Sample records for abiotic natural selection

  1. Cyclone tolerance in new world arecaceae: biogeographic variation and abiotic natural selection.

    PubMed

    Griffith, M Patrick; Noblick, Larry R; Dowe, John L; Husby, Chad E; Calonje, Michael A

    2008-10-01

    Consistent abiotic factors can affect directional selection; cyclones are abiotic phenomena with near-discrete geographic limits. The current study investigates selective pressure of cyclones on plants at the species level, testing for possible natural selection. New World Arecaceae (palms) are used as a model system, as plants with monopodial, unbranched arborescent form are most directly affected by the selective pressure of wind load. Living specimens of known provenance grown at a common site were affected by the same cyclone. Data on percentage mortality were compiled and analysed in biogeographic and phylogenetic contexts. Palms of cyclone-prone provenance exhibited a much lower (one order of magnitude) range in cyclone tolerance, and significantly lower (P < 0.001) mean percentage mortality than collections from cyclone-free areas. Palms of cyclone-free provenance had much greater variation in tolerance, and significantly greater mean percentage mortality. A test for serial independence recovered no significant phylogenetic autocorrelation of percentage mortality. Variation in cyclone tolerance in New World Arecaceae correlates with biogeography, and is not confounded with phylogeny. These results suggest natural selection of cyclone tolerance in cyclone-prone areas.

  2. A review of selection-based tests of abiotic surrogates for species representation.

    PubMed

    Beier, Paul; Sutcliffe, Patricia; Hjort, Jan; Faith, Daniel P; Pressey, Robert L; Albuquerque, Fabio

    2015-06-01

    Because conservation planners typically lack data on where species occur, environmental surrogates--including geophysical settings and climate types--have been used to prioritize sites within a planning area. We reviewed 622 evaluations of the effectiveness of abiotic surrogates in representing species in 19 study areas. Sites selected using abiotic surrogates represented more species than an equal number of randomly selected sites in 43% of tests (55% for plants) and on average improved on random selection of sites by about 8% (21% for plants). Environmental diversity (ED) (42% median improvement on random selection) and biotically informed clusters showed promising results and merit additional testing. We suggest 4 ways to improve performance of abiotic surrogates. First, analysts should consider a broad spectrum of candidate variables to define surrogates, including rarely used variables related to geographic separation, distance from coast, hydrology, and within-site abiotic diversity. Second, abiotic surrogates should be defined at fine thematic resolution. Third, sites (the landscape units prioritized within a planning area) should be small enough to ensure that surrogates reflect species' environments and to produce prioritizations that match the spatial resolution of conservation decisions. Fourth, if species inventories are available for some planning units, planners should define surrogates based on the abiotic variables that most influence species turnover in the planning area. Although species inventories increase the cost of using abiotic surrogates, a modest number of inventories could provide the data needed to select variables and evaluate surrogates. Additional tests of nonclimate abiotic surrogates are needed to evaluate the utility of conserving nature's stage as a strategy for conservation planning in the face of climate change. © 2015 Society for Conservation Biology.

  3. Can plant-natural enemy communication withstand disruption by biotic and abiotic factors?

    PubMed

    Clavijo McCormick, Andrea

    2016-12-01

    The attraction of natural enemies towards herbivore-induced plant volatiles is a well-documented phenomenon. However, the majority of published studies are carried under optimal water and nutrient regimes and with just one herbivore. But what happens when additional levels of ecological complexity are added? Does the presence of a second herbivore, microorganisms, and abiotic stress interfere with plant-natural enemy communication? or is communication stable enough to withstand disruption by additional biotic and abiotic factors?Investigating the effects of these additional levels of ecological complexity is key to understanding the stability of tritrophic interactions in natural ecosystems and may aid to forecast the impact of environmental disturbances on these, especially in climate change scenarios, which are often associated with modifications in plant and arthropod species distribution and increased levels of abiotic stress.This review explores the literature on natural enemy attraction to herbivore-induced volatiles when, besides herbivory, plants are challenged by additional biotic and abiotic factors.The aim of this review was to establish the impact of different biotic and abiotic factors on plant-natural enemy communication and to highlight critical aspects to guide future research efforts.

  4. A significant abiotic pathway for the formation of unknown nitrogen in nature

    NASA Astrophysics Data System (ADS)

    Jokic, A.; Schulten, H.-R.; Cutler, J. N.; Schnitzer, M.; Huang, P. M.

    2004-03-01

    The global nitrogen cycle is of prime importance in natural ecosystems. However, the origin and nature of up to one-half of total soil N remains obscure despite all attempts at elucidation. Our data provide, for the first time, unequivocal evidence that the promoting action of Mn (IV) oxide on the Maillard reaction (sugar-amino acid condensation) under ambient conditions results in the abiotic formation of heterocyclic N compounds, which are often referred to as unknown nitrogen, and of amides which are apparently the dominant N moieties in nature. The information presented is of fundamental significance in understanding the role of mineral colloids in abiotic transformations of organic N moieties, the incorporation of N in the organic matrix of fossil fuels, and the global N cycle.

  5. Abiotic dechlorination of chlorinated ethenes in natural clayey soils: Impacts of mineralogy and temperature

    NASA Astrophysics Data System (ADS)

    Schaefer, Charles E.; Ho, Paul; Gurr, Christopher; Berns, Erin; Werth, Charles

    2017-11-01

    Laboratory batch experiments were performed to assess the impacts of temperature and mineralogy on the abiotic dechlorination of tetrachloroethene (PCE) or trichloroethene (TCE) due to the presence of ferrous minerals in natural aquifer clayey soils under anaerobic conditions. A combination of x-ray diffraction (XRD), magnetic susceptibility, and ferrous mineral content were used to characterize each of the 3 natural soils tested in this study, and dechlorination at temperatures ranging from 20 to 55 °C were examined. Results showed that abiotic dechlorination occurred in all 3 soils examined, yielding reduced gas abiotic dechlorination products acetylene, butane, ethene, and/or propane. Bulk first-order dechlorination rate constants (kbulk), scaled to the soil:water ratio expected for in situ conditions, ranged from 2.0 × 10- 5 day- 1 at 20 °C, to 32 × 10- 5 day- 1 at 55 °C in the soil with the greatest ferrous mineral content. For the generation of acetylene and ethene from PCE, the reaction was well described by Arrhenius kinetics, with an activation energy of 91 kJ/mol. For the generation of coupling products butane and propane, the Arrhenius equation did not provide a satisfactory description of the data, likely owing to the complex reaction mechanisms associated with these products and/or diffusional mass transfer processes associated with the ferrous minerals likely responsible for these coupling reactions. Although the data set was too limited to determine a definitive correlation, the two soils with elevated ferrous mineral contents had elevated abiotic dechlorination rate constants, while the one soil with a low ferrous mineral content had a relatively low abiotic dechlorination rate constant. Overall, results suggest intrinsic abiotic dechlorination rates may be an important long-term natural attenuation component in site conceptual models for clays that have the appropriate iron mineralogy.

  6. A focus on natural variation for abiotic constraints response in the model species Arabidopsis thaliana.

    PubMed

    Lefebvre, Valérie; Kiani, Seifollah Poormohammad; Durand-Tardif, Mylène

    2009-08-13

    Plants are particularly subject to environmental stress, as they cannot move from unfavourable surroundings. As a consequence they have to react in situ. In any case, plants have to sense the stress, then the signal has to be transduced to engage the appropriate response. Stress response is effected by regulating genes, by turning on molecular mechanisms to protect the whole organism and its components and/or to repair damage. Reactions vary depending on the type of stress and its intensity, but some are commonly turned on because some responses to different abiotic stresses are shared. In addition, there are multiple ways for plants to respond to environmental stress, depending on the species and life strategy, but also multiple ways within a species depending on plant variety or ecotype. It is regularly accepted that populations of a single species originating from diverse geographic origins and/or that have been subjected to different selective pressure, have evolved retaining the best alleles for completing their life cycle. Therefore, the study of natural variation in response to abiotic stress, can help unravel key genes and alleles for plants to cope with their unfavourable physical and chemical surroundings. This review is focusing on Arabidopsis thaliana which has been largely adopted by the global scientific community as a model organism. Also, tools and data that facilitate investigation of natural variation and abiotic stress encountered in the wild are set out. Characterization of accessions, QTLs detection and cloning of alleles responsible for variation are presented.

  7. Contribution of biotic and abiotic factors in the natural attenuation of sulfamethoxazole: A path analysis approach.

    PubMed

    Li, Yan; Rashid, Azhar; Wang, Hongjie; Hu, Anyi; Lin, Lifeng; Yu, Chang-Ping; Chen, Meng; Sun, Qian

    2018-08-15

    Sulfamethoxazole (SMX) is a sulfonamide antibiotic, widely used as curative and preventive drug for human, animal, and aquaculture bacterial infections. Its residues have been ubiquitously detected in the surface waters and sediments. In the present study, SMX dissipation and kinetics was studied in the natural water samples from Jiulong River under simulated complex natural conditions as well as conditions to mimic various biotic and abiotic environmental conditions in isolation. Structural equation modeling (SEM) by employing partial least square technique in path coefficient analysis was used to investigate the direct and indirect contributions of different environmental factors in the natural attenuation of SMX. The model explained 81% of the variability in natural attenuation as a dependent variable under the influence of sole effects of direct photo-degradation, indirect photo-degradation, hydrolysis, microbial degradation and bacterial degradation. The results of SEM suggested that the direct and indirect photo-degradation were the major pathways in the SMX natural attenuation. However, other biotic and abiotic factors also play a mediatory role during the natural attenuation and other processes. Furthermore, the potential transformation products of SMX were identified and their toxicity was evaluated. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Abiotic Nitrous Oxide Production in Natural and Artificial Seawater

    NASA Astrophysics Data System (ADS)

    Ochoa, H.; Stanton, C. L.; Cavazos, A. R.; Ostrom, N. E.; Glass, J. B.

    2014-12-01

    The ocean contributes approximately one third of global sources of nitrous oxide (N2O) to the atmosphere. While nitrification is thought to be the dominant pathway for marine N2O production, mechanisms remain unresolved. Previous studies have carried the implicit assumption that marine N2O originates directly from enzymatic sources. However, abiotic production of N2O is possible via chemical reactions between nitrogenous intermediates and redox active trace metals in seawater. In this study, we investigated N2O production and isotopic composition in treatments with and without added hydroxylamine (NH2OH) and nitric oxide (NO), intermediates in microbial oxidation of ammonia to nitrite, and Fe(III). Addition of substrates to sterile artificial seawater was compared with filtered and unfiltered seawater from Sapelo Island, coastal Georgia, USA. N2O production was observed immediately after addition of Fe(III) in the presence of NH2OH at pH 8 in sterile artificial seawater. Highest N2O production was observed in the presence of Fe(III), NO, and NH2OH. The isotopomer site preference of abiotically produced N2O was consistent with previous studies (31 ± 2 ‰). Higher abiotic N2O production was observed in sterile artificial seawater (salinity: 35 ppt) than filtered Sapelo Island seawater (salinity: 25 ppt) whereas diluted sterile artificial seawater (18 ppt) showed lowest N2O production, suggesting that higher salinity promotes enhanced abiotic N2O production. Addition of Fe(III) to unfiltered Sapelo Island seawater stimulated N2O production. The presence of ammonia-oxidizing archaea (AOA), which lack known N2O producing enzymes, in Sapelo Island seawater was confirmed by successful amplification of the archaeal amoA gene, whereas ammonia-oxidizing bacteria (AOB), which contain N2O-producing enzymes were undetected. Given the few Fe-containing proteins present in AOA, it is likely that Fe(III) addition promoted N2O production via an abiotic vs. enzymatic N2O mechanism

  9. Abiotic Versus Biotic Weathering Of Olivine As Possible Biosignatures

    NASA Technical Reports Server (NTRS)

    Longazo, Teresa G.; Wentworth, Susan J.; Clemett, Simon J.; Southam, Gordon; McKay, David S.

    2001-01-01

    We are investigating the weathering of silicate minerals by both purely inorganic, and biologically mediated processes using field-emission scanning electron microscopy (FESEM) and energy dispersive x-ray spectroscopy (EDS). By resolving surface textures and chemical compositions of weathered surfaces at the sub-micron scale we hope to be able to distinguish abiotic from biotic weathering processes and so establish a new biosignature applicable to the study of astromaterials including but not limited to the Martian meteorites. Sterilized olivine grains (San Carlos, Arizona) no more than 1-2 mm in their longest dimension were optically assayed to be uniform in color and free of inclusions were selected as weathering subjects. Prior to all experiments surface morphologies and Fe/Mg ratios were determined for each grain using FE-SEM and EDS. Experiments were divided into two categories abiotic and biotic and were compared with "naturally" weathered samples. For the preliminary experiments, two trials (open and closed to the ambient laboratory environment) were performed under abiotic conditions, and three trials under biotic conditions (control, day 1 and day 2). The open system abiotic trials used sterile grains heated at 98 C and 200 C for both 24 and 48 hours in 1L double distilled de-ionized water. The closed system abiotic trials were conducted under the same conditions but in a sealed two layer steel/Teflon "bomb" apparatus. The biotic trials used sterile grains mounted in a flow-through device attached to a wellhead on the Columbia River aquifer. Several discolored, altered, grains were selected to document "natural" weathering surface textures for comparison with the experimental samples. Preliminary results indicate there are qualitative differences in weathered surface textures among all the designed experiments. The olivine grains in abiotic trials displayed etching, pitting, denticulate margins, dissolution and clay formation. The scale of the features

  10. Abiotic Bromination of Soil Organic Matter

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Leri, Alessandra C.; Ravel, Bruce

    Biogeochemical transformations of plant-derived soil organic matter (SOM) involve complex abiotic and microbially mediated reactions. One such reaction is halogenation, which occurs naturally in the soil environment and has been associated with enzymatic activity of decomposer organisms. Building on a recent finding that naturally produced organobromine is ubiquitous in SOM, we hypothesized that inorganic bromide could be subject to abiotic oxidations resulting in bromination of SOM. Through lab-based degradation treatments of plant material and soil humus, we have shown that abiotic bromination of particulate organic matter occurs in the presence of a range of inorganic oxidants, including hydrogen peroxide andmore » assorted forms of ferric iron, producing both aliphatic and aromatic forms of organobromine. Bromination of oak and pine litter is limited primarily by bromide concentration. Fresh plant material is more susceptible to bromination than decayed litter and soil humus, due to a labile pool of mainly aliphatic compounds that break down during early stages of SOM formation. As the first evidence of abiotic bromination of particulate SOM, this study identifies a mechanistic source of the natural organobromine in humic substances and the soil organic horizon. Formation of organobromine through oxidative treatments of plant material also provides insights into the relative stability of aromatic and aliphatic components of SOM.« less

  11. Abiotic Bromination of Soil Organic Matter.

    PubMed

    Leri, Alessandra C; Ravel, Bruce

    2015-11-17

    Biogeochemical transformations of plant-derived soil organic matter (SOM) involve complex abiotic and microbially mediated reactions. One such reaction is halogenation, which occurs naturally in the soil environment and has been associated with enzymatic activity of decomposer organisms. Building on a recent finding that naturally produced organobromine is ubiquitous in SOM, we hypothesized that inorganic bromide could be subject to abiotic oxidations resulting in bromination of SOM. Through lab-based degradation treatments of plant material and soil humus, we have shown that abiotic bromination of particulate organic matter occurs in the presence of a range of inorganic oxidants, including hydrogen peroxide and assorted forms of ferric iron, producing both aliphatic and aromatic forms of organobromine. Bromination of oak and pine litter is limited primarily by bromide concentration. Fresh plant material is more susceptible to bromination than decayed litter and soil humus, due to a labile pool of mainly aliphatic compounds that break down during early stages of SOM formation. As the first evidence of abiotic bromination of particulate SOM, this study identifies a mechanistic source of the natural organobromine in humic substances and the soil organic horizon. Formation of organobromine through oxidative treatments of plant material also provides insights into the relative stability of aromatic and aliphatic components of SOM.

  12. Individual Cell Based Traits Obtained by Scanning Flow-Cytometry Show Selection by Biotic and Abiotic Environmental Factors during a Phytoplankton Spring Bloom

    PubMed Central

    Pomati, Francesco; Kraft, Nathan J. B.; Posch, Thomas; Eugster, Bettina; Jokela, Jukka; Ibelings, Bas W.

    2013-01-01

    In ecology and evolution, the primary challenge in understanding the processes that shape biodiversity is to assess the relationship between the phenotypic traits of organisms and the environment. Here we tested for selection on physio-morphological traits measured by scanning flow-cytometry at the individual level in phytoplankton communities under a temporally changing biotic and abiotic environment. Our aim was to study how high-frequency temporal changes in the environment influence biodiversity dynamics in a natural community. We focused on a spring bloom in Lake Zurich (Switzerland), characterized by rapid changes in phytoplankton, water conditions, nutrients and grazing (mainly mediated by herbivore ciliates). We described bloom dynamics in terms of taxonomic and trait-based diversity and found that diversity dynamics of trait-based groups were more pronounced than those of identified phytoplankton taxa. We characterized the linkage between measured phytoplankton traits, abiotic environmental factors and abundance of the main grazers and observed weak but significant correlations between changing abiotic and biotic conditions and measured size-related and fluorescence-related traits. We tested for deviations in observed community-wide distributions of focal traits from random patterns and found evidence for both clustering and even spacing of traits, occurring sporadically over the time series. Patterns were consistent with environmental filtering and phenotypic divergence under herbivore pressure, respectively. Size-related traits showed significant even spacing during the peak of herbivore abundance, suggesting that morphology-related traits were under selection from grazing. Pigment distribution within cells and colonies appeared instead to be associated with acclimation to temperature and water chemistry. We found support for trade-offs among grazing resistance and environmental tolerance traits, as well as for substantial periods of dynamics in which

  13. Individual cell based traits obtained by scanning flow-cytometry show selection by biotic and abiotic environmental factors during a phytoplankton spring bloom.

    PubMed

    Pomati, Francesco; Kraft, Nathan J B; Posch, Thomas; Eugster, Bettina; Jokela, Jukka; Ibelings, Bas W

    2013-01-01

    In ecology and evolution, the primary challenge in understanding the processes that shape biodiversity is to assess the relationship between the phenotypic traits of organisms and the environment. Here we tested for selection on physio-morphological traits measured by scanning flow-cytometry at the individual level in phytoplankton communities under a temporally changing biotic and abiotic environment. Our aim was to study how high-frequency temporal changes in the environment influence biodiversity dynamics in a natural community. We focused on a spring bloom in Lake Zurich (Switzerland), characterized by rapid changes in phytoplankton, water conditions, nutrients and grazing (mainly mediated by herbivore ciliates). We described bloom dynamics in terms of taxonomic and trait-based diversity and found that diversity dynamics of trait-based groups were more pronounced than those of identified phytoplankton taxa. We characterized the linkage between measured phytoplankton traits, abiotic environmental factors and abundance of the main grazers and observed weak but significant correlations between changing abiotic and biotic conditions and measured size-related and fluorescence-related traits. We tested for deviations in observed community-wide distributions of focal traits from random patterns and found evidence for both clustering and even spacing of traits, occurring sporadically over the time series. Patterns were consistent with environmental filtering and phenotypic divergence under herbivore pressure, respectively. Size-related traits showed significant even spacing during the peak of herbivore abundance, suggesting that morphology-related traits were under selection from grazing. Pigment distribution within cells and colonies appeared instead to be associated with acclimation to temperature and water chemistry. We found support for trade-offs among grazing resistance and environmental tolerance traits, as well as for substantial periods of dynamics in which

  14. Natural abiotic formation of oxalic acid in soils: results from aromatic model compounds and soil samples.

    PubMed

    Studenroth, Sabine; Huber, Stefan G; Kotte, Karsten; Schöler, Heinz F

    2013-02-05

    Oxalic acid is the smallest dicarboxylic acid and plays an important role in soil processes (e.g., mineral weathering and metal detoxification in plants). We have first proven its abiotic formation in soils and investigated natural abiotic degradation processes based on the oxidation of soil organic matter, enhanced by Fe(3+) and H(2)O(2) as hydroxyl radical suppliers. Experiments with the model compound catechol and further hydroxylated benzenes were performed to examine a common degradation pathway and to presume a general formation mechanism of oxalic acid. Two soil samples were tested for the release of oxalic acid and the potential effects of various soil parameters on oxalic acid formation. Additionally, the soil samples were treated with different soil sterilization methods to prove the oxalic acid formation under abiotic soil conditions. Different series of model experiments were conducted to determine a range of factors including Fe(3+), H(2)O(2), reaction time, pH, and chloride concentration on oxalic acid formation. Under certain conditions, catechol is degraded up to 65.6% to oxalic acid referring to carbon. In serial experiments with two soil samples, oxalic acid was produced, and the obtained results are suggestive of an abiotic degradation process. In conclusion, Fenton-like conditions with low Fe(3+) concentrations and an excess of H(2)O(2) as well as acidic conditions were required for an optimal oxalic acid formation. The presence of chloride reduced oxalic acid formation.

  15. Abiotic gene transfer: rare or rampant?

    PubMed Central

    Kotnik, Tadej; Weaver, James C.

    2016-01-01

    Phylogenetic studies reveal that horizontal gene transfer (HGT) plays a prominent role in evolution and genetic variability of life. Five biotic mechanisms of HGT among prokaryotic organisms have been extensively characterized: conjugation, competence, transduction, gene-transfer-agent (GTA) particles, and transitory fusion with recombination, but it is not known whether they can account for all natural HGT. It is even less clear how HGT could have occurred before any of these mechanisms had developed. Here, we consider contemporary conditions and experiments on microorganisms to estimate possible roles of abiotic HGT – currently and throughout evolution. Candidate mechanisms include freeze-and-thaw, microbeads-agitation, and electroporation-based transformation, and we posit that these laboratory techniques have analogues in nature acting as mechanisms of abiotic HGT: freeze-and-thaw cycles in polar waters, sand-agitation at foreshores and riverbeds, and lightning-triggered electroporation in near-surface aqueous habitats. We derive conservative order-of-magnitude estimates for rates of microorganisms subjected to freeze-and-thaw cycles, sand-agitation, and lightning-triggered electroporation, at 1024, 1019, and 1017 per year, respectively. Considering the yield of viable transformants, which is by far the highest in electroporation, we argue this may still favor lightning-triggered transformation over the other two mechanisms. Electroporation-based gene transfer also appears to be the most general of these abiotic candidates, and perhaps even of all known HGT mechanisms. Future studies should provide improved estimates of gene transfer rates and cell viability, currently and in the past, but to assess the importance of abiotic HGT in nature, will likely require substantial progress – also in knowledge of biotic HGT. PMID:27067073

  16. Reference Gene Selection for Quantitative Real-Time Reverse-Transcriptase PCR in Annual Ryegrass (Lolium multiflorum) Subjected to Various Abiotic Stresses.

    PubMed

    Liu, Qiuxu; Qi, Xiao; Yan, Haidong; Huang, Linkai; Nie, Gang; Zhang, Xinquan

    2018-01-16

    To select the most stable reference genes in annual ryegrass ( Lolium multiflorum ), we studied annual ryegrass leaf tissues exposed to various abiotic stresses by qRT-PCR and selected 11 candidate reference genes, i.e., 18S rRNA, E2, GAPDH, eIF4A, HIS3, SAMDC, TBP-1, Unigene71, Unigene77, Unigene755, and Unigene14912. We then used GeNorm, NormFinder, and BestKeeper to analyze the expression stability of these 11 genes, and used RefFinder to comprehensively rank genes according to stability. Under different stress conditions, the most suitable reference genes for studies of leaf tissues of annual ryegrass were different. The expression of the eIF4A gene was the most stable under drought stress. Under saline-alkali stress, Unigene14912 has the highest expression stability. Under acidic aluminum stress, SAMDC expression stability was highest. Under heavy metal stress, Unigene71 expression had the highest stability. According to the software analyses, Unigene14912, HIS3, and eIF4A were the most suitable for analyses of abiotic stress in tissues of annual ryegrass. GAPDH was the least suitable reference gene. In conclusion, selecting appropriate reference genes under abiotic stress not only improves the accuracy of annual ryegrass gene expression analyses, but also provides a theoretical reference for the development of reference genes in plants of the genus Lolium .

  17. Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus.

    PubMed

    Whitney, Kenneth D; Randell, Rebecca A; Rieseberg, Loren H

    2010-07-01

    *Adaptive trait introgression is increasingly recognized as common. However, it is unclear whether adaptive genetic exchanges typically affect only a single trait, or instead affect multiple aspects of the phenotype. Here, we examine introgression of abiotic tolerance traits between two hybridizing North American sunflower species, Helianthus annuus and Helianthus debilis. *In two common gardens in the hybrid range, we measured 10 ecophysiological, phenological, and architectural traits for parents and their natural and artificial hybrids, and examined how fitness covaried with trait values. *Eight of the 10 traits showed patterns consistent with introgression from H. debilis into H. annuus, and suggested that H. debilis-like traits allowing rapid growth and reproduction before summer heat and drought have been favored in the hybrid range. Natural selection currently favors BC(1) hybrids with H. debilis-like branching traits. *We demonstrate that introgression has altered multiple aspects of the H. annuus phenotype in an adaptive manner, has affected traits relevant to both biotic and abiotic environments, and may have aided expansion of the H. annuus range into central Texas, USA.

  18. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions.

    PubMed

    Coari, Kristin M; Martin, Rebecca C; Jain, Kopal; McGown, Linda B

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  19. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    NASA Astrophysics Data System (ADS)

    Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  20. Enhanced abiotic reduction of Cr(VI) in a soil slurry system by natural biomaterial addition.

    PubMed

    Park, Donghee; Ahn, Chi Kyu; Kim, Young Mi; Yun, Yeoung-Sang; Park, Jong Moon

    2008-12-30

    Among various plant-based natural biomaterials, pine bark was chosen as an efficient biomaterial capable of removing toxic Cr(VI) from aqueous solution. XPS spectra indicated that Cr(VI) was abiotically reduced to Cr(III) in both liquid and solid phases. The Cr(VI)-reducing capacity of pine bark was determined as 545 (+/-1.3)mg-Cr(VI)g(-1) of it, which was 8.7 times higher than that of a common chemical Cr(VI)-reductant, FeSO4 x 7H2O. Because pine bark could completely reduce toxic Cr(VI) to less toxic or nontoxic Cr(III) even at neutral pH, it was used as an organic reductant to remediate Cr(VI)-contaminated soil in this study. Soil slurry system using a bottle roller was applied to ex situ slurry-phase remediation experiments. In the soil slurry system, pine bark completely reduced Cr(VI) to Cr(III) and adsorbed the reduced-Cr(III) on its surface. Abiotic remediation rate of Cr(VI)-contaminated soil increased with the increase of pine bark dosage and with the decreases of Cr(VI) and water contents. In conclusion, pine bark can be used to remediate Cr(VI)-contaminated soil efficiently and environmentally friendly.

  1. Demonstrating Natural Selection

    ERIC Educational Resources Information Center

    Hinds, David S.; Amundson, John C.

    1975-01-01

    Describes laboratory exercises with chickens selecting their food from dyed and natural corn kernels as a method of demonstrating natural selection. The procedure is based on the fact that organisms that blend into their surroundings escape predation. (BR)

  2. MICROSCALE METABOLIC, REDOX AND ABIOTIC REACTIONS IN HANFORD 300 AREA SUBSURFACE SEDIMENTS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beyenal, Haluk; McLEan, Jeff; Majors, Paul

    2013-11-14

    The Hanford 300 Area is a unique site due to periodic hydrologic influence of river water resulting in changes in groundwater elevation and flow direction. This area is also highly subject to uranium remobilization, the source of which is currently believed to be the region at the base of the vadose zone that is subject to period saturation due to the changes in the water levels in the Columbia River. We found that microbial processes and redox and abiotic reactions which operate at the microscale were critical to understanding factors controlling the macroscopic fate and transport of contaminants in themore » subsurface. The combined laboratory and field research showed how microscale conditions control uranium mobility and how biotic, abiotic and redox reactions relate to each other. Our findings extended the current knowledge to examine U(VI) reduction and immobilization using natural 300 Area communities as well as selected model organisms on redox-sensitive and redox-insensitive minerals. Using innovative techniques developed specifically to probe biogeochemical processes at the microscale, our research expanded our current understanding of the roles played by mineral surfaces, bacterial competition, and local biotic, abiotic and redox reaction rates on the reduction and immobilization of uranium.« less

  3. Area and percent of forest affected by abiotic agents beyond reference conditions

    Treesearch

    2012-01-01

    Criterion 3, Indicator 16, of the Montréal Process Criteria and Indicators for the Conservation and Sustainable Management of Temperate and Boreal Forests was designed to assess the impact of abiotic agents upon forests (Montréal Process Working Group 2007). Various abiotic agents, both natural and human-induced, can change forest structure and species composition....

  4. Abiotic drivers of Chihuahuan Desert plant communities

    Treesearch

    Laura Marie Ladwig

    2014-01-01

    Within grasslands, precipitation, fire, nitrogen (N) addition, and extreme temperatures influence community composition and ecosystem function. The differential influences of these abiotic factors on Chihuahuan Desert grassland communities was examined within the Sevilleta National Wildlife Refuge, located in central New Mexico, U.S.A. Although fire is a natural...

  5. Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

    PubMed Central

    McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

    2013-01-01

    Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

  6. Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

    PubMed

    McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

    2013-01-01

    Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

  7. A membraneless single compartment abiotic glucose fuel cell

    NASA Astrophysics Data System (ADS)

    Slaughter, Gymama; Sunday, Joshua

    2014-09-01

    A simple energy harvesting strategy has been developed to selectively catalyze glucose in the presence of oxygen in a glucose/O2 fuel cell. The anode consists of an abiotic catalyst Al/Au/ZnO, in which ZnO seed layer was deposited on the surface of Al/Au substrate using hydrothermal method. The cathode is constructed from a single rod of platinum with an outer diameter of 500 μm. The abiotic glucose fuel cell was studied in phosphate buffer solution (pH 7.4) containing 5 mM glucose at a temperature of 22 °C. The cell is characterized according to its open-circuit voltage, polarization profile, and power density plot. Under these conditions, the abiotic glucose fuel cell possesses an open-circuit voltage of 840 mV and delivered a maximum power density of 16.2 μW cm-2 at a cell voltage of 495 mV. These characteristics are comparable to biofuel cell utilizing a much more complex system design. Such low-cost lightweight abiotic catalyzed glucose fuel cells have a great promise to be optimized, miniaturized to power bio-implantable devices.

  8. Abiotic methane formation during experimental serpentinization of olivine

    PubMed Central

    2016-01-01

    Fluids circulating through actively serpentinizing systems are often highly enriched in methane (CH4). In many cases, the CH4 in these fluids is thought to derive from abiotic reduction of inorganic carbon, but the conditions under which this process can occur in natural systems remain unclear. In recent years, several studies have reported abiotic formation of CH4 during experimental serpentinization of olivine at temperatures at or below 200 °C. However, these results seem to contradict studies conducted at higher temperatures (300 °C to 400 °C), where substantial kinetic barriers to CH4 synthesis have been observed. Here, the potential for abiotic formation of CH4 from dissolved inorganic carbon during olivine serpentinization is reevaluated in a series of laboratory experiments conducted at 200 °C to 320 °C. A 13C-labeled inorganic carbon source was used to unambiguously determine the origin of CH4 generated in the experiments. Consistent with previous high-temperature studies, the results indicate that abiotic formation of CH4 from reduction of dissolved inorganic carbon during the experiments is extremely limited, with nearly all of the observed CH4 derived from background sources. The results indicate that the potential for abiotic synthesis of CH4 in low-temperature serpentinizing environments may be much more limited than some recent studies have suggested. However, more extensive production of CH4 was observed in one experiment performed under conditions that allowed an H2-rich vapor phase to form, suggesting that shallow serpentinization environments where a separate gas phase is present may be more favorable for abiotic synthesis of CH4. PMID:27821742

  9. Abiotic methane formation during experimental serpentinization of olivine.

    PubMed

    McCollom, Thomas M

    2016-12-06

    Fluids circulating through actively serpentinizing systems are often highly enriched in methane (CH 4 ). In many cases, the CH 4 in these fluids is thought to derive from abiotic reduction of inorganic carbon, but the conditions under which this process can occur in natural systems remain unclear. In recent years, several studies have reported abiotic formation of CH 4 during experimental serpentinization of olivine at temperatures at or below 200 °C. However, these results seem to contradict studies conducted at higher temperatures (300 °C to 400 °C), where substantial kinetic barriers to CH 4 synthesis have been observed. Here, the potential for abiotic formation of CH 4 from dissolved inorganic carbon during olivine serpentinization is reevaluated in a series of laboratory experiments conducted at 200 °C to 320 °C. A 13 C-labeled inorganic carbon source was used to unambiguously determine the origin of CH 4 generated in the experiments. Consistent with previous high-temperature studies, the results indicate that abiotic formation of CH 4 from reduction of dissolved inorganic carbon during the experiments is extremely limited, with nearly all of the observed CH 4 derived from background sources. The results indicate that the potential for abiotic synthesis of CH 4 in low-temperature serpentinizing environments may be much more limited than some recent studies have suggested. However, more extensive production of CH 4 was observed in one experiment performed under conditions that allowed an H 2 -rich vapor phase to form, suggesting that shallow serpentinization environments where a separate gas phase is present may be more favorable for abiotic synthesis of CH 4 .

  10. Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition.

    PubMed

    Striebel, Maren; Schabhüttl, Stefanie; Hodapp, Dorothee; Hingsamer, Peter; Hillebrand, Helmut

    2016-11-01

    Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.

  11. Regulation of MIR Genes in Response to Abiotic Stress in Hevea brasiliensis

    PubMed Central

    Gébelin, Virginie; Leclercq, Julie; Hu, Songnian; Tang, Chaorong; Montoro, Pascal

    2013-01-01

    Increasing demand for natural rubber (NR) calls for an increase in latex yield and also an extension of rubber plantations in marginal zones. Both harvesting and abiotic stresses lead to tapping panel dryness through the production of reactive oxygen species. Many microRNAs regulated during abiotic stress modulate growth and development. The objective of this paper was to study the regulation of microRNAs in response to different types of abiotic stress and hormone treatments in Hevea. Regulation of MIR genes differs depending on the tissue and abiotic stress applied. A negative co-regulation between HbMIR398b with its chloroplastic HbCuZnSOD target messenger is observed in response to salinity. The involvement of MIR gene regulation during latex harvesting and tapping panel dryness (TPD) occurrence is further discussed. PMID:24084713

  12. Variation in resource limitation of plant reproduction influences natural selection on floral traits of Asclepias syriaca.

    PubMed

    Caruso, Christina M; Remington, Davin L D; Ostergren, Kate E

    2005-11-01

    The availability of both pollen and resources can influence natural selection on floral traits, but their relative importance in shaping floral evolution is unclear. We experimentally manipulated pollinator and resource (fertilizer and water) availability in the perennial wildflower Asclepias syriaca L. Nine floral traits, one male fitness component (number of pollinia removed), and two female fitness components (number of pollinia inserted and number of fruits initiated) were measured for plants in each of three treatments (unmanipulated control, decreased pollinator access, and resource supplementation). Although decreasing pollinators' access to flowers did result in fewer pollinia inserted and removed, fruit set and phenotypic selection on floral traits via female and male fitness did not differ from the control. In contrast, resource supplementation increased fruit set, and phenotypic selection on seven out of nine floral traits was stronger via female than male fitness, consistent with the prediction that selection via female fitness would be greater when reproduction was less resource-limited. Our results support the hypothesis that abiotic resource availability can influence floral evolution by altering gender-specific selection.

  13. Abiotic vs. biotic influences on habitat selection of coexisting species: Climate change impacts?

    USGS Publications Warehouse

    Martin, T.E.

    2001-01-01

    Species are commonly segregated along gradients of microclimate and vegetation. I explore the question of whether segregation is the result of microhabitat partitioning (biotic effects) or choice of differing microclimates (abiotic effects). I explored this question for four ground-nesting bird species that are segregated along a microclimate and vegetation gradient in Arizona. Birds shifted position of their nests on the microhabitat and microclimate gradient in response to changing precipitation over nine years. Similarly, annual bird abundance varied with precipitation across 12 yr. Those shifts in abundance and nesting microhabitat with changing precipitation demonstrate the importance of abiotic influences on bird distributions and habitat choice. However, nest-site shifts and microhabitat use also appear to be influenced by interactions among coexisting species. Moreover, shifts in habitat use by all species caused nest predation (i.e., biotic) costs that increased with increasing distance along the microclimate gradient. These results indicate that abiotic and biotic costs can strongly interact to influence microhabitat choice and abundances of coexisting species. Global climate change impacts have been considered largely in terms of simple distributional shifts, but these results indicate that shifts can also increase biotic costs when species move into habitat types for which they are poorly adapted or that create new biotic interactions.

  14. Abiotic and biotic factors associated with the presence of Anopheles arabiensis immatures and their abundance in naturally occurring and man-made aquatic habitats

    PubMed Central

    2012-01-01

    Background Anopheles arabiensis (Diptera: Culicidae) is a potential malaria vector commonly present at low altitudes in remote areas in Reunion Island. Little attention has been paid to the environmental conditions driving larval development and abundance patterns in potential habitats. Two field surveys were designed to determine whether factors that discriminate between aquatic habitats with and without An. arabiensis larvae also drive larval abundance, comparatively in man-made and naturally occurring habitats. Methods In an initial preliminary survey, a representative sample of aquatic habitats that would be amenable to an intensive long-term study were selected and divided into positive and negative sites based on the presence or absence of Anopheles arabiensis larvae. Subsequently, a second survey was prompted to gain a better understanding of biotic and abiotic drivers of larval abundance, comparatively in man-made and naturally occurring habitats in the two studied locations. In both surveys, weekly sampling was performed to record mosquito species composition and larval density within individual habitats, as well as in situ biological characteristics and physico-chemical properties. Results Whilst virtually any stagnant water body could be a potential breeding ground for An. arabiensis, habitats occupied by their immatures had different structural and biological characteristics when compared to those where larvae were absent. Larval occurrence seemed to be influenced by flow velocity, macrofauna diversity and predation pressure. Interestingly, the relative abundance of larvae in man-made habitats (average: 0.55 larvae per dip, 95%CI [0.3–0.7]) was significantly lower than that recorded in naturally occurring ones (0.74, 95%CI [0.5–0.8]). Such differences may be accounted for in part by varying pressures that could be linked to a specific habitat. Conclusions If the larval ecology of An. arabiensis is in general very complex and factors affecting

  15. Cytosine Methylation Alteration in Natural Populations of Leymus chinensis Induced by Multiple Abiotic Stresses

    PubMed Central

    Yu, Yingjie; Yang, Xuejiao; Wang, Huaying; Shi, Fengxue; Liu, Ying; Liu, Jushan; Li, Linfeng; Wang, Deli; Liu, Bao

    2013-01-01

    Background Human activity has a profound effect on the global environment and caused frequent occurrence of climatic fluctuations. To survive, plants need to adapt to the changing environmental conditions through altering their morphological and physiological traits. One known mechanism for phenotypic innovation to be achieved is environment-induced rapid yet inheritable epigenetic changes. Therefore, the use of molecular techniques to address the epigenetic mechanisms underpinning stress adaptation in plants is an important and challenging topic in biological research. In this study, we investigated the impact of warming, nitrogen (N) addition, and warming+nitrogen (N) addition stresses on the cytosine methylation status of Leymus chinensis Tzvel. at the population level by using the amplified fragment length polymorphism (AFLP), methylation-sensitive amplified polymorphism (MSAP) and retrotransposon based sequence-specific amplification polymorphism (SSAP) techniques. Methodology/Principal Findings Our results showed that, although the percentages of cytosine methylation changes in SSAP are significantly higher than those in MSAP, all the treatment groups showed similar alteration patterns of hypermethylation and hypomethylation. It meant that the abiotic stresses have induced the alterations in cytosine methylation patterns, and the levels of cytosine methylation changes around the transposable element are higher than the other genomic regions. In addition, the identification and analysis of differentially methylated loci (DML) indicated that the abiotic stresses have also caused targeted methylation changes at specific loci and these DML might have contributed to the capability of plants in adaptation to the abiotic stresses. Conclusions/Significance Our results demonstrated that abiotic stresses related to global warming and nitrogen deposition readily evoke alterations of cytosine methylation, and which may provide a molecular basis for rapid adaptation by

  16. Natural selection promotes antigenic evolvability.

    PubMed

    Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

  17. Natural Selection Promotes Antigenic Evolvability

    PubMed Central

    Graves, Christopher J.; Ros, Vera I. D.; Stevenson, Brian; Sniegowski, Paul D.; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed ‘cassettes’ that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections

  18. Advances in crop proteomics: PTMs of proteins under abiotic stress.

    PubMed

    Wu, Xiaolin; Gong, Fangping; Cao, Di; Hu, Xiuli; Wang, Wei

    2016-03-01

    Under natural conditions, crop plants are frequently subjected to various abiotic environmental stresses such as drought and heat wave, which may become more prevalent in the coming decades. Plant acclimation and tolerance to an abiotic stress are always associated with significant changes in PTMs of specific proteins. PTMs are important for regulating protein function, subcellular localization and protein activity and stability. Studies of plant responses to abiotic stress at the PTMs level are essential to the process of plant phenotyping for crop improvement. The ability to identify and quantify PTMs on a large-scale will contribute to a detailed protein functional characterization that will improve our understanding of the processes of crop plant stress acclimation and stress tolerance acquisition. Hundreds of PTMs have been reported, but it is impossible to review all of the possible protein modifications. In this review, we briefly summarize several main types of PTMs regarding their characteristics and detection methods, review the advances in PTMs research of crop proteomics, and highlight the importance of specific PTMs in crop response to abiotic stress. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Natural Selection in the Great Apes

    PubMed Central

    Cagan, Alexander; Theunert, Christoph; Laayouni, Hafid; Santpere, Gabriel; Pybus, Marc; Casals, Ferran; Prüfer, Kay; Navarro, Arcadi; Marques-Bonet, Tomas; Bertranpetit, Jaume; Andrés, Aida M.

    2016-01-01

    Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population size. Thus, even the modest differences in population size among the closely related Hominidae lineages have resulted in differences in their ability to remove deleterious alleles and to adapt to changing environments. Most signatures of balancing and positive selection are species-specific, with signatures of balancing selection more often being shared among species. We also identify loci with evidence of positive selection across several lineages. Notably, we detect signatures of positive selection in several genes related to brain function, anatomy, diet and immune processes. Our results contribute to a better understanding of human evolution by putting the evidence of natural selection in humans within its larger evolutionary context. The global map of natural selection in our closest living relatives is available as an interactive browser at http://tinyurl.com/nf8qmzh. PMID:27795229

  20. Understanding the Interaction of Peptides and Proteins with Abiotic Surfaces: Towards Water-Free Biologics

    DTIC Science & Technology

    2018-02-03

    peptides immobilized on abiotic surfaces depends upon a) the chemical and physical nature of the abiotic surface; b) the physicochemical properties of... dependent model of protein aggregation, aggregation proceeds only after a lag phase in which the concentration of energetically unfavorable nuclei reaches...time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the

  1. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

    PubMed Central

    Meena, Kamlesh K.; Sorty, Ajay M.; Bitla, Utkarsh M.; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P.; Prabha, Ratna; Sahu, Pramod K.; Gupta, Vijai K.; Singh, Harikesh B.; Krishanani, Kishor K.; Minhas, Paramjit S.

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  2. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

    PubMed

    Meena, Kamlesh K; Sorty, Ajay M; Bitla, Utkarsh M; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P; Prabha, Ratna; Sahu, Pramod K; Gupta, Vijai K; Singh, Harikesh B; Krishanani, Kishor K; Minhas, Paramjit S

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  3. Salt lakes of Western Australia - Natural abiotic formation of volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Krause, T.; Studenroth, S.; Mulder, I.; Tubbesing, C.; Kotte, K.; Ofner, J.; Junkermann, W.; Schöler, H. F.

    2012-04-01

    Western Australia is a semi-/arid region that is heavily influenced by global climate change and agricultural land use. The area is known for its many ephemeral saline and hypersaline lakes with a wide range of hydrogeochemical parameters that have gradually changed over the last fifty years. Historically, the region was covered by eucalyptus trees and shrubs, but was cleared mainly within 10 years after WWII to make room for wheat and live stock. After the clearance of the deep rooted native plants the groundwater started to rise, bringing increased amounts of dissolved salts and minerals to the surface and discharging them into streams and lakes. Thus most of Western Australia is influenced by secondary salinisation (soil salting) [1]. Another problem is that the discharged minerals affect the pH of ground and surface water, which ranges from acidic to slightly basic. During the 2011 campaign surface water was measured with a pH between 2.5 and 7.1. Another phenomenon in Western Australia is the decrease of rainfall over the last decades assumed to be linked to the secondary salinisation. The rising saline and mineral rich groundwater increases the biotical and abiotical activity of the salt lakes. Halogenated and non-halogenated volatile organic compounds emitted from those lakes undergo fast oxidation and chemical reactions to form small particles modifying cloud microphysics and thus suppressing rain events [2]. Our objective is to gain a better understanding of this extreme environment with its hypersaline acidic lakes with regard to the potential abiotic formation of volatile organic compounds and its impact on the local climate. In spring 2011 fifty-three sediment samples from ten salt lakes in the Lake King region where taken, freeze-dried and ground. In order to simulate the abiotic formation of volatile organic compounds the soil samples were resuspended with water in gas-tight headspace vials. The headspace was measured using a purge and trap GC

  4. Unraveling the role of fungal symbionts in plant abiotic stress tolerance

    PubMed Central

    Singh, Lamabam Peter

    2011-01-01

    Fungal symbionts have been found to be associated with every plant studied in the natural ecosystem, where they colonize and reside entirely or partially in the internal tissues of their host plant. Fungal endophytes can express/form a range of different lifestyle/relationships with different host including symbiotic, mutualistic, commensalistic and parasitic in response to host genotype and environmental factors. In mutualistic association fungal endophyte can enhance growth, increase reproductive success and confer biotic and abiotic stress tolerance to its host plant. Since abiotic stress such as, drought, high soil salinity, heat, cold, oxidative stress and heavy metal toxicity is the common adverse environmental conditions that affect and limit crop productivity worldwide. It may be a promising alternative strategy to exploit fungal endophytes to overcome the limitations to crop production brought by abiotic stress. There is an increasing interest in developing the potential biotechnological applications of fungal endophytes for improving plant stress tolerance and sustainable production of food crops. Here we have described the fungal symbioses, fungal symbionts and their role in abiotic stress tolerance. A putative mechanism of stress tolerance by symbionts has also been covered. PMID:21512319

  5. Nitrogen fertility and abiotic stresses management in cotton crop: a review.

    PubMed

    Khan, Aziz; Tan, Daniel Kean Yuen; Afridi, Muhammad Zahir; Luo, Honghai; Tung, Shahbaz Atta; Ajab, Mir; Fahad, Shah

    2017-06-01

    This review outlines nitrogen (N) responses in crop production and potential management decisions to ameliorate abiotic stresses for better crop production. N is a primary constituent of the nucleotides and proteins that are essential for life. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. Therefore, increasing plant N use efficiency (NUE) is important for the development of sustainable agriculture. NUE has a key role in crop yield and can be enhanced by controlling loss of fertilizers by application of humic acid and natural polymers (hydrogels), having high water-holding capacity which can improve plant performance under field conditions. Abiotic stresses such as waterlogging, drought, heat, and salinity are the major limitations for successful crop production. Therefore, integrated management approaches such as addition of aminoethoxyvinylglycine (AVG), the film antitranspirant (di-1-p-menthene and pinolene) nutrients, hydrogels, and phytohormones may provide novel approaches to improve plant tolerance against abiotic stress-induced damage. Moreover, for plant breeders and molecular biologists, it is a challenge to develop cotton cultivars that can tolerate plant abiotic stresses while having high potential NUE for the future.

  6. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

    PubMed Central

    Shriram, Varsha; Kumar, Vinay; Devarumath, Rachayya M.; Khare, Tushar S.; Wani, Shabir H.

    2016-01-01

    The microRNAs (miRNAs) are small (20–24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed. PMID:27379117

  7. Natural selection in chemical evolution.

    PubMed

    Fernando, Chrisantha; Rowe, Jonathan

    2007-07-07

    We propose that chemical evolution can take place by natural selection if a geophysical process is capable of heterotrophic formation of liposomes that grow at some base rate, divide by external agitation, and are subject to stochastic chemical avalanches, in the absence of nucleotides or any monomers capable of modular heredity. We model this process using a simple hill-climbing algorithm, and an artificial chemistry that is unique in exhibiting conservation of mass and energy in an open thermodynamic system. Selection at the liposome level results in the stabilization of rarely occurring molecular autocatalysts that either catalyse or are consumed in reactions that confer liposome level fitness; typically they contribute in parallel to an increasingly conserved intermediary metabolism. Loss of competing autocatalysts can sometimes be adaptive. Steady-state energy flux by the individual increases due to the energetic demands of growth, but also of memory, i.e. maintaining variations in the chemical network. Self-organizing principles such as those proposed by Kauffman, Fontana, and Morowitz have been hypothesized as an ordering principle in chemical evolution, rather than chemical evolution by natural selection. We reject those notions as either logically flawed or at best insufficient in the absence of natural selection. Finally, a finite population model without elitism shows the practical evolutionary constraints for achieving chemical evolution by natural selection in the lab.

  8. Abiotic ligation of DNA oligomers templated by their liquid crystal ordering

    NASA Astrophysics Data System (ADS)

    Fraccia, Tommaso P.; Smith, Gregory P.; Zanchetta, Giuliano; Paraboschi, Elvezia; Yi, Yougwooo; Walba, David M.; Dieci, Giorgio; Clark, Noel A.; Bellini, Tommaso

    2015-03-01

    It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly. In mixtures of oligomers with various degree of complementarity, liquid crystal microdomains are formed via the selective aggregation of those oligomers that have a sufficient degree of duplexing and propensity for physical polymerization. Here we show that such domains act as fluid and permeable microreactors in which the order-stabilized molecular contacts between duplex terminals serve as physical templates for their chemical ligation. In the presence of abiotic condensing agents, liquid crystal ordering markedly enhances ligation efficacy, thereby enhancing its own phase stability. The coupling between order-templated ligation and selectivity provided by supramolecular ordering enables an autocatalytic cycle favouring the growth of DNA chains, up to biologically relevant lengths, from few-base long oligomers. This finding suggests a novel scenario for the abiotic origin of nucleic acids.

  9. Negative effects of heterospecific pollen receipt vary with abiotic conditions: ecological and evolutionary implications.

    PubMed

    Celaya, Ileana N; Arceo-Gómez, Gerardo; Alonso, Conchita; Parra-Tabla, Víctor

    2015-10-01

    Studies that have evaluated the effects of heterospecific pollen (HP) receipt on plant reproductive success have generally overlooked the variability of the natural abiotic environment in which plants grow. Variability in abiotic conditions, such as light and water availability, has the potential to affect pollen-stigma interactions (i.e. conspecific pollen germination and performance), which will probably influence the effects of HP receipt. Thus, a more complete understanding of the extent, strength and consequences of plant-plant interactions via HP transfer requires better consideration of the range of abiotic conditions in which these interactions occur. This study addresses this issue by evaluating the effects of two HP donors (Tamonea curassavica and Angelonia angustifolia) on the reproductive success of Cuphea gaumeri, an endemic species of the Yucatan Peninsula. Mixed (conspecific pollen and HP) and pure (conspecific pollen only) hand-pollinations were conducted under varying conditions of water and light availability in a full factorial design. Reproductive success was measured as the number of pollen tubes that reached the bottom of the style. Only one of the two HP donors had a significant effect on C. gaumeri reproductive success, but this effect was dependent on water and light availability. Specifically, HP receipt caused a decrease in pollen tube growth, but only when the availability of water, light or both was low, and not when the availability of both resources was high. The results show that the outcome of interspecific post-pollination interactions via HP transfer can be context-dependent and vary with abiotic conditions, thus suggesting that abiotic effects in natural populations may be under-estimated. Such context-dependency could lead to spatial and temporal mosaics in the ecological and evolutionary consequences of post-pollination interactions. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany

  10. Negative effects of heterospecific pollen receipt vary with abiotic conditions: ecological and evolutionary implications

    PubMed Central

    Celaya, Ileana N.; Arceo-Gómez, Gerardo; Alonso, Conchita; Parra-Tabla, Víctor

    2015-01-01

    Background and Aims Studies that have evaluated the effects of heterospecific pollen (HP) receipt on plant reproductive success have generally overlooked the variability of the natural abiotic environment in which plants grow. Variability in abiotic conditions, such as light and water availability, has the potential to affect pollen–stigma interactions (i.e. conspecific pollen germination and performance), which will probably influence the effects of HP receipt. Thus, a more complete understanding of the extent, strength and consequences of plant–plant interactions via HP transfer requires better consideration of the range of abiotic conditions in which these interactions occur. This study addresses this issue by evaluating the effects of two HP donors (Tamonea curassavica and Angelonia angustifolia) on the reproductive success of Cuphea gaumeri, an endemic species of the Yucatan Peninsula. Methods Mixed (conspecific pollen and HP) and pure (conspecific pollen only) hand-pollinations were conducted under varying conditions of water and light availability in a full factorial design. Reproductive success was measured as the number of pollen tubes that reached the bottom of the style. Key Results Only one of the two HP donors had a significant effect on C. gaumeri reproductive success, but this effect was dependent on water and light availability. Specifically, HP receipt caused a decrease in pollen tube growth, but only when the availability of water, light or both was low, and not when the availability of both resources was high. Conclusions The results show that the outcome of interspecific post-pollination interactions via HP transfer can be context-dependent and vary with abiotic conditions, thus suggesting that abiotic effects in natural populations may be under-estimated. Such context-dependency could lead to spatial and temporal mosaics in the ecological and evolutionary consequences of post-pollination interactions. PMID:26199385

  11. Natural selection. IV. The Price equation*

    PubMed Central

    Frank, Steven A.

    2012-01-01

    The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation’s greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection, and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. PMID:22487312

  12. Microsatellites as targets of natural selection.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2013-02-01

    The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich's ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants.

  13. Microsatellites as Targets of Natural Selection

    PubMed Central

    Haasl, Ryan J.; Payseur, Bret A.

    2013-01-01

    The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich’s ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants. PMID:23104080

  14. Natural selection stops the evolution of male attractiveness

    PubMed Central

    Hine, Emma; McGuigan, Katrina; Blows, Mark W.

    2011-01-01

    Sexual selection in natural populations acts on highly heritable traits and tends to be relatively strong, implicating sexual selection as a causal agent in many phenotypic radiations. Sexual selection appears to be ineffectual in promoting phenotypic divergence among contemporary natural populations, however, and there is little evidence from artificial selection experiments that sexual fitness can evolve. Here, we demonstrate that a multivariate male trait preferred by Drosophila serrata females can respond to selection and results in the maintenance of male mating success. The response to selection was associated with a gene of major effect increasing in frequency from 12 to 35% in seven generations. No further response to selection, or increase in frequency of the major gene, was observed between generations 7 and 11, indicating an evolutionary limit had been reached. Genetic analyses excluded both depletion of genetic variation and overdominance as causes of the evolutionary limit. Relaxing artificial selection resulted in the loss of 52% of the selection response after a further five generations, demonstrating that the response under artificial sexual selection was opposed by antagonistic natural selection. We conclude that male D. serrata sexually selected traits, and attractiveness to D. serrata females conferred by these traits, were held at an evolutionary limit by the lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness. Our results suggest that sexual selection is unlikely to cause divergence among natural populations without a concomitant change in natural selection, a conclusion consistent with observational evidence from natural populations. PMID:21321197

  15. Natural selection. IV. The Price equation.

    PubMed

    Frank, S A

    2012-06-01

    The Price equation partitions total evolutionary change into two components. The first component provides an abstract expression of natural selection. The second component subsumes all other evolutionary processes, including changes during transmission. The natural selection component is often used in applications. Those applications attract widespread interest for their simplicity of expression and ease of interpretation. Those same applications attract widespread criticism by dropping the second component of evolutionary change and by leaving unspecified the detailed assumptions needed for a complete study of dynamics. Controversies over approximation and dynamics have nothing to do with the Price equation itself, which is simply a mathematical equivalence relation for total evolutionary change expressed in an alternative form. Disagreements about approach have to do with the tension between the relative valuation of abstract versus concrete analyses. The Price equation's greatest value has been on the abstract side, particularly the invariance relations that illuminate the understanding of natural selection. Those abstract insights lay the foundation for applications in terms of kin selection, information theory interpretations of natural selection and partitions of causes by path analysis. I discuss recent critiques of the Price equation by Nowak and van Veelen. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  16. Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb)

    PubMed Central

    Wang, Peihong; Xiong, Aisheng; Gao, Zhihong; Yu, Xinyi; Li, Man; Hou, Yingjun; Sun, Chao; Qu, Shenchun

    2016-01-01

    The success of quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to quantify gene expression depends on the stability of the reference genes used for data normalization. To date, systematic screening for reference genes in persimmon (Diospyros kaki Thunb) has never been reported. In this study, 13 candidate reference genes were cloned from 'Nantongxiaofangshi' using information available in the transcriptome database. Their expression stability was assessed by geNorm and NormFinder algorithms under abiotic stress and hormone stimulation. Our results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT. In addition, UBC combined with RPII or TUA were found to be appropriate for the "abiotic stress" group and α-TUB combined with PP2A were found to be appropriate for the "hormone stimuli" group. For further validation, the transcript level of the DkDREB2C homologue under heat stress was studied with the selected genes (CYP, GAPDH, TUA, UBC, α-TUB, and EF1-α). The results suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions. Our study will be useful for future studies on gene expression in persimmon. PMID:27513755

  17. Induction of abiotic stress tolerance in plants by endophytic microbes.

    PubMed

    Lata, R; Chowdhury, S; Gond, S K; White, J F

    2018-04-01

    Endophytes are micro-organisms including bacteria and fungi that survive within healthy plant tissues and promote plant growth under stress. This review focuses on the potential of endophytic microbes that induce abiotic stress tolerance in plants. How endophytes promote plant growth under stressful conditions, like drought and heat, high salinity and poor nutrient availability will be discussed. The molecular mechanisms for increasing stress tolerance in plants by endophytes include induction of plant stress genes as well as biomolecules like reactive oxygen species scavengers. This review may help in the development of biotechnological applications of endophytic microbes in plant growth promotion and crop improvement under abiotic stress conditions. Increasing human populations demand more crop yield for food security while crop production is adversely affected by abiotic stresses like drought, salinity and high temperature. Development of stress tolerance in plants is a strategy to cope with the negative effects of adverse environmental conditions. Endophytes are well recognized for plant growth promotion and production of natural compounds. The property of endophytes to induce stress tolerance in plants can be applied to increase crop yields. With this review, we intend to promote application of endophytes in biotechnology and genetic engineering for the development of stress-tolerant plants. © 2018 The Society for Applied Microbiology.

  18. Massive production of abiotic methane during subduction evidenced in metamorphosed ophicarbonates from the Italian Alps

    PubMed Central

    Vitale Brovarone, Alberto; Martinez, Isabelle; Elmaleh, Agnès; Compagnoni, Roberto; Chaduteau, Carine; Ferraris, Cristiano; Esteve, Imène

    2017-01-01

    Alteration of ultramafic rocks plays a major role in the production of hydrocarbons and organic compounds via abiotic processes on Earth and beyond and contributes to the redistribution of C between solid and fluid reservoirs over geological cycles. Abiotic methanogenesis in ultramafic rocks is well documented at shallow conditions, whereas natural evidence at greater depths is scarce. Here we provide evidence for intense high-pressure abiotic methanogenesis by reduction of subducted ophicarbonates. Protracted (≥0.5–1 Ma), probably episodic infiltration of reduced fluids in the ophicarbonates and methanogenesis occurred from at least ∼40 km depth to ∼15–20 km depth. Textural, petrological and isotopic data indicate that methane reached saturation triggering the precipitation of graphitic C accompanied by dissolution of the precursor antigorite. Continuous infiltration of external reducing fluids caused additional methane production by interaction with the newly formed graphite. Alteration of high-pressure carbonate-bearing ultramafic rocks may represent an important source of abiotic methane, with strong implications for the mobility of deep C reservoirs. PMID:28223715

  19. Stable Carbon Isotopic Signatures of Abiotic Organics from Hydrothermal Synthesis Experiments

    NASA Technical Reports Server (NTRS)

    Stern, Jennifer C.; Summers, David P.; Kubo, Mike; Yassar, Saima

    2006-01-01

    Stable carbon isotopes can be powerful biogeochemical markers in the study of life's origins. Biogenic carbon fixation produces organics that are depleted in C-13 by about -20 to -30%0. Less attention has been paid to the isotopic signatures of abiotic processes. The possibility of abiotic processes producing organics with morphologies and isotopic signatures in the biogenic range has been at the center of recent debate over the Earth's earliest microfossils. The abiotic synthesis of organic compounds in hydrothermal environments is one possible source of endogenous organic matter to the prebiotic earth. Simulated hydrothermal settings have been shown to synthesize, among other things, single chain amphiphiles and simple lipids from a mix of CO, CO2, and H2. A key characteristic of these amphiphilic molecules is the ability to self-assemble in aqueous phases into more organized structures called vesicles, which form a selectively permeable boundary and serve the function of containing and concentrating other organic molecules. The ability to form cell like structures also makes these compounds more likely to be mistaken for biogenic. Hydrothermal simulation experiments were conducted from oxalic or formic acid in water at 175 C for 72 hr. The molecular and isotopic composition of the products of these reactions were determined and compared to biogenic fractionations . Preliminary results indicate isotopic fractionation during abiotic hydrocarbon synthesis in hydrothermal environments is on par with biological carbon fixation.

  20. Precise through-space control of an abiotic electrophilic aromatic substitution reaction

    NASA Astrophysics Data System (ADS)

    Murphy, Kyle E.; Bocanegra, Jessica L.; Liu, Xiaoxi; Chau, H.-Y. Katharine; Lee, Patrick C.; Li, Jianing; Schneebeli, Severin T.

    2017-04-01

    Nature has evolved selective enzymes for the efficient biosynthesis of complex products. This exceptional ability stems from adapted enzymatic pockets, which geometrically constrain reactants and stabilize specific reactive intermediates by placing electron-donating/accepting residues nearby. Here we perform an abiotic electrophilic aromatic substitution reaction, which is directed precisely through space. Ester arms--positioned above the planes of aromatic rings--enable it to distinguish between nearly identical, neighbouring reactive positions. Quantum mechanical calculations show that, in two competing reaction pathways, both [C-H...O]-hydrogen bonding and electrophile preorganization by coordination to a carbonyl group likely play a role in controlling the reaction. These through-space-directed mechanisms are inspired by dimethylallyl tryptophan synthases, which direct biological electrophilic aromatic substitutions by preorganizing dimethylallyl cations and by stabilizing reactive intermediates with [C-H...N]-hydrogen bonding. Our results demonstrate how the third dimension above and underneath aromatic rings can be exploited to precisely control electrophilic aromatic substitutions.

  1. Dynamic covalent chemistry enables formation of antimicrobial peptide quaternary assemblies in a completely abiotic manner

    NASA Astrophysics Data System (ADS)

    Reuther, James F.; Dees, Justine L.; Kolesnichenko, Igor V.; Hernandez, Erik T.; Ukraintsev, Dmitri V.; Guduru, Rusheel; Whiteley, Marvin; Anslyn, Eric V.

