Evolution of genome–phenome diversity under environmental stress

The genomic era revolutionized evolutionary biology. The enigma of genotypic-phenotypic diversity and biodiversity evolution of genes, genomes, phenomes, and biomes, reviewed here, was central in the research program of the Institute of Evolution, University of Haifa, since 1975. We explored the following questions. (i) How much of the genomic and phenomic diversity in nature is adaptive and processed by natural selection? (ii) What is the origin and evolution of adaptation and speciation processes under spatiotemporal variables and stressful macrogeographic and microgeographic environments? We advanced ecological genetics into ecological genomics and analyzed globally ecological, demographic, and life history variables in 1,200 diverse species across life, thousands of populations, and tens of thousands of individuals tested mostly for allozyme and partly for DNA diversity. Likewise, we tested thermal, chemical, climatic, and biotic stresses in several model organisms. Recently, we introduced genetic maps and quantitative trait loci to elucidate the genetic basis of adaptation and speciation. The genome–phenome holistic model was deciphered by the global regressive, progressive, and convergent evolution of subterranean mammals. Our results indicate abundant genotypic and phenotypic diversity in nature. The organization and evolution of molecular and organismal diversity in nature at global, regional, and local scales are nonrandom and structured; display regularities across life; and are positively correlated with, and partly predictable by, abiotic and biotic environmental heterogeneity and stress. Biodiversity evolution, even in small isolated populations, is primarily driven by natural selection, including diversifying, balancing, cyclical, and purifying selective regimes, interacting with, but ultimately overriding, the effects of mutation, migration, and stochasticity.

wrinkled1: A Novel, Low-Seed-Oil Mutant of Arabidopsis with a Deficiency in the Seed-Specific Regulation of Carbohydrate Metabolism1

During oil deposition in developing seeds of Arabidopsis, photosynthate is imported in the form of carbohydrates into the embryo and converted to triacylglycerols. To identify genes essential for this process and to investigate the molecular basis for the developmental regulation of oil accumulation, mutants producing wrinkled, incompletely filled seeds were isolated. A novel mutant locus, wrinkled1 (wri1), which maps to the bottom of chromosome 3 and causes an 80% reduction in seed oil content, was identified. Wild-type and homozygous wri1 mutant plantlets or mature plants were indistinguishable. However, developing homozygous wri1 seeds were impaired in the incorporation of sucrose and glucose into triacylglycerols, but incorporated pyruvate and acetate at an increased rate. Because the activities of several glycolytic enzymes, in particular hexokinase and pyrophosphate-dependent phosphofructokinase, are reduced in developing homozygous wri1 seeds, it is suggested that WRI1 is involved in the developmental regulation of carbohydrate metabolism during seed filling.

Environmental and developmental signals modulate proline homeostasis: evidence for a negative transcriptional regulator.

In many plants, osmotic stress induces a rapid accumulation of proline through de novo synthesis from glutamate. This response is thought to play a pivotal role in osmotic stress tolerance [Kishor, P. B. K., Hong, Z., Miao, G.-H., Hu, C.-A. A. and Verma, D. P. S. (1995) Plant Physiol. 108, 1387-1394]. During recovery from osmotic stress, accumulated proline is rapidly oxidized to glutamate and the first step of this process is catalyzed by proline oxidase. We have isolated a full-length cDNA from Arabidopsis thaliana, At-POX, which maps to a single locus on chromosome 3 and that encodes a predicted polypeptide of 499 amino acids showing significant similarity with proline oxidase sequences from Drosophila and Saccharomyces cerevisiae (55.5% and 45.1%, respectively). The predicted location of the encoded polypeptide is the inner mitochondrial membrane. RNA gel blot analysis revealed that At-POX mRNA levels declined rapidly upon osmotic stress and this decline preceded proline accumulation. On the other hand, At-POX mRNA levels rapidly increased during recovery. Free proline, exogenously added to plants, was found to be an effective inducer of At-POX expression; indeed, At-POX was highly expressed in flowers and mature seeds where the proline level is higher relative to other organs of Arabidopsis. Our results indicate that stress- and developmentally derived signals interact to determine proline homeostasis in Arabidopsis.

