of several static tests commonly used to characterize mine waste. The mining and ore processing practices employed at a specific mine site will vary on the basis of the commodities being targeted, the geology of the deposit, the geometry of the deposit, and the mining and ore processing methods used. Thus, these factors, in addition to the waste management practices used, can result in a variety of end-member mine waste features, each of which has its own set of challenges. Open pit mines and underground mines require waste rock to be removed to access ore. Waste rock presents unique problems because the rock is commonly mineralized at sub-economic grades and has not been processed to remove potentially problematic minerals, such as pyrite. Amos et al. examine the salient aspects of the geochemistry of waste rock. Mill tailings – the waste material after ore minerals have been removed – are a volumetrically important solid waste at many mine sites. Their fine grain size and the options for their management make their behavior in the environment distinct from that of waste rock. Lindsay et al. describe some of these differences through three case-study examples. Subaqueous disposal of tailings is another option described by Moncur et al. Cyanide leaching for gold extraction is a common method throughout the world. Johnson describes environmental aspects of cyanidation. Uranium mining presents unique environmental challenges, particularly since in-situ recovery has seen widespread use. Campbell et al. review the environmental geochemistry of uranium mining and current research on bioremediation. Ore concentrates from many types of metal mining undergo a pyrometallurgical technique known as smelting to extract the metal. Slag is the result of smelting, and it may be an environmental liability or a valuable byproduct, as described by Piatak et al. Finally, the open pits that result from surface mining commonly reach below the water table. At the end of mining, these pits may fill to form lakes that become part of the legacy of the mine. Castendyk et al., in two papers, review theoretical aspects of the environmental limnology of pit lakes. They also describe approaches that have been used to model pit lake water balance, wall-rock contributions to pit lake chemistry, pit lake water quality, and limnological processes, such as vertical mixing, through the use of three case studies.