    2018-01-01

    Naturally occurring peptides and proteins often use dynamic disulfide bonds to impart defined tertiary/quaternary structures for the formation of binding pockets with uniform size and function. Although peptide synthesis and modification are well established, controlling quaternary structure formation remains a significant challenge. Here, we report the facile incorporation of aryl aldehyde and acyl hydrazide functionalities into peptide oligomers via solid-phase copper-catalysed azide-alkyne cycloaddition (SP-CuAAC) click reactions. When mixed, these complementary functional groups rapidly react in aqueous media at neutral pH to form peptide-peptide intermolecular macrocycles with highly tunable ring sizes. Moreover, sequence-specific figure-of-eight, dumbbell-shaped, zipper-like and multi-loop quaternary structures were formed selectively. Controlling the proportions of reacting peptides with mismatched numbers of complementary reactive groups results in the formation of higher-molecular-weight sequence-defined ladder polymers. This also amplified antimicrobial effectiveness in select cases. This strategy represents a general approach to the creation of complex abiotic peptide quaternary structures.

  2. Natural Selection as Coarsening

    NASA Astrophysics Data System (ADS)

    Smerlak, Matteo

    2017-11-01

    Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

  3. Natural Selection as Coarsening

    NASA Astrophysics Data System (ADS)

    Smerlak, Matteo

    2018-07-01

    Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

  4. Characterization of expressed sequence tags (ESTs) of pigeonpea (Cajanus cajan L.) and functional validation of selected genes for abiotic stress tolerance in Arabidopsis thaliana.

    PubMed

    Priyanka, B; Sekhar, K; Sunita, T; Reddy, V D; Rao, Khareedu Venkateswara

    2010-03-01

    Pigeonpea, a major grain legume crop with remarkable drought tolerance traits, has been used for the isolation of stress-responsive genes. Herein, we report generation of ESTs, transcript profiles of selected genes and validation of candidate genes obtained from the subtracted cDNA libraries of pigeonpea plants subjected to PEG/water-deficit stress conditions. Cluster analysis of 124 selected ESTs yielded 75 high-quality ESTs. Homology searches disclosed that 55 ESTs share significant similarity with the known/putative proteins or ESTs available in the databases. These ESTs were characterized and genes relevant to the specific physiological processes were identified. Of the 75 ESTs obtained from the cDNA libraries of drought-stressed plants, 20 ESTs proved to be unique to the pigeonpea. These sequences are envisaged to serve as a potential source of stress-inducible genes of the drought stress-response transcriptome, and hence may be used for deciphering the mechanism of drought tolerance of the pigeonpea. Expression profiles of selected genes revealed increased levels of m-RNA transcripts in pigeonpea plants subjected to different abiotic stresses. Transgenic Arabidopsis lines, expressing Cajanus cajan hybrid-proline-rich protein (CcHyPRP), C. cajan cyclophilin (CcCYP) and C. cajan cold and drought regulatory (CcCDR) genes, exhibited marked tolerance, increased plant biomass and enhanced photosynthetic rates under PEG/NaCl/cold/heat stress conditions. This study represents the first report dealing with the isolation of drought-specific ESTs, transcriptome analysis and functional validation of drought-responsive genes of the pigeonpea. These genes, as such, hold promise for engineering crop plants bestowed with tolerance to major abiotic stresses.

  5. Populations, Natural Selection, and Applied Organizational Science.

    ERIC Educational Resources Information Center

    McKelvey, Bill; Aldrich, Howard

    1983-01-01

    Deficiencies in existing models in organizational science may be remedied by applying the population approach, with its concepts of taxonomy, classification, evolution, and population ecology; and natural selection theory, with its principles of variation, natural selection, heredity, and struggle for existence, to the idea of organizational forms…

  6. Comparing Patterns of Natural Selection across Species Using Selective Signatures

    PubMed Central

    Shapiro, B. Jesse; Alm, Eric J

    2008-01-01

    Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell. PMID:18266472

  7. The Real Difference between Biotic and Abiotic Methane

    NASA Astrophysics Data System (ADS)

    Cao, X.; Bao, H.; Peng, Y.

    2017-12-01

    Methane has both biotic and abiotic origins, and the identification of these two origins has important implications not only in understanding terrestrial processes but also in searching for extraterrestrial life. Carbon and hydrogen isotopes in methane have been used to identify certain biosignatures, but such efforts often suffer from ambiguity. Recent advancement in our capability in measuring multiply substituted isotopologues of methane (i.e. 13CDH3 and 12CD2H2) has found large 12CD2H2 depletion in abiotic methane. Quantum tunneling has been proposed to account for the apparent abiotic signature. However, quantum tunneling is neither unique to abiotic processes nor consistent with the observed not-so-depleted hydrogen isotope composition. Here we constructed a general kinetic model for methane formation from CO2, and validated it by fitting its parameters to observed 13CDH3, 12CD2H2, and 12CDH3. Our model revealed that the fundamental difference between biotic and abiotic methane isotopic signatures is in the source of hydrogens during methane formation. Hydrogens in biotic methane originate from the stronger carbon-hydrogen and sulfur-hydrogen bonds, while hydrogens in abiotic methane originate from the much weaker metal-hydrogen adsorption bond. This hydrogen source difference results in abiotic methane being more depleted in 12CD2H2 than the biotic one. Our model also shows that the primary kinetic hydrogen isotope effect is at approximately 0.6 for both abiotic and biotic pathways, a normal value further nullifying the role of quantum tunneling. The active and exclusive shuttling of reduced hydrogen via strong chemical bonds like carbon-hydrogen and sulfur-hydrogen in coenzymes is proposed here to be a unique signature of life. In an ironic sense, it is the equilibrated hydrogen isotope composition in the hydrogen donors that distinguishes the living from the non-living.

  8. Widespread abiotic methane in chromitites.

    PubMed

    Etiope, G; Ifandi, E; Nazzari, M; Procesi, M; Tsikouras, B; Ventura, G; Steele, A; Tardini, R; Szatmari, P

    2018-06-07

    Recurring discoveries of abiotic methane in gas seeps and springs in ophiolites and peridotite massifs worldwide raised the question of where, in which rocks, methane was generated. Answers will impact the theories on life origin related to serpentinization of ultramafic rocks, and the origin of methane on rocky planets. Here we document, through molecular and isotopic analyses of gas liberated by rock crushing, that among the several mafic and ultramafic rocks composing classic ophiolites in Greece, i.e., serpentinite, peridotite, chromitite, gabbro, rodingite and basalt, only chromitites, characterized by high concentrations of chromium and ruthenium, host considerable amounts of 13 C-enriched methane, hydrogen and heavier hydrocarbons with inverse isotopic trend, which is typical of abiotic gas origin. Raman analyses are consistent with methane being occluded in widespread microfractures and porous serpentine- or chlorite-filled veins. Chromium and ruthenium may be key metal catalysts for methane production via Sabatier reaction. Chromitites may represent source rocks of abiotic methane on Earth and, potentially, on Mars.

  9. Diagnosing Abiotic Degradation

    EPA Science Inventory

    The abiotic degradation of chlorinated solvents in ground water can be difficult to diagnose. Under current practice, most of the “evidence” is negative; specifically the apparent disappearance of chlorinated solvents with an accumulation of vinyl chloride, ethane, ethylene, or ...

  10. Effects of Abiotic Factors on HIPV-Mediated Interactions between Plants and Parasitoids

    PubMed Central

    Becker, Christine; Desneux, Nicolas; Monticelli, Lucie; Fernandez, Xavier; Michel, Thomas; Lavoir, Anne-Violette

    2015-01-01

    In contrast to constitutively emitted plant volatiles (PV), herbivore-induced plant volatiles (HIPV) are specifically emitted by plants when afflicted with herbivores. HIPV can be perceived by parasitoids and predators which parasitize or prey on the respective herbivores, including parasitic hymenoptera. HIPV act as signals and facilitate host/prey detection. They comprise a blend of compounds: main constituents are terpenoids and “green leaf volatiles.” Constitutive emission of PV is well known to be influenced by abiotic factors like temperature, light intensity, water, and nutrient availability. HIPV share biosynthetic pathways with constitutively emitted PV and might therefore likewise be affected by abiotic conditions. However, the effects of abiotic factors on HIPV-mediated biotic interactions have received only limited attention to date. HIPV being influenced by the plant's growing conditions could have major implications for pest management. Quantitative and qualitative changes in HIPV blends may improve or impair biocontrol. Enhanced emission of HIPV may attract a larger number of natural enemies. Reduced emission rates or altered compositions, however, may render blends imperceptible to parasitoides and predators. Predicting the outcome of these changes is highly important for food production and for ecosystems affected by global climate change. PMID:26788501

  11. Biotic and abiotic factors predicting the global distribution and population density of an invasive large mammal

    PubMed Central

    Lewis, Jesse S.; Farnsworth, Matthew L.; Burdett, Chris L.; Theobald, David M.; Gray, Miranda; Miller, Ryan S.

    2017-01-01

    Biotic and abiotic factors are increasingly acknowledged to synergistically shape broad-scale species distributions. However, the relative importance of biotic and abiotic factors in predicting species distributions is unclear. In particular, biotic factors, such as predation and vegetation, including those resulting from anthropogenic land-use change, are underrepresented in species distribution modeling, but could improve model predictions. Using generalized linear models and model selection techniques, we used 129 estimates of population density of wild pigs (Sus scrofa) from 5 continents to evaluate the relative importance, magnitude, and direction of biotic and abiotic factors in predicting population density of an invasive large mammal with a global distribution. Incorporating diverse biotic factors, including agriculture, vegetation cover, and large carnivore richness, into species distribution modeling substantially improved model fit and predictions. Abiotic factors, including precipitation and potential evapotranspiration, were also important predictors. The predictive map of population density revealed wide-ranging potential for an invasive large mammal to expand its distribution globally. This information can be used to proactively create conservation/management plans to control future invasions. Our study demonstrates that the ongoing paradigm shift, which recognizes that both biotic and abiotic factors shape species distributions across broad scales, can be advanced by incorporating diverse biotic factors. PMID:28276519

  12. Roots Withstanding their Environment: Exploiting Root System Architecture Responses to Abiotic Stress to Improve Crop Tolerance

    PubMed Central

    Koevoets, Iko T.; Venema, Jan Henk; Elzenga, J. Theo. M.; Testerink, Christa

    2016-01-01

    To face future challenges in crop production dictated by global climate changes, breeders and plant researchers collaborate to develop productive crops that are able to withstand a wide range of biotic and abiotic stresses. However, crop selection is often focused on shoot performance alone, as observation of root properties is more complex and asks for artificial and extensive phenotyping platforms. In addition, most root research focuses on development, while a direct link to the functionality of plasticity in root development for tolerance is often lacking. In this paper we review the currently known root system architecture (RSA) responses in Arabidopsis and a number of crop species to a range of abiotic stresses, including nutrient limitation, drought, salinity, flooding, and extreme temperatures. For each of these stresses, the key molecular and cellular mechanisms underlying the RSA response are highlighted. To explore the relevance for crop selection, we especially review and discuss studies linking root architectural responses to stress tolerance. This will provide a first step toward understanding the relevance of adaptive root development for a plant’s response to its environment. We suggest that functional evidence on the role of root plasticity will support breeders in their efforts to include root properties in their current selection pipeline for abiotic stress tolerance, aimed to improve the robustness of crops. PMID:27630659

  13. Abiotic CO2 reduction during geologic carbon sequestration facilitated by Fe(II)-bearing minerals

    NASA Astrophysics Data System (ADS)

    Nielsen, L. C.; Maher, K.; Bird, D. K.; Brown, G. E.; Thomas, B.; Johnson, N. C.; Rosenbauer, R. J.

    2012-12-01

    Redox reactions involving subsurface minerals and fluids and can lead to the abiotic generation of hydrocarbons from CO2 under certain conditions. Depleted oil reservoirs and saline aquifers targeted for geologic carbon sequestration (GCS) can contain significant quantities of minerals such as ferrous chlorite, which could facilitate the abiotic reduction of carbon dioxide to n-carboxylic acids, hydrocarbons, and amorphous carbon (C0). If such reactions occur, the injection of supercritical CO2 (scCO2) could significantly alter the oxidation state of the reservoir and cause extensive reorganization of the stable mineral assemblage via dissolution and reprecipitation reactions. Naturally occurring iron oxide minerals such as magnetite are known to catalyze CO2 reduction, resulting in the synthesis of organic compounds. Magnetite is thermodynamically stable in Fe(II) chlorite-bearing mineral assemblages typical of some reservoir formations. Thermodynamic calculations demonstrate that GCS reservoirs buffered by the chlorite-kaolinite-carbonate(siderite/magnesite)-quartz assemblage favor the reduction of CO2 to n-carboxylic acids, hydrocarbons, and C0, although the extent of abiotic CO2 reduction may be kinetically limited. To investigate the rates of abiotic CO2 reduction in the presence of magnetite, we performed batch abiotic CO2 reduction experiments using a Dickson-type rocking hydrothermal apparatus at temperatures (373 K) and pressures (100 bar) within the range of conditions relevant to GCS. Blank experiments containing CO2 and H2 were used to rule out the possibility of catalytic activity of the experimental apparatus. Reaction of brine-suspended magnetite nanoparticles with scCO2 at H2 partial pressures typical of reservoir rocks - up to 100 and 0.1 bars respectively - was used to investigate the kinetics of magnetite-catalyzed abiotic CO2 reduction. Later experiments introducing ferrous chlorite (ripidolite) were carried out to determine the potential for

  14. Abiotic Formation of Methyl Halides in the Terrestrial Environment

    NASA Astrophysics Data System (ADS)

    Keppler, F.

    2011-12-01

    Methyl chloride and methyl bromide are the most abundant chlorine and bromine containing organic compounds in the atmosphere. Since both compounds have relatively long tropospheric lifetimes they can effectively transport halogen atoms from the Earth's surface, where they are released, to the stratosphere and following photolytic oxidation form reactive halogen gases that lead to the chemical destruction of ozone. Methyl chloride and methyl bromide account for more than 20% of the ozone-depleting halogens delivered to the stratosphere and are predicted to grow in importance as the chlorine contribution to the stratosphere from anthropogenic CFCs decline. Today methyl chloride and methyl bromide originate mainly from natural sources with only a minor fraction considered to be of anthropogenic origin. However, until as recently as 2000 most of the methyl chloride and methyl bromide input to the atmosphere was considered to originate from the oceans, but investigations in recent years have clearly demonstrated that terrestrial sources such as biomass burning, wood-rotting fungi, coastal salt marshes, tropical vegetation and organic matter degradation must dominate the atmospheric budgets of these trace gases. However, many uncertainties still exist regarding strengths of both sources and sinks, as well as the mechanisms of formation of these naturally occurring halogenated gases. A better understanding of the atmospheric budget of both methyl chloride and methyl bromide is therefore required for reliable prediction of future ozone depletion. Biotic and abiotic methylation processes of chloride and bromide ion are considered to be the dominant pathways of formation of these methyl halides in nature. In this presentation I will focus on abiotic formation processes in the terrestrial environment and the potential parameters that control their emissions. Recent advances in our understanding of the abiotic formation pathway of methyl halides will be discussed. This will

  15. A quantum of natural selection

    NASA Astrophysics Data System (ADS)

    Lloyd, Seth

    2009-03-01

    The modern evolutionary synthesis, which marries Darwin's theory of natural selection with Mendel's genetics, was developed around the same time as quantum mechanics. Is there any connection between the two?

  16. Pathways for abiotic organic synthesis at submarine hydrothermal fields.

    PubMed

    McDermott, Jill M; Seewald, Jeffrey S; German, Christopher R; Sylva, Sean P

    2015-06-23

    Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond.

  17. Pathways for abiotic organic synthesis at submarine hydrothermal fields

    PubMed Central

    McDermott, Jill M.; Seewald, Jeffrey S.; German, Christopher R.; Sylva, Sean P.

    2015-01-01

    Arguments for an abiotic origin of low-molecular weight organic compounds in deep-sea hot springs are compelling owing to implications for the sustenance of deep biosphere microbial communities and their potential role in the origin of life. Theory predicts that warm H2-rich fluids, like those emanating from serpentinizing hydrothermal systems, create a favorable thermodynamic drive for the abiotic generation of organic compounds from inorganic precursors. Here, we constrain two distinct reaction pathways for abiotic organic synthesis in the natural environment at the Von Damm hydrothermal field and delineate spatially where inorganic carbon is converted into bioavailable reduced carbon. We reveal that carbon transformation reactions in a single system can progress over hours, days, and up to thousands of years. Previous studies have suggested that CH4 and higher hydrocarbons in ultramafic hydrothermal systems were dependent on H2 generation during active serpentinization. Rather, our results indicate that CH4 found in vent fluids is formed in H2-rich fluid inclusions, and higher n-alkanes may likely be derived from the same source. This finding implies that, in contrast with current paradigms, these compounds may form independently of actively circulating serpentinizing fluids in ultramafic-influenced systems. Conversely, widespread production of formate by ΣCO2 reduction at Von Damm occurs rapidly during shallow subsurface mixing of the same fluids, which may support anaerobic methanogenesis. Our finding of abiogenic formate in deep-sea hot springs has significant implications for microbial life strategies in the present-day deep biosphere as well as early life on Earth and beyond. PMID:26056279

  18. Pollinator-mediated natural selection in Penstemon digitalis.

    PubMed

    Parachnowitsch, Amy; Kessler, André

    2010-12-01

    Measuring the agents of natural selection is important because it allows us to understand not only which traits are expected to evolve but also why they will evolve. Natural selection by pollinators on floral traits is often assumed because in outcrossing animal-pollinated plants flowers are generally thought to function as advertisements of rewards directed at pollinators. We tested the role of bee pollinators in selection on Penstemon digitalis and found that pollinators were driving selection for larger and more flowers. However, what makes our publication unique is the additional information we gained from reviewing the few other studies that also directly tested whether pollinators were agents of selection on floral traits. As we would expect if pollinators are important agents of selection, selection on floral traits was significantly stronger when pollinators were present than when they were experimentally removed. Taken together, these results suggest that pollinators can be important drivers of selection in contemporary populations.

  19. Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet

    PubMed Central

    Shivhare, Radha; Lata, Charu

    2017-01-01

    Pearl millet is one of the most important small-grained C4 Panicoid crops with a large genome size (∼2352 Mb), short life cycle and outbreeding nature. It is highly resilient to areas with scanty rain and high temperature. Pearl millet is a nutritionally superior staple crop for people inhabiting hot, drought-prone arid and semi-arid regions of South Asia and Africa where it is widely grown and used for food, hay, silage, bird feed, building material, and fuel. Having excellent nutrient composition and exceptional buffering capacity against variable climatic conditions and pathogen attack makes pearl millet a wonderful model crop for stress tolerance studies. Pearl millet germplasm show a large range of genotypic and phenotypic variations including tolerance to abiotic and biotic stresses. Conventional breeding for enhancing abiotic and biotic stress resistance in pearl millet have met with considerable success, however, in last few years various novel approaches including functional genomics and molecular breeding have been attempted in this crop for augmenting yield under adverse environmental conditions, and there is still a lot of scope for further improvement using genomic tools. Discovery and use of various DNA-based markers such as EST-SSRs, DArT, CISP, and SSCP-SNP in pearl millet not only help in determining population structure and genetic diversity but also prove to be important for developing strategies for crop improvement at a faster rate and greater precision. Molecular marker-based genetic linkage maps and identification of genomic regions determining yield under abiotic stresses particularly terminal drought have paved way for marker-assisted selection and breeding of pearl millet cultivars. Reference collections and marker-assisted backcrossing have also been used to improve biotic stress resistance in pearl millet specifically to downy mildew. Whole genome sequencing of pearl millet genome will give new insights for processing of functional

  20. Coupled biotic-abiotic oxidation of organic matter by biogenic MnO_{2}

    NASA Astrophysics Data System (ADS)

    Gonzalez, Julia; Peña, Jasquelin

    2016-04-01

    Some reactive soil minerals are strongly implicated in stabilising organic matter. However, others can play an active role in the oxidation of organic molecules. In natural systems, layer-type manganese oxide minerals (MnO2) typically occur as biomineral assemblages consisting of mineral particles and microbial biomass. Both the mineral and biological fractions of the assemblage can be powerful oxidants of organic C. The biological compartment relies on a set of enzymes to drive oxidative transformations of reduced C-substrates, whereas MnO2 minerals are strong, less specific abiotic oxidants that are assumed to rely on interfacial interactions between C-substrates and the mineral surface. This project aims to understand the coupling between microbial C mineralization and abiotic C oxidation mediated by MnO2 in bacterial-MnO2 assemblages. Specifically, under conditions of high C turnover, microbial respiration can significantly alter local pH, dissolved oxygen and pool of available reductants, which may modify rates and mechanism of C oxidation by biotic and abiotic components. We first investigated changes in the solution chemistry of Pseudomonas putida suspensions exposed to varying concentrations of glucose, chosen to represent readily bioavailable substrates in soils. Glucose concentrations tested ranged between 0 and 5.5mM and changes in pH, dissolved oxygen and dissolved organic and inorganic carbon were tracked over 48h. We then combined literature review and wet-chemical experiments to compile the pH dependence of rates of organic substrate oxidation by MnO2, including glucose. Our results demonstrate a strong pH dependence for these abiotic reactions. In assemblages of P. putida - MnO2, kinetic limitations for abiotic C oxidation by MnO2 are overcome by changes in biogeochemical conditions that result from bacterial C metabolism. When extrapolated to a soil solution confronted to an input of fresh dissolved organic matter, bacterial C metabolism of the

  1. Phenotypic selection in natural populations: what limits directional selection?

    PubMed

    Kingsolver, Joel G; Diamond, Sarah E

    2011-03-01

    Studies of phenotypic selection document directional selection in many natural populations. What factors reduce total directional selection and the cumulative evolutionary responses to selection? We combine two data sets for phenotypic selection, representing more than 4,600 distinct estimates of selection from 143 studies, to evaluate the potential roles of fitness trade-offs, indirect (correlated) selection, temporally varying selection, and stabilizing selection for reducing net directional selection and cumulative responses to selection. We detected little evidence that trade-offs among different fitness components reduced total directional selection in most study systems. Comparisons of selection gradients and selection differentials suggest that correlated selection frequently reduced total selection on size but not on other types of traits. The direction of selection on a trait often changes over time in many temporally replicated studies, but these fluctuations have limited impact in reducing cumulative directional selection in most study systems. Analyses of quadratic selection gradients indicated stabilizing selection on body size in at least some studies but provided little evidence that stabilizing selection is more common than disruptive selection for most traits or study systems. Our analyses provide little evidence that fitness trade-offs, correlated selection, or stabilizing selection strongly constrains the directional selection reported for most quantitative traits.

  2. Natural Selection in the Field and the Classroom

    ERIC Educational Resources Information Center

    Andrews, Tessa Marie

    2012-01-01

    This dissertation examined natural selection in westslope cutthroat trout ("Oncorhynchus clarkii lewisi") and undergraduate learning in the subject area natural selection. Translocation--moving individuals to a new habitat to establish, re-establish or supplement a population--is a crucial management strategy for cutthroat trout. One of…

  3. Natural selection. VII. History and interpretation of kin selection theory.

    PubMed

    Frank, S A

    2013-06-01

    Kin selection theory is a kind of causal analysis. The initial form of kin selection ascribed cause to costs, benefits and genetic relatedness. The theory then slowly developed a deeper and more sophisticated approach to partitioning the causes of social evolution. Controversy followed because causal analysis inevitably attracts opposing views. It is always possible to separate total effects into different component causes. Alternative causal schemes emphasize different aspects of a problem, reflecting the distinct goals, interests and biases of different perspectives. For example, group selection is a particular causal scheme with certain advantages and significant limitations. Ultimately, to use kin selection theory to analyse natural patterns and to understand the history of debates over different approaches, one must follow the underlying history of causal analysis. This article describes the history of kin selection theory, with emphasis on how the causal perspective improved through the study of key patterns of natural history, such as dispersal and sex ratio, and through a unified approach to demographic and social processes. Independent historical developments in the multivariate analysis of quantitative traits merged with the causal analysis of social evolution by kin selection. © 2013 The Author. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  4. Elucidating the Role of Carbon Sources on Abiotic and Biotic Release of Arsenic into Cambodian Aquifers

    NASA Astrophysics Data System (ADS)

    Koeneke, M.

    2017-12-01

    Arsenic (As) is a naturally occurring contaminant in Cambodia that has been contaminating well-water sources of millions of people. Commonly, studies look into the biotic factors that cause the arsenic to be released from aquifer sediments to groundwater. However, abiotic release of As from sediments, though little studied, may also play key roles in As contamination of well water. The goal of this research is to quantitatively compare organic-carbon mediated abiotic and biotic release of arsenic from sediments to groundwater. Batch anaerobic incubation experiments under abiotic (sodium azide used to immobilize microbes) and biotic conditions were conducted using Cambodian aquifer sediments, four different organic carbon sources (sodium lactate, sodium citrate, sodium oxalate, and humic acid), and six different carbon concentrations (0, 1, 2.5, 5, 10, 25mg C/L). Dissolved arsenic, iron(Fe), and manganese(Mn) concentrations in the treatments were measured 112 days . In addition, sediment and solution carbon solution was measured . Collectively, these show how different carbon sources, different carbon concentrations, and how abiotic and biotic factors impact the release of arsenic from Cambodian sediments into aquifers. Overall, an introduction of organic carbon to the soil increases the amount of As released from the sediment. The biotic + abiotic and abiotic conditions seemed to play a minimal role in the amount of As released. Dissolved species analysis showed us that 100% of the As was As(V), Our ICP-MS results vary due to the heterogeneity of samples, but when high levels are Fe are seen in solution, we also see high levels of As. We also see higher As concentrations when there is a smaller amount of Mn in solution.

  5. Role of sugars under abiotic stress.

    PubMed

    Sami, Fareen; Yusuf, Mohammad; Faizan, Mohammad; Faraz, Ahmad; Hayat, Shamsul

    2016-12-01

    Sugars are the most important regulators that facilitate many physiological processes, such as photosynthesis, seed germination, flowering, senescence, and many more under various abiotic stresses. Exogenous application of sugars in low concentration promote seed germination, up regulates photosynthesis, promotes flowering, delayed senescence under various unfavorable environmental conditions. However, high concentration of sugars reverses all these physiological process in a concentration dependent manner. Thus, this review focuses the correlation between sugars and their protective functions in several physiological processes against various abiotic stresses. Keeping in mind the multifaceted role of sugars, an attempt has been made to cover the role of sugar-regulated genes associated with photosynthesis, seed germination and senescence. The concentration of sugars determines the expression of these sugar-regulated genes. This review also enlightens the interaction of sugars with several phytohormones, such as abscisic acid, ethylene, cytokinins and gibberellins and its effect on their biosynthesis under abiotic stress conditions. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  6. Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

    PubMed Central

    Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; Schranz, M Eric; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; Michelmore, Richard W; van Tienderen, Peter H

    2014-01-01

    The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. PMID:25360276

  7. Parallel shifts in ecology and natural selection in an island lizard

    PubMed Central

    Calsbeek, Ryan; Buermann, Wolfgang; Smith, Thomas B

    2009-01-01

    Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered both habitat use and natural selection in the brown anole, Anolis sagrei. Results In natural populations, lizards increased their use of vegetation in wet years and this was correlated with selection on limb length but not body size. By contrast, a die-back of vegetation caused by drought was followed by reduced arboreality, selection on body size, and relaxed selection on limb length. With the return of the rains and recovery of vegetation, selection reverted back to pre-drought pattern of selection acting on limb length but not body size. To test for the impact of vegetation loss on natural selection during the drought, we experimentally removed vegetation on a separate study island in a naturally wet year. The experiment revealed similar inter-annual changes in selection on body size but not limb length. Conclusion Our results illustrate the dynamic nature of ecology driving natural selection on Anolis morphology and emphasize the importance of inter-annual environmental variation in shaping adaptive variation. In addition, results illustrate the utility of using remote sensing data to examine ecology's role in driving natural selection. PMID:19126226

  8. The impact of individual and combined abiotic factors on daily otolith growth in a coral reef fish

    NASA Astrophysics Data System (ADS)

    Wenger, Amelia S.; Whinney, James; Taylor, Brett; Kroon, Frederieke

    2016-06-01

    Coral reefs are increasingly subjected to both local and global stressors, however, there is limited information on how reef organisms respond to their combined effects under natural conditions. This field study examined the growth response of the damselfish Neopomacentrus bankieri to the individual and combined effects of multiple abiotic factors. Turbidity, temperature, tidal movement, and wave action were recorded every 10 minutes for four months, after which the daily otolith growth of N. bankieri was aligned with corresponding abiotic conditions. Temperature was the only significant driver of daily otolith increment width, with increasing temperatures resulting in decreasing width. Although tidal movement was not a significant driver of increment width by itself, the combined effect of tidal movement and temperature had a greater negative effect on growth than temperature alone. Our results indicate that temperature can drive changes in growth even at very fine scales, and demonstrate that the cumulative impact of abiotic factors can be substantially greater than individual effects. As abiotic factors continue to change in intensity and duration, the combined impacts of them will become increasingly important drivers of physiological and ecological change.

  9. The impact of individual and combined abiotic factors on daily otolith growth in a coral reef fish.

    PubMed

    Wenger, Amelia S; Whinney, James; Taylor, Brett; Kroon, Frederieke

    2016-06-28

    Coral reefs are increasingly subjected to both local and global stressors, however, there is limited information on how reef organisms respond to their combined effects under natural conditions. This field study examined the growth response of the damselfish Neopomacentrus bankieri to the individual and combined effects of multiple abiotic factors. Turbidity, temperature, tidal movement, and wave action were recorded every 10 minutes for four months, after which the daily otolith growth of N. bankieri was aligned with corresponding abiotic conditions. Temperature was the only significant driver of daily otolith increment width, with increasing temperatures resulting in decreasing width. Although tidal movement was not a significant driver of increment width by itself, the combined effect of tidal movement and temperature had a greater negative effect on growth than temperature alone. Our results indicate that temperature can drive changes in growth even at very fine scales, and demonstrate that the cumulative impact of abiotic factors can be substantially greater than individual effects. As abiotic factors continue to change in intensity and duration, the combined impacts of them will become increasingly important drivers of physiological and ecological change.

  10. The impact of individual and combined abiotic factors on daily otolith growth in a coral reef fish

    PubMed Central

    Wenger, Amelia S.; Whinney, James; Taylor, Brett; Kroon, Frederieke

    2016-01-01

    Coral reefs are increasingly subjected to both local and global stressors, however, there is limited information on how reef organisms respond to their combined effects under natural conditions. This field study examined the growth response of the damselfish Neopomacentrus bankieri to the individual and combined effects of multiple abiotic factors. Turbidity, temperature, tidal movement, and wave action were recorded every 10 minutes for four months, after which the daily otolith growth of N. bankieri was aligned with corresponding abiotic conditions. Temperature was the only significant driver of daily otolith increment width, with increasing temperatures resulting in decreasing width. Although tidal movement was not a significant driver of increment width by itself, the combined effect of tidal movement and temperature had a greater negative effect on growth than temperature alone. Our results indicate that temperature can drive changes in growth even at very fine scales, and demonstrate that the cumulative impact of abiotic factors can be substantially greater than individual effects. As abiotic factors continue to change in intensity and duration, the combined impacts of them will become increasingly important drivers of physiological and ecological change. PMID:27350589

  11. Bridging Emergent Attributes and Darwinian Principles in Teaching Natural Selection

    ERIC Educational Resources Information Center

    Xu, Dongchen; Chi, Michelene T. H.

    2016-01-01

    Students often have misconceptions about natural selection as they misuse a direct causal schema to explain the process. Natural selection is in fact an emergent process where random interactions lead to changes in a population. The misconceptions stem from students' lack of emergent schema for natural selection. In order to help students…

  12. Reference gene selection for qRT-PCR assays in Stellera chamaejasme subjected to abiotic stresses and hormone treatments based on transcriptome datasets.

    PubMed

    Liu, Xin; Guan, Huirui; Song, Min; Fu, Yanping; Han, Xiaomin; Lei, Meng; Ren, Jingyu; Guo, Bin; He, Wei; Wei, Yahui

    2018-01-01

    Stellera chamaejasme Linn, an important poisonous plant of the China grassland, is toxic to humans and livestock. The rapid expansion of S. chamaejasme has greatly damaged the grassland ecology and, consequently, seriously endangered the development of animal husbandry. To draft efficient prevention and control measures, it has become more urgent to carry out research on its adaptive and expansion mechanisms in different unfavorable habitats at the genetic level. Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely used technique for studying gene expression at the transcript level; however, qRT-PCR requires reference genes (RGs) as endogenous controls for data normalization and only through appropriate RG selection and qRT-PCR can we guarantee the reliability and robustness of expression studies and RNA-seq data analysis. Unfortunately, little research on the selection of RGs for gene expression data normalization in S. chamaejasme has been reported. In this study, 10 candidate RGs namely, 18S , 60S , CYP , GAPCP1 , GAPDH2 , EF1B , MDH , SAND , TUA1 , and TUA6 , were singled out from the transcriptome database of S. chamaejasme , and their expression stability under three abiotic stresses (drought, cold, and salt) and three hormone treatments (abscisic acid, ABA; gibberellin, GA; ethephon, ETH) were estimated with the programs geNorm, NormFinder, and BestKeeper. Our results showed that GAPCP1 and EF1B were the best combination for the three abiotic stresses, whereas TUA6 and SAND , TUA1 and CYP , GAPDH2 and 60S were the best choices for ABA, GA, and ETH treatment, respectively. Moreover, GAPCP1 and 60S were assessed to be the best combination for all samples, and 18S was the least stable RG for use as an internal control in all of the experimental subsets. The expression patterns of two target genes ( P5CS2 and GI ) further verified that the RGs that we selected were suitable for gene expression normalization. This work is the first attempt to

  13. Using Card Games to Simulate the Process of Natural Selection

    ERIC Educational Resources Information Center

    Grilliot, Matthew E.; Harden, Siegfried

    2014-01-01

    In 1858, Darwin published "On the Origin of Species by Means of Natural Selection." His explanation of evolution by natural selection has become the unifying theme of biology. We have found that many students do not fully comprehend the process of evolution by natural selection. We discuss a few simple games that incorporate hands-on…

  14. Selection of reference genes for miRNA qRT-PCR under abiotic stress in grapevine.

    PubMed

    Luo, Meng; Gao, Zhen; Li, Hui; Li, Qin; Zhang, Caixi; Xu, Wenping; Song, Shiren; Ma, Chao; Wang, Shiping

    2018-03-13

    Grapevine is among the fruit crops with high economic value, and because of the economic losses caused by abiotic stresses, the stress resistance of Vitis vinifera has become an increasingly important research area. Among the mechanisms responding to environmental stresses, the role of miRNA has received much attention recently. qRT-PCR is a powerful method for miRNA quantitation, but the accuracy of the method strongly depends on the appropriate reference genes. To determine the most suitable reference genes for grapevine miRNA qRT-PCR, 15 genes were chosen as candidate reference genes. After eliminating 6 candidate reference genes with unsatisfactory amplification efficiency, the expression stability of the remaining candidate reference genes under salinity, cold and drought was analysed using four algorithms, geNorm, NormFinder, deltaCt and Bestkeeper. The results indicated that U6 snRNA was the most suitable reference gene under salinity and cold stresses; whereas miR168 was the best for drought stress. The best reference gene sets for salinity, cold and drought stresses were miR160e + miR164a, miR160e + miR168 and ACT + UBQ + GAPDH, respectively. The selected reference genes or gene sets were verified using miR319 or miR408 as the target gene.

  15. Hard and Soft Selection Revisited: How Evolution by Natural Selection Works in the Real World.

    PubMed

    Reznick, David

    2016-01-01

    The modern synthesis of evolutionary biology unified Darwin's natural selection with Mendelian genetics, but at the same time it created the dilemma of genetic load. Lewontin and Hubby's (1966) and Harris's (1966) characterization of genetic variation in natural populations increased the apparent burden of this load. Neutrality or near neutrality of genetic variation was one mechanism proposed for the revealed excessive genetic variation. Bruce Wallace coined the term "soft selection" to describe an alternative way for natural selection to operate that was consistent with observed variation. He envisioned nature as presenting ecological vacancies that could be filled by diverse genotypes. Survival and successful reproduction was a combined function of population density, genotype, and genotype frequencies, rather than a fixed value of the relative fitness of each genotype. My goal in this review is to explore the importance of soft selection in the real world. My motive and that of my colleagues as described here is not to explain what maintains genetic variation in natural populations, but rather to understand the factors that shape how organisms adapt to natural environments. We characterize how feedbacks between ecology and evolution shape both evolution and ecology. These feedbacks are mediated by density- and frequency-dependent selection, the mechanisms that underlie soft selection. Here, I report on our progress in characterizing these types of selection with a combination of a consideration of the published literature and the results from my collaborators' and my research on natural populations of guppies. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa?

    PubMed

    Atwell, Brian J; Wang, Han; Scafaro, Andrew P

    2014-02-01

    Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon). The extent of DNA sequence diversity and phenotypic variation is still being established in wild Oryza, with genetic barriers suggesting a vast range of morphologies and function even within species, such as has been demonstrated for Oryza meridionalis. With increasing climate variability and attempts to make more marginal land arable, abiotic and biotic stresses will be managed over the coming decades by tapping into the genetic diversity of wild relatives of O. sativa. To help create a more targeted approach to sourcing wild rice germplasm for abiotic stress tolerance, we have created a climate distribution map by plotting the natural occurrence of all Oryza species against corresponding temperature and moisture data. We then discuss interspecific variation in phenotype and its significance for rice, followed by a discussion of ways to integrate germplasm from wild relatives into domesticated rice. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

  17. [Transgenic rice breeding for abiotic stress tolerance--present and future].

    PubMed

    Zhao, Feng-Yun; Zhang, Hui

    2007-01-01

    Environmental stresses and the continuing deterioration of arable land, along with an explosive increase in world population, pose serious threats to global agricultural production and food security. Improving the tolerance of the major crop plants to abiotic stresses has been a main goal in agriculture for a long time. As rice is considered one of the major crops, the development of new cultivars with enhanced abiotic stress-tolerance will undoubtedly have an important effect on global food production. The transgenic approach offers an attractive alternative to conventional techniques for the genetic improvement of rice cultivars. In recent years, an array of stress-related genes has already been transferred to rice to improve its resistance against abiotic stresses. Many transgenic rice plants with enhanced abiotic stress-tolerance have been obtained. This article focuses on the progress in the study of abiotic stress tolerance in transgenic rice breeding.

  18. Oxygen and sulfur isotope systematics of sulfate produced by bacterial and abiotic oxidation of pyrite

    USGS Publications Warehouse

    Balci, N.; Shanks, Wayne C.; Mayer, B.; Mandernack, K.W.

    2007-01-01

    To better understand reaction pathways of pyrite oxidation and biogeochemical controls on ??18O and ??34S values of the generated sulfate in acid mine drainage (AMD) and other natural environments, we conducted a series of pyrite oxidation experiments in the laboratory. Our biological and abiotic experiments were conducted under aerobic conditions by using O2 as an oxidizing agent and under anaerobic conditions by using dissolved Fe(III)aq as an oxidant with varying ??18OH2O values in the presence and absence of Acidithiobacillus ferrooxidans. In addition, aerobic biological experiments were designed as short- and long-term experiments where the final pH was controlled at ???2.7 and 2.2, respectively. Due to the slower kinetics of abiotic sulfide oxidation, the aerobic abiotic experiments were only conducted as long term with a final pH of ???2.7. The ??34SSO4 values from both the biological and abiotic anaerobic experiments indicated a small but significant sulfur isotope fractionation (???-0.7???) in contrast to no significant fractionation observed from any of the aerobic experiments. Relative percentages of the incorporation of water-derived oxygen and dissolved oxygen (O2) to sulfate were estimated, in addition to the oxygen isotope fractionation between sulfate and water, and dissolved oxygen. As expected, during the biological and abiotic anaerobic experiments all of the sulfate oxygen was derived from water. The percentage incorporation of water-derived oxygen into sulfate during the oxidation experiments by O2 varied with longer incubation and lower pH, but not due to the presence or absence of bacteria. These percentages were estimated as 85%, 92% and 87% from the short-term biological, long-term biological and abiotic control experiments, respectively. An oxygen isotope fractionation effect between sulfate and water (??18 OSO4 s(-) H2 O) of ???3.5??? was determined for the anaerobic (biological and abiotic) experiments. This measured ??18 OSO42 - s(-) H2

  19. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk

    PubMed Central

    Kissoudis, Christos; van de Wiel, Clemens; Visser, Richard G. F.; van der Linden, Gerard

    2014-01-01

    Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops. PMID:24904607

  20. Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA

    DTIC Science & Technology

    2009-05-01

    FINAL REPORT Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA SERDP Project ER-1421 MAY 2009 James E. Szecsody...00-2009 4. TITLE AND SUBTITLE Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...investigate whether in situ coupled abiotic/biotic degradation of N-nitrosodimethylamine ( NDMA , an emerging contaminant) could be used as a permeable

  1. Six Classroom Exercises to Teach Natural Selection to Undergraduate Biology Students

    PubMed Central

    Kalinowski, Steven T.; Leonard, Mary J.; Andrews, Tessa M.; Litt, Andrea R.

    2013-01-01

    Students in introductory biology courses frequently have misconceptions regarding natural selection. In this paper, we describe six activities that biology instructors can use to teach undergraduate students in introductory biology courses how natural selection causes evolution. These activities begin with a lesson introducing students to natural selection and also include discussions on sexual selection, molecular evolution, evolution of complex traits, and the evolution of behavior. The set of six topics gives students the opportunity to see how natural selection operates in a variety of contexts. Pre- and postinstruction testing showed students’ understanding of natural selection increased substantially after completing this series of learning activities. Testing throughout this unit showed steadily increasing student understanding, and surveys indicated students enjoyed the activities. PMID:24006396

  2. Natural Selection in a Petri Dish.

    ERIC Educational Resources Information Center

    McCarty, Robbie V.; Marek, Edmund A.

    1997-01-01

    Presents an activity to teach natural selection that involves students in a microbiological investigation. Students discover that a change in environmental conditions tests a species' range of adaptations. (DDR)

  3. ELUCIDATING THE ROLE OF ELECTRON TRANSFER MEDIATORS IN REDUCTIVE TRANSFORMATIONS IN NATURAL SEDIMENTS

    EPA Science Inventory

    To study the identity and reactivity of electron transfer mediators (ETMs) in natural sediments, the reduction kinetics of a glass bead-azo dye complex were measured in abiotic and biotic model systems, as well as in natural sediments. In abiotic model systems, the bead-dye comp...

  4. Sexual selection expedites the evolution of pesticide resistance.

    PubMed

    Jacomb, Frances; Marsh, Jason; Holman, Luke

    2016-12-01

    The evolution of insecticide resistance by crop pests and disease vectors causes serious problems for agriculture and health. Sexual selection can accelerate or hinder adaptation to abiotic challenges in a variety of ways, but the effect of sexual selection on resistance evolution is little studied. Here, we examine this question using experimental evolution in the pest insect Tribolium castaneum. The experimental removal of sexual selection slowed the evolution of resistance in populations treated with pyrethroid pesticide, and also reduced the rate at which resistance was lost from pesticide-free populations. These results suggest that selection arising from variance in mating and fertilization success can augment natural selection on pesticide resistance, meaning that sexual selection should be considered when designing strategies to limit the evolution of pesticide resistance. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  5. Roles of melatonin in abiotic stress resistance in plants.

    PubMed

    Zhang, Na; Sun, Qianqian; Zhang, Haijun; Cao, Yunyun; Weeda, Sarah; Ren, Shuxin; Guo, Yang-Dong

    2015-02-01

    In recent years melatonin has emerged as a research highlight in plant studies. Melatonin has different functions in many aspects of plant growth and development. The most frequently mentioned functions of melatonin are related to abiotic stresses such as drought, radiation, extreme temperature, and chemical stresses. This review mainly focuses on the regulatory effects of melatonin when plants face harsh environmental conditions. Evidence indicates that environmental stress can increase the level of endogenous melatonin in plants. Overexpression of the melatonin biosynthetic genes elevates melatonin levels in transgenic plants. The transgenic plants show enhanced tolerance to abiotic stresses. Exogenously applied melatonin can also improve the ability of plants to tolerate abiotic stresses. The mechanisms by which melatonin alleviates abiotic stresses are discussed. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  6. Abiotic Supramolecular Systems

    DTIC Science & Technology

    2011-05-02

    REPORT Abiotic Supramolecular Systems 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The goal of this research project was to develop new concepts for the...decision, unless so designated by other documentation. 12. DISTRIBUTION AVAILIBILITY STATEMENT Approved for Public Release; Distribution Unlimited UU...9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES U.S. Army Research Office P.O

  7. Stressed out symbiotes: hypotheses for the influence of abiotic stress on arbuscular mycorrhizal fungi.

    PubMed

    Millar, Niall S; Bennett, Alison E

    2016-11-01

    Abiotic stress is a widespread threat to both plant and soil communities. Arbuscular mycorrhizal (AM) fungi can alleviate effects of abiotic stress by improving host plant stress tolerance, but the direct effects of abiotic stress on AM fungi are less well understood. We propose two hypotheses predicting how AM fungi will respond to abiotic stress. The stress exclusion hypothesis predicts that AM fungal abundance and diversity will decrease with persistent abiotic stress. The mycorrhizal stress adaptation hypothesis predicts that AM fungi will evolve in response to abiotic stress to maintain their fitness. We conclude that abiotic stress can have effects on AM fungi independent of the effects on the host plant. AM fungal communities will change in composition in response to abiotic stress, which may mean the loss of important individual species. This could alter feedbacks to the plant community and beyond. AM fungi will adapt to abiotic stress independent of their host plant. The adaptation of AM fungi to abiotic stress should allow the maintenance of the plant-AM fungal mutualism in the face of changing climates.

  8. Utilizing genetic resources and precision agriculture to enhance resistance to biotic and abiotic stress in watermelon

    USDA-ARS?s Scientific Manuscript database

    Originally from Africa, watermelon is a staple crop in South Carolina and rich source of important phytochemicals that promote human health. As a result of many years of domestication and selection for desired fruit quality, modern watermelon cultivars are susceptible to biotic and abiotic stress. T...

  9. LSU network hubs integrate abiotic and biotic stress responses via interaction with the superoxide dismutase FSD2

    PubMed Central

    Garcia-Molina, Antoni; Altmann, Melina; Alkofer, Angela; Epple, Petra M.; Dangl, Jeffery L.

    2017-01-01

    Abstract In natural environments, plants often experience different stresses simultaneously, and adverse abiotic conditions can weaken the plant immune system. Interactome mapping revealed that the LOW SULPHUR UPREGULATED (LSU) proteins are hubs in an Arabidopsis protein interaction network that are targeted by virulence effectors from evolutionarily diverse pathogens. Here we show that LSU proteins are up-regulated in several abiotic and biotic stress conditions, such as nutrient depletion or salt stress, by both transcriptional and post-translational mechanisms. Interference with LSU expression prevents chloroplastic reactive oxygen species (ROS) production and proper stomatal closure during sulphur stress. We demonstrate that LSU1 interacts with the chloroplastic superoxide dismutase FSD2 and stimulates its enzymatic activity in vivo and in vitro. Pseudomonas syringae virulence effectors interfere with this interaction and preclude re-localization of LSU1 to chloroplasts. We demonstrate that reduced LSU levels cause a moderately enhanced disease susceptibility in plants exposed to abiotic stresses such as nutrient deficiency, high salinity, or heavy metal toxicity, whereas LSU1 overexpression confers significant disease resistance in several of these conditions. Our data suggest that the network hub LSU1 plays an important role in co-ordinating plant immune responses across a spectrum of abiotic stress conditions. PMID:28207043

  10. ABIOTIC IN SITU TECHNOLOGIES FOR GROUNDWATER REMEDIATION CONFERENCE: PROCEEDINGS

    EPA Science Inventory

    The USEPA conference on Abiotic In Situ Technologies for Groundwater Remediation was held in Dallas, TX, 8/31-9/2/99. The goal of the meeting was to disseminate current information on abiotic in situ groundwater treatment echnologies. Although much information is being provided a...

  11. Spatial variation in abiotic and biotic factors in a floodplain determine anuran body size and growth rate at metamorphosis.

    PubMed

    Indermaur, Lukas; Schmidt, Benedikt R; Tockner, Klement; Schaub, Michael

    2010-07-01

    Body size at metamorphosis is a critical trait in the life history of amphibians. Despite the wide-spread use of amphibians as experimental model organisms, there is a limited understanding of how multiple abiotic and biotic factors affect the variation in metamorphic traits under natural conditions. The aim of our study was to quantify the effects of abiotic and biotic factors on spatial variation in the body size of tadpoles and size at metamorphosis of the European common toad (Bufo b. spinosus). Our study population was distributed over the riverbed (active tract) and the fringing riparian forest of a natural floodplain. The riverbed had warm ponds with variable hydroperiod and few predators, whereas the forest had ponds with the opposite characteristics. Spatial variation in body size at metamorphosis was governed by the interactive effects of abiotic and biotic factors. The particular form of the interaction between water temperature and intraspecific tadpole density suggests that abiotic factors laid the foundation for biotic factors: intraspecific density decreased growth only at high temperature. Predation and intraspecific density jointly reduced metamorphic size. Interspecific density had a negligible affect on body size at metamorphosis, suggesting weak inter-anuran interactions in the larval stage. Population density at metamorphosis was about one to two orders of magnitudes higher in the riverbed ponds than in the forest ponds, mainly because of lower tadpole mortality. Based on our results, we conclude that ponds in the riverbed appear to play a pivotal role for the population because tadpole growth and survival is best in this habitat.

  12. Concurrent natural and sexual selection in wild male sockeye salmon, Oncorhynchus nerka.

    PubMed

    Hamon, Troy R; Foote, Chris J

    2005-05-01

    Concurrent natural and sexual selection have been inferred from laboratory and comparative studies in a number of taxa, but are rarely measured in natural populations. Because the interaction of these two general categories of selection may be complex when they occur simultaneously, empirical evidence from natural populations would help us to understand this interaction and probably give us greater insight into each separate episode as well. In male sockeye salmon, sexual selection for larger body size has been indicated in both deep and shallow water habitats. However, in shallow habitats male sockeye are generally smaller and less deep-bodied than in deep habitats, a difference that has been ascribed to natural selection. We measured concurrent natural and sexual selection in two years on breeding male sockeye salmon with respect to body size, body shape, and time of arrival to the breeding grounds. Natural selection was variable in effect and sexual selection was variable in intensity in these two years. The patterns of selection also appear to be interdependent; areas where predation on spawning adults is not intense have yielded different patterns of sexual selection than those measured here. It appears that some of the body shape differences in sockeye salmon associated with different spawning habitats, which were previously attributed to selective mortality, may be a result of different patterns of sexual selection in the different habitats. Total selection resulting from the combination of both natural and sexual selection was less intense than either natural or sexual selection in most cases. Measurement of concurrent selection episodes in nature may help us to understand whether the pattern of differential sexual selection is common, and whether observed patterns of habitat-related differentiation may be due to differences in sexual selection.

  13. Designing cooperatively folded abiotic uni- and multimolecular helix bundles

    NASA Astrophysics Data System (ADS)

    de, Soumen; Chi, Bo; Granier, Thierry; Qi, Ting; Maurizot, Victor; Huc, Ivan

    2018-01-01

    Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.

  14. Systems biology approach in plant abiotic stresses.

    PubMed

    Mohanta, Tapan Kumar; Bashir, Tufail; Hashem, Abeer; Abd Allah, Elsayed Fathi

    2017-12-01

    Plant abiotic stresses are the major constraint on plant growth and development, causing enormous crop losses across the world. Plants have unique features to defend themselves against these challenging adverse stress conditions. They modulate their phenotypes upon changes in physiological, biochemical, molecular and genetic information, thus making them tolerant against abiotic stresses. It is of paramount importance to determine the stress-tolerant traits of a diverse range of genotypes of plant species and integrate those traits for crop improvement. Stress-tolerant traits can be identified by conducting genome-wide analysis of stress-tolerant genotypes through the highly advanced structural and functional genomics approach. Specifically, whole-genome sequencing, development of molecular markers, genome-wide association studies and comparative analysis of interaction networks between tolerant and susceptible crop varieties grown under stress conditions can greatly facilitate discovery of novel agronomic traits that protect plants against abiotic stresses. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  15. Recovery of white sturgeon populations through natural production: Understanding the influence of abiotic and biotic factors on spawning and subsequent recruitment

    USGS Publications Warehouse

    Parsley, M.J.; Anders, P.J.; Miller, Allen I.; Beckman, L.G.; McCabe, G.T.

    2002-01-01

    Recovery or maintenance of sturgeon populations through natural production in perturbed rivers requires adequate knowledge of the abiotic and biotic factors that influence spawning and cause mortality of embryonic, larval, and juvenile life stages. Although it is known that year-class strength of white sturgeon Acipenser transmontanus is determined within 2-3 months after spawning, little is known about specific causes of mortality to early life stages during this period. Initial spawning success is critical in the development of a strong year-class, and maximized recruitment may be dependent upon water temperature and the availability of optimal in-river habitat. Analyses have shown that increased river discharge combined with suitable water temperatures during spawning, egg incubation, yolk sac larvae dispersal, and first exogenous feeding result in greater recruitment. However, little is known about the importance of other variables, such as food availability or losses due to predation that influence year-class strength. ?? 2002 by the American Fisheries Society.

  16. A Gambler's Model of Natural Selection.

    ERIC Educational Resources Information Center

    Nolan, Michael J.; Ostrovsky, David S.

    1996-01-01

    Presents an activity that highlights the mechanism and power of natural selection. Allows students to think in terms of modeling a biological process and instills an appreciation for a mathematical approach to biological problems. (JRH)

  17. Development and Validation of the Conceptual Assessment of Natural Selection (CANS)

    ERIC Educational Resources Information Center

    Kalinowski, Steven T.; Leonard, Mary J.; Taper, Mark L.

    2016-01-01

    We developed and validated the Conceptual Assessment of Natural Selection (CANS), a multiple-choice test designed to assess how well college students understand the central principles of natural selection. The expert panel that reviewed the CANS concluded its questions were relevant to natural selection and generally did a good job sampling the…

  18. More than Meets the Eye--a Simulation of Natural Selection.

    ERIC Educational Resources Information Center

    Allen, J. A.; And Others

    1987-01-01

    Presents experiments using wild birds as predators and pastry as prey and colored stones as background to demonstrate natural selection. Describes the exercise as an exercise in simulating natural selection. (Author/CW)

  19. Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants

    PubMed Central

    Khan, M. Iqbal R.; Fatma, Mehar; Per, Tasir S.; Anjum, Naser A.; Khan, Nafees A.

    2015-01-01

    Abiotic stresses (such as metals/metalloids, salinity, ozone, UV-B radiation, extreme temperatures, and drought) are among the most challenging threats to agricultural system and economic yield of crop plants. These stresses (in isolation and/or combination) induce numerous adverse effects in plants, impair biochemical/physiological and molecular processes, and eventually cause severe reductions in plant growth, development and overall productivity. Phytohormones have been recognized as a strong tool for sustainably alleviating adverse effects of abiotic stresses in crop plants. In particular, the significance of salicylic acid (SA) has been increasingly recognized in improved plant abiotic stress-tolerance via SA-mediated control of major plant-metabolic processes. However, the basic biochemical/physiological and molecular mechanisms that potentially underpin SA-induced plant-tolerance to major abiotic stresses remain least discussed. Based on recent reports, this paper: (a) overviews historical background and biosynthesis of SA under both optimal and stressful environments in plants; (b) critically appraises the role of SA in plants exposed to major abiotic stresses; (c) cross-talks potential mechanisms potentially governing SA-induced plant abiotic stress-tolerance; and finally (d) briefly highlights major aspects so far unexplored in the current context. PMID:26175738

  20. Development and Validation of the Conceptual Assessment of Natural Selection (CANS)

    PubMed Central

    Kalinowski, Steven T.; Leonard, Mary J.; Taper, Mark L.

    2016-01-01

    We developed and validated the Conceptual Assessment of Natural Selection (CANS), a multiple-choice test designed to assess how well college students understand the central principles of natural selection. The expert panel that reviewed the CANS concluded its questions were relevant to natural selection and generally did a good job sampling the specific concepts they were intended to assess. Student interviews confirmed questions on the CANS provided accurate reflections of how students think about natural selection. And, finally, statistical analysis of student responses using item response theory showed that the CANS did a very good job of estimating how well students understood natural selection. The empirical reliability of the CANS was substantially higher than the Force Concept Inventory, a highly regarded test in physics that has a similar purpose. PMID:27856552

  1. Missing concepts in natural selection theory reconstructions.

    PubMed

    Ginnobili, Santiago

    2016-09-01

    The concept of fitness has generated a lot of discussion in philosophy of biology. There is, however, relative agreement about the need to distinguish at least two uses of the term: ecological fitness on the one hand, and population genetics fitness on the other. The goal of this paper is to give an explication of the concept of ecological fitness by providing a reconstruction of the theory of natural selection in which this concept was framed, that is, based on the way the theory was put to use in Darwin's main texts. I will contend that this reconstruction enables us to account for the current use of the theory of natural selection. The framework presupposed in the analysis will be that of metatheoretical structuralism. This framework will provide both a better understanding of the nature of ecological fitness and a more complete reconstruction of the theory. In particular, it will provide what I think is a better way of understanding how the concept of fitness is applied through heterogeneous cases. One of the major advantages of my way of thinking about natural selection theory is that it would not have the peculiar metatheoretical status that it has in other available views. I will argue that in order to achieve these goals it is necessary to make several concepts explicit, concepts that are frequently omitted in usual reconstructions.

  2. The insufficient part of abiogenesis theory - natural selection

    NASA Astrophysics Data System (ADS)

    Ploompuu, Tõnu

    2016-04-01

    Abiogenesis has already been studied for a whole century. There have been studies on the synthesis of precursors of biopolymers, concentration processes and polymerization pathways, sites of initiation of life. Autoreplication has been explained. Protocells have been constructed from abiogenic membranes. But one essential aspect for life - the natural selection - has been marginalized in these investigations. Despite the convincing use of natural selection in biology for one and half century, it has not been used sufficiently in the models of the beginning of life. Pictorially - Darwin's pond model is used without darwinism. This generates an unnecessary interruption on the path for understanding the process. Natural selection is essential in abiogenesis, in the genesis of biological information system. A selection of more collaborative autoreplicate biopolymers and the depolymerisation of others was required. Only natural selection was able to combine biopolymer molecules for life. The primary natural selection can operate only in an environment with variable physical and chemical conditions. The selective agent must constantly fluctuate during a long time span and a large area. Formation of the simplest complex of life needs homeostasis. The best sites for constant fluctuations are littoral areas of oceans. Two very constant fluctuations - waves and tides - occur there. The best conditions for the origin of life were exactly in the end of the Late Heavy Bombardment at temperature nealy 100° C. Earth's surface was then protected against the UV destruction by a thick cloud cover. High evaporation at the hotter parts of shore rocks increased the concentration of the primordial soup and there was excellent selective power by routine water level fluctuations. Because of the water level fluctuations salty ocean water and fresh water from continuous downpours alternated at the littoral zones. In low temperatures the formation of life would be hindered by UV

  3. Microbial Resistance to Triclosan: A Case Study in Natural Selection

    ERIC Educational Resources Information Center

    Serafini, Amanda; Matthews, Dorothy M.

    2009-01-01

    Natural selection is the mechanism of evolution caused by the environmental selection of organisms most fit to reproduce, sometimes explained as "survival of the fittest." An example of evolution by natural selection is the development of bacteria that are resistant to antimicrobial agents as a result of exposure to these agents. Triclosan, which…

  4. Symbiogenesis, natural selection, and the dynamic Earth.

    PubMed

    Kutschera, U

    2009-08-01

    One century ago, Constantin S. Mereschkowsky introduced the symbiogenesis theory for the origin of chloroplasts from ancient cyanobacteria which was later supplemented by Ivan E. Wallin's proposal that mitochondria evolved from once free-living bacteria. Today, this Mereschkowsky-Wallin principle of symbiogenesis, which is also known as the serial primary endosymbiosis theory, explains the evolutionary origin of eukaryotic cells and hence the emergence of all eukaryotes (protists, fungi, animals and plants). In 1858, the concept of natural selection was described independently by Charles Darwin and Alfred R. Wallace. In the same year, Antonio Snider-Pellegrini proposed the idea of shifting continents, which was later expanded by Alfred Wegener, who published his theory of continental drift eight decades ago. Today, directional selection is accepted as the major cause of adaptive evolution within natural populations of micro- and macro-organisms and the theory of the dynamic Earth (plate tectonics) is well supported. In this article, I combine the processes and principles of symbiogenesis, natural selection and the dynamic Earth and propose an integrative 'synade-model' of macroevolution which takes into account organisms from all five Kingdoms of life.

  5. Polyamines and abiotic stress in plants: a complex relationship1

    PubMed Central

    Minocha, Rakesh; Majumdar, Rajtilak; Minocha, Subhash C.

    2014-01-01

    The physiological relationship between abiotic stress in plants and polyamines was reported more than 40 years ago. Ever since there has been a debate as to whether increased polyamines protect plants against abiotic stress (e.g., due to their ability to deal with oxidative radicals) or cause damage to them (perhaps due to hydrogen peroxide produced by their catabolism). The observation that cellular polyamines are typically elevated in plants under both short-term as well as long-term abiotic stress conditions is consistent with the possibility of their dual effects, i.e., being protectors from as well as perpetrators of stress damage to the cells. The observed increase in tolerance of plants to abiotic stress when their cellular contents are elevated by either exogenous treatment with polyamines or through genetic engineering with genes encoding polyamine biosynthetic enzymes is indicative of a protective role for them. However, through their catabolic production of hydrogen peroxide and acrolein, both strong oxidizers, they can potentially be the cause of cellular harm during stress. In fact, somewhat enigmatic but strong positive relationship between abiotic stress and foliar polyamines has been proposed as a potential biochemical marker of persistent environmental stress in forest trees in which phenotypic symptoms of stress are not yet visible. Such markers may help forewarn forest managers to undertake amelioration strategies before the appearance of visual symptoms of stress and damage at which stage it is often too late for implementing strategies for stress remediation and reversal of damage. This review provides a comprehensive and critical evaluation of the published literature on interactions between abiotic stress and polyamines in plants, and examines the experimental strategies used to understand the functional significance of this relationship with the aim of improving plant productivity, especially under conditions of abiotic stress. PMID:24847338

  6. Contribution of hydrolysis in the abiotic attenuation of RDX and HMX in coastal waters.

    PubMed

    Monteil-Rivera, Fanny; Paquet, Louise; Giroux, Romain; Hawari, Jalal

    2008-01-01

    Sinking of military ships, dumping of munitions during the two World Wars, and military training have resulted in the undersea deposition of numerous unexploded ordnances (UXOs). Leaching of energetic compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) from these UXOs may cause adverse ecological effects so that the long-term fate of these chemicals in the sea should be known. The present study assesses the contribution of alkaline hydrolysis into the natural attenuation of RDX and HMX in coastal waters. Alkaline hydrolysis rates were shown to be unaffected by the presence of sodium chloride, the most common component in marine waters. Kinetic parameters (E(a), ln A, k(2)) quantified for the alkaline hydrolysis of RDX and HMX in deionized water (30-50 degrees C, pH 10-12) agreed relatively well with abiotic degradation rates determined in sterilized natural coastal waters (50 and 60 degrees C, variable salinity) even if the latter were generally slightly faster than the former. Furthermore, similar products (HCHO, NO(2)(-), O(2)NNHCH(2)NHCHO) were obtained on alkaline hydrolysis in deionized water and abiotic degradation in coastal waters. These two findings suggested that degradation of nitramines in sterilized natural coastal waters, away from light, was mainly governed by alkaline hydrolysis. Kinetic calculations using the present parameters showed that alkaline hydrolysis of RDX and HMX in marine waters at 10 degrees C would respectively take 112 +/- 10 and 2408 +/- 217 yr to be completed (99.0%). We concluded that under natural conditions hydrolysis should not contribute significantly to the natural attenuation of HMX in coastal waters whereas it could play an active role in the natural attenuation of RDX.