[C II] and 12^CO(1-0) emission maps in HLSJ091828.6+514223: a strongly lensed interacting system AT z = 5.24

We present Submillimeter Array [C II] 158 μm and Karl G. Jansky Very Large Array 12^CO(1-0) line emission maps for the bright, lensed, submillimeter source at z = 5.2430 behind A 773: HLSJ091828.6+514223 (HLS0918). We combine these measurements with previously reported line profiles, including multiple 12^CO rotational transitions, [C I], water, and [N II], providing some of the best constraints on the properties of the interstellar medium in a galaxy at z > 5. HLS0918 has a total far-infrared (FIR) luminosity L_FIR(8–1000 μm) = (1.6 ± 0.1) × 10^14 L_☉ μ^–1, where the total magnification μ_total = 8.9 ± 1.9, via a new lens model from the [C II] and continuum maps. Despite a HyLIRG luminosity, the FIR continuum shape resembles that of a local LIRG. We simultaneously fit all of the observed spectral line profiles, finding four components that correspond cleanly to discrete spatial structures identified in the maps. The two most redshifted spectral components occupy the nucleus of a massive galaxy, with a source-plane separation <1 kpc. The reddest dominates the continuum map (demagnified L_FIR, component = (1.1 ± 0.2) × 10^13 L_☉) and excites strong water emission in both nuclear components via a powerful FIR radiation field from the intense star formation. A third star-forming component is most likely a region of a merging companion (ΔV ~ 500 km s^–1) exhibiting generally similar gas properties. The bluest component originates from a spatially distinct region and photodissociation region analysis suggests that it is lower density, cooler, and forming stars less vigorously than the other components. Strikingly, it has very strong [N II] emission, which may suggest an ionized, molecular outflow. This comprehensive view of gas properties and morphology in HLS0918 previews the science possible for a large sample of high-redshift galaxies once ALMA attains full sensitivity.

A Case Study of the Economic and Environmental Impacts from a Bio-fuel Facility (Southwest Georgia Ethanol, LLC) on the Surrounding Communities, Southwest Georgia

Bio-fuels such as ethanol provide an extraordinary opportunity to address our dependency on foreign oil. This case study examines the economic and environmental impacts associated with constructing and operating a dry mill ethanol manufacturing facility in a Southwest Georgia town and surrounding communities. The case study found that the plant had little impact on air quality, water quality, and habitat fragmentation. However, economic results showed the plant produced $1.5 million in tax revenues, and 86 jobs. Ethanol producers and communities must consider both the economic and environmental impacts on a local community when searching or attracting a bio-fuels plant. Likewise, communities should be aware of these challenges when attracting ethanol production plants.

The Effects of Oil and Gas Exploration on Greater Sage Grouse Populations

Energy production throughout the greater Rocky Mountain Region has increased dramatically in the past decade. Pristine habitat areas historically home to the greater sage grouse are being impaired by these energy development actions. Ongoing studies by state and federal biologists have shown a decrease in overall reproductive activity and a decrease in population on historical mating grounds. This project identifies actions to conserve and restore the habitat of sage grouse populations and reverse the decline of the species. Recommended measures presented in this project include using directional drilling of multiple wells from one single drill pad, creating a GIS mapping data base, funding additional scientific studies regarding impacts from energy development and improved cooperation between state, federal and private agencies.

The Impacts of National Culture on Safety Culture in the Global Oil and Gas Industry

Safety culture is one of the most-studied subjects in the safety literature today, although no agreement exists on exactly what it means. Most safety culture research has been conducted in high-hazard industries such as nuclear power, aviation, and offshore oil and gas production. Only limited research has investigated links between safety culture and the prevailing national culture. This paper proposes that efforts to build safety culture and improve safety performance in the global oil and gas industry will be enhanced if the safety culture maturity and the prevailing national culture are assessed and a location-specific plan is developed based on these factors. A model plan to improve safety performance for one multinational oil and gas company is presented.

Thermogravimetric monitoring of oil refinery sludge

The present work has two dimensions: analytical and environmental. On the one hand we proved that thermogravimetric analysis can be used to perform fast characterization of oil refinery sludge. To this end, thermogravimetric curves were deconvoluted by using autocatalytic kinetics to take into account acceleratory phases in a thermal degradation performed in oxygen-containing atmosphere or at high heating rates. Based on thermogravimetric results, oil refinery sludge was modeled in terms of various fractions (pseudo-components) which degrade as major oil cuts. On the other hand, as an alternative to landfill, we have seen that Soxhlet extraction allows recovery almost half of the weight of sludge as a mixture of hydrocarbons, similar to gas–oil, which burns without residue. This ensures both, waste inerting and significant reduction in sludge volume.

