Natural variation in floral nectar proteins of two Nicotiana attenuata accessions

PubMed Central

2013-01-01

Background Floral nectar (FN) contains not only energy-rich compounds to attract pollinators, but also defense chemicals and several proteins. However, proteomic analysis of FN has been hampered by the lack of publically available sequence information from nectar-producing plants. Here we used next-generation sequencing and advanced proteomics to profile FN proteins in the opportunistic outcrossing wild tobacco, Nicotiana attenuata. Results We constructed a transcriptome database of N. attenuata and characterized its nectar proteome using LC-MS/MS. The FN proteins of N. attenuata included nectarins, sugar-cleaving enzymes (glucosidase, galactosidase, and xylosidase), RNases, pathogen-related proteins, and lipid transfer proteins. Natural variation in FN proteins of eleven N. attenuata accessions revealed a negative relationship between the accumulation of two abundant proteins, nectarin1b and nectarin5. In addition, microarray analysis of nectary tissues revealed that protein accumulation in FN is not simply correlated with the accumulation of transcripts encoding FN proteins and identified a group of genes that were specifically expressed in the nectary. Conclusions Natural variation of identified FN proteins in the ecological model plant N. attenuata suggests that nectar chemistry may have a complex function in plant-pollinator-microbe interactions. PMID:23848992

Natural and anthropogenic variations in methane sources during the past two millennia.

PubMed

Sapart, C J; Monteil, G; Prokopiou, M; van de Wal, R S W; Kaplan, J O; Sperlich, P; Krumhardt, K M; van der Veen, C; Houweling, S; Krol, M C; Blunier, T; Sowers, T; Martinerie, P; Witrant, E; Dahl-Jensen, D; Röckmann, T

2012-10-04

Methane is an important greenhouse gas that is emitted from multiple natural and anthropogenic sources. Atmospheric methane concentrations have varied on a number of timescales in the past, but what has caused these variations is not always well understood. The different sources and sinks of methane have specific isotopic signatures, and the isotopic composition of methane can therefore help to identify the environmental drivers of variations in atmospheric methane concentrations. Here we present high-resolution carbon isotope data (δ(13)C content) for methane from two ice cores from Greenland for the past two millennia. We find that the δ(13)C content underwent pronounced centennial-scale variations between 100 BC and AD 1600. With the help of two-box model calculations, we show that the centennial-scale variations in isotope ratios can be attributed to changes in pyrogenic and biogenic sources. We find correlations between these source changes and both natural climate variability--such as the Medieval Climate Anomaly and the Little Ice Age--and changes in human population and land use, such as the decline of the Roman empire and the Han dynasty, and the population expansion during the medieval period.

Modeling Natural Variation through Distribution

ERIC Educational Resources Information Center

Lehrer, Richard; Schauble, Leona

2004-01-01

This design study tracks the development of student thinking about natural variation as late elementary grade students learned about distribution in the context of modeling plant growth at the population level. The data-modeling approach assisted children in coordinating their understanding of particular cases with an evolving notion of data as an…

Genome-Wide Delineation of Natural Variation for Pod Shatter Resistance in Brassica napus

PubMed Central

Raman, Harsh; Raman, Rosy; Kilian, Andrzej; Detering, Frank; Carling, Jason; Coombes, Neil; Diffey, Simon; Kadkol, Gururaj; Edwards, David; McCully, Margaret; Ruperao, Pradeep; Parkin, Isobel A. P.; Batley, Jacqueline; Luckett, David J.; Wratten, Neil

2014-01-01

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified. PMID:25006804

Natural variations in the geomagnetically trapped electron population

NASA Technical Reports Server (NTRS)

Vampola, A. L.

1972-01-01

Temporal variations in the trapped natural electron flux intensities and energy spectra are discussed and demonstrated using recent satellite data. These data are intended to acquaint the space systems engineer with the types of natural variations that may be encountered during a mission and to augment the models of the electron environment currently being used in space system design and orbit selection. An understanding of the temporal variations which may be encountered should prove helpful. Some of the variations demonstrated here which are not widely known include: (1) addition of very energetic electrons to the outer zone during moderate magnetic storms: (2) addition of energetic electrons to the inner zone during major magnetic storms; (3) inversions in the outer zone electron energy spectrum during the decay phase of a storm injection event and (4) occasional formation of multiple maxima in the flux vs altitude profile of moderately energetic electrons.

Natural variation reveals that OsSAP16 controls low-temperature germination in rice.

PubMed

Wang, Xiang; Zou, Baohong; Shao, Qiaolin; Cui, Yongmei; Lu, Shan; Zhang, Yan; Huang, Quansheng; Huang, Ji; Hua, Jian

2018-01-23

Low temperature affects seed germination in plants, and low-temperature germination (LTG) is an important agronomic trait. Natural variation of LTG has been reported in rice, but the molecular basis for this variation is largely unknown. Here we report the phenotypic analysis of LTG in 187 rice natural accessions and a genome-wide association study (GWAS) of LTG in this collection. A total of 53 quantitative trait loci (QTLs) were found to be associated with LTG, of which 20 were located in previously reported QTLs. We further identified Stress-Associated Protein 16 (OsSAP16), coding for a zinc-finger domain protein, as a causal gene for one of the major LTG QTLs. Loss of OsSAP16 function reduces germination while greater expression of OsSAP16 enhances germination at low temperature. In addition, accessions with extremely high and low LTG values have correspondingly high and low OsSAP16 expression at low temperatures, suggesting that variation in expression of the OsSAP16 gene contributes to LTG variation. As the first case of identification of an LTG gene through GWAS, this study indicates that GWAS of natural accessions is an effective strategy in genetically dissecting LTG processes and gaining molecular understanding of low-temperature response and germination. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Deuterium: Natural variations used as a biological tracer

USGS Publications Warehouse

Gleason, J.D.; Friedman, I.

1970-01-01

The suggestion is made that isotope tracing be carried out by monitoring the natural variations in deuterium concentrations. As an example, the natural variations in deuterium concentrations between food and water collected in Illinois and food and water collected in Colorado were used to determine the residence time of water in the blood and urine of rats. We observed not only a 51/2-day turnover time of water in the blood and urine, but also evidence for the influx of water vapor from the atmosphere through the lungs into the blood.

AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana

PubMed Central

Chen, Zi-Ru; Kuang, Lu; Gao, Yi-Qun; Wang, Ya-Ling; Salt, David E.; Chao, Dai-Yin

2018-01-01

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 (HMA4) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation. PMID:29545819

AtHMA4 Drives Natural Variation in Leaf Zn Concentration of Arabidopsis thaliana.

PubMed

Chen, Zi-Ru; Kuang, Lu; Gao, Yi-Qun; Wang, Ya-Ling; Salt, David E; Chao, Dai-Yin

2018-01-01

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 ( HMA4 ) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation.

Genetic architecture of natural variation in Drosophila melanogaster aggressive behavior

PubMed Central

Shorter, John; Couch, Charlene; Huang, Wen; Carbone, Mary Anna; Peiffer, Jason; Anholt, Robert R. H.; Mackay, Trudy F. C.

2015-01-01

Aggression is an evolutionarily conserved complex behavior essential for survival and the organization of social hierarchies. With the exception of genetic variants associated with bioamine signaling, which have been implicated in aggression in many species, the genetic basis of natural variation in aggression is largely unknown. Drosophila melanogaster is a favorable model system for exploring the genetic basis of natural variation in aggression. Here, we performed genome-wide association analyses using the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and replicate advanced intercross populations derived from the most and least aggressive DGRP lines. We identified genes that have been previously implicated in aggressive behavior as well as many novel loci, including gustatory receptor 63a (Gr63a), which encodes a subunit of the receptor for CO2, and genes associated with development and function of the nervous system. Although genes from the two association analyses were largely nonoverlapping, they mapped onto a genetic interaction network inferred from an analysis of pairwise epistasis in the DGRP. We used mutations and RNAi knock-down alleles to functionally validate 79% of the candidate genes and 75% of the candidate epistatic interactions tested. Epistasis for aggressive behavior causes cryptic genetic variation in the DGRP that is revealed by changing allele frequencies in the outbred populations derived from extreme DGRP lines. This phenomenon may pertain to other fitness traits and species, with implications for evolution, applied breeding, and human genetics. PMID:26100892

Natural and engineered coding variation in antidepressant-sensitive serotonin transporters.

PubMed

Ye, R; Blakely, R D

2011-12-01

The presynaptic serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressant medications and psychostimulants. In recent years, studies of natural and engineered genetic variation in SERT have provided new opportunities to understand structural dimensions of drug interactions and regulation of the transporter, to explore 5-HT contributions to antidepressant action, and to assess the impact of SERT-mediated 5-HT contributions to neuropsychiatric disorders. Here we review three examples from our recent studies where genetic changes in SERT, identified or engineered, have led to new models, findings, and theories that cast light on new dimensions of 5-HT action in the CNS and periphery. First, we review our work to identify specific residues through which SERT recognizes antagonists, and the conversion of this knowledge to the creation of mice lacking high-affinity antidepressant and cocaine sensitivity. Second, we discuss our studies of functional coding variation in SERT that exists in commonly used strains of inbred mice, and how this variation is beginning to reveal novel 5-HT-associated phenotypes. Third, we review our identification and functional characterization of multiple, hyperactive SERT coding variants in subjects with autism. Each of these activities has driven the development of new model systems that can be further exploited to understand the contribution of 5-HT signaling to risk for neuropsychiatric disorders and their treatment. Copyright © 2011. Published by Elsevier Ltd.

NATURAL AND ENGINEERED CODING VARIATION IN ANTIDEPRESSANT-SENSITIVE SEROTONIN TRANSPORTERS

PubMed Central

YE, R.; BLAKELY, R. D.

2013-01-01

The presynaptic serotonin (5-HT) transporter (SERT) is a key regulator of 5-HT signaling and is a major target for antidepressant medications and psychostimulants. In recent years, studies of natural and engineered genetic variation in SERT have provided new opportunities to understand structural dimensions of drug interactions and regulation of the transporter, to explore 5-HT contributions to antidepressant action, and to assess the impact of SERT-mediated 5-HT contributions to neuropsychiatric disorders. Here we review three examples from our recent studies where genetic changes in SERT, identified or engineered, have led to new models, findings, and theories that cast light on new dimensions of 5-HT action in the CNS and periphery. First, we review our work to identify specific residues through which SERT recognizes antagonists, and the conversion of this knowledge to the creation of mice lacking high-affinity antidepressant and cocaine sensitivity. Second, we discuss our studies of functional coding variation in SERT that exists in commonly used strains of inbred mice, and how this variation is beginning to reveal novel 5-HT-associated phenotypes. Third, we review our identification and functional characterization of multiple, hyperactive SERT coding variants in subjects with autism. Each of these activities has driven the development of new model systems that can be further exploited to understand the contribution of 5-HT signaling to risk for neuropsychiatric disorders and their treatment. PMID:21893166

Analysis of natural variation in bermudagrass (Cynodon dactylon) reveals physiological responses underlying drought tolerance.

PubMed

Shi, Haitao; Wang, Yanping; Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

2012-01-01

Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H₂O₂ content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system.

Genome-wide association studies identify heavy metal ATPase3 as the primary determinant of natural variation in leaf cadmium in Arabidopsis thaliana

USDA-ARS?s Scientific Manuscript database

Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-...

Learning about natural variation of odor mixtures enhances categorization in early olfactory processing.

PubMed

Locatelli, Fernando F; Fernandez, Patricia C; Smith, Brian H

2016-09-01

Natural odors are typically mixtures of several chemical components. Mixtures vary in composition among odor objects that have the same meaning. Therefore a central 'categorization' problem for an animal as it makes decisions about odors in natural contexts is to correctly identify odor variants that have the same meaning and avoid variants that have a different meaning. We propose that identified mechanisms of associative and non-associative plasticity in early sensory processing in the insect antennal lobe and mammalian olfactory bulb are central to solving this problem. Accordingly, this plasticity should work to improve categorization of odors that have the opposite meanings in relation to important events. Using synthetic mixtures designed to mimic natural odor variation among flowers, we studied how honey bees learn about and generalize among floral odors associated with food. We behaviorally conditioned honey bees on a difficult odor discrimination problem using synthetic mixtures that mimic natural variation among snapdragon flowers. We then used calcium imaging to measure responses of projection neurons of the antennal lobe, which is the first synaptic relay of olfactory sensory information in the brain, to study how ensembles of projection neurons change as a result of behavioral conditioning. We show how these ensembles become 'tuned' through plasticity to improve categorization of odors that have the different meanings. We argue that this tuning allows more efficient use of the immense coding space of the antennal lobe and olfactory bulb to solve the categorization problem. Our data point to the need for a better understanding of the 'statistics' of the odor space. © 2016. Published by The Company of Biologists Ltd.

Analysis of Natural Variation in Bermudagrass (Cynodon dactylon) Reveals Physiological Responses Underlying Drought Tolerance

PubMed Central

Cheng, Zhangmin; Ye, Tiantian; Chan, Zhulong

2012-01-01

Bermudagrass (Cynodon dactylon) is a widely used warm-season turfgrass and one of the most drought tolerant species. Dissecting the natural variation in drought tolerance and physiological responses will bring us powerful basis and novel insight for plant breeding. In the present study, we evaluated the natural variation of drought tolerance among nine bermudagrass varieties by measuring physiological responses after drought stress treatment through withholding water. Three groups differing in drought tolerance were identified, including two tolerant, five moderately tolerant and two susceptible varieties. Under drought stress condition, drought sensitive variety (Yukon) showed relative higher water loss, more severe cell membrane damage (EL), and more accumulation of hydrogen peroxide (H2O2) and malondialdehyde (MDA), while drought tolerant variety (Tifgreen) exhibited significantly higher antioxidant enzymes activities. Further results indicated that drought induced cell injury in different varieties (Yukon, SR9554 and Tifgreen) exhibited liner correlation with leaf water content (LWC), H2O2 content, MDA content and antioxidant enzyme activities. Additionally, Tifgreen plants had significantly higher levels of osmolytes (proline level and soluble sugars) when compared with Yukon and SR9554 under drought stress condition. Taken together, our results indicated that natural variation of drought stress tolerance in bermudagrass varieties might be largely related to the induced changes of water status, osmolyte accumulation and antioxidant defense system. PMID:23285294

Scale-dependent variation in forest structures in naturally dynamic boreal forest landscapes

NASA Astrophysics Data System (ADS)

Kulha, Niko; Pasanen, Leena; De Grandpré, Louis; Kuuluvainen, Timo; Aakala, Tuomas

2017-04-01

Natural forest structures vary at multiple spatial scales. This variation reflects the occurrence of driving factors, such as disturbances and variation in soil or topography. To explore and understand the linkages of forest structural characteristics and factors driving their variation, we need to recognize how the structural characteristics vary in relation to spatial scale. This can be achieved by identifying scale-dependent features in forest structure within unmanaged forest landscapes. By identifying these features and examining their relationship with potential driving factors, we can better understand the dynamics of forest structural development. Here, we examine the spatial variation in forest structures at multiple spatial scales, utilizing data from old-growth boreal forests in two regions with contrasting disturbance regimes: northern Finland and north-eastern Québec, Canada ( 67° 45'N, 29° 36'E, 49° 39'N, 67° 55'W, respectively). The three landscapes (4 km2 each) in Finland are dominated by Pinus sylvestris and Picea abies, whereas the two landscapes in Québec are dominated by Abies balsamea and Picea mariana. Québec's forests are a subject to cyclic outbreaks of the eastern spruce budworm, causing extensive mortality especially in A. balsamea-dominated stands. In the Finnish landscapes, gap- to patch-scale disturbances due to tree senescence, fungi and wind, as well as infrequent surface fires in areas dominated by P. sylvestris, prevail. Owing to the differences in the species compositions and the disturbance regimes, we expect differing scales of variation between the landscapes. To quantify patterns of variation, we visually interpret stereopairs of recent aerial photographs. From the photographs, we collect information on forest canopy coverage, species composition and dead wood. For the interpretation, each 4 km2 plot is divided into 0.1ha square cells (4096 per plot). Interpretations are validated against field observations and compiled

Naturally occurring variation in tadpole morphology and performance linked to predator regime

Treesearch

James B. Johnson; Daniel Saenz; Cory K. Adams; Toby J. Hibbitts

2015-01-01

Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic...

Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness.

PubMed

Kerwin, Rachel; Feusier, Julie; Corwin, Jason; Rubin, Matthew; Lin, Catherine; Muok, Alise; Larson, Brandon; Li, Baohua; Joseph, Bindu; Francisco, Marta; Copeland, Daniel; Weinig, Cynthia; Kliebenstein, Daniel J

2015-04-13

Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana.

Discriminating Natural Variation from Legacies of Disturbance in Semi-Arid Forests, Southwestern USA

NASA Astrophysics Data System (ADS)

Swetnam, T. L.; Lynch, A. M.; Falk, D. A.; Yool, S. R.; Guertin, D. P.

2014-12-01

Characterizing differences in existing vegetation driven by natural variation versus disturbance legacies could become a critical component of applied forest management practice with important implications for monitoring ecologic succession and eco-hydrological interactions within the critical zone. Here we characterize variations in aerial LiDAR derived forest structure at individual tree scale in Arizona and New Mexico. Differences in structure result from both topographic and climatological variations and from natural and human related disturbances. We chose a priori undisturbed and disturbed sites that included preservation, development, logging and wildfire as exemplars. We compare two topographic indices, the topographic position index (TPI) and topographic wetness index (TWI), to two local indicators of spatial association (LISA): the Getis-Ord Gi and Anselin's Moran I. We found TPI and TWI correlate well to positive z-scores (tall trees in tall neighborhoods) in undisturbed areas and that disturbed areas are clearly defined by negative z-scores, in some cases better than what is visible from traditional orthophotography and existing GIS maps. These LISA methods also serve as a robust technique for creating like-clustered stands, i.e. common stands used in forest inventory monitoring. This research provides a significant advancement in the ability to (1) quantity variation in forest structure across topographically complex landscapes, (2) identify and map previously unrecorded disturbance locations, and (3) quantify the different impacts of disturbance within the perimeter of a stand or event at ecologically relevant scale.

Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes

PubMed Central

Delgado, Dolores; Alonso-Blanco, Carlos; Fenoll, Carmen; Mena, Montaña

2011-01-01

Background and Aims Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. Methods Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. Key Results and Conclusions Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and

Natural Variation in Resistance to Virus Infection in Dipteran Insects

PubMed Central

Palmer, William H.; Varghese, Finny S.

2018-01-01

The power and ease of Drosophila genetics and the medical relevance of mosquito-transmitted viruses have made dipterans important model organisms in antiviral immunology. Studies of virus–host interactions at the molecular and population levels have illuminated determinants of resistance to virus infection. Here, we review the sources and nature of variation in antiviral immunity and virus susceptibility in model dipteran insects, specifically the fruit fly Drosophila melanogaster and vector mosquitoes of the genera Aedes and Culex. We first discuss antiviral immune mechanisms and describe the virus-specificity of these responses. In the following sections, we review genetic and microbiota-dependent variation in antiviral immunity. In the final sections, we explore less well-studied sources of variation, including abiotic factors, sexual dimorphism, infection history, and endogenous viral elements. We borrow from work on other pathogen types and non-dipteran species when it parallels or complements studies in dipterans. Understanding natural variation in virus–host interactions may lead to the identification of novel restriction factors and immune mechanisms and shed light on the molecular determinants of vector competence. PMID:29522475

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield.

PubMed

Ma, Zhiying; He, Shoupu; Wang, Xingfen; Sun, Junling; Zhang, Yan; Zhang, Guiyin; Wu, Liqiang; Li, Zhikun; Liu, Zhihao; Sun, Gaofei; Yan, Yuanyuan; Jia, Yinhua; Yang, Jun; Pan, Zhaoe; Gu, Qishen; Li, Xueyuan; Sun, Zhengwen; Dai, Panhong; Liu, Zhengwen; Gong, Wenfang; Wu, Jinhua; Wang, Mi; Liu, Hengwei; Feng, Keyun; Ke, Huifeng; Wang, Junduo; Lan, Hongyu; Wang, Guoning; Peng, Jun; Wang, Nan; Wang, Liru; Pang, Baoyin; Peng, Zhen; Li, Ruiqiang; Tian, Shilin; Du, Xiongming

2018-05-07

Upland cotton is the most important natural-fiber crop. The genomic variation of diverse germplasms and alleles underpinning fiber quality and yield should be extensively explored. Here, we resequenced a core collection comprising 419 accessions with 6.55-fold coverage depth and identified approximately 3.66 million SNPs for evaluating the genomic variation. We performed phenotyping across 12 environments and conducted genome-wide association study of 13 fiber-related traits. 7,383 unique SNPs were significantly associated with these traits and were located within or near 4,820 genes; more associated loci were detected for fiber quality than fiber yield, and more fiber genes were detected in the D than the A subgenome. Several previously undescribed causal genes for days to flowering, fiber length, and fiber strength were identified. Phenotypic selection for these traits increased the frequency of elite alleles during domestication and breeding. These results provide targets for molecular selection and genetic manipulation in cotton improvement.

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

PubMed

Kang, Hyun Min; Subramaniam, Meena; Targ, Sasha; Nguyen, Michelle; Maliskova, Lenka; McCarthy, Elizabeth; Wan, Eunice; Wong, Simon; Byrnes, Lauren; Lanata, Cristina M; Gate, Rachel E; Mostafavi, Sara; Marson, Alexander; Zaitlen, Noah; Criswell, Lindsey A; Ye, Chun Jimmie

2018-01-01

Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

PubMed

Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

2015-06-01

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Genetic variation in natural honeybee populations, Apis mellifera capensis

NASA Astrophysics Data System (ADS)

Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

2004-09-01

Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

Natural variation in differentiated hemocytes is related to parasitoid resistance in Drosophila melanogaster.

PubMed

Gerritsma, Sylvia; Haan, Ammerins de; Zande, Louis van de; Wertheim, Bregje

2013-02-01

As a measure of parasitoid resistance, hemocyte load and encapsulation ability were measured in lines collected from natural populations of Drosophila melanogaster in Europe. Results show large geographic variation in resistance against the parasitoid wasp Asobara tabida among the field lines, but there was no clear correlation between resistance and total hemocyte load, neither before nor after parasitization. This was in contrast to the patterns that had been found in a comparison among species of Drosophila, where total hemocyte counts were positively correlated to encapsulation rates. This suggests that the mechanisms underlying between-species variation in parasitoid resistance do not extend to the natural variation that exists within a species. Although hemocyte counts did not correspond to encapsulation ability within D. melanogaster, the ratios of lamellocytes and crystal cells were very similar in lines with successful encapsulation responses. Apart from variation in the hemocytic response of the different hemocyte types, within-species variation was also observed for accurate targeting of the foreign body by the hemocytes. These results are discussed in the context of possible causes of variation in immune functions among natural populations. Copyright © 2012 Elsevier Ltd. All rights reserved.

A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa.

PubMed

Wu, Jian; Wei, Keyun; Cheng, Feng; Li, Shikai; Wang, Qian; Zhao, Jianjun; Bonnema, Guusje; Wang, Xiaowu

2012-08-28

Flowering time is an important trait in Brassica rapa crops. FLOWERING LOCUS C (FLC) is a MADS-box transcription factor that acts as a potent repressor of flowering. Expression of FLC is silenced when plants are exposed to low temperature, which activates flowering. There are four copies of FLC in B. rapa. Analyses of different segregating populations have suggested that BraA.FLC.a (BrFLC1) and BraA.FLC.b (BrFLC2) play major roles in controlling flowering time in B. rapa. We analyzed the BrFLC2 sequence in nine B. rapa accessions, and identified a 57-bp insertion/deletion (InDel) across exon 4 and intron 4 resulting in a non-functional allele. In total, three types of transcripts were identified for this mutated BrFLC2 allele. The InDel was used to develop a PCR-based marker, which was used to screen a collection of 159 B. rapa accessions. The deletion genotype was present only in oil-type B. rapa, including ssp. oleifera and ssp. tricolaris, and not in other subspecies. The deletion genotype was significantly correlated with variation in flowering time. In contrast, the reported splicing site variation in BrFLC1, which also leads to a non-functional locus, was detected but not correlated with variation in flowering time in oil-type B. rapa, although it was correlated with variation in flowering time in vegetable-type B. rapa. Our results suggest that the naturally occurring deletion mutation across exon 4 and intron 4 in BrFLC2 gene contributes greatly to variation in flowering time in oil-type B. rapa. The observed different relationship between BrFLC1 or BrFLC2 and flowering time variation indicates that the control of flowering time has evolved separately between oil-type and vegetable-type B. rapa groups.