  7. Abiotic regulation: a common way for proteins to modulate their functions.

    PubMed

    Zou, Zhi; Fu, Xinmiao

    2015-01-01

    Modulation of protein intrinsic activity in cells is generally carried out via a combination of four common ways, i.e., allosteric regulation, covalent modification, proteolytic cleavage and association of other regulatory proteins. Accumulated evidence indicate that changes of certain abiotic factors (e.g., temperature, pH, light and mechanical force) within or outside the cells directly influence protein structure and thus profoundly modulate the functions of a wide range of proteins, termed as abiotic regulatory proteins (e.g., heat shock factor, small heat shock protein, hemoglobin, zymogen, integrin, rhodopsin). Such abiotic regulation apparently differs from the four classic ways in perceiving and response to the signals. Importantly, it enables cells to directly and also immediately response to extracellular stimuli, thus facilitating the ability of organisms to resist against and adapt to the abiotic stress and thereby playing crucial roles in life evolution. Altogether, abiotic regulation may be considered as a common way for proteins to modulate their functions.

  8. Abiotic controls on N2O emissions from soils and wetlands

    NASA Astrophysics Data System (ADS)

    Horwath, W. R.

    2016-12-01

    The increase in atmospheric nitrous oxide (N2O) is a critical climate change issue contributing to global warming. Most studies on N2O production attribute microbial processes and their associated enzymatic reactions to be the main driver affecting emissions. The role of redox capable iron, manganese and organic compounds that can react with intermediates in the nitrogen cycle has also been shown to produce N2O abiotically. The importance of the abiotic pathways, however, is highly debated. The abiotic production of N2O is related to biophysiochemical controls and unique isotopic signatures of nitrogen cycle intermediates (hydroxylamine, nitric oxide, and nitrite), redox-active metals (iron and manganese) and organic matter (humic and fulvic acids). In a range of soils, we find that the iron directly associated with organic compounds is the strongest variable relating to N2O emissions. In addition to these factors, management is also assumed to affect abiotic N2O production through its impact on nitrogen cycle intermediates, but the environmental and physiochemical conditions that are changed by management are rarely considered in the abiotic production of N2O. We find that the amount and quality of organic compounds in soils directly determines the fate of soil N2O production (i.e. be emitted or consumed). Water depth in rice paddies and wetlands also plays a significant role in partitioning production and consumption of N2O. What is evident from studies on N2O emission is that abiotic reactions are coupled to biotic processes and they cannot be easily separated. The biotic/abiotic interactions have important ecological outcomes that influence abiotic production mechanisms and should be recognized as important controllers of N2O production and consumption processes in soils and sediments.

  9. Using David Lack's Observations of Finch Beak Size to Teach Natural Selection & the Nature of Science

    ERIC Educational Resources Information Center

    Bierema, Andrea M.-K.; Rudge, David W.

    2014-01-01

    One of the key aspects of natural selection is competition, yet the concept of competition is not necessarily emphasized in explanations of natural selection. Because of this, we developed an activity for our class that focuses on competition and provides an example of the effects of competition on natural selection. This hands-on activity models…

  10. Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress

    PubMed Central

    dos Reis, Sávio Pinho; Lima, Aline Medeiros; de Souza, Cláudia Regina Batista

    2012-01-01

    Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. PMID:22942725

  11. The Stable Isotope Fractionation of Abiotic Reactions: A Benchmark in the Detection of Life

    NASA Technical Reports Server (NTRS)

    Summers, David P.

    2003-01-01

    One very important tool in the analysis of biogenic, and potentially biogenic, samples is the study of their stable isotope distributions. The isotope distribution of a sample depends on the process(es) that created it. One important application of the analysis of C & N stable isotope ratios has been in the determination of whether organic matter in a sample is of biological origin or was produced abiotically. For example, the delta C-13 of organic material found embedded in phosphate grains was cited as a critical part of the evidence for life in 3.8 billion year old samples. The importance of such analysis in establishing biogenicity was highlighted again by the role this issue played in the recent debate over the validity of what had been accepted as the Earth s earliest microfossils. These kinds of analysis imply a comparison with the fractionation that one would have seen if the organic material had been produced by alternative, abiotic, pathways. Could abiotic reactions account for the same level of fractionation? Additionally, since the fractionation can vary between different abiotic reactions, understanding their fractionations can be important in distinguishing what reactions may have been significant in the formation of different abiological samples (such as extraterrestrial samples). There is however, a scarcity of data on the fractionation of carbon and nitrogen by abiotic reactions. In order to interpret properly what the stable isotope ratios of samples tell us about their biotic or abiotic nature, more needs to be known about how abiotic reactions fractionate C and N. Carbon isotope fractionations have been studied for a few abiotic processes. These studies presumed the presence of a reducing atmosphere, focusing on reactions involving spark discharge, W photolysis of reducing gas mixtures, and cyanide polymerization in the presence of ammonia. They did find that the initial products showed a depletion in I3C with values in the range of a few per

  12. LSU network hubs integrate abiotic and biotic stress responses via interaction with the superoxide dismutase FSD2.

    PubMed

    Garcia-Molina, Antoni; Altmann, Melina; Alkofer, Angela; Epple, Petra M; Dangl, Jeffery L; Falter-Braun, Pascal

    2017-02-01

    In natural environments, plants often experience different stresses simultaneously, and adverse abiotic conditions can weaken the plant immune system. Interactome mapping revealed that the LOW SULPHUR UPREGULATED (LSU) proteins are hubs in an Arabidopsis protein interaction network that are targeted by virulence effectors from evolutionarily diverse pathogens. Here we show that LSU proteins are up-regulated in several abiotic and biotic stress conditions, such as nutrient depletion or salt stress, by both transcriptional and post-translational mechanisms. Interference with LSU expression prevents chloroplastic reactive oxygen species (ROS) production and proper stomatal closure during sulphur stress. We demonstrate that LSU1 interacts with the chloroplastic superoxide dismutase FSD2 and stimulates its enzymatic activity in vivo and in vitro. Pseudomonas syringae virulence effectors interfere with this interaction and preclude re-localization of LSU1 to chloroplasts. We demonstrate that reduced LSU levels cause a moderately enhanced disease susceptibility in plants exposed to abiotic stresses such as nutrient deficiency, high salinity, or heavy metal toxicity, whereas LSU1 overexpression confers significant disease resistance in several of these conditions. Our data suggest that the network hub LSU1 plays an important role in co-ordinating plant immune responses across a spectrum of abiotic stress conditions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  13. Model for detection and assessment of abiotic stress caused by uranium mining in European Black Pine landscapes

    NASA Astrophysics Data System (ADS)

    Filchev, Lachezar; Roumenina, Eugenia

    2013-10-01

    The article presents the results obtained from a study for detection and assessment of abiotic stress through pollution with heavy metals, metalloids, and natural radionuclides in European Black Pine (Pinus nigra L.) forests caused by uranium mining using ground-based biogeochemical, biophysical, and field spectrometry data. The forests are located on a territory subject to underground and open uranium mining. An operational model of the study is proposed. The areas subject to technogeochemical load are outlined based on the aggregate pollution index Zc. Laboratory and field spectrometry data were used to detect the signals of abiotic stress at pixel level. The methods used for determination of stressed and unstressed black pine forests are: four vegetation indices (TCARI, MCARI, MTVI 2, and PRI 1) for stress detection, and the position, depth, asymmetry, and shift of the red-edge. Based on the "blue shift" and the depth and position of the red-edge, registered by the laboratory analysis and field spectral reflectance, it is established that coniferous forests subject to abiotic stress show an increase in total chlorophyll content and carotene. It has been found that the vegetation indices MTVI 2 and PRI 1, as well as the combination of vegetation indices and pigments may be used as a direct indicator of abiotic stress in coniferous forests caused by uranium mining.

  14. Life without water: cross-resistance of anhydrobiotic cell line to abiotic stresses

    NASA Astrophysics Data System (ADS)

    Gusev, Oleg

    2016-07-01

    Anhydrobiosis is an intriguing phenomenon of natural ability of some organisms to resist water loss. The larvae of Polypedilum vanderplanki, the sleeping chironomid is the largest and most complex anhydrobionts known to date. The larvae showed ability to survive variety of abiotic stresses, including outer space environment. Recently cell line (Pv11) derived from the embryonic mass of the chironomid was established. Initially sensitive to desiccation cells, are capable to "induced" anhydrobiosis, when the resistance to desiccation can be developed by pre-treatment of the cells with trehalose followed by quick desiccation. We have further conducted complex analysis of the whole genome transcription response of Pv11 cells to different abiotic stresses, including oxidative stress and irradiation. Comparative analysis showed that the gene set, responsible for formation of desiccation resistance (ARID regions in the genome) is also activated in response to other types of stresses and likely to contribute to general enhancing of the resistance of the cells to harsh environment. We have further demonstrated that the cells are able to protect recombinant proteins from harmful effect of desiccation

  15. Poaceae vs. Abiotic Stress: Focus on Drought and Salt Stress, Recent Insights and Perspectives

    PubMed Central

    Landi, Simone; Hausman, Jean-Francois; Guerriero, Gea; Esposito, Sergio

    2017-01-01

    Poaceae represent the most important group of crops susceptible to abiotic stress. This large family of monocotyledonous plants, commonly known as grasses, counts several important cultivated species, namely wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), and barley (Hordeum vulgare). These crops, notably, show different behaviors under abiotic stress conditions: wheat and rice are considered sensitive, showing serious yield reduction upon water scarcity and soil salinity, while barley presents a natural drought and salt tolerance. During the green revolution (1940–1960), cereal breeding was very successful in developing high-yield crops varieties; however, these cultivars were maximized for highest yield under optimal conditions, and did not present suitable traits for tolerance under unfavorable conditions. The improvement of crop abiotic stress tolerance requires a deep knowledge of the phenomena underlying tolerance, to devise novel approaches and decipher the key components of agricultural production systems. Approaches to improve food production combining both enhanced water use efficiency (WUE) and acceptable yields are critical to create a sustainable agriculture in the future. This paper analyzes the latest results on abiotic stress tolerance in Poaceae. In particular, the focus will be directed toward various aspects of water deprivation and salinity response efficiency in Poaceae. Aspects related to cell wall metabolism will be covered, given the importance of the plant cell wall in sensing environmental constraints and in mediating a response; the role of silicon (Si), an important element for monocots' normal growth and development, will also be discussed, since it activates a broad-spectrum response to different exogenous stresses. Perspectives valorizing studies on landraces conclude the survey, as they help identify key traits for breeding purposes. PMID:28744298

  16. The shifting influence of abiotic drivers during landslide succession in Puerto Rico

    Treesearch

    L. R. Walker; A. B. Shiels; P. J. Bellingham; A. D. Sparrow; N. Fetcher; F. H. Landau; D. J. Lodge

    2013-01-01

    Summary 1. Abiotic variables are critical drivers of succession in most primary seres, but how their influence on biota changes over time is rarely examined. Landslides provide good model systems for examining abiotic influences because they are spatially and temporally heterogeneous habitats with distinct abiotic and biotic gradients and post-landslide erosion. 2. In...

  17. The genetic consequences of selection in natural populations.

    PubMed

    Thurman, Timothy J; Barrett, Rowan D H

    2016-04-01

    The selection coefficient, s, quantifies the strength of selection acting on a genetic variant. Despite this parameter's central importance to population genetic models, until recently we have known relatively little about the value of s in natural populations. With the development of molecular genetic techniques in the late 20th century and the sequencing technologies that followed, biologists are now able to identify genetic variants and directly relate them to organismal fitness. We reviewed the literature for published estimates of natural selection acting at the genetic level and found over 3000 estimates of selection coefficients from 79 studies. Selection coefficients were roughly exponentially distributed, suggesting that the impact of selection at the genetic level is generally weak but can occasionally be quite strong. We used both nonparametric statistics and formal random-effects meta-analysis to determine how selection varies across biological and methodological categories. Selection was stronger when measured over shorter timescales, with the mean magnitude of s greatest for studies that measured selection within a single generation. Our analyses found conflicting trends when considering how selection varies with the genetic scale (e.g., SNPs or haplotypes) at which it is measured, suggesting a need for further research. Besides these quantitative conclusions, we highlight key issues in the calculation, interpretation, and reporting of selection coefficients and provide recommendations for future research. © 2016 John Wiley & Sons Ltd.

  18. Relative contribution of biotic and abiotic factors to the population density of the cassava green mite, Mononychellus tanajoa (Acari: Tetranychidae).

    PubMed

    Rêgo, Adriano S; Teodoro, Adenir V; Maciel, Anilde G S; Sarmento, Renato A

    2013-08-01

    The cassava green mite, Mononychellus tanajoa, is a key pest of cassava, Manihot esculenta Crantz (Euphorbiaceae), and it may be kept in check by naturally occurring predatory mites of the family Phytoseiidae. In addition to predatory mites, abiotic factors may also contribute to regulate pest mite populations in the field. Here, we evaluated the population densities of both M. tanajoa and the generalist predatory mite Euseius ho DeLeon (Acari: Phytoseiidae) over the cultivation cycle (11 months) of cassava in four study sites located around the city of Miranda do Norte, Maranhão, Brazil. The abiotic variables rainfall, temperature and relative humidity were also recorded throughout the cultivation cycle of cassava. We determined the relative importance of biotic (density of E. ho) and abiotic (rainfall, temperature and relative humidity) factors to the density of M. tanajoa. The density of M. tanajoa increased whereas the density of E. ho remained constant throughout time. A hierarchical partitioning analysis revealed that most of the variance for the density of M. tanajoa was explained by rainfall and relative humidity followed by E. ho density and temperature. We conclude that abiotic factors, especially rainfall, were the main mechanisms driving M. tanajoa densities.

  19. Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

    ERIC Educational Resources Information Center

    Thagard, Paul; Findlay, Scott

    2010-01-01

    Darwin's theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin's theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that…

  20. Simulating natural selection in landscape genetics

    Treesearch

    E. L. Landguth; S. A. Cushman; N. Johnson

    2012-01-01

    Linking landscape effects to key evolutionary processes through individual organism movement and natural selection is essential to provide a foundation for evolutionary landscape genetics. Of particular importance is determining how spatially- explicit, individual-based models differ from classic population genetics and evolutionary ecology models based on ideal...

  1. Identification and Characterization Methods for Reactive Minerals Responsible for Natural Attenuation of Chlorinated Organic Compounds in Ground Water

    EPA Science Inventory

    Over the past decade, there has been a growing awareness of the contribution of abiotic processes to the natural degradation of chlorinated organic contaminants in aquifer material. These abiotic processes contribute to risk management of the contaminants through monitored natur...

  2. Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress.

    PubMed

    Khan, Sardar-Ali; Li, Meng-Zhan; Wang, Suo-Min; Yin, Hong-Ju

    2018-05-31

    Owing to diverse abiotic stresses and global climate deterioration, the agricultural production worldwide is suffering serious losses. Breeding stress-resilient crops with higher quality and yield against multiple environmental stresses via application of transgenic technologies is currently the most promising approach. Deciphering molecular principles and mining stress-associate genes that govern plant responses against abiotic stresses is one of the prerequisites to develop stress-resistant crop varieties. As molecular switches in controlling stress-responsive genes expression, transcription factors (TFs) play crucial roles in regulating various abiotic stress responses. Hence, functional analysis of TFs and their interaction partners during abiotic stresses is crucial to perceive their role in diverse signaling cascades that many researchers have continued to undertake. Here, we review current developments in understanding TFs, with particular emphasis on their functions in orchestrating plant abiotic stress responses. Further, we discuss novel molecular mechanisms of their action under abiotic stress conditions. This will provide valuable information for understanding regulatory mechanisms to engineer stress-tolerant crops.

  3. Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

    PubMed Central

    2013-01-01

    stresses, further validates known resistance-associated genes, and highlights new potential target genes, some lineage specific to rice, that play important roles in response to stress, providing a roadmap to develop varieties of rice that are more resistant to multiple biotic and abiotic stresses, as encountered in nature. PMID:23398910

  4. Natural Selection in Large Populations

    NASA Astrophysics Data System (ADS)

    Desai, Michael

    2011-03-01

    I will discuss theoretical and experimental approaches to the evolutionary dynamics and population genetics of natural selection in large populations. In these populations, many mutations are often present simultaneously, and because recombination is limited, selection cannot act on them all independently. Rather, it can only affect whole combinations of mutations linked together on the same chromosome. Methods common in theoretical population genetics have been of limited utility in analyzing this coupling between the fates of different mutations. In the past few years it has become increasingly clear that this is a crucial gap in our understanding, as sequence data has begun to show that selection appears to act pervasively on many linked sites in a wide range of populations, including viruses, microbes, Drosophila, and humans. I will describe approaches that combine analytical tools drawn from statistical physics and dynamical systems with traditional methods in theoretical population genetics to address this problem, and describe how experiments in budding yeast can help us directly observe these evolutionary dynamics.

  5. Natural and sexual selection in a monogamous historical human population.

    PubMed

    Courtiol, Alexandre; Pettay, Jenni E; Jokela, Markus; Rotkirch, Anna; Lummaa, Virpi

    2012-05-22

    Whether and how human populations exposed to the agricultural revolution are still affected by Darwinian selection remains controversial among social scientists, biologists, and the general public. Although methods of studying selection in natural populations are well established, our understanding of selection in humans has been limited by the availability of suitable datasets. Here, we present a study comparing the maximum strengths of natural and sexual selection in humans that includes the effects of sex and wealth on different episodes of selection. Our dataset was compiled from church records of preindustrial Finnish populations characterized by socially imposed monogamy, and it contains a complete distribution of survival, mating, and reproductive success for 5,923 individuals born 1760-1849. Individual differences in early survival and fertility (natural selection) were responsible for most variation in fitness, even among wealthier individuals. Variance in mating success explained most of the higher variance in reproductive success in males compared with females, but mating success also influenced reproductive success in females, allowing for sexual selection to operate in both sexes. The detected opportunity for selection is in line with measurements for other species but higher than most previous reports for human samples. This disparity results from biological, demographic, economic, and social differences across populations as well as from failures by most previous studies to account for variation in fitness introduced by nonreproductive individuals. Our results emphasize that the demographic, cultural, and technological changes of the last 10,000 y did not preclude the potential for natural and sexual selection in our species.

  6. Natural and sexual selection in a monogamous historical human population

    PubMed Central

    Courtiol, Alexandre; Pettay, Jenni E.; Jokela, Markus; Rotkirch, Anna; Lummaa, Virpi

    2012-01-01

    Whether and how human populations exposed to the agricultural revolution are still affected by Darwinian selection remains controversial among social scientists, biologists, and the general public. Although methods of studying selection in natural populations are well established, our understanding of selection in humans has been limited by the availability of suitable datasets. Here, we present a study comparing the maximum strengths of natural and sexual selection in humans that includes the effects of sex and wealth on different episodes of selection. Our dataset was compiled from church records of preindustrial Finnish populations characterized by socially imposed monogamy, and it contains a complete distribution of survival, mating, and reproductive success for 5,923 individuals born 1760–1849. Individual differences in early survival and fertility (natural selection) were responsible for most variation in fitness, even among wealthier individuals. Variance in mating success explained most of the higher variance in reproductive success in males compared with females, but mating success also influenced reproductive success in females, allowing for sexual selection to operate in both sexes. The detected opportunity for selection is in line with measurements for other species but higher than most previous reports for human samples. This disparity results from biological, demographic, economic, and social differences across populations as well as from failures by most previous studies to account for variation in fitness introduced by nonreproductive individuals. Our results emphasize that the demographic, cultural, and technological changes of the last 10,000 y did not preclude the potential for natural and sexual selection in our species. PMID:22547810

  7. Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

    2013-10-24

    Uranium bioremediation has emerged as a potential strategy of cleanup of radionuclear contamination worldwide. An integrated geochemical & microbial community model is a promising approach to predict and provide insights into the bioremediation of a complicated natural subsurface. In this study, an integrated column-scale model of uranium bioremediation was developed, taking into account long-term interactions between biotic and abiotic processes. It is also combined with a comprehensive thermodynamic analysis to track the fate and cycling of biogenic species. As compared with other bioremediation models, the model increases the resolution of the connection of microbial community to geochemistry and establishes directmore » quantitative correlation between overall community evolution and geochemical variation, thereby accurately predicting the community dynamics under different sedimentary conditions. The thermodynamic analysis examined a recently identified homogeneous reduction of U(VI) by Fe(II) under dynamic sedimentary conditions across time and space. It shows that the biogenic Fe(II) from Geobacter metabolism can be removed rapidly by the biogenic sulphide from sulfate reducer metabolism, hence constituting one of the reasons that make the abiotic U(VI) reduction thermodynamically infeasible in the subsurface. Further analysis indicates that much higher influent concentrations of both Fe(II) and U(VI) than normal are required to for abiotic U(VI) reduction to be thermodynamically feasible, suggesting that the abiotic reduction cannot be an alternative to the biotic reduction in the remediation of uranium contaminated groundwater.« less

  8. Research advances in major cereal crops for adaptation to abiotic stresses

    PubMed Central

    Maiti, RK; Satya, Pratik

    2014-01-01

    With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers’ fields. PMID:25523172

  9. Research advances in major cereal crops for adaptation to abiotic stresses.

    PubMed

    Maiti, R K; Satya, Pratik

    2014-01-01

    With devastating increase in population there is a great necessity to increase crop productivity of staple crops but the productivity is greatly affected by various abiotic stress factors such as drought, salinity. An attempt has been made a brief account on abiotic stress resistance of major cereal crops viz. In spite of good successes obtained on physiological and use molecular biology, the benefits of this high cost technology are beyond the reach of developing countries. This review discusses several morphological, anatomical, physiological, biochemical and molecular mechanisms of major cereal crops related to the adaptation of these crop to abiotic stress factors. It discusses the effect of abiotic stresses on physiological processes such as flowering, grain filling and maturation and plant metabolisms viz. photosynthesis, enzyme activity, mineral nutrition, and respiration. Though significant progress has been attained on the physiological, biochemical basis of resistance to abiotic stress factors, very little progress has been achieved to increase productivity under sustainable agriculture. Therefore, there is a great necessity of inter-disciplinary research to address this issue and to evolve efficient technology and its transfer to the farmers' fields.

  10. Abiotic degradation of plastic films

    NASA Astrophysics Data System (ADS)

    Ángeles-López, Y. G.; Gutiérrez-Mayen, A. M.; Velasco-Pérez, M.; Beltrán-Villavicencio, M.; Vázquez-Morillas, A.; Cano-Blanco, M.

    2017-01-01

    Degradable plastics have been promoted as an option to mitigate the environmental impacts of plastic waste. However, there is no certainty about its degradability under different environmental conditions. The effect of accelerated weathering (AW), natural weathering (NW) and thermal oxidation (TO) on different plastics (high density polyethylene, HDPE; oxodegradable high density polyethylene, HDPE-oxo; compostable plastic, Ecovio ® metalized polypropylene, PP; and oxodegradable metalized polypropylene, PP-oxo) was studied. Plastics films were exposed to AW per 110 hours; to NW per 90 days; and to TO per 30 days. Plastic films exposed to AW and NW showed a general loss on mechanical properties. The highest reduction in elongation at break on AW occurred to HDPE-oxo (from 400.4% to 20.9%) and was higher than 90% for HDPE, HDPE-oxo, Ecovio ® and PP-oxo in NW. No substantial evidence of degradation was found on plastics exposed to TO. Oxo-plastics showed higher degradation rates than their conventional counterparts, and the compostable plastic was resistant to degradation in the studied abiotic conditions. This study shows that degradation of plastics in real life conditions will vary depending in both, their composition and the environment.

  11. Naturally acidified habitat selects for ocean acidification–tolerant mussels

    PubMed Central

    Thomsen, Jörn; Stapp, Laura S.; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K. Mathias; Melzner, Frank

    2017-01-01

    Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae (Mytilus edulis) in a periodically CO2-enriched habitat. The larval fitness of the population originating from the CO2-enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO2–adapted population showed higher fitness under elevated Pco2 (partial pressure of CO2) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO2 tolerance differed substantially between the families within the F1 generation, and survival was drastically decreased in the highest, yet realistic, Pco2 treatment. Selection of CO2-tolerant F1 animals resulted in higher calcification performance of F2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO2-enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change. PMID:28508039

  12. Naturally acidified habitat selects for ocean acidification-tolerant mussels.

    PubMed

    Thomsen, Jörn; Stapp, Laura S; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K Mathias; Melzner, Frank

    2017-04-01

    Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae ( Mytilus edulis ) in a periodically CO 2 -enriched habitat. The larval fitness of the population originating from the CO 2 -enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO 2 -adapted population showed higher fitness under elevated P co 2 (partial pressure of CO 2 ) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO 2 tolerance differed substantially between the families within the F 1 generation, and survival was drastically decreased in the highest, yet realistic, P co 2 treatment. Selection of CO 2 -tolerant F 1 animals resulted in higher calcification performance of F 2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO 2 -enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change.

  13. A Working Model of Natural Selection Illustrated by Table Tennis

    ERIC Educational Resources Information Center

    Dinc, Muhittin; Kilic, Selda; Aladag, Caner

    2013-01-01

    Natural selection is one of the most important topics in biology and it helps to clarify the variety and complexity of organisms. However, students in almost every stage of education find it difficult to understand the mechanism of natural selection and they can develop misconceptions about it. This article provides an active model of natural…

  14. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

    PubMed Central

    Dwivedi, Sangam L.; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

    2017-01-01

    There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and

  15. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes.

    PubMed

    Dwivedi, Sangam L; Scheben, Armin; Edwards, David; Spillane, Charles; Ortiz, Rodomiro

    2017-01-01

    There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and

  16. A Lesson on Evolution & Natural Selection

    ERIC Educational Resources Information Center

    Curtis, Anthony D.

    2010-01-01

    I describe three activities that allow students to explore the ideas of evolution, natural selection, extinction, mass extinction, and rates of evolutionary change by engaging a simple model using paper, pens, chalk, and a chalkboard. As a culminating activity that supports expository writing in the sciences, the students write an essay on mass…

  17. Natural Selection as an Emergent Process: Instructional Implications

    ERIC Educational Resources Information Center

    Cooper, Robert A.

    2017-01-01

    Student reasoning about cases of natural selection is often plagued by errors that stem from miscategorising selection as a direct, causal process, misunderstanding the role of randomness, and from the intuitive ideas of intentionality, teleology and essentialism. The common thread throughout many of these reasoning errors is a failure to apply…

  18. Microbiological and abiotic processes in modelling longer-term marine corrosion of steel.

    PubMed

    Melchers, Robert E

    2014-06-01

    Longer term exposure of mild steel in natural (biotic) waters progresses as a bimodal function of time, both for corrosion mass loss and for pit depth. Recent test results, however, found this also for immersion in clean fresh, almost pure and triply distilled waters. This shows chlorides or microbiological activity is not essential for the electrochemical processes producing bimodal behaviour. It is proposed that the first mode is aerobic corrosion that eventually produces a non-homogeneous corroded surface and rust coverage sufficient to allow formation of anoxic niches. Within these, aggressive autocatalytic reduction then occurs under anoxic abiotic conditions, caused by sulfide species originating from the MnS inclusions typical in steels. This is consistent with Wranglen's model for abiotic anoxic crevice and pitting corrosion without external aggressive ions. In biotic conditions, metabolites from anaerobic bacterial activity within and near the anoxic niches provides additional (sulfide) species to contribute to the severity of corrosion. Limited observational evidence that supports this hypothesis is given but further investigation is required to determine all contributor(s) to the cathodic current for the electrochemical reaction. The results are important for estimating the contribution of microbiological corrosion in infrastructure applications. © 2013.

  19. Stomata Prioritize Their Responses to Multiple Biotic and Abiotic Signal Inputs

    PubMed Central

    Chen, Peilei; Qiu, Muqing; Jiang, Kun; Wang, Genxuan

    2014-01-01

    Stomata are microscopic pores in leaf epidermis that regulate gas exchange between plants and the environment. Being natural openings on the leaf surface, stomata also serve as ports for the invasion of foliar pathogenic bacteria. Each stomatal pore is enclosed by a pair of guard cells that are able to sense a wide spectrum of biotic and abiotic stresses and respond by precisely adjusting the pore width. However, it is not clear whether stomatal responses to simultaneously imposed biotic and abiotic signals are mutually dependent on each other. Here we show that a genetically engineered Escherichia coli strain DH5α could trigger stomatal closure in Vicia faba, an innate immune response that might depend on NADPH oxidase-mediated ROS burst. DH5α-induced stomatal closure could be abolished or disguised under certain environmental conditions like low [CO2], darkness, and drought, etc. Foliar spraying of high concentrations of ABA could reduce stomatal aperture in high humidity-treated faba bean plants. Consistently, the aggressive multiplication of DH5α bacteria in Vicia faba leaves under high humidity could be alleviated by exogenous application of ABA. Our data suggest that a successful colonization of bacteria on the leaf surface is correlated with stomatal aperture regulation by a specific set of environmental factors. PMID:25003527

  20. Abiotic stresses affect Trichoderma harzianum T39-induced resistance to downy mildew in grapevine.

    PubMed

    Roatti, Benedetta; Perazzolli, Michele; Gessler, Cesare; Pertot, Ilaria

    2013-12-01

    Enhancement of plant defense through the application of resistance inducers seems a promising alternative to chemical fungicides for controlling crop diseases but the efficacy can be affected by abiotic factors in the field. Plants respond to abiotic stresses with hormonal signals that may interfere with the mechanisms of induced systemic resistance (ISR) to pathogens. In this study, we exposed grapevines to heat, drought, or both to investigate the effects of abiotic stresses on grapevine resistance induced by Trichoderma harzianum T39 (T39) to downy mildew. Whereas the efficacy of T39-induced resistance was not affected by exposure to heat or drought, it was significantly reduced by combined abiotic stresses. Decrease of leaf water potential and upregulation of heat-stress markers confirmed that plants reacted to abiotic stresses. Basal expression of defense-related genes and their upregulation during T39-induced resistance were attenuated by abiotic stresses, in agreement with the reduced efficacy of T39. The evidence reported here suggests that exposure of crops to abiotic stress should be carefully considered to optimize the use of resistance inducers, especially in view of future global climate changes. Expression analysis of ISR marker genes could be helpful to identify when plants are responding to abiotic stresses, in order to optimize treatments with resistance inducers in field.

  1. The Limits of Natural Selection in a Nonequilibrium World.

    PubMed

    Brandvain, Yaniv; Wright, Stephen I

    2016-04-01

    Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.

    PubMed

    Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

    2008-10-01

    Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.

  3. Abiotic formation of RNA-like oligomers by montmorillonite catalysis: part II

    NASA Astrophysics Data System (ADS)

    Ertem, Gözen; Snellinger-O'Brien, Ann M.; Ertem, M. C.; Rogoff, D. A.; Dworkin, Jason P.; Johnston, Murray V.; Hazen, Robert M.

    2008-01-01

    This work is an extension of our previous studies carried out to investigate the possible catalytic role of minerals in the abiotic synthesis of biologically important molecules. In the presence of montmorillonite, a member of the phyllosilicate group minerals that are abundant on Earth and identified on Mars, activated RNA monomers, namely 5‧-phosphorimidazolides of nucleosides (ImpNs), undergo condensation reactions in aqueous electrolyte solution producing oligomers with similar structures to short RNA fragments. Analysis of the linear trimer isomers formed in the reaction of a mixture of activated adenosine and cytidine monomers (ImpA and ImpC, respectively) employing high-performance liquid chromatography, selective enzymatic hydrolysis and matrix-assisted laser desorption/ionization mass spectroscopy molecular weight measurements demonstrate that montmorillonite catalysis facilitates the formation of hetero-isomers containing 56% A- and 44% C-monomer incorporated in their structure. The results also show that 56% of the monomer units are linked together by RNA-like 3‧, 5‧-phosphodiester bonds. These results follow the same trend observed in our most recent work studying the reaction of activated adenosine and uridine monomers, and support Bernal's hypothesis proposing the possible catalytic role of minerals in the abiotic processes in the course of chemical evolution.

  4. Natural selection and infectious disease in human populations

    PubMed Central

    Karlsson, Elinor K.; Kwiatkowski, Dominic P.; Sabeti, Pardis C.

    2015-01-01

    The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology. PMID:24776769

  5. A High-Resolution Multitechniques Approach to Characterize Bio-Organo-Mineral Associations Within Rock Samples: Tracking Biological vs Abiotic Processes? Towards a Better Understanding of the Deep Carbon Cycle.

    NASA Astrophysics Data System (ADS)

    Pisapia, C.

    2015-12-01

    Among all elements, carbon plays one of the major roles for the sustainability of life on Earth. Past considerations of the carbon cycle have mainly focused on surface processes occurring at the atmosphere, oceans and shallow crustal environments. By contrast, little is known about the Deep Carbon cycle whereas both geochemical and biological processes may induce organic carbon production and/or consumption at depth. Indeed, the nowadays-recognized capability of geochemical processes such as serpentinization to generate abiotic organic compounds as well as the existence of a potentially important intraterrestrial life raises questions about the limit of biotic/abiotic carbon on Earth's deep interior and how it impacts global biogeochemical cycles. It is then mandatory to increase our knowledge on the nature and extent of carbon reservoirs along with their sources, sinks and fluxes in the subsurface. This implies to be able to finely characterize organomineral associations within crustal rocks although it might be hampered by the scarceness and heterogeneous micrometric spatial distribution of organic molecules in natural rocks. We then developed an in situ analytical strategy based on the combination of high-resolution techniques to track organic molecules at the pore level in natural rocks and to determine their biological or abiotic origin. We associated classical high-resolution techniques and synchrotron-based imaging techniques in order to characterize their nature and localization (SEM/TEM, coupled CLSM/Raman spectroscopy, Tof-SIMS) along with their 3D-distribution relatively to mineral phases (S-FTIR, S-DeepUV, XANES, Biphoton microscopy). The effectiveness of this approach to shed light on the speciation and nature of carbon in subsurface environments will be illustrated through the study of (i) subsurface ecosystems and abiotic organic carbon within ultramafic rocks of the oceanic lithosphere as putative analogs for the nature and functioning of primitive

  6. Six Classroom Exercises to Teach Natural Selection to Undergraduate Biology Students

    ERIC Educational Resources Information Center

    Kalinowski, Steven T.; Leonard, Mary J.; Andrews, Tessa M.; Litt, Andrea R.

    2013-01-01

    Students in introductory biology courses frequently have misconceptions regarding natural selection. In this paper, we describe six activities that biology instructors can use to teach undergraduate students in introductory biology courses how natural selection causes evolution. These activities begin with a lesson introducing students to natural…

  7. The Darwin cure for apiculture? Natural selection and managed honeybee health.

    PubMed

    Neumann, Peter; Blacquière, Tjeerd

    2017-03-01

    Recent major losses of managed honeybee, Apis mellifera, colonies at a global scale have resulted in a multitude of research efforts to identify the underlying mechanisms. Numerous factors acting singly and/or in combination have been identified, ranging from pathogens, over nutrition to pesticides. However, the role of apiculture in limiting natural selection has largely been ignored. This is unfortunate, because honeybees are more exposed to environmental stressors compared to other livestock and management can severely compromise bee health. Here, we briefly review apicultural factors that influence bee health and focus on those most likely interfering with natural selection, which offers a broad range of evolutionary applications for field practice. Despite intense breeding over centuries, natural selection appears to be much more relevant for the health of managed A. mellifera colonies than previously thought. We conclude that sustainable solutions for the apicultural sector can only be achieved by taking advantage of natural selection and not by attempting to limit it.

  8. Quantitative Framework and Management Expectation Tool for the Selection of Bioremediation Approaches at Chlorinated Solvent Sites

    DTIC Science & Technology

    2015-03-19

    to Abiotic Degradation  Magnetite (FeO.Fe2O3) often occurs naturally in sediments formed by weathering of igneous or metamorphic rock  Magnetite...send questions at any time using the Q&A panel 6 SERDP & ESTCP Webinar Series (#11) SERDP & ESTCP Webinar Series SERDP and ESTCP Overview Andrea...Attenuation (MNA)  Integrate the decision-making framework into an easy to use application • Excel spreadsheet  Guide users in the selection of

  9. Darwinian natural selection: its enduring explanatory power

    PubMed Central

    2012-01-01

    Evolutionary theory has never had a stronger scientific foundation than it does today. In a short review I hope to portray the deep commitment of today's biologists to Darwinian natural selection and to discoveries made since Darwin's time. In spite of the scientific advances in the century and a half since the publication of On the Origin of Species, Darwin still remains the principal author of modern evolutionary theory. He is one of the greatest contributors of all time to our understanding of nature. PMID:22481845

  10. Evidence for abiotic sulfurization of marine dissolved organic matter in sulfidic environments

    NASA Astrophysics Data System (ADS)

    Pohlabeln, A. M.; Niggemann, J.; Dittmar, T.

    2016-02-01

    Sedimentary organic matter abiotically sulfurizes in sulfidic marine environments. Here we hypothesize that sulfurization also affects dissolved organic matter (DOM), and that sulfidic marine environments are sources of dissolved organic sulfur (DOS) to the ocean. To test these hypotheses we studied solid-phase extractable (SPE) DOS in the Black Sea at various water column depths (oxic and anoxic) and in sediment porewaters from the German Wadden Sea. The concentration and molecular composition of SPE-DOS from these sites and from the oxic water columns of the North Sea (Germany) and of the North Pacific were compared. In support of our hypotheses, SPE-DOS concentrations were elevated in sulfidic waters compared to oxic waters. For a detailed molecular characterization of SPE-DOS, selective wet-chemical alteration experiments targeting different sulfur-containing functional groups were applied prior to Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). These experiments included harsh hydrolysis, selective derivatization of thiols, oxidation, and deoxygenation to test for thioesters, sulfonic acid esters, alkylsulfates, thiols, non-aromatic thioethers, and sulfoxides. Additionally, collision-induced fragmentation experiments were applied to test for sulfonic acids. The tests revealed that the sulfonic acid group was the main structural feature in SPE-DOS, independent of the environmental conditions of the sampling site. Only in Wadden Sea anoxic porewater also non-aromatic thioethers were found which are presumably not stable in oxic waters. The findings from our field studies were confirmed in laboratory experiments, where we abiotically sulfurized marine and algal-derived DOM under conditions similar to that in anoxic marine sediments.

  11. Abiotic degradation of hexahydro-l,3,5-trinitro-1,3,5-triazine in the presence of hydrogen sulfide and black carbon.

    PubMed

    Kemper, Jerome M; Ammar, Emaan; Mitch, William A

    2008-03-15

    We report that hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was rapidly destroyed by sulfides in the presence of black carbon, forming nitrite and formaldehyde, rather than toxic nitrosated reduction products. Although traditionally viewed as inactive sorbents, black carbons have been noted to participate in the destruction of certain contaminants, such as azo dyes, via quinonoid groups. However, in our experiments sulfide modification of quinones did not seem to be involved. Although at least 1.2 mM sulfides were needed for the reaction to proceed, abiotic natural attenuation of RDX in marine sediments may occur, because these concentrations are found in certain marine sediments, together with black carbon. In the absence of natural black carbons, synthetic black carbons, such as activated carbon, may be added to sediments. As compared with other in situ techniques, such as bioremediation and zero-valent iron cutoff trenches, which often generate nitrosated byproducts, this in situ, abiotic technique may be an attractive alternative.

  12. Evolution of Students' Ideas about Natural Selection through a Constructivist Framework

    ERIC Educational Resources Information Center

    Baumgartner, Erin; Duncan, Kanesa

    2009-01-01

    Educating students about the process of evolution through natural selection is vitally important because not only is it the unifying theory of biological science, it is also widely regarded as difficult for students to fully comprehend. Anderson and colleagues (2002) describe alternative ideas and misconceptions about natural selection as highly…

  13. Biotic and abiotic degradation of CL-20 and RDX in soils.

    PubMed

    Crocker, Fiona H; Thompson, Karen T; Szecsody, James E; Fredrickson, Herbert L

    2005-01-01

    The caged cyclic nitramine 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) is a new explosive that has the potential to replace existing military explosives, but little is known about its environmental toxicity, transport, and fate. We quantified and compared the aerobic environmental fate of CL-20 to the widely used cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in surface and subsurface soil microcosms. Soil-free controls and biologically attenuated soil controls were used to separate abiotic processes from biologically mediated processes. Both abiotic and biological processes significantly degraded CL-20 in all soils examined. Apparent abiotic, first-order degradation rates (k) for CL-20 were not significantly different between soil-free controls (0.018 < k < 0.030 d(-1)) and biologically attenuated soil controls (0.003 < k < 0.277 d(-1)). The addition of glucose to biologically active soil microcosms significantly increased CL-20 degradation rates (0.068 < k < 1.22 d(-1)). Extents of mineralization of (14)C-CL-20 to (14)CO(2) in biologically active soil microcosms were 41.1 to 55.7%, indicating that the CL-20 cage was broken, since all carbons are part of the heterocyclic cage. Under aerobic conditions, abiotic degradation rates of RDX were generally slower (0 < k < 0.032 d(-1)) than abiotic CL-20 degradation rates. In biologically active soil microcosms amended with glucose aerobic RDX degradation rates varied between 0.010 and 0.474 d(-1). Biodegradation was a key factor in determining the environmental fate of RDX, while a combination of biotic and abiotic processes was important with CL-20. Our data suggest that CL-20 should be less recalcitrant than RDX in aerobic soils.

  14. Abiotic Stress Signaling in Wheat – An Inclusive Overview of Hormonal Interactions During Abiotic Stress Responses in Wheat

    PubMed Central

    Abhinandan, Kumar; Skori, Logan; Stanic, Matija; Hickerson, Neil M. N.; Jamshed, Muhammad; Samuel, Marcus A.

    2018-01-01

    Rapid global warming directly impacts agricultural productivity and poses a major challenge to the present-day agriculture. Recent climate change models predict severe losses in crop production worldwide due to the changing environment, and in wheat, this can be as large as 42 Mt/°C rise in temperature. Although wheat occupies the largest total harvested area (38.8%) among the cereals including rice and maize, its total productivity remains the lowest. The major production losses in wheat are caused more by abiotic stresses such as drought, salinity, and high temperature than by biotic insults. Thus, understanding the effects of these stresses becomes indispensable for wheat improvement programs which have depended mainly on the genetic variations present in the wheat genome through conventional breeding. Notably, recent biotechnological breakthroughs in the understanding of gene functions and access to whole genome sequences have opened new avenues for crop improvement. Despite the availability of such resources in wheat, progress is still limited to the understanding of the stress signaling mechanisms using model plants such as Arabidopsis, rice and Brachypodium and not directly using wheat as the model organism. This review presents an inclusive overview of the phenotypic and physiological changes in wheat due to various abiotic stresses followed by the current state of knowledge on the identified mechanisms of perception and signal transduction in wheat. Specifically, this review provides an in-depth analysis of different hormonal interactions and signaling observed during abiotic stress signaling in wheat. PMID:29942321

  15. What Is "Natural"? Consumer Responses to Selected Ingredients.

    PubMed

    Chambers, Edgar; Chambers, Edgar; Castro, Mauricio

    2018-04-23

    Interest in “natural” food has grown enormously over the last decade. Because the United States government has not set a legal definition for the term “natural”, customers have formed their own sensory perceptions and opinions on what constitutes natural. In this study, we examined 20 ingredients to determine what consumers consider to be natural. Using a national database, 630 consumers were sampled (50% male and 50% female) online, and the results were analyzed using percentages and chi-square tests. No ingredient was considered natural by more than 69% of respondents. We found evidence that familiarity may play a major role in consumers’ determination of naturalness. We also found evidence that chemical sounding names and the age of the consumer have an effect on whether an ingredient and potentially a food is considered natural. Interestingly, a preference towards selecting GMO (genetically modified organisms) foods had no significant impact on perceptions of natural.

  16. Coupled Abiotic-Biotic Degradation of Bisphenol A

    NASA Astrophysics Data System (ADS)

    Im, J.; Prevatte, C.; Campagna, S. R.; Loeffler, F.

    2014-12-01

    Bisphenol A (BPA) is a ubiquitous environmental contaminant with weak estrogenic activity. BPA is readily biodegradable with oxygen available, but is recalcitrant to microbial degradation under anoxic conditions. However, BPA is susceptible to abiotic transformation under anoxic conditions. To better understand the fate of BPA in anoxic environments, the kinetics of BPA transformation by manganese oxide (d-MnO2) were investigated. BPA was rapidly transformed by MnO2 with a pseudo-first-order rate constant of 0.413 min-1. NMR and LC-MS analyses identified 4-hydroxycumyl alcohol (HCA) as a major intermediate. Up to 64% of the initial amount of BPA was recovered as HCA within 5 min, but the conversion efficiency decreased with time, suggesting that HCA was further degraded by MnO2. Further experiments confirmed that HCA was also susceptible to transformation by MnO2, albeit at 5-fold lower rates than BPA transformation. Mass balance approaches suggested that HCA was the major BPA transformation intermediate, but other compounds may also be formed. The abiotic transformation of BPA by MnO2 was affected by pH, and 10-fold higher transformation rates were observed at pH 4.5 than at pH 10. Compared to BPA, HCA has a lower octanol-water partitioning coefficient (Log Kow) of 0.76 vs 2.76 for BPA and a higher aqueous solubility of 2.65 g L-1 vs 0.31 g L-1 for BPA, suggesting higher mobility of HCA in the environment. Microcosms established with freshwater sediment materials collected from four geographically distinct locations and amended with HCA demonstrated rapid HCA biodegradation under oxic, but not under anoxic conditions. These findings suggest that BPA is not inert under anoxic conditions and abiotic reactions with MnO2 generate HCA, which has increased mobility and is susceptible to aerobic degradation. Therefore, coupled abiotic-biotic processes can affect the fate and longevity of BPA in terrestrial environments.

  17. Opportunity for natural selection among five population groups of Manipur, North East India.

    PubMed

    Asghar, M; Meitei, S Y; Luxmi, Y; Achoubi, N; Meitei, K S; Murry, B; Sachdeva, M P; Saraswathy, K N

    2014-01-01

    Opportunity for natural selection among five population groups of Manipur in comparison with other North East Indian population has been studied. Crow's index as well as Johnston and Kensinger's index for natural selection were calculated based on differential fertility and mortality. The mortality component was found to be lower compared to fertility component in all the populations which may attribute to comparatively improved and easily accessible health care facilities. However, different selection pressures, artificial and natural, seem to be influencing the selection intensity through induced abortion and spontaneous abortion among the two non-tribal migrant groups: Bamon and Muslims, respectively. This study highlights the probable interaction of artificial and natural selection in determining the evolutionary fate of any population group.

  18. Chiral Selective Chemistry Induced by Natural Selection of Spin-Polarized Electrons.

    PubMed

    Rosenberg, Richard A; Mishra, Debabrata; Naaman, Ron

    2015-06-15

    The search to understand the origin of homochirality in nature has been ongoing since the time of Pasteur. Previous work has shown that DNA can act as a spin filter for low-energy electrons and that spin-polarized secondary electrons produced by X-ray irradiation of a magnetic substrate can induce chiral selective chemistry. In the present work it is demonstrated that secondary electrons from a substrate that are transmitted through a chiral overlayer cause enantiomeric selective chemistry in an adsorbed adlayer. We determine the quantum yields (QYs) for dissociation of (R)- or (S)-epichlorohydrin adsorbed on a chiral self-assembled layer of DNA on gold and on bare gold (for control). The results show that there is a significant difference in the QYs between the two enantiomers when adsorbed on DNA, but none when they are adsorbed on bare Au. We propose that the effect results from natural spin filtering effects cause by the chiral monolayer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Natural selection on plant physiological traits in an urban environment

    NASA Astrophysics Data System (ADS)

    Lambrecht, Susan C.; Mahieu, Stephanie; Cheptou, Pierre-Olivier

    2016-11-01

    Current rates of urbanization are creating new opportunities for studying urban plant ecology, but our knowledge of urban plant physiology lags behind that of other ecosystems. Moreover, higher temperatures, elevated CO2, and increased inorganic nitrogen deposition along with altered moisture regimes of urban as compared to rural areas creates a compelling analog for studying adaptations of plants to climate change. We grew plants under common conditions in a greenhouse to determine whether populations of Crepis sancta (Asteraceae) differed in phenological, morphological, and physiological traits. We also used a field experiment to test for natural selection on these traits in urban Montpellier, France. Urban plants flowered and senesced later than rural plants, and natural selection favored later phenology in the urban habitat. Natural selection also favored larger plants with more leaves, and increased photosynthesis and leaf nitrogen concentration. Ours is the first study to document selection on plant functional traits in an urban habitat and, as such, advances our understanding of urban plant ecology and possible adaptations to climate change.

  20. The natural selection of altruistic traits.

    PubMed

    Boehm, C

    1999-09-01

    Proponents of the standard evolutionary biology paradigm explain human "altruism" in terms of either nepotism or strict reciprocity. On that basis our underlying nature is reduced to a function of inclusive fitness: human nature has to be totally selfish or nepotistic. Proposed here are three possible paths to giving costly aid to nonrelatives, paths that are controversial because they involve assumed pleiotropic effects or group selection. One path is pleiotropic subsidies that help to extend nepotistic helping behavior from close family to nonrelatives. Another is "warfare"-if and only if warfare recurred in the Paleolithic. The third and most plausible hypothesis is based on the morally based egalitarian syndrome of prehistoric hunter-gatherers, which reduced phenotypic variation at the within-group level, increased it at the between-group level, and drastically curtailed the advantages of free riders. In an analysis consistent with the fundamental tenets of evolutionary biology, these three paths are evaluated as explanations for the evolutionary development of a rather complicated human social nature.

  1. Abiotic tooth enamel

    NASA Astrophysics Data System (ADS)

    Yeom, Bongjun; Sain, Trisha; Lacevic, Naida; Bukharina, Daria; Cha, Sang-Ho; Waas, Anthony M.; Arruda, Ellen M.; Kotov, Nicholas A.

    2017-03-01

    Tooth enamel comprises parallel microscale and nanoscale ceramic columns or prisms interlaced with a soft protein matrix. This structural motif is unusually consistent across all species from all geological eras. Such invariability—especially when juxtaposed with the diversity of other tissues—suggests the existence of a functional basis. Here we performed ex vivo replication of enamel-inspired columnar nanocomposites by sequential growth of zinc oxide nanowire carpets followed by layer-by-layer deposition of a polymeric matrix around these. We show that the mechanical properties of these nanocomposites, including hardness, are comparable to those of enamel despite the nanocomposites having a smaller hard-phase content. Our abiotic enamels have viscoelastic figures of merit (VFOM) and weight-adjusted VFOM that are similar to, or higher than, those of natural tooth enamels—we achieve values that exceed the traditional materials limits of 0.6 and 0.8, respectively. VFOM values describe resistance to vibrational damage, and our columnar composites demonstrate that light-weight materials of unusually high resistance to structural damage from shocks, environmental vibrations and oscillatory stress can be made using biomimetic design. The previously inaccessible combinations of high stiffness, damping and light weight that we achieve in these layer-by-layer composites are attributed to efficient energy dissipation in the interfacial portion of the organic phase. The in vivo contribution of this interfacial portion to macroscale deformations along the tooth’s normal is maximized when the architecture is columnar, suggesting an evolutionary advantage of the columnar motif in the enamel of living species. We expect our findings to apply to all columnar composites and to lead to the development of high-performance load-bearing materials.

  2. Review of recent transgenic studies on abiotic stress tolerance and future molecular breeding in potato.

    PubMed

    Kikuchi, Akira; Huynh, Huu Duc; Endo, Tsukasa; Watanabe, Kazuo

    2015-03-01

    Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.

  3. Natural image statistics and low-complexity feature selection.

    PubMed

    Vasconcelos, Manuela; Vasconcelos, Nuno

    2009-02-01

    Low-complexity feature selection is analyzed in the context of visual recognition. It is hypothesized that high-order dependences of bandpass features contain little information for discrimination of natural images. This hypothesis is characterized formally by the introduction of the concepts of conjunctive interference and decomposability order of a feature set. Necessary and sufficient conditions for the feasibility of low-complexity feature selection are then derived in terms of these concepts. It is shown that the intrinsic complexity of feature selection is determined by the decomposability order of the feature set and not its dimension. Feature selection algorithms are then derived for all levels of complexity and are shown to be approximated by existing information-theoretic methods, which they consistently outperform. The new algorithms are also used to objectively test the hypothesis of low decomposability order through comparison of classification performance. It is shown that, for image classification, the gain of modeling feature dependencies has strongly diminishing returns: best results are obtained under the assumption of decomposability order 1. This suggests a generic law for bandpass features extracted from natural images: that the effect, on the dependence of any two features, of observing any other feature is constant across image classes.

  4. Abscisic Acid and Abiotic Stress Tolerance in Crop Plants

    PubMed Central

    Sah, Saroj K.; Reddy, Kambham R.; Li, Jiaxu

    2016-01-01

    Abiotic stress is a primary threat to fulfill the demand of agricultural production to feed the world in coming decades. Plants reduce growth and development process during stress conditions, which ultimately affect the yield. In stress conditions, plants develop various stress mechanism to face the magnitude of stress challenges, although that is not enough to protect them. Therefore, many strategies have been used to produce abiotic stress tolerance crop plants, among them, abscisic acid (ABA) phytohormone engineering could be one of the methods of choice. ABA is an isoprenoid phytohormone, which regulates various physiological processes ranging from stomatal opening to protein storage and provides adaptation to many stresses like drought, salt, and cold stresses. ABA is also called an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to different environmental stress conditions. In this review, we will discuss the role of ABA in response to abiotic stress at the molecular level and ABA signaling. The review also deals with the effect of ABA in respect to gene expression. PMID:27200044

  5. The Relative Abundances of Resolved 12CH2D2 and 13CH3D and Mechanisms Controlling Isotopic Bond Ordering in Abiotic and Biotic Methane Gases

    NASA Astrophysics Data System (ADS)

    Young, E. D.; Kohl, I. E.; Sherwood Lollar, B.; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K.; Foustoukos, D.; Sutcliffe, C. N.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Perez-Rodriguez, I. M.; Rowe, A. R.; LaRowe, D.; Magnabosco, C.; Bryndzia, T.

    2016-12-01

    We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide important information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis versus biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature of abiotic CH4 formation may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of

  6. Exploring biotic vs. abiotic controls on syngenetic carbonate and clay mineral precipitation

    NASA Astrophysics Data System (ADS)

    Nascimento, Gabriela S.; McKenzie, Judith A.; Martinez Ruiz, Francisca; Bontognali, Tomaso R. R.; Vasconcelos, Crisogono

    2016-04-01

    A possible syngenetic relationship between carbonate and clay mineral precipitation has been reported for sedimentary rocks deposited in both lacustrine and marine sedimentary environments throughout the geological record. In particular, the mineral dolomite is often found associated with Mg-rich clays, such as stevensite. It is notable that this carbonate/clay association has been recorded in numerous samples taken from modern dolomite precipitating environments; for example, the Coorong lakes, South Australia, coastal sabkhas, Abu Dhabi, UAE and coastal hypersaline lagoons (Lagoa Vermelha and Brejo do Espinho) east of Rio de Janeiro, Brazil. An HRTEM study of samples from these three locations indicates a possible physical/chemical association between the Ca-dolomite and Mg-rich clays, demonstrating a probable co-precipitation. To test this hypothesis, we have conducted a series of biotic and abiotic laboratory experiments. If this syngenesis actually occurs in nature, what, if any, are the biogeochemical processes controlling these precipitation reactions? Our experiments were designed to determine the extent of the biotic versus abiotic component influencing the mineral precipitation and, in the case of a biotic influence, to understand the mechanism through which microorganisms might mediate the formation of clay minerals. The experiments were carried out in the Geomicrobiology Laboratory of ETH Zürich using cultures of living microbes and artificial organic compounds that simulate functional groups present in natural biofilms formed under both aerobic and anaerobic conditions. In addition, pure inorganic experiments were designed to understand possible physico-chemical conditions for diagenetic processes that could induce dissolution of Mg-carbonates and precipitation of Mg-rich clays. Our results show a remarkable biotic influence during the formation of clay minerals. Specifically, extracellular polymeric substances (EPS), released by microbes in their

  7. The Late Embryogenesis Abundant Protein Family in Cassava (Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress.

    PubMed

    Wu, Chunlai; Hu, Wei; Yan, Yan; Tie, Weiwei; Ding, Zehong; Guo, Jianchun; He, Guangyuan

    2018-05-17

    Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection. Transcriptomic analysis showed the expression profiles of MeLEAs in different tissues of stem, leaves, and storage roots of three accessions. Comparative transcriptomic analysis revealed that the function of MeLEAs in response to drought may be differentiated in different accessions. Compared with the wild subspecies W14, more MeLEA genes were activated in cultivated varieties Arg7 and SC124 after drought treatment. Several MeLEA genes showed induction under various stresses and related signaling treatments. Taken together, this study demonstrates the transcriptional control of MeLEAs in tissue development and the responses to abiotic stress in cassava and identifies candidate genes for improving crop resistance to abiotic stress.

  8. Abiotic ozone and oxygen in atmospheres similar to prebiotic Earth

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Domagal-Goldman, Shawn D.; Segura, Antígona; Claire, Mark W.

    The search for life on planets outside our solar system will use spectroscopic identification of atmospheric biosignatures. The most robust remotely detectable potential biosignature is considered to be the detection of oxygen (O{sub 2}) or ozone (O{sub 3}) simultaneous to methane (CH{sub 4}) at levels indicating fluxes from the planetary surface in excess of those that could be produced abiotically. Here we use an altitude-dependent photochemical model with the enhanced lower boundary conditions necessary to carefully explore abiotic O{sub 2} and O{sub 3} production on lifeless planets with a wide variety of volcanic gas fluxes and stellar energy distributions. Onmore » some of these worlds, we predict limited O{sub 2} and O{sub 3} buildup, caused by fast chemical production of these gases. This results in detectable abiotic O{sub 3} and CH{sub 4} features in the UV-visible, but no detectable abiotic O{sub 2} features. Thus, simultaneous detection of O{sub 3} and CH{sub 4} by a UV-visible mission is not a strong biosignature without proper contextual information. Discrimination between biological and abiotic sources of O{sub 2} and O{sub 3} is possible through analysis of the stellar and atmospheric context—particularly redox state and O atom inventory—of the planet in question. Specifically, understanding the spectral characteristics of the star and obtaining a broad wavelength range for planetary spectra should allow more robust identification of false positives for life. This highlights the importance of wide spectral coverage for future exoplanet characterization missions. Specifically, discrimination between true and false positives may require spectral observations that extend into infrared wavelengths and provide contextual information on the planet's atmospheric chemistry.« less

  9. Abiotic dechlorination in rock matrices impacted by long-term exposure to TCE.

    PubMed

    Schaefer, Charles E; Towne, Rachael M; Lippincott, David R; Lacombe, Pierre J; Bishop, Michael E; Dong, Hailiang

    2015-01-01

    Field and laboratory tests were performed to evaluate the abiotic reaction of trichloroethene (TCE) in sedimentary rock matrices. Hydraulically conductive fractures, and the rock directly adjacent to the hydraulically conductive fractures, within a historically contaminated TCE bedrock aquifer were used as the basis for this study. These results were compared to previous work using rock that had not been exposed to TCE (Schaefer et al., 2013) to assess the impact of long-term TCE exposure on the abiotic dechlorination reaction, as the longevity of these reactions after long-term exposure to TCE was hitherto unknown. Results showed that potential abiotic TCE degradation products, including ethane, ethene, and acetylene, were present in the conductive fractures. Using minimally disturbed slices of rock core at and near the fracture faces, laboratory testing on the rocks confirmed that abiotic dechlorination reactions between the rock matrix and TCE were occurring. Abiotic daughter products measured in the laboratory under controlled conditions were consistent with those measured in the conductive fractures, except that propane also was observed as a daughter product. TCE degradation measured in the laboratory was well described by a first order rate constant through the 118-d study. Observed bulk first-order TCE degradation rate constants within the rock matrix were 1.3×10(-8) s(-1). These results clearly show that abiotic dechlorination of TCE is occurring within the rock matrix, despite decades of exposure to TCE. Furthermore, these observed rates of TCE dechlorination are expected to have a substantial impact on TCE migration and uptake/release from rock matrices. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Selective MAO-B inhibitors: a lesson from natural products.

    PubMed

    Carradori, Simone; D'Ascenzio, Melissa; Chimenti, Paola; Secci, Daniela; Bolasco, Adriana

    2014-02-01

    Monoamine oxidases (MAOs) are mitochondrial bound enzymes, which catalyze the oxidative deamination of monoamine neurotransmitters. Inside the brain, MAOs are present in two isoforms: MAO-A and MAO-B. The activity of MAO-B is generally higher in patients affected by neurodegenerative diseases like Alzheimer's and Parkinson's. Therefore, the search for potent and selective MAO-B inhibitors is still a challenge for medicinal chemists. Nature has always been a source of inspiration for the discovery of new lead compounds. Moreover, natural medicine is a major component in all traditional medicine systems. In this review, we present the latest discoveries in the search for selective MAO-B inhibitors from natural sources. For clarity, compounds have been classified on the basis of structural analogy or source: flavonoids, xanthones, tannins, proanthocyanidins, iridoid glucosides, curcumin, alkaloids, cannabinoids, and natural sources extracts. MAO inhibition values reported in the text are not always consistent due to the high variability of MAO sources (bovine, pig, rat brain or liver, and human) and to the heterogeneity of the experimental protocols used.

  11. WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

    PubMed Central

    Banerjee, Aditya

    2015-01-01

    WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of the WRKY genes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research. PMID:25879071

  12. WRKY proteins: signaling and regulation of expression during abiotic stress responses.

    PubMed

    Banerjee, Aditya; Roychoudhury, Aryadeep

    2015-01-01

    WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of the WRKY genes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

  13. Energy harvesting by implantable abiotically catalyzed glucose fuel cells

    NASA Astrophysics Data System (ADS)

    Kerzenmacher, S.; Ducrée, J.; Zengerle, R.; von Stetten, F.

    Implantable glucose fuel cells are a promising approach to realize an autonomous energy supply for medical implants that solely relies on the electrochemical reaction of oxygen and glucose. Key advantage over conventional batteries is the abundant availability of both reactants in body fluids, rendering the need for regular replacement or external recharging mechanisms obsolete. Implantable glucose fuel cells, based on abiotic catalysts such as noble metals and activated carbon, have already been developed as power supply for cardiac pacemakers in the late-1960s. Whereas, in vitro and preliminary in vivo studies demonstrated their long-term stability, the performance of these fuel cells is limited to the μW-range. Consequently, no further developments have been reported since high-capacity lithium iodine batteries for cardiac pacemakers became available in the mid-1970s. In recent years research has been focused on enzymatically catalyzed glucose fuel cells. They offer higher power densities than their abiotically catalyzed counterparts, but the limited enzyme stability impedes long-term application. In this context, the trend towards increasingly energy-efficient low power MEMS (micro-electro-mechanical systems) implants has revived the interest in abiotic catalysts as a long-term stable alternative. This review covers the state-of-the-art in implantable abiotically catalyzed glucose fuel cells and their development since the 1960s. Different embodiment concepts are presented and the historical achievements of academic and industrial research groups are critically reviewed. Special regard is given to the applicability of the concept as sustainable micro-power generator for implantable devices.