Using causal maps to support ex-post assessment of social impacts of dams

This paper presents the results of an ex-post assessment of two important dams in Brazil. The study follows the principles of Social Impact Management, which offer a suitable framework for analyzing the complex social transformations triggered by hydroelectric dams. In the implementation of this approach, participative causal maps were used to identify the ex-post social impacts of the Porto Primavera and Rosana dams on the community of Porto Rico, located along the High Paraná River. We found that in the operation of dams there are intermediate causes of a political nature, stemming from decisions based on values and interests not determined by neutral, exclusively technical reasons; and this insight opens up an area of action for managing the negative impacts of dams.

Synthesis, Modification, and Application of Siloxane Materials for Environmental Sensing

As human populations and resource consumption increase, it is increasingly important to monitor the quality of our environment. While laboratory instruments offer useful information, portable, easy to use sensors would allow environmental analysis to occur on-site, at lower cost, and with minimal operator training. We explore the synthesis, modification, and applications of modified polysiloxane in environmental sensing. Multiple methods of producing modified siloxanes were investigated. Oligomers were formed by using functionalized monomers, producing siloxane materials containing silicon hydride, methyl, and phenyl side chains. Silicon hydride-functionalized oligomers were further modified by hydrosilylation to incorporate methyl ester and naphthyl side chains. Modifications to the siloxane materials were also carried out using post-curing treatments. Methyl ester-functionalized siloxane was incorporated into the surface of a cured poly(dimethylsiloxane) film by siloxane equilibration. The materials containing methyl esters were hydrolyzed to reveal carboxylic acids, which could later be used for covalent protein immobilization. Finally, the siloxane surfaces were modified to incorporate antibodies by covalent, affinity, and adsorption-based attachment. These modifications were characterized by a variety of methods, including contact angle, attenuated total reflectance Fourier transform infrared spectroscopy, dye labels, and 1H nuclear magnetic resonance spectroscopy. The modified siloxane materials were employed in a variety of sensing schemes. Volatile organic compounds were detected using methyl, phenyl, and naphthyl-functionalized materials on a Fabry-Perot interferometer and a refractometer. The Fabry-Perot interferometer was found to detect the analytes upon siloxane extraction by deformation of the Bragg reflectors. The refractometer was used to determine that naphthyl-functionalized siloxanes had elevated refractive indices, rendering these materials more sensitive to some analytes. Antibody-modified siloxanes were used to detect biological analytes through a solid phase microextraction-mediated enzyme linked immunosorbent assay (SPME ELISA). The SPME ELISA was found to have higher analyte sensitivity compared to a conventional ELISA system. The detection scheme was used to detect Escherichia coli at 8500 CFU/mL. These results demonstrate the variety of methods that can be used to modify siloxanes and the wide range of applications of modified siloxanes has been demonstrated through chemical and biological sensing schemes.

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.

Solar sensitivity experiments for the pre-industrial time period using the comprehensive global climate model CCSM3 (Community Climate System Model 3)

The Southern Hemisphere Westerly Winds (SWW) constitute an important zonal circulation that influences large-scale precipitation patterns and ocean circulation. Variations in their intensity and latitudinal position have been suggested to exert a strong influence on the CO2 budget in the Southern Ocean, thus making them a potential factor affecting the global climate. The possible influence of solar forcing on SWW variability during the Holocene is addressed. Solar sensitivity experiments with a comprehensive global climate model (CCSM3) are carried out to study the response of SWW to solar variability. In addition, It is shown that a high-resolution iron record from the Chilean continental slope (41° S), which is interpreted to reflect changes in the position of the SWW, is significantly correlated with reconstructed solar activity during the past 3000 years. Taken together, the proxy and model results suggest that centennial-scale periods of lower (higher) solar activity caused equatorward (southward) shifts of the annual mean SWW.

Sensitivity of soil regions to acid precipitation /

Mode of access: Internet.

Groundwater quality monitoring of Western oil shale development : identification and priority ranking of potential pollution sources /

Mode of access: Internet.

Chemical shoreline cleaning agents for oil spills : update state-of-the-art on mechanisms of action and factors influencing performance /

"EPA contract no. 68-C8-0062, Work assignment no. 3-48, SAIC project no. 01-0895-03-1000."