Genetic fidelity under harsh conditions: Analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius

Microbes whose genomes are encoded by DNA and for which adequate information is available display similar genomic mutation rates (average 0.0034 mutations per chromosome replication, range 0.0025 to 0.0046). However, this value currently is based on only a few well characterized microbes reproducing within a narrow range of environmental conditions. In particular, no genomic mutation rate has been determined either for a microbe whose natural growth conditions may extensively damage DNA or for any member of the archaea, a prokaryotic lineage deeply diverged from both bacteria and eukaryotes. Both of these conditions are met by the extreme thermoacidophile Sulfolobus acidocaldarius. We determined the genomic mutation rate for this species when growing at pH 3.5 and 75°C based on the rate of forward mutation at the pyrE gene and the nucleotide changes identified in 101 independent mutants. The observed value of about 0.0018 extends the range of DNA-based microbes with rates close to the standard rate simultaneously to an archaeon and to an extremophile whose cytoplasmic pH and normal growth temperature greatly accelerate the spontaneous decomposition of DNA. The mutations include base pair substitutions (BPSs) and additions and deletions of various sizes, but the S. acidocaldarius spectrum differs from those of other DNA-based organisms in being relatively poor in BPSs. The paucity of BPSs cannot yet be explained by known properties of DNA replication or repair enzymes of Sulfolobus spp. It suggests, however, that molecular evolution per genome replication may proceed more slowly in S. acidocaldarius than in other DNA-based organisms examined to date.

Remaking Movie Making: The Environmental Impacts of the Film Industry in Southern California

The film and television industry is integral to the economics and culture of the Southern California region. It is also a major contributing factor to the environmental problems in the region. Currently the Motion Picture, Television, and Commercial Industries Act of 1984 is the only regulation written specifically for the entertainment industry. This regulation was created with the purpose of streamlining the film permitting process to prevent run-away production, taking production out of state, and encourage growth. A change in this regulation is needed since studios routinely fail to meet environmental standards or work towards improvement during on-location filming. Amendments to this regulation requiring permits to contain environmental conditions would improve environmental conditions and stay true to the original purpose of the act.

Response of Catch-Per-Unit-Effort to Spatial and Environmental Factors: an Exploratory Data Analysis Using Generalized Additive Models

Understanding spatial distributions and how environmental conditions influence catch-per-unit-effort (CPUE) is important for increased fishing efficiency and sustainable fisheries management. This study investigated the relationship between CPUE, spatial factors, temperature, and depth using generalized additive models. Combinations of factors, and not one single factor, were frequently included in the best model. Parameters which best described CPUE varied by geographic region. The amount of variance, or deviance, explained by the best models ranged from a low of 29% (halibut, Charlotte region) to a high of 94% (sablefish, Charlotte region). Depth, latitude, and longitude influenced most species in several regions. On the broad geographic scale, depth was associated with CPUE for every species, except dogfish. Latitude and longitude influenced most species, except halibut (Areas 4 A/D), sablefish, and cod. Temperature was important for describing distributions of halibut in Alaska, arrowtooth flounder in British Columbia, dogfish, Alaska skate, and Aleutian skate. The species-habitat relationships revealed in this study can be used to create improved fishing and management strategies.

Long-term Responses of Mountain Ecosystems to Environmental Changes: Resilience, Adjustment, and Vulnerability