Potassium Retention under Salt Stress Is Associated with Natural Variation in Salinity Tolerance among Arabidopsis Accessions

PubMed Central

Sun, Yanling; Kong, Xiangpei; Li, Cuiling; Liu, Yongxiu; Ding, Zhaojun

2015-01-01

Plants are exposed to various environmental stresses during their life cycle such as salt, drought and cold. Natural variation mediated plant growth adaptation has been employed as an effective approach in response to the diverse environmental cues such as salt stress. However, the molecular mechanism underlying this process is not well understood. In the present study, a collection of 82 Arabidopsis thaliana accessions (ecotypes) was screened with a view to identify variation for salinity tolerance. Seven accessions showed a higher level of tolerance than Col-0. The young seedlings of the tolerant accessions demonstrated a higher K+ content and a lower Na+/K+ ratio when exposed to salinity stress, but its Na+ content was the same as that of Col-0. The K+ transporter genes AtHAK5, AtCHX17 and AtKUP1 were up-regulated significantly in almost all the tolerant accessions, even in the absence of salinity stress. There was little genetic variation or positive transcriptional variation between the selections and Col-0 with respect to Na+-related transporter genes, as AtSOS genes, AtNHX1 and AtHKT1;1. In addition, under salinity stress, these selections accumulated higher compatible solutes and lower reactive oxygen species than did Col-0. Taken together, our results showed that natural variation in salinity tolerance of Arabidopsis seems to have been achieved by the strong capacity of K+ retention. PMID:25993093

Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals.

PubMed

Suzuki, Taichi A

2017-10-01

Recent studies in model organisms have shown that compositional variation in the microbiome can affect a variety of host phenotypes including those related to digestion, development, immunity, and behavior. Natural variation in the microbiome within and between natural populations and species may also affect host phenotypes and thus fitness in the wild. Here, I review recent evidence that compositional variation in the microbiome may affect host phenotypes and fitness in wild mammals. Studies over the last decade indicate that natural variation in the mammalian microbiome may be important in the assistance of energy uptake from different diet types, detoxification of plant secondary compounds, protection from pathogens, chemical communication, and behavior. I discuss the importance of combining both field observations and manipulative experiments in a single system to fully characterize the functions and fitness effects of the microbiome. Finally, I discuss the evolutionary consequences of mammal-microbiome associations by proposing a framework to test how natural selection on hosts is mediated by the microbiome. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice.

PubMed

Duan, Penggen; Xu, Jinsong; Zeng, Dali; Zhang, Baolan; Geng, Mufan; Zhang, Guozheng; Huang, Ke; Huang, Luojiang; Xu, Ran; Ge, Song; Qian, Qian; Li, Yunhai

2017-05-01

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5 DEL1+IN1 , and GSE5 DEL2 ) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5 DEL1+IN1 haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5 DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Coupled Effects of Natural and Anthropogenic Controls on Seasonal and Spatial Variations of River Water Quality during Baseflow in a Coastal Watershed of Southeast China

PubMed Central

Huang, Jinliang; Huang, Yaling; Zhang, Zhenyu

2014-01-01

Surface water samples of baseflow were collected from 20 headwater sub-watersheds which were classified into three types of watersheds (natural, urban and agricultural) in the flood, dry and transition seasons during three consecutive years (2010–2012) within a coastal watershed of Southeast China. Integrating spatial statistics with multivariate statistical techniques, river water quality variations and their interactions with natural and anthropogenic controls were examined to identify the causal factors and underlying mechanisms governing spatiotemporal patterns of water quality. Anthropogenic input related to industrial effluents and domestic wastewater, agricultural activities associated with the precipitation-induced surface runoff, and natural weathering process were identified as the potential important factors to drive the seasonal variations in stream water quality for the transition, flood and dry seasons, respectively. All water quality indicators except SRP had the highest mean concentrations in the dry and transition seasons. Anthropogenic activities and watershed characteristics led to the spatial variations in stream water quality in three types of watersheds. Concentrations of NH4 +-N, SRP, K+, CODMn, and Cl− were generally highest in urban watersheds. NO3 –N Concentration was generally highest in agricultural watersheds. Mg2+ concentration in natural watersheds was significantly higher than that in agricultural watersheds. Spatial autocorrelations analysis showed similar levels of water pollution between the neighboring sub-watersheds exhibited in the dry and transition seasons while non-point source pollution contributed to the significant variations in water quality between neighboring sub-watersheds. Spatial regression analysis showed anthropogenic controls played critical roles in variations of water quality in the JRW. Management implications were further discussed for water resource management. This research demonstrates that the

Natural variations in OsγTMT contribute to diversity of the α-tocopherol content in rice.

PubMed

Wang, Xiao-Qiang; Yoon, Min-Young; He, Qiang; Kim, Tae-Sung; Tong, Wei; Choi, Bu-Woong; Lee, Young-Sang; Park, Yong-Jin

2015-12-01

Tocopherols and tocotrienols, collectively known as tocochromanols, are lipid-soluble molecules that belong to the group of vitamin E compounds. Among them, α-tocopherol (αΤ) is one of the antioxidants with diverse functions and benefits for humans and animals. Thus, understanding the genetic basis of these traits would be valuable to improve nutritional quality by breeding in rice. Genome-wide association study (GWAS) has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. To discover the genes or QTLs underlying the naturally occurring variations of αΤ content in rice, we performed GWAS using 1.44 million high-quality single-nucleotide polymorphisms acquired from re-sequencing of 137 accessions from a diverse rice core collection. Thirteen candidate genes were found across 2-year phenotypic data, among which gamma-tocopherol methyltransferase (OsγTMT) was identified as the major factor responsible for the αΤ content among rice accessions. Nucleotide variations in the coding region of OsγTMT were significantly associated with the αΤ content variations, while nucleotide polymorphisms in the promoter region of OsγTMT also could partly demonstrate the correlation with αΤ content variations, according to our RNA expression analyses. This study provides useful information for genetic factors underlying αΤ content variations in rice, which will significantly contribute the research on αΤ biosynthesis mechanisms and αΤ improvement of rice.

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster.

PubMed

Lee, Yuh Chwen G; Yang, Qian; Chi, Wanhao; Turkson, Susie A; Du, Wei A; Kemkemer, Claus; Zeng, Zhao-Bang; Long, Manyuan; Zhuang, Xiaoxi

2017-05-01

Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Natural Variation in the Pto Pathogen Resistance Gene Within Species of Wild Tomato (Lycopersicon). I. Functional Analysis of Pto Alleles

PubMed Central

Rose, Laura E.; Langley, Charles H.; Bernal, Adriana J.; Michelmore, Richard W.

2005-01-01

Disease resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) in the cultivated tomato, Lycopersicon esculentum, and the closely related L. pimpinellifolium is triggered by the physical interaction between plant disease resistance protein, Pto, and the pathogen avirulence protein, AvrPto. To investigate the extent to which variation in the Pto gene is responsible for naturally occurring variation in resistance to Pst, we determined the resistance phenotype of 51 accessions from seven species of Lycopersicon to isogenic strains of Pst differing in the presence of avrPto. One-third of the plants displayed resistance specifically when the pathogen expressed AvrPto, consistent with a gene-for-gene interaction. To test whether this resistance in these species was conferred specifically by the Pto gene, alleles of Pto were amplified and sequenced from 49 individuals and a subset (16) of these alleles was tested in planta using Agrobacterium-mediated transient assays. Eleven alleles conferred a hypersensitive resistance response (HR) in the presence of AvrPto, while 5 did not. Ten amino acid substitutions associated with the absence of AvrPto recognition and HR were identified, none of which had been identified in previous structure-function studies. Additionally, 3 alleles encoding putative pseudogenes of Pto were isolated from two species of Lycopersicon. Therefore, a large proportion, but not all, of the natural variation in the reaction to strains of Pst expressing AvrPto can be attributed to sequence variation in the Pto gene. PMID:15944360

Naturally occurring variation in tadpole morphology and performance linked to predator regime

PubMed Central

Johnson, James B; Saenz, Daniel; Adams, Cory K; Hibbitts, Toby J

2015-01-01

Divergent natural selection drives a considerable amount of the phenotypic and genetic variation observed in natural populations. For example, variation in the predator community can generate conflicting selection on behavioral, life-history, morphological, and performance traits. Differences in predator regime can subsequently increase phenotypic and genetic variations in the population and result in the evolution of reproductive barriers (ecological speciation) or phenotypic plasticity. We evaluated morphology and swimming performance in field collected Bronze Frog larvae (Lithobates clamitans) in ponds dominated by predatory fish and those dominated by invertebrate predators. Based on previous experimental findings, we hypothesized that tadpoles from fish-dominated ponds would have small bodies, long tails, and large tail muscles and that these features would facilitate fast-start speed. We also expected to see increased tail fin depth (i.e., the tail-lure morphology) in tadpoles from invertebrate-dominated ponds. Our results support our expectations with respect to morphology in affecting swimming performance of tadpoles in fish-dominated ponds. Furthermore, it is likely that divergent natural selection is playing a role in the diversification on morphology and locomotor performance in this system. PMID:26357533

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

PubMed Central

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria

2017-01-01

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain[OPEN

PubMed Central

Diepenbrock, Christine H.; Kandianis, Catherine B.; Lipka, Alexander E.; Magallanes-Lundback, Maria; Vaillancourt, Brieanne; Cepela, Jason; Bradbury, Peter J.; Mateos-Hernandez, Maria; Hamilton, John; Owens, Brenda F.; Tiede, Tyler; Rocheford, Torbert

2017-01-01

Tocopherols, tocotrienols, and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are nonphotosynthetic, remains limited. To understand the genetic control of tocochromanols in grain, we conducted a joint linkage and genome-wide association study in the 5000-line U.S. maize (Zea mays) nested association mapping panel. Fifty-two quantitative trait loci for individual and total tocochromanols were identified, and of the 14 resolved to individual genes, six encode novel activities affecting tocochromanols in plants. These include two chlorophyll biosynthetic enzymes that explain the majority of tocopherol variation, which was not predicted given that, like most major cereal crops, maize grain is nonphotosynthetic. This comprehensive assessment of natural variation in vitamin E levels in maize establishes the foundation for improving tocochromanol and vitamin E content in seeds of maize and other major cereal crops. PMID:28970338

The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

PubMed

Roux, F; Bergelson, J

2016-01-01

In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. © 2016 Elsevier Inc. All rights reserved.

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

PubMed Central

Lira-Medeiros, Catarina Fonseca; Parisod, Christian; Fernandes, Ricardo Avancini; Mata, Camila Souza; Cardoso, Monica Aires; Ferreira, Paulo Cavalcanti Gomes

2010-01-01

Background Epigenetic modifications, such as cytosine methylation, are inherited in plant species and may occur in response to biotic or abiotic stress, affecting gene expression without changing genome sequence. Laguncularia racemosa, a mangrove species, occurs in naturally contrasting habitats where it is subjected daily to salinity and nutrient variations leading to morphological differences. This work aims at unraveling how CpG-methylation variation is distributed among individuals from two nearby habitats, at a riverside (RS) or near a salt marsh (SM), with different environmental pressures and how this variation is correlated with the observed morphological variation. Principal Findings Significant differences were observed in morphological traits such as tree height, tree diameter, leaf width and leaf area between plants from RS and SM locations, resulting in smaller plants and smaller leaf size in SM plants. Methyl-Sensitive Amplified Polymorphism (MSAP) was used to assess genetic and epigenetic (CpG-methylation) variation in L. racemosa genomes from these populations. SM plants were hypomethylated (14.6% of loci had methylated samples) in comparison to RS (32.1% of loci had methylated samples). Within-population diversity was significantly greater for epigenetic than genetic data in both locations, but SM also had less epigenetic diversity than RS. Frequency-based (GST) and multivariate (βST) methods that estimate population structure showed significantly greater differentiation among locations for epigenetic than genetic data. Co-Inertia analysis, exploring jointly the genetic and epigenetic data, showed that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment, suggesting that CpG-methylation changes may be associated with environmental heterogeneity. Conclusions In spite of significant morphological dissimilarities, individuals of L. racemosa from salt

Natural variation of rice blast resistance gene Pi-d2

USDA-ARS?s Scientific Manuscript database

Studying natural variation of rice resistance (R) genes in cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of rice R gene Pi-d2 in 35 rice accessions of subgroups, aus (AUS), indica (IND), temperate japonica (...

Extensive Natural Intraspecific Variation in Stoichiometric (C:N:P) Composition in Two Terrestrial Insect Species

PubMed Central

Bertram, S. M.; Bowen, M.; Kyle, M.; Schade, J. D.

2008-01-01

Heterotrophic organisms must obtain essential elements in sufficient quantities from their food. Because plants naturally exhibit extensive variation in their elemental content, it is important to quantify the within-species stoichiometric variation of consumers. If extensive stoichiometric variation exists, it may help explain consumer variation in life-history strategy and fitness. To date, however, research on stoichiometric variation has focused on interspecific differences and assumed minimal intraspecific differences. Here this assumption is tested. Natural variation is quantified in body stoichiometry of two terrestrial insects: the generalist field cricket, Gryllus texensis Cade and Otte (Orthoptera: Gryllidae) and a specialist curculionid weevil, Sabinia setosa (Le Conte) (Coleoptera: Curculionidae). Both species exhibited extensive intraspecific stoichiometric variation. Cricket body nitrogen content ranged from 8–12% and there was a four-fold difference in body phosphorus content, ranging from 0.32–1.27%. Body size explained half this stoichiometric variation, with larger individuals containing less nitrogen and phosphorus. Weevils exhibited an almost three-fold difference in body phosphorus content, ranging from 0.38–0.97%. Overall, the variation observed within each of these species is comparable to the variation previously observed across almost all terrestrial insect species. PMID:20298114

Natural and anthropogenic variations in methane sources during the past two millennia

NASA Astrophysics Data System (ADS)

Sapart, C. J.; Monteil, G.; Prokopiou, M.; Vandewal, R.; Kaplan, J. O.; Sperlich, P.; Krumhardt, K.; van der Veen, C.; Houweling, S.; Krol, M. C.; Blunier, T.; Sowers, T. A.; Martinerie, P.; Witrant, E.; Dahl-Jensen, D.; Roeckmann, T.

2012-12-01

Methane (CH4) is an important greenhouse gas that is emitted from multiple natural and anthropogenic sources. Atmospheric levels of CH4 have varied on various timescales in the past, but in many cases the causes of these variations are not understood. Analysis of the isotopic composition of CH4 provides evidence for the environmental drivers of variations in CH4 atmospheric abundance, because different sources and sinks affect the isotopic composition of CH4 specifically. Our data from air trapped in the NEEM and EUROCORE Greenland ice cores show that the carbon isotopic composition (δ13C) of CH4 underwent pronounced centennial-scale variations between 100 BC and 1600 AD. Two-box model calculations suggest that the centennial-scale variations in isotope ratios are due to changes in both pyrogenic and biogenic sources. These changes are correlated with both natural climate variability including the Medieval Climate Anomaly and the Little Ice Age and with changes in human population, land-use and with the decline of both the Roman Empire and the Han dynasty and the Medieval period. Our findings suggest that between 100 BC and 1600 AD human activities may have been responsible for about 20-30 per cent of the total pyrogenic methane emissions and that they have therefore contributed to variations in methane emissions long before the onset of the industrial revolution.

The effects of oil spills on marine fish: Implications of spatial variation in natural mortality.

PubMed

Langangen, Ø; Olsen, E; Stige, L C; Ohlberger, J; Yaragina, N A; Vikebø, F B; Bogstad, B; Stenseth, N C; Hjermann, D Ø

2017-06-15

The effects of oil spills on marine biological systems are of great concern, especially in regions with high biological production of harvested resources such as in the Northeastern Atlantic. The scientific studies of the impact of oil spills on fish stocks tend to ignore that spatial patterns of natural mortality may influence the magnitude of the impact over time. Here, we first illustrate how spatial variation in natural mortality may affect the population impact by considering a thought experiment. Second, we consider an empirically based example of Northeast Arctic cod to extend the concept to a realistic setting. Finally, we present a scenario-based investigation of how the degree of spatial variation in natural mortality affects the impact over a gradient of oil spill sizes. Including the effects of spatial variations in natural mortality tends to widen the impact distribution, hence increasing the probability of both high and low impact events. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster.

PubMed

Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

2015-11-14

Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

Phase relations of natural 65 year SST variations, ocean sea level variations over 260 years, and Arctic sea-ice retreat of the satellite era - issues of cause and effect.

NASA Astrophysics Data System (ADS)

Asten, Michael

2017-04-01

We study sea level variations over the past 300yr in order to quantify what fraction of variations may be considered cyclic, and what phase relations exist with respect to those cycles. The 64yr cycle detected by Chambers et al (2012) is found in the 1960-2000 data set which Hamlington et al (2013) interpreted as an expression of the PDO; we show that fitting a 64yr cycle is a better fit, accounting for 92% of variance. In a 300yr GMSL tide guage record Jeverejeva et al (2008) identified a 60-65yr cycle superimposed on an upward trend from 1800CE. Using break-points and removal of centennial trends identified by Kemp et al (2015), we produce a detrended GMSL record for 1700-2000CE which emphasizes the 60-65yr oscillations. A least-square fit using a 64yr period cosine yields an amplitude 12mm and origin at year 1958.6, which accounts for 30% of the variance. A plot of the cosine against the entire length of the 300yr detrended GMSL record shows a clear phase lock for the interval 1740 to 2000CE, denoting either a very consistent timing of an internally generated natural variation, or adding to evidence for an external forcing of astronomical origin (Scafetta 2012, 2013). Barcikowska et al (2016) have identified a 65yr cyclic variation in sea surface temperature in the first multidecadal component of Multi- Channel Singular Spectrum Analysis (MSSA) on the Hadley SST data set (RC60). A plot of RC60 versus our fitted cosine shows the phase shift to be 16 yr, close to a 90 degree phase lag of GMSL relative to RC60. This is the relation to be expected for a simple low-pass or integrating filter, which suggests that cyclic natural variations in sea-surface temperature drive similar variations in GMSL. We compare the extent of Arctic sea-ice using the time interval of 1979- 2016 (window of satellite imagery). The decrease in summer ice cover has been subject of many predictions as to when summer ice will reach zero. The plot of measured ice area can be fitted with many

Spatio-temporal distribution and natural variation of metabolites in citrus fruits.

PubMed

Wang, Shouchuang; Tu, Hong; Wan, Jian; Chen, Wei; Liu, Xianqing; Luo, Jie; Xu, Juan; Zhang, Hongyan

2016-05-15

To study the natural variation and spatio-temporal accumulation of citrus metabolites, liquid chromatography tandem mass spectrometry (LC-MS) based metabolome analysis was performed on four fruit tissues (flavedo, albedo, segment membrane and juice sacs) and different Citrus species (lemon, pummelo and grapefruit, sweet orange and mandarin). Using a non-targeted metabolomics approach, more than 2000 metabolite signals were detected, from which more than 54 metabolites, including amino acids, flavonoids and limonoids, were identified/annotated. Differential accumulation patterns of both primary metabolites and secondary metabolites in various tissues and species were revealed by our study. Further investigation indicated that flavedo accumulates more flavonoids while juice sacs contain more amino acids. Besides this, cluster analysis based on the levels of metabolites detected in 47 individual Citrus accessions clearly grouped them into four distinct clusters: pummelos and grapefruits, lemons, sweet oranges and mandarins, while the cluster of pummelos and grapefruits lay distinctly apart from the other three species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition

PubMed Central

Bouain, Nadia; Saenchai, Chorpet

2018-01-01

Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating primary root length depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of growth and immune responses in plants. PMID:29608565

Natural genetic variation in social environment choice: context-dependent gene-environment correlation in Drosophila melanogaster.

PubMed

Saltz, Julia B

2011-08-01

Gene-environment correlation (rGE) occurs when an individual's genotype determines its choice of environment, generating a correlation between environment and genotype frequency. In particular, social rGE, caused by genetic variation in social environment choice, can critically determine both individual development and the course of social selection. Despite its foundational role in social evolution and developmental psychology theory, natural genetic variation in social environment choice has scarcely been examined empirically. Drosophila melanogaster provides an ideal system for investigating social rGE. Flies live socially in nature and have many opportunities to make social decisions; and natural, heterozygous genotypes may be replicated, enabling comparisons between genotypes across environments. Using this approach, I show that all aspects of social environment choice vary among natural genotypes, demonstrating pervasive social rGE. Surprisingly, genetic variation in group-size preference was density dependent, indicating that the behavioral and evolutionary consequences of rGE may depend on the context in which social decisions are made. These results provide the first detailed investigation of social rGE, and illustrate that that genetic variation may influence organismal performance by specifying the environment in which traits are expressed. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Natural genetic variation of freezing tolerance in Arabidopsis.

PubMed

Hannah, Matthew A; Wiese, Dana; Freund, Susanne; Fiehn, Oliver; Heyer, Arnd G; Hincha, Dirk K

2006-09-01

Low temperature is a primary determinant of plant growth and survival. Using accessions of Arabidopsis (Arabidopsis thaliana) originating from Scandinavia to the Cape Verde Islands, we show that freezing tolerance of natural accessions correlates with habitat winter temperatures, identifying low temperature as an important selective pressure for Arabidopsis. Combined metabolite and transcript profiling show that during cold exposure, global changes of transcripts, but not of metabolites, correlate with the ability of Arabidopsis to cold acclimate. There are, however, metabolites and transcripts, including several transcription factors, that correlate with freezing tolerance, indicating regulatory pathways that may be of primary importance for this trait. These data identify that enhanced freezing tolerance is associated with the down-regulation of photosynthesis and hormonal responses and the induction of flavonoid metabolism, provide evidence for naturally increased nonacclimated freezing tolerance due to the constitutive activation of the C-repeat binding factors pathway, and identify candidate transcriptional regulators that correlate with freezing tolerance.

A newly identified variation at the entry of the recurrent laryngeal nerve into the larynx.

PubMed

Shao, Tanglei; Yang, Weiping; Zhang, Tao; Wang, Yang; Jin, Xiaotai; Li, Qinyu; Kuang, Jie; Qiu, Weihua; Chu, Peiguo G; Yen, Yun

2010-12-01

We aimed to highlight a new anatomical variation of the recurrent laryngeal nerve (RLN), and to emphasize its implications for thyroid surgery. A prospective study was carried out in a group of 3,078 consecutive thyroidectomies from 1998 to 2008. Total, near-total, subtotal, and partial thyroidectomy were performed for various thyroid diseases. The RLN was routinely identified and exposed in its entire course until the entry into the larynx. The postoperative complications of patients with different variations were compared. 4,241 RLNs were successfully identified in all patients unilaterally or bilaterally. In addition to extralaryngeal branching and nonrecurrent laryngeal nerves, an unreported variation was identified in 44 RLNs (1.04%) at their entries into the larynx. The variation happened at the trunk or the branches of the RLN entering the larynx far from the posterior of cricothyroid joint, and the entry was higher than the superior cornu of the thyroid cartilage and the arch of the cricoid. The median distance from the entry to the posterior of cricothyroid joint was more than 5 mm. As the trunk or the branches had to travel along the lateral edge of the upper 1/3 of the thyroid before entering the larynx, the incidence of RLN palsy was higher than that in extralaryngeal branching variations (p < .05). This newly discovered variation of the RLN is more vulnerable to injury and should be brought to the attention of surgeons.

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value.

PubMed

Pacheco-Villalobos, David; Hardtke, Christian S

2012-06-05

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.

Genomic Variation in Natural Populations of Drosophila melanogaster

PubMed Central

Langley, Charles H.; Stevens, Kristian; Cardeno, Charis; Lee, Yuh Chwen G.; Schrider, Daniel R.; Pool, John E.; Langley, Sasha A.; Suarez, Charlyn; Corbett-Detig, Russell B.; Kolaczkowski, Bryan; Fang, Shu; Nista, Phillip M.; Holloway, Alisha K.; Kern, Andrew D.; Dewey, Colin N.; Song, Yun S.; Hahn, Matthew W.; Begun, David J.

2012-01-01

This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5′- and 3′-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species. PMID:22673804

Identification of natural high-oleate mutants from the USDA Peanut Germplasm Collection

USDA-ARS?s Scientific Manuscript database

Natural genetic variation may exist in plant germplasm collections. Identifying genetic variation may provide useful materials for breeders to develop new cultivars. After screening 8,846 cultivated peanut germplasm accessions by gas chromatography analysis, we identified three natural mutant lines ...