  14. Ecological genomics of natural plant populations: the Israeli perspective.

    PubMed

    Nevo, Eviatar

    2009-01-01

    The genomic era revolutionized evolutionary population biology. The ecological genomics of the wild progenitors of wheat and barley reviewed here was central in the research program of the Institute of Evolution, University of Haifa, since 1975 ( http://evolution.haifa.ac.il ). We explored the following questions: (1) How much of the genomic and phenomic diversity of wild progenitors of cultivars (wild emmer wheat, Triticum dicoccoides, the progenitor of most wheat, plus wild relatives of the Aegilops species; wild barley, Hordeum spontaneum, the progenitor of cultivated barley; wild oat, Avena sterilis, the progenitor of cultivated oats; and wild lettuce species, Lactuca, the progenitor and relatives of cultivated lettuce) are adaptive and processed by natural selection at both coding and noncoding genomic regions? (2) What is the origin and evolution of genomic adaptation and speciation processes and their regulation by mutation, recombination, and transposons under spatiotemporal variables and stressful macrogeographic and microgeographic environments? (3) How much genetic resources are harbored in the wild progenitors for crop improvement? We advanced ecological genetics into ecological genomics and analyzed (regionally across Israel and the entire Near East Fertile Crescent and locally at microsites, focusing on the "Evolution Canyon" model) hundreds of populations and thousands of genotypes for protein (allozyme) and deoxyribonucleic acid (DNA) (coding and noncoding) diversity, partly combined with phenotypic diversity. The environmental stresses analyzed included abiotic (climatic and microclimatic, edaphic) and biotic (pathogens, demographic) stresses. Recently, we introduced genetic maps, cloning, and transformation of candidate genes. Our results indicate abundant genotypic and phenotypic diversity in natural plant populations. The organization and evolution of molecular and organismal diversity in plant populations, at all genomic regions and

  15. Expression of an Engineered Heterologous Antimicrobial Peptide in Potato Alters Plant Development and Mitigates Normal Abiotic and Biotic Responses

    PubMed Central

    Goyal, Ravinder K.; Hancock, Robert E. W.; Mattoo, Autar K.; Misra, Santosh

    2013-01-01

    Antimicrobial cationic peptides (AMPs) are ubiquitous small proteins used by living cells to defend against a wide spectrum of pathogens. Their amphipathic property helps their interaction with negatively charged cellular membrane of the pathogen causing cell lysis and death. AMPs also modulate signaling pathway(s) and cellular processes in animal models; however, little is known of cellular processes other than the pathogen-lysis phenomenon modulated by AMPs in plants. An engineered heterologous AMP, msrA3, expressed in potato was previously shown to cause resistance of the transgenic plants against selected fungal and bacterial pathogens. These lines together with the wild type were studied for growth habits, and for inducible defense responses during challenge with biotic (necrotroph Fusarium solani) and abiotic stressors (dark-induced senescence, wounding and temperature stress). msrA3-expression not only conferred protection against F. solani but also delayed development of floral buds and prolonged vegetative phase. Analysis of select gene transcript profiles showed that the transgenic potato plants were suppressed in the hypersensitive (HR) and reactive oxygen species (ROS) responses to both biotic and abiotic stressors. Also, the transgenic leaves accumulated lesser amounts of the defense hormone jasmonic acid upon wounding with only a slight change in salicylic acid as compared to the wild type. Thus, normal host defense responses to the pathogen and abiotic stressors were mitigated by msrA3 expression suggesting MSRA3 regulates a common step(s) of these response pathways. The stemming of the pathogen growth and mitigating stress response pathways likely contributes to resource reallocation for higher tuber yield. PMID:24147012

  16. Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks

    PubMed Central

    Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C.; Pepper, John W.

    2017-01-01

    Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of “cancer” and for why this convergent condition becomes life-threatening. PMID:28148564

  17. Natural Selection in Cancer Biology: From Molecular Snowflakes to Trait Hallmarks.

    PubMed

    Fortunato, Angelo; Boddy, Amy; Mallo, Diego; Aktipis, Athena; Maley, Carlo C; Pepper, John W

    2017-02-01

    Evolution by natural selection is the conceptual foundation for nearly every branch of biology and increasingly also for biomedicine and medical research. In cancer biology, evolution explains how populations of cells in tumors change over time. It is a fundamental question whether this evolutionary process is driven primarily by natural selection and adaptation or by other evolutionary processes such as founder effects and drift. In cancer biology, as in organismal evolutionary biology, there is controversy about this question and also about the use of adaptation through natural selection as a guiding framework for research. In this review, we discuss the differences and similarities between evolution among somatic cells versus evolution among organisms. We review what is known about the parameters and rate of evolution in neoplasms, as well as evidence for adaptation. We conclude that adaptation is a useful framework that accurately explains the defining characteristics of cancer. Further, convergent evolution through natural selection provides the only satisfying explanation both for how a group of diverse pathologies have enough in common to usefully share the descriptive label of "cancer" and for why this convergent condition becomes life-threatening. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  18. Evaluation and selection of reliable reference genes for gene expression under abiotic stress in cotton (Gossypium hirsutum L.).

    PubMed

    Wang, Min; Wang, Qinglian; Zhang, Baohong

    2013-11-01

    Reference genes are critical for normalization of the gene expression level of target genes. The widely used housekeeping genes may change their expression levels at different tissue under different treatment or stress conditions. Therefore, systematical evaluation on the housekeeping genes is required for gene expression analysis. Up to date, no work was performed to evaluate the housekeeping genes in cotton under stress treatment. In this study, we chose 10 housekeeping genes to systematically assess their expression levels at two different tissues (leaves and roots) under two different abiotic stresses (salt and drought) with three different concentrations. Our results show that there is no best reference gene for all tissues at all stress conditions. The reliable reference gene should be selected based on a specific condition. For example, under salt stress, UBQ7, GAPDH and EF1A8 are better reference genes in leaves; TUA10, UBQ7, CYP1, GAPDH and EF1A8 were better in roots. Under drought stress, UBQ7, EF1A8, TUA10, and GAPDH showed less variety of expression level in leaves and roots. Thus, it is better to identify reliable reference genes first before performing any gene expression analysis. However, using a combination of housekeeping genes as reference gene may provide a new strategy for normalization of gene expression. In this study, we found that combination of four housekeeping genes worked well as reference genes under all the stress conditions. © 2013.

  19. The interaction between abiotic photodegradation and microbial decomposition under ultraviolet radiation.

    PubMed

    Wang, Jing; Liu, Lingli; Wang, Xin; Chen, Yiwei

    2015-05-01

    Elevated ultraviolet (UV) radiation has been demonstrated to stimulate litter decomposition. Despite years of research, it is still not fully understood whether the acceleration in litter degradation is primarily attributed to abiotic photodegradation or the combined effects of abiotic photodegradation and microbial decomposition. In this study, we used meta-analysis to synthesize photodegradation studies and compared the effects of UV radiation on litter decomposition between abiotic and biotic conditions. We also conducted a microcosm experiment to assess the effects of UV radiation on litter biodegradability and microbial activity. Overall, our meta-analysis found that under abiotic photodegradation, UV radiation reduced the remaining litter mass by 1.44% (95% CI: 0.85% to 2.08%), did not affect the remaining lignin and increased the dissolved organic carbon (DOC) concentration by 14.01% (1.49-23.67%). Under combined abiotic photodegradation and microbial decomposition, UV radiation reduced the remaining litter mass and lignin by 1.60% (0.04-3.58%) and 16.07% (9.27-24.23%), respectively, but did not alter DOC concentration. UV radiation had no significant impact on soil microbial biomass carbon (MBC), but it reduced microbial respiration by 44.91% (2.26-78.62%) and altered the composition of the microbial community. In addition, UV radiation reduced nitrogen (N) immobilization by 19.44% (4.77-37.92%). Our microcosm experiment further indicated that DOC concentration and the amount of respired C in UV-treated litter increased with UV exposure time, suggesting that longer UV exposure resulted in greater biodegradability. Overall, our study suggested that UV exposure could increase litter biodegradability by increasing the microbial accessibility of lignin, as well as the labile carbon supply to microbes. However, the remaining litter mass was not different between the abiotic and biotic conditions, most likely because the positive effect of UV radiation on litter

  20. Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda.

    PubMed

    Safran, Rebecca J; Scordato, Elizabeth S C; Symes, Laurel B; Rodríguez, Rafael L; Mendelson, Tamra C

    2013-11-01

    Speciation by divergent natural selection is well supported. However, the role of sexual selection in speciation is less well understood due to disagreement about whether sexual selection is a mechanism of evolution separate from natural selection, as well as confusion about various models and tests of sexual selection. Here, we outline how sexual selection and natural selection are different mechanisms of evolutionary change, and suggest that this distinction is critical when analyzing the role of sexual selection in speciation. Furthermore, we clarify models of sexual selection with respect to their interaction with ecology and natural selection. In doing so, we outline a research agenda for testing hypotheses about the relative significance of divergent sexual and natural selection in the evolution of reproductive isolation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Genetic evidence for natural selection in humans in the contemporary United States.

    PubMed

    Beauchamp, Jonathan P

    2016-07-12

    Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals' genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 who participated in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 mo of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Although they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving-albeit slowly, especially compared with the rapid changes that have occurred over the past few generations due to cultural and environmental factors.

  2. Genetic evidence for natural selection in humans in the contemporary United States

    PubMed Central

    Beauchamp, Jonathan P.

    2016-01-01

    Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals’ genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 who participated in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about −1.5 mo of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Although they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving—albeit slowly, especially compared with the rapid changes that have occurred over the past few generations due to cultural and environmental factors. PMID:27402742

  3. Directional, stabilizing, and disruptive trait selection as alternative mechanisms for plant community assembly.

    PubMed

    Rolhauser, Andrés G; Pucheta, Eduardo

    2017-03-01

    How plant functional traits (e.g., seed mass) drive species abundance within communities remains an unsolved question. Borrowing concepts from natural selection theory, we propose that trait-abundance relationships can generally correspond to one of three modes of trait selection: directional (a rectilinear relationship, where species at one end of a trait axis are most abundant), stabilizing (an n-shaped relationship), and disruptive (a u-shaped relationship). Stabilizing selection (i.e., the functional convergence of abundant species) would result from positive density-dependent interactions (e.g., facilitation) or due to generalized trade-offs in resource acquisition/use, while disruptive selection (i.e., the divergence of abundant species) would result from negative density-dependent interactions (e.g., competition) or due to environmental heterogeneity. These selection modes can be interpreted as proxies for community-level trait-fitness functions, which establish the degree to which traits are truly "functional". We searched for selection modes in a desert annual-plant community in Argentina (which was divided into winter and summer guilds) to test the hypothesis that the relative importance of disruptive mechanisms (competition, disturbances) decreases with the increase of abiotic stress, a stabilizing agent. Average density was analyzed as a function of eight traits generally linked to resource acquisition and competitive ability (maximum plant height, leaf size, specific leaf area, specific root length), resource retention and stress tolerance (leaf dissection, leaf dry matter content, specific root volume), and regeneration (seed mass) using multiple quadratic-regression models. Trait selection was stabilizing and/or directional when the environment was harshest (winter) and disruptive and/or directional when conditions were milder (summer). Selection patterns differed between guilds for two important traits: plant height and seed mass. These results

  4. Genetic engineering strategies for biotic and abiotic stress tolerance and quality enhancement in horticultural crops: a comprehensive review.

    PubMed

    Parmar, Nehanjali; Singh, Kunwar Harendra; Sharma, Deepika; Singh, Lal; Kumar, Pankaj; Nanjundan, J; Khan, Yasin Jeshima; Chauhan, Devendra Kumar; Thakur, Ajay Kumar

    2017-08-01

    Genetic engineering technique offers myriads of applications in improvement of horticultural crops for biotic and abiotic stress tolerance, and produce quality enhancement. During last two decades, a large number of transgenic horticultural crops has been developed and more are underway. A number of genes including natural and synthetic Cry genes, protease inhibitors, trypsin inhibitors and cystatin genes have been used to incorporate insect and nematode resistance. For providing protection against fungal and bacterial diseases, various genes like chitinase, glucanase, osmotin, defensin and pathogenesis-related genes are being transferred to many horticultural crops world over. RNAi technique has been found quite successful in inducing virus resistance in horticultural crops in addition to coat protein genes. Abiotic stresses such as drought, heat and salinity adversely affect production and productivity of horticultural crops and a number of genes encoding for biosynthesis of stress protecting compounds including mannitol, glycine betaine and heat shock proteins have been employed for abiotic stress tolerance besides various transcription factors like DREB1, MAPK, WRKY, etc. Antisense gene and RNAi technologies have revolutionized the pace of improvement of horticultural crops, particularly ornamentals for color modification, increasing shelf-life and reducing post-harvest losses. Precise genome editing tools, particularly CRISPR/Cas9, have been efficiently applied in tomato, petunia, citrus, grape, potato and apple for gene mutation, repression, activation and epigenome editing. This review provides comprehensive overview to draw the attention of researchers for better understanding of genetic engineering advancements in imparting biotic and abiotic stress tolerance as well as on improving various traits related to quality, texture, plant architecture modification, increasing shelf-life, etc. in different horticultural crops.

  5. Sperm selection in natural conception: what can we learn from Mother Nature to improve assisted reproduction outcomes?

    PubMed Central

    Sakkas, Denny; Ramalingam, Mythili; Garrido, Nicolas; Barratt, Christopher L.R.

    2015-01-01

    BACKGROUND In natural conception only a few sperm cells reach the ampulla or the site of fertilization. This population is a selected group of cells since only motile cells can pass through cervical mucus and gain initial entry into the female reproductive tract. In animals, some studies indicate that the sperm selected by the reproductive tract and recovered from the uterus and the oviducts have higher fertilization rates but this is not a universal finding. Some species show less discrimination in sperm selection and abnormal sperm do arrive at the oviduct. In contrast, assisted reproductive technologies (ART) utilize a more random sperm population. In this review we contrast the journey of the spermatozoon in vivo and in vitro and discuss this in the context of developing new sperm preparation and selection techniques for ART. METHODS A review of the literature examining characteristics of the spermatozoa selected in vivo is compared with recent developments in in vitro selection and preparation methods. Contrasts and similarities are presented. RESULTS AND CONCLUSIONS New technologies are being developed to aid in the diagnosis, preparation and selection of spermatozoa in ART. To date progress has been frustrating and these methods have provided variable benefits in improving outcomes after ART. It is more likely that examining the mechanisms enforced by nature will provide valuable information in regard to sperm selection and preparation techniques in vitro. Identifying the properties of those spermatozoa which do reach the oviduct will also be important for the development of more effective tests of semen quality. In this review we examine the value of sperm selection to see how much guidance for ART can be gleaned from the natural selection processes in vivo. PMID:26386468

  6. Titania may produce abiotic oxygen atmospheres on habitable exoplanets

    PubMed Central

    Narita, Norio; Enomoto, Takafumi; Masaoka, Shigeyuki; Kusakabe, Nobuhiko

    2015-01-01

    The search for habitable exoplanets in the Universe is actively ongoing in the field of astronomy. The biggest future milestone is to determine whether life exists on such habitable exoplanets. In that context, oxygen in the atmosphere has been considered strong evidence for the presence of photosynthetic organisms. In this paper, we show that a previously unconsidered photochemical mechanism by titanium (IV) oxide (titania) can produce abiotic oxygen from liquid water under near ultraviolet (NUV) lights on the surface of exoplanets. Titania works as a photocatalyst to dissociate liquid water in this process. This mechanism offers a different source of a possibility of abiotic oxygen in atmospheres of exoplanets from previously considered photodissociation of water vapor in upper atmospheres by extreme ultraviolet (XUV) light. Our order-of-magnitude estimation shows that possible amounts of oxygen produced by this abiotic mechanism can be comparable with or even more than that in the atmosphere of the current Earth, depending on the amount of active surface area for this mechanism. We conclude that titania may act as a potential source of false signs of life on habitable exoplanets. PMID:26354078

  7. Titania may produce abiotic oxygen atmospheres on habitable exoplanets.

    PubMed

    Narita, Norio; Enomoto, Takafumi; Masaoka, Shigeyuki; Kusakabe, Nobuhiko

    2015-09-10

    The search for habitable exoplanets in the Universe is actively ongoing in the field of astronomy. The biggest future milestone is to determine whether life exists on such habitable exoplanets. In that context, oxygen in the atmosphere has been considered strong evidence for the presence of photosynthetic organisms. In this paper, we show that a previously unconsidered photochemical mechanism by titanium (IV) oxide (titania) can produce abiotic oxygen from liquid water under near ultraviolet (NUV) lights on the surface of exoplanets. Titania works as a photocatalyst to dissociate liquid water in this process. This mechanism offers a different source of a possibility of abiotic oxygen in atmospheres of exoplanets from previously considered photodissociation of water vapor in upper atmospheres by extreme ultraviolet (XUV) light. Our order-of-magnitude estimation shows that possible amounts of oxygen produced by this abiotic mechanism can be comparable with or even more than that in the atmosphere of the current Earth, depending on the amount of active surface area for this mechanism. We conclude that titania may act as a potential source of false signs of life on habitable exoplanets.

  8. Cell Wall Metabolism in Response to Abiotic Stress

    PubMed Central

    Gall, Hyacinthe Le; Philippe, Florian; Domon, Jean-Marc; Gillet, Françoise; Pelloux, Jérôme; Rayon, Catherine

    2015-01-01

    This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions. PMID:27135320

  9. Biotic and abiotic pathways of phosphorus cycling in minerals and sediments: insights from oxygen isotopes in phosphate

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jaisi, Deb P.; Kukkadapu, Ravi K.; Stout, Lisa M.

    2011-07-06

    A key question to address in the development of oxygen isotope ratios in phosphate (18Op) as a tracer of biogeochemical cycling of phosphorus in ancient and modern environments is the nature of isotopic signatures associated with uptake and cycling of mineral-bound phosphate by microorganisms. Here we present experimental results aimed at understanding the biotic and abiotic pathway of P cycling during biological uptake of phosphate sorbed to ferrihydrite and the selective uptake of specific sedimentary phosphate phases by Escherichia coli, Vibrio fischeri and Marinobacter aquaeolei. Results indicate that a significant fraction of ferrihydrite-bound phosphate is biologically available. The fraction ofmore » phosphate taken up by E. coli attained an equilibrium isotopic composition in a short time (<50 hrs) due to efficient O-isotope exchange between phosphate and water (biotic pathway). The difference in isotopic composition between newly equilibrated aqueous and residual sorbed phosphate promoted the exchange of intact phosphate radicals (abiotic pathway) so that this difference gradually became negligible. In sediment containing different P phases, E. coli and V. fischeri ‘extracted’ loosely sorbed phosphate first while M. aquaeolei preferred iron-oxide bound phosphate. Each bacterium imprinted a biotic isotopic signature on each P phase that it took up and cycled. For example, the 18Op value of the sorbed phosphate phase shifted gradually towards equilibrium isotopic composition and the value of Fe oxide-bound phosphate showed slight changes at first, but when new iron oxides were formed, co-precipitated/occluded phosphate retained 18O values of aqueous phosphate at that time. Concentrations and isotopic compositions of authigenic and detrital phosphates did not change, suggesting that these phosphate phases were not utilized by bacteria. These findings support burgeoning applications of 18Op as a tracer of phosphorus cycling in sediments, soils and

  10. The Nature of Selected English Teachers' Online Participation

    ERIC Educational Resources Information Center

    Rodesiler, Luke

    2015-01-01

    This article documents an investigation into the nature of selected secondary English teachers' online participation across platforms (i.e., blogs, microblogs, social networking sites) as they explored issues related to teaching, learning, and literacy. Ethnographic content analysis of online artifacts generated over approximately 10 months…

  11. Sampling protocol for monitoring abiotic and biotic characteristics of mountain ponds and lakes

    USGS Publications Warehouse

    Hoffman, Robert L.; Tyler, Torrey J.; Larson, Gary L.; Adams, Michael J.; Wente, Wendy; Galvan, Stephanie

    2005-01-01

    This document describes field techniques and procedures used for sampling mountain ponds and lakes. These techniques and procedures will be used primarily to monitor, as part of long-term programs in National Parks and other protected areas, the abiotic and biotic characteristics of naturally occurring permanent montane lentic systems up to 75 ha in surface area. However, the techniques and procedures described herein also can be used to sample temporary or ephemeral montane lentic sites. Each Standard Operating Procedure (SOP) section addresses a specific component of the limnological investigation, and describes in detail field sampling methods pertaining to parameters to be measured for each component.

  12. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

    PubMed

    Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

    2016-08-01

    A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

  13. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

    PubMed Central

    Phung, Tanya N.; Lohmueller, Kirk E.

    2016-01-01

    A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

  14. Transgenic Alfalfa Plants Expressing the Sweetpotato Orange Gene Exhibit Enhanced Abiotic Stress Tolerance

    PubMed Central

    Wang, Zhi; Ke, Qingbo; Kim, Myoung Duck; Kim, Sun Ha; Ji, Chang Yoon; Jeong, Jae Cheol; Lee, Haeng-Soon; Park, Woo Sung; Ahn, Mi-Jeong; Li, Hongbing; Xu, Bingcheng; Deng, Xiping; Lee, Sang-Hoon; Lim, Yong Pyo; Kwak, Sang-Soo

    2015-01-01

    Alfalfa (Medicago sativa L.), a perennial forage crop with high nutritional content, is widely distributed in various environments worldwide. We recently demonstrated that the sweetpotato Orange gene (IbOr) is involved in increasing carotenoid accumulation and enhancing resistance to multiple abiotic stresses. In this study, in an effort to improve the nutritional quality and environmental stress tolerance of alfalfa, we transferred the IbOr gene into alfalfa (cv. Xinjiang Daye) under the control of an oxidative stress-inducible peroxidase (SWPA2) promoter through Agrobacterium tumefaciens-mediated transformation. Among the 11 transgenic alfalfa lines (referred to as SOR plants), three lines (SOR2, SOR3, and SOR8) selected based on their IbOr transcript levels were examined for their tolerance to methyl viologen (MV)-induced oxidative stress in a leaf disc assay. The SOR plants exhibited less damage in response to MV-mediated oxidative stress and salt stress than non-transgenic plants. The SOR plants also exhibited enhanced tolerance to drought stress, along with higher total carotenoid levels. The results suggest that SOR alfalfa plants would be useful as forage crops with improved nutritional value and increased tolerance to multiple abiotic stresses, which would enhance the development of sustainable agriculture on marginal lands. PMID:25946429

  15. Transgenic alfalfa plants expressing the sweetpotato Orange gene exhibit enhanced abiotic stress tolerance.

    PubMed

    Wang, Zhi; Ke, Qingbo; Kim, Myoung Duck; Kim, Sun Ha; Ji, Chang Yoon; Jeong, Jae Cheol; Lee, Haeng-Soon; Park, Woo Sung; Ahn, Mi-Jeong; Li, Hongbing; Xu, Bingcheng; Deng, Xiping; Lee, Sang-Hoon; Lim, Yong Pyo; Kwak, Sang-Soo

    2015-01-01

    Alfalfa (Medicago sativa L.), a perennial forage crop with high nutritional content, is widely distributed in various environments worldwide. We recently demonstrated that the sweetpotato Orange gene (IbOr) is involved in increasing carotenoid accumulation and enhancing resistance to multiple abiotic stresses. In this study, in an effort to improve the nutritional quality and environmental stress tolerance of alfalfa, we transferred the IbOr gene into alfalfa (cv. Xinjiang Daye) under the control of an oxidative stress-inducible peroxidase (SWPA2) promoter through Agrobacterium tumefaciens-mediated transformation. Among the 11 transgenic alfalfa lines (referred to as SOR plants), three lines (SOR2, SOR3, and SOR8) selected based on their IbOr transcript levels were examined for their tolerance to methyl viologen (MV)-induced oxidative stress in a leaf disc assay. The SOR plants exhibited less damage in response to MV-mediated oxidative stress and salt stress than non-transgenic plants. The SOR plants also exhibited enhanced tolerance to drought stress, along with higher total carotenoid levels. The results suggest that SOR alfalfa plants would be useful as forage crops with improved nutritional value and increased tolerance to multiple abiotic stresses, which would enhance the development of sustainable agriculture on marginal lands.

  16. Exchange of adsorbed serum proteins during adhesion of Staphylococcus aureus to an abiotic surface and Candida albicans hyphae--an AFM study.

    PubMed

    Ovchinnikova, Ekaterina S; van der Mei, Henny C; Krom, Bastiaan P; Busscher, Henk J

    2013-10-01

    Staphylococcus aureus and Candida albicans are the second and third most commonly isolated microorganisms in hospital-related-infections, that are often multi-species in nature causing high morbidity and mortality. Here, adhesion forces between a S. aureus strain and abiotic (tissue-culture-polystyrene, TCPS) or partly biotic (TCPS with adhering hyphae of C. albicans) surfaces were investigated in presence of fetal-bovine-serum or individual serum proteins and related with staphylococcal adhesion. Atomic-force-microscopy was used to measure adhesion forces between S. aureus and the abiotic and biotic surfaces. Adsorption of individual serum proteins like albumin and apo-transferrin to abiotic TCPS surfaces during 60min, impeded development of strong adhesion forces as compared to fibronectin, while 60min adsorption of proteins from fetal-bovine-serum yielded a decrease in adhesion force from -5.7nN in phosphate-buffered-saline to -0.6nN. Adsorption of albumin and apo-transferrin also decreased staphylococcal adhesion forces to hyphae as compared with fibronectin. During 60min exposure to fetal-bovine-serum however, initial (5min protein adsorption) staphylococcal adhesion forces were low (-1.6nN), but strong adhesion forces of around -5.5nN were restored within 60min. This suggests for the first time that in whole fetal-bovine-serum exchange of non-adhesive proteins by fibronectin occurs on biotic C. albicans hyphal surfaces. No evidence was found for such protein exchange on abiotic TCPS surfaces. Staphylococcal adhesion of abiotic and biotic surfaces varied in line with the adhesion forces and was low on TCPS in presence of fetal-bovine-serum. On partly biotic TCPS, staphylococci aggregated in presence of fetal-bovine-serum around adhering C. albicans hyphae. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Experiments on the abiotic amplification of optical activity

    NASA Technical Reports Server (NTRS)

    Bonner, W. A.; Blair, N. E.; Dirbas, F. M.

    1981-01-01

    Experiments concerning the physical mechanisms for the abiotic generation and chemical mechanisms for the amplification of optical activity in biological compounds are reviewed. Attention is given to experiments involving the determination of the differential adsorption of racemic amino acids on d- and l-quartz, the asymmetric photolysis of racemic amino acids by circularly polarized light, and the asymmetric radiolysis of solid amino acids by longitudinally polarized electrons, and the enantiomeric enrichments thus obtained are noted. Further experiments on the amplification of the chirality in the polymerization of D, L-amino acid mixtures and the hydrolysis of D-, L-, and D, L-polypeptides are discussed. It is suggested that a repetitive cycle of partial polymerization-hydrolyses may account for the abiotic genesis of optically enriched polypeptides on the primitive earth.

  18. Effective Assessment: Probing Students' Understanding of Natural Selection

    ERIC Educational Resources Information Center

    Stern, Luli

    2004-01-01

    Evolution by natural selection provides the conceptual framework upon which much of modern biology is based: therefore understanding core ideas about biological evolution is an essential part of scientific literacy. Nonetheless, research repeatedly shows that high school and college students have difficulties understanding the notion of natural…

  19. Hydrogen peroxide priming modulates abiotic oxidative stress tolerance: insights from ROS detoxification and scavenging

    PubMed Central

    Hossain, Mohammad A.; Bhattacharjee, Soumen; Armin, Saed-Moucheshi; Qian, Pingping; Xin, Wang; Li, Hong-Yu; Burritt, David J.; Fujita, Masayuki; Tran, Lam-Son P.

    2015-01-01

    Plants are constantly challenged by various abiotic stresses that negatively affect growth and productivity worldwide. During the course of their evolution, plants have developed sophisticated mechanisms to recognize external signals allowing them to respond appropriately to environmental conditions, although the degree of adjustability or tolerance to specific stresses differs from species to species. Overproduction of reactive oxygen species (ROS; hydrogen peroxide, H2O2; superoxide, O2⋅-; hydroxyl radical, OH⋅ and singlet oxygen, 1O2) is enhanced under abiotic and/or biotic stresses, which can cause oxidative damage to plant macromolecules and cell structures, leading to inhibition of plant growth and development, or to death. Among the various ROS, freely diffusible and relatively long-lived H2O2 acts as a central player in stress signal transduction pathways. These pathways can then activate multiple acclamatory responses that reinforce resistance to various abiotic and biotic stressors. To utilize H2O2 as a signaling molecule, non-toxic levels must be maintained in a delicate balancing act between H2O2 production and scavenging. Several recent studies have demonstrated that the H2O2-priming can enhance abiotic stress tolerance by modulating ROS detoxification and by regulating multiple stress-responsive pathways and gene expression. Despite the importance of the H2O2-priming, little is known about how this process improves the tolerance of plants to stress. Understanding the mechanisms of H2O2-priming-induced abiotic stress tolerance will be valuable for identifying biotechnological strategies to improve abiotic stress tolerance in crop plants. This review is an overview of our current knowledge of the possible mechanisms associated with H2O2-induced abiotic oxidative stress tolerance in plants, with special reference to antioxidant metabolism. PMID:26136756

  20. A Conceptual Characterization of Online Videos Explaining Natural Selection

    NASA Astrophysics Data System (ADS)

    Bohlin, Gustav; Göransson, Andreas; Höst, Gunnar E.; Tibell, Lena A. E.

    2017-11-01

    Educational videos on the Internet comprise a vast and highly diverse source of information. Online search engines facilitate access to numerous videos claiming to explain natural selection, but little is known about the degree to which the video content match key evolutionary content identified as important in evolution education research. In this study, we therefore analyzed the content of 60 videos accessed through the Internet, using a criteria catalog with 38 operationalized variables derived from research literature. The variables were sorted into four categories: (a) key concepts (e.g. limited resources and inherited variation), (b) threshold concepts (abstract concepts with a transforming and integrative function), (c) misconceptions (e.g. that evolution is driven by need), and (d) organismal context (e.g. animal or plant). The results indicate that some concepts are frequently communicated, and certain taxa are commonly used to illustrate concepts, while others are seldom included. In addition, evolutionary phenomena at small temporal and spatial scales, such as subcellular processes, are rarely covered. Rather, the focus is on population-level events over time scales spanning years or longer. This is consistent with an observed lack of explanations regarding how randomly occurring mutations provide the basis for variation (and thus natural selection). The findings imply, among other things, that some components of natural selection warrant far more attention in biology teaching and science education research.

  1. The Ascorbate-glutathione-α-tocopherol Triad in Abiotic Stress Response

    PubMed Central

    Szarka, András; Tomasskovics, Bálint; Bánhegyi, Gábor

    2012-01-01

    The life of any living organism can be defined as a hurdle due to different kind of stresses. As with all living organisms, plants are exposed to various abiotic stresses, such as drought, salinity, extreme temperatures and chemical toxicity. These primary stresses are often interconnected, and lead to the overproduction of reactive oxygen species (ROS) in plants, which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA, which ultimately results in oxidative stress. Stress-induced ROS accumulation is counteracted by enzymatic antioxidant systems and non-enzymatic low molecular weight metabolites, such as ascorbate, glutathione and α-tocopherol. The above mentioned low molecular weight antioxidants are also capable of chelating metal ions, reducing thus their catalytic activity to form ROS and also scavenge them. Hence, in plant cells, this triad of low molecular weight antioxidants (ascorbate, glutathione and α-tocopherol) form an important part of abiotic stress response. In this work we are presenting a review of abiotic stress responses connected to these antioxidants. PMID:22605990

  2. Wheat EST resources for functional genomics of abiotic stress

    PubMed Central

    Houde, Mario; Belcaid, Mahdi; Ouellet, François; Danyluk, Jean; Monroy, Antonio F; Dryanova, Ani; Gulick, Patrick; Bergeron, Anne; Laroche, André; Links, Matthew G; MacCarthy, Luke; Crosby, William L; Sarhan, Fathey

    2006-01-01

    Background Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. Results We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. Conclusion We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals. PMID

  3. The Creativity of Natural Selection? Part I: Darwin, Darwinism, and the Mutationists.

    PubMed

    Beatty, John

    2016-12-01

    This is the first of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. Here I focus on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled "mutationists." The second part focuses on the evolutionary synthesis and some of its critics, especially the "neutralists" and "neo-mutationists." Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as "Darwinism." I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection being responsible for the presence of the variation it acts upon, for example by directing the course of variation. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.

  4. Origin of Abiotic Methane in Submarine Hydrothermal Systems

    NASA Astrophysics Data System (ADS)

    Seewald, J. S.; German, C. R.; Grozeva, N. G.; Klein, F.; McDermott, J. M.; Ono, S.; Reeves, E. P.; Wang, D. T.

    2018-05-01

    Results of recent investigations into the chemical and isotopic composition of actively venting submarine hydrothermal fluids and volatile species trapped in fluid inclusions will be discussed in the context of processes responsible for abiotic CH4 formation.

  5. De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum).

    PubMed

    Li, Meng-Yao; Tan, Hua-Wei; Wang, Feng; Jiang, Qian; Xu, Zhi-Sheng; Tian, Chang; Xiong, Ai-Sheng

    2014-01-01

    Parsley is an important biennial Apiaceae species that is widely cultivated as herb, spice, and vegetable. Previous studies on parsley principally focused on its physiological and biochemical properties, including phenolic compound and volatile oil contents. However, little is known about the molecular and genetic properties of parsley. In this study, 23,686,707 high-quality reads were obtained and assembled into 81,852 transcripts and 50,161 unigenes for the first time. Functional annotation showed that 30,516 unigenes had sequence similarity to known genes. In addition, 3,244 putative simple sequence repeats were detected in curly parsley. Finally, 1,569 of the identified unigenes belonged to 58 transcription factor families. Various abiotic stresses have a strong detrimental effect on the yield and quality of parsley. AP2/ERF transcription factors have important functions in plant development, hormonal regulation, and abiotic response. A total of 88 putative AP2/ERF factors were identified from the transcriptome sequence of parsley. Seven AP2/ERF transcription factors were selected in this study to analyze the expression profiles of parsley under different abiotic stresses. Our data provide a potentially valuable resource that can be used for intensive parsley research.

  6. De Novo Transcriptome Sequence Assembly and Identification of AP2/ERF Transcription Factor Related to Abiotic Stress in Parsley (Petroselinum crispum)

    PubMed Central

    Wang, Feng; Jiang, Qian; Xu, Zhi-Sheng; Tian, Chang; Xiong, Ai-Sheng

    2014-01-01

    Parsley is an important biennial Apiaceae species that is widely cultivated as herb, spice, and vegetable. Previous studies on parsley principally focused on its physiological and biochemical properties, including phenolic compound and volatile oil contents. However, little is known about the molecular and genetic properties of parsley. In this study, 23,686,707 high-quality reads were obtained and assembled into 81,852 transcripts and 50,161 unigenes for the first time. Functional annotation showed that 30,516 unigenes had sequence similarity to known genes. In addition, 3,244 putative simple sequence repeats were detected in curly parsley. Finally, 1,569 of the identified unigenes belonged to 58 transcription factor families. Various abiotic stresses have a strong detrimental effect on the yield and quality of parsley. AP2/ERF transcription factors have important functions in plant development, hormonal regulation, and abiotic response. A total of 88 putative AP2/ERF factors were identified from the transcriptome sequence of parsley. Seven AP2/ERF transcription factors were selected in this study to analyze the expression profiles of parsley under different abiotic stresses. Our data provide a potentially valuable resource that can be used for intensive parsley research. PMID:25268141

  7. Fast Abiotic Production of Methane at Temperatures Below 100°C

    NASA Astrophysics Data System (ADS)

    Etiope, G.; Ionescu, A.

    2015-12-01

    Fischer-Tropsch Type (FTT) reactions, e.g., the Sabatier synthesis between H2 and CO2, are considered a main source of abiotic methane on Earth and likely on other planets. Several laboratory FTT experiments demonstrated abiotic CH4 production at temperatures above 200°C, by using Fe, Ni or Cr catalysts, simulating hydrothermal conditions in peridotite-hosted systems in mid-ocean ridges. Nevertheless, at least on laboratory experiment time-scale, Fe-Ni-Cr catalysts do not support CH4 generation at T<100°C, such as those of land-based serpentinization systems. We have recently reported rapid production of considerable amounts of CH4 (>800 ppmv in 155 mL bottles after 1 day) via Sabatier reaction at 90, 50 and 25°C, using small concentrations of non-pretreated ruthenium (Ru) equivalent to those occurring in chromitites in continental ultramafic rocks (Etiope & Ionescu, 2014; Geofluids, doi:10.1111/gfl.12106). We have repeated the experiments by using 13C-enriched CO2 and we confirm fast production of CH4at percentage levels. The experiments performed so far show that: 1. considerable amounts of CH4can be produced in dry conditions below 100°C with small quantities of Ru; 2. under the same experimental conditions (<100°C), Fe, Ni and Cr oxides do not produce CH4; 3. low T Sabatier reaction can produce CH4 with a large C isotope fractionation between CO2 and CH4, leading to relatively " light" (13C-depleted) CH4, resembling microbial gas; 4. the CO2-CH4isotope separation decreases over time and by increasing the temperature; 5. minor amounts of C2-C6hydrocarbons are also generated. Our laboratory data are compatible with the isotopic patterns of CH4 naturally occurring in land-based seeps and springs. Our experiments suggest that Ru-enriched chromitites could potentially generate CH4 at low T. Since Ru is reported in Martian meteorites, low T abiotic CH4 production on Mars via Sabatier reaction cannot be excluded (Etiope et al. 2013, Icarus, 224, 276-285).

  8. Young children can be taught basic natural selection using a picture-storybook intervention.

    PubMed

    Kelemen, Deborah; Emmons, Natalie A; Seston Schillaci, Rebecca; Ganea, Patricia A

    2014-04-01

    Adaptation by natural selection is a core mechanism of evolution. It is also one of the most widely misunderstood scientific processes. Misconceptions are rooted in cognitive biases found in preschoolers, yet concerns about complexity mean that adaptation by natural selection is generally not comprehensively taught until adolescence. This is long after untutored theoretical misunderstandings are likely to have become entrenched. In a novel approach, we explored 5- to 8-year-olds' capacities to learn a basic but theoretically coherent mechanistic explanation of adaptation through a custom storybook intervention. Experiment 1 showed that children understood the population-based logic of natural selection and also generalized it. Furthermore, learning endured 3 months later. Experiment 2 replicated these results and showed that children understood and applied an even more nuanced mechanistic causal explanation. The findings demonstrate that, contrary to conventional educational wisdom, basic natural selection is teachable in early childhood. Theory-driven interventions using picture storybooks with rich explanatory structure are beneficial.

  9. Understanding Tropical Forest Abiotic Responses to Canopy Loss and Biomass Deposition from an Experimental Hurricane Manipulation

    NASA Astrophysics Data System (ADS)

    Van Beusekom, A.; González, G.; Stankavitch, S.; Zimmerman, J. K.

    2017-12-01

    Understanding the nature and duration of the response of tropical forests to the extreme weather events of hurricanes is critical to understanding future forest regimes, as hurricanes are expected to increase in frequency with climate change. Here we present results from a manipulative experiment on hurricane disturbance effects in the Luquillo Experimental Forest (LEF) in Puerto Rico. The LEF is an example of a forest that would be in a frequent-hurricane region in Earth System Models (ESMs). Thus, the Canopy Trimming Experiment (CTE) was designed to study the key mechanisms behind such a forest's response after a major hurricane (category 4), and guide how repeated hurricanes might be expected to alter such ecosystems using these key mechanisms. Furthermore, with explicit forest manipulation instead of natural occurrence, it is possible to separate out which aspects of hurricane disturbance are most important to be accurately included in ESMs. Phase one of the experiments ran from 2005-2012, where it was found that short-term biotic responses of the forests were driven by canopy openness rather than by debris deposition. In phase two, running from 2014 through the present, we focus here on the abiotic changes forcing the overall response of the ecosystem. The manner in which these abiotic characteristics are disturbed and the speed at which they recover will be key to the continued existence of tropical forests under a climate with more frequent hurricane activity.

  10. Getting to Darwin: Obstacles to Accepting Evolution by Natural Selection

    NASA Astrophysics Data System (ADS)

    Thagard, Paul; Findlay, Scott

    2010-06-01

    Darwin’s theory of evolution by natural selection is central to modern biology, but is resisted by many people. This paper discusses the major psychological obstacles to accepting Darwin’s theory. Cognitive obstacles to adopting evolution by natural selection include conceptual difficulties, methodological issues, and coherence problems that derive from the intuitiveness of alternative theories. The main emotional obstacles to accepting evolution are its apparent conflict with valued beliefs about God, souls, and morality. We draw on the philosophy of science and on a psychological theory of cognitive and emotional belief revision to make suggestions about what can be done to improve acceptance of Darwinian ideas.

  11. Natural and sexual selection against immigrants maintains differentiation among micro-allopatric populations.

    PubMed

    Tobler, M; Riesch, R; Tobler, C M; Schulz-Mirbach, T; Plath, M

    2009-11-01

    Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence lead to speciation. But what mechanisms contribute to reproductive isolation among diverging populations? We tested for natural and sexual selection against immigrants in a fish species inhabiting (and adapting to) nonsulphidic surface habitats, sulphidic surface habitats and a sulphidic cave. Gene flow is strong among sample sites situated within the same habitat type, but low among divergent habitat types. Our results indicate that females of both sulphidic populations discriminate against immigrant males during mate choice. Furthermore, using reciprocal translocation experiments, we document natural selection against migrants between nonsulphidic and sulphidic habitats, whereas migrants between sulphidic cave and surface habitats did not exhibit increased mortality within the same time period. Consequently, both natural and sexual selection may contribute to isolation among parapatric populations, and selection against immigrants may be a powerful mechanism facilitating speciation among locally adapted populations even over very small spatial distances.

  12. Novel NAC Transcription Factor TaNAC67 Confers Enhanced Multi-Abiotic Stress Tolerances in Arabidopsis

    PubMed Central

    Mao, Xinguo; Chen, Shuangshuang; Li, Ang; Zhai, Chaochao; Jing, Ruilian

    2014-01-01

    Abiotic stresses are major environmental factors that affect agricultural productivity worldwide. NAC transcription factors play pivotal roles in abiotic stress signaling in plants. As a staple crop, wheat production is severely constrained by abiotic stresses whereas only a few NAC transcription factors have been characterized functionally. To promote the application of NAC genes in wheat improvement by biotechnology, a novel NAC gene designated TaNAC67 was characterized in common wheat. To determine its role, transgenic Arabidopsis overexpressing TaNAC67-GFP controlled by the CaMV-35S promoter was generated and subjected to various abiotic stresses for morphological and physiological assays. Gene expression showed that TaNAC67 was involved in response to drought, salt, cold and ABA treatments. Localization assays revealed that TaNAC67 localized in the nucleus. Morphological analysis indicated the transgenics had enhanced tolerances to drought, salt and freezing stresses, simultaneously supported by enhanced expression of multiple abiotic stress responsive genes and improved physiological traits, including strengthened cell membrane stability, retention of higher chlorophyll contents and Na+ efflux rates, improved photosynthetic potential, and enhanced water retention capability. Overexpression of TaNAC67 resulted in pronounced enhanced tolerances to drought, salt and freezing stresses, therefore it has potential for utilization in transgenic breeding to improve abiotic stress tolerance in crops. PMID:24427285

  13. The abiotic degradation of soil organic matter to oxalic acid

    NASA Astrophysics Data System (ADS)

    Studenroth, Sabine; Huber, Stefan; Schöler, H. F.

    2010-05-01

    The abiotic degradation of soil organic matter to volatile organic compounds was studied intensely over the last years (Keppler et al., 2000; Huber et al., 2009). It was shown that soil organic matter is oxidised due to the presence of iron (III), hydrogen peroxide and chloride and thereby produces diverse alkyl halides, which are emitted into the atmosphere. The formation of polar halogenated compounds like chlorinated acetic acids which are relevant toxic environmental substances was also found in soils and sediments (Kilian et al., 2002). The investigation of the formation of other polar halogenated and non-halogenated compounds like diverse mono- and dicarboxylic acids is going to attain more and more importance. Due to its high acidity oxalic acid might have impacts on the environment e.g., nutrient leaching, plant diseases and negative influence on microbial growth. In this study, the abiotic formation of oxalic acid in soil is examined. For a better understanding of natural degradation processes mechanistic studies were conducted using the model compound catechol as representative for structural elements of the humic substances and its reaction with iron (III) and hydrogen peroxide. Iron is one of the most abundant elements on earth and hydrogen peroxide is produced by bacteria or through incomplete reduction of oxygen. To find suitable parameters for an optimal reaction and a qualitative and quantitative analysis method the following reaction parameters are varied: concentration of iron (III) and hydrogen peroxide, time dependence, pH-value and influence of chloride. Analysis of oxalic acid was performed employing an ion chromatograph equipped with a conductivity detector. The time dependent reaction shows a relatively fast formation of oxalic acid, the optimum yield is achieved after 60 minutes. Compared to the concentration of catechol an excess of hydrogen peroxide as well as a low concentration of iron (III) are required. In absence of chloride the

  14. Natural selection on thermal preference, critical thermal maxima and locomotor performance.

    PubMed

    Gilbert, Anthony L; Miles, Donald B

    2017-08-16

    Climate change is resulting in a radical transformation of the thermal quality of habitats across the globe. Whereas species have altered their distributions to cope with changing environments, the evidence for adaptation in response to rising temperatures is limited. However, to determine the potential of adaptation in response to thermal variation, we need estimates of the magnitude and direction of natural selection on traits that are assumed to increase persistence in warmer environments. Most inferences regarding physiological adaptation are based on interspecific analyses, and those of selection on thermal traits are scarce. Here, we estimate natural selection on major thermal traits used to assess the vulnerability of ectothermic organisms to altered thermal niches. We detected significant directional selection favouring lizards with higher thermal preferences and faster sprint performance at their optimal temperature. Our analyses also revealed correlational selection between thermal preference and critical thermal maxima, where individuals that preferred warmer body temperatures with cooler critical thermal maxima were favoured by selection. Recent published estimates of heritability for thermal traits suggest that, in concert with the strong selective pressures we demonstrate here, evolutionary adaptation may promote long-term persistence of ectotherms in altered thermal environments. © 2017 The Author(s).

  15. Ideas on the emergence of life by a quantity-to-quality transition of the abiotic matter

    NASA Astrophysics Data System (ADS)

    Kolb, Vera M.

    2005-09-01

    We review and re-examine the idea that life emerged by a quantity-to-quality transition of the abiotic matter. This idea was originally proposed by the dialectical materialists, who are the proponents of the materialistic approach to the Hegel's laws of dialectics. We propose in this paper that the universal feature of the quantity-to-quality transitions is a change in the organization of the system. We also discuss Jean-Paul Sartre's view on the application of the laws of dialectics to the nature and to the origins of life.

  16. Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses

    PubMed Central

    Chen, Zhehao; Yuan, Ye; Fu, Di; Shen, Chenjia; Yang, Yanjun

    2017-01-01

    Auxin response factor (ARF) proteins play roles in plant responses to diverse environmental stresses by binding specifically to the auxin response element in the promoters of target genes. Using our latest public Dendrobium transcriptomes, a comprehensive characterization and analysis of 14 DnARF genes were performed. Three selected DnARFs, including DnARF1, DnARF4, and DnARF6, were confirmed to be nuclear proteins according to their transient expression in epidermal cells of Nicotiana benthamiana leaves. Furthermore, the transcription activation abilities of DnARF1, DnARF4, and DnARF6 were tested in a yeast system. Our data showed that DnARF6 is a transcriptional activator in Dendrobium officinale. To uncover the basic information of DnARF gene responses to abiotic stresses, we analyzed their expression patterns under various hormones and abiotic treatments. Based on our data, several hormones and significant stress responsive DnARF genes have been identified. Since auxin and ARF genes have been identified in many plant species, our data is imperative to reveal the function of ARF mediated auxin signaling in the adaptation to the challenging Dendrobium environment. PMID:28471373

  17. Identification and Expression Profiling of the Auxin Response Factors in Dendrobium officinale under Abiotic Stresses.

    PubMed

    Chen, Zhehao; Yuan, Ye; Fu, Di; Shen, Chenjia; Yang, Yanjun

    2017-05-04

    Auxin response factor (ARF) proteins play roles in plant responses to diverse environmental stresses by binding specifically to the auxin response element in the promoters of target genes. Using our latest public Dendrobium transcriptomes, a comprehensive characterization and analysis of 14 DnARF genes were performed. Three selected DnARFs , including DnARF1 , DnARF4 , and DnARF6 , were confirmed to be nuclear proteins according to their transient expression in epidermal cells of Nicotiana benthamiana leaves. Furthermore, the transcription activation abilities of DnARF1 , DnARF4 , and DnARF6 were tested in a yeast system. Our data showed that DnARF6 is a transcriptional activator in Dendrobium officinale . To uncover the basic information of DnARF gene responses to abiotic stresses, we analyzed their expression patterns under various hormones and abiotic treatments. Based on our data, several hormones and significant stress responsive DnARF genes have been identified. Since auxin and ARF genes have been identified in many plant species, our data is imperative to reveal the function of ARF mediated auxin signaling in the adaptation to the challenging Dendrobium environment.

  18. Polyamines and abiotic stress in plants: a complex relationship Frontiers in Plant Science

    Treesearch

    Rakesh Minocha; Rajtilak Majumdar; Subhash C. Minocha

    2014-01-01

    The physiological relationship between abiotic stress in plants and polyamines was reported more than 40 years ago. Ever since there has been a debate as to whether increased polyamines protect plants against abiotic stress (e.g., due to their ability to deal with oxidative radicals) or cause damage to them (perhaps due to hydrogen peroxide produced by their catabolism...

  19. Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties

    PubMed Central

    Kandianis, Catherine B.; Michenfelder, Abigail S.; Simmons, Susan J.; Grusak, Michael A.; Stapleton, Ann E.

    2013-01-01

    The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks. PMID:24363659

  20. Natural selection on immune defense: A field experiment.

    PubMed

    Langeloh, Laura; Behrmann-Godel, Jasminca; Seppälä, Otto

    2017-02-01

    Predicting the evolution of phenotypic traits requires an understanding of natural selection on them. Despite its indispensability in the fight against parasites, selection on host immune defense has remained understudied. Theory predicts immune traits to be under stabilizing selection due to associated trade-offs with other fitness-related traits. Empirical studies, however, report mainly positive directional selection. This discrepancy could be caused by low phenotypic variation in the examined individuals and/or variation in host resource level that confounds trade-offs in empirical studies. In a field experiment where we maintained Lymnaea stagnalis snails individually in cages in a lake, we investigated phenotypic selection on two immune defense traits, phenoloxidase (PO)-like activity and antibacterial activity, in hemolymph. We used a diverse laboratory population and manipulated snail resource level by limiting their food supply. For six weeks, we followed immune activity, growth, and two fitness components, survival and fecundity of snails. We found that PO-like activity and growth were under stabilizing selection, while antibacterial activity was under positive directional selection. Selection on immune traits was mainly driven by variation in survival. The form of selection on immune defense apparently depends on the particular trait, possibly due to its importance for countering the present parasite community. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  1. Hormone balance and abiotic stress tolerance in crop plants.

    PubMed

    Peleg, Zvi; Blumwald, Eduardo

    2011-06-01

    Plant hormones play central roles in the ability of plants to adapt to changing environments, by mediating growth, development, nutrient allocation, and source/sink transitions. Although ABA is the most studied stress-responsive hormone, the role of cytokinins, brassinosteroids, and auxins during environmental stress is emerging. Recent evidence indicated that plant hormones are involved in multiple processes. Cross-talk between the different plant hormones results in synergetic or antagonic interactions that play crucial roles in response of plants to abiotic stress. The characterization of the molecular mechanisms regulating hormone synthesis, signaling, and action are facilitating the modification of hormone biosynthetic pathways for the generation of transgenic crop plants with enhanced abiotic stress tolerance. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Do positive interactions increase with abiotic stress? A test from a semi-arid steppe.

    PubMed Central

    Maestre, Fernando T; Cortina, Jordi

    2004-01-01

    Theoretical models predict that the relative importance of facilitation and competition may vary inversely across gradients of abiotic stress. However, these predictions have not been thoroughly tested in the field, especially in semi-arid environments. In this study, we evaluated how the net effect of the tussock grass Stipa tenacissima on the shrub Pistacia lentiscus varied across a gradient of abiotic stress in semi-arid Mediterranean steppes. We fitted the relationship between accumulated rainfall and the relative neighbour index (our measures of abiotic stress and of the net effect of S. tenacissima on P. lentiscus, respectively), which varied across this gradient, to a quadratic model. Competitive interactions dominated at both extremes of the gradient. Our results do not support established theory. Instead, they suggest that a shift from facilitation to competition under high abiotic stress conditions is likely to occur when the levels of the most limiting resource are so low that the benefits provided by the facilitator cannot overcome its own resource uptake. PMID:15504009

  3. Serotonin, behavior, and natural selection in New World monkeys.

    PubMed

    Reales, Guillermo; Paixão-Côrtes, Vanessa R; Cybis, Gabriela B; Gonçalves, Gislene L; Pissinatti, Alcides; Salzano, Francisco M; Bortolini, Maria CÁtira

    2018-06-26

    Traits that undergo massive natural selection pressure, with multiple events of positive selection, are hard to find. Social behaviour, in social animals, is crucial for survival, and genetic networks involved in behaviour, such as those of serotonin (5-HT) and other neurotransmitters, must be the target of natural selection. Here, we used molecular analyses to search for signals of positive selection in the 5-HT system and found such signals in the M3-M4 intracellular domain of the 5-HT3A serotonin receptor subunit (HTR3A) in primates. We detected four amino acid sites with signs of putatively positive selection (398, 403, 432 and 416); the first three showed indications of being selected in New World monkeys (NWM, Platyrrhini), specifically in the Callitrichinae branch. Additionally, we searched for associations of these amino acid variants with social behavioural traits (i.e. sex-biased dispersal, dominance and social monogamy) using classical and Bayesian methods, and found statistically significant associations for unbiased sex dispersal (398L and 416S), unbiased sex dominance (416S) and social monogamy (416S), as well as significant positive correlation between female dispersal and 403G. Furthermore, we found putatively functional protein motifs determined by three selected sites, of which we highlight a ligand motif to GSK3 in the 416S variant, appearing only in Platyrrhini. 5-HT, 5-HT3A receptor and GSK3 are part of a network that participates in neurodevelopment and regulates behaviour, among other functions. We suggest that these genetic variations, together with those found in other neurotransmitter systems, must contribute to adaptive behaviours and consequently to fitness in NWMs. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

  4. Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans.

    PubMed

    Sharma, Manmohan D; Hunt, John; Hosken, David J

    2012-03-01

    Natural and sexual selection are classically thought to oppose one another, and although there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. Here, we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (CHCs), a character subject to both modes of selection, in Drosophila simulans. Natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experimental evolution, the responses of male and female CHCs were assessed. The effects of natural and sexual selection differed greatly across the sexes. The responses of female CHCs were generally small, but CHCs evolved predominantly in the direction of natural selection. For males, profiles evolved via sexual and natural selection, as well as through the interaction between the two, with some male CHC components only evolving in the direction of natural selection when sexual selection was relaxed. These results indicate sex-specific responses to selection, and that sexual and natural selection act antagonistically for at least some combinations of CHCs. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  5. Abiotic stress responses in plants: roles of calmodulin-regulated proteins.

    PubMed

    Virdi, Amardeep S; Singh, Supreet; Singh, Prabhjeet

    2015-01-01

    Intracellular changes in calcium ions (Ca(2+)) in response to different biotic and abiotic stimuli are detected by various sensor proteins in the plant cell. Calmodulin (CaM) is one of the most extensively studied Ca(2+)-sensing proteins and has been shown to be involved in transduction of Ca(2+) signals. After interacting with Ca(2+), CaM undergoes conformational change and influences the activities of a diverse range of CaM-binding proteins. A number of CaM-binding proteins have also been implicated in stress responses in plants, highlighting the central role played by CaM in adaptation to adverse environmental conditions. Stress adaptation in plants is a highly complex and multigenic response. Identification and characterization of CaM-modulated proteins in relation to different abiotic stresses could, therefore, prove to be essential for a deeper understanding of the molecular mechanisms involved in abiotic stress tolerance in plants. Various studies have revealed involvement of CaM in regulation of metal ions uptake, generation of reactive oxygen species and modulation of transcription factors such as CAMTA3, GTL1, and WRKY39. Activities of several kinases and phosphatases have also been shown to be modulated by CaM, thus providing further versatility to stress-associated signal transduction pathways. The results obtained from contemporary studies are consistent with the proposed role of CaM as an integrator of different stress signaling pathways, which allows plants to maintain homeostasis between different cellular processes. In this review, we have attempted to present the current state of understanding of the role of CaM in modulating different stress-regulated proteins and its implications in augmenting abiotic stress tolerance in plants.

  6. Natural selection on thermal performance in a novel thermal environment

    PubMed Central

    Logan, Michael L.; Cox, Robert M.; Calsbeek, Ryan

    2014-01-01

    Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation to changing conditions. Here, we mimic the effects of climate change by experimentally transplanting a population of Anolis sagrei lizards to a novel thermal environment. Transplanted lizards experienced warmer and more thermally variable conditions, which resulted in strong directional selection on thermal performance traits. These same traits were not under selection in a reference population studied in a less thermally stressful environment. Our results indicate that climate change can exert strong natural selection on tropical ectotherms, despite their ability to thermoregulate behaviorally. To the extent that thermal performance traits are heritable, populations may be capable of rapid adaptation to anthropogenic warming. PMID:25225361

  7. Natural selection on thermal performance in a novel thermal environment.

    PubMed

    Logan, Michael L; Cox, Robert M; Calsbeek, Ryan

    2014-09-30

    Tropical ectotherms are thought to be especially vulnerable to climate change because they are adapted to relatively stable temperature regimes, such that even small increases in environmental temperature may lead to large decreases in physiological performance. One way in which tropical organisms may mitigate the detrimental effects of warming is through evolutionary change in thermal physiology. The speed and magnitude of this response depend, in part, on the strength of climate-driven selection. However, many ectotherms use behavioral adjustments to maintain preferred body temperatures in the face of environmental variation. These behaviors may shelter individuals from natural selection, preventing evolutionary adaptation to changing conditions. Here, we mimic the effects of climate change by experimentally transplanting a population of Anolis sagrei lizards to a novel thermal environment. Transplanted lizards experienced warmer and more thermally variable conditions, which resulted in strong directional selection on thermal performance traits. These same traits were not under selection in a reference population studied in a less thermally stressful environment. Our results indicate that climate change can exert strong natural selection on tropical ectotherms, despite their ability to thermoregulate behaviorally. To the extent that thermal performance traits are heritable, populations may be capable of rapid adaptation to anthropogenic warming.

  8. Birth-order differences can drive natural selection on aging.

    PubMed

    Gillespie, Duncan O S; Trotter, Meredith V; Krishna-Kumar, Siddharth; Tuljapurkar, Shripad D

    2014-03-01

    Senescence-the deterioration of survival and reproductive capacity with increasing age-is generally held to be an evolutionary consequence of the declining strength of natural selection with increasing age. The diversity in rates of aging observed in nature suggests that the rate at which age-specific selection weakens is determined by species-specific ecological factors. We propose that, in iteroparous species, relationships between parental age, offspring birth order, and environment may affect selection on senescence. Later-born siblings have, on average, older parents than do first borns. Offspring born to older parents may experience different environments in terms of family support or inherited resources, factors often mediated by competition from siblings. Thus, age-specific selection on parents may change if the environment produces birth-order related gradients in reproductive success. We use an age-and-stage structured population model to investigate the impact of sibling environmental inequality on the expected evolution of senescence. We show that accelerated senescence evolves when later-born siblings are likely to experience an environment detrimental to lifetime reproduction. In general, sibling inequality is likely to be of particular importance for the evolution of senescence in species such as humans, where family interactions and resource inheritance have important roles in determining lifetime reproduction. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  9. The Role of Tomato WRKY Genes in Plant Responses to Combined Abiotic and Biotic Stresses

    PubMed Central

    Bai, Yuling; Sunarti, Sri; Kissoudis, Christos; Visser, Richard G. F.; van der Linden, C. G.

    2018-01-01

    In the field, plants constantly face a plethora of abiotic and biotic stresses that can impart detrimental effects on plants. In response to multiple stresses, plants can rapidly reprogram their transcriptome through a tightly regulated and highly dynamic regulatory network where WRKY transcription factors can act as activators or repressors. WRKY transcription factors have diverse biological functions in plants, but most notably are key players in plant responses to biotic and abiotic stresses. In tomato there are 83 WRKY genes identified. Here we review recent progress on functions of these tomato WRKY genes and their homologs in other plant species, such as Arabidopsis and rice, with a special focus on their involvement in responses to abiotic and biotic stresses. In particular, we highlight WRKY genes that play a role in plant responses to a combination of abiotic and biotic stresses.

  10. Transcription Factors and Their Roles in Signal Transduction in Plants under Abiotic Stresses

    PubMed Central

    Hoang, Xuan Lan Thi; Nhi, Du Ngoc Hai; Thu, Nguyen Binh Anh; Thao, Nguyen Phuong; Tran, Lam-Son Phan

    2017-01-01

    Abstract: In agricultural production, abiotic stresses are known as the main disturbance leading to negative impacts on crop performance. Research on elucidating plant defense mechanisms against the stresses at molecular level has been addressed for years in order to identify the major contributors in boosting the plant tolerance ability. From literature, numerous genes from different species, and from both functional and regulatory gene categories, have been suggested to be on the list of potential candidates for genetic engineering. Noticeably, enhancement of plant stress tolerance by manipulating expression of Transcription Factors (TFs) encoding genes has emerged as a popular approach since most of them are early stress-responsive genes and control the expression of a set of downstream target genes. Consequently, there is a higher chance to generate novel cultivars with better tolerance to either single or multiple stresses. Perhaps, the difficult task when deploying this approach is selecting appropriate gene(s) for manipulation. In this review, on the basis of the current findings from molecular and post-genomic studies, our interest is to highlight the current understanding of the roles of TFs in signal transduction and mediating plant responses towards abiotic stressors. Furthermore, interactions among TFs within the stress-responsive network will be discussed. The last section will be reserved for discussing the potential applications of TFs for stress tolerance improvement in plants. PMID:29204078

  11. Characterization of reference genes for RT-qPCR in the desert moss Syntrichia caninervis in response to abiotic stress and desiccation/rehydration

    PubMed Central

    Li, Xiaoshuang; Zhang, Daoyuan; Li, Haiyan; Gao, Bei; Yang, Honglan; Zhang, Yuanming; Wood, Andrew J.

    2015-01-01

    Syntrichia caninervis is the dominant bryophyte of the biological soil crusts found in the Gurbantunggut desert. The extreme desert environment is characterized by prolonged drought, temperature extremes, high radiation and frequent cycles of hydration and dehydration. S. caninervis is an ideal organism for the identification and characterization of genes related to abiotic stress tolerance. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) expression analysis is a powerful analytical technique that requires the use of stable reference genes. Using available S. caninervis transcriptome data, we selected 15 candidate reference genes and analyzed their relative expression stabilities in S. caninervis gametophores exposed to a range of abiotic stresses or a hydration-desiccation-rehydration cycle. The programs geNorm, NormFinder, and RefFinder were used to assess and rank the expression stability of the 15 candidate genes. The stability ranking results of reference genes under each specific experimental condition showed high consistency using different algorithms. For abiotic stress treatments, the combination of two genes (α-TUB2 and CDPK) were sufficient for accurate normalization. For the hydration-desiccation-rehydration process, the combination of two genes (α-TUB1 and CDPK) were sufficient for accurate normalization. 18S was among the least stable genes in all of the experimental sets and was unsuitable as reference gene in S. caninervis. This is the first systematic investigation and comparison of reference gene selection for RT-qPCR work in S. caninervis. This research will facilitate gene expression studies in S. caninervis, related moss species from the Syntrichia complex and other mosses. PMID:25699066

  12. The Effect of Different Oceanic Abiotic Factors on Prokaryotic Body Sizes

    NASA Astrophysics Data System (ADS)

    Pidathala, S.; Bellon, M.; Heim, N.; Payne, J.