The steep environmental gradients of mountain ecosystems over short distances reflect large gradients of several climatic parameters and hence provide excellent possibilities for ecological research on the effects of environmental change. To gain a better understanding of the dynamics of abiotic and biotic parameters of mountain ecosystems, long-term records are required since permanent plots in mountain regions cover in the best case about 50 - 70 years. In order to extend investigations of ecological dynamics beyond these temporal limitations of permanent plots, paleoecological approaches can be used if the sampling resolution can be adapted to ecological research questions, e.g. a sample every 10 years. Paleoecological studies in mountain ecosystems can provide new ecological insights through the combination of different spatial and temporal scales. [f we thus improve our understanding of processes across both steep environmental gradients and different time scales, we may be able to better estimate ecosystem responses to current and future environmental change (Ammann et al. 1993; Lotter et al. 1997). The complexity of ecological interactions in mountain regions forces us to concentrate on a number of sub-systems - without losing sight of the wider context. Here, we summarize a few case studies on the effects of Holocene climate change and disturbance on the vegetation of the Western Alps. To categorize the main response modes of vegetation to climatic change and disturbance in the Alps we use three classes of ecological behaviour: "resilience", "adjustment", and "vulnerability", We assume a resilient (or elastic) behaviour if vegetation is able to recover to its former state, regaining important ecosystem characteristics, such as floristic composition, biodiversity, species abundances, and biomass (e.g. Küttel 1990; Aber and Melillo 199 1). Conversely, vegetation displacements may occur in response to climatic change and/or disturbance. In some cases, this may culminate in irreversible large-scale processes such as species and/or community extinctions. Such drastic developments indicate high ecosystem vulnerability (or inelasticity or instability, for detailed definitions see Küttel 1990; Aber and Melillo 199 1) to climatic change and/or disturbance. In this sense, the "vulnerability" (or instability) of an ecosystem is expressed by the degree of failure to recover to the original state before disturbance and/or climatic change. Between these two extremes (resilience vs. vulnerability), ecosystem adjustments to climatic change and/or disturbance may occur, including the appearance of new and/or the disappearance of old species. The term "adjustment" is hence used to indicate the response of vegetational communities, which adapted to new environmental conditions without losing their main character. For forest ecosystems, we assume vegetational adjustments (rather than vulnerability) if the dominant (or co-dominant) tree species are not outnumbered or replaced by formerly unimportant plant species or new invaders. Adaptation as a genetic process is not discussed here and will require additional pbylogeographical studies (that incorporate the analysis of ancient DNA) in order to fully understand the distributions of ecotypes.

Ensemble prediction distribution maps of macroalgae for current conditions and four climate change scenarios and high resultion bathymetry for Potter Cove, WAP, Antarctica

Species distribution models (SDM) predict species occurrence based on statistical relationships with environmental conditions. The R-package biomod2 which includes 10 different SDM techniques and 10 different evaluation methods was used in this study. Macroalgae are the main biomass producers in Potter Cove, King George Island (Isla 25 de Mayo), Antarctica, and they are sensitive to climate change factors such as suspended particulate matter (SPM). Macroalgae presence and absence data were used to test SDMs suitability and, simultaneously, to assess the environmental response of macroalgae as well as to model four scenarios of distribution shifts by varying SPM conditions due to climate change. According to the averaged evaluation scores of Relative Operating Characteristics (ROC) and True scale statistics (TSS) by models, those methods based on a multitude of decision trees such as Random Forest and Classification Tree Analysis, reached the highest predictive power followed by generalized boosted models (GBM) and maximum-entropy approaches (Maxent). The final ensemble model used 135 of 200 calculated models (TSS > 0.7) and identified hard substrate and SPM as the most influencing parameters followed by distance to glacier, total organic carbon (TOC), bathymetry and slope. The climate change scenarios show an invasive reaction of the macroalgae in case of less SPM and a retreat of the macroalgae in case of higher assumed SPM values.

Environmental controls on zooplankton composition and distribution in Muchalat Inlet, Nootka Sound, B.C., Canada

Senior thesis written for Oceanography 445

Non-linear principal components analysis: an alternative method for finding patterns in environmental data

The main purpose of this article is to gain an insight into the relationships between variables describing the environmental conditions of the Far Northern section of the Great Barrier Reef, Australia, Several of the variables describing these conditions had different measurement levels and often they had non-linear relationships. Using non-linear principal component analysis, it was possible to acquire an insight into these relationships. Furthermore. three geographical areas with unique environmental characteristics could be identified. Copyright (c) 2005 John Wiley & Sons, Ltd.

Practice report: the role of environmental factors in industrial site selection activities: a case of limestone quarry expansion in Barbados, West Indies

Site selection is a key activity for quarry expansion to support cement production, and is governed by factors such as resource availability, logistics, costs, and socio-environmental factors. Adequate consideration of all factors facilitates both industrial productivity and sustainable economic growth. This study illustrates the site selection process that was undertaken for the expansion of limestone quarry operations to support cement production in Barbados. First, alternate sites with adequate resources to support a 25-year development horizon were identified. Second, socio-environmental conditions were described and potential impacts identified. Third, a comparative matrix was constructed to evaluate relative site characteristics with respect to physical, ecological, socio-cultural and economic factors. The study shows that environmental factors were essential to the final site recommendation.