Identifying the cellular targets of natural products using T7 phage display.

PubMed

Piggott, Andrew M; Karuso, Peter

2016-05-04

Covering: up to the end of 2015While Nature continues to deliver a myriad of potent and structurally diverse biologically active small molecules, the cellular targets and modes of action of these natural products are rarely identified, significantly hindering their development as new chemotherapeutic agents. This article provides an introductory tutorial on the use of T7 phage display as a tool to rapidly identify the cellular targets of natural products and is aimed specifically at natural products chemists who may have only limited experience in molecular biology. A brief overview of T7 phage display is provided, including its strengths, weaknesses, and the type of problems that can and cannot be tackled with this technology. Affinity probe construction is reviewed, including linker design and natural product derivatisation strategies. A detailed description of the T7 phage biopanning procedure is provided, with valuable tips for optimising each step in the process, as well as advice for identifying and avoiding the most commonly encountered challenges and pitfalls along the way. Finally, a brief discussion is provided on techniques for validating the cellular targets identified using T7 phage display.

Molecular mechanisms of epigenetic variation in plants.

PubMed

Fujimoto, Ryo; Sasaki, Taku; Ishikawa, Ryo; Osabe, Kenji; Kawanabe, Takahiro; Dennis, Elizabeth S

2012-01-01

Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.

Temporal variations of natural soil salinity in an arid environment using satellite images

NASA Astrophysics Data System (ADS)

Gutierrez, M.; Johnson, E.

2010-11-01

In many remote arid areas the scarce amount of conventional soil salinity data precludes detailed analyses of salinity variations for the purpose of predicting its impact on agricultural production. A tool that is an appropriate surrogate for on-ground testing in determining temporal variations of soil salinity is Landsat satellite data. In this study six Landsat scenes over El Cuervo, a closed basin adjacent to the middle Rio Conchos basin in northern Mexico, were used to show temporal variation of natural salts from 1986 to 2005. Natural salts were inferred from ground reference data and spectral responses. Transformations used were Tasseled Cap, Principal Components and several (band) ratios. Classification of each scene was performed from the development of Regions Of Interest derived from geochemical data collected by SGM, spectral responses derived from ENVI software, and a small amount of field data collected by the authors. The resultant land cover classes showed a relationship between climatic drought and areal coverage of natural salts. When little precipitation occurred three months prior to the capture of the Landsat scene, approximately 15%-20% of the area was classified as salt. This is compared to practically no classified salt in the wetter years of 1992 and 2005 Landsat scenes.

Natural variation and genetic make-up of leaf blade area in spring barley.

PubMed

Alqudah, Ahmad M; Youssef, Helmy M; Graner, Andreas; Schnurbusch, Thorsten

2018-04-01

GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes. Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals. To better understand the natural genetic variation of LA at four developmental stages, main culm LA was measured from 215 worldwide spring barleys including 92 photoperiod-sensitive accessions [PHOTOPERIOD RESPONSE LOCUS 1 (Ppd-H1)] and 123 accessions with reduced photoperiod sensitivity (ppd-H1) locus under controlled greenhouse conditions (long-day; 16/8 h; ~ 20/~ 16 °C day/night). The LA of Ppd-H1-carrying accessions was always smaller than in ppd-H1-carrying accessions. We found that nine SNPs from the Ppd-H1 gene were present in the collection of which marker 9 (M9; G/T in the CCT-domain) showed the most significant and consistent effect on LA at all studied developmental stages. Genome-wide association scans (GWAS) showed that the accessions carrying the ppd-H1 allele T/M9 (late heading) possessed more genetic variation in LA than the Ppd-H1 group carrying G/M9 (early heading). Several QTL with major effects on LA variation were found close to plant stature-related heading time, phytohormone- and sugar-related genes. The results provide evidence that natural variation of LA is an important source for improving grain yield, adaptation and canopy architecture of temperate cereals.

Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature.

PubMed

Roux, Fabrice; Colomé-Tatché, Maria; Edelist, Cécile; Wardenaar, René; Guerche, Philippe; Hospital, Frédéric; Colot, Vincent; Jansen, Ritsert C; Johannes, Frank

2011-08-01

We extensively phenotyped 6000 Arabidopsis plants with experimentally perturbed DNA methylomes as well as a diverse panel of natural accessions in a common garden. We found that alterations in DNA methylation not only caused heritable phenotypic diversity but also produced heritability patterns closely resembling those of the natural accessions. Our findings indicate that epigenetically induced and naturally occurring variation in complex traits share part of their polygenic architecture and may offer complementary adaptation routes in ecological settings.

Meiotic sex ratio variation in natural populations of Ceratodon purpureus (Ditrichaceae).

PubMed

Norrell, Tatum E; Jones, Kelly S; Payton, Adam C; McDaniel, Stuart F

2014-09-01

• Sex ratio variation is a common but often unexplained phenomenon in species across the tree of life. Here we evaluate the hypothesis that meiotic sex ratio variation can contribute to the biased sex ratios found in natural populations of the moss Ceratodon purpureus.• We obtained sporophytes from several populations of C. purpureus from eastern North America. From each sporophyte, we estimated the mean spore viability by germinating replicate samples on agar plates. We estimated the meiotic sex ratio of each sporophyte by inferring the sex of a random sample of germinated spores (mean = 77) using a PCR-RFLP test. We tested for among-sporophyte variation in viability using an ANOVA and for deviations from 1:1 sex ratio using a χ(2)-test and evaluated the relationship between these quantities using a linear regression.• We found among-sporophyte variation in spore viability and meiotic sex ratio, suggesting that genetic variants that contribute to variation in both of these traits segregate within populations of this species. However, we found no relationship between these quantities, suggesting that factors other than sex ratio distorters contribute to variation in spore viability within populations.• These results demonstrate that sex ratio distortion may partially explain the population sex ratio variation seen in C. purpureus, but more generally that genetic conflict over meiotic segregation may contribute to fitness variation in this species. Overall, this study lays the groundwork for future studies on the genetic basis of meiotic sex ratio variation. © 2014 Botanical Society of America, Inc.

Natural Variation in Elicitation of Defense-Signaling Associates to Field Resistance Against the Spot Blotch Disease in Bread Wheat (Triticum aestivum L.)

PubMed Central

Sharma, Sandeep; Sahu, Ranabir; Navathe, Sudhir; Mishra, Vinod K.; Chand, Ramesh; Singh, Pawan K.; Joshi, Arun K.; Pandey, Shree P.

2018-01-01

Spot blotch, caused by the hemibiotropic fungus Bipolaris sorokiniana, is amongst the most damaging diseases of wheat. Still, natural variation in expression of biochemical traits that determine field resistance to spot blotch in wheat remain unaddressed. To understand how genotypic variations relate to metabolite profiles of the components of defense-signaling and the plant performance, as well as to discover novel sources of resistance against spot blotch, we have conducted field studies using 968 wheat genotypes at 5 geographical locations in South-Asia in 2 years. 46 genotypes were identified as resistant. Further, in independent confirmatory trials in subsequent 3 years, over 5 geographical locations, we re-characterized 55 genotypes for their resistance (above 46 along with Yangmai#6, a well characterized resistant genotype, and eight susceptible genotypes). We next determined time-dependent spot blotch-induced metabolite profiles of components of defense-signaling as well as levels of enzymatic components of defense pathway (such as salicylic acid (SA), phenolic acids, and redox components), and derived co-variation patterns with respect to resistance in these 55 genotypes. Spot blotch-induced SA accumulation was negatively correlated to disease progression. Amongst phenolic acids, syringic acid was most strongly inversely correlated to disease progression, indicating a defensive function, which was independently confirmed. Thus, exploring natural variation proved extremely useful in determining traits influencing phenotypic plasticity and adaptation to complex environments. Further, by overcoming environmental heterogeneity, our study identifies germplasm and biochemical traits that are deployable for spot blotch resistance in wheat along South-Asia. PMID:29868089

Natural Variation in Elicitation of Defense-Signaling Associates to Field Resistance Against the Spot Blotch Disease in Bread Wheat (Triticum aestivum L.).

PubMed

Sharma, Sandeep; Sahu, Ranabir; Navathe, Sudhir; Mishra, Vinod K; Chand, Ramesh; Singh, Pawan K; Joshi, Arun K; Pandey, Shree P

2018-01-01

Spot blotch, caused by the hemibiotropic fungus Bipolaris sorokiniana , is amongst the most damaging diseases of wheat. Still, natural variation in expression of biochemical traits that determine field resistance to spot blotch in wheat remain unaddressed. To understand how genotypic variations relate to metabolite profiles of the components of defense-signaling and the plant performance, as well as to discover novel sources of resistance against spot blotch, we have conducted field studies using 968 wheat genotypes at 5 geographical locations in South-Asia in 2 years. 46 genotypes were identified as resistant. Further, in independent confirmatory trials in subsequent 3 years, over 5 geographical locations, we re-characterized 55 genotypes for their resistance (above 46 along with Yangmai#6, a well characterized resistant genotype, and eight susceptible genotypes). We next determined time-dependent spot blotch-induced metabolite profiles of components of defense-signaling as well as levels of enzymatic components of defense pathway (such as salicylic acid (SA), phenolic acids, and redox components), and derived co-variation patterns with respect to resistance in these 55 genotypes. Spot blotch-induced SA accumulation was negatively correlated to disease progression. Amongst phenolic acids, syringic acid was most strongly inversely correlated to disease progression, indicating a defensive function, which was independently confirmed. Thus, exploring natural variation proved extremely useful in determining traits influencing phenotypic plasticity and adaptation to complex environments. Further, by overcoming environmental heterogeneity, our study identifies germplasm and biochemical traits that are deployable for spot blotch resistance in wheat along South-Asia.

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Yang, Zhigang; Okazaki, Yozo; Yonemaru, Jun-ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2015-01-01

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications. PMID:25267402

Strategies to identify natural antisense transcripts.

PubMed

Sun, Yulong; Li, Dijie; Zhang, Ru; Peng, Shang; Zhang, Ge; Yang, Tuanmin; Qian, Airong

2017-01-01

Natural antisense transcripts, originally considered as transcriptional noises arising from so-called "junk DNA″, are recently recognized as important modulators for gene regulation. They are prevalent in nearly all realms of life and have been found to modulate gene expression positively or negatively. By affecting almost all stages of gene expression range from pre-transcriptional, transcriptional and post-transcriptional to translation, NATs are fundamentally involved in various biological processes. However, compared to increasing huge data from transcriptional analysis especially high-throughput sequencing technologies (such as RNA-seq), limited functional NATs (around 70) are so far reported, which hinder our advanced comprehensive understanding for this field. Hence, efficient strategies for identifying NATs are urgently desired. In this review, we discussed the current strategies for identifying NATs, with a focus on the advantages, disadvantages, and applications of methods isolating functional NATs. Moreover, publicly available databases for NATs were also discussed. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Hsp90 and environmental stress transform the adaptive value of natural genetic variation.

PubMed

Jarosz, Daniel F; Lindquist, Susan

2010-12-24

How can species remain unaltered for long periods yet also undergo rapid diversification? By linking genetic variation to phenotypic variation via environmental stress, the Hsp90 protein-folding reservoir might promote both stasis and change. However, the nature and adaptive value of Hsp90-contingent traits remain uncertain. In ecologically and genetically diverse yeasts, we find such traits to be both common and frequently adaptive. Most are based on preexisting variation, with causative polymorphisms occurring in coding and regulatory sequences alike. A common temperature stress alters phenotypes similarly. Both selective inhibition of Hsp90 and temperature stress increase correlations between genotype and phenotype. This system broadly determines the adaptive value of standing genetic variation and, in so doing, has influenced the evolution of current genomes.

Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

PubMed Central

Poupin, Nathalie; Mariotti, François; Huneau, Jean-François; Hermier, Dominique; Fouillet, Hélène

2014-01-01

Body tissues are generally 15N-enriched over the diet, with a discrimination factor (Δ15N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both 15N bioaccumulation and intra- and inter-individual Δ15N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ15N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ15N system, by explicitly linking the sizes and Δ15N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to 15N accumulation in tissues, (ii) the Δ15N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ15N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ15N, and (v) Δ15N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ15N measurements. This work provides proof of concept that Δ15N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such

CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit.

PubMed

Brand, Arnon; Borovsky, Yelena; Hill, Theresa; Rahman, Khalis Afnan Abdul; Bellalou, Aharon; Van Deynze, Allen; Paran, Ilan

2014-10-01

We provide multiple evidences that CaGLK2 underlies a quantitative trait locus controlling natural variation in chlorophyll content and immature fruit color of pepper via modulating chloroplast compartment size. Pepper fruit quality is attributed to a variety of traits, affecting visual appearance, flavor, chemical composition and nutritional value. Among the quality traits, fruit color is of primary importance because the pigments that confer color are associated with nutrition, health and flavor. Although gene models have been proposed for qualitative aspects of fruit color, large natural variation in quantitative pigment content and fruit color exists in pepper. However, its genetic basis is largely unknown which hampers its utilization for plant improvement. We studied the role of GLK2, a GOLDEN2-like transcription factor that regulates chloroplast development in controlling natural variation for chlorophyll content and immature fruit color of pepper. The role of GLK2 in regulating fruit development has been studied previously in tomato using ectopic expression and the uniform ripening mutant analyses. However, pepper provides a unique opportunity to further study the function of this gene because of the wide natural variation of fruit colors in this species. Segregation, sequencing and expression analyses indicated that pepper GLK2 (CaGLK2) corresponds to the recently reported pc10 QTL that controls chloroplast development and chlorophyll content in pepper. CaGLK2 exerts its effect on chloroplast compartment size predominantly during immature fruit development. We show that the genetic background, sequence variation and expression pattern confer a complex and multi-level regulation of CaGLK2 and fruit color in Capsicum. The positive effect on fruit quality predominantly at the green stage conferred by CaGLK2 can be utilized to breed green pepper varieties with improved nutritional values and taste.

Mining and harnessing natural variation - a little MAGIC

USDA-ARS?s Scientific Manuscript database

As has been frequently noted, exotic germplasm ( lines unadapted to local conditions) can be sources of very beneficial genes. The trouble is that it's often difficult to identify these genes. We propose an approach in which mutations can be used to uncover useful variants of natural genes....

Identifying natural flow regimes using fish communities

NASA Astrophysics Data System (ADS)

Chang, Fi-John; Tsai, Wen-Ping; Wu, Tzu-Ching; Chen, Hung-kwai; Herricks, Edwin E.

2011-10-01

SummaryModern water resources management has adopted natural flow regimes as reasonable targets for river restoration and conservation. The characterization of a natural flow regime begins with the development of hydrologic statistics from flow records. However, little guidance exists for defining the period of record needed for regime determination. In Taiwan, the Taiwan Eco-hydrological Indicator System (TEIS), a group of hydrologic statistics selected for fisheries relevance, is being used to evaluate ecological flows. The TEIS consists of a group of hydrologic statistics selected to characterize the relationships between flow and the life history of indigenous species. Using the TEIS and biosurvey data for Taiwan, this paper identifies the length of hydrologic record sufficient for natural flow regime characterization. To define the ecological hydrology of fish communities, this study connected hydrologic statistics to fish communities by using methods to define antecedent conditions that influence existing community composition. A moving average method was applied to TEIS statistics to reflect the effects of antecedent flow condition and a point-biserial correlation method was used to relate fisheries collections with TEIS statistics. The resulting fish species-TEIS (FISH-TEIS) hydrologic statistics matrix takes full advantage of historical flows and fisheries data. The analysis indicates that, in the watersheds analyzed, averaging TEIS statistics for the present year and 3 years prior to the sampling date, termed MA(4), is sufficient to develop a natural flow regime. This result suggests that flow regimes based on hydrologic statistics for the period of record can be replaced by regimes developed for sampled fish communities.

Natural biological variation of white matter microstructure is accentuated in Huntington's disease.

PubMed

Gregory, Sarah; Crawford, Helen; Seunarine, Kiran; Leavitt, Blair; Durr, Alexandra; Roos, Raymund A C; Scahill, Rachael I; Tabrizi, Sarah J; Rees, Geraint; Langbehn, Douglas; Orth, Michael

2018-04-22

Huntington's disease (HD) is a monogenic neurodegenerative disorder caused by a CAG-repeat expansion in the Huntingtin gene. Presence of this expansion signifies certainty of disease onset, but only partly explains age at which onset occurs. Genome-wide association studies have shown that naturally occurring genetic variability influences HD pathogenesis and disease onset. Investigating the influence of biological traits in the normal population, such as variability in white matter properties, on HD pathogenesis could provide a complementary approach to understanding disease modification. We have previously shown that while white matter diffusivity patterns in the left sensorimotor network were similar in controls and HD gene-carriers, they were more extreme in the HD group. We hypothesized that the influence of natural variation in diffusivity on effects of HD pathogenesis on white matter is not limited to the sensorimotor network but extends to cognitive, limbic, and visual networks. Using tractography, we investigated 32 bilateral pathways within HD-related networks, including motor, cognitive, and limbic, and examined diffusivity metrics using principal components analysis. We identified three independent patterns of diffusivity common to controls and HD gene-carriers that predicted HD status. The first pattern involved almost all tracts, the second was limited to sensorimotor tracts, and the third encompassed cognitive network tracts. Each diffusivity pattern was associated with network specific performance. The consistency in diffusivity patterns across both groups coupled with their association with disease status and task performance indicates that naturally-occurring patterns of diffusivity can become accentuated in the presence of the HD gene mutation to influence clinical brain function. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Variation in Genomic Methylation in Natural Populations of Chinese White Poplar

PubMed Central

Ma, Kaifeng; Song, Yuepeng; Yang, Xiaohui; Zhang, Zhiyi; Zhang, Deqiang

2013-01-01

Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match. PMID:23704963

Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways

PubMed Central

Singh, Kapil Dev; Roschitzki, Bernd; Snoek, L. Basten; Grossmann, Jonas; Zheng, Xue; Elvin, Mark; Kamkina, Polina; Schrimpf, Sabine P.; Poulin, Gino B.; Kammenga, Jan E.; Hengartner, Michael O.

2016-01-01

Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels. PMID:26985669

Natural Variation in the Thermotolerance of Neural Function and Behavior due to a cGMP-Dependent Protein Kinase

PubMed Central

Dawson-Scully, Ken; Armstrong, Gary A.B.; Kent, Clement; Robertson, R. Meldrum; Sokolowski, Marla B.

2007-01-01

Although it is acknowledged that genetic variation contributes to individual differences in thermotolerance, the specific genes and pathways involved and how they are modulated by the environment remain poorly understood. We link natural variation in the thermotolerance of neural function and behavior in Drosophila melanogaster to the foraging gene (for, which encodes a cGMP-dependent protein kinase (PKG)) as well as to its downstream target, protein phosphatase 2A (PP2A). Genetic and pharmacological manipulations revealed that reduced PKG (or PP2A) activity caused increased thermotolerance of synaptic transmission at the larval neuromuscular junction. Like synaptic transmission, feeding movements were preserved at higher temperatures in larvae with lower PKG levels. In a comparative assay, pharmacological manipulations altering thermotolerance in a central circuit of Locusta migratoria demonstrated conservation of this neuroprotective pathway. In this circuit, either the inhibition of PKG or PP2A induced robust thermotolerance of neural function. We suggest that PKG and therefore the polymorphism associated with the allelic variation in for may provide populations with natural variation in heat stress tolerance. for's function in behavior is conserved across most organisms, including ants, bees, nematodes, and mammals. PKG's role in thermotolerance may also apply to these and other species. Natural variation in thermotolerance arising from genes involved in the PKG pathway could impact the evolution of thermotolerance in natural populations. PMID:17712421

Natural Variation of Molecular and Morphological Gibberellin Responses.

PubMed

Nam, Youn-Jeong; Herman, Dorota; Blomme, Jonas; Chae, Eunyoung; Kojima, Mikiko; Coppens, Frederik; Storme, Veronique; Van Daele, Twiggy; Dhondt, Stijn; Sakakibara, Hitoshi; Weigel, Detlef; Inzé, Dirk; Gonzalez, Nathalie

2017-01-01

Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis (Arabidopsis thaliana). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signaling. © 2017 American Society of Plant Biologists. All Rights Reserved.

Natural Variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Gordon, Sean

2013-03-01

Sean Gordon of the USDA on Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Natural variation in virulence of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes.

PubMed

Valero-Jiménez, Claudio A; Debets, Alfons J M; van Kan, Jan A L; Schoustra, Sijmen E; Takken, Willem; Zwaan, Bas J; Koenraadt, Constantianus J M

2014-12-06

Insecticide resistance is greatly hampering current efforts to control malaria and therefore alternative methods are needed. Entomopathogenic fungi have been proposed as an alternative with a special focus on the cosmopolitan species Beauveria bassiana. However, few studies have analysed the effects of natural variation within fungal isolates on mosquito survival, and the implications and possible exploitation for malaria control. Laboratory bioassays were performed on adult female mosquitoes (Anopheles coluzzii) with spores from 29 isolates of B. bassiana, originating from different parts of the world. In addition, phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth rate were studied to explore their relationship with virulence. All tested isolates of B. bassiana killed An. coluzzii mosquitoes, and the rate at which this happened differed significantly among the isolates. The risk of mosquitoes dying was around ten times higher when they were exposed to the most virulent as compared to the least virulent isolate. There was significant variation among isolates in spore size, growth rate and sporulation, but none of these morphological characteristics were correlated, and thus predictive, for the ability of the fungal isolate to kill malaria mosquitoes. This study shows that there is a wide natural variation in virulence of isolates of B. bassiana, and that selecting an appropriate fungal isolate is highly relevant in killing and thus controlling malaria mosquitoes, particularly if used as part of an integrated vector management strategy. Also, the wide variation observed in virulence offers the opportunity to better understand the molecular and genetic mechanisms that drive this variation and thus to address the potential development of resistance against entomopathogenic fungi.

Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data.

PubMed

Bigham, Abigail; Bauchet, Marc; Pinto, Dalila; Mao, Xianyun; Akey, Joshua M; Mei, Rui; Scherer, Stephen W; Julian, Colleen G; Wilson, Megan J; López Herráez, David; Brutsaert, Tom; Parra, Esteban J; Moore, Lorna G; Shriver, Mark D

2010-09-09

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

PubMed Central

Bigham, Abigail; Bauchet, Marc; Pinto, Dalila; Mao, Xianyun; Akey, Joshua M.; Mei, Rui; Scherer, Stephen W.; Julian, Colleen G.; Wilson, Megan J.; López Herráez, David; Brutsaert, Tom; Parra, Esteban J.; Moore, Lorna G.; Shriver, Mark D.

2010-01-01

High-altitude hypoxia (reduced inspired oxygen tension due to decreased barometric pressure) exerts severe physiological stress on the human body. Two high-altitude regions where humans have lived for millennia are the Andean Altiplano and the Tibetan Plateau. Populations living in these regions exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. Although these responses have been well characterized physiologically, their underlying genetic basis remains unknown. We performed a genome scan to identify genes showing evidence of adaptation to hypoxia. We looked across each chromosome to identify genomic regions with previously unknown function with respect to altitude phenotypes. In addition, groups of genes functioning in oxygen metabolism and sensing were examined to test the hypothesis that particular pathways have been involved in genetic adaptation to altitude. Applying four population genetic statistics commonly used for detecting signatures of natural selection, we identified selection-nominated candidate genes and gene regions in these two populations (Andeans and Tibetans) separately. The Tibetan and Andean patterns of genetic adaptation are largely distinct from one another, with both populations showing evidence of positive natural selection in different genes or gene regions. Interestingly, one gene previously known to be important in cellular oxygen sensing, EGLN1 (also known as PHD2), shows evidence of positive selection in both Tibetans and Andeans. However, the pattern of variation for this gene differs between the two populations. Our results indicate that several key HIF-regulatory and targeted genes are responsible for adaptation to high altitude in Andeans and Tibetans, and several different chromosomal regions are implicated in the putative response to selection. These data suggest a genetic role in high-altitude adaption and provide a basis for future genotype/phenotype association studies necessary

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.

Molecular basis of natural variation and environmental control of trichome patterning

PubMed Central

Hauser, Marie-Theres

2014-01-01

Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

Egg discrimination along a gradient of natural variation in eggshell coloration.