    2016-12-01

    We are studying the impact of abiotic factors in the Pacific and Atlantic on prokaryotic body sizes and genome sizes because we are interested in the manner in which abiotic factors influence genome sizes independent of their influence on body sizes. Some research has been done in the past on marine bacterial evolution, including data collection on marine ecology in relation to bacterial body sizes (Straza 2009). We are using the abiotic factors: temperature, salinity, and pH to compare the biovolumes/genome sizes of different phyla by using R. We made 9 scatter plots to model these relationships. Regardless of the phyla or the ocean, we found that there is no relation between pH, temperature, and body size, with several exceptions: Deinococcus. thermus has an indirect relationship with size in respect to temperature; size only correlates to temperature for phyla that are thermophiles. We also found that bacteria like D. thermus and Thermotogae are taxa only found in higher temperatures. Additionally, almost all phyla have genome sizes restricted by certain pH levels:, Proteobacteria only reach genomes with acidity levels greater than 6. In terms of salinity levels, certain bacteria are only found within a small range, and others, like Proteobacteria, can only reach genomes at low salinity levels. Finally, Proteobacteria have large genome sizes between 30 and 40 °, and Crenarchaeota have constant genome sizes in higher temperatures. Conclusively, we discovered that these abiotic factors generally do not affect body size, with the exception of D. thermus' indirect relationship to temperature due to its small biovolume in high temperatures. However, we determined that these abiotic factors have a great impact on genome sizes. This is due to genome size independence from body size. Also, genome size could have served as an adaptive feature for bacteria in marine environments, explaining why different phyla may have diverged to accommodate their lifestyles.

  13. Nonconsumptive predator-driven mortality causes natural selection on prey.

    PubMed

    Siepielski, Adam M; Wang, Jason; Prince, Garrett

    2014-03-01

    Predators frequently exert natural selection through differential consumption of their prey. However, predators may also cause prey mortality through nonconsumptive effects, which could cause selection if different prey phenotypes are differentially susceptible to this nonconsumptive mortality. Here we present an experimental test of this hypothesis, which reveals that nonconsumptive mortality imposed by predatory dragonflies causes selection on their damselfly prey favoring increased activity levels. These results are consistent with other studies of predator-driven selection, however, they reveal that consumption alone is not the only mechanism by which predators can exert selection on prey. Uncovering this mechanism also suggests that prey defensive traits may represent adaptations to not only avoid being consumed, but also for dealing with other sources of mortality caused by predators. Demonstrating selection through both consumptive and nonconsumptive predator mortality provides us with insight into the diverse effects of predators as an evolutionary force. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  14. The basic science and mathematics of random mutation and natural selection.

    PubMed

    Kleinman, Alan

    2014-12-20

    The mutation and natural selection phenomenon can and often does cause the failure of antimicrobial, herbicidal, pesticide and cancer treatments selection pressures. This phenomenon operates in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures. The mathematical behavior of mutation and selection is derived using the principles given by probability theory. The derivation of the equations describing the mutation and selection phenomenon is carried out in the context of an empirical example. Copyright © 2014 John Wiley & Sons, Ltd.

  15. Site-specific 15N isotopic signatures of abiotically produced N2O

    NASA Astrophysics Data System (ADS)

    Heil, Jannis; Wolf, Benjamin; Brüggemann, Nicolas; Emmenegger, Lukas; Tuzson, Béla; Vereecken, Harry; Mohn, Joachim

    2014-08-01

    Efficient nitrous oxide (N2O) mitigation strategies require the identification of the main source and sink processes and their contribution to total soil N2O production. Several abiotic reactions of nitrification intermediates leading to N2O production are known, but their contribution to total N2O production in soils is uncertain. As the site preference (SP) of 15N in N2O is a promising tool to give more insight into N2O production processes, we investigated the SP of N2O produced by different abiotic reactions in a laboratory study. All reactions involved the nitrification intermediate hydroxylamine (NH2OH) in combination with nitrite (NO2-), Fe3+, Fe2+ and Cu2+, reactants commonly or potentially found in soils, at different concentrations and pH values. N2O production and its four main isotopic species (14N14N16O, 15N14N16O, 14N15N16O, and 14N14N18O) were quantified simultaneously and online at high temporal resolution using quantum cascade laser absorption spectroscopy. Thereby, our study presents the first continuous analysis of δ18O in N2O. The experiments revealed the possibility of purely abiotic reactions over a wide range of acidity (pH 3-8) by different mechanisms. All studied abiotic pathways produced N2O with a characteristic SP in the range of 34-35‰, unaffected by process conditions and remaining constant over the course of the experiments. These findings reflect the benefit of continuous N2O isotopic analysis by laser spectroscopy, contribute new information to the challenging source partitioning of N2O emissions from soils, and emphasize the potentially significant role of coupled biotic-abiotic reactions in soils.

  16. The relative abundances of resolved l2CH2D2 and 13CH3D and mechanisms controlling isotopic bond ordering in abiotic and biotic methane gases

    NASA Astrophysics Data System (ADS)

    Young, E. D.; Kohl, I. E.; Lollar, B. Sherwood; Etiope, G.; Rumble, D.; Li, S.; Haghnegahdar, M. A.; Schauble, E. A.; McCain, K. A.; Foustoukos, D. I.; Sutclife, C.; Warr, O.; Ballentine, C. J.; Onstott, T. C.; Hosgormez, H.; Neubeck, A.; Marques, J. M.; Pérez-Rodríguez, I.; Rowe, A. R.; LaRowe, D. E.; Magnabosco, C.; Yeung, L. Y.; Ash, J. L.; Bryndzia, L. T.

    2017-04-01

    We report measurements of resolved 12CH2D2 and 13CH3D at natural abundances in a variety of methane gases produced naturally and in the laboratory. The ability to resolve 12CH2D2 from 13CH3D provides unprecedented insights into the origin and evolution of CH4. The results identify conditions under which either isotopic bond order disequilibrium or equilibrium are expected. Where equilibrium obtains, concordant Δ12CH2D2 and Δ13CH3D temperatures can be used reliably for thermometry. We find that concordant temperatures do not always match previous hypotheses based on indirect estimates of temperature of formation nor temperatures derived from CH4/H2 D/H exchange, underscoring the importance of reliable thermometry based on the CH4 molecules themselves. Where Δ12CH2D2 and Δ13CH3D values are inconsistent with thermodynamic equilibrium, temperatures of formation derived from these species are spurious. In such situations, while formation temperatures are unavailable, disequilibrium isotopologue ratios nonetheless provide novel information about the formation mechanism of the gas and the presence or absence of multiple sources or sinks. In particular, disequilibrium isotopologue ratios may provide the means for differentiating between methane produced by abiotic synthesis vs. biological processes. Deficits in 12CH2D2 compared with equilibrium values in CH4 gas made by surface-catalyzed abiotic reactions are so large as to point towards a quantum tunneling origin. Tunneling also accounts for the more moderate depletions in 13CH3D that accompany the low 12CH2D2 abundances produced by abiotic reactions. The tunneling signature may prove to be an important tracer of abiotic methane formation, especially where it is preserved by dissolution of gas in cool hydrothermal systems (e.g., Mars). Isotopologue signatures of abiotic methane production can be erased by infiltration of microbial communities, and Δ12CH2D2 values are a key tracer of microbial recycling.

  17. Pollinators exert natural selection on flower size and floral display in Penstemon digitalis.

    PubMed

    Parachnowitsch, Amy L; Kessler, André

    2010-10-01

    • A major gap in our understanding of floral evolution, especially micro-evolutionary processes, is the role of pollinators in generating patterns of natural selection on floral traits. Here we explicitly tested the role of pollinators in selecting floral traits in a herbaceous perennial, Penstemon digitalis. • We manipulated the effect of pollinators on fitness through hand pollinations and compared phenotypic selection in open- and hand-pollinated plants. • Despite the lack of pollen limitation in our population, pollinators mediated selection on floral size and floral display. Hand pollinations removed directional selection for larger flowers and stabilizing selection on flower number, suggesting that pollinators were the agents of selection on both of these traits. • We reviewed studies that measured natural selection on floral traits by biotic agents and generally found stronger signatures of selection imposed by pollinators than by herbivores and co-flowering plant species. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

  18. The Arabidopsis PLAT domain protein1 is critically involved in abiotic stress tolerance.

    PubMed

    Hyun, Tae Kyung; van der Graaff, Eric; Albacete, Alfonso; Eom, Seung Hee; Großkinsky, Dominik K; Böhm, Hannah; Janschek, Ursula; Rim, Yeonggil; Ali, Walid Wahid; Kim, Soo Young; Roitsch, Thomas

    2014-01-01

    Despite the completion of the Arabidopsis genome sequence, for only a relatively low percentage of the encoded proteins experimental evidence concerning their function is available. Plant proteins that harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and belong to the PLAT-plant-stress protein family are ubiquitously present in monocot and dicots. However, the function of PLAT-plant-stress proteins is still poorly understood. Therefore, we have assessed the function of the uncharacterised Arabidopsis PLAT-plant-stress family members through a combination of functional genetic and physiological approaches. PLAT1 overexpression conferred increased abiotic stress tolerance, including cold, drought and salt stress, while loss-of-function resulted in opposite effects on abiotic stress tolerance. Strikingly, PLAT1 promoted growth under non-stressed conditions. Abiotic stress treatments induced PLAT1 expression and caused expansion of its expression domain. The ABF/ABRE transcription factors, which are positive mediators of abscisic acid signalling, activate PLAT1 promoter activity in transactivation assays and directly bind to the ABRE elements located in this promoter in electrophoretic mobility shift assays. This suggests that PLAT1 represents a novel downstream target of the abscisic acid signalling pathway. Thus, we showed that PLAT1 critically functions as positive regulator of abiotic stress tolerance, but also is involved in regulating plant growth, and thereby assigned a function to this previously uncharacterised PLAT domain protein. The functional data obtained for PLAT1 support that PLAT-plant-stress proteins in general could be promising targets for improving abiotic stress tolerance without yield penalty.

  19. The Arabidopsis PLAT Domain Protein1 Is Critically Involved in Abiotic Stress Tolerance

    PubMed Central

    Eom, Seung Hee; Großkinsky, Dominik K.; Böhm, Hannah; Janschek, Ursula; Rim, Yeonggil; Ali, Walid Wahid; Kim, Soo Young; Roitsch, Thomas

    2014-01-01

    Despite the completion of the Arabidopsis genome sequence, for only a relatively low percentage of the encoded proteins experimental evidence concerning their function is available. Plant proteins that harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and belong to the PLAT-plant-stress protein family are ubiquitously present in monocot and dicots. However, the function of PLAT-plant-stress proteins is still poorly understood. Therefore, we have assessed the function of the uncharacterised Arabidopsis PLAT-plant-stress family members through a combination of functional genetic and physiological approaches. PLAT1 overexpression conferred increased abiotic stress tolerance, including cold, drought and salt stress, while loss-of-function resulted in opposite effects on abiotic stress tolerance. Strikingly, PLAT1 promoted growth under non-stressed conditions. Abiotic stress treatments induced PLAT1 expression and caused expansion of its expression domain. The ABF/ABRE transcription factors, which are positive mediators of abscisic acid signalling, activate PLAT1 promoter activity in transactivation assays and directly bind to the ABRE elements located in this promoter in electrophoretic mobility shift assays. This suggests that PLAT1 represents a novel downstream target of the abscisic acid signalling pathway. Thus, we showed that PLAT1 critically functions as positive regulator of abiotic stress tolerance, but also is involved in regulating plant growth, and thereby assigned a function to this previously uncharacterised PLAT domain protein. The functional data obtained for PLAT1 support that PLAT-plant-stress proteins in general could be promising targets for improving abiotic stress tolerance without yield penalty. PMID:25396746

  20. Image statistics underlying natural texture selectivity of neurons in macaque V4

    PubMed Central

    Okazawa, Gouki; Tajima, Satohiro; Komatsu, Hidehiko

    2015-01-01

    Our daily visual experiences are inevitably linked to recognizing the rich variety of textures. However, how the brain encodes and differentiates a plethora of natural textures remains poorly understood. Here, we show that many neurons in macaque V4 selectively encode sparse combinations of higher-order image statistics to represent natural textures. We systematically explored neural selectivity in a high-dimensional texture space by combining texture synthesis and efficient-sampling techniques. This yielded parameterized models for individual texture-selective neurons. The models provided parsimonious but powerful predictors for each neuron’s preferred textures using a sparse combination of image statistics. As a whole population, the neuronal tuning was distributed in a way suitable for categorizing textures and quantitatively predicts human ability to discriminate textures. Together, we suggest that the collective representation of visual image statistics in V4 plays a key role in organizing the natural texture perception. PMID:25535362

  1. Arbuscular mycorrhizal fungal responses to abiotic stresses: A review.

    PubMed

    Lenoir, Ingrid; Fontaine, Joël; Lounès-Hadj Sahraoui, Anissa

    2016-03-01

    The majority of plants live in close collaboration with a diversity of soil organisms among which arbuscular mycorrhizal fungi (AMF) play an essential role. Mycorrhizal symbioses contribute to plant growth and plant protection against various environmental stresses. Whereas the resistance mechanisms induced in mycorrhizal plants after exposure to abiotic stresses, such as drought, salinity and pollution, are well documented, the knowledge about the stress tolerance mechanisms implemented by the AMF themselves is limited. This review provides an overview of the impacts of various abiotic stresses (pollution, salinity, drought, extreme temperatures, CO2, calcareous, acidity) on biodiversity, abundance and development of AMF and examines the morphological, biochemical and molecular mechanisms implemented by AMF to survive in the presence of these stresses. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Relationships between biotic and abiotic factors and regeneration of chestnut oak, white oak, and northern red oak

    Treesearch

    Songlin Fei; Kim C. Steiner; James C. Finley; Marc E. McDill

    2003-01-01

    A series of substantial field surveys of 38 mixed-oak stands in central Pennsylvania were carried out during 1996-2000. All the stands were surveyed 1 year prior to harvest, and 16 stands have been surveyed 1 year after harvest. Three abiotic factors at stand scale, four abiotic factors at plot scale, and two biotic factors and one abiotic factor at subplot scale was...

  3. Abiotic stress responses in plants: roles of calmodulin-regulated proteins

    PubMed Central

    Virdi, Amardeep S.; Singh, Supreet; Singh, Prabhjeet

    2015-01-01

    Intracellular changes in calcium ions (Ca2+) in response to different biotic and abiotic stimuli are detected by various sensor proteins in the plant cell. Calmodulin (CaM) is one of the most extensively studied Ca2+-sensing proteins and has been shown to be involved in transduction of Ca2+ signals. After interacting with Ca2+, CaM undergoes conformational change and influences the activities of a diverse range of CaM-binding proteins. A number of CaM-binding proteins have also been implicated in stress responses in plants, highlighting the central role played by CaM in adaptation to adverse environmental conditions. Stress adaptation in plants is a highly complex and multigenic response. Identification and characterization of CaM-modulated proteins in relation to different abiotic stresses could, therefore, prove to be essential for a deeper understanding of the molecular mechanisms involved in abiotic stress tolerance in plants. Various studies have revealed involvement of CaM in regulation of metal ions uptake, generation of reactive oxygen species and modulation of transcription factors such as CAMTA3, GTL1, and WRKY39. Activities of several kinases and phosphatases have also been shown to be modulated by CaM, thus providing further versatility to stress-associated signal transduction pathways. The results obtained from contemporary studies are consistent with the proposed role of CaM as an integrator of different stress signaling pathways, which allows plants to maintain homeostasis between different cellular processes. In this review, we have attempted to present the current state of understanding of the role of CaM in modulating different stress-regulated proteins and its implications in augmenting abiotic stress tolerance in plants. PMID:26528296

  4. Effects of soil abiotic factors on the plant morphology in an intertidal salt marsh, Yellow River Delta, China

    NASA Astrophysics Data System (ADS)

    Li, Shanze; Cui, Baoshan; Bai, Junhong; Xie, Tian; Yan, Jiaguo; Wang, Qing; Zhang, Shuyan

    2018-02-01

    Plant morphology plays important role in studying biogeography in many ecosystems. Suadea salsa, as a native plant community of northern China and an important habitat for diversity of waterbirds and macrobenthos, has often been overlooked. Nowadays, S. salsa community is facing great loss due to coastal reclamation activities and natural disturbances. To maintain and restore S. salsa community, it's important to address the plant morphology across marsh zones, as well as its relationships with local soil abiotic conditions. In our studied intertidal salt marsh, we found that less flood disturbance frequency, softer soil conditions, rich soil organic matter, total carbon and total nitrogen, lower water depth and water content, less species competition will benefit S. salsa plant in the morphology of high coverage, above-ground biomass, shoot height and leaf length. Lower soil porewater salinity will benefit the below-ground biomass of S. salsa. Thus, we recommend managers help alleviate soil abiotic stresses in the intertidal salt marshes, making the soil conditions more suitable for S. salsa growth and succession.

  5. The Unit of Natural Selection: Groups, Families, Individuals, or Genes?

    ERIC Educational Resources Information Center

    Reiss, Michael J.

    1985-01-01

    Offers perspectives on natural selection and the phenomenon of altruism. Presents evidence for and against the theories that evolution acts essentially on genes, on individuals, on kin, or on larger groups. (ML)

  6. Natural Selection Is a Sorting Process: What Does that Mean?

    ERIC Educational Resources Information Center

    Price, Rebecca M.

    2013-01-01

    To learn why natural selection acts only on existing variation, students categorize processes as either creative or sorting. This activity helps students confront the misconception that adaptations evolve because species need them.

  7. Olivine Weathering: Abiotic Versus Biotic Processes as Possible Biosignatures

    NASA Technical Reports Server (NTRS)

    Longazo, T. G.; Wentworth, S. J.; McKay, D. S.; Southam, G.; Clemett, S. J.

    2001-01-01

    A preliminary study to determine how abiotic versus biotic processes affect the weathering of olivine crystals. Perhaps the differences between these weathering processes could be used as biosignatures. Additional information is contained in the original extended abstract.

  8. Cortex proliferation in the root is a protective mechanism against abiotic stress.

    PubMed

    Cui, Hongchang

    2015-01-01

    Although as an organ the root plays a pivotal role in nutrient and water uptake as well anchorage, individual cell types function distinctly. Cortex is regarded as the least differentiated cell type in the root, but little is known about its role in plant growth and physiology. In recent studies, we found that cortex proliferation can be induced by oxidative stress. Since all types of abiotic stress lead to oxidative stress, this finding suggests a role for cortex in coping with abiotic stress. This hypothesis was tested in this study using the spy mutant, which has an extra layer of cortex in the root. Interestingly, the spy mutant was shown to be hypersensitive to salt and oxidizing reagent applied to the leaves, but it was as tolerant as the wild type to these compounds in the soil. This result lends support to the notion that cortex has a protective role against abiotic stress arising from the soil.

  9. MONITORED NATURAL ATTENUATION FOR INORGANIC CONTAMINANT REMEDIATION IN GROUNDWATER

    EPA Science Inventory

    Monitored natural attenuation (MNA) has been applied as a knowledge-based remediation technology for organic contaminants in ground water. Development of a site-specific assessment of biotic and abiotic processes that lead to organic contaminant degradation provides the technica...

  10. Global genetic differentiation of complex traits shaped by natural selection in humans.

    PubMed

    Guo, Jing; Wu, Yang; Zhu, Zhihong; Zheng, Zhili; Trzaskowski, Maciej; Zeng, Jian; Robinson, Matthew R; Visscher, Peter M; Yang, Jian

    2018-05-14

    There are mean differences in complex traits among global human populations. We hypothesize that part of the phenotypic differentiation is due to natural selection. To address this hypothesis, we assess the differentiation in allele frequencies of trait-associated SNPs among African, Eastern Asian, and European populations for ten complex traits using data of large sample size (up to ~405,000). We show that SNPs associated with height ([Formula: see text]), waist-to-hip ratio ([Formula: see text]), and schizophrenia ([Formula: see text]) are significantly more differentiated among populations than matched "control" SNPs, suggesting that these trait-associated SNPs have undergone natural selection. We further find that SNPs associated with height ([Formula: see text]) and schizophrenia ([Formula: see text]) show significantly higher variance in linkage disequilibrium (LD) scores across populations than control SNPs. Our results support the hypothesis that natural selection has shaped the genetic differentiation of complex traits, such as height and schizophrenia, among worldwide populations.

  11. The Emergence of Physiology and Form: Natural Selection Revisited

    PubMed Central

    Torday, John S.

    2016-01-01

    Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution. PMID:27534726

  12. Biotic and abiotic transformations of methyl tertiary butyl ether (MTBE).

    PubMed

    Fischer, Axel; Oehm, Claudia; Selle, Michael; Werner, Peter

    2005-11-01

    Methyl tertiary butyl ether (MTBE) is a fuel additive which is used all over the world. In recent years it has often been found in groundwater, mainly in the USA, but also in Europe. Although MTBE seems to be a minor toxic, it affects the taste and odour of water at concentrations of < 30 microg/L. Although MTBE is often a recalcitrant compound, it is known that many ethers can be degraded by abiotic means. The aim of this study was to examine biotic and abiotic transformations of MTBE with respect to the particular conditions of a contaminated site (former refinery) in Leuna, Germany. Groundwater samples from wells of a contaminated site were used for aerobic and anaerobic degradation experiments. The abiotic degradation experiment (hydrolysis) was conducted employing an ion-exchange resin and MTBE solutions in distilled water. MTBE, tertiary butyl formate (TBF) and tertiary butyl alcohol (TBA) were measured by a gas chromatograph with flame ionisation detector (FID). Aldehydes and organic acids were respectively analysed by a gas chromatograph with electron capture detector (ECD) and high-performance ion chromatography (HPIC). Under aerobic conditions, MTBE was degraded in laboratory experiments. Only 4 of a total of 30 anaerobic experiments exhibited degradation, and the process was very slow. In no cases were metabolites detected, but a few degradation products (TBF, TBA and formic acid) were found on the site, possibly due to the lower temperatures in groundwater. The abiotic degradation of MTBE with an ion-exchange resin as a catalyst at pH 3.5 was much faster than hydrolysis in diluted hydrochloric acid (pH 1.0). Although the aerobic degradation of MTBE in the environment seems to be possible, the specific conditions responsible are widely unknown. Successful aerobic degradation only seems to take place if there is a lack of other utilisable compounds. However, MTBE is often accompanied by other fuel compounds on contaminated sites and anaerobic conditions

  13. Student concepts of Natural Selection from a resource-based perspective

    NASA Astrophysics Data System (ADS)

    Benjamin, Scott Shawn

    The past two decades have produced a substantial amount of research about the teaching and learning of evolution; however, recent research often lacks a theoretical foundation. Application of a new theoretical framework could help fill the void and improve research about student concepts of evolution. This study seeks to show that a resource-based framework (Hammer et al., 2005) can improve research into student concepts of natural selection. Concepts of natural selection from urban community college students were assessed via qualitative (interviews, written open-response questions, and write/think aloud procedures) and quantitative methods (coded open response analysis, Concept Inventory for Natural Selection (CINS)(Anderson, Fisher, & Norman, 2002). Results showed that students demonstrate four important aspects of resource-based framework: the multi-faceted construction of concepts, context sensitivity/ concept flexibility, at-the-moment activation of resources, and perceptual frames. In open response assessment, evolutionary-gain responses produced significantly different responses than evolutionary-loss questions with: 1) significantly more correct answers for the gain than loss question (Wilcoxon signed rank test, z = -3.68, p=0.0002); 2) more Lamarckian responses to loss than the gain question (Fisher exact, p=0.0039); and significantly different distributions in expanded need vs basic need answers (Fishers exact, p = 0.02). Results from CINS scores showed significant differences in post activity scores between students that held different naive concepts associated with origin of variation, origin of species, differential reproduction, and limited survival suggesting that some naive ideas facilitate learning. Outcomes also suggest that an everyday or self-experience typological perceptual frame is an underlying source of many incorrect ideas about evolution. Interview and write/think aloud assessments propose four process resources applied by students as

  14. Emerging trends in the functional genomics of the abiotic stress response in crop plants.

    PubMed

    Vij, Shubha; Tyagi, Akhilesh K

    2007-05-01

    Plants are exposed to different abiotic stresses, such as water deficit, high temperature, salinity, cold, heavy metals and mechanical wounding, under field conditions. It is estimated that such stress conditions can potentially reduce the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms developed during evolution to mitigate against stress by plants. Before the advent of the genomics era, researchers primarily used a gene-by-gene approach to decipher the function of the genes involved in the abiotic stress response. However, abiotic stress tolerance is a complex trait and, although large numbers of genes have been identified to be involved in the abiotic stress response, there remain large gaps in our understanding of the trait. The availability of the genome sequences of certain important plant species has enabled the use of strategies, such as genome-wide expression profiling, to identify the genes associated with the stress response, followed by the verification of gene function by the analysis of mutants and transgenics. Certain components of both abscisic acid-dependent and -independent cascades involved in the stress response have already been identified. Information originating from the genome-wide analysis of abiotic stress tolerance will help to provide an insight into the stress-responsive network(s), and may allow the modification of this network to reduce the loss caused by stress and to increase agricultural productivity.

  15. A NAP-Family Histone Chaperone Functions in Abiotic Stress Response and Adaptation1[OPEN

    PubMed Central

    Pareek, Ashwani; Singla-Pareek, Sneh Lata

    2016-01-01

    Modulation of gene expression is one of the most significant molecular mechanisms of abiotic stress response in plants. Via altering DNA accessibility, histone chaperones affect the transcriptional competence of genomic loci. However, in contrast to other factors affecting chromatin dynamics, the role of plant histone chaperones in abiotic stress response and adaptation remains elusive. Here, we studied the physiological function of a stress-responsive putative rice (Oryza sativa) histone chaperone of the NAP superfamily: OsNAPL6. We show that OsNAPL6 is a nuclear-localized H3/H4 histone chaperone capable of assembling a nucleosome-like structure. Utilizing overexpression and knockdown approaches, we found a positive correlation between OsNAPL6 expression levels and adaptation to multiple abiotic stresses. Results of comparative transcriptome profiling and promoter-recruitment studies indicate that OsNAPL6 functions during stress response via modulation of expression of various genes involved in diverse functions. For instance, we show that OsNAPL6 is recruited to OsRad51 promoter, activating its expression and leading to more efficient DNA repair and abrogation of programmed cell death under salinity and genotoxic stress conditions. These results suggest that the histone chaperone OsNAPL6 may serve a regulatory role in abiotic stress physiology possibly via modulating nucleosome dynamics at various stress-associated genomic loci. Taken together, our findings establish a hitherto unknown link between histone chaperones and abiotic stress response in plants. PMID:27342307

  16. Using Different Examples of Natural Selection When Teaching Biology.

    ERIC Educational Resources Information Center

    Perry, Robert T.

    1993-01-01

    Describes the following examples of natural selection for use in science instruction: sickle-cell anemia and human beings, clogged crabs, the rounding of the human head, shell color in land snails, pollinator behavior and flower color, copper tolerance in a grass, lizards and quick change, and Darwin's finches. (PR)

  17. The Living Dead: Transformative Experiences in Modelling Natural Selection

    ERIC Educational Resources Information Center

    Petersen, Morten Rask

    2017-01-01

    This study considers how students change their coherent conceptual understanding of natural selection through a hands-on simulation. The results show that most students change their understanding. In addition, some students also underwent a transformative experience and used their new knowledge in a leisure time activity. These transformative…

  18. Abscisic Acid and abiotic stress signaling.

    PubMed

    Tuteja, Narendra

    2007-05-01

    Abiotic stress is severe environmental stress, which impairs crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in responce to changing physiological and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to stress include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression through interacting with their corrosponding cis-acting elements such as DRE/CRT, ABRE and MYCRS/MYBRS, respectively. Understanding these mechanisms is important to improve stress tolerance in crops plants. This article first describes the general pathway for plant stress response followed by roles of ABA and transcription factors in stress tolerance including the regulation of ABA biosynthesis.

  19. Abscisic Acid and Abiotic Stress Signaling

    PubMed Central

    2007-01-01

    Abiotic stress is severe environmental stress, which impairs crop production on irrigated land worldwide. Overall, the susceptibility or tolerance to the stress in plants is a coordinated action of multiple stress responsive genes, which also cross-talk with other components of stress signal transduction pathways. Plant responses to abiotic stress can be determined by the severity of the stress and by the metabolic status of the plant. Abscisic acid (ABA) is a phytohormone critical for plant growth and development and plays an important role in integrating various stress signals and controlling downstream stress responses. Plants have to adjust ABA levels constantly in responce to changing physiological and environmental conditions. To date, the mechanisms for fine-tuning of ABA levels remain elusive. The mechanisms by which plants respond to stress include both ABA-dependent and ABA-independent processes. Various transcription factors such as DREB2A/2B, AREB1, RD22BP1 and MYC/MYB are known to regulate the ABA-responsive gene expression through interacting with their corrosponding cis-acting elements such as DRE/CRT, ABRE and MYCRS/MYBRS, respectively. Understanding these mechanisms is important to improve stress tolerance in crops plants. This article first describes the general pathway for plant stress response followed by roles of ABA and transcription factors in stress tolerance including the regulation of ABA biosynthesis. PMID:19516981

  20. ABIOTIC DEGRADATION OF TRICHLOROETHYLENE UNDER THERMAL REMEDIATION CONDITIONS

    EPA Science Inventory

    The degradation of TCE (C2HCl3) to carbon dioxide (CO2) and chloride (Cl-) has been reported to occur during thermal remediation of subsurface environments. The overall goal of this study was to evaluate abiotic degradation of TCE at el...

  1. Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses.

    PubMed

    Behr, Marc; Legay, Sylvain; Hausman, Jean-Francois; Guerriero, Gea

    2015-07-16

    Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop.

  2. Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses

    PubMed Central

    Behr, Marc; Legay, Sylvain; Hausman, Jean-Francois; Guerriero, Gea

    2015-01-01

    Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop. PMID:26193255

  3. The Neural Dynamics of Attentional Selection in Natural Scenes.

    PubMed

    Kaiser, Daniel; Oosterhof, Nikolaas N; Peelen, Marius V

    2016-10-12

    The human visual system can only represent a small subset of the many objects present in cluttered scenes at any given time, such that objects compete for representation. Despite these processing limitations, the detection of object categories in cluttered natural scenes is remarkably rapid. How does the brain efficiently select goal-relevant objects from cluttered scenes? In the present study, we used multivariate decoding of magneto-encephalography (MEG) data to track the neural representation of within-scene objects as a function of top-down attentional set. Participants detected categorical targets (cars or people) in natural scenes. The presence of these categories within a scene was decoded from MEG sensor patterns by training linear classifiers on differentiating cars and people in isolation and testing these classifiers on scenes containing one of the two categories. The presence of a specific category in a scene could be reliably decoded from MEG response patterns as early as 160 ms, despite substantial scene clutter and variation in the visual appearance of each category. Strikingly, we find that these early categorical representations fully depend on the match between visual input and top-down attentional set: only objects that matched the current attentional set were processed to the category level within the first 200 ms after scene onset. A sensor-space searchlight analysis revealed that this early attention bias was localized to lateral occipitotemporal cortex, reflecting top-down modulation of visual processing. These results show that attention quickly resolves competition between objects in cluttered natural scenes, allowing for the rapid neural representation of goal-relevant objects. Efficient attentional selection is crucial in many everyday situations. For example, when driving a car, we need to quickly detect obstacles, such as pedestrians crossing the street, while ignoring irrelevant objects. How can humans efficiently perform such tasks

  4. Internalization of Escherichia coli O157:H7 gfp+ in rocket and Swiss chard baby leaves as affected by abiotic and biotic damage.

    PubMed

    Hartmann, R; Fricke, A; Stützel, H; Mansourian, S; Dekker, T; Wohanka, W; Alsanius, B

    2017-07-01

    Internalization of human pathogens in edible parts of vegetables eaten raw is a major concern, since once internalized they are protected from sanitizing treatments. In this study, we examined the invasion of gfp-labelled Escherichia coli O157:H7 into intact and biotically (infection with Xanthomonas campestris/Pseudomonas syringae) and abiotically (grating with silicon carbide) damaged leaves of wild rocket (Diplotaxis tenuifolia) and Swiss chard (Beta vulgaris subsp. cicla) using laser scanning confocal microscopy. Bacterial cells were found in internal locations of the tissue, irrespective of tissue health status. Contaminated leaf sections of biotically and abiotically damaged wild rocket leaves showed higher susceptibility to microbial invasion, while the pathogen was internalized in greater numbers into intact Swiss chard leaf sections when abiotically, but not biotically, damaged. The greatest differences were observed between the plant species; after surface sanitization, E. coli O157:H7 was still detected in wild rocket leaves, but not in Swiss chard leaves. Contamination of leafy vegetables with Escherichia coli O157:H7 is a growing problem, as reported outbreaks are increasing. However, establishment of this human pathogen in the phyllosphere is not completely understood. Using laser scanning confocal microscopy, we demonstrated that E. coli O157:H7gfp+ can invade plant tissue of Swiss chard and wild rocket leaves and that the bacterium is more sensitive to surface sanitization of Swiss chard leaves. Damage to leaf tissue promoted leaf invasion, but the nature of the damage (abiotic or biotic) and plant species had an impact. © 2017 The Society for Applied Microbiology.

  5. A Conceptual Characterization of Online Videos Explaining Natural Selection

    ERIC Educational Resources Information Center

    Bohlin, Gustav; Göransson, Andreas; Höst, Gunnar E.; Tibell, Lena A. E.

    2017-01-01

    Educational videos on the Internet comprise a vast and highly diverse source of information. Online search engines facilitate access to numerous videos claiming to explain natural selection, but little is known about the degree to which the video content match key evolutionary content identified as important in evolution education research. In…

  6. Comparison of the Abiotic Preferences of Macroinvertebrates in Tropical River Basins

    PubMed Central

    Everaert, Gert; De Neve, Jan; Boets, Pieter; Dominguez-Granda, Luis; Mereta, Seid Tiku; Ambelu, Argaw; Hoang, Thu Huong; Goethals, Peter L. M.; Thas, Olivier

    2014-01-01

    We assessed and compared abiotic preferences of aquatic macroinvertebrates in three river basins located in Ecuador, Ethiopia and Vietnam. Upon using logistic regression models we analyzed the relationship between the probability of occurrence of five macroinvertebrate families, ranging from pollution tolerant to pollution sensitive, (Chironomidae, Baetidae, Hydroptilidae, Libellulidae and Leptophlebiidae) and physical-chemical water quality conditions. Within the investigated physical-chemical ranges, nine out of twenty-five interaction effects were significant. Our analyses suggested river basin dependent associations between the macroinvertebrate families and the corresponding physical-chemical conditions. It was found that pollution tolerant families showed no clear abiotic preference and occurred at most sampling locations, i.e. Chironomidae were present in 91%, 84% and 93% of the samples taken in Ecuador, Ethiopia and Vietnam. Pollution sensitive families were strongly associated with dissolved oxygen and stream velocity, e.g. Leptophlebiidae were only present in 48%, 2% and 18% of the samples in Ecuador, Ethiopia and Vietnam. Despite some limitations in the study design, we concluded that associations between macroinvertebrates and abiotic conditions can be river basin-specific and hence are not automatically transferable across river basins in the tropics. PMID:25279673

  7. A Central Role for Thiols in Plant Tolerance to Abiotic Stress

    PubMed Central

    Zagorchev, Lyuben; Seal, Charlotte E.; Kranner, Ilse; Odjakova, Mariela

    2013-01-01

    Abiotic stress poses major problems to agriculture and increasing efforts are being made to understand plant stress response and tolerance mechanisms and to develop new tools that underpin successful agriculture. However, the molecular mechanisms of plant stress tolerance are not fully understood, and the data available is incomplete and sometimes contradictory. Here, we review the significance of protein and non-protein thiol compounds in relation to plant tolerance of abiotic stress. First, the roles of the amino acids cysteine and methionine, are discussed, followed by an extensive discussion of the low-molecular-weight tripeptide, thiol glutathione, which plays a central part in plant stress response and oxidative signalling and of glutathione-related enzymes, including those involved in the biosynthesis of non-protein thiol compounds. Special attention is given to the glutathione redox state, to phytochelatins and to the role of glutathione in the regulation of the cell cycle. The protein thiol section focuses on glutaredoxins and thioredoxins, proteins with oxidoreductase activity, which are involved in protein glutathionylation. The review concludes with a brief overview of and future perspectives for the involvement of plant thiols in abiotic stress tolerance. PMID:23549272

  8. Comparison of the abiotic preferences of macroinvertebrates in tropical river basins.

    PubMed

    Everaert, Gert; De Neve, Jan; Boets, Pieter; Dominguez-Granda, Luis; Mereta, Seid Tiku; Ambelu, Argaw; Hoang, Thu Huong; Goethals, Peter L M; Thas, Olivier

    2014-01-01

    We assessed and compared abiotic preferences of aquatic macroinvertebrates in three river basins located in Ecuador, Ethiopia and Vietnam. Upon using logistic regression models we analyzed the relationship between the probability of occurrence of five macroinvertebrate families, ranging from pollution tolerant to pollution sensitive, (Chironomidae, Baetidae, Hydroptilidae, Libellulidae and Leptophlebiidae) and physical-chemical water quality conditions. Within the investigated physical-chemical ranges, nine out of twenty-five interaction effects were significant. Our analyses suggested river basin dependent associations between the macroinvertebrate families and the corresponding physical-chemical conditions. It was found that pollution tolerant families showed no clear abiotic preference and occurred at most sampling locations, i.e. Chironomidae were present in 91%, 84% and 93% of the samples taken in Ecuador, Ethiopia and Vietnam. Pollution sensitive families were strongly associated with dissolved oxygen and stream velocity, e.g. Leptophlebiidae were only present in 48%, 2% and 18% of the samples in Ecuador, Ethiopia and Vietnam. Despite some limitations in the study design, we concluded that associations between macroinvertebrates and abiotic conditions can be river basin-specific and hence are not automatically transferable across river basins in the tropics.

  9. Comparative study of biogenic and abiotic iron-containing materials

    NASA Astrophysics Data System (ADS)

    Cherkezova-Zheleva, Z.; Shopska, M.; Paneva, D.; Kovacheva, D.; Kadinov, G.; Mitov, I.

    2016-12-01

    Series of iron-based biogenic materials prepared by cultivation of Leptothrix group of bacteria in different feeding media ( Sphaerotilus-Leptothrix group of bacteria isolation medium, Adler, Lieske and silicon-iron-glucose-peptone) were studied. Control samples were obtained in the same conditions and procedures but the nutrition media were not infected with bacteria, i.e. they were sterile. Room and low temperature Mössbauer spectroscopy, powder X-ray diffraction (XRD), and infrared spectroscopy (IRS) were used to reveal the composition and physicochemical properties of biomass and respective control samples. Comparative analysis showed differences in their composition and dispersity of present phases. Sample composition included different ratio of nanodimensional iron oxyhydroxide and oxide phases. Relaxation phenomena such as superparamagnetism or collective magnetic excitation behaviour were registered for some of them. The experimental data showed that the biogenic materials were enriched in oxyhydroxides of high dispersion. Catalytic behaviour of a selected biomass and abiotic material were studied in the reaction of CO oxidation. In situ diffuse-reflectance (DR) IRS was used to monitor the phase transformations in the biomass and CO conversion.

  10. Changes in abiotic influences on seed plants and ferns during 18 years of primary succession on Puerto Rican landslides

    Treesearch

    Lawrence R. Walker; Aaron B. Shiels; Peter J. Bellingham; Ashley D. Sparrow; Ned Fetcher; Fred H. Landau; Deborah J. Lodge

    2013-01-01

    Abiotic variables are critical drivers of succession in most primary seres, but how their influence on biota changes over time is rarely examined. Landslides provide good model systems for examining abiotic influences because they are spatially and temporally heterogeneous habitats with distinct abiotic and biotic gradients and post-landslide erosion. In an 18-year...

  11. Transcriptomic Profiling of the Maize (Zea mays L.) Leaf Response to Abiotic Stresses at the Seedling Stage.

    PubMed

    Li, Pengcheng; Cao, Wei; Fang, Huimin; Xu, Shuhui; Yin, Shuangyi; Zhang, Yingying; Lin, Dezhou; Wang, Jianan; Chen, Yufei; Xu, Chenwu; Yang, Zefeng

    2017-01-01

    Abiotic stresses, including drought, salinity, heat, and cold, negatively affect maize ( Zea mays L.) development and productivity. To elucidate the molecular mechanisms of resistance to abiotic stresses in maize, RNA-seq was used for global transcriptome profiling of B73 seedling leaves exposed to drought, salinity, heat, and cold stress. A total of 5,330 differentially expressed genes (DEGs) were detected in differential comparisons between the control and each stressed sample, with 1,661, 2,019, 2,346, and 1,841 DEGs being identified in comparisons of the control with salinity, drought, heat, and cold stress, respectively. Functional annotations of DEGs suggested that the stress response was mediated by pathways involving hormone metabolism and signaling, transcription factors (TFs), very-long-chain fatty acid biosynthesis and lipid signaling, among others. Of the obtained DEGs (5,330), 167 genes are common to these four abiotic stresses, including 10 up-regulated TFs (five ERFs, two NACs, one ARF, one MYB, and one HD-ZIP) and two down-regulated TFs (one b-ZIP and one MYB-related), which suggested that common mechanisms may be initiated in response to different abiotic stresses in maize. This study contributes to a better understanding of the molecular mechanisms of maize leaf responses to abiotic stresses and could be useful for developing maize cultivars resistant to abiotic stresses.

  12. Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

    PubMed

    Colautti, Robert I; Lau, Jennifer A

    2015-05-01

    Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

  13. Naturally seeded versus planted ponderosa pine seedlings in group-selection openings

    Treesearch

    Philip M. McDonald; Gary Fiddler; Martin Ritchie; Paula Anderson

    2009-01-01

    The purpose of this article was to determine whether natural regeneration or planted seedlings should be used in group-selection openings. The answer dependson the survival and growth rate of both types of seedlings, and that could depend on the size of the openings and the effect of trees on their edge. In thisside-by-side study, the natural pine seedlings originated...

  14. Modeling Natural Selection

    ERIC Educational Resources Information Center

    Bogiages, Christopher A.; Lotter, Christine

    2011-01-01

    In their research, scientists generate, test, and modify scientific models. These models can be shared with others and demonstrate a scientist's understanding of how the natural world works. Similarly, students can generate and modify models to gain a better understanding of the content, process, and nature of science (Kenyon, Schwarz, and Hug…

  15. Short-term alteration of biotic and abiotic components of the pelagic system in a shallow bay produced by a strong natural hypoxia event.

    PubMed

    Hernández-Miranda, Eduardo; Veas, Rodrigo; Anabalón, Valeria; Quiñones, Renato A

    2017-01-01

    In January 2008 there was an intensive and extensive upwelling event in the southern Humboldt Current System. This event produced an intrusion of water with low dissolved oxygen into Coliumo Bay, which caused massive mortality and the beaching of pelagic and benthic organisms, including zooplankton. During this event, which lasted 3 to 5 days, we studied and evaluated the effect of the hypoxic water in the bay on the abundance of macrozooplankton, nanoplankton and microphytoplankton, the concentration of several nutrients and hydrographic conditions. At the beginning of the hypoxia event the water column had very low dissolved oxygen concentrations (<0.5 mL O2 L-1), low temperatures and high salinity which are characteristics of the oxygen minimum zone from the Humboldt Current System. Redox, pH, nitrate, phosphate, silicate and chlorophyll-a values were the lowest, while nitrate and the phaeopigment values were the highest. The N:P ratio was below 16, and the abundance of nano- and microphytoplankton were at their lowest, the latter also with the lowest proportion of live organisms. Macrozooplankton had the greatest abundance during hypoxia, dominated mainly by crustacean, fish eggs and amphipods. The hypoxia event generated a strong short-term alteration of all biotic and abiotic components of the pelagic system in Coliumo Bay and the neighboring coastal zone. These negative effects associated with strong natural hypoxia events could have important consequences for the productivity and ecosystem functioning of the coastal zone of the Humboldt Current System if, as suggested by several models, winds favorable to upwelling should increase due to climate change. The effects of natural hypoxia in this coastal zone can be dramatic especially for pelagic and benthic species not adapted to endure conditions of low dissolved oxygen.

  16. Short-term alteration of biotic and abiotic components of the pelagic system in a shallow bay produced by a strong natural hypoxia event

    PubMed Central

    Veas, Rodrigo; Anabalón, Valeria; Quiñones, Renato A.

    2017-01-01

    In January 2008 there was an intensive and extensive upwelling event in the southern Humboldt Current System. This event produced an intrusion of water with low dissolved oxygen into Coliumo Bay, which caused massive mortality and the beaching of pelagic and benthic organisms, including zooplankton. During this event, which lasted 3 to 5 days, we studied and evaluated the effect of the hypoxic water in the bay on the abundance of macrozooplankton, nanoplankton and microphytoplankton, the concentration of several nutrients and hydrographic conditions. At the beginning of the hypoxia event the water column had very low dissolved oxygen concentrations (<0.5 mL O2 L-1), low temperatures and high salinity which are characteristics of the oxygen minimum zone from the Humboldt Current System. Redox, pH, nitrate, phosphate, silicate and chlorophyll-a values were the lowest, while nitrate and the phaeopigment values were the highest. The N:P ratio was below 16, and the abundance of nano- and microphytoplankton were at their lowest, the latter also with the lowest proportion of live organisms. Macrozooplankton had the greatest abundance during hypoxia, dominated mainly by crustacean, fish eggs and amphipods. The hypoxia event generated a strong short-term alteration of all biotic and abiotic components of the pelagic system in Coliumo Bay and the neighboring coastal zone. These negative effects associated with strong natural hypoxia events could have important consequences for the productivity and ecosystem functioning of the coastal zone of the Humboldt Current System if, as suggested by several models, winds favorable to upwelling should increase due to climate change. The effects of natural hypoxia in this coastal zone can be dramatic especially for pelagic and benthic species not adapted to endure conditions of low dissolved oxygen. PMID:28715447

  17. Natural selection and the evolution of reproductive effort.

    PubMed

    Hirshfield, M F; Tinkle, D W

    1975-06-01

    Reproductive effort is defined as that proportion of the total energy budget of an organism that is devoted to reproductive processes. Reproductive effort at a given age within a species will be selected to maximize reproductive value at that age. Reproductive effort is not directly affected by changes in juvenile survivorship, nor necessarily reduced by an increase in adult survivorship. Selection for high levels of reproductive effort should occur when extrinsic adult mortality is high, in environments with constant juvenile survivorship, and in good years for juvenile survivorship in a variable environment, provided that the quality of the year is predictable by adults. Data necessary to measure reproductive effort and to understand how selection results in different levels of effort between individuals and species are discussed. We make several predictions about the effect of increased resource availability on reproductive effort. The empirical bases for testing these predictions are presently inadequate, and we consider data on energy budgets of organisms in nature to be essential for such test. We also conclude that variance in life table parameters must be known in detail to understand the selective bases of levels of reproductive effort.

  18. Selecting and applying indicators of ecosystem collapse for risk assessments.

    PubMed

    Rowland, Jessica A; Nicholson, Emily; Murray, Nicholas J; Keith, David A; Lester, Rebecca E; Bland, Lucie M

    2018-03-12

    Ongoing ecosystem degradation and transformation are key threats to biodiversity. Measuring ecosystem change towards collapse relies on monitoring indicators that quantify key ecological processes. Yet little guidance is available on selecting and implementing indicators for ecosystem risk assessment. Here, we reviewed indicator use in ecological studies of decline towards collapse in marine pelagic and temperate forest ecosystems. We evaluated the use of indicator selection methods, indicator types (geographic distribution, abiotic, biotic), methods of assessing multiple indicators, and temporal quality of time series. We compared these ecological studies to risk assessments in the International Union for the Conservation of Nature Red List of Ecosystems (RLE), where indicators are used to estimate ecosystem collapse risk. We found that ecological studies and RLE assessments rarely reported how indicators were selected, particularly in terrestrial ecosystems. Few ecological studies and RLE assessments quantified ecosystem change with all three indicator types, and indicators types used varied between marine and terrestrial ecosystem. Several studies used indices or multivariate analyses to assess multiple indicators simultaneously, but RLE assessments did not, as RLE guidelines advise against them. Most studies and RLE assessments used time series spanning at least 30 years, increasing the chance of reliably detecting change. Limited use of indicator selection protocols and infrequent use of all three indicator types may hamper the ability to accurately detect changes. To improve the value of risk assessments for informing policy and management, we recommend using: (i) explicit protocols, including conceptual models, to identify and select indicators; (ii) a range of indicators spanning distributional, abiotic and biotic features; (iii) indices and multivariate analyses with extreme care until guidelines are developed; (iv) time series with sufficient data to

  19. Substitution rate and natural selection in parvovirus B19

    PubMed Central

    Stamenković, Gorana G.; Ćirković, Valentina S.; Šiljić, Marina M.; Blagojević, Jelena V.; Knežević, Aleksandra M.; Joksić, Ivana D.; Stanojević, Maja P.

    2016-01-01

    The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open reading frames ORF1 and ORF2, respectively, collected 1973–2012 and including 9 newly sequenced isolates from Serbia. Phylogenetic clustering assigned majority of studied isolates to G1A. Nucleotide substitution rate for total coding DNA was 1.03 (0.6–1.27) x 10−4 substitutions/site/year, with higher values for analyzed genome partitions. In spite of the highest evolutionary rate, VP2 codons were found to be under purifying selection with rare episodic positive selection, whereas codons under diversifying selection were found in the unique part of VP1, known to contain B19 immune epitopes important in persistent infection. Analyses of overlapping gene regions identified nucleotide positions under opposite selective pressure in different ORFs, suggesting complex evolutionary mechanisms of nucleotide changes in B19 viral genomes. PMID:27775080

  20. From Ends to Causes (and Back Again) by Metaphor: The Paradox of Natural Selection

    NASA Astrophysics Data System (ADS)

    Blancke, Stefaan; Schellens, Tammy; Soetaert, Ronald; Van Keer, Hilde; Braeckman, Johan

    2014-04-01

    Natural selection is one of the most famous metaphors in the history of science. Charles Darwin used the metaphor and the underlying analogy to frame his ideas about evolution and its main driving mechanism into a full-fledged theory. Because the metaphor turned out to be such a powerful epistemic tool, Darwin naturally assumed that he could also employ it as an educational tool to inform his contemporaries about his findings. Moreover, by using the metaphor Darwin was able to bring his theory in accordance with both the dominant philosophy of science in his time and the respected tradition of natural theology. However, as he introduced his theory of evolution by natural selection in On the origin of species in 1859, the metaphor also turned out to have a serious downside. Because of its intentional overtones, his contemporaries systematically misunderstood his metaphor not as a natural mechanism causing evolution to occur but as an agent who works towards particular ends. The difference in success between natural selection as an epistemic tool and its failure as an educational tool is labelled as a paradox. We explain the paradox from a cognitive perspective and discuss the implications for teaching evolution.

  1. The paradoxical advantages and disadvantages of natural selection: the case history of Charles Darwin.

    PubMed

    Lieb, J

    2007-01-01

    The biology of natural selection is an enduring mystery, as is the nature of Charles Darwin's chronic illness. Of the theories advanced to explain the latter, Oedipal conflicts and Chagas' disease are preeminent. Hypomania, however, propelled Darwin to the pinnacle of scientific achievement and good health, the depression that followed condemning him to intellectual stagnation, lethargy, impaired memory and concentration, and incapacitating gastrointestinal disorders. Examples of natural selection in humans are much sought after when, ironically, one need look no further than Darwin himself.

  2. Resistance Responses of Potato to Vesicular-Arbuscular Mycorrhizal Fungi under Varying Abiotic Phosphorus Levels.

    PubMed

    McArthur, D A; Knowles, N R

    1992-09-01

    In mycorrhizal symbioses, susceptibility of a host plant to infection by fungi is influenced by environmental factors, especially the availability of soil phosphorus. This study describes morphological and biochemical details of interactions between a vesicular-arbuscular mycorrhizal (VAM) fungus and potato (Solanum tuberosum L. cv Russet Burbank) plants, with a particular focus on the physiological basis for P-induced resistance of roots to infection. Root infection by the VAM fungus Glomus fasciculatum ([Thaxt. sensu Gerdemann] Gerdemann and Trappe) was extensive for plants grown with low abiotic P supply, and plant biomass accumulation was enhanced by the symbiosis. The capacity of excised roots from P-deficient plants to produce ethylene in the presence or absence of exogenous 1-amino cyclopropane-1-carboxylic acid (ACC) was markedly reduced by VAM infection. This apparent inhibition of ACC oxidase (ACC(ox)) activity was localized to areas containing infected roots, as demonstrated in split-root studies. Furthermore, leachate from VAM roots contained a potent water-soluble inhibitor of ethylene generation from exogenous ACC by nonmycorrhizal (NM) roots. The leachate from VAM-infected roots had a higher concentration of phenolics, relative to that from NM roots. Moreover, the rates of ethylene formation and phenolic concentration in leachates from VAM roots were inversely correlated, suggesting that this inhibitor may be of a phenolic nature. The specific activity of extracellular peroxidase recovered in root leachates was not stimulated by VAM infection, although activity on a fresh weight basis was significantly enhanced, reflecting the fact that VAM roots had higher protein content than NM roots. Polyphenol oxidase activity of roots did not differ between NM and VAM roots. These results characterize the low resistance response of P-deficient plants to VAM infection. When plants were grown with higher abiotic P supply, the relative benefit of the VAM symbiosis

  3. Unweaving misconceptions: Guided learning, simulations, and misconceptions in learning principles of natural selection

    NASA Astrophysics Data System (ADS)

    Weeks, Brian E.

    College students often come to the study of evolutionary biology with many misconceptions of how the processes of natural selection and speciation occur. How to relinquish these misconceptions with learners is a question that many educators face in introductory biology courses. Constructivism as a theoretical framework has become an accepted and promoted model within the epistemology of science instruction. However, constructivism is not without its skeptics who see some problems of its application in lacking necessary guidance for novice learners. This study within a quantitative, quasi-experimental format tested whether guided online instruction in a video format of common misconceptions in evolutionary biology produced higher performance on a survey of knowledge of natural selection versus more constructivist style learning in the form of student exploration of computer simulations of the evolutionary process. Performances on surveys were also explored for a combination of constructivist and guided techniques to determine if a consolidation of approaches produced higher test scores. Out of the 94 participants 95% displayed at least one misconception of natural selection in the pre-test while the study treatments produced no statistically significant improvements in post-test scores except within the video (guided learning treatment). These overall results demonstrated the stubbornness of misconceptions involving natural selection for adult learners and the difficulty of helping them overcome them. It also bolsters the idea that some misconceptions of natural selection and evolution may be hardwired in a neurological sense and that new, more long-term teaching techniques may be warranted. Such long-term strategies may not be best implemented with constructivist techniques alone, and it is likely that some level of guidance may be necessary for novice adult learners. A more substantial, nuanced approach for undergraduates is needed that consolidates successful

  4. Are karrikins involved in plant abiotic stress responses?

    PubMed

    Li, Weiqiang; Tran, Lam-Son Phan

    2015-09-01

    Recent reports have shown that strigolactones play a positive role in plant responses to drought and salt stress through MAX2 (More Axillary Growth 2). Increasing evidence suggests that MAX2 is also involved in karrikin signaling, raising the question whether karrikins play any role in plant adaptation to abiotic stresses. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli

    PubMed Central

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1α and TUB were the most stable genes for abiotic stresses, whereas EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley. PMID:27746803

  6. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli.

    PubMed

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley ( GAPDH, ACTIN, eIF-4 α, SAND, UBC, TIP41, EF-1 α, and TUB ) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1 α and TUB were the most stable genes for abiotic stresses, whereas EF-1 α, GAPDH , and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1 α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley.

  7. Selection criteria for forested natural areas in New England, USA

    Treesearch

    William B. Leak; Mariko Yamasaki; Marie-Louise Smith; David T. Funk

    1994-01-01

    The selection of forested natural areas for research and educational purposes is discussed. Five factors are important: sufficient size; representation of typical communities and sites; documented disturbance histories; acceptable current condition in terms of age, tree size, and successional stage; and administrative feasibility.

  8. Methane clumped isotopes in the Songliao Basin (China): New insights into abiotic vs. biotic hydrocarbon formation

    NASA Astrophysics Data System (ADS)

    Shuai, Yanhua; Etiope, Giuseppe; Zhang, Shuichang; Douglas, Peter M. J.; Huang, Ling; Eiler, John M.

    2018-01-01

    Abiotic hydrocarbon gas, typically generated in serpentinized ultramafic rocks and crystalline shields, has important implications for the deep biosphere, petroleum systems, the carbon cycle and astrobiology. Distinguishing abiotic gas (produced by chemical reactions like Sabatier synthesis) from biotic gas (produced from degradation of organic matter or microbial activity) is sometimes challenging because their isotopic and molecular composition may overlap. Abiotic gas has been recognized in numerous locations on the Earth, although there are no confirmed instances where it is the dominant source of commercially valuable quantities in reservoir rocks. The deep hydrocarbon reservoirs of the Xujiaweizi Depression in the Songliao Basin (China) have been considered to host significant amounts of abiotic methane. Here we report methane clumped-isotope values (Δ18) and the isotopic composition of C1-C3 alkanes, CO2 and helium of five gas samples collected from those Xujiaweizi deep reservoirs. Some geochemical features of these samples resemble previously suggested identifiers of abiotic gas (13C-enriched CH4; decrease in 13C/12C ratio with increasing carbon number for the C1-C4 alkanes; abundant, apparently non-biogenic CO2; and mantle-derived helium). However, combining these constraints with new measurements of the clumped-isotope composition of methane and careful consideration of the geological context, suggests that the Xujiaweizi depression gas is dominantly, if not exclusively, thermogenic and derived from over-mature source rocks, i.e., from catagenesis of buried organic matter at high temperatures. Methane formation temperatures suggested by clumped-isotopes (167-213 °C) are lower than magmatic gas generation processes and consistent with the maturity of local source rocks. Also, there are no geological conditions (e.g., serpentinized ultramafic rocks) that may lead to high production of H2 and thus abiotic production of CH4 via CO2 reduction. We propose

  9. Abiotic uptake of gases by organic soils

    NASA Astrophysics Data System (ADS)

    Smagin, A. V.

    2007-12-01

    Methodological and experimental studies of the abiotic uptake of gaseous substances by organic soils were performed. The static adsorption method of closed vessels for assessing the interaction of gases with the solid and liquid soil phases and the dynamic method of determining the sorption isotherms of gases by soils were analyzed. The theoretical substantiation of the methods and their practical implementations on the basis of a PGA-7 portable gas analyzer (Russia) were considered. Good agreement between the equilibrium sorption isotherms of the gases and the Langmuir model was revealed; for the real ranges of natural gas concentrations, this model can be reduced to the linear Henry equation. The limit values of the gas sorption (Langmuir monolayer capacity) are typical for dry samples; they vary from 670 4000 g/m3 for methane and oxygen to 20 000 25 000 g/m3 for carbon dioxide. The linear distribution coefficients of gases between the solid and gas phases of organic soils (Henry constants) are 8 18 units for poorly sorbed gases (O2, CH4) and 40 60 units for CO2. The kinetics of the chemicophysical uptake of gases by the soil studied is linear in character and obeys the relaxation kinetic model of the first order with the corresponding relaxation constants, which vary from 1 h -1 in wet samples to 10 h -1 in dry samples.

  10. The Effects of Abiotic Factors on Induced Volatile Emissions in Corn Plants1

    PubMed Central

    Gouinguené, Sandrine P.; Turlings, Ted C.J.

    2002-01-01

    Many plants respond to herbivory by releasing a specific blend of volatiles that is attractive to natural enemies of the herbivores. In corn (Zea mays), this induced odor blend is mainly composed of terpenoids and indole. The induced signal varies with plant species and genotype, but little is known about the variation due to abiotic factors. Here, we tested the effect of soil humidity, air humidity, temperature, light, and fertilization rate on the emission of induced volatiles in young corn plants. Each factor was tested separately under constant conditions for the other factors. Plants released more when standing in dry soil than in wet soil, whereas for air humidity, the optimal release was found at around 60% relative humidity. Temperatures between 22°C and 27°C led to a higher emission than lower or higher temperatures. Light intensity had a dramatic effect. The emission of volatiles did not occur in the dark and increased steadily with an increase in the light intensity. An experiment with an unnatural light-dark cycle showed that the release was fully photophase dependent. Fertilization also had a strong positive effect; the emission of volatiles was minimal when plants were grown under low nutrition, even when results were corrected for plant biomass. Changes in all abiotic factors caused small but significant changes in the relative ratios among the different compounds (quality) in the induced odor blends, except for air humidity. Hence, climatic conditions and nutrient availability can be important factors in determining the intensity and variability in the release of induced plant volatiles. PMID:12114583

  11. Abiotic synthesis of organic compounds from carbon disulfide under hydrothermal conditions.

    PubMed

    Rushdi, Ahmed I; Simoneit, Bernd R T

    2005-12-01

    Abiotic formation of organic compounds under hydrothermal conditions is of interest to bio, geo-, and cosmochemists. Oceanic sulfur-rich hydrothermal systems have been proposed as settings for the abiotic synthesis of organic compounds. Carbon disulfide is a common component of magmatic and hot spring gases, and is present in marine and terrestrial hydrothermal systems. Thus, its reactivity should be considered as another carbon source in addition to carbon dioxide in reductive aqueous thermosynthesis. We have examined the formation of organic compounds in aqueous solutions of carbon disulfide and oxalic acid at 175 degrees C for 5 and 72 h. The synthesis products from carbon disulfide in acidic aqueous solutions yielded a series of organic sulfur compounds. The major compounds after 5 h of reaction included dimethyl polysulfides (54.5%), methyl perthioacetate (27.6%), dimethyl trithiocarbonate (6.8%), trithianes (2.7%), hexathiepane (1.4%), trithiolanes (0.8%), and trithiacycloheptanes (0.3%). The main compounds after 72 h of reaction consisted of trithiacycloheptanes (39.4%), pentathiepane (11.6%), tetrathiocyclooctanes (11.5%), trithiolanes (10.6%), tetrathianes (4.4%), trithianes (1.2%), dimethyl trisulfide (1.1%), and numerous minor compounds. It is concluded that the abiotic formation of aliphatic straight-chain and cyclic polysulfides is possible under hydrothermal conditions and warrants further studies.

  12. When Bad Guys Become Good Ones: The Key Role of Reactive Oxygen Species and Nitric Oxide in the Plant Responses to Abiotic Stress

    PubMed Central

    Farnese, Fernanda S.; Menezes-Silva, Paulo E.; Gusman, Grasielle S.; Oliveira, Juraci A.

    2016-01-01

    The natural environment of plants is composed of a complex set of abiotic stresses and their ability to respond to these stresses is highly flexible and finely balanced through the interaction between signaling molecules. In this review, we highlight the integrated action between reactive oxygen species (ROS) and reactive nitrogen species (RNS), particularly nitric oxide (NO), involved in the acclimation to different abiotic stresses. Under stressful conditions, the biosynthesis transport and the metabolism of ROS and NO influence plant response mechanisms. The enzymes involved in ROS and NO synthesis and scavenging can be found in different cells compartments and their temporal and spatial locations are determinant for signaling mechanisms. Both ROS and NO are involved in long distances signaling (ROS wave and GSNO transport), promoting an acquired systemic acclimation to abiotic stresses. The mechanisms of abiotic stresses response triggered by ROS and NO involve some general steps, as the enhancement of antioxidant systems, but also stress-specific mechanisms, according to the stress type (drought, hypoxia, heavy metals, etc.), and demand the interaction with other signaling molecules, such as MAPK, plant hormones, and calcium. The transduction of ROS and NO bioactivity involves post-translational modifications of proteins, particularly S-glutathionylation for ROS, and S-nitrosylation for NO. These changes may alter the activity, stability, and interaction with other molecules or subcellular location of proteins, changing the entire cell dynamics and contributing to the maintenance of homeostasis. However, despite the recent advances about the roles of ROS and NO in signaling cascades, many challenges remain, and future studies focusing on the signaling of these molecules in planta are still necessary. PMID:27148300

  13. When Bad Guys Become Good Ones: The Key Role of Reactive Oxygen Species and Nitric Oxide in the Plant Responses to Abiotic Stress.