Environmental quality in residential areas : a social survey approach to improvement priorities

The research is concerned with the measurement of residents' evaluations of the environmental quality of residential areas. The research reflects the increased attention being given to residents' values in planning decisions affecting the residential environment. The work was undertaken in co-operation with a local authority which was in the process of revising its housing strategy, and in particular the priorities for improvement action. The study critically examines the existing evidence on environmental values and their relationship to the environment and points to a number of methodological and conceptual deficiencies. The research strategy developed on the basis of the research review was constrained by the need to keep any survey methods simple so that they could easily be repeated, when necessary, by the sponsoring authority. A basic perception model was assumed, and a social survey carried out to measure residents' responses to different environmental conditions. The data was only assumed to have ordinal properties, necessitating the extensive use of non-parametric statistics. Residents' expressions of satisfaction with the component elements of the environment (ranging from convenience to upkeep and privacy) were successfully related to 'objective' measures of the environment. However the survey evidence did not justify the use of the 'objective' variables as environmental standards. A method of using the social survey data directly as an aid to decision-making is discussed. Alternative models of the derivation of overall satisfaction with the environment are tested, and the values implied by the additive model compared with residents' preferences as measured directly in the survey. Residents' overall satisfactions with the residential environment were most closely related to their satisfactions with the "Appearance" and the "Reputation" of their areas. By contrast the most important directly measured preference was "Friendliness of area". The differences point to the need to define concepts used in social research clearly in operational terms, and to take care in the use of values 'measured' by different methods.

A goal-based modeling approach to develop requirements of an adaptive system with environmental uncertainty

Dynamically adaptive systems (DASs) are intended to monitor the execution environment and then dynamically adapt their behavior in response to changing environmental conditions. The uncertainty of the execution environment is a major motivation for dynamic adaptation; it is impossible to know at development time all of the possible combinations of environmental conditions that will be encountered. To date, the work performed in requirements engineering for a DAS includes requirements monitoring and reasoning about the correctness of adaptations, where the DAS requirements are assumed to exist. This paper introduces a goal-based modeling approach to develop the requirements for a DAS, while explicitly factoring uncertainty into the process and resulting requirements. We introduce a variation of threat modeling to identify sources of uncertainty and demonstrate how the RELAX specification language can be used to specify more flexible requirements within a goal model to handle the uncertainty. © 2009 Springer Berlin Heidelberg.

The role of environmental factors in industrial site selection activities:a case of limestone quarry expansion in Barbados, West Indies

Site selection is a key activity for quarry expansion to support cement production, and is governed by factors such as resource availability, logistics, costs, and socio-environmental factors. Adequate consideration of all factors facilitates both industrial productivity and sustainable economic growth. This study illustrates the site selection process that was undertaken for the expansion of limestone quarry operations to support cement production in Barbados. First, alternate sites with adequate resources to support a 25-year development horizon were identified. Second, socio-environmental conditions were described and potential impacts identified. Third, a comparative matrix was constructed to evaluate relative site characteristics with respect to physical, ecological, socio-cultural and economic factors. The study shows that environmental factors were essential to the final site recommendation.

Blood Lead Levels in Children and Environmental Lead Contamination in Miami Inner City, Florida

Studies have shown that the environmental conditions of the home are important predictors of health, especially in low-income communities. Understanding the relationship between the environment and health is crucial in the management of certain diseases. One health outcome related to the home environment among urban, minority, and low-income children is childhood lead poisoning. The most common sources of lead exposure for children are lead paint in older, dilapidated housing and contaminated dust and soil produced by accumulated residue of leaded gasoline. Blood lead levels (BLL) as low as 10 μg/dL in children are associated with impaired cognitive function, behavior difficulties, and reduced intelligence. Recently, it is suggested that the standard for intervention be lowered to BLL of 5 μg /dl. The objectives of our report were to assess the prevalence of lead poisoning among children under six years of age and to quantify and test the correlations between BLL in children and lead exposure levels in their environment. This cross-sectional analysis was restricted to 75 children under six years of age who lived in 6 zip code areas of inner city Miami. These locations exhibited unacceptably high levels of lead dust and soil in areas where children live and play. Using the 5 μg/dL as the cutoff point, the prevalence of lead poisoning among the study sample was 13.33%. The study revealed that lead levels in floor dust and window sill samples were positively and significantly correlated with BLL among children (p < 0.05). However, the correlations between BLL and the soil, air, and water samples were not significant. Based on this pilot study, a more comprehensive environmental study in surrounding inner city areas is warranted. Parental education on proper housecleaning techniques may also benefit those living in the high lead-exposed communities of inner city Miami.