PubMed

Hanley, Daniel; Grim, Tomáš; Igic, Branislav; Samaš, Peter; López, Analía V; Shawkey, Matthew D; Hauber, Mark E

2017-02-08

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs' colours. We tested hosts' responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of egg colours. Hosts rejected brown eggs and accepted blue-green eggs along the natural egg colour gradient, irrespective of the total perceived dissimilarity from their own egg's colour. By contrast, their responses did not vary along the artificial colour gradient. Our results demonstrate that egg recognition is specifically tuned to the natural gradient of avian eggshell colour and suggest a novel decision rule. These results highlight the importance of considering sensory reception and decision rules when studying perception, and illustrate that our understanding of recognition processes benefits from examining natural variation in phenotypes. © 2017 The Authors.

Egg discrimination along a gradient of natural variation in eggshell coloration

PubMed Central

Grim, Tomáš; Igic, Branislav; Samaš, Peter; López, Analía V.; Shawkey, Matthew D.; Hauber, Mark E.

2017-01-01

Accurate recognition of salient cues is critical for adaptive responses, but the underlying sensory and cognitive processes are often poorly understood. For example, hosts of avian brood parasites have long been assumed to reject foreign eggs from their nests based on the total degree of dissimilarity in colour to their own eggs, regardless of the foreign eggs' colours. We tested hosts' responses to gradients of natural (blue-green to brown) and artificial (green to purple) egg colours, and demonstrate that hosts base rejection decisions on both the direction and degree of colour dissimilarity along the natural, but not artificial, gradient of egg colours. Hosts rejected brown eggs and accepted blue-green eggs along the natural egg colour gradient, irrespective of the total perceived dissimilarity from their own egg's colour. By contrast, their responses did not vary along the artificial colour gradient. Our results demonstrate that egg recognition is specifically tuned to the natural gradient of avian eggshell colour and suggest a novel decision rule. These results highlight the importance of considering sensory reception and decision rules when studying perception, and illustrate that our understanding of recognition processes benefits from examining natural variation in phenotypes. PMID:28179521

Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time.

PubMed

Johanson, U; West, J; Lister, C; Michaels, S; Amasino, R; Dean, C

2000-10-13

Vernalization, the acceleration of flowering by a long period of cold temperature, ensures that many plants overwinter vegetatively and flower in spring. In Arabidopsis, allelic variation at the FRIGIDA (FRI) locus is a major determinant of natural variation in flowering time. Dominant alleles of FRI confer late flowering, which is reversed to earliness by vernalization. We cloned FRI and analyzed the molecular basis of the allelic variation. Most of the early-flowering ecotypes analyzed carry FRI alleles containing one of two different deletions that disrupt the open reading frame. Loss-of-function mutations at FRI have thus provided the basis for the evolution of many early-flowering ecotypes.

Identifying Variations in Baseline Behavior of Killer Whales (Orcinus orca) to Contextualize Their Responses to Anthropogenic Noise.

PubMed

Samarra, Filipa I P; Miller, Patrick J O

2016-01-01

Determining the baseline behavior of a whale requires understanding natural variations occurring due to environmental context, such as changes in prey behavior. Killer whales feeding on herring consistently encircle herring schools; however, depth of feeding differs from near the surface in winter to deeper than 10 m in spring and summer. These variations in feeding depth are probably due to the depth of the prey and the balance between the costs and benefits of bringing schools of herring to the surface. Such variation in baseline behavior may incur different energetic costs and consequently change the motivation of whales to avoid a feeding area. Here, we discuss these variations in feeding behavior in the context of exposure to noise and interpret observed responses to simulated navy sonar signals.

Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

PubMed

Tomar, Parul; Bhatia, Aatish; Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

2013-01-01

Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.

Sporulation Genes Associated with Sporulation Efficiency in Natural Isolates of Yeast

PubMed Central

Ramdas, Shweta; Diao, Liyang; Bhanot, Gyan; Sinha, Himanshu

2013-01-01

Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes – HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast. PMID:23874994

Retrospectively reported month-to-month variation in sleeping problems of people naturally exposed to high-amplitude annual variation in daylength and/or temperature.

PubMed

Putilov, Arcady A

2017-01-01

Compared to literature on seasonal variation in mood and well-being, reports on seasonality of trouble sleeping are scarce and contradictive. To extend geography of such reports on example of people naturally exposed to high-amplitude annual variation in daylength and/or temperature. Participants were the residents of Turkmenia, West Siberia, South and North Yakutia, Chukotka, and Alaska. Health and sleep-wake adaptabilities, month-to-month variation in sleeping problems, well-being and behaviors were self-assessed. More than a half of 2398 respondents acknowledged seasonality of sleeping problems. Four of the assessed sleeping problems demonstrated three different patterns of seasonal variation. Rate of the problems significantly increased in winter months with long nights and cold days (daytime sleepiness and difficulties falling and staying asleep) as well as in summer months with either long days (premature awakening and difficulties falling and staying asleep) or hot nights and days (all 4 sleeping problems). Individual differences between respondents in pattern and level of seasonality of sleeping problems were significantly associated with differences in several other domains of individual variation, such as gender, age, ethnicity, physical health, morning-evening preference, sleep quality, and adaptability of the sleep-wake cycle. These results have practical relevance to understanding of the roles playing by natural environmental factors in seasonality of sleeping problems as well as to research on prevalence of sleep disorders and methods of their prevention and treatment in regions with large seasonal differences in temperature and daylength.

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

PubMed Central

Strauch, Renee C.; Svedin, Elisabeth; Dilkes, Brian; Chapple, Clint; Li, Xu

2015-01-01

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. As an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite–gene associations led to the identification of N-malonyl-d-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5′-phosphate for its activity. This study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. It also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism. PMID:26324904

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

DOE PAGES

Strauch, Renee C.; Svedin, Elisabeth; Dilkes, Brian; ...

2015-08-31

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. Here, as an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-genemore » associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. In conclusion, this study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. As a result, it also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.« less

Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana

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

Strauch, Renee C.; Svedin, Elisabeth; Dilkes, Brian

Plants produce diverse low-molecular-weight compounds via specialized metabolism. Discovery of the pathways underlying production of these metabolites is an important challenge for harnessing the huge chemical diversity and catalytic potential in the plant kingdom for human uses, but this effort is often encumbered by the necessity to initially identify compounds of interest or purify a catalyst involved in their synthesis. Here, as an alternative approach, we have performed untargeted metabolite profiling and genome-wide association analysis on 440 natural accessions of Arabidopsis thaliana. This approach allowed us to establish genetic linkages between metabolites and genes. Investigation of one of the metabolite-genemore » associations led to the identification of N-malonyl-D-allo-isoleucine, and the discovery of a novel amino acid racemase involved in its biosynthesis. This finding provides, to our knowledge, the first functional characterization of a eukaryotic member of a large and widely conserved phenazine biosynthesis protein PhzF-like protein family. Unlike most of known eukaryotic amino acid racemases, the newly discovered enzyme does not require pyridoxal 5'-phosphate for its activity. In conclusion, this study thus identifies a new d-amino acid racemase gene family and advances our knowledge of plant d-amino acid metabolism that is currently largely unexplored. As a result, it also demonstrates that exploitation of natural metabolic variation by integrating metabolomics with genome-wide association is a powerful approach for functional genomics study of specialized metabolism.« less

Environmental and biomedical applications of natural metal stable isotope variations

USGS Publications Warehouse

Bullen, T.D.; Walczyk, T.

2009-01-01

etal stable isotopes are now being used to trace metal contaminants in the environment and as indicators of human systemic function where metals play a role. Stable isotope abundance variations provide information about metal sources and the processes affecting metals in complex natural systems, complementing information gained from surrogate tracers, such as metal abundance ratios or biochemical markers of metal metabolism. The science is still in its infancy, but the results of initial studies confirm that metal stable isotopes can provide a powerful tool for forensic and biomedical investigations.

Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study

PubMed Central

Wang, Quanxiu; Zhao, Hu; Jiang, Junpeng; Xu, Jiuyue; Xie, Weibo; Fu, Xiangkui; Liu, Chang; He, Yuqing; Wang, Gongwei

2017-01-01

The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels) within a 6,997-bp DNA fragment of OsPsbS1, but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1. The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2, the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice. PMID:29081789

Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study.

PubMed

Wang, Quanxiu; Zhao, Hu; Jiang, Junpeng; Xu, Jiuyue; Xie, Weibo; Fu, Xiangkui; Liu, Chang; He, Yuqing; Wang, Gongwei

2017-01-01

The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice ( Oryza sativa ), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified. To check the validity of the GWAS signals, three F2 mapping populations with parents selected from the association panel were constructed and assayed. All QTLs detected in mapping populations could correspond to at least one GWAS signal, indicating the GWAS results were quite reliable. OsPsbS1 was repeatedly detected and explained more than 40% of the variation in the whole association population in two years, and demonstrated to be a common major QTL in all three mapping populations derived from inter-group crosses. We revealed 43 single nucleotide polymorphisms (SNPs) and 7 insertions and deletions (InDels) within a 6,997-bp DNA fragment of OsPsbS1 , but found no non-synonymous SNPs or InDels in the coding region, indicating the PsbS1 protein sequence is highly conserved. Haplotypes with the 2,674-bp insertion in the promoter region exhibited significantly higher NPQ values and higher expression levels of OsPsbS1 . The OsPsbS1 RNAi plants and CRISPR/Cas9 mutants exhibited drastically decreased NPQ values. OsPsbS1 had specific and high-level expression in green tissues of rice. However, we didn't find significant function for OsPsbS2 , the other rice PsbS homologue. Manipulation of the significant loci or candidate genes identified may enhance photoprotection and improve photosynthesis and yield in rice.

Natural time analysis on the ultra-low frequency magnetic field variations prior to the 2016 Kumamoto (Japan) earthquakes

NASA Astrophysics Data System (ADS)

Potirakis, Stelios M.; Schekotov, Alexander; Asano, Tomokazu; Hayakawa, Masashi

2018-04-01

On 15 April 2016 a very strong and shallow earthquake (EQ) (MW = 7.0 , depth ∼ 10 km) occurred in Southwest Japan under the city of Kumamoto, while two very strong foreshocks (MW = 6.2 and MW = 6.0) preceded by about one day. The Kumamoto EQs being very catastrophic, have already attracted much attention among the scientific community in a quest for understanding the generation mechanism, as well as for reporting any preseismic anomalies in various observables and assessing the effectivity of the current early warning systems. In the present article we report precursory behavior of the ground-based observed ultra-low frequency (ULF) magnetic field variations before the Kumamoto EQs. By analyzing specific ULF magnetic field characteristics in terms of the recently introduced natural time (NT) analysis method, we identified that ULF magnetic field variations presented critical features from 2 weeks up to 1 month before the Kumamoto EQs. Specifically, the ULF magnetic field characteristics Fh , Fz , Dh and δDep were analyzed. The first two represent variations of the horizontal and vertical components of the geomagnetic field. The third and fourth characteristics correspond to the depression (decrease) and a relative depression of the horizontal magnetic field variations, respectively. The latter depends on the degree of ionospheric disturbance. All of them were found to reach criticality before the Kumamoto EQs; however, in different time periods for each characteristic.

Natural Genetic Variation for Acclimation of Photosynthetic Light Use Efficiency to Growth Irradiance in Arabidopsis1[OPEN

PubMed Central

Harbinson, Jeremy

2015-01-01

Plants are known to be able to acclimate their photosynthesis to the level of irradiance. Here, we present the analysis of natural genetic variation for photosynthetic light use efficiency (ΦPSII) in response to five light environments among 12 genetically diverse Arabidopsis (Arabidopsis thaliana) accessions. We measured the acclimation of ΦPSII to constant growth irradiances of four different levels (100, 200, 400, and 600 µmol m−2 s−1) by imaging chlorophyll fluorescence after 24 d of growth and compared these results with acclimation of ΦPSII to a step-wise change in irradiance where the growth irradiance was increased from 100 to 600 µmol m−2 s−1 after 24 d of growth. Genotypic variation for ΦPSII is shown by calculating heritability for the short-term ΦPSII response to different irradiance levels as well as for the relation of ΦPSII measured at light saturation (a measure of photosynthetic capacity) to growth irradiance level and for the kinetics of the response to a step-wise increase in irradiance from 100 to 600 µmol m−2 s−1. A genome-wide association study for ΦPSII measured 1 h after a step-wise increase in irradiance identified several new candidate genes controlling this trait. In conclusion, the different photosynthetic responses to a changing light environment displayed by different Arabidopsis accessions are due to genetic differences, and we have identified candidate genes for the photosynthetic response to an irradiance change. The genetic variation for photosynthetic acclimation to irradiance found in this study will allow future identification and analysis of the causal genes for the regulation of ΦPSII in plants. PMID:25670817

Sequence variation identified in the 18S rRNA gene of Theileria mutans and Theileria velifera from the African buffalo (Syncerus caffer).

PubMed

Chaisi, Mamohale E; Collins, Nicola E; Potgieter, Fred T; Oosthuizen, Marinda C

2013-01-16

The African buffalo (Syncerus caffer) is a natural reservoir host for both pathogenic and non-pathogenic Theileria species. These often occur naturally as mixed infections in buffalo. Although the benign and mildly pathogenic forms do not have any significant economic importance, their presence could complicate the interpretation of diagnostic test results aimed at the specific diagnosis of the pathogenic Theileria parva in cattle and buffalo in South Africa. The 18S rRNA gene has been used as the target in a quantitative real-time PCR (qPCR) assay for the detection of T. parva infections. However, the extent of sequence variation within this gene in the non-pathogenic Theileria spp. of the Africa buffalo is not well known. The aim of this study was, therefore, to characterise the full-length 18S rRNA genes of Theileria mutans, Theileria sp. (strain MSD) and T. velifera and to determine the possible influence of any sequence variation on the specific detection of T. parva using the 18S rRNA qPCR. The reverse line blot (RLB) hybridization assay was used to select samples which either tested positive for several different Theileria spp., or which hybridised only with the Babesia/Theileria genus-specific probe and not with any of the Babesia or Theileria species-specific probes. The full-length 18S rRNA genes from 14 samples, originating from 13 buffalo and one bovine from different localities in South Africa, were amplified, cloned and the resulting recombinants sequenced. Variations in the 18S rRNA gene sequences were identified in T. mutans, Theileria sp. (strain MSD) and T. velifera, with the greatest diversity observed amongst the T. mutans variants. This variation possibly explained why the RLB hybridization assay failed to detect T. mutans and T. velifera in some of the analysed samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Application of the Mathar Method to Identify Internal Stress Variation in Steel as a Welding Process Result

NASA Astrophysics Data System (ADS)

Kowalski, Dariusz

2017-06-01

The paper deals with the method to identify internal stresses in two-dimensional steel members. Steel members were investigated in the delivery stage and after assembly, by means of electric-arc welding. In order to perform the member assessment two methods to identify the stress variation were applied. The first is a non-destructive measurement method employing local external magnetic field and to detecting the induced voltage, including Barkhausen noise The analysis of the latter allows to assess internal stresses in a surface layer of the material. The second method, essential in the paper, is a semi-trepanation Mathar method of tensometric strain variation measurement in the course of a controlled void-making in the material. Variation of internal stress distribution in the material led to the choice of welding technology to join. The assembly process altered the actual stresses and made up new stresses, triggering post-welding stresses as a response for the excessive stress variation.

Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.).

PubMed

Bahri, Bochra A; Daverdin, Guillaume; Xu, Xiangyang; Cheng, Jan-Fang; Barry, Kerrie W; Brummer, E Charles; Devos, Katrien M

2018-06-14

Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima's test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in

Tuning up mind's pattern to nature's own idea: Eddington's early twenties case for variational derivatives

NASA Astrophysics Data System (ADS)

Smadja, Ivahn

This paper sets out to show how Eddington's early twenties case for variational derivatives significantly bears witness to a steady and consistent shift in focus from a resolute striving for objectivity towards "selective subjectivism" and structuralism. While framing his so-called "Hamiltonian derivatives" along the lines of previously available variational methods allowing to derive gravitational field equations from an action principle, Eddington assigned them a theoretical function of his own devising in The Mathematical Theory of Relativity (1923). I make clear that two stages should be marked out in Eddington's train of thought if the meaning of such variational derivatives is to be adequately assessed. As far as they were originally intended to embody the mind's collusion with nature by linking atomicity of matter with atomicity of action, variational derivatives were at first assigned a dual role requiring of them not only to express mind's craving for permanence but also to tune up mind's privileged pattern to "Nature's own idea". Whereas at a later stage, as affine field theory would provide a framework for world-building, such "Hamiltonian differentiation" would grow out of tune through gauge-invariance and, by disregarding how mathematical theory might precisely come into contact with actual world, would be turned into a mere heuristic device for structural knowledge.

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

PubMed

Herrera, C M; Bazaga, P

2011-04-01

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions. © 2011 Blackwell Publishing Ltd.

Wild rodents as a model to discover genes and pathways underlying natural variation in infectious disease susceptibility.

PubMed

Turner, A K; Paterson, S

2013-11-01

Individuals vary in their susceptibility to infectious disease, and it is now well established that host genetic factors form a major component of this variation. The discovery of genes underlying susceptibility has the potential to lead to improved disease control, through the identification and management of vulnerable individuals and the discovery of novel therapeutic targets. Laboratory rodents have proved invaluable for ascertaining the function of genes involved in immunity to infection. However, these captive animals experience conditions very different to the natural environment, lacking the genetic diversity and environmental pressures characteristic of natural populations, including those of humans. It has therefore often proved difficult to translate basic laboratory research to the real world. In order to further our understanding of the genetic basis of infectious disease resistance, and the evolutionary forces that drive variation in susceptibility, we propose that genetic research traditionally conducted on laboratory animals is expanded to the more ecologically valid arena of natural populations. In this article, we highlight the potential of using wild rodents as a new resource for biomedical research, to link the functional genetic knowledge gained from laboratory rodents with the variation in infectious disease susceptibility observed in humans and other natural populations. © 2013 John Wiley & Sons Ltd.

Mapping the natural variation in whole bone stiffness and strength across skeletal sites.

PubMed

Schlecht, Stephen H; Bigelow, Erin M R; Jepsen, Karl J

2014-10-01

Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this 'complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p<0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7-2.3 times less stiff and strong in men and 1.3-2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. Copyright © 2014 Elsevier Inc. All rights reserved.

Mapping the natural variation in whole bone stiffness and strength across skeletal sites

PubMed Central

Schlecht, Stephen H.; Bigelow, Erin M.R.; Jepsen, Karl J.

2016-01-01

Traits of the skeletal system are coordinately adjusted to establish mechanical homeostasis in response to genetic and environmental factors. Prior work demonstrated that this `complex adaptive' process is not perfect, revealing a two-fold difference in whole bone stiffness of the tibia across a population. Robustness (specifically, total cross-sectional area relative to length) varies widely across skeletal sites and between sexes. However, it is unknown whether the natural variation in whole bone stiffness and strength also varies across skeletal sites and between men and women. We tested the hypotheses that: 1) all major long bones of the appendicular skeleton demonstrate inherent, systemic constraints in the degree to which morphological and compositional traits can be adjusted for a given robustness; and 2) these traits covary in a predictable manner independent of body size and robustness. We assessed the functional relationships among robustness, cortical area (Ct.Ar), cortical tissue mineral density (Ct.TMD), and bone strength index (BSI) across the long bones of the upper and lower limbs of 115 adult men and women. All bones showed a significant (p < 0.001) positive regression between BSI and robustness after adjusting for body size, with slender bones being 1.7–2.3 times less stiff and strong in men and 1.3–2.8 times less stiff and strong in women compared to robust bones. Our findings are the first to document the natural inter-individual variation in whole bone stiffness and strength that exist within populations and that is predictable based on skeletal robustness for all major long bones. Documenting and further understanding this natural variation in strength may be critical for differentially diagnosing and treating skeletal fragility. PMID:24999223

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.

A systematic approach to identify therapeutic effects of natural products based on human metabolite information.

PubMed

Noh, Kyungrin; Yoo, Sunyong; Lee, Doheon

2018-06-13

Natural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug development. Many researchers have focused on identifying therapeutic effects of natural products, yet the resemblance of natural products and human metabolites has been rarely touched. We propose a novel method which predicts therapeutic effects of natural products based on their similarity with human metabolites. In this study, we compare the structure, target and phenotype similarities between natural products and human metabolites to capture molecular and phenotypic properties of both compounds. With the generated similarity features, we train support vector machine model to identify similar natural product and human metabolite pairs. The known functions of human metabolites are then mapped to the paired natural products to predict their therapeutic effects. With our selected three feature sets, structure, target and phenotype similarities, our trained model successfully paired similar natural products and human metabolites. When applied to the natural product derived drugs, we could successfully identify their indications with high specificity and sensitivity. We further validated the found therapeutic effects of natural products with the literature evidence. These results suggest that our model can match natural products to similar human metabolites and provide possible therapeutic effects of natural products. By utilizing the similar human metabolite information, we expect to find new indications of natural products which could not be covered by previous in silico methods.

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning

PubMed Central

Fakhro, Khalid A.; Choi, Murim; Ware, Stephanie M.; Belmont, John W.; Towbin, Jeffrey A.; Lifton, Richard P.; Khokha, Mustafa K.; Brueckner, Martina

2011-01-01

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10−4). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10−6). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning. PMID:21282601

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning.

PubMed

Fakhro, Khalid A; Choi, Murim; Ware, Stephanie M; Belmont, John W; Towbin, Jeffrey A; Lifton, Richard P; Khokha, Mustafa K; Brueckner, Martina

2011-02-15

Dominant human genetic diseases that impair reproductive fitness and have high locus heterogeneity constitute a problem for gene discovery because the usual criterion of finding more mutations in specific genes than expected by chance may require extremely large populations. Heterotaxy (Htx), a congenital heart disease resulting from abnormalities in left-right (LR) body patterning, has features suggesting that many cases fall into this category. In this setting, appropriate model systems may provide a means to support implication of specific genes. By high-resolution genotyping of 262 Htx subjects and 991 controls, we identify a twofold excess of subjects with rare genic copy number variations in Htx (14.5% vs. 7.4%, P = 1.5 × 10(-4)). Although 7 of 45 Htx copy number variations were large chromosomal abnormalities, 38 smaller copy number variations altered a total of 61 genes, 22 of which had Xenopus orthologs. In situ hybridization identified 7 of these 22 genes with expression in the ciliated LR organizer (gastrocoel roof plate), a marked enrichment compared with 40 of 845 previously studied genes (sevenfold enrichment, P < 10(-6)). Morpholino knockdown in Xenopus of Htx candidates demonstrated that five (NEK2, ROCK2, TGFBR2, GALNT11, and NUP188) strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning. These effects were specific, because 0 of 13 control genes from rare Htx or control copy number variations produced significant LR abnormalities (P = 0.001). These findings identify genes not previously implicated in LR patterning.

Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici

PubMed Central

McDonald, Megan C.; McGinness, Lachlan; Hane, James K.; Williams, Angela H.; Milgate, Andrew; Solomon, Peter S.

2016-01-01

Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene. PMID:26837952

Seasonal and clonal variations in technological and thermal properties of raw Hevea natural rubber

USDA-ARS?s Scientific Manuscript database

This study was undertaken over a ten-month period, under the environmental conditions within the state of Mato Grosso, Brazil, to evaluate the causes of variation in technological and thermal properties of raw natural rubber from different clones of Hevea brasiliensis (GT 1, PR 255, FX 3864 and RRIM...

Using natural range of variation to set decision thresholds: a case study for great plains grasslands

USGS Publications Warehouse

Symstad, Amy J.; Jonas, Jayne L.; Edited by Guntenspergen, Glenn R.

2014-01-01

Natural range of variation (NRV) may be used to establish decision thresholds or action assessment points when ecological thresholds are either unknown or do not exist for attributes of interest in a managed ecosystem. The process for estimating NRV involves identifying spatial and temporal scales that adequately capture the heterogeneity of the ecosystem; compiling data for the attributes of interest via study of historic records, analysis and interpretation of proxy records, modeling, space-for-time substitutions, or analysis of long-term monitoring data; and quantifying the NRV from those data. At least 19 National Park Service (NPS) units in North America’s Great Plains are monitoring plant species richness and evenness as indicators of vegetation integrity in native grasslands, but little information on natural, temporal variability of these indicators is available. In this case study, we use six long-term vegetation monitoring datasets to quantify the temporal variability of these attributes in reference conditions for a variety of Great Plains grassland types, and then illustrate the implications of using different NRVs based on these quantities for setting management decision thresholds. Temporal variability of richness (as measured by the coefficient of variation, CV) is fairly consistent across the wide variety of conditions occurring in Colorado shortgrass prairie to Minnesota tallgrass sand savanna (CV 0.20–0.45) and generally less than that of production at the same sites. Temporal variability of evenness spans a greater range of CV than richness, and it is greater than that of production in some sites but less in other sites. This natural temporal variability may mask undesirable changes in Great Plains grasslands vegetation. Consequently, we suggest that managers consider using a relatively narrow NRV (interquartile range of all richness or evenness values observed in reference conditions) for designating a surveillance threshold, at which

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Inter-observer variation in identifying mammals from their tracks at enclosed track plate stations

Treesearch

William J. Zielinski; Fredrick V. Schlexer

2009-01-01

Enclosed track plate stations are a common method to detect mammalian carnivores. Studies rely on these data to make inferences about geographic range, population status and detectability. Despite their popularity, there has been no effort to document inter-observer variation in identifying the species that leave their tracks. Four previous field crew leaders...