    PubMed

    Farnese, Fernanda S; Menezes-Silva, Paulo E; Gusman, Grasielle S; Oliveira, Juraci A

    2016-01-01

    The natural environment of plants is composed of a complex set of abiotic stresses and their ability to respond to these stresses is highly flexible and finely balanced through the interaction between signaling molecules. In this review, we highlight the integrated action between reactive oxygen species (ROS) and reactive nitrogen species (RNS), particularly nitric oxide (NO), involved in the acclimation to different abiotic stresses. Under stressful conditions, the biosynthesis transport and the metabolism of ROS and NO influence plant response mechanisms. The enzymes involved in ROS and NO synthesis and scavenging can be found in different cells compartments and their temporal and spatial locations are determinant for signaling mechanisms. Both ROS and NO are involved in long distances signaling (ROS wave and GSNO transport), promoting an acquired systemic acclimation to abiotic stresses. The mechanisms of abiotic stresses response triggered by ROS and NO involve some general steps, as the enhancement of antioxidant systems, but also stress-specific mechanisms, according to the stress type (drought, hypoxia, heavy metals, etc.), and demand the interaction with other signaling molecules, such as MAPK, plant hormones, and calcium. The transduction of ROS and NO bioactivity involves post-translational modifications of proteins, particularly S-glutathionylation for ROS, and S-nitrosylation for NO. These changes may alter the activity, stability, and interaction with other molecules or subcellular location of proteins, changing the entire cell dynamics and contributing to the maintenance of homeostasis. However, despite the recent advances about the roles of ROS and NO in signaling cascades, many challenges remain, and future studies focusing on the signaling of these molecules in planta are still necessary.

  14. Gis-Based Site Selection for Underground Natural Resources Using Fuzzy Ahp-Owa

    NASA Astrophysics Data System (ADS)

    Sabzevari, A. R.; Delavar, M. R.

    2017-09-01

    Fuel consumption has significantly increased due to the growth of the population. A solution to address this problem is the underground storage of natural gas. The first step to reach this goal is to select suitable places for the storage. In this study, site selection for the underground natural gas reservoirs has been performed using a multi-criteria decision-making in a GIS environment. The "Ordered Weighted Average" (OWA) operator is one of the multi-criteria decision-making methods for ranking the criteria and consideration of uncertainty in the interaction among the criteria. In this paper, Fuzzy AHP_OWA (FAHP_OWA) is used to determine optimal sites for the underground natural gas reservoirs. Fuzzy AHP_OWA considers the decision maker's risk taking and risk aversion during the decision-making process. Gas consumption rate, temperature, distance from main transportation network, distance from gas production centers, population density and distance from gas distribution networks are the criteria used in this research. Results show that the northeast and west of Iran and the areas around Tehran (Tehran and Alborz Provinces) have a higher attraction for constructing a natural gas reservoir. The performance of the used method was also evaluated. This evaluation was performed using the location of the existing natural gas reservoirs in the country and the site selection maps for each of the quantifiers. It is verified that the method used in this study is capable of modeling different decision-making strategies used by the decision maker with about 88 percent of agreement between the modeling and test data.

  15. Using abiotic variables to predict importance of sites for species representation.

    PubMed

    Albuquerque, Fabio; Beier, Paul

    2015-10-01

    In systematic conservation planning, species distribution data for all sites in a planning area are used to prioritize each site in terms of the site's importance toward meeting the goal of species representation. But comprehensive species data are not available in most planning areas and would be expensive to acquire. As a shortcut, ecologists use surrogates, such as occurrences of birds or another well-surveyed taxon, or land types defined from remotely sensed data, in the hope that sites that represent the surrogates also represent biodiversity. Unfortunately, surrogates have not performed reliably. We propose a new type of surrogate, predicted importance, that can be developed from species data for a q% subset of sites. With species data from this subset of sites, importance can be modeled as a function of abiotic variables available at no charge for all terrestrial areas on Earth. Predicted importance can then be used as a surrogate to prioritize all sites. We tested this surrogate with 8 sets of species data. For each data set, we used a q% subset of sites to model importance as a function of abiotic variables, used the resulting function to predict importance for all sites, and evaluated the number of species in the sites with highest predicted importance. Sites with the highest predicted importance represented species efficiently for all data sets when q = 25% and for 7 of 8 data sets when q = 20%. Predicted importance requires less survey effort than direct selection for species representation and meets representation goals well compared with other surrogates currently in use. This less expensive surrogate may be useful in those areas of the world that need it most, namely tropical regions with the highest biodiversity, greatest biodiversity loss, most severe lack of inventory data, and poorly developed protected area networks. © 2015 Society for Conservation Biology.

  16. BIOTIC AND ABIOTIC CONTRIBUTIONS TO REDUCTIVE TRANSFORMATION OF ORGANIC POLLUTANTS

    EPA Science Inventory

    The relative contributions of biotic and abiotic reductive transformation reactions were probed in two anoxic freshwater sediments by following the transformation of nitrobenzene, and 2,4 dichlorophenol (compounds with different one electron reduction potentials). The sediments d...

  17. Valine-glutamine (VQ) motif coding genes are ancient and non-plant-specific with comprehensive expression regulation by various biotic and abiotic stresses.

    PubMed

    Jiang, Shu-Ye; Sevugan, Mayalagu; Ramachandran, Srinivasan

    2018-05-09

    Valine-glutamine (VQ) motif containing proteins play important roles in abiotic and biotic stress responses in plants. However, little is known about the origin and evolution as well as comprehensive expression regulation of the VQ gene family. In this study, we systematically surveyed this gene family in 50 plant genomes from algae, moss, gymnosperm and angiosperm and explored their presence in other species from animals, bacteria, fungi and viruses. No VQs were detected in all tested algae genomes and all genomes from moss, gymnosperm and angiosperm encode varying numbers of VQs. Interestingly, some of fungi, lower animals and bacteria also encode single to a few VQs. Thus, they are not plant-specific and should be regarded as an ancient family. Their family expansion was mainly due to segmental duplication followed by tandem duplication and mobile elements. Limited contribution of gene conversion was detected to the family evolution. Generally, VQs were very much conserved in their motif coding region and were under purifying selection. However, positive selection was also observed during species divergence. Many VQs were up- or down-regulated by various abiotic / biotic stresses and phytohormones in rice and Arabidopsis. They were also co-expressed with some of other stress-related genes. All of the expression data suggest a comprehensive expression regulation of the VQ gene family. We provide new insights into gene expansion, divergence, evolution and their expression regulation of this VQ family. VQs were detectable not only in plants but also in some of fungi, lower animals and bacteria, suggesting the evolutionary conservation and the ancient origin. Overall, VQs are non-plant-specific and play roles in abiotic / biotic responses or other biological processes through comprehensive expression regulation.

  18. Soil heterogeneity in Mojave Desert shrublands: Biotic and abiotic processes

    NASA Astrophysics Data System (ADS)

    Caldwell, Todd G.; Young, Michael H.; McDonald, Eric V.; Zhu, Jianting

    2012-09-01

    Geological and ecological processes play critical roles in the evolution of desert piedmonts. Feedback between fast cyclic biotic and slow cumulative pedogenic processes on arid alluvial fan systems results in a heterogeneous landscape of interspace and canopy microsites. Defining the spatial extent between these processes will allow a better connection to ecosystem service and climate change. We use a soil chronosequence in the Mojave Desert and high spatial resolution infiltrometer measurements along transects radiating from canopies of perennial shrubs to assess the extent of biotic and abiotic processes and the heterogeneity of soil properties in arid shrublands. Results showed higher saturated conductivity under vegetation regardless of surface age, but it was more conspicuous on older, developed soils. At proximal locations to the shrub, bulk density, soil structure grade, silt, and clay content significantly increased radially from the canopy, while sand and organic material decreased. Soil properties at distal locations 2-5 times the canopy radius had no significant spatial correlation. The extent of the biotic influence of the shrub was 1.34 ± 0.32 times the canopy radius. Hydraulic properties were weakly correlated in space, but 75% of the variance could be attributed to sand content, soil structure grade, mean-particle diameter, and soil organic material, none of which are exclusively biotic or abiotic. The fast cyclic biotic processes occurring under vegetation are clearly overprinted on slow cumulative abiotic processes, resulting in the deterministic variability observed at the plant scale.

  19. Translating knowledge about abiotic stress tolerance to breeding programmes.

    PubMed

    Gilliham, Matthew; Able, Jason A; Roy, Stuart J

    2017-06-01

    Plant breeding and improvements in agronomic practice are making a consistent contribution to increasing global crop production year upon year. However, the rate of yield improvement currently lags behind the targets set to produce enough food to meet the demands of the predicted global population in 2050. Furthermore, crops that are exposed to harmful abiotic environmental factors (abiotic stresses, e.g. water limitation, salinity, extreme temperature) are prone to reduced yields. Here, we briefly describe the processes undertaken in conventional breeding programmes, which are usually designed to improve yields in near-optimal conditions rather than specifically breeding for improved crop yield stability under stressed conditions. While there is extensive fundamental research activity that examines mechanisms of plant stress tolerance, there are few examples that apply this research to improving commercial crop yields. There are notable exceptions, and we highlight some of these to demonstrate the magnitude of yield gains that could be made by translating agronomic, phenological and genetic solutions focused on improving or mitigating the effect of abiotic stress in the field; in particular, we focus on improvements in crop water-use efficiency and salinity tolerance. We speculate upon the reasons for the disconnect between research and research translation. We conclude that to realise untapped rapid gains towards food security targets new funding structures need to be embraced. Such funding needs to serve both the core and collaborative activities of the fundamental, pre-breeding and breeding research communities in order to expedite the translation of innovative research into the fields of primary producers. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  20. Effects of the Ordering of Natural Selection and Population Regulation Mechanisms on Wright-Fisher Models

    PubMed Central

    He, Zhangyi; Beaumont, Mark; Yu, Feng

    2017-01-01

    We explore the effect of different mechanisms of natural selection on the evolution of populations for one- and two-locus systems. We compare the effect of viability and fecundity selection in the context of the Wright-Fisher model with selection under the assumption of multiplicative fitness. We show that these two modes of natural selection correspond to different orderings of the processes of population regulation and natural selection in the Wright-Fisher model. We find that under the Wright-Fisher model these two different orderings can affect the distribution of trajectories of haplotype frequencies evolving with genetic recombination. However, the difference in the distribution of trajectories is only appreciable when the population is in significant linkage disequilibrium. We find that as linkage disequilibrium decays the trajectories for the two different models rapidly become indistinguishable. We discuss the significance of these findings in terms of biological examples of viability and fecundity selection, and speculate that the effect may be significant when factors such as gene migration maintain a degree of linkage disequilibrium. PMID:28500051

  1. Natural selection drives chemical resistance of Datura stramonium

    PubMed Central

    Miranda-Pérez, Adán; Castillo, Guillermo; Hernández-Cumplido, Johnattan; Valverde, Pedro L.; Borbolla, María; Cruz, Laura L.; Tapia-López, Rosalinda; Fornoni, Juan; Flores-Ortiz, César M.

    2016-01-01

    Plant resistance to herbivores involves physical and chemical plant traits that prevent or diminish damage by herbivores, and hence may promote coevolutionary arm-races between interacting species. Although Datura stramonium’s concentration of tropane alkaloids is under selection by leaf beetles, it is not known whether chemical defense reduces seed predation by the specialist weevil, Trichobaris soror, and if it is evolving by natural selection. We measured infestation by T. soror as well as the concentration of the plants’ two main tropane alkaloids in 278 D. stramonium plants belonging to 31 populations in central Mexico. We assessed whether the seed predator exerted preferences on the levels of both alkaloids and whether they affect plant fitness. Results show great variation across populations in the concentration of scopolamine and atropine in both leaves and seeds of plants of D. stramonium, as well as in the intensity of infestation and the proportion of infested fruits by T. soror. The concentration of scopolamine in seeds and leaves are negatively associated across populations. We found that scopolamine concentration increases plant fitness. Our major finding was the detection of a positive relationship between the population average concentrations of scopolamine with the selection differentials of scopolamine. Such spatial variation in the direction and intensity of selection on scopolamine may represent a coevolutionary selective mosaic. Our results support the view that variation in the concentration of scopolamine among-populations of D. stramonium in central Mexico is being driven, in part, by selection exerted by T. soror, pointing an adaptive role of tropane alkaloids in this plant species. PMID:27114866

  2. DEMONSTRATION BULLETIN: METAL-ENHANCED ABIOTIC DEGRADATION TECHNOLOGY - ENVIROMETAL TECHNOLOGIES, INC.

    EPA Science Inventory

    EnviroMetal Technologies, Inc. (ETI), of Guelph, ON, Canada, has developed the metal-enhanced abiotic degradation technology to treat halogenated volatile organic compounds (VOC) in water. A reactive, zero-valent, granular iron medium causes reductive dehalogenation of VOCs yield...

  3. Are heritability and selection related to population size in nature? Meta-analysis and conservation implications.

    PubMed

    Wood, Jacquelyn L A; Yates, Matthew C; Fraser, Dylan J

    2016-06-01

    It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h (2)) and found no reduction in h (2) with decreasing N; surveyed populations ranged from four to one million individuals (1735 h (2) estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N and found little evidence for systematic differences in the strength, direction or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h (2) in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, under-represented taxonomic groups, and nongeneralist species, (ii) adaptive potential using multidimensional approaches and (iii) the nature of selective pressures for specific traits.

  4. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    PubMed Central

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-01-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. PMID:26340626

  5. Natural selection of memory-one strategies for the iterated prisoner's dilemma.

    PubMed

    Kraines, D P; Kraines, V Y

    2000-04-21

    In the iterated Prisoner's Dilemma, mutually cooperative behavior can become established through Darwinian natural selection. In simulated interactions of stochastic memory-one strategies for the Iterated Prisoner's Dilemma, Nowak and Sigmund discovered that cooperative agents using a Pavlov (Win-Stay Lose-Switch) type strategy eventually dominate a random population. This emergence follows more directly from a deterministic dynamical system based on differential reproductive success or natural selection. When restricted to an environment of memory-one agents interacting in iterated Prisoner's Dilemma games with a 1% noise level, the Pavlov agent is the only cooperative strategy and one of very few others that cannot be invaded by a similar strategy. Pavlov agents are trusting but no suckers. They will exploit weakness but repent if punished for cheating. Copyright 2000 Academic Press.

  6. Strong and consistent natural selection associated with armour reduction in sticklebacks.

    PubMed

    LE Rouzic, Arnaud; Østbye, Kjartan; Klepaker, Tom O; Hansen, Thomas F; Bernatchez, Louis; Schluter, Dolph; Vøllestad, L Asbjørn

    2011-06-01

    Measuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading with the reduction or loss of the bony lateral armour, has occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic changes were tracked for 20 years. Fish from the last generation were genotyped for the Ectodysplasin-A (Eda) locus, the major gene involved in armour development. We found a strong fitness advantage for the freshwater-type fish (on average, 20% fitness advantage for the freshwater morph, and 92% for the freshwater genotype). The trend is best explained by assuming that this fitness advantage is maximum at the beginning of the invasion and decreases with time. Such fitness differences provide a quantifiable example of rapid selection-driven phenotypic evolution associated with environmental change in a natural population. © 2011 Blackwell Publishing Ltd.

  7. SERDP ER-1421 Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA: Final Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Szecsody, James E.; McKinley, James P.; Crocker, Fiona H.

    This laboratory-scale project was initiated to investigate in situ abiotic/biotic mineralization of NDMA. Under iron-reducing conditions, aquifer sediments showed rapid abiotic NDMA degradation to dimethylamine (DMA), nitrate, formate, and finally, CO2. These are the first reported experiments of abiotic NDMA mineralization. The NDMA reactivity of these different iron phases showed that adsorbed ferrous iron was the dominant reactive phase that promoted NDMA reduction, and other ferrous phases present (siderite, iron sulfide, magnetite, structural ferrous iron in 2:1 clays) did not promote NDMA degradation. In contrast, oxic sediments that were biostimulated with propane promoted biomineralization of NDMA by a cometabolic monooxygenasemore » enzyme process. Other monooxygenase enzyme processes were not stimulated with methane or toluene additions, and acetylene addition did not block mineralization. Although NDMA mineralization extent was the highest in oxic, biostimulated sediments (30 to 82%, compared to 10 to 26% for abiotic mineralization in reduced sediments), large 1-D column studies (high sediment/water ratio of aquifers) showed 5.6 times higher NDMA mineralization rates in reduced sediment (half-life 410 ± 147 h) than oxic biomineralization (half life 2293 ± 1866 h). Sequential reduced/oxic biostimulated sediment mineralization (half-life 3180 ± 1094 h) was also inefficient compared to reduced sediment. These promising laboratory-scale results for NDMA mineralization should be investigated at field scale. Future studies of NDMA remediation should focus on the comparison of this in situ abiotic NDMA mineralization (iron-reducing environments) to ex situ biomineralization, which has been shown successful in other studies.« less

  8. Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in Fragaria vesca.

    PubMed

    Wang, Yong; Ding, Guanqun; Gu, Tingting; Ding, Jing; Li, Yi

    2017-08-01

    Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved. We characterized the expression profiles of FveNCED and FveCCD genes during flower and fruit development, and in response to several abiotic stresses. FveNCED1 expression positively responded to osmotic, cold, and heat stresses, whereas FveNCED2 was only induced under cold stress. In contrast, FveNCED2 was the unique gene highly and continuously increasing in receptacle during fruit ripening, which co-occurred with the increase in endogenous abscisic acid (ABA) content previously reported in octoploid strawberry. The differential expression patterns suggested that FveNCED1 and FveNCED2 were key genes for ABA biosynthesis in abiotic stress responses and fruit ripening, respectively. FveCCD1 exhibited the highest expression in most stages of flower and fruit development, while the other FveCCDs were expressed in a subset of stages and tissues. Our study suggests distinct functions of FveNCED and FveCCD genes in fruit development and stress responses and lays a foundation for future study to understand the roles of these genes and their metabolites, including ABA and other apocarotenoid products, in the growth and development of strawberry.

  9. Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

    PubMed Central

    2012-01-01

    Background Plasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed. Methods Fifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs. Results Thirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII. Conclusions PvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine. PMID:22380592

  10. The Promoter of AtUSP Is Co-regulated by Phytohormones and Abiotic Stresses in Arabidopsis thaliana.

    PubMed

    Bhuria, Monika; Goel, Parul; Kumar, Sanjay; Singh, Anil K

    2016-01-01

    Universal stress proteins (USPs) are known to be expressed in response to various abiotic stresses in a wide variety of organisms, such as bacteria, archaebacteria, protists, algae, fungi, plants, and animals. However, in plants, biological function of most of the USPs still remains obscure. In the present study, Arabidopsis USP gene ( AtUSP ) showed induction in response to abscisic acid (ABA) and various abiotic stresses viz . heat, dehydration, salt, osmotic, and cold stresses. Additionally, in silico analysis of AtUSP promoter identified several cis -elements responsive to phytohormones and abiotic stresses such as ABRE, ERE, DRE, and HSE, etc. To functionally validate the AtUSP promoter, the 1115 bp region of promoter was characterized under phytohormone and abiotic stress treatments. Deletion analysis of promoter was carried out by cloning the full length promoter (D0) and its three 5' deletion derivatives, D1 (964 bp), D2 (660 bp), and D3 (503 bp) upstream of the β-glucuronidase (GUS) reporter gene, which were then stably transformed in Arabidopsis plants. The AtUSP promoter (D0) showed minimal activity under non-stress conditions which was enhanced in response to phytohormone treatments (ABA and ACC) and abiotic stresses such as dehydration, heat, cold, salt, and osmotic stresses. The seedlings harboring D1 and D2 deletion fragments showed constitutive GUS expression even under control condition with increased activity almost under all the treatments. However, D3 seedlings exhibited complete loss of activity under control condition with induction under ACC treatment, dehydration, heat, oxidative, salt, and osmotic stresses. Thus, present study clearly showed that AtUSP promoter is highly inducible by phytohormones and multiple abiotic stresses and it can be exploited as stress inducible promoter to generate multi-stress tolerant crops with minimal effects on their other important traits.

  11. Sexual dichromatism in frogs: natural selection, sexual selection and unexpected diversity.

    PubMed

    Bell, Rayna C; Zamudio, Kelly R

    2012-12-07

    Sexual dichromatism, a form of sexual dimorphism in which males and females differ in colour, is widespread in animals but has been predominantly studied in birds, fishes and butterflies. Moreover, although there are several proposed evolutionary mechanisms for sexual dichromatism in vertebrates, few studies have examined this phenomenon outside the context of sexual selection. Here, we describe unexpectedly high diversity of sexual dichromatism in frogs and create a comparative framework to guide future analyses of the evolution of these sexual colour differences. We review what is known about evolution of colour dimorphism in frogs, highlight alternative mechanisms that may contribute to the evolution of sexual colour differences, and compare them to mechanisms active in other major groups of vertebrates. In frogs, sexual dichromatism can be dynamic (temporary colour change in males) or ontogenetic (permanent colour change in males or females). The degree and the duration of sexual colour differences vary greatly across lineages, and we do not detect phylogenetic signal in the distribution of this trait, therefore frogs provide an opportunity to investigate the roles of natural and sexual selection across multiple independent derivations of sexual dichromatism.

  12. Genetic signatures of natural selection in a model invasive ascidian

    NASA Astrophysics Data System (ADS)

    Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

    2017-03-01

    Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.

  13. Genetic signatures of natural selection in a model invasive ascidian

    PubMed Central

    Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

    2017-01-01

    Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta. PMID:28266616

  14. Resistance Responses of Potato to Vesicular-Arbuscular Mycorrhizal Fungi under Varying Abiotic Phosphorus Levels 1

    PubMed Central

    McArthur, David A. J.; Knowles, N. Richard

    1992-01-01

    In mycorrhizal symbioses, susceptibility of a host plant to infection by fungi is influenced by environmental factors, especially the availability of soil phosphorus. This study describes morphological and biochemical details of interactions between a vesicular-arbuscular mycorrhizal (VAM) fungus and potato (Solanum tuberosum L. cv Russet Burbank) plants, with a particular focus on the physiological basis for P-induced resistance of roots to infection. Root infection by the VAM fungus Glomus fasciculatum ([Thaxt. sensu Gerdemann] Gerdemann and Trappe) was extensive for plants grown with low abiotic P supply, and plant biomass accumulation was enhanced by the symbiosis. The capacity of excised roots from P-deficient plants to produce ethylene in the presence or absence of exogenous 1-amino cyclopropane-1-carboxylic acid (ACC) was markedly reduced by VAM infection. This apparent inhibition of ACC oxidase (ACCox) activity was localized to areas containing infected roots, as demonstrated in split-root studies. Furthermore, leachate from VAM roots contained a potent water-soluble inhibitor of ethylene generation from exogenous ACC by nonmycorrhizal (NM) roots. The leachate from VAM-infected roots had a higher concentration of phenolics, relative to that from NM roots. Moreover, the rates of ethylene formation and phenolic concentration in leachates from VAM roots were inversely correlated, suggesting that this inhibitor may be of a phenolic nature. The specific activity of extracellular peroxidase recovered in root leachates was not stimulated by VAM infection, although activity on a fresh weight basis was significantly enhanced, reflecting the fact that VAM roots had higher protein content than NM roots. Polyphenol oxidase activity of roots did not differ between NM and VAM roots. These results characterize the low resistance response of P-deficient plants to VAM infection. When plants were grown with higher abiotic P supply, the relative benefit of the VAM symbiosis

  15. Generation of RNA in abiotic conditions.

    NASA Astrophysics Data System (ADS)

    di Mauro, Ernesto

    Generation of RNA in abiotic conditions. Ernesto Di Mauro Dipartimento di Genetica Bi-ologia Molecolare, Universit` "Sapienza" Roma, Italy. a At least four conditions must be satisfied for the spontaneous generation of (pre)-genetic poly-mers: 1) availability of precursors that are activated enough to spontaneously polymerize. Preliminary studies showed that (a) nucleic bases and acyclonucleosides can be synthesized from formamide H2NCOH by simply heating with prebiotically available mineral catalysts [last reviewed in (1)], and that b) nucleic bases can be phosphorylated in every possible posi-tion [2'; 3'; 5'; cyclic 2',3'; cyclic 3',5' (2)]. The higher stability of the cyclic forms allows their accumulation. 2) A polymerization mechanism. A reaction showing the formation of RNA polymers starting from prebiotically plausible precursors (3',5' cyclic GMP and 3', 5'cyclic AMP) was recently reported (3). Polymerization in these conditions is thermodynamically up-hill and an equilibrium is attained that limits the maximum length of the polymer produced to about 40 nucleotides for polyG and 100 nucleotides for polyA. 3) Ligation of the synthesized oligomers. If this type of reaction could occur according to a terminal-joining mechanism and could generate canonical 3',5' phosphodiester bonds, exponential growth would be obtained of the generated oligomers. This type of reaction has been reported (4) , limited to homogeneous polyA sequences and leading to the production of polyA dimers and tetramers. What is still missing are: 4) mechanisms that provide the proof of principle for the generation of sequence complexity. We will show evidence for two mechanisms providing this proof of principle for simple complementary sequences. Namely: abiotic sequence complementary-driven terminal ligation and sequence-complementary terminal growth. In conclusion: all the steps leading to the generation of RNA in abiotic conditions are satisfied. (1) R Saladino, C Crestini, F

  16. Proteins in phytohormone signaling pathways for abiotic stress in plants

    USDA-ARS?s Scientific Manuscript database

    Plant hormones and their signaling network systems have an essential role in activating and regulating plant responses to both biotic and abiotic stress factors. This chapter describes proteins that are involved in hormone biosynthesis, long distance and intra-cellular transport, the signaling sensi...

  17. Genetic and Computational Approaches for Studying Plant Development and Abiotic Stress Responses Using Image-Based Phenotyping

    NASA Astrophysics Data System (ADS)

    Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.

    2017-12-01

    The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.

  18. Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana

    PubMed Central

    Hu, Wei; Hou, Xiaowan; Huang, Chao; Yan, Yan; Tie, Weiwei; Ding, Zehong; Wei, Yunxie; Liu, Juhua; Miao, Hongxia; Lu, Zhiwei; Li, Meiying; Xu, Biyu; Jin, Zhiqiang

    2015-01-01

    Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars. PMID:26307965

  19. Notice of release of Amethyst Germplasm hoaty tansyaster: Selected class of natural germplasm

    Treesearch

    Derek J. Tilley

    2015-01-01

    The US Department of Agriculture (USDA), Natural Resources Conservation Service (NRCS), Aberdeen Plant Materials Center, Aberdeen, Idaho, announces the release of Amethyst Germplasm hoary tansyaster (Machaeronthero canescens (Pursh) A. Gray [Asteraceae]}, a selected class natural track germplasm identified by NRCS accession number 9076670 for conservation plantings in...

  20. Identification and expression of the WRKY transcription factors of Carica papaya in response to abiotic and biotic stresses.

    PubMed

    Pan, Lin-Jie; Jiang, Ling

    2014-03-01

    The WRKY transcription factor (TF) plays a very important role in the response of plants to various abiotic and biotic stresses. A local papaya database was built according to the GenBank expressed sequence tag database using the BioEdit software. Fifty-two coding sequences of Carica papaya WRKY TFs were predicted using the tBLASTn tool. The phylogenetic tree of the WRKY proteins was classified. The expression profiles of 13 selected C. papaya WRKY TF genes under stress induction were constructed by quantitative real-time polymerase chain reaction. The expression levels of these WRKY genes in response to 3 abiotic and 2 biotic stresses were evaluated. TF807.3 and TF72.14 are upregulated by low temperature; TF807.3, TF43.76, TF12.199 and TF12.62 are involved in the response to drought stress; TF9.35, TF18.51, TF72.14 and TF12.199 is involved in response to wound; TF12.199, TF807.3, TF21.156 and TF18.51 was induced by PRSV pathogen; TF72.14 and TF43.76 are upregulated by SA. The regulated expression levels of above eight genes normalized against housekeeping gene actin were significant at probability of 0.01 levels. These WRKY TFs could be related to corresponding stress resistance and selected as the candidate genes, especially, the two genes TF807.3 and TF12.199, which were regulated notably by four stresses respectively. This study may provide useful information and candidate genes for the development of transgenic stress tolerant papaya varieties.

  1. MicroRNAs play critical roles during plant development and in response to abiotic stresses.

    PubMed

    de Lima, Júlio César; Loss-Morais, Guilherme; Margis, Rogerio

    2012-12-01

    MicroRNAs (miRNAs) have been identified as key molecules in regulatory networks. The fine-tuning role of miRNAs in addition to the regulatory role of transcription factors has shown that molecular events during development are tightly regulated. In addition, several miRNAs play crucial roles in the response to abiotic stress induced by drought, salinity, low temperatures, and metals such as aluminium. Interestingly, several miRNAs have overlapping roles with regard to development, stress responses, and nutrient homeostasis. Moreover, in response to the same abiotic stresses, different expression patterns for some conserved miRNA families among different plant species revealed different metabolic adjustments. The use of deep sequencing technologies for the characterisation of miRNA frequency and the identification of new miRNAs adds complexity to regulatory networks in plants. In this review, we consider the regulatory role of miRNAs in plant development and abiotic stresses, as well as the impact of deep sequencing technologies on the generation of miRNA data.

  2. Novel perspectives for the engineering of abiotic stress tolerance in plants.

    PubMed

    Cabello, Julieta V; Lodeyro, Anabella F; Zurbriggen, Matias D

    2014-04-01

    Adverse environmental conditions pose serious limitations to agricultural production. Classical biotechnological approaches towards increasing abiotic stress tolerance focus on boosting plant endogenous defence mechanisms. However, overexpression of regulatory elements or effectors is usually accompanied by growth handicap and yield penalties due to crosstalk between developmental and stress-response networks. Herein we offer an overview on novel strategies with the potential to overcome these limitations based on the engineering of regulatory systems involved in the fine-tuning of the plant response to environmental hardships, including post-translational modifications, small RNAs, epigenetic control of gene expression and hormonal networks. The development and application of plant synthetic biology tools and approaches will add new functionalities and perspectives to genetic engineering programs for enhancing abiotic stress tolerance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Adaptive Value of Phenological Traits in Stressful Environments: Predictions Based on Seed Production and Laboratory Natural Selection

    PubMed Central

    Glorieux, Cédric; Cuguen, Joel; Roux, Fabrice

    2012-01-01

    Phenological traits often show variation within and among natural populations of annual plants. Nevertheless, the adaptive value of post-anthesis traits is seldom tested. In this study, we estimated the adaptive values of pre- and post-anthesis traits in two stressful environments (water stress and interspecific competition), using the selfing annual species Arabidopsis thaliana. By estimating seed production and by performing laboratory natural selection (LNS), we assessed the strength and nature (directional, disruptive and stabilizing) of selection acting on phenological traits in A. thaliana under the two tested stress conditions, each with four intensities. Both the type of stress and its intensity affected the strength and nature of selection, as did genetic constraints among phenological traits. Under water stress, both experimental approaches demonstrated directional selection for a shorter life cycle, although bolting time imposes a genetic constraint on the length of the interval between bolting and anthesis. Under interspecific competition, results from the two experimental approaches showed discrepancies. Estimation of seed production predicted directional selection toward early pre-anthesis traits and long post-anthesis periods. In contrast, the LNS approach suggested neutrality for all phenological traits. This study opens questions on adaptation in complex natural environment where many selective pressures act simultaneously. PMID:22403624

  4. Does natural variation in diversity affect biotic resistance?

    USGS Publications Warehouse

    Harrison, Susan; Cornell, Howard; Grace, James B.

    2015-01-01

    Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

  5. Phenotypic selection on leaf water use efficiency and related ecophysiological traits for natural populations of desert sunflowers.

    PubMed

    Donovan, Lisa A; Dudley, Susan A; Rosenthal, David M; Ludwig, Fulco

    2007-05-01

    Plant water-use efficiency (WUE) is expected to affect plant fitness and thus be under natural selection in arid habitats. Although many natural population studies have assessed plant WUE, only a few related WUE to fitness. The further determination of whether selection on WUE is direct or indirect through functionally related traits has yielded no consistent results. For natural populations of two desert annual sunflowers, Helianthus anomalus and H. deserticola, we used phenotypic selection analysis with vegetative biomass as the proxy for fitness to test (1) whether there was direct and indirect selection on WUE (carbon isotope ratio) and related traits (leaf N, area, succulence) and (2) whether direct selection was consistent with hypothesized drought/dehydration escape and avoidance strategies. There was direct selection for lower WUE in mesic and dry H. anomalus populations, consistent with dehydration escape, even though it is the longer lived of the two species. For mesic H. anomalus, direct selection favored lower WUE and higher N, suggesting that plants may be "wasting water" to increase N delivery via the transpiration stream. For the shorter lived H. deserticola in the direr habitat, there was indirect selection for lower WUE, inconsistent with drought escape. There was also direct selection for higher leaf N, succulence and leaf size. There was no direct selection for higher WUE consistent with dehydration avoidance in either species. Thus, in these natural populations of two desert dune species higher fitness was associated with some combination direct and indirect selection for lower WUE, higher leaf N and larger leaf size. Our understanding of the adaptive value of plant ecophysiological traits will benefit from further consideration of related traits such as leaf nitrogen and more tests in natural populations.

  6. Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

    PubMed Central

    Muleke, Everlyne M’mbone; Jabir, Bashir Mohammed; Xie, Yang; Zhu, Xianwen; Cheng, Wanwan

    2017-01-01

    NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish. PMID:29259849

  7. Constraint, natural selection, and the evolution of human body form

    PubMed Central

    Savell, Kristen R. R.; Auerbach, Benjamin M.; Roseman, Charles C.

    2016-01-01

    Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics. PMID:27482101

  8. Constraint, natural selection, and the evolution of human body form.

    PubMed

    Savell, Kristen R R; Auerbach, Benjamin M; Roseman, Charles C

    2016-08-23

    Variation in body form among human groups is structured by a blend of natural selection driven by local climatic conditions and random genetic drift. However, attempts to test ecogeographic hypotheses have not distinguished between adaptive traits (i.e., those that evolved as a result of selection) and those that evolved as a correlated response to selection on other traits (i.e., nonadaptive traits), complicating our understanding of the relationship between climate and morphological distinctions among populations. Here, we use evolutionary quantitative methods to test if traits previously identified as supporting ecogeographic hypotheses were actually adaptive by estimating the force of selection on individual traits needed to drive among-group differentiation. Our results show that not all associations between trait means and latitude were caused by selection acting directly on each individual trait. Although radial and tibial length and biiliac and femoral head breadth show signs of responses to directional selection matching ecogeographic hypotheses, the femur was subject to little or no directional selection despite having shorter values by latitude. Additionally, in contradiction to ecogeographic hypotheses, the humerus was under directional selection for longer values by latitude. Responses to directional selection in the tibia and radius induced a nonadaptive correlated response in the humerus that overwhelmed its own trait-specific response to selection. This result emphasizes that mean differences between groups are not good indicators of which traits are adaptations in the absence of information about covariation among characteristics.

  9. Genome-Wide Analysis of the GRF Family Reveals Their Involvement in Abiotic Stress Response in Cassava.

    PubMed

    Shang, Sang; Wu, Chunlai; Huang, Chao; Tie, Weiwei; Yan, Yan; Ding, Zehong; Xia, Zhiqiang; Wang, Wenquan; Peng, Ming; Tian, Libo; Hu, Wei

    2018-02-20

    GENERAL REGULATORY FACTOR (GRF) proteins play vital roles in the regulation of plant growth, development, and response to abiotic stress. However, little information is known for this gene family in cassava ( Manihot esculenta ). In this study, 15 MeGRFs were identified from the cassava genome and were clustered into the ε and the non-ε groups according to phylogenetic, conserved motif, and gene structure analyses. Transcriptomic analyses showed eleven Me GRFs with constitutively high expression in stems, leaves, and storage roots of two cassava genotypes. Expression analyses revealed that the majority of GRFs showed transcriptional changes under cold, osmotic, salt, abscisic acid (ABA), and H₂O₂ treatments. Six Me GRFs were found to be commonly upregulated by abiotic stress, ABA, and H₂O₂ treatments, which may be the converging points of multiple signaling pathways. Interaction network analysis identified 18 possible interactors of MeGRFs. Taken together, this study elucidates the transcriptional control of Me GRFs in tissue development and the responses of abiotic stress and related signaling in cassava. Some constitutively expressed, tissue-specific, and abiotic stress-responsive candidate MeGRF genes were identified for the further genetic improvement of crops.

  10. Abiotic Organic Chemistry in Hydrothermal Systems.

    NASA Astrophysics Data System (ADS)

    Simoneit, B. R.; Rushdi, A. I.

    2004-12-01

    Abiotic organic chemistry in hydrothermal systems is of interest to biologists, geochemists and oceanographers. This chemistry consists of thermal alteration of organic matter and minor prebiotic synthesis of organic compounds. Thermal alteration has been extensively documented to yield petroleum and heavy bitumen products from contemporary organic detritus. Carbon dioxide, carbon monoxide, ammonia and sulfur species have been used as precursors in prebiotic synthesis experiments to organic compounds. These inorganic species are common components of hot spring gases and marine hydrothermal systems. It is of interest to further test their reactivities in reductive aqueous thermolysis. We have synthesized organic compounds (lipids) in aqueous solutions of oxalic acid, and with carbon disulfide or ammonium bicarbonate at temperatures from 175-400° C. The synthetic lipids from oxalic acid solutions consisted of n-alkanols, n-alkanoic acids, n-alkyl formates, n-alkanones, n-alkenes and n-alkanes, typically to C30 with no carbon number preferences. The products from CS2 in acidic aqueous solutions yielded cyclic thioalkanes, alkyl polysulfides, and thioesters with other numerous minor compounds. The synthesis products from oxalic acid and ammonium bicarbonate solutions were homologous series of n-alkyl amides, n-alkyl amines, n-alkanes and n-alkanoic acids, also to C30 with no carbon number predominance. Condensation (dehydration) reactions also occur under elevated temperatures in aqueous medium as tested by model reactions to form amide, ester and nitrile bonds. It is concluded that the abiotic formation of aliphatic lipids, condensation products (amides, esters, nitriles, and CS2 derivatives (alkyl polysulfides, cyclic polysulfides) is possible under hydrothermal conditions and warrants further studies.

  11. Rational selection of structurally diverse natural product scaffolds with favorable ADME properties for drug discovery.

    PubMed

    Samiulla, D S; Vaidyanathan, V V; Arun, P C; Balan, G; Blaze, M; Bondre, S; Chandrasekhar, G; Gadakh, A; Kumar, R; Kharvi, G; Kim, H O; Kumar, S; Malikayil, J A; Moger, M; Mone, M K; Nagarjuna, P; Ogbu, C; Pendhalkar, D; Rao, A V S Raja; Rao, G Venkateshwar; Sarma, V K; Shaik, S; Sharma, G V R; Singh, S; Sreedhar, C; Sonawane, R; Timmanna, U; Hardy, L W

    2005-01-01

    Natural product analogs are significant sources for therapeutic agents. To capitalize efficiently on the effective features of naturally occurring substances, a natural product-based library production platform has been devised at Aurigene for drug lead discovery. This approach combines the attractive biological and physicochemical properties of natural product scaffolds, provided by eons of natural selection, with the chemical diversity available from parallel synthetic methods. Virtual property analysis, using computational methods described here, guides the selection of a set of natural product scaffolds that are both structurally diverse and likely to have favorable pharmacokinetic properties. The experimental characterization of several in vitro ADME properties of twenty of these scaffolds, and of a small set of designed congeners based upon one scaffold, is also described. These data confirm that most of the scaffolds and the designed library members have properties favorable to their utilization for creating libraries of lead-like molecules.

  12. Progress and challenges for abiotic stress proteomics of crop plants.

    PubMed

    Barkla, Bronwyn J; Vera-Estrella, Rosario; Pantoja, Omar

    2013-06-01

    Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS-based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Species associations overwhelm abiotic conditions to dictate the structure and function of wood-decay fungal communities.

    PubMed

    Maynard, Daniel S; Covey, Kristofer R; Crowther, Thomas W; Sokol, Noah W; Morrison, Eric W; Frey, Serita D; van Diepen, Linda T A; Bradford, Mark A

    2018-04-01

    Environmental conditions exert strong controls on the activity of saprotrophic microbes, yet abiotic factors often fail to adequately predict wood decomposition rates across broad spatial scales. Given that species interactions can have significant positive and negative effects on wood-decay fungal activity, one possibility is that biotic processes serve as the primary controls on community function, with abiotic controls emerging only after species associations are accounted for. Here we explore this hypothesis in a factorial field warming- and nitrogen-addition experiment by examining relationships among wood decomposition rates, fungal activity, and fungal community structure. We show that functional outcomes and community structure are largely unrelated to abiotic conditions, with microsite and plot-level abiotic variables explaining at most 19% of the total variability in decomposition and fungal activity, and 2% of the variability in richness and evenness. In contrast, taxonomic richness, evenness, and species associations (i.e., co-occurrence patterns) exhibited strong relationships with community function, accounting for 52% of the variation in decomposition rates and 73% in fungal activity. A greater proportion of positive vs. negative species associations in a community was linked to strong declines in decomposition rates and richness. Evenness emerged as a key mediator between richness and function, with highly even communities exhibiting a positive richness-function relationship and uneven communities exhibiting a negative or null response. These results suggest that community-assembly processes and species interactions are important controls on the function of wood-decay fungal communities, ultimately overwhelming substantial differences in abiotic conditions. © 2018 by the Ecological Society of America.

  14. Comprehensive Genomic Analysis and Expression Profiling of Phospholipase C Gene Family during Abiotic Stresses and Development in Rice

    PubMed Central

    Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K.; Sopory, Sudhir K.; Kapoor, Sanjay; Pandey, Girdhar K.

    2013-01-01

    Background Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. Methodology/Principal Findings An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. Conclusion/Significance The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future. PMID

  15. Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice.

    PubMed

    Singh, Amarjeet; Kanwar, Poonam; Pandey, Amita; Tyagi, Akhilesh K; Sopory, Sudhir K; Kapoor, Sanjay; Pandey, Girdhar K

    2013-01-01

    Phospholipase C (PLC) is one of the major lipid hydrolysing enzymes, implicated in lipid mediated signaling. PLCs have been found to play a significant role in abiotic stress triggered signaling and developmental processes in various plant species. Genome wide identification and expression analysis have been carried out for this gene family in Arabidopsis, yet not much has been accomplished in crop plant rice. An exhaustive in-silico exploration of rice genome using various online databases and tools resulted in the identification of nine PLC encoding genes. Based on sequence, motif and phylogenetic analysis rice PLC gene family could be divided into phosphatidylinositol-specific PLCs (PI-PLCs) and phosphatidylcholine- PLCs (PC-PLC or NPC) classes with four and five members, respectively. A comparative analysis revealed that PLCs are conserved in Arabidopsis (dicots) and rice (monocot) at gene structure and protein level but they might have evolved through a separate evolutionary path. Transcript profiling using gene chip microarray and quantitative RT-PCR showed that most of the PLC members expressed significantly and differentially under abiotic stresses (salt, cold and drought) and during various developmental stages with condition/stage specific and overlapping expression. This finding suggested an important role of different rice PLC members in abiotic stress triggered signaling and plant development, which was also supported by the presence of relevant cis-regulatory elements in their promoters. Sub-cellular localization of few selected PLC members in Nicotiana benthamiana and onion epidermal cells has provided a clue about their site of action and functional behaviour. The genome wide identification, structural and expression analysis and knowledge of sub-cellular localization of PLC gene family envisage the functional characterization of these genes in crop plants in near future.

  16. Survival of the biological control agent Candida sake CPA-1 on grapes under the influence of abiotic factors.

    PubMed

    Calvo-Garrido, C; Viñas, I; Usall, J; Rodríguez-Romera, M; Ramos, M C; Teixidó, N

    2014-09-01

    As reliability of preharvest applications of biological control agents (BCAs) to control fruit pathogens is highly dependent on the survival of the selected organism, this study aimed to describe the population dynamics of the yeast-BCA Candida sake (Saito & Ota) CPA-1 on grape berries under the effect of abiotic factors such as temperature, relative humidity, sunlight and rainfall. Candida sake (5 × 10(7) CFU ml(-1)), combined with different concentrations of the food additive Fungicover(®), was applied on grape berry clusters. Treated clusters were then exposed to abiotic factors in field or laboratory conditions, recovering populations to describe C. sake population dynamics. The addition of Fungicover significantly increased C. sake multiplication under optimal growth conditions and improved survival under fluctuating abiotic factors. After field applications, significant differences in populations on grape bunches exposed or covered by fine foliage were detected. Simulated rainfall washed off C. sake populations by 0·6-0·9 log units after 20 mm of rain volume. Allowing populations to establish for 24 h or more, prior to a rain event, persistence on grape berries significantly increased and the effect of rain intensity was not observable. Candida sake demonstrated high survival ability under unfavourable environmental conditions and persistence under intense rain. The study evidenced the importance of the first period just after application for C. sake survival on grape tissues and also the protective effect of the additive Fungicover. This research provides new information on the survival of C. sake under field conditions and its practical implications for recommending timing of spray with this antagonist. Our results could be useful for other yeast antagonists applied before harvest. This work, for the first time, defines population dynamics of a yeast BCA using simulated rainfall. © 2014 The Society for Applied Microbiology.

  17. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    PubMed

    Priest, Henry D; Fox, Samuel E; Rowley, Erik R; Murray, Jessica R; Michael, Todd P; Mockler, Todd C

    2014-01-01

    Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  18. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    PubMed

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  19. Pre-mRNA splicing repression triggers abiotic stress signaling in plants.

    PubMed

    Ling, Yu; Alshareef, Sahar; Butt, Haroon; Lozano-Juste, Jorge; Li, Lixin; Galal, Aya A; Moustafa, Ahmed; Momin, Afaque A; Tashkandi, Manal; Richardson, Dale N; Fujii, Hiroaki; Arold, Stefan; Rodriguez, Pedro L; Duque, Paula; Mahfouz, Magdy M

    2017-01-01

    Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  20. Natural selection and sex differences in morbidity and mortality in early life.

    PubMed

    Wells, J C

    2000-01-07

    Both morbidity and mortality are consistently reported to be higher in males than in females in early life, but no explanation for these findings has been offered. This paper argues that the sex difference in early vulnerability can be attributed to the natural selection of optimal maternal strategies for maximizing lifetime reproductive success, as modelled previously by Trivers and Willard. These authors theorized that males and females offer different returns on parental investment depending on the state of the environment. Natural selection has therefore favoured maternal ability to manipulate offspring sex in response to environmental conditions in early life, as shown in variation in the sex ratio at birth. This argument can be extended to the whole period of parental investment until weaning. Male vulnerability in response to environmental stress in early life is predicted to have been favoured by natural selection. This vulnerability is most evident in the harsh conditions resulting from pre-term birth, but can also be seen in term infants, and manifests as greater morbidity and mortality persisting into early childhood. Malnutrition, interacting with infection after birth, is suggested as the fundamental trigger mechanism. The model suggests that whatever improvements are made in medical care, any environmental stress will always affect males more severely than females in early life. Copyright 2000 Academic Press.

  1. Overexpression of Arabidopsis AnnAt8 Alleviates Abiotic Stress in Transgenic Arabidopsis and Tobacco

    PubMed Central

    Yadav, Deepanker; Ahmed, Israr; Shukla, Pawan; Boyidi, Prasanna; Kirti, Pulugurtha Bharadwaja

    2016-01-01

    Abiotic stress results in massive loss of crop productivity throughout the world. Because of our limited knowledge of the plant defense mechanisms, it is very difficult to exploit the plant genetic resources for manipulation of traits that could benefit multiple stress tolerance in plants. To achieve this, we need a deeper understanding of the plant gene regulatory mechanisms involved in stress responses. Understanding the roles of different members of plant gene families involved in different stress responses, would be a step in this direction. Arabidopsis, which served as a model system for the plant research, is also the most suitable system for the functional characterization of plant gene families. Annexin family in Arabidopsis also is one gene family which has not been fully explored. Eight annexin genes have been reported in the genome of Arabidopsis thaliana. Expression studies of different Arabidopsis annexins revealed their differential regulation under various abiotic stress conditions. AnnAt8 (At5g12380), a member of this family has been shown to exhibit ~433 and ~175 fold increase in transcript levels under NaCl and dehydration stress respectively. To characterize Annexin8 (AnnAt8) further, we have generated transgenic Arabidopsis and tobacco plants constitutively expressing AnnAt8, which were evaluated under different abiotic stress conditions. AnnAt8 overexpressing transgenic plants exhibited higher seed germination rates, better plant growth, and higher chlorophyll retention when compared to wild type plants under abiotic stress treatments. Under stress conditions transgenic plants showed comparatively higher levels of proline and lower levels of malondialdehyde compared to the wild-type plants. Real-Time PCR analyses revealed that the expression of several stress-regulated genes was altered in AnnAt8 over-expressing transgenic tobacco plants, and the enhanced tolerance exhibited by the transgenic plants can be correlated with altered expressions of

  2. The nature of selection on the major histocompatibility complex.

    PubMed

    Apanius, V; Penn, D; Slev, P R; Ruff, L R; Potts, W K

    1997-01-01

    Only natural selection can account for the extreme genetic diversity of genes of the major histocompatibility complex (MHC). Although the structure and function of classic MHC genes is well understood at the molecular and cellular levels, there is controversy about how MHC diversity is selectively maintained. The diversifying selection can be driven by pathogen interactions and inbreeding avoidance mechanisms. Pathogen-driven selection can maintain MHC polymorphism based on heterozygote advantage or frequency-dependent selection due to pathogen evasion of MHC-dependent immune recognition. Empirical evidence demonstrates that specific MHC haplotypes are resistant to certain infectious agents, while susceptible to others. These data are consistent with both heterozygote advantage and frequency-dependent models. Additional research is needed to discriminate between these mechanisms. Infectious agents can precipitate autoimmunity and can potentially contribute to MHC diversity through molecular mimicry and by favoring immunodominance. MHC-dependent abortion and mate choice, based on olfaction, can also maintain MHC diversity and probably functions both to avoid genome-wide inbreeding and produce MHC-heterozygous offspring with increased immune responsiveness. Although this diverse set of hypotheses are often treated as competing alternatives, we believe that they all fit into a coherent, internally consistent thesis. It is likely that at least in some species, all of these mechanisms operate, leading to the extreme diversification found in MHC genes.

  3. Natural and sexual selection giveth and taketh away reproductive barriers: models of population divergence in guppies.

    PubMed

    Labonne, Jacques; Hendry, Andrew P

    2010-07-01

    The standard predictions of ecological speciation might be nuanced by the interaction between natural and sexual selection. We investigated this hypothesis with an individual-based model tailored to the biology of guppies (Poecilia reticulata). We specifically modeled the situation where a high-predation population below a waterfall colonizes a low-predation population above a waterfall. Focusing on the evolution of male color, we confirm that divergent selection causes the appreciable evolution of male color within 20 generations. The rate and magnitude of this divergence were reduced when dispersal rates were high and when female choice did not differ between environments. Adaptive divergence was always coupled to the evolution of two reproductive barriers: viability selection against immigrants and hybrids. Different types of sexual selection, however, led to contrasting results for another potential reproductive barrier: mating success of immigrants. In some cases, the effects of natural and sexual selection offset each other, leading to no overall reproductive isolation despite strong adaptive divergence. Sexual selection acting through female choice can thus strongly modify the effects of divergent natural selection and thereby alter the standard predictions of ecological speciation. We also found that under no circumstances did divergent selection cause appreciable divergence in neutral genetic markers.

  4. Selecting the Best Mobile Information Service with Natural Language User Input

    NASA Astrophysics Data System (ADS)

    Feng, Qiangze; Qi, Hongwei; Fukushima, Toshikazu

    Information services accessed via mobile phones provide information directly relevant to subscribers’ daily lives and are an area of dynamic market growth worldwide. Although many information services are currently offered by mobile operators, many of the existing solutions require a unique gateway for each service, and it is inconvenient for users to have to remember a large number of such gateways. Furthermore, the Short Message Service (SMS) is very popular in China and Chinese users would prefer to access these services in natural language via SMS. This chapter describes a Natural Language Based Service Selection System (NL3S) for use with a large number of mobile information services. The system can accept user queries in natural language and navigate it to the required service. Since it is difficult for existing methods to achieve high accuracy and high coverage and anticipate which other services a user might want to query, the NL3S is developed based on a Multi-service Ontology (MO) and Multi-service Query Language (MQL). The MO and MQL provide semantic and linguistic knowledge, respectively, to facilitate service selection for a user query and to provide adaptive service recommendations. Experiments show that the NL3S can achieve 75-95% accuracies and 85-95% satisfactions for processing various styles of natural language queries. A trial involving navigation of 30 different mobile services shows that the NL3S can provide a viable commercial solution for mobile operators.

  5. Genome-wide characterization and analysis of bZIP transcription factor gene family related to abiotic stress in cassava.

    PubMed

    Hu, Wei; Yang, Hubiao; Yan, Yan; Wei, Yunxie; Tie, Weiwei; Ding, Zehong; Zuo, Jiao; Peng, Ming; Li, Kaimian

    2016-03-07

    The basic leucine zipper (bZIP) transcription factor family plays crucial roles in various aspects of biological processes. Currently, no information is available regarding the bZIP family in the important tropical crop cassava. Herein, 77 bZIP genes were identified from cassava. Evolutionary analysis indicated that MebZIPs could be divided into 10 subfamilies, which was further supported by conserved motif and gene structure analyses. Global expression analysis suggested that MebZIPs showed similar or distinct expression patterns in different tissues between cultivated variety and wild subspecies. Transcriptome analysis of three cassava genotypes revealed that many MebZIP genes were activated by drought in the root of W14 subspecies, indicating the involvement of these genes in the strong resistance of cassava to drought. Expression analysis of selected MebZIP genes in response to osmotic, salt, cold, ABA, and H2O2 suggested that they might participate in distinct signaling pathways. Our systematic analysis of MebZIPs reveals constitutive, tissue-specific and abiotic stress-responsive candidate MebZIP genes for further functional characterization in planta, yields new insights into transcriptional regulation of MebZIP genes, and lays a foundation for understanding of bZIP-mediated abiotic stress response.

  6. Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates.

    PubMed

    Kang, Jung-Mi; Lee, Jinyoung; Moe, Mya; Jun, Hojong; Lê, Hương Giang; Kim, Tae Im; Thái, Thị Lam; Sohn, Woon-Mok; Myint, Moe Kyaw; Lin, Khin; Shin, Ho-Joon; Kim, Tong-Soo; Na, Byoung-Kuk

    2018-02-07

    Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is one of leading blood stage malaria vaccine candidates. However, genetic variation and antigenic diversity identified in global PfAMA-1 are major hurdles in the development of an effective vaccine based on this antigen. In this study, genetic structure and the effect of natural selection of PfAMA-1 among Myanmar P. falciparum isolates were analysed. Blood samples were collected from 58 Myanmar patients with falciparum malaria. Full-length PfAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. PfAMA-1 sequence of each isolate was sequenced. Polymorphic characteristics and effect of natural selection were analysed with using DNASTAR, MEGA4, and DnaSP programs. Polymorphic nature and natural selection in 459 global PfAMA-1 were also analysed. Thirty-seven different haplotypes of PfAMA-1 were identified in 58 Myanmar P. falciparum isolates. Most amino acid changes identified in Myanmar PfAMA-1 were found in domains I and III. Overall patterns of amino acid changes in Myanmar PfAMA-1 were similar to those in global PfAMA-1. However, frequencies of amino acid changes differed by country. Novel amino acid changes in Myanmar PfAMA-1 were also identified. Evidences for natural selection and recombination event were observed in global PfAMA-1. Among 51 commonly identified amino acid changes in global PfAMA-1 sequences, 43 were found in predicted RBC-binding sites, B-cell epitopes, or IUR regions. Myanmar PfAMA-1 showed similar patterns of nucleotide diversity and amino acid polymorphisms compared to those of global PfAMA-1. Balancing natural selection and intragenic recombination across PfAMA-1 are likely to play major roles in generating genetic diversity in global PfAMA-1. Most common amino acid changes in global PfAMA-1 were located in predicted B-cell epitopes where high levels of nucleotide diversity and balancing natural selection were found. These results highlight the

  7. Reasoning about Natural Selection: Diagnosing Contextual Competency Using the ACORNS Instrument

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Beggrow, Elizabeth P.; Opfer, John E.; Ha, Minsu

    2012-01-01

    Studies of students' thinking about natural selection have revealed that the scenarios in which students reason evoke different types, magnitudes, and arrangements of knowledge elements and misconceptions. Diagnostic tests are needed that probe students' thinking across a representative array of evolutionary contexts. The ACORNS is a diagnostic…

  8. Review of Abiotic Degradation of Chlorinated Solvents by Reactive Iron Minerals

    EPA Science Inventory

    Abiotic degradation of chlorinated solvents by reactive iron minerals such as iron sulfides, magnetite, green rust, and other Fe(II)-containing minerals has been observed in both laboratory and field conditions. These reactive iron minerals typically form under iron and sulfate ...

  9. Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress.

    PubMed

    Leisner, Courtney P; Yendrek, Craig R; Ainsworth, Elizabeth A

    2017-12-12

    Understanding how intensification of abiotic stress due to global climate change affects crop yields is important for continued agricultural productivity. Coupling genomic technologies with physiological crop responses in a dynamic field environment is an effective approach to dissect the mechanisms underpinning crop responses to abiotic stress. Soybean (Glycine max L. Merr. cv. Pioneer 93B15) was grown in natural production environments with projected changes to environmental conditions predicted for the end of the century, including decreased precipitation, increased tropospheric ozone concentrations ([O 3 ]), or increased temperature. All three environmental stresses significantly decreased leaf-level photosynthesis and stomatal conductance, leading to significant losses in seed yield. This was driven by a significant decrease in the number of pods per node for all abiotic stress treatments. To understand the underlying transcriptomic response involved in the yield response to environmental stress, RNA-Sequencing analysis was performed on the soybean seed coat, a tissue that plays an essential role in regulating carbon and nitrogen transport to developing seeds. Gene expression analysis revealed 49, 148 and 1,576 differentially expressed genes in the soybean seed coat in response to drought, elevated [O 3 ] and elevated temperature, respectively. Elevated [O 3 ] and drought did not elicit substantive transcriptional changes in the soybean seed coat. However, this may be due to the timing of sampling and does not preclude impacts of those stresses on different tissues or different stages in seed coat development. Expression of genes involved in DNA replication and metabolic processes were enriched in the seed coat under high temperate stress, suggesting that the timing of events that are important for cell division and proper seed development were altered in a stressful growth environment.

  10. How can we improve crop genotypes to increase stress resilience and productivity in a future climate? A new crop screening method based on productivity and resistance to abiotic stress

    PubMed Central

    Thiry, Arnauld A.; Chavez Dulanto, Perla N.; Reynolds, Matthew P.; Davies, William J.

    2016-01-01

    The need to accelerate the selection of crop genotypes that are both resistant to and productive under abiotic stress is enhanced by global warming and the increase in demand for food by a growing world population. In this paper, we propose a new method for evaluation of wheat genotypes in terms of their resilience to stress and their production capacity. The method quantifies the components of a new index related to yield under abiotic stress based on previously developed stress indices, namely the stress susceptibility index, the stress tolerance index, the mean production index, the geometric mean production index, and the tolerance index, which were created originally to evaluate drought adaptation. The method, based on a scoring scale, offers simple and easy visualization and identification of resilient, productive and/or contrasting genotypes according to grain yield. This new selection method could help breeders and researchers by defining clear and strong criteria to identify genotypes with high resilience and high productivity and provide a clear visualization of contrasts in terms of grain yield production under stress. It is also expected that this methodology will reduce the time required for first selection and the number of first-selected genotypes for further evaluation by breeders and provide a basis for appropriate comparisons of genotypes that would help reveal the biology behind high stress productivity of crops. PMID:27677299

  11. Identification of reference genes for RT-qPCR in the Antarctic moss Sanionia uncinata under abiotic stress conditions

    PubMed Central

    Park, Mira; Hong, Soon Gyu; Park, Hyun; Lee, Byeong-ha

    2018-01-01

    Sanionia uncinata is a dominant moss species in the maritime Antarctic. Due to its high adaptability to harsh environments, this extremophile plant has been considered a good target for studying the molecular adaptation mechanisms of plants to a variety of environmental stresses. Despite the importance of S. uncinata as a representative Antarctic plant species for the identification and characterization of genes associated with abiotic stress tolerance, suitable reference genes, which are critical for RT-qPCR analyses, have not yet been identified. In this report, 11 traditionally used and 6 novel candidate reference genes were selected from transcriptome data of S. uncinata and the expression stability of these genes was evaluated under various abiotic stress conditions using three statistical algorithms; geNorm, NormFinder, and BestKeeper. The stability ranking analysis selected the best reference genes depending on the stress conditions. Among the 17 candidates, the most stable references were POB1 and UFD2 for cold stress, POB1 and AKB for drought treatment, and UFD2 and AKB for the field samples from a different water contents in Antarctica. Overall, novel genes POB1 and AKB were the most reliable references across all samples, irrespective of experimental conditions. In addition, 6 novel candidate genes including AKB, POB1 and UFD2, were more stable than the housekeeping genes traditionally used for internal controls, indicating that transcriptome data can be useful for identifying novel robust normalizers. The reference genes validated in this study will be useful for improving the accuracy of RT-qPCR analysis for gene expression studies of S. uncinata in Antarctica and for further functional genomic analysis of bryophytes. PMID:29920565

  12. The Nature of Selection and Judging for the Teacher of the Year Award.

    ERIC Educational Resources Information Center

    McKenna, Bonnie; And Others

    This paper reports on the investigation of the operation of the Teacher of the Year Award program in 28 states. It focuses on the method of selection for recipients of this award, and explores the nature of the judging process used in selecting candidates at both the state and national levels. Specific objectives are: (1) to determine the criteria…

  13. Hydrologic, abiotic and biotic interactions: plant density, windspeed, leaf size and groundwater all affect oak water use efficiency

    Treesearch

    Darin J. Law; Deborah M. Finch

    2011-01-01

    Plant water use in drylands can be complex due to variation in hydrologic, abiotic and biotic factors, particularly near ephemeral or intermittent streams. Plant use of groundwater may be important but is usually uncertain. Disturbances like fire contribute to complex spatiotemporal heterogeneity. Improved understanding of how such hydrologic, abiotic, and biotic...

  14. Photochemically assisted fast abiotic oxidation of manganese and formation of δ-MnO 2 nanosheets in nitrate solution

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jung, Haesung; Chadha, Tandeep S.; Kim, Doyoon

    This study introduces a new and previously unconsidered fast abiotic formation of Mn(IV) oxides. We report photochemically assisted fast abiotic oxidation of Mn 2+ (aq) to Mn(IV) (s) by superoxide radicals generated from nitrate photolysis. This photochemical pathway generates randomly stacked layered birnessite (δ-MnO 2) nanosheets.