Coral disease dynamics and environmental drivers in the northern Florida Keys and Lee Stocking Island, Bahamas

Coral reefs are experiencing declines worldwide and recently coral diseases have been identified as significant contributors to coral mortality. However, little is known regarding the factors that drive coral disease distributions and dynamics. Current knowledge of the organisms that cause coral diseases is also limited, with pathogens having been identified for only 5 of the 21 described coral diseases. The study presented here describes coral disease dynamics in terms of occurrence, prevalence, spatial distribution, and host species susceptibility from 2002--2004 on reefs of the Northern Florida Keys (NFK) and Lee Stocking Island (LSI) in the Bahamas' Exuma chain. In addition, this research investigated the influence of temperature, sediment, and nutrient availability on coral disease prevalence and severity. Finally, microbial communities associated with a polymicrobial disease, black band, were examined to address spatial and temporal variability. ^ Four scleractinian diseases were observed in repeated surveys conducted during June-August of each year: black band disease (BBD), white plague type 2 (WP), dark spots syndrome (DSS), and yellow band disease-(YBD). Coral disease prevalence was generally low in both the NFK and LSI as compared to epizootic levels reported previously in the NFK and other regions of the Caribbean. Disease prevalence and species susceptibility varied spatially and temporally. Massive framework species, including Siderastrea siderea, Colpophyllia natans, and Montastraea annularis, along with relatively smaller colonies of Meandrina meandrites and Dichocoenia stokesi, were most susceptible to disease. Temperature, sedimentation, and dissolved inorganic nitrogen were positively correlated with BBD infections. Furthermore, experimental nutrient enrichment exacerbated coral tissue loss to BBD both in situ and in vivo. Profiling of BBD microbial communities using length heterogeneity PCR revealed variation over space and time, with significantly distinct bacterial assemblages in the NFK, LSI, and US Virgin Islands. ^ This study contributes to knowledge of the relationship between coral diseases and the environment, and facilitates predictions regarding potential changes in coral reef communities under differing environmental conditions. Additionally, this research provides further understanding of coral disease dynamics at both the host and microbial pathogen levels.^

Distribution of Diatoms Along Environmental Gradients in the Charlotte Harbor, Florida (USA), Estuary and Its Watershed: Implications for Bioassessment of Salinity and Nutrient Concentrations

The relative abundance of diatom species in different habitats can be used as a tool to infer prior environmental conditions and evaluate management decisions that influence habitat quality. Diatom distribution patterns were examined to characterize relationships between assemblage composition and environmental gradients in a subtropical estuarine watershed. We identified environmental correlates of diatom distribution patterns across the Charlotte Harbor, Florida, watershed; evaluated differences among three major river drainages; and determined how accurately local environmental conditions can be predicted using inference models based on diatom assemblages. Sampling locations ranged from freshwater to marine (0.1–37.2 ppt salinity) and spanned broad nutrient concentration gradients. Salinity was the predominant driver of difference among diatom assemblages across the watershed, but other environmental variables had stronger correlations with assemblages within the subregions of the three rivers and harbor. Eighteen indicator taxa were significantly affiliated with subregions. Relationships between diatom taxon distributions and salinity, distance from the harbor, total phosphorus (TP), and total nitrogen (TN) were evaluated to determine the utility of diatom assemblages to predict environmental values using a weighted averaging-regression approach. Diatom-based inferences of these variables were strong (salinity R 2 = 0.96; distance R 2 = 0.93; TN R 2 = 0.83; TP R 2 = 0.83). Diatom assemblages provide reliable estimates of environmental parameters on different spatial scales across the watershed. Because many coastal diatom taxa are ubiquitous, the diatom training sets provided here should enable diatom-based environmental reconstructions in subtropical estuaries that are being rapidly altered by land and water use changes and sea level rise.