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of CNVs using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intak...

Cultural variation is part of human nature : Literary universals, context-sensitivity, and "shakespeare in the bush".

PubMed

Sugiyama, Michelle Scalise

2003-12-01

In 1966, Laura Bohannan wrote her classic essay challenging the supposition that great literary works speak to universal human concerns and conditions and, by extension, that human nature is the same everywhere. Her evidence: the Tiv of West Africa interpret Hamlet differently from Westerners. While Bohannan's essay implies that cognitive universality and cultural variation are mutually exclusive phenomena, adaptationist theory suggests otherwise. Adaptive problems ("the human condition") and cognitive adaptations ("human nature") are constant across cultures. What differs between cultures is habitat: owing to environmental variation, the means and information relevant to solving adaptive problems differ from place to place. Thus, we find differences between cultures not because human minds differ in design but largely because human habitats differ in resources and history. On this view, we would expect world literature to express both human universals and cultural particularities. Specifically, we should expect to find literary universality at the macro level (e.g., adaptive problems, cognitive adaptations) and literary variation at the micro level (e.g., local solutions to adaptive problems).

Genetic variation in plant volatile emission does not result in differential attraction of natural enemies in the field.

PubMed

Wason, Elizabeth L; Hunter, Mark D

2014-02-01

Volatile organic chemical (VOC) emission by plants may serve as an adaptive plant defense by attracting the natural enemies of herbivores. For plant VOC emission to evolve as an adaptive defense, plants must show genetic variability for the trait. To date, such variability has been investigated primarily in agricultural systems, yet relatively little is known about genetic variation in VOCs emitted by natural populations of native plants. Here, we investigate intraspecific variation in constitutive and herbivore-induced plant VOC emission using the native common milkweed plant (Asclepias syriaca) and its monarch caterpillar herbivore (Danaus plexippus) in complementary field and common garden greenhouse experiments. In addition, we used a common garden field experiment to gauge natural enemy attraction to milkweed VOCs induced by monarch damage. We found evidence of genetic variation in the total constitutive and induced concentrations of VOCs and the composition of VOC blends emitted by milkweed plants. However, all milkweed genotypes responded similarly to induction by monarchs in terms of their relative change in VOC concentration and blend. Natural enemies attacked decoy caterpillars more frequently on damaged than on undamaged milkweed, and natural enemy visitation was associated with higher total VOC concentrations and with VOC blend. Thus, we present evidence that induced VOCs emitted by milkweed may function as a defense against herbivores. However, plant genotypes were equally attractive to natural enemies. Although milkweed genotypes diverge phenotypically in their VOC concentrations and blends, they converge into similar phenotypes with regard to magnitude of induction and enemy attraction.

Genome-Wide Analysis of ZmDREB Genes and Their Association with Natural Variation in Drought Tolerance at Seedling Stage of Zea mays L

PubMed Central

Wang, Hongwei; Xin, Haibo; Yang, Xiaohong; Yan, Jianbing; Li, Jiansheng; Tran, Lam-Son Phan; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko; Qin, Feng

2013-01-01

The worldwide production of maize (Zea mays L.) is frequently impacted by water scarcity and as a result, increased drought tolerance is a priority target in maize breeding programs. While DREB transcription factors have been demonstrated to play a central role in desiccation tolerance, whether or not natural sequence variations in these genes are associated with the phenotypic variability of this trait is largely unknown. In the present study, eighteen ZmDREB genes present in the maize B73 genome were cloned and systematically analyzed to determine their phylogenetic relationship, synteny with rice, maize and sorghum genomes; pattern of drought-responsive gene expression, and protein transactivation activity. Importantly, the association between the nucleic acid variation of each ZmDREB gene with drought tolerance was evaluated using a diverse population of maize consisting of 368 varieties from tropical and temperate regions. A significant association between the genetic variation of ZmDREB2.7 and drought tolerance at seedling stage was identified. Further analysis found that the DNA polymorphisms in the promoter region of ZmDREB2.7, but not the protein coding region itself, was associated with different levels of drought tolerance among maize varieties, likely due to distinct patterns of gene expression in response to drought stress. In vitro, protein-DNA binding assay demonstrated that ZmDREB2.7 protein could specifically interact with the target DNA sequences. The transgenic Arabidopsis overexpressing ZmDREB2.7 displayed enhanced tolerance to drought stress. Moreover, a favorable allele of ZmDREB2.7, identified in the drought-tolerant maize varieties, was effective in imparting plant tolerance to drought stress. Based upon these findings, we conclude that natural variation in the promoter of ZmDREB2.7 contributes to maize drought tolerance, and that the gene and its favorable allele may be an important genetic resource for the genetic improvement of drought

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

PubMed Central

Routaboul, Jean-Marc; Dubos, Christian; Beck, Gilles; Marquis, Catherine; Bidzinski, Przemyslaw; Loudet, Olivier; Lepiniec, Loïc

2012-01-01

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11–64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation. PMID:22442426

VWF mutations and new sequence variations identified in healthy controls are more frequent in the African-American population.

PubMed

Bellissimo, Daniel B; Christopherson, Pamela A; Flood, Veronica H; Gill, Joan Cox; Friedman, Kenneth D; Haberichter, Sandra L; Shapiro, Amy D; Abshire, Thomas C; Leissinger, Cindy; Hoots, W Keith; Lusher, Jeanne M; Ragni, Margaret V; Montgomery, Robert R

2012-03-01

Diagnosis and classification of VWD is aided by molecular analysis of the VWF gene. Because VWF polymorphisms have not been fully characterized, we performed VWF laboratory testing and gene sequencing of 184 healthy controls with a negative bleeding history. The controls included 66 (35.9%) African Americans (AAs). We identified 21 new sequence variations, 13 (62%) of which occurred exclusively in AAs and 2 (G967D, T2666M) that were found in 10%-15% of the AA samples, suggesting they are polymorphisms. We identified 14 sequence variations reported previously as VWF mutations, the majority of which were type 1 mutations. These controls had VWF Ag levels within the normal range, suggesting that these sequence variations might not always reduce plasma VWF levels. Eleven mutations were found in AAs, and the frequency of M740I, H817Q, and R2185Q was 15%-18%. Ten AA controls had the 2N mutation H817Q; 1 was homozygous. The average factor VIII level in this group was 99 IU/dL, suggesting that this variation may confer little or no clinical symptoms. This study emphasizes the importance of sequencing healthy controls to understand ethnic-specific sequence variations so that asymptomatic sequence variations are not misidentified as mutations in other ethnic or racial groups.

Measurement of isotope abundance variations in nature by gravimetric spiking isotope dilution analysis (GS-IDA).

PubMed

Chew, Gina; Walczyk, Thomas

2013-04-02

Subtle variations in the isotopic composition of elements carry unique information about physical and chemical processes in nature and are now exploited widely in diverse areas of research. Reliable measurement of natural isotope abundance variations is among the biggest challenges in inorganic mass spectrometry as they are highly sensitive to methodological bias. For decades, double spiking of the sample with a mix of two stable isotopes has been considered the reference technique for measuring such variations both by multicollector-inductively coupled plasma mass spectrometry (MC-ICPMS) and multicollector-thermal ionization mass spectrometry (MC-TIMS). However, this technique can only be applied to elements having at least four stable isotopes. Here we present a novel approach that requires measurement of three isotope signals only and which is more robust than the conventional double spiking technique. This became possible by gravimetric mixing of the sample with an isotopic spike in different proportions and by applying principles of isotope dilution for data analysis (GS-IDA). The potential and principle use of the technique is demonstrated for Mg in human urine using MC-TIMS for isotopic analysis. Mg is an element inaccessible to double spiking methods as it consists of three stable isotopes only and shows great potential for metabolically induced isotope effects waiting to be explored.

[Variation trends of natural vegetation net primary productivity in China under climate change scenario].

PubMed

Zhao, Dong-sheng; Wu, Shao-hong; Yin, Yun-he

2011-04-01

Based on the widely used Lund-Potsdam-Jena Dynamic Global Vegetation Model (LPJ) for climate change study, and according to the features of natural environment in China, the operation mechanism of the model was adjusted, and the parameters were modified. With the modified LPJ model and taking 1961-1990 as baseline period, the responses of natural vegetation net primary productivity (NPP) in China to climate change in 1991-2080 were simulated under the Special Report on Emissions Scenarios (SRES) B2 scenario. In 1961-1990, the total NPP of natural vegetation in China was about 3.06 Pg C a(-1); in 1961-2080, the total NPP showed a fluctuant decreasing trend, with an accelerated decreasing rate. Under the condition of slight precipitation change, the increase of mean air temperature would have definite adverse impact on the NPP. Spatially, the NPP decreased from southeast coast to northwest inland, and this pattern would have less variation under climate change. In eastern China with higher NPP, especially in Northeast China, east of North China, and Loess Plateau, the NPP would mainly have a decreasing trend; while in western China with lower NPP, especially in the Tibetan Plateau and Tarim Basin, the NPP would be increased. With the intensive climate change, such a variation trend of NPP would be more obvious.

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity.

PubMed

Granados-Cifuentes, Camila; Bellantuono, Anthony J; Ridgway, Tyrone; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

2013-04-08

Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

PubMed Central

2013-01-01

Background Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is

Assessment of Genetically Modified Soybean in Relation to Natural Variation in the Soybean Seed Metabolome

PubMed Central

Clarke, Joseph D.; Alexander, Danny C.; Ward, Dennis P.; Ryals, John A.; Mitchell, Matthew W.; Wulff, Jacob E.; Guo, Lining

2013-01-01

Genetically modified (GM) crops currently constitute a significant and growing part of agriculture. An important aspect of GM crop adoption is to demonstrate safety and equivalence with respect to conventional crops. Untargeted metabolomics has the ability to profile diverse classes of metabolites and thus could be an adjunct for GM crop substantial equivalence assessment. To account for environmental effects and introgression of GM traits into diverse genetic backgrounds, we propose that the assessment for GM crop metabolic composition should be understood within the context of the natural variation for the crop. Using a non-targeted metabolomics platform, we profiled 169 metabolites and established their dynamic ranges from the seeds of 49 conventional soybean lines representing the current commercial genetic diversity. We further demonstrated that the metabolome of a GM line had no significant deviation from natural variation within the soybean metabolome, with the exception of changes in the targeted engineered pathway. PMID:24170158

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

PubMed

Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

2014-11-29

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation

CaAP2 transcription factor is a candidate gene for a flowering repressor and a candidate for controlling natural variation of flowering time in Capsicum annuum.

PubMed

Borovsky, Yelena; Sharma, Vinod K; Verbakel, Henk; Paran, Ilan

2015-06-01

The APETALA2 transcription factor homolog CaAP2 is a candidate gene for a flowering repressor in pepper, as revealed by induced-mutation phenotype, and a candidate underlying a major QTL controlling natural variation in flowering time. To decipher the genetic control of transition to flowering in pepper (Capsicum spp.) and determine the extent of gene function conservation compared to model species, we isolated and characterized several ethyl methanesulfonate (EMS)-induced mutants that vary in their flowering time compared to the wild type. In the present study, we report on the isolation of an early-flowering mutant that flowers after four leaves on the primary stem compared to nine leaves in the wild-type 'Maor'. By genetic mapping and sequencing of putative candidate genes linked to the mutant phenotype, we identified a member of the APETALA2 (AP2) transcription factor family, CaAP2, which was disrupted in the early-flowering mutant. CaAP2 is a likely ortholog of AP2 that functions as a repressor of flowering in Arabidopsis. To test whether CaAP2 has an effect on controlling natural variation in the transition to flowering in pepper, we performed QTL mapping for flowering time in a cross between early and late-flowering C. annuum accessions. We identified a major QTL in a region of chromosome 2 in which CaAP2 was the most significant marker, explaining 52 % of the phenotypic variation of the trait. Sequence comparison of the CaAP2 open reading frames in the two parents used for QTL mapping did not reveal significant variation. In contrast, significant differences in expression level of CaAP2 were detected between near-isogenic lines that differ for the flowering time QTL, supporting the putative function of CaAP2 as a major repressor of flowering in pepper.

Natural variation in gene expression in the early development of dauer larvae of Caenorhabditis elegans.

PubMed

Harvey, Simon C; Barker, Gary L A; Shorto, Alison; Viney, Mark E

2009-07-18

The free-living nematode Caenorhabditis elegans makes a developmental decision based on environmental conditions: larvae either arrest as dauer larva, or continue development into reproductive adults. There is natural variation among C. elegans lines in the sensitivity of this decision to environmental conditions; that is, there is variation in the phenotypic plasticity of dauer larva development. We hypothesised that these differences may be transcriptionally controlled in early stage larvae. We investigated this by microarray analysis of different C. elegans lines under different environmental conditions, specifically the presence and absence of dauer larva-inducing pheromone. There were substantial transcriptional differences between four C. elegans lines under the same environmental conditions. The expression of approximately 2,000 genes differed between genetically different lines, with each line showing a largely line-specific transcriptional profile. The expression of genes that are markers of larval moulting suggested that the lines may be developing at different rates. The expression of a total of 89 genes was putatively affected by dauer larva or non-dauer larva-inducing conditions. Among the upstream regions of these genes there was an over-representation of DAF-16-binding motifs. Under the same environmental conditions genetically different lines of C. elegans had substantial transcriptional differences. This variation may be due to differences in the developmental rates of the lines. Different environmental conditions had a rather smaller effect on transcription. The preponderance of DAF-16-binding motifs upstream of these genes was consistent with these genes playing a key role in the decision between development into dauer or into non-dauer larvae. There was little overlap between the genes whose expression was affected by environmental conditions and previously identified loci involved in the plasticity of dauer larva development.

Using Opinions and Knowledge to Identify Natural Groups of Gambling Employees.

PubMed

Gray, Heather M; Tom, Matthew A; LaPlante, Debi A; Shaffer, Howard J

2015-12-01

Gaming industry employees are at higher risk than the general population for health conditions including gambling disorder. Responsible gambling training programs, which train employees about gambling and gambling-related problems, might be a point of intervention. However, such programs tend to use a "one-size-fits-all" approach rather than multiple tiers of instruction. We surveyed employees of one Las Vegas casino (n = 217) and one online gambling operator (n = 178) regarding their gambling-related knowledge and opinions prior to responsible gambling training, to examine the presence of natural knowledge groups among recently hired employees. Using k-means cluster analysis, we observed four natural groups within the Las Vegas casino sample and two natural groups within the online operator sample. We describe these natural groups in terms of opinion/knowledge differences as well as distributions of demographic/occupational characteristics. Gender and language spoken at home were correlates of cluster group membership among the sample of Las Vegas casino employees, but we did not identify demographic or occupational correlates of cluster group membership among the online gambling operator employees. Gambling operators should develop more sophisticated training programs that include instruction that targets different natural knowledge groups.

Natural variation in germination responses of Arabidopsis to seasonal cues and their associated physiological mechanisms

PubMed Central

Barua, Deepak; Butler, Colleen; Tisdale, Tracy E.; Donohue, Kathleen

2012-01-01

Background and Aims Despite the intense interest in phenological adaptation to environmental change, the fundamental character of natural variation in germination is almost entirely unknown. Specifically, it is not known whether different genotypes within a species are germination specialists to particular conditions, nor is it known what physiological mechanisms of germination regulation vary in natural populations and how they are associated with responses to particular environmental factors. Methods We used a set of recombinant inbred genotypes of Arabidopsis thaliana, in which linkage disequilibrium has been disrupted over seven generations, to test for genetic variation and covariation in germination responses to distinct environmental factors. We then examined physiological mechanisms associated with those responses, including seed-coat permeability and sensitivity to the phytohormones gibberellic acid (GA) and abscisic acid (ABA). Key Results Genetic variation for germination was environment-dependent, but no evidence for specialization of germination to different conditions was found. Hormonal sensitivities also exhibited significant genetic variation, but seed-coat properties did not. GA sensitivity was associated with germination responses to multiple environmental factors, but seed-coat permeability and ABA sensitivity were associated with specific germination responses, suggesting that an evolutionary change in GA sensitivity could affect germination in multiple environments, but that of ABA sensitivity may affect germination under more restricted conditions. Conclusions The physiological mechanisms of germination responses to specific environmental factors therefore can influence the ability to adapt to diverse seasonal environments encountered during colonization of new habitats or with future predicted climate change. PMID:22012958

Is biotic resistance enhanced by natural variation in diversity?

USGS Publications Warehouse

Grace, James B.; Harrison, Susan P.; Cornell, Howard

2017-01-01

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 underlying processes by dissecting how biotic resistance to new invaders may be shaped by the same environmental influences that determine diversity and other community properties.In grasslands with heterogeneous soils, we added invaders and removed competitors to analyze the causes of invasion resistance. Abiotic resistance was measured using invader success in the absence of the resident community. Biotic resistance was measured as the reduction in invader success in the presence of the resident community.Invaders were most successful where biotic resistance was lowest and abiotic resistance was highest, confirming the dominant role of biotic resistance. Contrary to theory, though, biotic resistance was highest where both species richness and functional diversity were lowest. In the multivariate framework of a structural equation model, biotic resistance was independent of community diversity, and was highest where fertile soils led to high community biomass.Seed predation slightly augmented biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results.We conclude that in natural systems, diversity may be correlated with invasibility and yet have little effect on biotic resistance to invasion. More generally, the environmental causes of variation in diversity should be considered when examining the potential functional consequences of diversity.

Causal Genetic Variation Underlying Metabolome Differences.

PubMed

Swain-Lenz, Devjanee; Nikolskiy, Igor; Cheng, Jiye; Sudarsanam, Priya; Nayler, Darcy; Staller, Max V; Cohen, Barak A

2017-08-01

An ongoing challenge in biology is to predict the phenotypes of individuals from their genotypes. Genetic variants that cause disease often change an individual's total metabolite profile, or metabolome. In light of our extensive knowledge of metabolic pathways, genetic variants that alter the metabolome may help predict novel phenotypes. To link genetic variants to changes in the metabolome, we studied natural variation in the yeast Saccharomyces cerevisiae We used an untargeted mass spectrometry method to identify dozens of metabolite Quantitative Trait Loci (mQTL), genomic regions containing genetic variation that control differences in metabolite levels between individuals. We mapped differences in urea cycle metabolites to genetic variation in specific genes known to regulate amino acid biosynthesis. Our functional assays reveal that genetic variation in two genes, AUA1 and ARG81 , cause the differences in the abundance of several urea cycle metabolites. Based on knowledge of the urea cycle, we predicted and then validated a new phenotype: sensitivity to a particular class of amino acid isomers. Our results are a proof-of-concept that untargeted mass spectrometry can reveal links between natural genetic variants and metabolome diversity. The interpretability of our results demonstrates the promise of using genetic variants underlying natural differences in the metabolome to predict novel phenotypes from genotype. Copyright © 2017 by the Genetics Society of America.

Characterizing Male–Female Interactions Using Natural Genetic Variation in Drosophila melanogaster

PubMed Central

Reinhart, Michael; Carney, Tara; Clark, Andrew G.

2015-01-01

Drosophila melanogaster females commonly mate with multiple males establishing the opportunity for pre- and postcopulatory sexual selection. Traits impacting sexual selection can be affected by a complex interplay of the genotypes of the competing males, the genotype of the female, and compatibilities between the males and females. We scored males from 96 2nd and 94 3rd chromosome substitution lines for traits affecting reproductive success when mated with females from 3 different genetic backgrounds. The traits included male-induced female refractoriness, male remating ability, the proportion of offspring sired under competitive conditions and male-induced female fecundity. We observed significant effects of male line, female genetic background, and strong male by female interactions. Some males appeared to be “generalists” and performed consistently across the different females; other males appeared to be “specialists” and performed very well with a particular female and poorly with others. “Specialist” males did not, however, prefer to court those females with whom they had the highest reproductive fitness. Using 143 polymorphisms in male reproductive genes, we mapped several genes that had consistent effects across the different females including a derived, high fitness allele in Acp26Aa that may be the target of adaptive evolution. We also identified a polymorphism upstream of PebII that may interact with the female genetic background to affect male-induced refractoriness to remating. These results suggest that natural variation in PebII might contribute to the observed male–female interactions. PMID:25425680

Natural variations in xenobiotic-metabolizing enzymes: developing tools for coral monitoring

NASA Astrophysics Data System (ADS)

Rougée, L. R. A.; Richmond, R. H.; Collier, A. C.

2014-06-01

The continued deterioration of coral reefs worldwide demonstrates the need to develop diagnostic tools for corals that go beyond general ecological monitoring and can identify specific stressors at sublethal levels. Cellular diagnostics present an approach to defining indicators (biomarkers) that have the potential to reflect the impact of stress at the cellular level, allowing for the detection of intracellular changes in corals prior to outright mortality. Detoxification enzymes, which may be readily induced or inhibited by environmental stressors, present such a set of indicators. However, in order to apply these diagnostic tools for the detection of stress, a detailed understanding of their normal, homeostatic levels within healthy corals must first be established. Herein, we present molecular and biochemical evidence for the expression and activity of major Phase I detoxification enzymes cytochrome P450 (CYP450), CYP2E1, and CYP450 reductase, as well as the Phase II enzymes UDP, glucuronosyltransferase (UGT), β-glucuronidase, glutathione- S-transferase (GST), and arylsulfatase C (ASC) in the coral Pocillopora damicornis. Additionally, we characterized enzyme expression and activity variations over a reproductive cycle within a coral's life history to determine natural endogenous changes devoid of stress exposure. Significant changes in enzyme activity over the coral's natural lunar reproductive cycle were observed for CYP2E1 and CYP450 reductase as well as UGT and GST, while β-glucuronidase and ASC did not fluctuate significantly. The data represent a baseline description of `health' for the expression and activity of these enzymes that can be used toward understanding the impact of environmental stressors on corals. Such knowledge can be applied to address causes of coral reef ecosystem decline and to monitor effectiveness of mitigation strategies. Achieving a better understanding of cause-and-effect relationships between putative stressors and biological

Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products

PubMed Central

Potts, Malia B.; Kim, Hyun Seok; Fisher, Kurt W.; Hu, Youcai; Carrasco, Yazmin P.; Bulut, Gamze Betul; Ou, Yi-Hung; Herrera-Herrera, Mireya L.; Cubillos, Federico; Mendiratta, Saurabh; Xiao, Guanghua; Hofree, Matan; Ideker, Trey; Xie, Yang; Huang, Lily Jun-shen; Lewis, Robert E.; MacMillan, John B.; White, Michael A.

2014-01-01

A challenge for biomedical research is the development of pharmaceuticals that appropriately target disease mechanisms. Natural products can be a rich source of bioactive chemicals for medicinal applications but can act through unknown mechanisms and can be difficult to produce or obtain. To address these challenges, we developed a new marine-derived, renewable natural products resource and a method for linking bioactive derivatives of this library to the proteins and biological processes that they target in cells. We used cell-based screening and computational analysis to match gene expression signatures produced by natural products to those produced by siRNA and synthetic microRNA libraries. With this strategy, we matched proteins and microRNAs with diverse biological processes and also identified putative protein targets and mechanisms of action for several previously undescribed marine-derived natural products. We confirmed mechanistic relationships for selected short-interfering RNAs, microRNAs, and compounds with functional roles in autophagy, chemotaxis mediated by discoidin domain receptor 2, or activation of the kinase AKT. Thus, this approach may be an effective method for screening new drugs while simultaneously identifying their targets. PMID:24129700

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors.

PubMed

Patin, Etienne; Hasan, Milena; Bergstedt, Jacob; Rouilly, Vincent; Libri, Valentina; Urrutia, Alejandra; Alanio, Cécile; Scepanovic, Petar; Hammer, Christian; Jönsson, Friederike; Beitz, Benoît; Quach, Hélène; Lim, Yoong Wearn; Hunkapiller, Julie; Zepeda, Magge; Green, Cherie; Piasecka, Barbara; Leloup, Claire; Rogge, Lars; Huetz, François; Peguillet, Isabelle; Lantz, Olivier; Fontes, Magnus; Di Santo, James P; Thomas, Stéphanie; Fellay, Jacques; Duffy, Darragh; Quintana-Murci, Lluís; Albert, Matthew L

2018-03-01

The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.