  15. Abiotic and Biotic Formation of Amino Acids in the Enceladus Ocean.

    PubMed

    Steel, Elliot L; Davila, Alfonso; McKay, Christopher P

    2017-09-01

    The active plume at Enceladus' south pole makes the indirect sampling of its global ocean possible. The partially resolved chemistry of the plume, which points to conditions that are seemingly compatible with life, has made orbital sampling missions a priority. We present a conceptual model of energy flux, hydrothermal H 2 production, and both abiotic and biotic production of amino acids. Based on the energy flux observed at the south pole and the inferred internal hydrothermal activity, we estimate an H 2 production of 0.6-34 mol/s from serpentinization, sufficient to sustain abiotic and biotic amino acid synthesis of 1.6-87 and 1-44 g/s, respectively. Two-dimensional (2D) numerical simulations of the hydrothermal vent suggest that the vent fluids could reach the ice-water boundary in less than 11-55 days for a 50 km deep ocean diluted by ambient ocean water 10 to 1. Concentrations of glycine, alanine, α-amino isobutyric acid, and glutamic acid in the plume and in the ambient ocean could all be above 0.01 μM just due to abiotic production. Biological synthesis, if occurring, could produce a maximum of 90 μM concentrations of amino acids based on a methanogenic ecosystem consuming H 2 and CO 2 . Racemization timescales in the ocean are short compared with production timescales. Thus, no enantiomeric excess is expected in the ambient ocean, and if biology is present, enantiomeric excess at the vent fluids is expected to be less than 10% in the plume. From vent H 2 concentrations of 7.8 mM (e.g., Lost City) and assuming complete H 2 use and conversion to chemical energy by methanogens, cell production is estimated. Annual biomass production in the methanogenic-based biology model is 4 × 10 4 -2 × 10 6 kg/year. This corresponds to cell concentrations ∼10 9 cells/cm 3 in the vents and ∼10 8 cells/cm 3 in the plume, and when diluted into the ambient ocean, we predict cell concentrations of 80-4250 cells/cm 3 . Key Words: Abiotic organic

  16. High-Resolution Electrospray Ionization/Ion Mobility Spectrometer for Detection of Abiotic Amino Acids

    NASA Technical Reports Server (NTRS)

    Beegle, L. W.; Terrell, C. A.; Kim, H.; Kanik, I.

    2003-01-01

    One of the primary goals of the current NASA thrust in Astrobiology is the detection and identification of organic molecules as part of an in-situ lander platform on the surface of Mars or Europa. The identification of these molecules should help determine whether indigenous organisms exist on the surface of Mars or in an undersea environment on Europa. In addition, a detailed organic chemical inventory of surface and near surface molecules will help elucidate the possibilities of life elsewhere in the Universe. Terrestrial life has, as its backbone, the family of molecules known as the amino acids (AA), and while AA can be found in the terrestrial environments as part of more complex molecules, such as peptides, and proteins, they also exist as individual molecules due to of the hydrolyses of biopolymers. In terrestrial biochemistry, there are 20 principal amino acids which are necessary for life. However, some forms of these molecules can be found in nature synthesized via abiotic process. For example, they are known to exist extraterrestrially as a component of carbonaceous meteorites. The idea that amino acids are readily created by abiotic means has been demonstrated by their positive identification in the Murchison CM2 meteorite, which fell in 1969. This meteorite was analyzed before contamination by terrestrial microbes could result. Three laboratories individually tested parts of the meteorite and concluded that the amino acids present in them were indigenous to the meteorite because, among other reasons, they had equal L- and D- enantiomers. Final identification of the constituents of the Murchison included 33 amino acids which have no known biotic source, 11 amino acids which have limited distribution and 8 (Glycine, Alanine, Valine, Proline, Leucine, Isoleucine, Aspartic Acid, and Glutamic Acid), which readily occur in terrestrial proteins.

  17. An experimental demonstration of Fisher's principle: evolution of sexual proportion by natural selection.

    PubMed Central

    Carvalho, A B; Sampaio, M C; Varandas, F R; Klaczko, L B

    1998-01-01

    Most sexually reproducing species have sexual proportions around 1:1. This major biological phenomenon remained unexplained until 1930, when FISHER proposed that it results from a mechanism of natural selection. Here we report the first experimental test of his model that obeys all its assumptions. We used a naturally occurring X-Y meiotic drive system--the sex-ratio trait of Drosophila mediopunctat--to generate female-biased experimental populations. As predicted by FISHER, these populations evolved toward equal sex proportions due to natural selection, by accumulation of autosomal alleles that direct the parental reproductive effort toward the rare sex. Classical Fisherian evolution is a rather slow mechanism: despite a very large amount of genetic variability, the experimental populations evolved from 16% of males to 32% of males in 49 generations and would take 330 generations (29 years) to reach 49%. This slowness has important implications for species potentially endangered by skewed sexual proportions, such as reptiles with temperature sex determination. PMID:9504919

  18. Assessment of derelict soil quality: Abiotic, biotic and functional approaches.

    PubMed

    Vincent, Quentin; Auclerc, Apolline; Beguiristain, Thierry; Leyval, Corinne

    2018-02-01

    The intensification and subsequent closing down of industrial activities during the last century has left behind large surfaces of derelict lands. Derelict soils have low fertility, can be contaminated, and many of them remain unused. However, with the increasing demand of soil surfaces, they might be considered as a resource, for example for non-food biomass production. The study of their physico-chemical properties and of their biodiversity and biological activity may provide indications for their potential re-use. The objective of our study was to investigate the quality of six derelict soils, considering abiotic, biotic, and functional parameters. We studied (i) the soil bacteria, fungi, meso- and macro-fauna and plant communities of six different derelict soils (two from coking plants, one from a settling pond, two constructed ones made from different substrates and remediated soil, and an inert waste storage one), and (ii) their decomposition function based on the decomposer trophic network, enzyme activities, mineralization activity, and organic pollutant degradation. Biodiversity levels in these soils were high, but all biotic parameters, except the mycorrhizal colonization level, discriminated them. Multivariate analysis showed that biotic parameters co-varied more with fertility proxies than with soil contamination parameters. Similarly, functional parameters significantly co-varied with abiotic parameters. Among functional parameters, macro-decomposer proportion, enzyme activity, average mineralization capacity, and microbial polycyclic aromatic hydrocarbon degraders were useful to discriminate the soils. We assessed their quality by combining abiotic, biotic, and functional parameters: the compost-amended constructed soil displayed the highest quality, while the settling pond soil and the contaminated constructed soil displayed the lowest. Although differences among the soils were highlighted, this study shows that derelict soils may provide a

  19. Manipulation of arginase expression modulates abiotic stress tolerance in Arabidopsis: effect on arginine metabolism and ROS accumulation

    PubMed Central

    Chan, Zhulong

    2013-01-01

    Arginine is an important medium for the transport and storage of nitrogen, and arginase (also known as arginine amidohydrolase, ARGAH) is responsible for catalyse of arginine into ornithine and urea in plants. In this study, the impact of AtARGAHs on abiotic stress response was investigated by manipulating AtARGAHs expression. In the knockout mutants of AtARGAHs, enhanced tolerances were observed to multiple abiotic stresses including water deficit, salt, and freezing stresses, while AtARGAH1- and AtARGAH2-overexpressing lines exhibited reduced abiotic stress tolerances compared to the wild type. Consistently, the enhanced tolerances were confirmed by the changes of physiological parameters including electrolyte leakage, water loss rate, stomatal aperture, and survival rate. Interestingly, the direct downstream products of arginine catabolism including polyamines and nitric oxide (NO) concentrations significantly increased in the AtARGAHs-knockout lines, but decreased in overexpressing lines under control conditions. Additionally, the AtARGAHs-overexpressing and -knockout lines displayed significantly reduced relative arginine (% of total free amino acids) relative to the wild type. Similarly, reactive oxygen species accumulation was remarkably regulated by AtARGAHs under abiotic stress conditions, as shown from hydrogen peroxide (H2O2), superoxide radical () concentrations, and antioxidant enzyme activities. Taken together, this is the first report, as far as is known, to provide evidence that AtARGAHs negatively regulate many abiotic stress tolerances, at least partially, attribute to their roles in modulating arginine metabolism and reactive oxygen species accumulation. Biotechnological strategy based on manipulation of AtARGAHs expression will be valuable for future crop breeding. PMID:23378380

  20. Estimating selection through male fitness: three complementary methods illuminate the nature and causes of selection on flowering time

    PubMed Central

    Austen, Emily J.; Weis, Arthur E.

    2016-01-01

    Our understanding of selection through male fitness is limited by the resource demands and indirect nature of the best available genetic techniques. Applying complementary, independent approaches to this problem can help clarify evolution through male function. We applied three methods to estimate selection on flowering time through male fitness in experimental populations of the annual plant Brassica rapa: (i) an analysis of mating opportunity based on flower production schedules, (ii) genetic paternity analysis, and (iii) a novel approach based on principles of experimental evolution. Selection differentials estimated by the first method disagreed with those estimated by the other two, indicating that mating opportunity was not the principal driver of selection on flowering time. The genetic and experimental evolution methods exhibited striking agreement overall, but a slight discrepancy between the two suggested that negative environmental covariance between age at flowering and male fitness may have contributed to phenotypic selection. Together, the three methods enriched our understanding of selection on flowering time, from mating opportunity to phenotypic selection to evolutionary response. The novel experimental evolution method may provide a means of examining selection through male fitness when genetic paternity analysis is not possible. PMID:26911957

  1. Overexpression of SlGRAS40 in Tomato Enhances Tolerance to Abiotic Stresses and Influences Auxin and Gibberellin Signaling

    PubMed Central

    Liu, Yudong; Huang, Wei; Xian, Zhiqiang; Hu, Nan; Lin, Dongbo; Ren, Hua; Chen, Jingxuan; Su, Deding; Li, Zhengguo

    2017-01-01

    Abiotic stresses are major environmental factors that inhibit plant growth and development impacting crop productivity. GRAS transcription factors play critical and diverse roles in plant development and abiotic stress. In this study, SlGRAS40, a member of the tomato (Solanum lycopersicum) GRAS family, was functionally characterized. In wild-type (WT) tomato, SlGRAS40 was upregulated by abiotic stress induced by treatment with D-mannitol, NaCl, or H2O2. Transgenic tomato plants overexpressing SlGRAS40 (SlGRAS40-OE) were more tolerant of drought and salt stress than WT. SlGRAS40-OE plants displayed pleiotropic phenotypes reminiscent of those resulting from altered auxin and/or gibberellin signaling. A comparison of WT and SlGRAS40-OE transcriptomes showed that the expression of a large number of genes involved in hormone signaling and stress responses were modified. Our study of SlGRAS40 protein provides evidence of how another GRAS plays roles in resisting abiotic stress and regulating auxin and gibberellin signaling during vegetative and reproductive growth in tomato. PMID:29018467

  2. Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

    PubMed Central

    Barbeau, Myriam A.

    2016-01-01

    Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

  3. Hydrolysis and photolysis of diacylhydrazines-type insect growth regulator JS-118 in aqueous solutions under abiotic conditions.

    PubMed

    Hu, J-Y; Liu, C; Zhang, Y-C; Zheng, Z-X

    2009-05-01

    JS-118 is a diacylhydrazines-type insect growth regulator which is now used extensively in China. The hydrolysis and photolysis of the pesticide JS-118 in aqueous solutions have been assessed under natural and controlled conditions in this project. Hydrolysis experimental results show that JS-118 is quite stable in aqueous solutions in dark, with no significant variations be observed in degradation under various conditions. Abiotic hydrolysis is relatively unimportant compared to photolysis. The rate of photodecomposition of JS-118 in aqueous solutions follows first-order kinetics both in UV radiation and natural sunlight. The degradation rates are faster under UV light than sunlight, with the half-lives (t (1/2) = ln2/k) of 6.00-10.85 min and 6.63-10.16 day, respectively. Under UV light, two major photoproducts are detected, and tentatively identified according to HPLC-MS spectral information as N-t-butyl-N-(3,5-dimethylbenzoyl) and 3,7-dimethyl-benzoatedihydrofuran. The corresponding photolysis pathways of JS-118 are also proposed. The results obtained indicate that direct photoreaction is an important dissipation pathway of JS-118 in natural water systems.

  4. Abiotic stress signaling and responses in plants

    PubMed Central

    Zhu, Jian-Kang

    2016-01-01

    Summary As sessile organisms, plants must cope with abiotic stress such as soil salinity, drought, and extreme temperatures. Core stress signaling pathways involve protein kinases related to the yeast SNF1 and mammalian AMPK, suggesting that stress signaling in plants evolved from energy sensing. Stress signaling regulates proteins critical for ion and water transport and for metabolic and gene-expression reprogramming to bring about ionic and water homeostasis and cellular stability under stress conditions. Understanding stress signaling and responses will increase our ability to improve stress resistance in crops to achieve agricultural sustainability and food security for a growing world population. PMID:27716505

  5. Selective Determination of Lipid Hydroperoxides in Natural Waters Using a Fluorescent Probe

    NASA Astrophysics Data System (ADS)

    Sunday, M. O.; Sakugawa, H.

    2016-12-01

    The presence of various lipids in natural waters and the availability of conditions needed for their oxidation to lipid hydroperoxides (LHPs) suggest that LHPs may be part of the hydroperoxide mix in natural waters. While other hydroperoxides, including H2O2, methyl hydroperoxide (MHP) and ethyl hydroperoxide (EHP) etc. have been investigated, there is no information on LHPs in natural waters. In this study, we report the presence of LHPs in natural waters. Firstly, a method selective to LHPs determination was developed using 2-(4-diphenylphosphanyl-phenyl)-9-(3,6,9,12-tetraoxatridecyl)-anthra[2,1,9-def:6,5,10-d'e'f']diisoquinoline-1,3,8,10-tetraone, Liperfluo, as a fluorescent probe. A flow injector analysis equipped with fluorescence detector was used for fluorescence measurement of Liperfluo-Ox formed from the reaction between Liperfluo and LHP. Under the optimized conditions, the reaction of Liperfluo with LHP in MilliQ and river water had a linear range of 0-500 nM LHP. The method detection limit was 10.1 nM and 7.3 nM in riverwater and MilliQ respectively. The coefficient of variation for five replicate measurements each for 100 nM and 500 nM LHP was ≤ 3.8%. The probe and the conditions used in this study showed high selectivity for LHP over other natural water hydroperoxides, including H2O2, MHP and EHP. The method was applied in the quantification of LHPs in water from the Kurose River (Japan). The concentration ranged from below detection limit to 98 nM (ave. 37.2 nM; n=12). Increase in H2O2 formation upon irradiation of LHP-spiked riverwater in a solar simulator suggests H2O2 formation as one of the possible sinks of LHPs in natural waters. For the first time, this study reveals that LHPs are part of the hydroperoxide mix in natural waters and provides insight on its fate in natural waters.

  6. Warning signals are under positive frequency-dependent selection in nature

    PubMed Central

    Chouteau, Mathieu; Arias, Mónica; Joron, Mathieu

    2016-01-01

    Positive frequency-dependent selection (FDS) is a selection regime where the fitness of a phenotype increases with its frequency, and it is thought to underlie important adaptive strategies resting on signaling and communication. However, whether and how positive FDS truly operates in nature remains unknown, which hampers our understanding of signal diversity. Here, we test for positive FDS operating on the warning color patterns of chemically defended butterflies forming multiple coexisting mimicry assemblages in the Amazon. Using malleable prey models placed in localities showing differences in the relative frequencies of warningly colored prey, we demonstrate that the efficiency of a warning signal increases steadily with its local frequency in the natural community, up to a threshold where protection stabilizes. The shape of this relationship is consistent with the direct effect of the local abundance of each warning signal on the corresponding avoidance knowledge of the local predator community. This relationship, which differs from purifying selection acting on each mimetic pattern, indicates that predator knowledge, integrated over the entire community, is saturated only for the most common warning signals. In contrast, among the well-established warning signals present in local prey assemblages, most are incompletely known to local predators and enjoy incomplete protection. This incomplete predator knowledge should generate strong benefits to life history traits that enhance warning efficiency by increasing the effective frequency of prey visible to predators. Strategies such as gregariousness or niche convergence between comimics may therefore readily evolve through their effects on predator knowledge and warning efficiency. PMID:26858416

  7. Inter-annual variability of carbon fluxes in temperate forest ecosystems: effects of biotic and abiotic factors

    NASA Astrophysics Data System (ADS)

    Chen, M.; Keenan, T. F.; Hufkens, K.; Munger, J. W.; Bohrer, G.; Brzostek, E. R.; Richardson, A. D.

    2014-12-01

    Carbon dynamics in terrestrial ecosystems are influenced by both abiotic and biotic factors. Abiotic factors, such as variation in meteorological conditions, directly drive biophysical and biogeochemical processes; biotic factors, referring to the inherent properties of the ecosystem components, reflect the internal regulating effects including temporal dynamics and memory. The magnitude of the effect of abiotic and biotic factors on forest ecosystem carbon exchange has been suggested to vary at different time scales. In this study, we design and conduct a model-data fusion experiment to investigate the role and relative importance of the biotic and abiotic factors for inter-annual variability of the net ecosystem CO2 exchange (NEE) of temperate deciduous forest ecosystems in the Northeastern US. A process-based model (FöBAAR) is parameterized at four eddy-covariance sites using all available flux and biometric measurements. We conducted a "transplant" modeling experiment, that is, cross- site and parameter simulations with different combinations of site meteorology and parameters. Using wavelet analysis and variance partitioning techniques, analysis of model predictions identifies both spatial variant and spatially invariant parameters. Variability of NEE was primarily modulated by gross primary productivity (GPP), with relative contributions varying from hourly to yearly time scales. The inter-annual variability of GPP and NEE is more regulated by meteorological forcing, but spatial variability in certain model parameters (biotic response) has more substantial effects on the inter-annual variability of ecosystem respiration (Reco) through the effects on carbon pools. Both the biotic and abiotic factors play significant roles in modulating the spatial and temporal variability in terrestrial carbon cycling in the region. Together, our study quantifies the relative importance of both, and calls for better understanding of them to better predict regional CO2

  8. Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythm

    PubMed Central

    Singh, Anupama; Kushwaha, Hemant R.; Soni, Praveen; Gupta, Himanshu; Singla-Pareek, Sneh L.; Pareek, Ashwani

    2015-01-01

    Two-component system (TCS) is one of the key signal sensing machinery which enables species to sense environmental stimuli. It essentially comprises of three major components, sensory histidine kinase proteins (HKs), histidine phosphotransfer proteins (Hpts), and response regulator proteins (RRs). The members of the TCS family have already been identified in Arabidopsis and rice but the knowledge about their functional indulgence during various abiotic stress conditions remains meager. Current study is an attempt to carry out comprehensive analysis of the expression of TCS members in response to various abiotic stress conditions and in various plant tissues in Arabidopsis and rice using MPSS and publicly available microarray data. The analysis suggests that despite having almost similar number of genes, rice expresses higher number of TCS members during various abiotic stress conditions than Arabidopsis. We found that the TCS machinery is regulated by not only various abiotic stresses, but also by the tissue specificity. Analysis of expression of some representative members of TCS gene family showed their regulation by the diurnal cycle in rice seedlings, thus bringing-in another level of their transcriptional control. Thus, we report a highly complex and tight regulatory network of TCS members, as influenced by the tissue, abiotic stress signal, and diurnal rhythm. The insights on the comparative expression analysis presented in this study may provide crucial leads toward dissection of diverse role(s) of the various TCS family members in Arabidopsis and rice. PMID:26442025

  9. Differentiating biotic from abiotic methane genesis in hydrothermally active planetary surfaces

    PubMed Central

    Oze, Christopher; Jones, L. Camille; Goldsmith, Jonas I.; Rosenbauer, Robert J.

    2012-01-01

    Molecular hydrogen (H2) is derived from the hydrothermal alteration of olivine-rich planetary crust. Abiotic and biotic processes consume H2 to produce methane (CH4); however, the extent of either process is unknown. Here, we assess the temporal dependence and limit of abiotic CH4 related to the presence and formation of mineral catalysts during olivine hydrolysis (i.e., serpentinization) at 200 °C and 0.03 gigapascal. Results indicate that the rate of CH4 production increases to a maximum value related to magnetite catalyzation. By identifying the dynamics of CH4 production, we kinetically model how the H2 to CH4 ratio may be used to assess the origin of CH4 in deep subsurface serpentinization systems on Earth and Mars. Based on our model and available field data, low H2/CH4 ratios (less than approximately 40) indicate that life is likely present and active. PMID:22679287

  10. Differentiating biotic from abiotic methane genesis in hydrothermally active planetary surfaces.

    PubMed

    Oze, Christopher; Jones, L Camille; Goldsmith, Jonas I; Rosenbauer, Robert J

    2012-06-19

    Molecular hydrogen (H(2)) is derived from the hydrothermal alteration of olivine-rich planetary crust. Abiotic and biotic processes consume H(2) to produce methane (CH(4)); however, the extent of either process is unknown. Here, we assess the temporal dependence and limit of abiotic CH(4) related to the presence and formation of mineral catalysts during olivine hydrolysis (i.e., serpentinization) at 200 °C and 0.03 gigapascal. Results indicate that the rate of CH(4) production increases to a maximum value related to magnetite catalyzation. By identifying the dynamics of CH(4) production, we kinetically model how the H(2) to CH(4) ratio may be used to assess the origin of CH(4) in deep subsurface serpentinization systems on Earth and Mars. Based on our model and available field data, low H(2)/CH(4) ratios (less than approximately 40) indicate that life is likely present and active.

  11. ABIOTIC REACTIONS MAY BE THE MOST IMPORTANT MECHANISM IN NATURAL ATTENUATION OF CHLORINATED SOLVENTS

    EPA Science Inventory

    The EPA Technical Protocol for Evaluating Natural Attenuation of Chlorinated Solvents in Ground Water was developed with the assumption that natural biological reductive dechlorination was the only important mechanism for destruction of chlorinated solvents and their reduction ...

  12. Minerals Masquerading As Enzymes: Abiotic Oxidation Of Soil Organic Matter In An Iron-Rich Humid Tropical Forest Soil

    NASA Astrophysics Data System (ADS)

    Hall, S. J.; Silver, W. L.

    2010-12-01

    ). Tyrosinase generated a red compound (dopachrome) that is the target analyte of the traditional L-DOPA oxidative enzyme assay, whereas our soil slurries generated purple melanin-like compounds that were likely generated by more extensive oxidation. To investigate the importance of Fe(II) for L-DOPA oxidation, we added realistic concentrations of Fe(II) (equivalent to 10 - 500 μg Fe g-1 soil) to an L-DOPA buffer solution under oxic conditions, and found rates of L-DOPA oxidation comparable to those from soil slurries. Molecular oxygen and Fe(II) are known to generate strong oxidants via Fenton reactions. We decreased L-DOPA oxidation rates in soil slurries by adding catalase and superoxide-dismutase enzymes to scavenge reactive oxygen species, suggesting that a free-radical mechanism contributed to L-DOPA oxidation. We obtained similar results using another humic model compound, tetramethylbenzidine (TMB). Although abiotic oxidative reactions involving iron have been employed to degrade anthropogenic organic contaminants, this study is among the first to demonstrate their potential importance for oxidizing organic matter in natural ecosystems. In soils rich in Fe(II), abiotic reactions could complement, or even obviate, the role of microbial oxidative enzymes in degrading recalcitrant organic compounds.

  13. Goal-Side Selection in Soccer Penalty Kicking When Viewing Natural Scenes

    PubMed Central

    Weigelt, Matthias; Memmert, Daniel

    2012-01-01

    The present study investigates the influence of goalkeeper displacement on goal-side selection in soccer penalty kicking. Facing a penalty situation, participants viewed photo-realistic images of a goalkeeper and a soccer goal. In the action selection task, they were asked to kick to the greater goal-side, and in the perception task, they indicated the position of the goalkeeper on the goal line. To this end, the goalkeeper was depicted in a regular goalkeeping posture, standing either in the exact middle of the goal or being displaced at different distances to the left or right of the goal’s center. Results showed that the goalkeeper’s position on the goal line systematically affected goal-side selection, even when participants were not aware of the displacement. These findings provide further support for the notion that the implicit processing of the stimulus layout in natural scenes can effect action selection in complex environments, such in soccer penalty shooting. PMID:22973246

  14. Natural selection and the predictability of evolution in Timema stick insects.

    PubMed

    Nosil, Patrik; Villoutreix, Romain; de Carvalho, Clarissa F; Farkas, Timothy E; Soria-Carrasco, Víctor; Feder, Jeffrey L; Crespi, Bernard J; Gompert, Zach

    2018-02-16

    Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time ( r 2 = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection ( r 2 = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  15. Interactions between Biological and Abiotic Pathways in the Reduction of Chlorinated Solvents

    EPA Science Inventory

    While biologically mediated reductive dechlorination continues to be a significant focus of chlorinated solvent remediation, there has been an increased interest in abiotic reductive processes for the remediation of chlorinated solvents. In situ chemical reduction (ISCR) uses zer...

  16. Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth.

    PubMed

    Xie, Xueshu; Backman, Daniel; Lebedev, Albert T; Artaev, Viatcheslav B; Jiang, Liying; Ilag, Leopold L; Zubarev, Roman A

    2015-09-28

    Sixty years after the seminal Miller-Urey experiment that abiotically produced a mixture of racemized amino acids, we provide a definite proof that this primordial soup, when properly cooked, was edible for primitive organisms. Direct admixture of even small amounts of Miller-Urey mixture strongly inhibits E. coli bacteria growth due to the toxicity of abundant components, such as cyanides. However, these toxic compounds are both volatile and extremely reactive, while bacteria are highly capable of adaptation. Consequently, after bacterial adaptation to a mixture of the two most abundant abiotic amino acids, glycine and racemized alanine, dried and reconstituted MU soup was found to support bacterial growth and even accelerate it compared to a simple mixture of the two amino acids. Therefore, primordial Miller-Urey soup was perfectly suitable as a growth media for early life forms.

  17. Interaction-based evolution: how natural selection and nonrandom mutation work together.

    PubMed

    Livnat, Adi

    2013-10-18

    The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation-while not Lamarckian, or "directed" to increase fitness-is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination's fitness. This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional theory can actually experience selection on interactions and thus has a much greater adaptive

  18. Interaction-based evolution: how natural selection and nonrandom mutation work together

    PubMed Central

    2013-01-01

    Background The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Presentation of the hypothesis Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. Testing and implications of the hypothesis This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional

  19. Darwin's Arguments in Favour of Natural Selection and against Special Creationism

    ERIC Educational Resources Information Center

    Nola, Robert

    2013-01-01

    In many places in "The Origin of Species", Darwin compares his own theory of Natural Selection favourably with Special Creationism which comes off as a bad second best. He does this using some version of the argument form known as "Inference to the Best Explanation". The first part of this paper is methodological. It considers Whewell's notion of…

  20. How can we estimate natural selection on endocrine traits? Lessons from evolutionary biology

    PubMed Central

    2016-01-01

    An evolutionary perspective can enrich almost any endeavour in biology, providing a deeper understanding of the variation we see in nature. To this end, evolutionary endocrinologists seek to describe the fitness consequences of variation in endocrine traits. Much of the recent work in our field, however, follows a flawed approach to the study of how selection shapes endocrine traits. Briefly, this approach relies on among-individual correlations between endocrine phenotypes (often circulating hormone levels) and fitness metrics to estimate selection on those endocrine traits. Adaptive plasticity in both endocrine and fitness-related traits can drive these correlations, generating patterns that do not accurately reflect natural selection. We illustrate why this approach to studying selection on endocrine traits is problematic, referring to work from evolutionary biologists who, decades ago, described this problem as it relates to a variety of other plastic traits. We extend these arguments to evolutionary endocrinology, where the likelihood that this flaw generates bias in estimates of selection is unusually high due to the exceptional responsiveness of hormones to environmental conditions, and their function to induce adaptive life-history responses to environmental variation. We end with a review of productive approaches for investigating the fitness consequences of variation in endocrine traits that we expect will generate exciting advances in our understanding of endocrine system evolution. PMID:27881753

  1. Carbohydrates protect protein against abiotic fragmentation by soil minerals

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Reardon, Patrick N.; Walter, Eric D.; Marean-Reardon, Carrie L.

    The degradation and turnover of soil organic matter is an important part of global carbon cycling and of particular importance with respect to attempts to predict the response of ecosystems to global climate change. Thus, it is important to mechanistically understand the processes by which organic matter can be degraded in the soil environment, including contact with reactive or catalytic mineral surfaces. We have characterized the outcome of the interaction of two minerals, birnessite and kaolinite, with two disaccharides, cellobiose and trehalose. These results show that birnessite reacts with and degrades the carbohydrates, while kaolinite does not. The reaction ofmore » disaccharides with birnessite produces Mn(II), indicating that degradation of the disaccharides is the result of their oxidation by birnessite. Furthermore, we find that both sugars can inhibit the degradation of a model protein by birnessite, demonstrating that the presence of one organic constituent can impact abiotic degradation of another. Therefore, both the reactivity of the mineral matrix and the presence of certain organic constituents influence the outcomes of abiotic degradation. These results suggest the possibility that microorganisms may be able to control the functionality of exoenzymes through the concomitant excretion of protective organic substances, such as those found in biofilms.« less

  2. Alfalfa Cellulose Synthase Gene Expression under Abiotic Stress: A Hitchhiker’s Guide to RT-qPCR Normalization

    PubMed Central

    Guerriero, Gea; Legay, Sylvain; Hausman, Jean-Francois

    2014-01-01

    Abiotic stress represents a serious threat affecting both plant fitness and productivity. One of the promptest responses that plants trigger following abiotic stress is the differential expression of key genes, which enable to face the adverse conditions. It is accepted and shown that the cell wall senses and broadcasts the stress signal to the interior of the cell, by triggering a cascade of reactions leading to resistance. Therefore the study of wall-related genes is particularly relevant to understand the metabolic remodeling triggered by plants in response to exogenous stresses. Despite the agricultural and economical relevance of alfalfa (Medicago sativa L.), no study, to our knowledge, has addressed specifically the wall-related gene expression changes in response to exogenous stresses in this important crop, by monitoring the dynamics of wall biosynthetic gene expression. We here identify and analyze the expression profiles of nine cellulose synthases, together with other wall-related genes, in stems of alfalfa plants subjected to different abiotic stresses (cold, heat, salt stress) at various time points (e.g. 0, 24, 72 and 96 h). We identify 2 main responses for specific groups of genes, i.e. a salt/heat-induced and a cold/heat-repressed group of genes. Prior to this analysis we identified appropriate reference genes for expression analyses in alfalfa, by evaluating the stability of 10 candidates across different tissues (namely leaves, stems, roots), under the different abiotic stresses and time points chosen. The results obtained confirm an active role played by the cell wall in response to exogenous stimuli and constitute a step forward in delineating the complex pathways regulating the response of plants to abiotic stresses. PMID:25084115

  3. Global Expressions Landscape of NAC Transcription Factor Family and Their Responses to Abiotic Stresses in Citrullus lanatus

    PubMed Central

    Lv, Xiaolong; Lan, Shanrong; Guy, Kateta Malangisha; Yang, Jinghua; Zhang, Mingfang; Hu, Zhongyuan

    2016-01-01

    Watermelon (Citrullus lanatus) is one xerophyte that has relative higher tolerance to drought and salt stresses as well as more sensitivity to cold stress, compared with most model plants. These characteristics facilitate it a potential model crop for researches on salt, drought or cold tolerance. In this study, a genome-wide comprehensive analysis of the ClNAC transcription factor (TF) family was carried out for the first time, to investigate their transcriptional profiles and potential functions in response to these abiotic stresses. The expression profiling analysis reveals that several NAC TFs are highly responsive to abiotic stresses and development, for instance, subfamily IV NACs may play roles in maintaining water status under drought or salt conditions, as well as water and metabolites conduction and translocation toward fruit. In contrast, rapid and negative responses of most of the ClNACs to low-temperature adversity may be related to the sensitivity to cold stress. Crosstalks among these abiotic stresses and hormone (abscisic acid and jasmonic acid) pathways were also discussed based on the expression of ClNAC genes. Our results will provide useful insights for the functional mining of NAC family in watermelon, as well as into the mechanisms underlying abiotic tolerance in other cash crops. PMID:27491393

  4. Global Expressions Landscape of NAC Transcription Factor Family and Their Responses to Abiotic Stresses in Citrullus lanatus.

    PubMed

    Lv, Xiaolong; Lan, Shanrong; Guy, Kateta Malangisha; Yang, Jinghua; Zhang, Mingfang; Hu, Zhongyuan

    2016-08-05

    Watermelon (Citrullus lanatus) is one xerophyte that has relative higher tolerance to drought and salt stresses as well as more sensitivity to cold stress, compared with most model plants. These characteristics facilitate it a potential model crop for researches on salt, drought or cold tolerance. In this study, a genome-wide comprehensive analysis of the ClNAC transcription factor (TF) family was carried out for the first time, to investigate their transcriptional profiles and potential functions in response to these abiotic stresses. The expression profiling analysis reveals that several NAC TFs are highly responsive to abiotic stresses and development, for instance, subfamily IV NACs may play roles in maintaining water status under drought or salt conditions, as well as water and metabolites conduction and translocation toward fruit. In contrast, rapid and negative responses of most of the ClNACs to low-temperature adversity may be related to the sensitivity to cold stress. Crosstalks among these abiotic stresses and hormone (abscisic acid and jasmonic acid) pathways were also discussed based on the expression of ClNAC genes. Our results will provide useful insights for the functional mining of NAC family in watermelon, as well as into the mechanisms underlying abiotic tolerance in other cash crops.

  5. The wheat transcription factor, TabHLH39, improves tolerance to multiple abiotic stressors in transgenic plants.

    PubMed

    Zhai, Yiqian; Zhang, Lichao; Xia, Chuan; Fu, Silu; Zhao, Guangyao; Jia, Jizeng; Kong, Xiuying

    2016-05-13

    Although bHLH transcription factors play important roles regulating plant development and abiotic stress response and tolerance, few functional studies have been performed in wheat. In this study, we isolated and characterized a bHLH gene, TabHLH39, from wheat. The TabHLH39 gene is located on wheat chromosome 5DL, and the protein localized to the nucleus and activated transcription. TabHLH39 showed variable expression in roots, stems, leaves, glumes, pistils and stamens and was induced by polyethylene glycol, salt and cold treatments. Further analysis revealed that TabHLH39 overexpression in Arabidopsis significantly enhanced tolerance to drought, salt and freezing stress during the seedling stage, which was also demonstrated by enhanced abiotic stress-response gene expression and changes to several physiological indices. Therefore, TabHLH39 has potential in transgenic breeding applications to improve abiotic stress tolerance in crops. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. From Ends to Causes (and Back Again) by Metaphor: The Paradox of Natural Selection

    ERIC Educational Resources Information Center

    Blancke, Stefaan; Schellens, Tammy; Soetaert, Ronald; Van Keer, Hilde; Braeckman, Johan

    2014-01-01

    Natural selection is one of the most famous metaphors in the history of science. Charles Darwin used the metaphor and the underlying analogy to frame his ideas about evolution and its main driving mechanism into a full-fledged theory. Because the metaphor turned out to be such a powerful epistemic tool, Darwin naturally assumed that he could also…

  7. Using biotechnology and genomics to improve biotic and abiotic stress in apple

    USDA-ARS?s Scientific Manuscript database

    Genomic sequencing, molecular biology, and transformation technologies are providing valuable tools to better understand the complexity of how plants develop, function, and respond to biotic and abiotic stress. These approaches should complement but not replace a solid understanding of whole plant ...

  8. Penetration enhancing effects of selected natural oils utilized in topical dosage forms.

    PubMed

    Viljoen, Joe M; Cowley, Amé; du Preez, Jan; Gerber, Minja; du Plessis, Jeanetta

    2015-01-01

    Various natural products, including oils, have been utilized as penetration enhancers due to their "safety profiles". These oils contain fatty acids promoting skin permeability through lipid fluidization within the stratum corneum; and might therefore be able to effectively enhance transdermal drug delivery. We investigated possible penetration enhancing properties of selected oils, utilizing flurbiprofen as marker compound in emulgel formulations. The formulations were compared to a liquid paraffin emulgel and a hydrogel to establish any significant penetration enhancing effects. Gas chromatographic analysis of the natural oils was performed at ambient temperature to determine the fatty acid composition in each selected natural oils. Franz cell diffusion studies and tape stripping methods were employed to study delivery of the marker into, and through the skin. The following rank order for the emulgel flux-values was obtained: Hydrogel > olive oil > liquid paraffin > coconut oil > grape seed oil > Avocado oil ≥ Crocodile oil > Emu oil. Results suggested that oils containing predominantly mono-unsaturated oleic acid, on average increased the flux of the marker to a larger extent than oils containing an almost even mixture of both mono- and poly-unsaturated fatty acids. Oils comprising saturated fatty acids (SFAs) with alkyl chains between C12 and C14, increased the marker flux to a higher extent than oils containing C16-C18 SFAs. Effects observed for branched fatty acids, however, did not vary significantly from effects for unbranched fatty acids with the same carbon chain length. Natural oils possess penetration enhancing effects.

  9. Measuring Knowledge of Natural Selection: A Comparison of the CINS, an Open-Response Instrument, and an Oral Interview

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Schonfeld, Irvin Sam

    2008-01-01

    Growing recognition of the central importance of fostering an in-depth understanding of natural selection has, surprisingly, failed to stimulate work on the development and rigorous evaluation of instruments that measure knowledge of it. We used three different methodological tools, the Conceptual Inventory of Natural Selection (CINS), a modified…

  10. Influences of Teleological and Lamarckian Thinking on Student Understanding of Natural Selection

    ERIC Educational Resources Information Center

    Stover, Shawn K.; Mabry, Michelle L.

    2007-01-01

    Previous research has demonstrated creationist, Lamarckian, and teleological reasoning in high school and college students. These lines of thinking conflict with the Darwinian notion of natural selection, which serves as the primary catalyst for biological evolution. The current study assessed evolutionary conceptions in non-science majors,…

  11. Induced responses to competition and herbivory: natural selection on multi-trait phenotypic plasticity.

    PubMed

    Boege, Karina

    2010-09-01

    Herbivory and competition are two of the most common biotic stressors for plants. When occurring simultaneously, responses to one interaction can constrain the induction of responses to the other interaction due to resource limitation and other interactive effects. Thus, to maximize fitness when interacting with competitors and herbivores, plants are likely to express particular combinations of plastic responses. This study reports the interactive effects of herbivory and competition on responses induced in Tithonia tubaeformis plants and describes how natural selection acts on particular plastic responses and on their different combinations. Competition induced a stem elongation response, expressed through an increase in height and mean internode length, together with a decrease in basal diameter. Interestingly, realized resistance increased in both competition and herbivory treatments, suggesting a plastic response in both constitutive and induced resistance traits. Particular combinations of plastic responses defined three plant phenotypes: vigorous, elongated, and resistant plants. The ecological context in which plants grew modified the traits and the particular combinations of plastic responses that were favored by selection. Vigorous plants were favored by selection in all environments, except when they were damaged by herbivores in the absence of neighbors. The combination of responses defining an elongated plant phenotype was favored by selection in crowded conditions. Resistance was negatively selected in the absence of competition and herbivory but favored in the presence of both interactions. In addition, contextual analyses detected that population structure in heterogeneous environments can also influence the outcomes of selection. These findings suggest that natural selection can act on particular combinations of plastic responses, which may allow plants to adjust their phenotypes to those that promote greater fitness under particular ecological

  12. Spatially-Correlated Risk in Nature Reserve Site Selection

    PubMed Central

    Albers, Heidi J.; Busby, Gwenlyn M.; Hamaide, Bertrand; Ando, Amy W.; Polasky, Stephen

    2016-01-01

    Establishing nature reserves protects species from land cover conversion and the resulting loss of habitat. Even within a reserve, however, many factors such as fires and defoliating insects still threaten habitat and the survival of species. To address the risk to species survival after reserve establishment, reserve networks can be created that allow some redundancy of species coverage to maximize the expected number of species that survive in the presence of threats. In some regions, however, the threats to species within a reserve may be spatially correlated. As examples, fires, diseases, and pest infestations can spread from a starting point and threaten neighboring parcels’ habitats, in addition to damage caused at the initial location. This paper develops a reserve site selection optimization framework that compares the optimal reserve networks in cases where risks do and do not reflect spatial correlation. By exploring the impact of spatially-correlated risk on reserve networks on a stylized landscape and on an Oregon landscape, this analysis demonstrates an appropriate and feasible method for incorporating such post-reserve establishment risks in the reserve site selection literature as an additional tool to be further developed for future conservation planning. PMID:26789127

  13. The Origin of Mutants Under Selection: How Natural Selection Mimics Mutagenesis (Adaptive Mutation)

    PubMed Central

    Maisnier-Patin, Sophie; Roth, John R.

    2015-01-01

    Selection detects mutants but does not cause mutations. Contrary to this dictum, Cairns and Foster plated a leaky lac mutant of Escherichia coli on lactose medium and saw revertant (Lac+) colonies accumulate with time above a nongrowing lawn. This result suggested that bacteria might mutagenize their own genome when growth is blocked. However, this conclusion is suspect in the light of recent evidence that revertant colonies are initiated by preexisting cells with multiple copies the conjugative F′lac plasmid, which carries the lac mutation. Some plated cells have multiple copies of the simple F′lac plasmid. This provides sufficient LacZ activity to support plasmid replication but not cell division. In nongrowing cells, repeated plasmid replication increases the likelihood of a reversion event. Reversion to lac+ triggers exponential cell growth leading to a stable Lac+ revertant colony. In 10% of these plated cells, the high-copy plasmid includes an internal tandem lac duplication, which provides even more LacZ activity—sufficient to support slow growth and formation of an unstable Lac+ colony. Cells with multiple copies of the F′lac plasmid have an increased mutation rate, because the plasmid encodes the error-prone (mutagenic) DNA polymerase, DinB. Without DinB, unstable and stable Lac+ revertant types form in equal numbers and both types arise with no mutagenesis. Amplification and selection are central to behavior of the Cairns–Foster system, whereas mutagenesis is a system-specific side effect or artifact caused by coamplification of dinB with lac. Study of this system has revealed several broadly applicable principles. In all populations, gene duplications are frequent stable genetic polymorphisms, common near-neutral mutant alleles can gain a positive phenotype when amplified under selection, and natural selection can operate without cell division when variability is generated by overreplication of local genome subregions. PMID:26134316

  14. Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora.

    PubMed

    Valadez-Cano, Cecilio; Olivares-Hernández, Roberto; Resendis-Antonio, Osbaldo; DeLuna, Alexander; Delaye, Luis

    2017-04-14

    Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore. We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by

  15. Effects of environmental changes on natural selection active on human polygenic traits.

    PubMed

    Ulizzi, L

    1993-06-01

    During the last century, industrialized countries experienced such an improvement in socioeconomic conditions and in sanitation that it is likely that the selective forces active on human metric traits have been modified. Perinatal mortality as a function of birth weight is one of the clearest examples of natural selection in humans. Here, trends over time of stabilizing and directional selection associated with birth weight have been analyzed in Japan from 1969 to 1989. The population of newborns has been subdivided according to gestational age, which is one of the main covariates of birth weight. The results show that in full-term babies both stabilizing and directional selection are coming to an end, whereas in babies born after 8 months of gestation these selective forces are still active, even if at much lower levels than in the past. The peculiar results found in the 7-month-gestation population are probably due to grossly abnormal cases of immaturity.

  16. The effects of climate change associated abiotic stresses on maize phytochemical defenses

    USDA-ARS?s Scientific Manuscript database

    Reliable large-scale maize production is an essential component of global food security; however, sustained efforts are needed to ensure optimized resilience under diverse crop stress conditions. Climate changes are expected to increase the frequency and intensity of both abiotic and biotic stress. ...

  17. Earth Without Life: A Systems Model of a Global Abiotic Nitrogen Cycle

    NASA Astrophysics Data System (ADS)

    Laneuville, M.; Kameya, M.; Cleaves, H. J.

    2017-07-01

    N is the major component of the atmosphere and plays important roles in biochemistry. Presently, the surface N-cycle is dominated by biology. However, before the origin of life, abiotic N-cycling would have set the stage for the origin of life.

  18. The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients

    PubMed Central

    Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

    2015-01-01

    We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages. PMID:26091266

  19. The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients.

    PubMed

    Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

    2015-01-01

    We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages.

  20. Influence of abiotic stress signals on secondary metabolites in plants

    PubMed Central

    Ramakrishna, Akula; Ravishankar, Gokare Aswathanarayana

    2011-01-01

    Plant secondary metabolites are unique sources for pharmaceuticals, food additives, flavors, and industrially important biochemicals. Accumulation of such metabolites often occurs in plants subjected to stresses including various elicitors or signal molecules. Secondary metabolites play a major role in the adaptation of plants to the environment and in overcoming stress conditions. Environmental factors viz. temperature, humidity, light intensity, the supply of water, minerals, and CO2 influence the growth of a plant and secondary metabolite production. Drought, high salinity, and freezing temperatures are environmental conditions that cause adverse effects on the growth of plants and the productivity of crops. Plant cell culture technologies have been effective tools for both studying and producing plant secondary metabolites under in vitro conditions and for plant improvement. This brief review summarizes the influence of different abiotic factors include salt, drought, light, heavy metals, frost etc. on secondary metabolites in plants. The focus of the present review is the influence of abiotic factors on secondary metabolite production and some of important plant pharmaceuticals. Also, we describe the results of in vitro cultures and production of some important secondary metabolites obtained in our laboratory. PMID:22041989

  1. Natural and induced reduction of hexavalent chromium in soil

    NASA Astrophysics Data System (ADS)

    Leita, Liviana; Margon, Alja; Sinicco, Tania; Mondini, Claudio; Valentini, Massimiliano; Cantone, Pierpaolo

    2013-04-01

    Even though naturally elevated levels of chromium can be found naturally in some soils, distressing amounts of the hexavalent form (CrVI) are largely restricted to sites contaminated by anthropogenic activities. In fact, the widespread use of chromium in various industries and the frequently associated inadequate disposal of its by-products and wastes have created serious environmental pollution problems in many parts of the world. CrVI is toxic to plants, animals and humans and exhibits also mutagenic effects. However, being a strong oxidant, CrVI can be readily reduced to the much less harmful trivalent form (CrIII) when suitable electron donors are present in the environment. CrIII is relatively insoluble, less available for biological uptake, and thus definitely less toxic for web-biota. Various electron donors in soil can be involved in CrVI reduction in soil. The efficiency of CrVI reducing abiotic agents such as ferrous iron and sulphur compounds is well documented. Furthermore, CrVI reduction is also known to be significantly enhanced by a wide variety of cell-produced monosaccharides, including glucose. In this study we evaluated the dynamics of hexavalent chromium (CrVI) reduction in contaminated soil amended or not with iron sulphate or/and glucose and assessed the effects of CrVI on native or glucose-induced soil microbial biomass size and activity. CrVI negatively affected both soil microbial activity and the size of the microbial biomass. During the incubation period, the concentration of CrVI in soil decreased over time whether iron sulphate or/and glucose was added or not, but with different reduction rates. Soil therefore displayed a natural attenuation capacity towards chromate reduction. Addition of iron sulphate or/and glucose, however, increased the reduction rate by both abiotic and biotic mechanisms. Our data suggest that glucose is likely to have exerted an indirect role in the increased rate of CrVI reduction by promoting growth of

  2. Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data.

    PubMed Central

    Orr, H A

    1998-01-01

    Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed. PMID:9691061

  3. Notice of release for Eagle Germplasm western yarrow (selected germplasm, natural track)

    Treesearch

    Scott M. Lambert; Stephen B. Monsen; Nancy Shaw

    2011-01-01

    The United States Department of Agriculture, Forest Service, Rocky Mountain Research Station; United States Department of the Interior, Bureau of Land Management, Idaho State Office; Utah State University, Agricultural Experiment Station; and University of Idaho, Agricultural Experiment Station, announce the release of a selected germplasm (natural track) of western...

  4. Genome Patterns of Selection and Introgression of Haplotypes in Natural Populations of the House Mouse (Mus musculus)

    PubMed Central

    Staubach, Fabian; Lorenc, Anna; Messer, Philipp W.; Tang, Kun; Petrov, Dmitri A.; Tautz, Diethard

    2012-01-01

    General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have

  5. On the Nature of the First Galaxies Selected at 350 Micrometers

    NASA Technical Reports Server (NTRS)

    Khan, Sophia A.; Chanial, Pierre F.; Willner, S. P.; Pearson, Chris P.; Ashby, M. L. N.; Benford, Dominic J.; Clements, David L.; Dye, Simon; Farrah, Duncan; Fazio, G. G.; hide

    2009-01-01

    We present constraints on the nature of the first galaxies selected at 350 micrometers. The sample includes galaxies discovered in the deepest blank-field survey at 350 micrometers (in the Bo6tes Deep Field) and also later serendipitous detections in the Lockman Hole. In determining multiwavelength identifications, the 350 lam position and map resolution of the second generation Submillimeter High Angular Resolution Camera are critical, especially in the cases where multiple radio sources exist and the 24 micrometer counterparts are unresolved. Spectral energy distribution templates are fitted to identified counterparts, and the sample is found to comprise IR-luminous galaxies at 1 < z < 3 predominantly powered by star formation. The first spectrum of a 350 micrometer selected galaxy provides an additional confirmation, showing prominent dust grain features typically associated with star-forming galaxies. Compared to submillimeter galaxies selected at 850 and 1100 micrometers, galaxies selected at 350 micrometers have a similar range of far-infrared color temperatures. However, no 350 micrometer selected sources are reliably detected at 850 or 1100 micrometers. Galaxies in our sample with redshifts 1 < z < 2 show a tight correlation between the far- and mid-infrared flux densities, but galaxies at higher redshifts show a large dispersion in their mid- to far-infrared colors. This implies a limit to which the mid-IR emission traces the far-IR emission in star-forming galaxies. The 350 micrometer flux densities (15 < S(sub 350) < 40 mJy) place these objects near the Herschel/SPIRE 350 micrometer confusion threshold, with the lower limit on the star formation rate density suggesting the bulk of the 350 micrometers contribution will come from less luminous infrared sources and normal galaxies. Therefore, the nature of the dominant source of the 350 micrometers background-star-forming galaxies in the epoch of peak star formation in the universe-could be more effectively

  6. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    PubMed

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. Copyright © 2016 by the Genetics Society of America.

  7. Nitrogen isotopic fractionation during abiotic synthesis of organic solid particles

    NASA Astrophysics Data System (ADS)

    Kuga, Maïa; Carrasco, Nathalie; Marty, Bernard; Marrocchi, Yves; Bernard, Sylvain; Rigaudier, Thomas; Fleury, Benjamin; Tissandier, Laurent

    2014-05-01

    The formation of organic compounds is generally assumed to result from abiotic processes in the Solar System, with the exception of biogenic organics on Earth. Nitrogen-bearing organics are of particular interest, notably for prebiotic perspectives but also for overall comprehension of organic formation in the young Solar System and in planetary atmospheres. We have investigated abiotic synthesis of organics upon plasma discharge, with special attention to N isotope fractionation. Organic aerosols were synthesized from N2-CH4 and N2-CO gaseous mixtures using low-pressure plasma discharge experiments, aimed at simulating chemistry occurring in Titan's atmosphere and in the protosolar nebula, respectively. The nitrogen content, the N speciation and the N isotopic composition were analyzed in the resulting organic aerosols. Nitrogen is efficiently incorporated into the synthesized solids, independently of the oxidation degree, of the N2 content of the starting gas mixture, and of the nitrogen speciation in the aerosols. The aerosols are depleted in 15N by 15-25‰ relative to the initial N2 gas, whatever the experimental setup is. Such an isotopic fractionation is attributed to mass-dependent kinetic effect(s). Nitrogen isotope fractionation upon electric discharge cannot account for the large N isotope variations observed among Solar System objects and reservoirs. Extreme N isotope signatures in the Solar System are more likely the result of self-shielding during N2 photodissociation, exotic effect during photodissociation of N2 and/or low temperature ion-molecule isotope exchange. Kinetic N isotope fractionation may play a significant role in the Titan's atmosphere. On the Titan's night side, 15N-depletion resulting from electron driven reactions may counterbalance photo-induced 15N enrichments occurring on the day's side. We also suggest that the low δ15N values of Archaean organic matter (Beaumont and Robert, 1999) are partly the result of abiotic synthesis of

  8. Correlation between macrobenthic structure (biotic) and water-sediment characteristics (abiotic) adjacent aquaculture areas at Tembelas Island, indonesia

    NASA Astrophysics Data System (ADS)

    Sharani, Jeanny; Hidayat, Jafron W.; Putro, Sapto P.

    2018-05-01

    Macrobenthic community play important role in sedimentary habitats as a part of food chain. Their structure may be influenced by environmental characteristic spatially and temporally. The purpose of this study is to access the correlation between macrobenthic structure (biotic) and water-sediment characteristics (abiotic) adjacent aquaculture areas at Tembelas Island, Indonesia. Water and sediments samples were taken twice, where the first and second sampling time were taken in June and October 2016, respectively. Samples were taken in the area of fish farming at coastal area of policulture/IMTA (as Location I), site of 1 km away from fish farming area as a reference site (as Location II), and monoculture sites (as Location III), with three stations for each location. Data of abiotic parameters included the composition of sediment substrate and DO, pH, salinity, temperature, and. Sediment samples were taken using Ekman grab. The organisms were 1 mm -size sieved and fixed using 10% formalin for further analysis, i.e. sorting, preserving, enumerating, identifying, and grouping. The relationship between biotics (macrobentos) and abiotics (physical-chemical factors) was assessed using a non-parametric multivariate procedure (BIOENV). This study found 61 species consisting of 46 families and 5 classes of macrobenthos. The most common classes were member of Mollusca and Polychaeta. Total nitrogen, silt, and clay were the abiotic factors most influencing macrobenthic structure (BIO-ENV; r = 0.46; R2 = 21.16%).

  9. Implications of quantum metabolism and natural selection for the origin of cancer cells and tumor progression

    NASA Astrophysics Data System (ADS)

    Davies, Paul; Demetrius, Lloyd A.; Tuszynski, Jack A.

    2012-03-01

    Empirical studies give increased support for the hypothesis that the sporadic form of cancer is an age-related metabolic disease characterized by: (a) metabolic dysregulation with random abnormalities in mitochondrial DNA, and (b) metabolic alteration - the compensatory upregulation of glycolysis to offset mitochondrial impairments. This paper appeals to the theory of Quantum Metabolism and the principles of natural selection to formulate a conceptual framework for a quantitative analysis of the origin and proliferation of the disease. Quantum Metabolism, an analytical theory of energy transduction in cells inspired by the methodology of the quantum theory of solids, elucidates the molecular basis for differences in metabolic rate between normal cells, utilizing predominantly oxidative phosphorylation, and cancer cells utilizing predominantly glycolysis. The principles of natural selection account for the outcome of competition between the two classes of cells. Quantum Metabolism and the principles of natural selection give an ontogenic and evolutionary rationale for cancer proliferation and furnish a framework for effective therapeutic strategies to impede the spread of the disease.

  10. Selection by pollinators on floral traits in generalized Trollius ranunculoides (Ranunculaceae) along altitudinal gradients.

    PubMed

    Zhao, Zhi-Gang; Wang, Yi-Ke

    2015-01-01

    Abundance and visitation of pollinator assemblages tend to decrease with altitude, leading to an increase in pollen limitation. Thus increased competition for pollinators may generate stronger selection on attractive traits of flowers at high elevations and cause floral adaptive evolution. Few studies have related geographically variable selection from pollinators and intraspecific floral differentiation. We investigated the variation of Trollius ranunculoides flowers and its pollinators along an altitudinal gradient on the eastern Qinghai-Tibet Plateau, and measured phenotypic selection by pollinators on floral traits across populations. The results showed significant decline of visitation rate of bees along altitudinal gradients, while flies was unchanged. When fitness is estimated by the visitation rate rather than the seed number per plant, phenotypic selection on the sepal length and width shows a significant correlation between the selection strength and the altitude, with stronger selection at higher altitudes. However, significant decreases in the sepal length and width of T. ranunculoides along the altitudinal gradient did not correspond to stronger selection of pollinators. In contrast to the pollinator visitation, mean annual precipitation negatively affected the sepal length and width, and contributed more to geographical variation in measured floral traits than the visitation rate of pollinators. Therefore, the sepal size may have been influenced by conflicting selection pressures from biotic and abiotic selective agents. This study supports the hypothesis that lower pollinator availability at high altitude can intensify selection on flower attractive traits, but abiotic selection is preventing a response to selection from pollinators.

  11. A database of annotated tentative orthologs from crop abiotic stress transcripts.

    PubMed

    Balaji, Jayashree; Crouch, Jonathan H; Petite, Prasad V N S; Hoisington, David A

    2006-10-07

    A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species. For this purpose, ESTs from stress cDNA libraries across 16 crop species including 6 important cereal crops and 10 dicots were systematically collated and subjected to bioinformatics analysis such as clustering, grouping of tentative orthologous sets, identification of protein motifs/patterns in the predicted protein sequence, and annotation with stress conditions, tissue/library source and putative function. All data are available to the scientific community at http://intranet.icrisat.org/gt1/tog/homepage.htm. We believe that the availability of annotated plant abiotic stress ortholog sets will be a valuable resource for researchers studying the biology of environmental stresses in plant systems, molecular evolution and genomics.

  12. Pharmacological Evidence for Calcium Involvement in the Long-Term Processing of Abiotic Stimuli in Plants

    PubMed Central

    Verdus, Marie-Claire; Le Sceller, Lois; Norris, Victor; Thellier, Michel

    2007-01-01

    Information about abiotic conditions is stored for long periods in plants and, in flax seedlings, can lead to the production of meristems. To investigate the underlying mechanism, flax seedlings were given abiotic stimuli that included a mechanical stimulus (by manipulation), one or two cold shocks, a slow cold treatment and a drought stress and, if these seedlings were then subjected to a temporary (1 to 3 days) depletion of calcium, epidermal meristems were produced in the seedling hypocotyls. This production was inhibited by the addition to the nutrient media of EGTA, ruthenium red, lanthanum or gadolinium that affect calcium availability or calcium transport. Use of these agents revealed a period of vulnerability in information processing that was less than two min for mechanical stimuli and over five min for other abiotic stimuli, consistent with information about mechanical stimuli being stored particularly fast. We propose that external calcium is needed for the transduction/storage of the information for meristem production whilst a temporary depletion of external calcium is needed for the actual production of meristems. Such roles for calcium would be consistent with a mechanism based on ion condensation on charged polymers. PMID:19516991

  13. Pharmacological evidence for calcium involvement in the long-term processing of abiotic stimuli in plants.

    PubMed

    Verdus, Marie-Claire; Le Sceller, Lois; Norris, Victor; Thellier, Michel; Ripoll, Camille

    2007-07-01

    Information about abiotic conditions is stored for long periods in plants and, in flax seedlings, can lead to the production of meristems. To investigate the underlying mechanism, flax seedlings were given abiotic stimuli that included a mechanical stimulus (by manipulation), one or two cold shocks, a slow cold treatment and a drought stress and, if these seedlings were then subjected to a temporary (1 to 3 days) depletion of calcium, epidermal meristems were produced in the seedling hypocotyls. This production was inhibited by the addition to the nutrient media of EGTA, ruthenium red, lanthanum or gadolinium that affect calcium availability or calcium transport. Use of these agents revealed a period of vulnerability in information processing that was less than two min for mechanical stimuli and over five min for other abiotic stimuli, consistent with information about mechanical stimuli being stored particularly fast. We propose that external calcium is needed for the transduction/storage of the information for meristem production whilst a temporary depletion of external calcium is needed for the actual production of meristems. Such roles for calcium would be consistent with a mechanism based on ion condensation on charged polymers.

  14. Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model.

    PubMed

    Lany, Nina K; Zarnetske, Phoebe L; Schliep, Erin M; Schaeffer, Robert N; Orians, Colin M; Orwig, David A; Preisser, Evan L

    2018-05-01

    A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions. © 2018 by the Ecological Society of America.

  15. Collective Syntheses of Icetexane Natural Products Based on Biogenetic Hypotheses.

    PubMed

    Thommen, Christophe; Neuburger, Markus; Gademann, Karl

    2017-01-01

    A divergent synthesis of 10 icetexane natural products based on a proposed biogenetic cationic ring expansion of a reduced carnosic acid derivative is described. Of these icetexanes, (+)-salvicanol, (-)-cyclocoulterone, (-)-coulterone, (-)-obtusinone D, and (-)-obtusinone E have been synthesized for the first time. In addition, the hypothesis for the non-enzymatic biogenesis of benzo[1,3]dioxole natural products has been experimentally investigated. Additional experimental evidence for the abiotic formation of the methylenedioxy unit is provided, as photolysis of the quinone (+)-komaroviquinone resulted in the formation of the [1,3]dioxole-containing natural product (-)-cyclocoulterone and (+)-komarovispirone. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. African Orphan Crops under Abiotic Stresses: Challenges and Opportunities.

    PubMed

    Tadele, Zerihun

    2018-01-01

    A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as "orphan crops") including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented.

  17. African Orphan Crops under Abiotic Stresses: Challenges and Opportunities

    PubMed Central

    2018-01-01

    A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as “orphan crops”) including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented. PMID:29623231

  18. Genome-wide detection of natural selection in African Americans pre- and post-admixture

    PubMed Central

    Jin, Wenfei; Xu, Shuhua; Wang, Haifeng; Yu, Yongguo; Shen, Yiping; Wu, Bailin; Jin, Li

    2012-01-01

    It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped in 5210 individuals and conducted a genome-wide search for selection signals in 1890 AfA. Several genomic regions showing an excess of African or European ancestry, which were considered the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre- and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA-specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to a new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than those in IAF, which is consistent with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre- and post-population admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs. PMID:22128132

  19. The Power of Natural Selection: A Guided Investigation of Three Case Studies

    ERIC Educational Resources Information Center

    Beachly, William

    2010-01-01

    I describe a quantitative approach to three case studies in evolution that can be used to challenge college freshmen to explore the power of natural selection and ask questions that foster a deeper understanding of its operation and relevance. Hemochromatosis, the peppered moth, and hominid cranial capacity are investigated with a common algebraic…

  20. Using the FAR Guide to Teach Simulations: An Example with Natural Selection

    ERIC Educational Resources Information Center

    Sickel, Aaron J.; Friedrichsen, Patricia J.

    2012-01-01

    Engaging students in a predator-prey simulation to teach natural selection is a common activity in secondary biology classrooms. The purpose of this article is to demonstrate how the authors have changed their approach to teaching this activity from a laboratory investigation to a class-constructed simulation. Specifically, the authors drew upon a…

  1. Identification of QTL in a tepary bean RIL population under abiotic stress

    USDA-ARS?s Scientific Manuscript database

    High temperatures and drought are critical abiotic factors that limit the production of grain legumes, especially in tropical countries. Tepary bean (Phaseolus acutifolius A. Gray) is a species that is tolerant to high temperatures and drought. It is also closely related to common bean (Phaseolus vu...

  2. Evidence of Natural Selection Acting on a Polymorphic Hybrid Incompatibility Locus in Mimulus

    PubMed Central

    Sweigart, Andrea L.; Flagel, Lex E.

    2015-01-01

    As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci—hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)—to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species. PMID:25428983

  3. Evidence of natural selection acting on a polymorphic hybrid incompatibility locus in Mimulus.

    PubMed

    Sweigart, Andrea L; Flagel, Lex E

    2015-02-01

    As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci-hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)-to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species. Copyright © 2015 by the Genetics Society of America.