Geographical variation in parasitism shapes larval immune function in a phytophagous insect

NASA Astrophysics Data System (ADS)

Vogelweith, Fanny; Dourneau, Morgane; Thiéry, Denis; Moret, Yannick; Moreau, Jérôme

2013-12-01

Two of the central goals of immunoecology are to understand natural variation in the immune system among populations and to identify those selection pressures that shape immune traits. Maintenance of the immune system can be costly, and both food quality and parasitism selection pressure are factors potentially driving immunocompetence. In tritrophic interactions involving phytophagous insects, host plants, and natural enemies, the immunocompetence of phytophagous insects is constrained by selective forces from both the host plants and the natural enemies. Here, we assessed the roles of host plants and natural enemies as selective pressures on immune variation among natural populations of Lobesia botrana. Our results showed marked geographical variation in immune defenses and parasitism among different natural populations. Larval immune functions were dependent of the host plant quality and were positively correlated to parasitism, suggesting that parasitoids select for greater investment into immunity in moth. Furthermore, investment in immune defense was negatively correlated with body size, suggesting that it is metabolically expensive. The findings emphasize the roles of host plants and parasitoids as selective forces shaping host immune functions in natural conditions. We argue that kinds of study are central to understanding natural variations in immune functions, and the selective forces beyond.

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

PubMed Central

Li, Dapeng; Baldwin, Ian T.; Gaquerel, Emmanuel

2015-01-01

Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States—including the well-characterized Utah 30th generation inbred accession—and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis. PMID:26170304

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes

PubMed Central

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-01-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. PMID:29367403

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

PubMed

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-04-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

Natural diversity of potato (Solanum tuberosum) invertases

PubMed Central

2010-01-01

Background Invertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (Solanum tuberosum), invertases are involved in 'cold-induced sweetening' of tubers, an adaptive response to cold stress, which negatively affects the quality of potato chips and French fries. Linkage and association studies have identified quantitative trait loci (QTL) for tuber sugar content and chip quality that colocalize with three independent potato invertase loci, which together encode five invertase genes. The role of natural allelic variation of these genes in controlling the variation of tuber sugar content in different genotypes is unknown. Results For functional studies on natural variants of five potato invertase genes we cloned and sequenced 193 full-length cDNAs from six heterozygous individuals (three tetraploid and three diploid). Eleven, thirteen, ten, twelve and nine different cDNA alleles were obtained for the genes Pain-1, InvGE, InvGF, InvCD141 and InvCD111, respectively. Allelic cDNA sequences differed from each other by 4 to 9%, and most were genotype specific. Additional variation was identified by single nucleotide polymorphism (SNP) analysis in an association-mapping population of 219 tetraploid individuals. Haplotype modeling revealed two to three major haplotypes besides a larger number of minor frequency haplotypes. cDNA alleles associated with chip quality, tuber starch content and starch yield were identified. Conclusions Very high natural allelic variation was uncovered in a set of five potato invertase genes. This variability is a consequence of the cultivated potato's reproductive biology. Some of the structural variation found might underlie functional variation that influences important agronomic traits such as tuber sugar content. The associations found between specific invertase alleles and

The nature of solar brightness variations

NASA Astrophysics Data System (ADS)

Shapiro, A. I.; Solanki, S. K.; Krivova, N. A.; Cameron, R. H.; Yeo, K. L.; Schmutz, W. K.

2017-09-01

Determining the sources of solar brightness variations1,2, often referred to as solar noise3, is important because solar noise limits the detection of solar oscillations3, is one of the drivers of the Earth's climate system4,5 and is a prototype of stellar variability6,7—an important limiting factor for the detection of extrasolar planets. Here, we model the magnetic contribution to solar brightness variability using high-cadence8,9 observations from the Solar Dynamics Observatory (SDO) and the Spectral And Total Irradiance REconstruction (SATIRE)10,11 model. The brightness variations caused by the constantly evolving cellular granulation pattern on the solar surface were computed with the Max Planck Institute for Solar System Research (MPS)/University of Chicago Radiative Magnetohydrodynamics (MURaM)12 code. We found that the surface magnetic field and granulation can together precisely explain solar noise (that is, solar variability excluding oscillations) on timescales from minutes to decades, accounting for all timescales that have so far been resolved or covered by irradiance measurements. We demonstrate that no other sources of variability are required to explain the data. Recent measurements of Sun-like stars by the COnvection ROtation and planetary Transits (CoRoT)13 and Kepler14 missions uncovered brightness variations similar to that of the Sun, but with a much wider variety of patterns15. Our finding that solar brightness variations can be replicated in detail with just two well-known sources will greatly simplify future modelling of existing CoRoT and Kepler as well as anticipated Transiting Exoplanet Survey Satellite16 and PLAnetary Transits and Oscillations of stars (PLATO)17 data.

The genetic basis of natural variation for iron homeostasis in the maize IBM population

PubMed Central

2014-01-01

Background Iron (Fe) deficiency symptoms in maize (Zea mays subsp. mays) express as leaf chlorosis, growth retardation, as well as yield reduction and are typically observed when plants grow in calcareous soils at alkaline pH. To improve our understanding of genotypical variability in the tolerance to Fe deficiency-induced chlorosis, the objectives of this study were to (i) determine the natural genetic variation of traits related to Fe homeostasis in the maize intermated B73 × Mo17 (IBM) population, (ii) to identify quantitative trait loci (QTLs) for these traits, and (iii) to analyze expression levels of genes known to be involved in Fe homeostasis as well as of candidate genes obtained from the QTL analysis. Results In hydroponically-grown maize, a total of 47 and 39 QTLs were detected for the traits recorded under limited and adequate supply of Fe, respectively. Conclusions From the QTL results, we were able to identify new putative candidate genes involved in Fe homeostasis under a deficient or adequate Fe nutritional status, like Ferredoxin class gene, putative ferredoxin PETF, metal tolerance protein MTP4, and MTP8. Furthermore, our expression analysis of candidate genes suggested the importance of trans-acting regulation for 2’-deoxymugineic acid synthase 1 (DMAS1), nicotianamine synthase (NAS3, NAS1), formate dehydrogenase 1 (FDH1), methylthioribose-1-phosphate isomerase (IDI2), aspartate/tyrosine/aromatic aminotransferase (IDI4), and methylthioribose kinase (MTK). PMID:24400634

Genetic and Cytological Analyses of the Natural Variation of Seed Number per Pod in Rapeseed (Brassica napus L.)

PubMed Central

Yang, Yuhua; Wang, Ying; Zhan, Jiepeng; Shi, Jiaqin; Wang, Xinfa; Liu, Guihua; Wang, Hanzhong

2017-01-01

Seed number is one of the key traits related to plant evolution/domestication and crop improvement/breeding. In rapeseed germplasm, the seed number per pod (SNPP) shows a very wide variation from several to nearly 30; however, the underlying causations/mechanisms for this variation are poorly known. In the current study, the genetic and cytological bases for the natural variation of SNPP in rapeseed was firstly and systematically investigated using the representative four high-SNPP and five low-SNPP lines. The results of self- or cross-pollination experiment between the high- and low-SNPP lines showed that the natural variation of SNPP was mainly controlled by maternal effect (mean = 0.79), followed by paternal effect (mean = 0.21). Analysis of the data using diploid seed embryo–cytoplasmic–maternal model further showed that the maternal genotype, embryo, and cytoplasm effects, respectively, explained 47.6, 35.2, and 7.5% of the genetic variance. In addition, the analysis of combining ability showed that for the SNPP of hybrid F1 was mainly determined by the general combining ability of parents (63.0%), followed by special combining ability of parental combination (37.0%). More importantly, the cytological observation showed that the SNPP difference between the high- and low-SNPP lines was attributable to the accumulative differences in its components. Of which, the number of ovules, the proportion of fertile ovules, the proportion of fertile ovules to be fertilized, and the proportion of fertilized ovules to develop into seeds accounted for 30.7, 18.2, 7.1, and 43.9%, respectively. The accordant results of both genetic and cytological analyses provide solid evidences and systematic insights to further understand the mechanisms underlying the natural variation of SNPP, which will facilitate the development of high-yield cultivars in rapeseed. PMID:29163611

Exploring natural variation of photosynthetic, primary metabolism and growth parameters in a large panel of Capsicum chinense accessions.

PubMed

Rosado-Souza, Laise; Scossa, Federico; Chaves, Izabel S; Kleessen, Sabrina; Salvador, Luiz F D; Milagre, Jocimar C; Finger, Fernando; Bhering, Leonardo L; Sulpice, Ronan; Araújo, Wagner L; Nikoloski, Zoran; Fernie, Alisdair R; Nunes-Nesi, Adriano

2015-09-01

Collectively, the results presented improve upon the utility of an important genetic resource and attest to a complex genetic basis for differences in both leaf metabolism and fruit morphology between natural populations. Diversity of accessions within the same species provides an alternative method to identify physiological and metabolic traits that have large effects on growth regulation, biomass and fruit production. Here, we investigated physiological and metabolic traits as well as parameters related to plant growth and fruit production of 49 phenotypically diverse pepper accessions of Capsicum chinense grown ex situ under controlled conditions. Although single-trait analysis identified up to seven distinct groups of accessions, working with the whole data set by multivariate analyses allowed the separation of the 49 accessions in three clusters. Using all 23 measured parameters and data from the geographic origin for these accessions, positive correlations between the combined phenotypes and geographic origin were observed, supporting a robust pattern of isolation-by-distance. In addition, we found that fruit set was positively correlated with photosynthesis-related parameters, which, however, do not explain alone the differences in accession susceptibility to fruit abortion. Our results demonstrated that, although the accessions belong to the same species, they exhibit considerable natural intraspecific variation with respect to physiological and metabolic parameters, presenting diverse adaptation mechanisms and being a highly interesting source of information for plant breeders. This study also represents the first study combining photosynthetic, primary metabolism and growth parameters for Capsicum to date.

Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus.

PubMed

Riyahi, Sepand; Vilatersana, Roser; Schrey, Aaron W; Ghorbani Node, Hassan; Aliabadian, Mansour; Senar, Juan Carlos

2017-11-01

Epigenetic modifications can respond rapidly to environmental changes and can shape phenotypic variation in accordance with environmental stimuli. One of the most studied epigenetic marks is DNA methylation. In the present study, we used the methylation-sensitive amplified polymorphism (MSAP) technique to investigate the natural variation in DNA methylation within and among subspecies of the house sparrow, Passer domesticus We focused on five subspecies from the Middle East because they show great variation in many ecological traits and because this region is the probable origin for the house sparrow's commensal relationship with humans. We analysed house sparrows from Spain as an outgroup. The level of variation in DNA methylation was similar among the five house sparrow subspecies from the Middle East despite high phenotypic and environmental variation, but the non-commensal subspecies was differentiated from the other four (commensal) Middle Eastern subspecies. Further, the European subspecies was differentiated from all other subspecies in DNA methylation. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We detected a correlation between methylation level and some morphological traits, such as standardized bill length, and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected 10 differentially methylated loci among subspecies and three loci that differentiated between commensal or non-commensal status. Therefore, the MSAP technique detected larger scale differences among the European and non-commensal subspecies, but did not detect finer scale differences among the other Middle Eastern subspecies. © 2017. Published by The Company of Biologists Ltd.

Is It Feasible to Identify Natural Clusters of TSC-Associated Neuropsychiatric Disorders (TAND)?

PubMed

Leclezio, Loren; Gardner-Lubbe, Sugnet; de Vries, Petrus J

2018-04-01

Tuberous sclerosis complex (TSC) is a genetic disorder with multisystem involvement. The lifetime prevalence of TSC-Associated Neuropsychiatric Disorders (TAND) is in the region of 90% in an apparently unique, individual pattern. This "uniqueness" poses significant challenges for diagnosis, psycho-education, and intervention planning. To date, no studies have explored whether there may be natural clusters of TAND. The purpose of this feasibility study was (1) to investigate the practicability of identifying natural TAND clusters, and (2) to identify appropriate multivariate data analysis techniques for larger-scale studies. TAND Checklist data were collected from 56 individuals with a clinical diagnosis of TSC (n = 20 from South Africa; n = 36 from Australia). Using R, the open-source statistical platform, mean squared contingency coefficients were calculated to produce a correlation matrix, and various cluster analyses and exploratory factor analysis were examined. Ward's method rendered six TAND clusters with good face validity and significant convergence with a six-factor exploratory factor analysis solution. The "bottom-up" data-driven strategies identified a "scholastic" cluster of TAND manifestations, an "autism spectrum disorder-like" cluster, a "dysregulated behavior" cluster, a "neuropsychological" cluster, a "hyperactive/impulsive" cluster, and a "mixed/mood" cluster. These feasibility results suggest that a combination of cluster analysis and exploratory factor analysis methods may be able to identify clinically meaningful natural TAND clusters. Findings require replication and expansion in larger dataset, and could include quantification of cluster or factor scores at an individual level. Copyright © 2018 Elsevier Inc. All rights reserved.

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

PubMed Central

Kesari, Ravi; Lasky, Jesse R.; Villamor, Joji Grace; Des Marais, David L.; Chen, Ying-Jiun C.; Liu, Tzu-Wen; Juenger, Thomas E.; Verslues, Paul E.

2012-01-01

Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the Arabidopsis accession Shakdara (Sha) was threefold less than that of Landsberg erecta (Ler) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme Δ1-pyrroline-5-carboxylate synthetase1 (P5CS1) as a basis for the lower proline of Sha. Sha P5CS1 had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip P5CS1). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip P5CS1 splice variant constituted as much as half of the total P5CS1 transcript. In a larger panel of Arabidopsis accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip P5CS1 among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that P5CS1 may have evolved under positive selection, and more extensive correlation of exon 3-skip P5CS1 production than proline abundance with climate conditions of natural accessions also suggest a role of P5CS1 in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip P5CS1 in natural variation of proline metabolism, and suggest an association of P5CS1 and its alternative splicing with environmental adaptation. PMID:22615385

Cortical Tracking of Global and Local Variations of Speech Rhythm during Connected Natural Speech Perception.

PubMed

Alexandrou, Anna Maria; Saarinen, Timo; Kujala, Jan; Salmelin, Riitta

2018-06-19

During natural speech perception, listeners must track the global speaking rate, that is, the overall rate of incoming linguistic information, as well as transient, local speaking rate variations occurring within the global speaking rate. Here, we address the hypothesis that this tracking mechanism is achieved through coupling of cortical signals to the amplitude envelope of the perceived acoustic speech signals. Cortical signals were recorded with magnetoencephalography (MEG) while participants perceived spontaneously produced speech stimuli at three global speaking rates (slow, normal/habitual, and fast). Inherently to spontaneously produced speech, these stimuli also featured local variations in speaking rate. The coupling between cortical and acoustic speech signals was evaluated using audio-MEG coherence. Modulations in audio-MEG coherence spatially differentiated between tracking of global speaking rate, highlighting the temporal cortex bilaterally and the right parietal cortex, and sensitivity to local speaking rate variations, emphasizing the left parietal cortex. Cortical tuning to the temporal structure of natural connected speech thus seems to require the joint contribution of both auditory and parietal regions. These findings suggest that cortical tuning to speech rhythm operates on two functionally distinct levels: one encoding the global rhythmic structure of speech and the other associated with online, rapidly evolving temporal predictions. Thus, it may be proposed that speech perception is shaped by evolutionary tuning, a preference for certain speaking rates, and predictive tuning, associated with cortical tracking of the constantly changing rate of linguistic information in a speech stream.

Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones

PubMed Central

Mayer, Melanie G.; Sommer, Ralf J.

2011-01-01

Many free-living nematodes, including the laboratory model organisms Caenorhabditis elegans and Pristionchus pacificus, have a choice between direct and indirect development, representing an important case of phenotypic plasticity. Under harsh environmental conditions, these nematodes form dauer larvae, which arrest development, show high resistance to environmental stress and constitute a dispersal stage. Pristionchus pacificus occurs in a strong association with scarab beetles in the wild and remains in the dauer stage on the living beetle. Here, we explored the circumstances under which P. pacificus enters and exits the dauer stage by using a natural variation approach. The analysis of survival, recovery and fitness after dauer exit of eight P. pacificus strains revealed that dauer larvae can survive for up to 1 year under experimental conditions. In a second experiment, we isolated dauer pheromones from 16 P. pacificus strains, and tested for natural variation in pheromone production and sensitivity in cross-reactivity assays. Surprisingly, 13 of the 16 strains produce a pheromone that induces the highest dauer formation in individuals of other genotypes. These results argue against a simple adaptation model for natural variation in dauer formation and suggest that strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains. We therefore discuss intraspecific competition among genotypes as a previously unconsidered aspect of dauer formation. PMID:21307052

Exploiting genomics and natural genetic variation to decode macrophage enhancers

PubMed Central

Romanoski, Casey E.; Link, Verena M.; Heinz, Sven; Glass, Christopher K.

2015-01-01

The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease. PMID:26298065

TEMPLE: analysing population genetic variation at transcription factor binding sites.

PubMed

Litovchenko, Maria; Laurent, Stefan

2016-11-01

Genetic variation occurring at the level of regulatory sequences can affect phenotypes and fitness in natural populations. This variation can be analysed in a population genetic framework to study how genetic drift and selection affect the evolution of these functional elements. However, doing this requires a good understanding of the location and nature of regulatory regions and has long been a major hurdle. The current proliferation of genomewide profiling experiments of transcription factor occupancies greatly improves our ability to identify genomic regions involved in specific DNA-protein interactions. Although software exists for predicting transcription factor binding sites (TFBS), and the effects of genetic variants on TFBS specificity, there are no tools currently available for inferring this information jointly with the genetic variation at TFBS in natural populations. We developed the software Transcription Elements Mapping at the Population LEvel (TEMPLE), which predicts TFBS, evaluates the effects of genetic variants on TFBS specificity and summarizes the genetic variation occurring at TFBS in intraspecific sequence alignments. We demonstrate that TEMPLE's TFBS prediction algorithms gives identical results to PATSER, a software distribution commonly used in the field. We also illustrate the unique features of TEMPLE by analysing TFBS diversity for the TF Senseless (SENS) in one ancestral and one cosmopolitan population of the fruit fly Drosophila melanogaster. TEMPLE can be used to localize TFBS that are characterized by strong genetic differentiation across natural populations. This will be particularly useful for studies aiming to identify adaptive mutations. TEMPLE is a java-based cross-platform software that easily maps the genetic diversity at predicted TFBSs using a graphical interface, or from the Unix command line. © 2016 John Wiley & Sons Ltd.

Identifying localized and scale-specific multivariate controls of soil organic matter variations using multiple wavelet coherence.

PubMed

Zhao, Ruiying; Biswas, Asim; Zhou, Yin; Zhou, Yue; Shi, Zhou; Li, Hongyi

2018-06-23

Environmental factors have shown localized and scale-dependent controls over soil organic matter (SOM) distribution in the landscape. Previous studies have explored the relationships between SOM and individual controlling factors; however, few studies have indicated the combined control from multiple environmental factors. In this study, we compared the localized and scale-dependent univariate and multivariate controls of SOM along two long transects (northeast, NE transect and north, N transect) from China. Bivariate wavelet coherence (BWC) between SOM and individual factors and multiple wavelet coherence (MWC) between SOM and factor combinations were calculated. Average wavelet coherence (AWC) and percent area of significant coherence (PASC) were used to assess the relative dominance of individual and a combination of factors to explain SOM variations at different scales and locations. The results showed that (in BWC analysis) mean annual temperature (MAT) with the largest AWC (0.39) and PASC (16.23%) was the dominant factor in explaining SOM variations along the NE transect. The topographic wetness index (TWI) was the dominant factor (AWC = 0.39 and PASC = 20.80%) along the N transect. MWC identified the combination of Slope, net primary production (NPP) and mean annual precipitation (MAP) as the most important combination in explaining SOM variations along the NE transect with a significant increase in AWC and PASC at different scales and locations (e.g. AWC = 0.91 and PASC = 58.03% at all scales). The combination of TWI, NPP and normalized difference vegetation index (NDVI) was the most influential along the N transect (AWC = 0.83 and PASC = 32.68% at all scales). The results indicated that the combined controls of environmental factors on SOM variations at different scales and locations in a large area can be identified by MWC. This is promising for a better understanding of the multivariate controls in SOM variations at larger spatial

Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana.

PubMed

Alonso-Blanco, Carlos; Bentsink, Leónie; Hanhart, Corrie J; Blankestijn-de Vries, Hetty; Koornneef, Maarten

2003-06-01

Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a quantitative trait loci (QTL) mapping approach to identify loci affecting the after-ripening requirement measured as the number of days of seed dry storage required to reach 50% germination. Thus, seven QTL were identified and named delay of germination (DOG) 1-7. To confirm and characterize these loci, we developed 12 near-isogenic lines carrying single and double Cvi introgression fragments in a Ler genetic background. The analysis of these lines for germination in water confirmed four QTL (DOG1, DOG2, DOG3, and DOG6) as showing large additive effects in Ler background. In addition, it was found that DOG1 and DOG3 genetically interact, the strong dormancy determined by DOG1-Cvi alleles depending on DOG3-Ler alleles. These genotypes were further characterized for seed dormancy/germination behavior in five other test conditions, including seed coat removal, gibberellins, and an abscisic acid biosynthesis inhibitor. The role of the Ler/Cvi allelic variation in affecting dormancy is discussed in the context of current knowledge of Arabidopsis germination.

Morphological Variation in the Adult Hard Palate and Posterior Pharyngeal Wall

PubMed Central

Lammert, Adam; Proctor, Michael; Narayanan, Shrikanth

2013-01-01

Purpose Adult human vocal tracts display considerable morphological variation across individuals, but the nature and extent of this variation has not been extensively studied for many vocal tract structures. There exists a need to analyze morphological variation and, even more basically, to develop a methodology for morphological analysis of the vocal tract. Such analysis will facilitate fundamental characterization of the speech production system, with broad implications from modeling to explaining inter-speaker variability. Method A data-driven methodology to automatically analyze the extent and variety of morphological variation is proposed and applied to a diverse subject pool of 36 adults. Analysis is focused on two key aspects of vocal tract structure: the midsagittal shape of the hard palate and the posterior pharyngeal wall. Result Palatal morphology varies widely in its degree of concavity, but also in anteriority and sharpness. Pharyngeal wall morphology, by contrast, varies mostly in terms of concavity alone. The distribution of morphological characteristics is complex, and analysis suggests that certain variations may be categorical in nature. Conclusion Major modes of morphological variation are identified, including their relative magnitude, distribution and categorical nature. Implications of these findings for speech articulation strategies and speech acoustics are discussed. PMID:23690566

Warning signal brightness variation: sexual selection may work under the radar of natural selection in populations of a polytypic poison frog.

PubMed

Crothers, Laura R; Cummings, Molly E

2013-05-01

Though theory predicts consistency of warning signals in aposematic species to facilitate predator learning, variation in these signals often occurs in nature. The strawberry poison frog Dendrobates pumilio is an exceptionally polytypic (populations are phenotypically distinct) aposematic frog exhibiting variation in warning color and brightness. In the Solarte population, males and females both respond differentially to male brightness variation. Here, we demonstrate through spectrophotometry and visual modeling that aposematic brightness variation within this population is likely visible to two putative predators (crabs, snakes) and conspecifics but not to the presumed major predator (birds). This study thus suggests that signal brightness within D. pumilio populations can be shaped by sexual selection, with limited opportunity for natural selection to influence this trait due to predator sensory constraints. Because signal brightness changes can ultimately lead to changes in hue, our findings at the within-population level can provide insights into understanding this polytypism at across-population scales.

Introduction to natural disturbances and historic range of variation: type, frequency, severity, and post-disturbance structure in central hardwood forests

Treesearch

Katie Greenberg; Beverly S. Collins; Henry McNab; Douglas K. Miller; Gary R. Wein

2015-01-01

EXCERPT FROM: Natural Disturbances and Historic Range Variation 2015. Throughout the history of upland hardwood forests of the Central Hardwood Region, natural disturbances have been integral to shaping forest structure and composition, and essential in maintaining diverse biotic...

Chemical proteomics approaches for identifying the cellular targets of natural products

PubMed Central

Sieber, S. A.

2016-01-01

Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed. PMID:27098809

Chemical proteomics approaches for identifying the cellular targets of natural products.

PubMed

Wright, M H; Sieber, S A

2016-05-04

Covering: 2010 up to 2016Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied "in situ" - in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide-alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss 'competitive mode' approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.

Accounting for regional variation in both natural environment and human disturbance to improve performance of multimetric indices of lotic benthic diatoms.

PubMed

Tang, Tao; Stevenson, R Jan; Infante, Dana M

2016-10-15

Regional variation in both natural environment and human disturbance can influence performance of ecological assessments. In this study we calculated 5 types of benthic diatom multimetric indices (MMIs) with 3 different approaches to account for variation in ecological assessments. We used: site groups defined by ecoregions or diatom typologies; the same or different sets of metrics among site groups; and unmodeled or modeled MMIs, where models accounted for natural variation in metrics within site groups by calculating an expected reference condition for each metric and each site. We used data from the USEPA's National Rivers and Streams Assessment to calculate the MMIs and evaluate changes in MMI performance. MMI performance was evaluated with indices of precision, bias, responsiveness, sensitivity and relevancy which were respectively measured as MMI variation among reference sites, effects of natural variables on MMIs, difference between MMIs at reference and highly disturbed sites, percent of highly disturbed sites properly classified, and relation of MMIs to human disturbance and stressors. All 5 types of MMIs showed considerable discrimination ability. Using different metrics among ecoregions sometimes reduced precision, but it consistently increased responsiveness, sensitivity, and relevancy. Site specific metric modeling reduced bias and increased responsiveness. Combined use of different metrics among site groups and site specific modeling significantly improved MMI performance irrespective of site grouping approach. Compared to ecoregion site classification, grouping sites based on diatom typologies improved precision, but did not improve overall performance of MMIs if we accounted for natural variation in metrics with site specific models. We conclude that using different metrics among ecoregions and site specific metric modeling improve MMI performance, particularly when used together. Applications of these MMI approaches in ecological assessments

Degradation of blending vulcanized natural rubber and nitril rubber (NR/NBR) by dimethyl ether through variation of elastomer ratio

NASA Astrophysics Data System (ADS)

Saputra, A. H.; Juneva, S.; Sari, T. I.; Cifriadi, A.

2018-04-01

Dimethyl ether can cause degradation of the rubber material seal in some applications. In order to use of natural rubber in industry, research about a blending of natural rubber (NR) and nitrile rubber (NBR) to produce rubber to meet the standard seal material application were conducted. This study will observe the degradation mechanisms that occur in the blending natural rubber and nitrile rubber (NR/NBR) by dimethyl ether. Nitrile rubber types used in this study is medium quality nitrile rubber with 33% of acrylonitrile content (NBR33). The observed parameters are percent change in mass, mechanical properties and surface morphology. This study is limited to see the effect of variation vulcanized blending ratio (NR/NBR33) against to swelling. The increase of nitrile rubber (NBR33) ratio of blending rubber vulcanized can reduce the tensile strength and elongation. The best elastomer variation was obtained after comparing with the standard feasibility material of seal is rubber vulcanized blending (NR/NBR33) with ratio 40:60 NR: NBR.

The nature of an object-oriented program: How do practitioners understand the nature of what they are creating?

NASA Astrophysics Data System (ADS)

Thompson, Errol; Kinshuk

2011-09-01

Object-oriented programming is seen as a difficult skill to master. There is considerable debate about the most appropriate way to introduce novice programmers to object-oriented concepts. Is it possible to uncover what the critical aspects or features are that enhance the learning of object-oriented programming? Practitioners have differing understandings of the nature of an object-oriented program. Uncovering these different ways of understanding leads to agreater understanding of the critical aspects and their relationship tothe structure of the program produced. A phenomenographic studywas conducted to uncover practitioner understandings of the nature of an object-oriented program. The study identified five levels of understanding and three dimensions of variation within these levels. These levels and dimensions of variation provide a framework for fostering conceptual change with respect to the nature of an object-oriented program.

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.

Natural Variation Underlies Differences in ETHYLENE RESPONSE FACTOR17 Activity in Fruit Peel Degreening1[OPEN

PubMed Central

Han, Zhenyun; Hu, Yanan; Lv, Yuanda; Sun, Yaqiang; Shen, Fei; Wang, Yi; Zhang, Xinzhong; Xu, Xuefeng

2018-01-01

Through natural or human selection, many fleshy fruits have evolved vivid external or internal coloration, which often develops during ripening. Such developmental changes in color are associated with the biosynthesis of pigments as well as with degreening through chlorophyll degradation. Here, we demonstrated that natural variation in the coding region of the gene ETHYLENE RESPONSE FACTOR17 (ERF17) contributes to apple (Malus domestica) fruit peel degreening. Specifically, ERF17 mutant alleles with different serine (Ser) repeat insertions in the coding region exhibited enhanced transcriptional regulation activity in a dual-luciferase reporter assay when more Ser repeats were present. Notably, surface plasmon resonance analysis showed that the number of Ser repeats affected the binding activity of ERF17 to the promoter sequences of chlorophyll degradation-related genes. In addition, overexpression of ERF17 in evergreen apples altered the accumulation of chlorophyll. Furthermore, we demonstrated that ERF17 has been under selection since the origin of apple tree cultivation. Taken together, these results reveal allelic variation underlying an important fruit quality trait and a molecular genetic mechanism associated with apple domestication. PMID:29431631

Use of natural variation reveals core genes in the transcriptome of iron-deficient Arabidopsis thaliana roots

PubMed Central

Stein, Ricardo J.; Waters, Brian M.

2012-01-01

Iron (Fe) is an essential mineral micronutrient for plants and animals. Plants respond to Fe deficiency by increasing root uptake capacity. Identification of gene networks for Fe uptake and homeostasis could result in improved crop growth and nutritional value. Previous studies have used microarrays to identify a large number of genes regulated by Fe deficiency in roots of three Arabidopsis ecotypes. However, a large proportion of these genes may be involved in secondary or genotype-influenced responses rather than in a universal role in Fe uptake or homeostasis. Here we show that a small percentage of the Fe deficiency transcriptome of two contrasting ecotypes, Kas-1 and Tsu-1, was shared with other ecotypes. Kas-1 and Tsu-1 had different timing and magnitude of ferric reductase activity upon Fe withdrawal, and different categories of overrepresented Fe-regulated genes. To gain insights into universal responses of Arabidopsis to Fe deficiency, the Kas-1 and Tsu-1 transcriptomes were compared with those of Col-0, Ler, and C24. In early Fe deficiency (24–48 h), no Fe-downregulated genes and only 10 upregulated genes were found in all ecotypes, and only 20 Fe-downregulated and 58 upregulated genes were found in at least three of the five ecotypes. Supernode gene networks were constructed to visualize conserved Fe homeostasis responses. Contrasting gene expression highlighted different responses to Fe deficiency between ecotypes. This study demonstrates the use of natural variation to identify central Fe-deficiency-regulated genes in plants, and identified genes with potential new roles in signalling during Fe deficiency. PMID:22039296

Natural or Induced: Identifying Natural and Induced Swarms from Pre-production and Co-production Microseismic Catalogs at the Coso Geothermal Field

USGS Publications Warehouse

Schoenball, Martin; Kaven, Joern; Glen, Jonathan M. G.; Davatzes, Nicholas C.

2015-01-01

Increased levels of seismicity coinciding with injection of reservoir fluids have prompted interest in methods to distinguish induced from natural seismicity. Discrimination between induced and natural seismicity is especially difficult in areas that have high levels of natural seismicity, such as the geothermal fields at the Salton Sea and Coso, both in California. Both areas show swarm-like sequences that could be related to natural, deep fluid migration as part of the natural hydrothermal system. Therefore, swarms often have spatio-temporal patterns that resemble fluid-induced seismicity, and might possibly share other characteristics. The Coso Geothermal Field and its surroundings is one of the most seismically active areas in California with a large proportion of its activity occurring as seismic swarms. Here we analyze clustered seismicity in and surrounding the currently produced reservoir comparatively for pre-production and co-production periods. We perform a cluster analysis, based on the inter-event distance in a space-time-energy domain to identify notable earthquake sequences. For each event j, the closest previous event i is identified and their relationship categorized. If this nearest neighbor’s distance is below a threshold based on the local minimum of the bimodal distribution of nearest neighbor distances, then the event j is included in the cluster as a child to this parent event i. If it is above the threshold, event j begins a new cluster. This process identifies subsets of events whose nearest neighbor distances and relative timing qualify as a cluster as well as a characterizing the parent-child relationships among events in the cluster. We apply this method to three different catalogs: (1) a two-year microseismic survey of the Coso geothermal area that was acquired before exploration drilling in the area began; (2) the HYS_catalog_2013 that contains 52,000 double-difference relocated events and covers the years 1981 to 2013; and (3) a

Natural variation of piRNA expression affects immunity to transposable elements.

PubMed

Ryazansky, Sergei; Radion, Elizaveta; Mironova, Anastasia; Akulenko, Natalia; Abramov, Yuri; Morgunova, Valeriya; Kordyukova, Maria Y; Olovnikov, Ivan; Kalmykova, Alla

2017-04-01

In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements. The permissivity to I-element activity of R females, called reactivity, varies considerably in natural R populations, indicating the existence of a strong natural polymorphism in defense systems targeting transposons. To reveal the nature of such polymorphisms, we compared ovarian small RNAs between R strains with low and high reactivity and show that reactivity negatively correlates with the ancestral I-element-specific piRNA content. Analysis of piRNA clusters containing remnants of I-elements shows increased expression of the piRNA precursors and enrichment by the Heterochromatin Protein 1 homolog, Rhino, in weak R strains, which is in accordance with stronger piRNA expression by these regions. To explore the nature of the differences in piRNA production, we focused on two R strains, weak and strong, and showed that the efficiency of maternal inheritance of piRNAs as well as the I-element copy number are very similar in both strains. At the same time, germline and somatic uni-strand piRNA clusters generate more piRNAs in strains with low reactivity, suggesting the relationship between the efficiency of primary piRNA production and variable response to TE invasions. The strength of adaptive genome defense is likely driven by naturally occurring polymorphisms in the rapidly evolving piRNA pathway proteins. We hypothesize that hyper-efficient piRNA production is contributing to elimination of a telomeric retrotransposon He

Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones.

PubMed

Mayer, Melanie G; Sommer, Ralf J

2011-09-22

Many free-living nematodes, including the laboratory model organisms Caenorhabditis elegans and Pristionchus pacificus, have a choice between direct and indirect development, representing an important case of phenotypic plasticity. Under harsh environmental conditions, these nematodes form dauer larvae, which arrest development, show high resistance to environmental stress and constitute a dispersal stage. Pristionchus pacificus occurs in a strong association with scarab beetles in the wild and remains in the dauer stage on the living beetle. Here, we explored the circumstances under which P. pacificus enters and exits the dauer stage by using a natural variation approach. The analysis of survival, recovery and fitness after dauer exit of eight P. pacificus strains revealed that dauer larvae can survive for up to 1 year under experimental conditions. In a second experiment, we isolated dauer pheromones from 16 P. pacificus strains, and tested for natural variation in pheromone production and sensitivity in cross-reactivity assays. Surprisingly, 13 of the 16 strains produce a pheromone that induces the highest dauer formation in individuals of other genotypes. These results argue against a simple adaptation model for natural variation in dauer formation and suggest that strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains. We therefore discuss intraspecific competition among genotypes as a previously unconsidered aspect of dauer formation. This journal is © 2011 The Royal Society

Machine learning with naturally labeled data for identifying abbreviation definitions.

PubMed

Yeganova, Lana; Comeau, Donald C; Wilbur, W John

2011-06-09

The rapid growth of biomedical literature requires accurate text analysis and text processing tools. Detecting abbreviations and identifying their definitions is an important component of such tools. Most existing approaches for the abbreviation definition identification task employ rule-based methods. While achieving high precision, rule-based methods are limited to the rules defined and fail to capture many uncommon definition patterns. Supervised learning techniques, which offer more flexibility in detecting abbreviation definitions, have also been applied to the problem. However, they require manually labeled training data. In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data. Positive training examples are naturally occurring potential abbreviation-definition pairs in text. Negative training examples are generated by randomly mixing potential abbreviations with unrelated potential definitions. The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form. This approach does not require manually labeled training data. We evaluate the performance of our algorithm on the Ab3P, BIOADI and Medstract corpora. Our system demonstrated results that compare favourably to the existing Ab3P and BIOADI systems. We achieve an F-measure of 91.36% on Ab3P corpus, and an F-measure of 87.13% on BIOADI corpus which are superior to the results reported by Ab3P and BIOADI systems. Moreover, we outperform these systems in terms of recall, which is one of our goals.

Exploring natural variation of Pinus pinaster Aiton using metabolomics: Is it possible to identify the region of origin of a pine from its metabolites?

PubMed

Meijón, Mónica; Feito, Isabel; Oravec, Michal; Delatorre, Carolina; Weckwerth, Wolfram; Majada, Juan; Valledor, Luis

2016-02-01

Natural variation of the metabolome of Pinus pinaster was studied to improve understanding of its role in the adaptation process and phenotypic diversity. The metabolomes of needles and the apical and basal section of buds were analysed in ten provenances of P. pinaster, selected from France, Spain and Morocco, grown in a common garden for 5 years. The employment of complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) together with bioinformatics tools allowed the reliable quantification of 2403 molecular masses. The analysis of the metabolome showed that differences were maintained across provenances and that the metabolites characteristic of each organ are mainly related to amino acid metabolism, while provenances were distinguishable essentially through secondary metabolism when organs were analysed independently. Integrative analyses of metabolome, environmental and growth data provided a comprehensive picture of adaptation plasticity in conifers. These analyses defined two major groups of plants, distinguished by secondary metabolism: that is, either Atlantic or Mediterranean provenance. Needles were the most sensitive organ, where strong correlations were found between flavonoids and the water regime of the geographic origin of the provenance. The data obtained point to genome specialization aimed at maximizing the drought stress resistance of trees depending on their origin. © 2016 John Wiley & Sons Ltd.

Beliefs About Pharmaceutical Medicines and Natural Remedies Explain Individual Variation in Placebo Analgesia.

PubMed

Watkinson, Andrew; Chapman, Sarah C E; Horne, Rob

2017-08-01

This study examined whether placebo responses were predicted by a theoretical model of specific and general treatment beliefs. Using a randomized crossover, experimental design (168 healthy individuals) we assessed whether responses to a cold pressor task were influenced by 2 placebo creams described as pharmaceutical versus natural. We assessed whether placebo responses were predicted by pretreatment beliefs about the treatments (placebo) and by beliefs about the pain. The efficacy of pharmaceutical as well as natural placebos in reducing pain intensity was predicted by aspects of pain catastrophizing including feelings of helplessness (pharmaceutical: B = .03, P < .01, natural: B = .02, P < .05) and magnification of pain (pharmaceutical: B = .04, P < .05, natural: B = .05, P < .05) but also by pretreatment necessity beliefs (pharmaceutical: B = .21, P < .01, natural: B = .16, P < .05) and, for the pharmaceutical condition, by more general beliefs about personal sensitivity to pharmaceuticals (B = .14, P < .05). Treatment necessity beliefs also partially mediated the effects of helplessness on placebo responses. Treatment necessity beliefs for the pharmaceutical placebo were influenced by general pharmaceutical beliefs whereas necessity beliefs for the natural placebo were informed by general background beliefs about holistic treatments. Our findings show that treatment beliefs influence the placebo effect suggesting that they may offer an additional approach for understanding the placebo effect. Placebo effects contribute to responses to active analgesics. Understanding how beliefs about different types of treatment influence placebo analgesia may be useful in understanding variations in treatment response. Using the cold pressor paradigm we found that placebo analgesia was influenced by beliefs about natural remedies, pharmaceutical medicines, and about pain. Copyright © 2017. Published by Elsevier Inc.

Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana.

PubMed Central

Alonso-Blanco, Carlos; Bentsink, Leónie; Hanhart, Corrie J; Blankestijn-de Vries, Hetty; Koornneef, Maarten

2003-01-01

Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a quantitative trait loci (QTL) mapping approach to identify loci affecting the after-ripening requirement measured as the number of days of seed dry storage required to reach 50% germination. Thus, seven QTL were identified and named delay of germination (DOG) 1-7. To confirm and characterize these loci, we developed 12 near-isogenic lines carrying single and double Cvi introgression fragments in a Ler genetic background. The analysis of these lines for germination in water confirmed four QTL (DOG1, DOG2, DOG3, and DOG6) as showing large additive effects in Ler background. In addition, it was found that DOG1 and DOG3 genetically interact, the strong dormancy determined by DOG1-Cvi alleles depending on DOG3-Ler alleles. These genotypes were further characterized for seed dormancy/germination behavior in five other test conditions, including seed coat removal, gibberellins, and an abscisic acid biosynthesis inhibitor. The role of the Ler/Cvi allelic variation in affecting dormancy is discussed in the context of current knowledge of Arabidopsis germination. PMID:12807791

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

PubMed Central

Wang, Mi

2017-01-01

Abstract Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximizes data usage by borrowing information from the whole data set and combines several SNPs per transcript to detect ASE. Of 2,576 transcripts analyzed in collared flycatcher, ASE was detected in 185 (7.2%) and a similar frequency was seen in the pied flycatcher. Transcripts with statistically significant ASE commonly showed the major allele in >90% of the reads, reflecting that power was highest when expression was heavily biased toward one of the alleles. This would suggest that the observed frequencies of ASE likely are underestimates. The proportion of ASE transcripts varied among tissues, being lowest in testis and highest in muscle. Individuals often showed ASE of particular transcripts in more than one tissue (73.4%), consistent with a genetic basis for regulation of gene expression. The results suggest that genetic variation in regulatory sequences commonly affects gene expression in natural populations and that it provides a seedbed for phenotypic evolution via divergence in gene expression. PMID:28453623

Using DNA Barcodes to Identify Road-Killed Animals in Two Atlantic Forest Nature Reserves, Brazil

PubMed Central

Klippel, Angélica H.; Oliveira, Pablo V.; Britto, Karollini B.; Freire, Bárbara F.; Moreno, Marcel R.; dos Santos, Alexandre R.; Banhos, Aureo; Paneto, Greiciane G.

2015-01-01

Road mortality is the leading source of biodiversity loss in the world, especially due to fragmentation of natural habitats and loss of wildlife. The survey of the main species victims of roadkill is of fundamental importance for the better understanding of the problem, being necessary, for this, the correct species identification. The aim of this study was to verify if DNA barcodes can be applied to identify road-killed samples that often cannot be determined morphologically. For this purpose, 222 vertebrate samples were collected in a stretch of the BR-101 highway that crosses two Discovery Coast Atlantic Forest Natural Reserves, the Sooretama Biological Reserve and the Vale Natural Reserve, in Espírito Santo, Brazil. The mitochondrial COI gene was amplified, sequenced and confronted with the BOLD database. It was possible to identify 62.16% of samples, totaling 62 different species, including Pyrrhura cruentata, Chaetomys subspinosus, Puma yagouaroundi and Leopardus wiedii considered Vulnerable in the National Official List of Species of Endangered Wildlife. The most commonly identified animals were a bat (Molossus molossus), an opossum (Didelphis aurita) and a frog (Trachycephalus mesophaeus) species. Only one reptile was identified using the technique, probably due to lack of reference sequences in BOLD. These data may contribute to a better understanding of the impact of roads on species biodiversity loss and to introduce the DNA barcode technique to road ecology scenarios. PMID:26244644

Differences in glycosyltransferase family 61 accompany variation in seed coat mucilage composition in Plantago spp.

PubMed

Phan, Jana L; Tucker, Matthew R; Khor, Shi Fang; Shirley, Neil; Lahnstein, Jelle; Beahan, Cherie; Bacic, Antony; Burton, Rachel A

2016-12-01

Xylans are the most abundant non-cellulosic polysaccharide found in plant cell walls. A diverse range of xylan structures influence tissue function during growth and development. Despite the abundance of xylans in nature, details of the genes and biochemical pathways controlling their biosynthesis are lacking. In this study we have utilized natural variation within the Plantago genus to examine variation in heteroxylan composition and structure in seed coat mucilage. Compositional assays were combined with analysis of the glycosyltransferase family 61 (GT61) family during seed coat development, with the aim of identifying GT61 sequences participating in xylan backbone substitution. The results reveal natural variation in heteroxylan content and structure, particularly in P. ovata and P. cunninghamii, species which show a similar amount of heteroxylan but different backbone substitution profiles. Analysis of the GT61 family identified specific sequences co-expressed with IRREGULAR XYLEM 10 genes, which encode putative xylan synthases, revealing a close temporal association between xylan synthesis and substitution. Moreover, in P. ovata, several abundant GT61 sequences appear to lack orthologues in P. cunninghamii. Our results indicate that natural variation in Plantago species can be exploited to reveal novel details of seed coat development and polysaccharide biosynthetic pathways. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Genetic variation of natural antibodies in milk of Dutch Holstein-Friesian cows.

PubMed

Ploegaert, T C W; Wijga, S; Tijhaar, E; van der Poel, J J; Lam, T J G M; Savelkoul, H F J; Parmentier, H K; van Arendonk, J A M

2010-11-01

Defense mechanisms of dairy cows against diseases partly rest on their naturally present disease resistance capacity. Natural antibodies (NAb) form a soluble part of the innate immune system, being defined as antibodies circulating in animals without prior intentional antigenic stimulation. Genetic selection on NAb titers in milk, therefore, might improve disease resistance. We estimated genetic parameters of NAb titers binding lipopolysaccharide, lipoteichoic acid (LTA), peptidoglycan, and keyhole limpet hemocyanin, and titers of the NAb isotypes IgG1, IgM, and IgA binding LTA in milk of Dutch Holstein-Friesian heifers. Natural antibody titers were measured in 1 milk sample from each of 1,939 Holstein-Friesian heifers and used for estimating genetic parameters of NAb titers. The data show that phenotypic variation exists among heifers in NAb titers binding lipopolysaccharide, LTA, peptidoglycan, and keyhole limpet hemocyanin, and the NAb isotypes IgG1, IgM, and IgA binding LTA in milk. High genetic correlations among NAb (ranging from 0.45 to 0.99) indicated a common genetic basis for the levels of different NAb in bovine milk. Intra-herd heritability estimates for NAb ranged from 0.10 to 0.53. The results indicated that NAb levels have potential for genetic selection. Copyright © 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Most genetic risk for autism resides with common variation.

PubMed

Gaugler, Trent; Klei, Lambertus; Sanders, Stephan J; Bodea, Corneliu A; Goldberg, Arthur P; Lee, Ann B; Mahajan, Milind; Manaa, Dina; Pawitan, Yudi; Reichert, Jennifer; Ripke, Stephan; Sandin, Sven; Sklar, Pamela; Svantesson, Oscar; Reichenberg, Abraham; Hultman, Christina M; Devlin, Bernie; Roeder, Kathryn; Buxbaum, Joseph D

2014-08-01

A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. Individual risk-associated genes have been identified from rare variation, especially de novo mutations. From this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial impact en masse. At issue is how much of an impact relative to rare variation this common variation has. Using a unique epidemiological sample from Sweden, new methods that distinguish total narrow-sense heritability from that due to common variation and synthesis of results from other studies, we reach several conclusions about autism's genetic architecture: its narrow-sense heritability is ∼52.4%, with most due to common variation, and rare de novo mutations contribute substantially to individual liability, yet their contribution to variance in liability, 2.6%, is modest compared to that for heritable variation.

Spatiotemporal variation of radon and carbon dioxide concentrations in an underground quarry: coupled processes of natural ventilation, barometric pumping and internal mixing.

PubMed

Perrier, Frédéric; Richon, Patrick

2010-04-01

Radon-222 and carbon dioxide concentrations have been measured during several years at several points in the atmosphere of an underground limestone quarry located at a depth of 18 m in Vincennes, near Paris, France. Both concentrations showed a seasonal cycle. Radon concentration varied from 1200 to 2000 Bq m(-3) in summer to about 800-1400 Bq m(-3) in winter, indicating winter ventilation rates varying from 0.6 to 2.5 x 10(-6) s(-1). Carbon dioxide concentration varied from 0.9 to 1.0% in summer, to about 0.1-0.3% in winter. Radon concentration can be corrected for natural ventilation using temperature measurements. The obtained model also accounts for the measured seasonal variation of carbon dioxide. After correction, radon concentrations still exhibit significant temporal variation, mostly associated with the variation of atmospheric pressure, with coupling coefficients varying from -7 to -26 Bq m(-3) hPa(-1). This variation can be accounted for using a barometric pumping model, coupled with natural ventilation in winter, and including internal mixing as well. After correction, radon concentrations exhibit residual temporal variation, poorly correlated between different points, with standard deviations varying from 3 to 6%. This study shows that temporal variation of radon concentrations in underground cavities can be understood to a satisfactory level of detail using non-linear and time-dependent modelling. It is important to understand the temporal variation of radon concentrations and the limitations in their modelling to monitor the properties of natural or artificial underground settings, and to be able to assess the existence of new processes, for example associated with the preparatory phases of volcanic eruptions or earthquakes. Copyright 2009 Elsevier Ltd. All rights reserved.