  4. DISTINGUISHING A HYPOTHETICAL ABIOTIC PLANET–MOON SYSTEM FROM A SINGLE INHABITED PLANET

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Tong; Tian, Feng; Wei, Wanjing

    It has recently been suggested that an exomoon with a CH{sub 4} atmosphere, orbiting an abiotic Earth-mass planet with an O{sub 2}-rich atmosphere, can produce a false positive biosignature at a low–moderate spectral resolution (R = λ/Δλ ≤ 2000). If this were true, inferring the presence of life on exoplanets will be beyond our reach in the next several decades. Here we use a line-by-line radiative transfer model to compute the relevant reflection spectrum between 1 and 3.3 μm. We show that it is possible to separate the combined spectra of such planet–moon systems from an inhabited planet by multiple-band NIR observations.more » We suggest that future observations near the 2.3 μm CH{sub 4} absorption band at a resolution of 100 and an SNR of 10 or more may be a good way to distinguish an abiotic planet–moon system from a inhabited single planet.« less

  5. Growth, viability and architecture of biofilms of Listeria monocytogenes formed on abiotic surfaces.

    PubMed

    Reis-Teixeira, Fernanda Barbosa Dos; Alves, Virgínia Farias; de Martinis, Elaine Cristina Pereira

    The pathogenic bacterium Listeria monocytogenes can persist in food processing plants for many years, even when appropriate hygienic measures are in place, with potential for contaminating ready-to-eat products and, its ability to form biofilms on abiotic surfaces certainly contributes for the environmental persistence. In this research, L. monocytogenes was grown in biofilms up 8 days attached to stainless steel and glass surfaces, contributing for advancing the knowledge on architecture of mature biofilms, since many literature studies carried out on this topic considered only early stages of cell adhesion. In this study, biofilm populations of two strains of L. monocytogenes (serotypes 1/2a and 4b) on stainless steel coupons and glass were examined using regular fluorescence microscopy, confocal laser scanning microscopy and classic culture method. The biofilms formed were not very dense and microscopic observations revealed uneven biofilm structures, with presence of exopolymeric matrix surrounding single cells, small aggregates and microcolonies, in a honeycomb-like arrangement. Moreover, planktonic population of L. monocytogenes (present in broth media covering the abiotic surface) remained stable throughout the incubation time, which indicates an efficient dispersal mechanism, since the culture medium was replaced daily. In conclusion, even if these strains of L. monocytogenes were not able to form thick multilayer biofilms, it was noticeable their high persistence on abiotic surfaces, reinforcing the need to focus on measures to avoid biofilm formation, instead of trying to eradicate mature biofilms. Copyright © 2017. Published by Elsevier Editora Ltda.

  6. Using thermodynamics to assess biotic and abiotic impediments to root water uptake

    NASA Astrophysics Data System (ADS)

    Bechmann, Marcel; Hildebrandt, Anke; Kleidon, Axel

    2016-04-01

    Root water uptake has been the subject of extensive research, dealing with understanding the processes limiting transpiration and understanding strategies of plants to avoid water stress. Many of those studies use models of water flow from the soil through the plant into the atmosphere to learn about biotic and abiotic factors affecting plant water relations. One important question in this context is to identify those processes that are most limiting to water transport, and specifically whether these processes lie within the plant or the soil? Here, we propose to use a thermodynamic formulation of root water uptake to answer this question. The method allows us to separate the energy exported at the root collar into a sum of energy fluxes related to all processes along the flow path, notably including the effect of increasing water retention in drier soils. Evaluation of the several contributions allows us to identify and rank the processes by how much these impede water flow from the soil to the atmosphere. The application of this approach to a complex 3-dimensional root water uptake model reveals insights on the role of root versus soil resistances to limit water flow. We investigate the efficiency of root water uptake in an ensemble of root systems with varying root hydraulic properties. While root morphology is kept the same, root radial and axial resistances are artificially varied. Starting with entirely young systems (uptake roots, high radial, low axial conductance) we increasingly add older roots (transport roots, high axial, low radial conductance) to improve transport within root systems. This yields a range of root hydraulic architectures, where the extremes are limited either by radial uptake capacity or low capacity to transport water along the root system. We model root water uptake in this range of root systems with a 3-dimensional root water uptake model in two different soils, applying constant flux boundary conditions in a dry down experiment and

  7. Assessing the effects of abiotic stress and livestock grazing disturbance on an alpine grassland with CSR model

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Luo, Peng; Mou, Chengxiang; Yang, Hao; Mo, Li; Luo, Chuan; Kattge, Jens

    2016-04-01

    How the abiotic factors represented by cold environment and biotic factors represented by livestock grazing will affect the vegetation structure of alpine grassland is a core issue in understanding the cause of biodiversity change on Tibetan Plateau. Past studies on changes of floristic composition, growth forms did not adequately answer question. Given the fact that the response of plant to environment change depend on its life strategy, a synthetical method that based on plant life strategy may deepen our understanding of the mechanism. Using Grime's concept of CSR plant classification, we carried out a vegetation survey along a gradient (three levels) of graze intensity on the south-east of Tibet Plateau, in order to evaluate the role and mechanism of abiotic stress and grazing disturbance in driving plant diversity change, by analyzing the plant life strategy compositions in each of the community and by comparing the characteristic of the strategy compositions along the graze gradient. When the graze intensity was relative low, the dominant plant life strategy gathered in the stress tolerance corner, which conformed the theory of environmental filter, indicating that the ideal top plant community may be dominated by the species with stress tolerant strategy. We also found that the response of strategy dominance to graze intensity increase is positively correlated with the competitive capacity (R 2=0.671; P<0.001) and negatively correlated with the capacity of tolerating stress (R 2=0.378; P=0.011), but is not affected by the ruderal strategy (R 2=0.047; P=0.42). This reflected a general shift of plant strategy from stress tolerant to competitive (rather than ruderal as expected) and suggested that the mechanism of graze to affect plant community is different from that of other disturbance like fire, clipping, till, etc. The particular selective foraging and escaping from feces may provide more opportunities for competitive than ruderal strategy to dominant the

  8. Active insecticides for Diaphania hyalinata selective for the natural enemy Solenopsis saevissima.

    PubMed

    Aguiar, Alex R; Alvarenga, Elson S; Lopes, Mayara C; Santos, Izailda B Dos; Galdino, Tarcisio V; Picanço, Marcelo C

    2016-09-01

    The objective of this study was to determine the toxicity of the nine synthetic dienamides against the insect pest Diaphania hyalinata (melonworm) and the selectivity of these substances for the predator Solenopsis saevissima (fire ant). Four bioassays were conducted. To begin with, the dienamides that caused high mortality of D. hyalinata have been selected. In the second bioassay the dose-mortality curves of the selected dienamides have been constructed. In the third bioassay, the survival curves for D. hyalinata and the elapsed time to kill 50% of their population have been determined. In the fourth biological test, the selectivity of the substances to the predator S. saevissima has been evaluated. The most active (2E,4E)-N-butylhexa-2,4-dienamide 3d has killed 95% of the melonworm, D. hyalinata, and less than 10% of the natural enemy S. saevissima. The results presented by this compound are superior to the outcome displayed by the commercial insecticide Malathion®. Three of the dienamides prepared in this manuscript have proven to be selective in killing the pest, but not the beneficial insect.

  9. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves.

    PubMed

    Schweizer, Rena M; Durvasula, Arun; Smith, Joel; Vohr, Samuel H; Stahler, Daniel R; Galaverni, Marco; Thalmann, Olaf; Smith, Douglas W; Randi, Ettore; Ostrander, Elaine A; Green, Richard E; Lohmueller, Kirk E; Novembre, John; Wayne, Robert K

    2018-05-01

    Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.

  10. Compensatory selection for roads over natural linear features by wolves in northern Ontario: Implications for caribou conservation

    PubMed Central

    Patterson, Brent R.; Anderson, Morgan L.; Rodgers, Arthur R.; Vander Vennen, Lucas M.; Fryxell, John M.

    2017-01-01

    Woodland caribou (Rangifer tarandus caribou) in Ontario are a threatened species that have experienced a substantial retraction of their historic range. Part of their decline has been attributed to increasing densities of anthropogenic linear features such as trails, roads, railways, and hydro lines. These features have been shown to increase the search efficiency and kill rate of wolves. However, it is unclear whether selection for anthropogenic linear features is additive or compensatory to selection for natural (water) linear features which may also be used for travel. We studied the selection of water and anthropogenic linear features by 52 resident wolves (Canis lupus x lycaon) over four years across three study areas in northern Ontario that varied in degrees of forestry activity and human disturbance. We used Euclidean distance-based resource selection functions (mixed-effects logistic regression) at the seasonal range scale with random coefficients for distance to water linear features, primary/secondary roads/railways, and hydro lines, and tertiary roads to estimate the strength of selection for each linear feature and for several habitat types, while accounting for availability of each feature. Next, we investigated the trade-off between selection for anthropogenic and water linear features. Wolves selected both anthropogenic and water linear features; selection for anthropogenic features was stronger than for water during the rendezvous season. Selection for anthropogenic linear features increased with increasing density of these features on the landscape, while selection for natural linear features declined, indicating compensatory selection of anthropogenic linear features. These results have implications for woodland caribou conservation. Prey encounter rates between wolves and caribou seem to be strongly influenced by increasing linear feature densities. This behavioral mechanism–a compensatory functional response to anthropogenic linear feature

  11. Compensatory selection for roads over natural linear features by wolves in northern Ontario: Implications for caribou conservation.

    PubMed

    Newton, Erica J; Patterson, Brent R; Anderson, Morgan L; Rodgers, Arthur R; Vander Vennen, Lucas M; Fryxell, John M

    2017-01-01

    Woodland caribou (Rangifer tarandus caribou) in Ontario are a threatened species that have experienced a substantial retraction of their historic range. Part of their decline has been attributed to increasing densities of anthropogenic linear features such as trails, roads, railways, and hydro lines. These features have been shown to increase the search efficiency and kill rate of wolves. However, it is unclear whether selection for anthropogenic linear features is additive or compensatory to selection for natural (water) linear features which may also be used for travel. We studied the selection of water and anthropogenic linear features by 52 resident wolves (Canis lupus x lycaon) over four years across three study areas in northern Ontario that varied in degrees of forestry activity and human disturbance. We used Euclidean distance-based resource selection functions (mixed-effects logistic regression) at the seasonal range scale with random coefficients for distance to water linear features, primary/secondary roads/railways, and hydro lines, and tertiary roads to estimate the strength of selection for each linear feature and for several habitat types, while accounting for availability of each feature. Next, we investigated the trade-off between selection for anthropogenic and water linear features. Wolves selected both anthropogenic and water linear features; selection for anthropogenic features was stronger than for water during the rendezvous season. Selection for anthropogenic linear features increased with increasing density of these features on the landscape, while selection for natural linear features declined, indicating compensatory selection of anthropogenic linear features. These results have implications for woodland caribou conservation. Prey encounter rates between wolves and caribou seem to be strongly influenced by increasing linear feature densities. This behavioral mechanism-a compensatory functional response to anthropogenic linear feature

  12. Abiotic Transformation Of Estrogens In Synthetic Municipal Wastewater: An Alternative For Treatment?

    EPA Science Inventory

    The abiotic transformation of estrogens, including estrone (E1), estradiol (E2), estriol (E3) and ethinylestradiol (EE2), in the presence of model vegetable matter was confirmed in this study. Batch experiments were performed to model the catalytic conversion of E1, E2, E3, and ...

  13. Norwegian honey bees surviving Varroa destructor mite infestations by means of natural selection.

    PubMed

    Oddie, Melissa A Y; Dahle, Bjørn; Neumann, Peter

    2017-01-01

    Managed, feral and wild populations of European honey bee subspecies, Apis mellifera , are currently facing severe colony losses globally. There is consensus that the ectoparasitic mite Varroa destructor , that switched hosts from the Eastern honey bee Apis cerana to the Western honey bee A. mellifera , is a key factor driving these losses. For >20 years, breeding efforts have not produced European honey bee colonies that can survive infestations without the need for mite control. However, at least three populations of European honey bees have developed this ability by means of natural selection and have been surviving for >10 years without mite treatments. Reduced mite reproductive success has been suggested as a key factor explaining this natural survival. Here, we report a managed A. mellifera population in Norway, that has been naturally surviving consistent V. destructor infestations for >17 years. Surviving colonies and local susceptible controls were evaluated for mite infestation levels, mite reproductive success and two potential mechanisms explaining colony survival: grooming of adult worker bees and Varroa Sensitive Hygiene (VSH): adult workers specifically detecting and removing mite-infested brood. Mite infestation levels were significantly lower in surviving colonies and mite reproductive success was reduced by 30% when compared to the controls. No significant differences were found between surviving and control colonies for either grooming or VSH. Our data confirm that reduced mite reproductive success seems to be a key factor for natural survival of infested A. mellifera colonies. However, neither grooming nor VSH seem to explain colony survival. Instead, other behaviors of the adult bees seem to be sufficient to hinder mite reproductive success, because brood for this experiment was taken from susceptible donor colonies only. To mitigate the global impact of V. destructor , we suggest learning more from nature, i.e., identifying the obviously

  14. Norwegian honey bees surviving Varroa destructor mite infestations by means of natural selection

    PubMed Central

    Dahle, Bjørn; Neumann, Peter

    2017-01-01

    Background Managed, feral and wild populations of European honey bee subspecies, Apis mellifera, are currently facing severe colony losses globally. There is consensus that the ectoparasitic mite Varroa destructor, that switched hosts from the Eastern honey bee Apis cerana to the Western honey bee A. mellifera, is a key factor driving these losses. For >20 years, breeding efforts have not produced European honey bee colonies that can survive infestations without the need for mite control. However, at least three populations of European honey bees have developed this ability by means of natural selection and have been surviving for >10 years without mite treatments. Reduced mite reproductive success has been suggested as a key factor explaining this natural survival. Here, we report a managed A. mellifera population in Norway, that has been naturally surviving consistent V. destructor infestations for >17 years. Methods Surviving colonies and local susceptible controls were evaluated for mite infestation levels, mite reproductive success and two potential mechanisms explaining colony survival: grooming of adult worker bees and Varroa Sensitive Hygiene (VSH): adult workers specifically detecting and removing mite-infested brood. Results Mite infestation levels were significantly lower in surviving colonies and mite reproductive success was reduced by 30% when compared to the controls. No significant differences were found between surviving and control colonies for either grooming or VSH. Discussion Our data confirm that reduced mite reproductive success seems to be a key factor for natural survival of infested A. mellifera colonies. However, neither grooming nor VSH seem to explain colony survival. Instead, other behaviors of the adult bees seem to be sufficient to hinder mite reproductive success, because brood for this experiment was taken from susceptible donor colonies only. To mitigate the global impact of V. destructor, we suggest learning more from nature, i

  15. The role of water tracks in altering biotic and abiotic soil properties and processes in a polar desert in Antarctica

    NASA Astrophysics Data System (ADS)

    Ball, Becky A.; Levy, Joseph

    2015-02-01

    Groundwater discharge via water tracks is a largely unexplored passageway routing salts and moisture from high elevations to valley floors in the McMurdo Dry Valleys (MDV) of Antarctica. Given the influence that water tracks have on the distribution of liquid water in seasonally thawed Antarctic soils, it is surprising how little is known about their role in structuring biotic and abiotic processes this cold desert ecosystem. Particularly, it is unclear how soil biota will respond to the activation of new water tracks resulting from enhanced active layer thickening or enhanced regional snowmelt. In the MDV, water tracks are both wetter and more saline than the surrounding soils, constituting a change in soil habitat suitability for soil biology and therefore the ecological processes they carry out. To investigate the net impact that water tracks have on Dry Valley soil biology, and therefore the ecosystem processes for which they are responsible, we analyzed microbial biomass and activity in soils inside and outside of three water tracks and relate this to the physical soil characteristics. Overall, our results suggest that water tracks can significantly influence soil properties, which can further impact biological biovolume and both biotic and abiotic fluxes of CO2. However, the nature of its impact differs with water track, further suggesting that not all water tracks can be regarded the same.

  16. Selective Removal of Natural Occlusal Caries by Coupling Near-infrared Imaging with a CO2 Laser

    PubMed Central

    Tao, You-Chen; Fried, Daniel

    2011-01-01

    Laser removal of dental hard tissue can be combined with optical, spectral or acoustic feedback systems to selectively ablate dental caries and restorative materials. Near-infrared (NIR) imaging has considerable potential for the optical discrimination of sound and demineralized tissue. Last year we successfully demonstrated that near-IR images can be used to guide a CO2 laser ablation system for the selective removal of artificial caries lesions on smooth surfaces. The objective of this study was to test the hypothesis that two-dimensional near-infrared images of natural occlusal caries can be used to guide a CO2 laser for selective removal. Two-dimensional NIR images were acquired at 1310-nm of extracted human molar teeth with occlusal caries. Polarization sensitive optical coherence tomography (PS-OCT) was also used to acquire depth-resolved images of the lesion areas. An imaging processing module was developed to analyze the NIR imaging output and generate optical maps that were used to guide a CO2 laser to selectively remove the lesions at a uniform depth. Post-ablation NIR images were acquired to verify caries removal. Based on the analysis of the NIR images, caries lesions were selectively removed with a CO2 laser while sound tissues were conserved. However, the removal rate varied markedly with the severity of decay and multiple passes were required for caries removal. These initial results are promising but indicate that the selective removal of natural caries is more challenging than the selective removal of artificial lesions due to varying tooth geometry, the highly variable organic/mineral ratio in natural lesions and more complicated lesion structure. PMID:21909225

  17. Selective removal of natural occlusal caries by coupling near-infrared imaging with a CO II laser

    NASA Astrophysics Data System (ADS)

    Tao, You-Chen; Fried, Daniel

    2008-02-01

    Laser removal of dental hard tissue can be combined with optical, spectral or acoustic feedback systems to selectively ablate dental caries and restorative materials. Near-infrared (NIR) imaging has considerable potential for the optical discrimination of sound and demineralized tissue. Last year we successfully demonstrated that near-IR images can be used to guide a CO2 laser ablation system for the selective removal of artificial caries lesions on smooth surfaces. The objective of this study was to test the hypothesis that two-dimensional near-infrared images of natural occlusal caries can be used to guide a CO2 laser for selective removal. Two-dimensional NIR images were acquired at 1310-nm of extracted human molar teeth with occlusal caries. Polarization sensitive optical coherence tomography (PS-OCT) was also used to acquire depth-resolved images of the lesion areas. An imaging processing module was developed to analyze the NIR imaging output and generate optical maps that were used to guide a CO2 laser to selectively remove the lesions at a uniform depth. Post-ablation NIR images were acquired to verify caries removal. Based on the analysis of the NIR images, caries lesions were selectively removed with a CO2 laser while sound tissues were conserved. However, the removal rate varied markedly with the severity of decay and multiple passes were required for caries removal. These initial results are promising but indicate that the selective removal of natural caries is more challenging than the selective removal of artificial lesions due to varying tooth geometry, the highly variable organic/mineral ratio in natural lesions and more complicated lesion structure.

  18. Selective Removal of Natural Occlusal Caries by Coupling Near-infrared Imaging with a CO(2) Laser.

    PubMed

    Tao, You-Chen; Fried, Daniel

    2008-03-01

    Laser removal of dental hard tissue can be combined with optical, spectral or acoustic feedback systems to selectively ablate dental caries and restorative materials. Near-infrared (NIR) imaging has considerable potential for the optical discrimination of sound and demineralized tissue. Last year we successfully demonstrated that near-IR images can be used to guide a CO(2) laser ablation system for the selective removal of artificial caries lesions on smooth surfaces. The objective of this study was to test the hypothesis that two-dimensional near-infrared images of natural occlusal caries can be used to guide a CO(2) laser for selective removal. Two-dimensional NIR images were acquired at 1310-nm of extracted human molar teeth with occlusal caries. Polarization sensitive optical coherence tomography (PS-OCT) was also used to acquire depth-resolved images of the lesion areas. An imaging processing module was developed to analyze the NIR imaging output and generate optical maps that were used to guide a CO(2) laser to selectively remove the lesions at a uniform depth. Post-ablation NIR images were acquired to verify caries removal. Based on the analysis of the NIR images, caries lesions were selectively removed with a CO(2) laser while sound tissues were conserved. However, the removal rate varied markedly with the severity of decay and multiple passes were required for caries removal. These initial results are promising but indicate that the selective removal of natural caries is more challenging than the selective removal of artificial lesions due to varying tooth geometry, the highly variable organic/mineral ratio in natural lesions and more complicated lesion structure.

  19. Sexual and natural selection in the evolution of extended phenotypes: the use of green nesting material in starlings.

    PubMed

    Rubalcaba, J G; Polo, V; Maia, R; Rubenstein, D R; Veiga, J P

    2016-08-01

    Although sexual selection is typically considered the predominant force driving the evolution of ritualized sexual behaviours, natural selection may also play an important and often underappreciated role. The use of green aromatic plants among nesting birds has been interpreted as a component of extended phenotype that evolved either via natural selection due to potential sanitary functions or via sexual selection as a signal of male attractiveness. Here, we compared both hypotheses using comparative methods in starlings, a group where this behaviour is widespread. We found that the use of green plants was positively related to male-biased size dimorphism and that it was most likely to occur among cavity-nesting species. These results suggest that this behaviour is likely favoured by sexual selection, but also related to its sanitary use in response to higher parasite loads in cavities. We speculate that the use of green plants in starlings may be facilitated by cavity nesting and was subsequently co-opted as a sexual signal by males. Our results represent an example of how an extended phenotypic component of males becomes sexually selected by females. Thus, both natural selection and sexual selection are necessary to fully understand the evolution of ritualized behaviours involved in courtship. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  20. Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations.

    PubMed

    Will, Jessica L; Kim, Hyun Seok; Clarke, Jessica; Painter, John C; Fay, Justin C; Gasch, Audrey P

    2010-04-01

    A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw-tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function-providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments-contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.

  1. Incipient Balancing Selection through Adaptive Loss of Aquaporins in Natural Saccharomyces cerevisiae Populations

    PubMed Central

    Will, Jessica L.; Kim, Hyun Seok; Clarke, Jessica; Painter, John C.; Fay, Justin C.; Gasch, Audrey P.

    2010-01-01

    A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw–tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function—providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments—contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection. PMID:20369021

  2. Successful introgression of abiotic stress tolerance from wild tepary bean to common bean

    USDA-ARS?s Scientific Manuscript database

    Common bean (Phaseolus vulgaris L.) production is severely limited due to abiotic stresses, including drought and sub-zero temperatures. Tepary bean (Phaseolus acutifolius Gray), a relative of common bean, has demonstrated tolerance to these stresses. Preliminary studies screening tepary accessions ...

  3. Evidence of rock matrix back-diffusion and abiotic dechlorination using a field testing approach

    NASA Astrophysics Data System (ADS)

    Schaefer, Charles E.; Lippincott, David R.; Klammler, Harald; Hatfield, Kirk

    2018-02-01

    An in situ field demonstration was performed in fractured rock impacted with trichloroethene (TCE) and cis-1,2-dichloroethene (DCE) to assess the impacts of contaminant rebound after removing dissolved contaminants within hydraulically conductive fractures. Using a bedrock well pair spaced 2.4 m apart, TCE and DCE were first flushed with water to create a decrease in dissolved contaminant concentrations. While hydraulically isolating the well pair from upgradient contaminant impacts, contaminant rebound then was observed between the well pair over 151 days. The magnitude, but not trend, of TCE rebound was reasonably described by a matrix back-diffusion screening model that employed an effective diffusion coefficient and first-order abiotic TCE dechlorination rate constant that was based on bench-scale testing. Furthermore, a shift in the TCE:DCE ratio and carbon isotopic enrichment was observed during the rebound, suggesting that both biotic and abiotic dechlorination were occurring within the rock matrix. The isotopic data and back-diffusion model together served as a convincing argument that matrix back-diffusion was the mechanism responsible for the observed contaminant rebound. Results of this field demonstration highlight the importance and applicability of rock matrix parameters determined at the bench-scale, and suggest that carbon isotopic enrichment can be used as a line of evidence for abiotic dechlorination within rock matrices.

  4. Anionic Cerium Oxide Nanoparticles Protect Plant Photosynthesis from Abiotic Stress by Scavenging Reactive Oxygen Species.

    PubMed

    Wu, Honghong; Tito, Nicholas; Giraldo, Juan P

    2017-11-28

    Plant abiotic stress leads to accumulation of reactive oxygen species (ROS) and a consequent decrease in photosynthetic performance. We demonstrate that a plant nanobionics approach of localizing negatively charged, sub-11 nm, spherical cerium oxide nanoparticles (nanoceria) inside chloroplasts in vivo augments ROS scavenging and photosynthesis of Arabidopsis thaliana plants under excess light (2000 μmol m -2 s -1 , 1.5 h), heat (35 °C, 2.5 h), and dark chilling (4 °C, 5 days). Poly(acrylic acid) nanoceria (PNC) with a hydrodynamic diameter (10.3 nm)-lower than the maximum plant cell wall porosity-and negative ζ-potential (-16.9 mV) exhibit significantly higher colocalization (46%) with chloroplasts in leaf mesophyll cells than aminated nanoceria (ANC) (27%) of similar size (12.6 nm) but positive charge (9.7 mV). Nanoceria are transported into chloroplasts via nonendocytic pathways, influenced by the electrochemical gradient of the plasma membrane potential. PNC with a low Ce 3+ /Ce 4+ ratio (35.0%) reduce leaf ROS levels by 52%, including hydrogen peroxide, superoxide anion, and hydroxyl radicals. For the latter ROS, there is no known plant enzyme scavenger. Plants embedded with these PNC that were exposed to abiotic stress exhibit an increase up to 19% in quantum yield of photosystem II, 67% in carbon assimilation rates, and 61% in Rubisco carboxylation rates relative to plants without nanoparticles. In contrast, PNC with high Ce 3+ /Ce 4+ ratio (60.8%) increase overall leaf ROS levels and do not protect photosynthesis from oxidative damage during abiotic stress. This study demonstrates that anionic, spherical, sub-11 nm PNC with low Ce 3+ /Ce 4+ ratio can act as a tool to study the impact of oxidative stress on plant photosynthesis and to protect plants from abiotic stress.

  5. An alternative pathway for marine nitrous oxide production at oxic-anoxic interfaces from coupled biotic-abiotic reactions

    NASA Astrophysics Data System (ADS)

    Glass, J. B.; Stanton, C. L.; Ochoa, H.; Haslun, J. A.; Gandhi, H.; Taillefert, M.; Dichristina, T. J.; Stewart, F. J.; Klotz, M. G.; Ostrom, N. E.

    2016-02-01

    Marine emissions of nitrous oxide (N2O), a potent greenhouse gas, comprise approximately a third of global sources. Recent evidence suggests that the dominant source of N2O in seawater is the activity of ammonia-oxidizing Thaumarchaeota that lack characterized N2O-generating enzymes. Nitrous oxide may arise from a novel enzyme and/or abiotic reactions between nitrification intermediates, hydroxylamine (NH2OH) and nitric oxide (NO), and redox-active metals in seawater. Isotopic site preference, or difference in δ15N between the two nitrogen atoms in N2O, has been used as tracer for microbial N2O production pathways (-10 to 0‰ for nitrifier-denitrification and denitrification vs. 30-37‰ for nitrification via NH2OH oxidation). Seawater N2O site preference falls in between these two characterized end members, suggesting simultaneous production via a combination of both microbial pathways or via a novel mechanism with intermediate site preference. Here we show significant N2O production in abiotic experiments after addition of iron to seawater containing NH2OH and NO. The N2O produced from chemical reduction of NO by Fe(II) had a site preference of 16‰ whereas N2O produced from abiotic NH2OH oxidation had a site preference of 31‰. We propose that coupled biotic-abiotic N2O production pathways could contribute significant sources of N2O at marine oxic-anoxic interfaces.

  6. The Right "Fit": Exploring Science Teacher Candidates' Approaches to Natural Selection Within a Clinical Simulation

    NASA Astrophysics Data System (ADS)

    Dotger, Benjamin; Dotger, Sharon; Masingila, Joanna; Rozelle, Jeffrey; Bearkland, Mary; Binnert, Ashley

    2018-06-01

    Teachers and students struggle with the complexities surrounding the evolution of species and the process of natural selection. This article examines how science teacher candidates (STCs) engage in a clinical simulation that foregrounds two common challenges associated with natural selection—students' understanding of "survival of the fittest" and the variation of species over time. We outline the medical education pedagogy of clinical simulations and its recent diffusion to teacher education. Then, we outline the study that situates each STC in a one-to-one interaction with a standardized student who is struggling to accurately interpret natural selection concepts. In simulation with the standardized student, each STC is challenged to recognize content misconceptions and respond with appropriate instructional strategies and accurate explanations. Findings and implications center on the STCs' instructional practices in the simulation and the use of clinical learning environments to foster science teacher learning.

  7. The Right "Fit": Exploring Science Teacher Candidates' Approaches to Natural Selection Within a Clinical Simulation

    NASA Astrophysics Data System (ADS)

    Dotger, Benjamin; Dotger, Sharon; Masingila, Joanna; Rozelle, Jeffrey; Bearkland, Mary; Binnert, Ashley

    2017-04-01

    Teachers and students struggle with the complexities surrounding the evolution of species and the process of natural selection. This article examines how science teacher candidates (STCs) engage in a clinical simulation that foregrounds two common challenges associated with natural selection—students' understanding of "survival of the fittest" and the variation of species over time. We outline the medical education pedagogy of clinical simulations and its recent diffusion to teacher education. Then, we outline the study that situates each STC in a one-to-one interaction with a standardized student who is struggling to accurately interpret natural selection concepts. In simulation with the standardized student, each STC is challenged to recognize content misconceptions and respond with appropriate instructional strategies and accurate explanations. Findings and implications center on the STCs' instructional practices in the simulation and the use of clinical learning environments to foster science teacher learning.

  8. Role of Biotic and Abiotic Processes on Soil CO2 Dynamics in the McMurdo Dry Valleys, Antarctica

    NASA Astrophysics Data System (ADS)

    Risk, D. A.; Macintyre, C. M.; Lee, C.; Cary, C.; Shanhun, F.; Almond, P. C.

    2016-12-01

    In the harsh conditions of the Antarctic Dry Valleys, microbial activity has been recorded via measurements of soil carbon dioxide (CO2) concentration and surface efflux. However, high temporal resolution studies in the Dry Valleys have also shown that abiotic solubility-driven processes can strongly influence (and perhaps even dominate) the CO2 dynamics in these low flux environments and suggests that biological activity may be lower than previously thought. In this study, we aim to improve our understanding of CO2 dynamics (biotic and abiotic) in Antarctic Dry Valley soils using long-term automated measurements of soil CO2 surface flux and soil profile concentration at several sites, often at sub-diel frequency. We hypothesize that soil CO2 variations are driven primarily by environmental factors affecting CO2 solubility in soil solution, mainly temperature, and that these processes may even overprint biologic production in representative Dry Valley soils. Monitoring of all sites revealed only one likely biotic CO2 production event, lasting three weeks during the Austral summer and reaching fluxes of 0.4 µmol/m2/s. Under more typical low flux conditions (<0.10 µmol/m2/s) we observed a cyclical daily sink/source pattern consistent with CO2 solubility cycling that would not generally have been evident with normal synoptic afternoon sampling campaigns. Subsurface CO2 monitoring and a lab-controlled Antarctic soil simulation experiment confirmed that abiotic processes are capable of dominating soil CO2 variability. Diel temperature cycles crossing the freezing boundary revealed a dual abiotic cycle of solubility cycling and gas exclusion from ice formation observed only by high temporal frequency measurements (30 min). This work demonstrates a need for a numerical model to partition the dynamic abiotic processes underlying any biotic CO2 production in order to understand potential climate-change induced increases in microbial productivity in terrestrial Antarctica.

  9. In Darwinian evolution, feedback from natural selection leads to biased mutations.

    PubMed

    Caporale, Lynn Helena; Doyle, John

    2013-12-01

    Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as "random." Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context).  This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory. © 2013 New York Academy of Sciences.

  10. The abiotic environment of the interstitial of a small Swiss river in the foothills of the Alps and its influence on gravel spawning brown trout (Salmo trutta L.)

    NASA Astrophysics Data System (ADS)

    Schindler, Yael; Michel, Christian; Holm, Patricia; Alewell, Christine

    2010-05-01

    The hyporheic zone can be characterized by multiple abiotic parameters (e.g. bulk density, texture, temperature, oxygen, ammonium, nitrate) which are all influenced directly or indirectly by the exchange processes between surface water and groundwater. These processes can vary both in time and space and are mainly driven by river discharge, ground water level and flow patterns. The input of fine sediment particles can change water-riverbed interactions through river bed clogging potentially affecting the embryonal development and survival of gravel spawning fish, such as brown trout (Salmo trutta L.). With our investigations we aim to understand these complex interactions spatially and temporally on a relevant small scale, i.e. within individual artificial brown trout redds. We designed an experimental field setup to directly investigate i) the influence of the abiotic river and redd environment on brown trout embryo development and ii) the hydrological dynamics affecting the abiotic environment in artificial brown trout. Additionally, our setup allows investigating the temporal dynamics of i) fine-sediment infiltration into the artificial redds and ii) embryo survival to two distinct developmental stages (i.e. eyed stage and hatch) The experiment was conducted in three sites of a typical Swiss river (Enziwigger, Canton of Luzern) with a strongly modified morphology. Individual sites represented a high, medium and low fine-sediment load. In each site, six artificial redds (18 in total) were built and data were collected during the entire incubation phase. Redds were located in places where natural spawning of brown trout is present. We adapted multiple established methods to the smaller scale of our river to study the dynamics of the most relevant abiotic parameters potentially affecting embryo development: Oxygen content and temperature was monitored continuously in different depths, fine sediment (bedload, suspended sediment load and its input in the river bed

  11. Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress.

    PubMed

    Singh, Roshan Kumar; Jaishankar, Jananee; Muthamilarasan, Mehanathan; Shweta, Shweta; Dangi, Anand; Prasad, Manoj

    2016-09-02

    Heat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.

  12. An analysis of phenotypic selection in natural stands of northern red oak (Quercus rubra L.)

    Treesearch

    Jeffery W. Stringer; David B. Wagner; Scott E. Schlarbaum; Daniel B. Houston

    1995-01-01

    Comparison of growth and stem quality parameters of 19-year-old progeny from superior and comparison trees indicates that rigorous phenotypic selection of trees in natural stands may not be an efficient method of parent tree selection for Quercus rubra L. Total tree height, dbh, number of branches in the butt log, fork height, and number of mainstem...

  13. Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa).

    PubMed

    Nguyen Dinh, Sy; Sai, Than Zaw Tun; Nawaz, Ghazala; Lee, Kwanuk; Kang, Hunseung

    2016-08-20

    Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. The impacts of selective logging and clear-cutting on woody plant diversity after 40years of natural recovery in a tropical montane rain forest, south China.

    PubMed

    Ding, Yi; Zang, Runguo; Lu, Xinghui; Huang, Jihong

    2017-02-01

    Historically, clear-cutting and selective logging have been the commercial logging practices. However, the effect of these pervasive timber extraction methods on biodiversity in tropical forests is still poorly understood. In this study, we compared abiotic factors, species diversity, community composition, and structure between ca. 40-year-old clear-cut (MCC); ca. 40-year-old selectively logged (MSL); and tropical old growth montane rain forests (MOG) on Hainan Island, China. Results showed that there were a large number of trees with a diameter at breast height (DBH) <30cm in the two logged forests. Additionally, the two logged forests only had 40% of the basal area of the large trees (DBH≥30cm) found in the old growth forest. The species richness and Shannon-Wiener diversity indices generally showed no difference among the three forest types. MCC had 70% of the species richness of the large trees in the MOG, whereas MSL and MOG had similar species richness. High value timber species had similar species richness among the three forest types, but a lower abundance and basal area of large trees in MCC. The species composition was distinct between the three forests. Large trees belonging to the family Fagaceae dominated in the logged forests and played a more important role in the old growth forest. Huge trees (DBH≥70cm) were rare in MCC, but were frequently found in MSL. Most abiotic factors varied inconsistently among the three forest types and few variables related to species diversity, community structure and composition. Our study indicated that MSL had a relatively faster recovery rate than MCC in a tropical montane rain forest after 40years, but both logged forests had a high recovery potential over a long-term. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Flowering phenology, growth forms, and pollination syndromes in tropical dry forest species: Influence of phylogeny and abiotic factors.

    PubMed

    Cortés-Flores, Jorge; Hernández-Esquivel, Karen Beatriz; González-Rodríguez, Antonio; Ibarra-Manríquez, Guillermo

    2017-01-01

    Analyses of the influence of temporal variation in abiotic factors on flowering phenology of tropical dry forest species have not considered the possible response of species with different growth forms and pollination syndromes, while controlling for phylogenetic relationships among species. Here, we investigated the relationship between flowering phenology, abiotic factors, and plant functional attributes, while controlling for phylogenetic relationship among species, in a dry forest community in Mexico. We characterized flowering phenology (time and duration) and pollination syndromes of 55 tree species, 49 herbs, 24 shrubs, 15 lianas, and 11 vines. We tested the influence of pollination syndrome, growth form, and abiotic factors on flowering phenology using phylogenetic generalized least squares. We found a relationship between flowering duration and time. Growth form was related to flowering time, and the pollination syndrome had a more significant relationship with flowering duration. Flowering time variation in the community was explained mainly by abiotic variables, without an important phylogenetic effect. Flowering time in lianas and trees was negatively and positively correlated with daylength, respectively. Functional attributes, environmental cues, and phylogeny interact with each other to shape the diversity of flowering patterns. Phenological differentiation among species groups revealed multiples strategies associated with growth form and pollination syndromes that can be important for understanding species coexistence in this highly diverse plant community. © 2017 Botanical Society of America.

  16. High-throughput profiling and analysis of plant responses over time to abiotic stress

    USDA-ARS?s Scientific Manuscript database

    Energy sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass, annual crop prized for abiotic stress tolerance. Measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. High throughput phenotyping within controlled environments has been proposed as a po...

  17. Biological Principles and Threshold Concepts for Understanding Natural Selection. Implications for Developing Visualizations as a Pedagogic Tool

    NASA Astrophysics Data System (ADS)

    Tibell, Lena A. E.; Harms, Ute

    2017-11-01

    Modern evolutionary theory is both a central theory and an integrative framework of the life sciences. This is reflected in the common references to evolution in modern science education curricula and contexts. In fact, evolution is a core idea that is supposed to support biology learning by facilitating the organization of relevant knowledge. In addition, evolution can function as a pivotal link between concepts and highlight similarities in the complexity of biological concepts. However, empirical studies in many countries have for decades identified deficiencies in students' scientific understanding of evolution mainly focusing on natural selection. Clearly, there are major obstacles to learning natural selection, and we argue that to overcome them, it is essential to address explicitly the general abstract concepts that underlie the biological processes, e.g., randomness or probability. Hence, we propose a two-dimensional framework for analyzing and structuring teaching of natural selection. The first—purely biological—dimension embraces the three main principles variation, heredity, and selection structured in nine key concepts that form the core idea of natural selection. The second dimension encompasses four so-called thresholds, i.e., general abstract and/or non-perceptual concepts: randomness, probability, spatial scales, and temporal scales. We claim that both of these dimensions must be continuously considered, in tandem, when teaching evolution in order to allow development of a meaningful understanding of the process. Further, we suggest that making the thresholds tangible with the aid of appropriate kinds of visualizations will facilitate grasping of the threshold concepts, and thus, help learners to overcome the difficulties in understanding the central theory of life.

  18. The importance of disturbance by fire and other abiotic and biotic factors in driving cheatgrass invasion varies based on invasion stage

    Treesearch

    Becky K. Kerns; Michelle A. Day

    2017-01-01

    Disturbances create fluctuations in resource availability that alter abiotic and biotic constraints. Exotic invader response may be due to multiple factors related to disturbance regimes and complex interactions between other small- and largescale abiotic and biotic processes that may vary across invasion stages. We explore how cheatgrass responds to both frequency and...

  19. Charles Darwin, Richard Owen, and Natural Selection: A Question of Priority.

    PubMed

    Johnson, Curtis N

    2018-05-03

    No single author presented Darwin with a more difficult question about his priority in discovering natural selection than the British comparative anatomist and paleontologist Richard Owen. Owen was arguably the most influential biologist in Great Britain in Darwin's time. Darwin wanted his approbation for what he believed to be his own theory of natural selection. Unfortunately for Darwin, when Owen first commented in publication about Darwin's theory of descent he was openly hostile (Edinb. Rev. vol. 111, Article VIII, 1860, pp. 487-533, anonymous). Darwin was taken off-guard. In private meetings and correspondence prior to 1860 Owen had been nothing but polite and friendly, even helping Darwin in cataloguing and analyzing Darwin's zoological specimens from the Beagle voyage. Every early indication predicted a life-long friendship and collaboration. But that was not to be. Owen followed his slashing review with a mounting campaign in the 1860s to denounce and discredit both Darwin and his small but ascendant circle of friends and supporters. But that was not enough for Owen. Starting in 1866, perhaps by now realizing Darwin had landed the big fish, Owen launched a new campaign, to claim the discovery of "Darwin's theory" for himself. Darwin naturally fought back, mainly in the "Historical Sketch" that he prefaced to Origin starting in 1861. But when we peel back the layers of personal animus and escalating vituperation we discover in fact their quarrel was generated more by mutual misunderstanding than scientific disagreement. The battle ended only when Darwin finally penetrated to the crux of the matter and put an end to the rivalry in 1872, in the final version of the Sketch.

  20. Selection by Pollinators on Floral Traits in Generalized Trollius ranunculoides (Ranunculaceae) along Altitudinal Gradients

    PubMed Central

    Zhao, Zhi-Gang; Wang, Yi-Ke

    2015-01-01

    Abundance and visitation of pollinator assemblages tend to decrease with altitude, leading to an increase in pollen limitation. Thus increased competition for pollinators may generate stronger selection on attractive traits of flowers at high elevations and cause floral adaptive evolution. Few studies have related geographically variable selection from pollinators and intraspecific floral differentiation. We investigated the variation of Trollius ranunculoides flowers and its pollinators along an altitudinal gradient on the eastern Qinghai-Tibet Plateau, and measured phenotypic selection by pollinators on floral traits across populations. The results showed significant decline of visitation rate of bees along altitudinal gradients, while flies was unchanged. When fitness is estimated by the visitation rate rather than the seed number per plant, phenotypic selection on the sepal length and width shows a significant correlation between the selection strength and the altitude, with stronger selection at higher altitudes. However, significant decreases in the sepal length and width of T. ranunculoides along the altitudinal gradient did not correspond to stronger selection of pollinators. In contrast to the pollinator visitation, mean annual precipitation negatively affected the sepal length and width, and contributed more to geographical variation in measured floral traits than the visitation rate of pollinators. Therefore, the sepal size may have been influenced by conflicting selection pressures from biotic and abiotic selective agents. This study supports the hypothesis that lower pollinator availability at high altitude can intensify selection on flower attractive traits, but abiotic selection is preventing a response to selection from pollinators. PMID:25692295

  1. On the unfitness of natural selection to explain sexual reproduction, and the difficulties that remain.

    PubMed

    van Rossum, Joris

    2006-01-01

    In its essence, the explanatory potential of the theory of natural selection is based on the iterative process of random production and variation, and subsequent non-random, directive selection. It is shown that within this explanatory framework, there is no place for the explanation of sexual reproduction. Thus in Darwinistic literature, sexual reproduction - one of nature's most salient characteristics - is often either assumed or ignored, but not explained. This fundamental and challenging gap within a complete naturalistic understanding of living beings calls for the need of a cybernetic account for sexual reproduction, meaning an understanding of the dynamic and creative potential of living beings to continuously and autonomously produce new organisms with unique and specific constellations.

  2. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealedmore » substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.« less

  3. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealedmore » substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.« less

  4. Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta

    PubMed Central

    Karlsson, Elinor K.; Harris, Jason B.; Tabrizi, Shervin; Rahman, Atiqur; Shlyakhter, Ilya; Patterson, Nick; O'Dushlaine, Colm; Schaffner, Stephen F.; Gupta, Sameer; Chowdhury, Fahima; Sheikh, Alaullah; Shin, Ok Sarah; Ellis, Crystal; Becker, Christine E.; Stuart, Lynda M.; Calderwood, Stephen B.; Ryan, Edward T.; Qadri, Firdausi; Sabeti, Pardis C.; LaRocque, Regina C.

    2015-01-01

    As an ancient disease with high fatality, cholera has likely exerted strong selective pressure on affected human populations. We performed a genome-wide study of natural selection in a population from the Ganges River Delta, the historic geographic epicenter of cholera. We identified 305 candidate selected regions using the Composite of Multiple Signals (CMS) method. The regions were enriched for potassium channel genes involved in cyclic AMP-mediated chloride secretion and for components of the innate immune system involved in NF-κB signaling. We demonstrate that a number of these strongly selected genes are associated with cholera susceptibility in two separate cohorts. We further identify repeated examples of selection and association in an NF-kB / inflammasome-dependent pathway that is activated in vitro by Vibrio cholerae. Our findings shed light on the genetic basis of cholera resistance in a population from the Ganges River Delta and present a promising approach for identifying genetic factors influencing susceptibility to infectious diseases. PMID:23825302

  5. Protein Tyrosine Nitration during Development and Abiotic Stress Response in Plants

    PubMed Central

    Mata-Pérez, Capilla; Begara-Morales, Juan C.; Chaki, Mounira; Sánchez-Calvo, Beatriz; Valderrama, Raquel; Padilla, María N.; Corpas, Francisco J.; Barroso, Juan B.

    2016-01-01

    In recent years, the study of nitric oxide (NO) in plant systems has attracted the attention of many researchers. A growing number of investigations have shown the significance of NO as a signal molecule or as a molecule involved in the response against (a)biotic processes. NO can be responsible of the post-translational modifications (NO-PTM) of target proteins by mechanisms such as the nitration of tyrosine residues. The study of protein tyrosine nitration during development and under biotic and adverse environmental conditions has increased in the last decade; nevertheless, there is also an endogenous nitration which seems to have regulatory functions. Moreover, the advance in proteome techniques has enabled the identification of new nitrated proteins, showing the high variability among plant organs, development stage and species. Finally, it may be important to discern between a widespread protein nitration because of greater RNS content, and the specific nitration of key targets which could affect cell-signaling processes. In view of the above point, we present a mini-review that offers an update about the endogenous protein tyrosine nitration, during plant development and under several abiotic stress conditions. PMID:27895655

  6. Interaction of abiotic and microbial processes in hexachloroethane reduction in groundwater

    USGS Publications Warehouse

    Roberts, A. Lynn; Gschwend, Philip M.

    1994-01-01

    In order to gain insight into mechanisms of hexachloroethane reduction, hexa- and pentachloroethane transformation rates were measured in anaerobic groundwater samples. For samples spiked with pentachloroethane, disappearance of pentachloroethane was accompanied by tetrachloroethylene production. Transformation rates were similar in unpoisoned and in HgCl2-poisoned samples, and rates were within ±20% of predictions based on measured pH and second-order dehydrochlorination rate constants determined in clean laboratory systems, indicating that the fate of pentachloroethane in this system is dominated by abiotic reactions. No hexachloroethane transformation was observed in HgCl2-poisoned samples, whereas in unpoisoned samples, hexachloroethane disappearance was accompanied by production of tetrachloroethylene as well as traces of pentachloroethane. Although only minor amounts of pentachloroethane accumulated, as much as 30% of the hexachloroethane transformation pathway proceeds via a pentachloroethane intermediate. This suggests that the microbial reduction of hexachloroethane proceeds at least in part through a free-radical mechanism. To the extent that hexachloroethane reduction to tetrachloroethylene occurs through a pentachloroethane intermediate, the first step in the sequence, the microbially-mediated step, is the slow step; the subsequent abiotic dehydrohalogenation step occurs much more rapidly.

  7. Abiotic and biotic controls over biogeochemical cycles in drylands: Insights from climate change and nitrogen deposition experiments on the Colorado Plateau

    NASA Astrophysics Data System (ADS)

    Reed, S.; Ferrenberg, S.; Tucker, C.; Rutherford, W. A.; Wertin, T. M.; McHugh, T. A.; Morrissey, E.; Kuske, C.; Mueller, R.; Belnap, J.

    2016-12-01

    As for all ecosystems, biogeochemical cycling in drylands represents numerous intricate connections between biotic and abiotic controls. However, patterns of many fundamental ecosystem processes that generally hold across global gradients fall apart at the arid and semiarid end of the spectrum, and data point to an exceptionally strong role for abiotic controls in explaining these patterns. Further, there are multiple dryland characteristics - such as extreme aridity and high UV radiation, as well as specialized biological communities - which can point to a conclusion that "drylands are different". Indeed, drylands are often characterized by their harsh environment, by the diverse classes of biota representing a range of traits aimed at surviving such harsh conditions, and, more recently, by the suggestion of dramatic biotic responses to seemingly subtle changes in abiotic factors. In this talk, we will explore a range of biotic and abiotic controls over fundamental biogeochemical cycling in drylands using data from a suite of manipulation experiments on the Colorado Plateau, USA. We will present results from field treatments that speak to the effects of increasing temperature, altered precipitation regimes, increased nitrogen availability via deposition, and the effects of altered litterfall inputs. Biogeochemical processes we explore will include plant photosynthesis, soil photosynthesis and respiration (with a focus on biological soil crusts), litter decomposition, and nutrient cycling. In addition, we will assess how treatments alter dryland community composition, as well as the resultant feedbacks of community shifts to environmental change. Taken together we will use these diverse datasets to ask questions about what makes drylands different or, instead, if a holistic joining of biotic and abiotic perspectives suggests they are not so different after all. These data will not only lend insight into the partitioning of and balance between biotic and abiotic

  8. Epigenetics as an answer to Darwin’s “special difficulty,” Part 2: natural selection of metastable epialleles in honeybee castes

    PubMed Central

    Ruden, Douglas M.; Cingolani, Pablo E.; Sen, Arko; Qu, Wen; Wang, Luan; Senut, Marie-Claude; Garfinkel, Mark D.; Sollars, Vincent E.; Lu, Xiangyi

    2015-01-01

    In a recent perspective in this journal, Herb (2014) discussed how epigenetics is a possible mechanism to circumvent Charles Darwin’s “special difficulty” in using natural selection to explain the existence of the sterile-fertile dimorphism in eusocial insects. Darwin’s classic book “On the Origin of Species by Means of Natural Selection” explains how natural selection of the fittest individuals in a population can allow a species to adapt to a novel or changing environment. However, in bees and other eusocial insects, such as ants and termites, there exist two or more castes of genetically similar females, from fertile queens to multiple sub-castes of sterile workers, with vastly different phenotypes, lifespans, and behaviors. This necessitates the selection of groups (or kin) rather than individuals in the evolution of honeybee hives, but group and kin selection theories of evolution are controversial and mechanistically uncertain. Also, group selection would seem to be prohibitively inefficient because the effective population size of a colony is reduced from thousands to a single breeding queen. In this follow-up perspective, we elaborate on possible mechanisms for how a combination of both epigenetics, specifically, the selection of metastable epialleles, and genetics, the selection of mutations generated by the selected metastable epialleles, allows for a combined means for selection amongst the fertile members of a species to increase colony fitness. This “intra-caste evolution” hypothesis is a variation of the epigenetic directed genetic error hypothesis, which proposes that selected metastable epialleles increase genetic variability by directing mutations specifically to the epialleles. Natural selection of random metastable epialleles followed by a second round of natural selection of random mutations generated by the metastable epialleles would allow a way around the small effective population size of eusocial insects. PMID:25759717

  9. On the laws for the emergence of life from the abiotic matter

    NASA Astrophysics Data System (ADS)

    Kolb, Vera M.

    2012-10-01

    In this work we pose a question if the laws for the emergence of life from the abiotic matter can exist even before carbon and the organic compounds were available. Carbon as an element became available via nucleosynthesis in the stars, and various carbon compounds were later made in the interstellar space and on the various objects in space. Is the emergence of life blue-printed as some general law which would then guarantee that life would evolve in the universe, or is it a law which co-evolved with the organic compounds and the environment in which they existed and which may be a subject to chance? This question is of a fundamental importance for astrobiology, which seeks extraterrestrial life without really knowing if it exists. Numerous articles and books have been written on the subject of the inevitability of life in the universe, on the evolution of matter which leads to life, and on the role of chance in the emergence of life. We select from these resources, critically examine them, and provide an inclusive summary, which we believe will be useful to astrobiologists.

  10. Evolving Better Cars: Teaching Evolution by Natural Selection with a Digital Inquiry Activity

    ERIC Educational Resources Information Center

    Royer, Anne M.; Schultheis, Elizabeth H.

    2014-01-01

    Evolutionary experiments are usually difficult to perform in the classroom because of the large sizes and long timescales of experiments testing evolutionary hypotheses. Computer applications give students a window to observe evolution in action, allowing them to gain comfort with the process of natural selection and facilitating inquiry…

  11. Mycobacterium ulcerans dynamics in aquatic ecosystems are driven by a complex interplay of abiotic and biotic factors

    PubMed Central

    Garchitorena, Andrés; Guégan, Jean-François; Léger, Lucas; Eyangoh, Sara; Marsollier, Laurent; Roche, Benjamin

    2015-01-01

    Host–parasite interactions are often embedded within complex host communities and can be influenced by a variety of environmental factors, such as seasonal variations in climate or abiotic conditions in water and soil, which confounds our understanding of the main drivers of many multi-host pathogens. Here, we take advantage of a combination of large environmental data sets on Mycobacterium ulcerans (MU), an environmentally persistent microorganism associated to freshwater ecosystems and present in a large variety of aquatic hosts, to characterize abiotic and biotic factors driving the dynamics of this pathogen in two regions of Cameroon. We find that MU dynamics are largely driven by seasonal climatic factors and certain physico-chemical conditions in stagnant and slow-flowing ecosystems, with an important role of pH as limiting factor. Furthermore, water conditions can modify the effect of abundance and diversity of aquatic organisms on MU dynamics, which suggests a different contribution of two MU transmission routes for aquatic hosts (trophic vs environmental transmission) depending on local abiotic factors. DOI: http://dx.doi.org/10.7554/eLife.07616.001 PMID:26216042

  12. Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model.

    PubMed

    Yosef, Ido; Edgar, Rotem; Levy, Asaf; Amitai, Gil; Sorek, Rotem; Munitz, Ariel; Qimron, Udi

    2016-04-18

    The emergence of mutations following growth-limiting conditions underlies bacterial drug resistance, viral escape from the immune system and fundamental evolution-driven events. Intriguingly, whether mutations are induced by growth limitation conditions or are randomly generated during growth and then selected by growth limitation conditions remains an open question(1). Here, we show that bacteriophage T7 undergoes apparent stress-induced mutagenesis when selected for improved recognition of its host's receptor. In our unique experimental set-up, the growth limitation condition is physically and temporally separated from mutagenesis: growth limitation occurs while phage DNA is outside the host, and spontaneous mutations occur during phage DNA replication inside the host. We show that the selected beneficial mutations are not pre-existing and that the initial slow phage growth is enabled by the phage particle's low-efficiency DNA injection into the host. Thus, the phage particle allows phage populations to initially extend their host range without mutagenesis by virtue of residual recognition of the host receptor. Mutations appear during non-selective intracellular replication, and the frequency of mutant phages increases by natural selection acting on free phages, which are not capable of mutagenesis.

  13. Abiotic mechanism for the formation of atmospheric nitrous oxide from ammonium nitrate.

    PubMed

    Rubasinghege, Gayan; Spak, Scott N; Stanier, Charles O; Carmichael, Gregory R; Grassian, Vicki H

    2011-04-01

    Nitrous oxide (N2O) is an important greenhouse gas and a primary cause of stratospheric ozone destruction. Despite its importance, there remain missing sources in the N2O budget. Here we report the formation of atmospheric nitrous oxide from the decomposition of ammonium nitrate via an abiotic mechanism that is favorable in the presence of light, relative humidity and a surface. This source of N2O is not currently accounted for in the global N2O budget. Annual production of N2O from atmospheric aerosols and surface fertilizer application over the continental United States from this abiotic pathway is estimated from results of an annual chemical transport simulation with the Community Multiscale Air Quality model (CMAQ). This pathway is projected to produce 9.3(+0.7/-5.3) Gg N2O annually over North America. N2O production by this mechanism is expected globally from both megacities and agricultural areas and may become more important under future projected changes in anthropogenic emissions.

  14. Recognition of Time-Compressed and Natural Speech with Selective Temporal Enhancements by Young and Elderly Listeners

    ERIC Educational Resources Information Center

    Gordon-Salant, Sandra; Fitzgibbons, Peter J.; Friedman, Sarah A.

    2007-01-01

    Purpose: The goal of this experiment was to determine whether selective slowing of speech segments improves recognition performance by young and elderly listeners. The hypotheses were (a) the benefits of time expansion occur for rapid speech but not for natural-rate speech, (b) selective time expansion of consonants produces greater score…

  15. Consequences of least tern (Sternula antillarum) microhabitat nest-site selection on natural and mechanically constructed sandbars in the Missouri River

    USGS Publications Warehouse

    Stucker, Jennifer H.; Buhl, Deborah A.; Sherfy, Mark H.

    2013-01-01

    Nest-habitat selection in colonial species has rarely been assessed at multiple spatial scales to evaluate its fitness consequences. Management for the federally endangered U.S. Interior population of Least Terns (Sternula antillarum) has focused on maintenance of breeding habitats, including mechanical construction of sandbars from dredged material. Least Terns are attracted to large areas of unvegetated substrate, yet small-scale habitat features are thought to trigger selection for nesting. We evaluated nest-scale habitat selection to determine (1) whether selection differs between constructed and natural sandbars and (2) the subsequent consequences of habitat selection on nest success. During 2006–2008, we examined 869 Least Tern nest sites on constructed and natural sandbars in the Missouri River for evidence of microhabitat selection at the nest in relation to habitat within the surrounding 3-m area. Least Tern nest sites had coarser and larger substrate materials at the nest, more debris, and less vegetation than the surrounding area. Nests in constructed habitats had a greater percentage of coarse substrates and less vegetation or debris than nests in naturally created habitats. Apparent nest success was 1.8× greater on constructed than on natural sandbars. Nest success was best predicted by models with two spatial scales of predictors, including substrates (nest) and vegetation and debris (nest or surrounding area). Our results indicate that Least Terns select nest microhabitat characteristics that are associated with wind- and water-scoured habitats, and that nest success increases when these habitats are selected.

  16. Unweaving Misconceptions: Guided Learning, Simulations, and Misconceptions in Learning Principles of Natural Selection

    ERIC Educational Resources Information Center

    Weeks, Brian E.

    2013-01-01

    College students often come to the study of evolutionary biology with many misconceptions of how the processes of natural selection and speciation occur. How to relinquish these misconceptions with learners is a question that many educators face in introductory biology courses. Constructivism as a theoretical framework has become an accepted and…

  17. RING E3 ligases: key regulatory elements are involved in abiotic stress responses in plants

    PubMed Central

    Cho, Seok Keun; Ryu, Moon Young; Kim, Jong Hum; Hong, Jeong Soo; Oh, Tae Rin; Kim, Woo Taek; Yang, Seong Wook

    2017-01-01

    Plants are constantly exposed to a variety of abiotic stresses, such as drought, heat, cold, flood, and salinity. To survive under such unfavorable conditions, plants have evolutionarily developed their own resistant-mechanisms. For several decades, many studies have clarified specific stress response pathways of plants through various molecular and genetic studies. In particular, it was recently discovered that ubiquitin proteasome system (UPS), a regulatory mechanism for protein turn over, is greatly involved in the stress responsive pathways. In the UPS, many E3 ligases play key roles in recognizing and tethering poly-ubiquitins on target proteins for subsequent degradation by the 26S proteasome. Here we discuss the roles of RING ligases that have been defined in related to abiotic stress responses in plants. PMID:28712388

  18. DRIFTSEL: an R package for detecting signals of natural selection in quantitative traits.

    PubMed

    Karhunen, M; Merilä, J; Leinonen, T; Cano, J M; Ovaskainen, O

    2013-07-01

    Approaches and tools to differentiate between natural selection and genetic drift as causes of population differentiation are of frequent demand in evolutionary biology. Based on the approach of Ovaskainen et al. (2011), we have developed an R package (DRIFTSEL) that can be used to differentiate between stabilizing selection, diversifying selection and random genetic drift as causes of population differentiation in quantitative traits when neutral marker and quantitative genetic data are available. Apart from illustrating the use of this method and the interpretation of results using simulated data, we apply the package on data from three-spined sticklebacks (Gasterosteus aculeatus) to highlight its virtues. DRIFTSEL can also be used to perform usual quantitative genetic analyses in common-garden study designs. © 2013 John Wiley & Sons Ltd.

  19. Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry

    PubMed Central

    Qi, Yanxiang; Liu, Xiaomei; Pu, Jinji

    2018-01-01

    The NAC transcription factors involved plant development and response to various stress stimuli. However, little information is available concerning the NAC family in the woodland strawberry. Herein, 37 NAC genes were identified from the woodland strawberry genome and were classified into 13 groups based on phylogenetic analysis. And further analyses of gene structure and conserved motifs showed closer relationship of them in every subgroup. Quantitative real-time PCR evaluation different tissues revealed distinct spatial expression profiles of the FvNAC genes. The comprehensive expression of FvNAC genes revealed under abiotic stress (cold, heat, drought, salt), signal molecule treatments (H2O2, ABA, melatonin, rapamycin), biotic stress (Colletotrichum gloeosporioides and Ralstonia solanacearum). Expression profiles derived from quantitative real-time PCR suggested that 5 FvNAC genes responded dramatically to the various abiotic and biotic stresses, indicating their contribution to abiotic and biotic stresses resistance in woodland strawberry. Interestingly, FvNAC genes showed greater extent responded to the cold treatment than other abiotic stress, and H2O2 exhibited a greater response than ABA, melatonin, and rapamycin. For biotic stresses, 3 FvNAC genes were up-regulated during infection with C. gloeosporioides, while 6 FvNAC genes were down-regulated during infection with R. solanacearum. In conclusion, this study identified candidate FvNAC genes to be used for the genetic improvement of abiotic and biotic stress tolerance in woodland strawberry. PMID:29897926

  20. S-Nitrosylated proteins in pea (Pisum sativum L.) leaf peroxisomes: changes under abiotic stress.

    PubMed

    Ortega-Galisteo, Ana P; Rodríguez-Serrano, María; Pazmiño, Diana M; Gupta, Dharmendra K; Sandalio, Luisa M; Romero-Puertas, María C

    2012-03-01

    Peroxisomes, single-membrane-bounded organelles with essentially oxidative metabolism, are key in plant responses to abiotic and biotic stresses. Recently, the presence of nitric oxide (NO) described in peroxisomes opened the possibility of new cellular functions, as NO regulates diverse biological processes by directly modifying proteins. However, this mechanism has not yet been analysed in peroxisomes. This study assessed the presence of S-nitrosylation in pea-leaf peroxisomes, purified S-nitrosylated peroxisome proteins by immunoprecipitation, and identified the purified proteins by two different mass-spectrometry techniques (matrix-assisted laser desorption/ionization tandem time-of-flight and two-dimensional nano-liquid chromatography coupled to ion-trap tandem mass spectrometry). Six peroxisomal proteins were identified as putative targets of S-nitrosylation involved in photorespiration, β-oxidation, and reactive oxygen species detoxification. The activity of three of these proteins (catalase, glycolate oxidase, and malate dehydrogenase) is inhibited by NO donors. NO metabolism/S-nitrosylation and peroxisomes were analysed under two different types of abiotic stress, i.e. cadmium and 2,4-dichlorophenoxy acetic acid (2,4-D). Both types of stress reduced NO production in pea plants, and an increase in S-nitrosylation was observed in pea extracts under 2,4-D treatment while no total changes were observed in peroxisomes. However, the S-nitrosylation levels of catalase and glycolate oxidase changed under cadmium and 2,4-D treatments, suggesting that this post-translational modification could be involved in the regulation of H(2)O(2) level under abiotic stress.