Sensitivity of simulated deep ocean natural radiocarbon to gas exchange velocity and historical atmospheric Δ14C variations

NASA Astrophysics Data System (ADS)

Wagner, Hannes; Koeve, Wolfgang; Kriest, Iris; Oschlies, Andreas

2015-04-01

Simulated deep ocean natural radiocarbon is frequently used to assess model performance of deep ocean ventilation in Ocean General Circulation Models (OGCMs). It has been shown to be sensitive to a variety of model parameters, such as the mixing parameterization, convection scheme and vertical resolution. Here we use three different ocean models (MIT2.8, ECCO, UVic) to evaluate the sensitivity of simulated deep ocean natural radiocarbon to two other factors, while keeping the model physics constant: (1) the gas exchange velocity and (2) historic variations in atmospheric Δ^1^4C boundary conditions. We find that simulated natural Δ^1^4C decreases by 14-20 ‰ throughout the deep ocean and consistently in all three models, if the gas exchange velocity is lowered by 30 % with respect to the OCMIP-2 protocol, to become more consistent with newer estimates of the oceans uptake of bomb derived ^1^4C. Simulated deep ocean natural Δ^1^4C furthermore decreases by 3-9 ‰ throughout the deep Pacific, Indian and Southern Oceans and consistently in all three models, if the models are forced with the observed atmospheric Δ^1^4C history, instead of an often made pragmatic assumption of a constant atmospheric Δ^1^4C value of zero. Applying both improvements (gas exchange reduction, as well as atmospheric Δ^1^4C history implementation) concomitantly and accounting for the present uncertainty in gas exchange velocity estimates (between 10 and 40 % reduction with respect to the OCMIP-2 protocol) simulated deep ocean Δ^1^4C decreases by 10-30 ‰ throughout the deep Pacific, Indian and Southern Ocean. This translates to a ^1^4C-age increase of 100-300 years and indicates, that models, which in former assessments (based on the OCMIP-2 protocol) had been identified to have an accurate deep ocean ventilation, should now be regarded as rather having a bit too sluggish a ventilation. Models, which on the other hand had been identified to have a bit too fast a deep ocean ventilation

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.

PubMed

Sharma, Vivekanand; Law, Wayne; Balick, Michael J; Sarkar, Indra Neil

2017-01-01

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement.

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts

PubMed Central

Sharma, Vivekanand; Law, Wayne; Balick, Michael J.; Sarkar, Indra Neil

2017-01-01

The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use information from natural language text is a challenging task for ethnobotanists. To date, there have been only limited adoption of informatics approaches used for supporting the identification of ethnobotanical information associated with medicinal uses. This study explored the feasibility of using biomedical terminologies and natural language processing approaches for extracting relevant plant-associated therapeutic use information from historical biodiversity literature collection available from the Biodiversity Heritage Library. The results from this preliminary study suggest that there is potential utility of informatics methods to identify medicinal plant knowledge from digitized resources as well as highlight opportunities for improvement. PMID:29854223

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers

PubMed Central

2011-01-01

Background Most information on genomic variations and their associations with phenotypes are covered exclusively in scientific publications rather than in structured databases. These texts commonly describe variations using natural language; database identifiers are seldom mentioned. This complicates the retrieval of variations, associated articles, as well as information extraction, e. g. the search for biological implications. To overcome these challenges, procedures to map textual mentions of variations to database identifiers need to be developed. Results This article describes a workflow for normalization of variation mentions, i.e. the association of them to unique database identifiers. Common pitfalls in the interpretation of single nucleotide polymorphism (SNP) mentions are highlighted and discussed. The developed normalization procedure achieves a precision of 98.1 % and a recall of 67.5% for unambiguous association of variation mentions with dbSNP identifiers on a text corpus based on 296 MEDLINE abstracts containing 527 mentions of SNPs. The annotated corpus is freely available at http://www.scai.fraunhofer.de/snp-normalization-corpus.html. Conclusions Comparable approaches usually focus on variations mentioned on the protein sequence and neglect problems for other SNP mentions. The results presented here indicate that normalizing SNPs described on DNA level is more difficult than the normalization of SNPs described on protein level. The challenges associated with normalization are exemplified with ambiguities and errors, which occur in this corpus. PMID:21992066

Natural experimentation is a challenging method for identifying headache triggers.

PubMed

Houle, Timothy T; Turner, Dana P

2013-04-01

In this study, we set out to determine whether individual headache sufferers can learn about the potency of their headache triggers (causes) using only natural experimentation. Headache patients naturally use the covariation of the presence-absence of triggers with headache attacks to assess the potency of triggers. The validity of this natural experimentation has never been investigated. A companion study has proposed 3 assumptions that are important for assigning causal status to triggers. This manuscript examines one of these assumptions, constancy in trigger presentation, using real-world conditions. The similarity of day-to-day weather conditions over 4 years, as well as the similarity of ovarian hormones and perceived stress over a median of 89 days in 9 regularly cycling headache sufferers, was examined using several available time series. An arbitrary threshold of 90% similarity using Gower's index identified similar days for comparison. The day-to-day variability in just these 3 headache triggers is substantial enough that finding 2 naturally similar days for which to contrast the effect of a fourth trigger (eg, drinking wine vs not drinking wine) will only infrequently occur. Fluctuations in weather patterns resulted in a median of 2.3 days each year that were similar (range 0-27.4). Considering fluctuations in stress patterns and ovarian hormones, only 1.5 days/month (95% confidence interval 1.2-2.9) and 2.0 days/month (95% confidence interval 1.9-2.2), respectively, met our threshold for similarity. Although assessing the personal causes of headache is an age-old endeavor, the great many candidate triggers exhibit variability that may prevent sound conclusions without assistance from formal experimentation or statistical balancing. © 2013 American Headache Society.

Natural experimentation is a challenging method for identifying headache triggers

PubMed Central

Houle, Timothy T.; Turner, Dana P.

2015-01-01

Objective In this study we set out to determine whether individual headache sufferers can learn about the potency of their headache triggers (causes) using only natural experimentation. Background Headache patients naturally use the covariation of the presence-absence of triggers with headache attacks to assess the potency of triggers. The validity of this natural experimentation has never been investigated. A companion study has proposed three assumptions that are important for assigning causal status to triggers. This manuscript examines one of these assumptions, constancy in trigger presentation, using real-world conditions. Methods The similarity of day-to-day weather conditions over four years, as well as the similarity of ovarian hormones and perceived stress over a median of 89 days in nine regularly cycling headache sufferers were examined using several available time-series. An arbitrary threshold of 90% similarity using Gower's index identified similar days for comparison. Results The day-to-day variability in just these three headache triggers is substantial enough that finding two naturally similar days for which to contrast the effect of a fourth trigger (e.g., drinking wine versus not drinking wine) will only infrequently occur. Fluctuations in weather patterns resulted in a median of 2.3 days each year that were similar (range: 0 to 27.4). Considering fluctuations in stress patterns and ovarian hormones, only 1.5 days/month (95%CI: 1.2 to 2.9) and 2.0 days/month (95%CI: 1.9 to 2.2), respectively, met our threshold for similarity.. Conclusion Although assessing the personal causes of headache is an age-old endeavor, the great many candidate triggers exhibit variability that may prevent sound conclusions without assistance from formal experimentation or statistical balancing. PMID:23534852

Reaction Norms in Natural Conditions: How Does Metabolic Performance Respond to Weather Variations in a Small Endotherm Facing Cold Environments?

PubMed Central

Petit, Magali; Vézina, François

2014-01-01

Reaction norms reflect an organisms' capacity to adjust its phenotype to the environment and allows for identifying trait values associated with physiological limits. However, reaction norms of physiological parameters are mostly unknown for endotherms living in natural conditions. Black-capped chickadees (Poecile atricapillus) increase their metabolic performance during winter acclimatization and are thus good model to measure reaction norms in the wild. We repeatedly measured basal (BMR) and summit (Msum) metabolism in chickadees to characterize, for the first time in a free-living endotherm, reaction norms of these parameters across the natural range of weather variation. BMR varied between individuals and was weakly and negatively related to minimal temperature. Msum varied with minimal temperature following a Z-shape curve, increasing linearly between 24°C and −10°C, and changed with absolute humidity following a U-shape relationship. These results suggest that thermal exchanges with the environment have minimal effects on maintenance costs, which may be individual-dependent, while thermogenic capacity is responding to body heat loss. Our results suggest also that BMR and Msum respond to different and likely independent constraints. PMID:25426860

[Spatiotemporal variations of natural wetland CH4 emissions over China under future climate change].

PubMed

Liu, Jian-gong; Zhu, Qiu-an; Shen, Yan; Yang, Yan-zheng; Luo, Yun-peng; Peng, Chang-hui

2015-11-01

Based on a new process-based model, TRIPLEX-GHG, this paper analyzed the spatio-temporal variations of natural wetland CH4 emissions over China under different future climate change scenarios. When natural wetland distributions were fixed, the amount of CH4 emissions from natural wetland ecosystem over China would increase by 32.0%, 55.3% and 90.8% by the end of 21st century under three representative concentration pathways (RCPs) scenarios, RCP2. 6, RCP4.5 and RCP8.5, respectively, compared with the current level. Southern China would have higher CH4 emissions compared to that from central and northern China. Besides, there would be relatively low emission fluxes in western China while relatively high emission fluxes in eastern China. Spatially, the areas with relatively high CH4 emission fluxes would be concentrated in the middle-lower reaches of the Yangtze River, the Northeast and the coasts of the Pearl River. In the future, most natural wetlands would emit more CH4 for RCP4.5 and RCP8.5 than that of 2005. However, under RCP2.6 scenario, the increasing trend would be curbed and CH4 emissions (especially from the Qinghai-Tibet Plateau) begin to decrease in the late 21st century.

Effects of source and seasonal variations of natural organic matters on the fate and transport of CeO2 nanoparticles in the environment

EPA Science Inventory

Natural organic matter (NOM) affects the stability and transport of nanoparticles (NPs) in natural waters by modifying their physiochemical properties. Source location, and seasonal variations, influence their molecular, physical and electrical charge properties. To understand th...

Most genetic risk for autism resides with common variation

PubMed Central

Gaugler, Trent; Klei, Lambertus; Sanders, Stephan J.; Bodea, Corneliu A.; Goldberg, Arthur P.; Lee, Ann B.; Mahajan, Milind; Manaa, Dina; Pawitan, Yudi; Reichert, Jennifer; Ripke, Stephan; Sandin, Sven; Sklar, Pamela; Svantesson, Oscar; Reichenberg, Abraham; Hultman, Christina M.; Devlin, Bernie

2014-01-01

A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (henceforth autism) the nature of its allelic spectrum is uncertain. Individual risk genes have been identified from rare variation, especially de novo mutations1–8. From this evidence one might conclude that rare variation dominates its allelic spectrum, yet recent studies show that common variation, individually of small effect, has substantial impact en masse9,10. At issue is how much of an impact relative to rare variation. Using a unique epidemiological sample from Sweden, novel methods that distinguish total narrow-sense heritability from that due to common variation, and by synthesizing results from other studies, we reach several conclusions about autism’s genetic architecture: its narrow-sense heritability is ≈54% and most traces to common variation; rare de novo mutations contribute substantially to individuals’ liability; still their contribution to variance in liability, 2.6%, is modest compared to heritable variation. PMID:25038753

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize.

PubMed

Chen, Jiafa; Zhang, Luyan; Liu, Songtao; Li, Zhimin; Huang, Rongrong; Li, Yongming; Cheng, Hongliang; Li, Xiantang; Zhou, Bo; Wu, Suowei; Chen, Wei; Wu, Jianyu; Ding, Junqiang

2016-01-01

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed.

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize

PubMed Central

Liu, Songtao; Li, Zhimin; Huang, Rongrong; Li, Yongming; Cheng, Hongliang; Li, Xiantang; Zhou, Bo; Wu, Suowei; Chen, Wei; Wu, Jianyu; Ding, Junqiang

2016-01-01

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed. PMID:27070143

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

PubMed Central

Wen, Xi; Yang, Sizhong; Horn, Fabian; Winkel, Matthias; Wagner, Dirk; Liebner, Susanne

2017-01-01

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis. PMID:28769904

Algorithm for Identifying Erroneous Rain-Gauge Readings

NASA Technical Reports Server (NTRS)

Rickman, Doug

2005-01-01

An algorithm analyzes rain-gauge data to identify statistical outliers that could be deemed to be erroneous readings. Heretofore, analyses of this type have been performed in burdensome manual procedures that have involved subjective judgements. Sometimes, the analyses have included computational assistance for detecting values falling outside of arbitrary limits. The analyses have been performed without statistically valid knowledge of the spatial and temporal variations of precipitation within rain events. In contrast, the present algorithm makes it possible to automate such an analysis, makes the analysis objective, takes account of the spatial distribution of rain gauges in conjunction with the statistical nature of spatial variations in rainfall readings, and minimizes the use of arbitrary criteria. The algorithm implements an iterative process that involves nonparametric statistics.

Natural Changes in Brain Temperature Underlie Variations in Song Tempo during a Mating Behavior

PubMed Central

Aronov, Dmitriy; Fee, Michale S.

2012-01-01

The song of a male zebra finch is a stereotyped motor sequence whose tempo varies with social context – whether or not the song is directed at a female bird – as well as with the time of day. The neural mechanisms underlying these changes in tempo are unknown. Here we show that brain temperature recorded in freely behaving male finches exhibits a global increase in response to the presentation of a female bird. This increase strongly correlates with, and largely explains, the faster tempo of songs directed at a female compared to songs produced in social isolation. Furthermore, we find that the observed diurnal variations in song tempo are also explained by natural variations in brain temperature. Our findings suggest that brain temperature is an important variable that can influence the dynamics of activity in neural circuits, as well as the temporal features of behaviors that some of these circuits generate. PMID:23112858

Natural variation in learning rate and memory dynamics in parasitoid wasps: opportunities for converging ecology and neuroscience

PubMed Central

Hoedjes, Katja M.; Kruidhof, H. Marjolein; Huigens, Martinus E.; Dicke, Marcel; Vet, Louise E. M.; Smid, Hans M.

2011-01-01

Although the neural and genetic pathways underlying learning and memory formation seem strikingly similar among species of distant animal phyla, several more subtle inter- and intraspecific differences become evident from studies on model organisms. The true significance of such variation can only be understood when integrating this with information on the ecological relevance. Here, we argue that parasitoid wasps provide an excellent opportunity for multi-disciplinary studies that integrate ultimate and proximate approaches. These insects display interspecific variation in learning rate and memory dynamics that reflects natural variation in a daunting foraging task that largely determines their fitness: finding the inconspicuous hosts to which they will assign their offspring to develop. We review bioassays used for oviposition learning, the ecological factors that are considered to underlie the observed differences in learning rate and memory dynamics, and the opportunities for convergence of ecology and neuroscience that are offered by using parasitoid wasps as model species. We advocate that variation in learning and memory traits has evolved to suit an insect's lifestyle within its ecological niche. PMID:21106587

Role of geospatial technology in identifying natural habitat of malarial vectors in South Andaman, India.

PubMed

Shankar, Shiva; Agrawal, Deepak Kumar

2016-03-01

Malaria is a serious disease which has repeatedly threatened Andaman, an island territory of India. Uncharted dense vegetation and inaccessibility are the salient features of the area and the major areas are covered by remotely sensed data to identify the malaria vector's natural habitat. The present investigation appraises the role of geospatial technologies in identifying the natural habitat of malarial vectors. The base map was prepared from Survey of India's toposheets, the landuse map was prepared from indices techniques like normalised difference vegetation index (NDVI), normalised difference water index (NDWI), modified normalised difference water index (MNDWI), normalised difference pond index (NDPI), and normalized difference turbidity index (NDTI) in conjugation with visual interpretation. The soil moisture content map was reproduced from the soil atlas of Andaman and Nicobar Islands followed by generation of an aspect profile from ASTER-GDEM satellite data. Both the landuse map and aspect profile were validated for accuracy in the field. A weighted overlay analysis of the classes like landuse, soil moisture and aspect profile of the study area resulted in identification of the potential natural habitat map of malaria vector surrounding the areas of Tushnabad, Garacharma, Manglutan, Chouldari, Ferrargunj and Wimberlygunj hamlets. The natural habitat of malaria vector indicated that Tushnabad, Garacharma, Manglutan, Chouldari, Ferrargunj and Wimberlygunj hamlets are within the proximity of 2.5 km from the prime habitat location with more number of malaria positive cases. Also these hamlets are surrounded by dense evergreen forest and the land surface is draped by clay loam and clay soil texture exhibiting high soil moisture content warranting high rates of survival and proliferation of the vector ensuring resurgence of malaria every year. It is thus concluded that application of geospatial technologies plays an important role in identifying the natural

High throughput screening to identify natural human monoamine oxidase B inhibitors.

PubMed

Mazzio, E; Deiab, S; Park, K; Soliman, K F A

2013-06-01

Age-related increase in monoamine oxidase B (MAO-B) may contribute to CNS neurodegenerative diseases. Moreover, MAO-B inhibitors are used in the treatment of idiopathic Parkinson disease as preliminary monotherapy or adjunct therapy with L-dopa. To date, meager natural sources of MAO-B inhibitors have been identified, and the relative strength, potency and rank of many plants relative to standard drugs such as Selegiline (L-deprenyl,Eldepryl) are not known. In this work, we developed and utilized a high throughput enzyme microarray format to screen and evaluate 905 natural product extracts (0.025-.7 mg/ml) to inhibit human MAO-B derived from BTI-TN-5B1-4 cells infected with recombinant baculovirus. The protein sequence of purified enzyme was confirmed using 1D gel electrophoresis-matrix assisted laser desorption ionization -time-of-flight-tandem mass spectroscopy, and enzyme activity was confirmed by [1] substrate conversion (3-mM benzylamine) to H202 and [2] benzaldehyde. Of the 905 natural extracts tested, the lowest IC50s [<0.07 mg/ml] were obtained with extracts of Amur Corktree (Phellodendron amurense), Bakuchi Seed(Cyamopsis psoralioides), Licorice Root (Glycyrrhiza glabra/uralensis), Babchi (Psoralea corylifolia seed). The data also show, albeit to a lesser extent, inhibitory properties of herbs originating from the mint family (Lamiaceae) and Turmeric, Comfrey, Bringraj, Skullcap, Kava-kava, Wild Indigo, Gentian and Green Tea. In conclusion, the data reflect relative potency information by rank of commonly used herbs and plants that contain human MAO-B inhibitory properties in their natural form. Copyright © 2012 John Wiley & Sons, Ltd.

Natural variation in expression of genes associated with carotenoid biosynthesis and accumulation in cassava (Manihot esculenta Crantz) storage root

USDA-ARS?s Scientific Manuscript database

Several groups have reported on massive accumulation of total carotenoids in cassava storage root (CSR). Naturally occurring color variation associated with carotenoid accumulation was observed in cassava (Manihot esculenta Crantz) storage root of landraces from Amazon. Here carotenoid profiles from...

Analysis of Natural and Induced Variation in Tomato Glandular Trichome Flavonoids Identifies a Gene Not Present in the Reference Genome[W][OPEN

PubMed Central

Kim, Jeongwoon; Matsuba, Yuki; Ning, Jing; Schilmiller, Anthony L.; Hammar, Dagan; Jones, A. Daniel; Pichersky, Eran; Last, Robert L.

2014-01-01

Flavonoids are ubiquitous plant aromatic specialized metabolites found in a variety of cell types and organs. Methylated flavonoids are detected in secreting glandular trichomes of various Solanum species, including the cultivated tomato (Solanum lycopersicum). Inspection of the sequenced S. lycopersicum Heinz 1706 reference genome revealed a close homolog of Solanum habrochaites MOMT1 3′/5′ myricetin O-methyltransferase gene, but this gene (Solyc06g083450) is missing the first exon, raising the question of whether cultivated tomato has a distinct 3′ or 3′/5′ O-methyltransferase. A combination of mining genome and cDNA sequences from wild tomato species and S. lycopersicum cultivar M82 led to the identification of Sl-MOMT4 as a 3′ O-methyltransferase. In parallel, three independent ethyl methanesulfonate mutants in the S. lycopersicum cultivar M82 background were identified as having reduced amounts of di- and trimethylated myricetins and increased monomethylated myricetin. Consistent with the hypothesis that Sl-MOMT4 is a 3′ O-methyltransferase gene, all three myricetin methylation defective mutants were found to have defects in MOMT4 sequence, transcript accumulation, or 3′-O-methyltransferase enzyme activity. Surprisingly, no MOMT4 sequence is found in the Heinz 1706 reference genome sequence, and this cultivar accumulates 3-methyl myricetin and is deficient in 3′-methyl myricetins, demonstrating variation in this gene among cultivated tomato varieties. PMID:25128240

Natural variability in Drosophila larval and pupal NaCl tolerance.

PubMed

Riedl, Craig A L; Oster, Sara; Busto, Macarena; Mackay, Trudy F C; Sokolowski, Marla B

2016-05-01

The regulation of NaCl is essential for the maintenance of cellular tonicity and functionality, and excessive salt exposure has many adverse effects. The fruit fly, Drosophila melanogaster, is a good osmoregulator and some strains can survive on media with very low or high NaCl content. Previous analyses of mutant alleles have implicated various stress signaling cascades in NaCl sensitivity or tolerance; however, the genes influencing natural variability of NaCl tolerance remain for the most part unknown. Here, we use two approaches to investigate natural variation in D. melanogaster NaCl tolerance. We describe four D. melanogaster lines that were selected for different degrees of NaCl tolerance, and present data on their survival, development, and pupation position when raised on varying NaCl concentrations. After finding evidence for natural variation in salt tolerance, we present the results of Quantitative Trait Loci (QTL) mapping of natural variation in larval and pupal NaCl tolerance, and identify different genomic regions associated with NaCl tolerance during larval and pupal development. Copyright © 2016 Elsevier Ltd. All rights reserved.

Benchmarking to Identify Practice Variation in Test Ordering: A Potential Tool for Utilization Management.

PubMed

Signorelli, Heather; Straseski, Joely A; Genzen, Jonathan R; Walker, Brandon S; Jackson, Brian R; Schmidt, Robert L

2015-01-01

Appropriate test utilization is usually evaluated by adherence to published guidelines. In many cases, medical guidelines are not available. Benchmarking has been proposed as a method to identify practice variations that may represent inappropriate testing. This study investigated the use of benchmarking to identify sites with inappropriate utilization of testing for a particular analyte. We used a Web-based survey to compare 2 measures of vitamin D utilization: overall testing intensity (ratio of total vitamin D orders to blood-count orders) and relative testing intensity (ratio of 1,25(OH)2D to 25(OH)D test orders). A total of 81 facilities contributed data. The average overall testing intensity index was 0.165, or approximately 1 vitamin D test for every 6 blood-count tests. The average relative testing intensity index was 0.055, or one 1,25(OH)2D test for every 18 of the 25(OH)D tests. Both indexes varied considerably. Benchmarking can be used as a screening tool to identify outliers that may be associated with inappropriate test utilization. Copyright© by the American Society for Clinical Pathology (ASCP).

Features and Natural Classes in ASL Handshapes

ERIC Educational Resources Information Center

Whitworth, Cecily

2011-01-01

This article argues for the necessity of phonetic analysis in signed language linguistics and presents a case study of one analytical system being used in a preliminary attempt to identify natural classes and investigate variation in ASL handshapes. Robbin Battison (1978) first described what is now a widely accepted list of basic handshapes,…

Ploidy-Regulated Variation in Biofilm-Related Phenotypes in Natural Isolates of Saccharomyces cerevisiae

PubMed Central

Hope, Elyse A.; Dunham, Maitreya J.

2014-01-01

The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and “flocs” (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. PMID:25060625

Ploidy-regulated variation in biofilm-related phenotypes in natural isolates of Saccharomyces cerevisiae.

PubMed

Hope, Elyse A; Dunham, Maitreya J

2014-07-24

The ability of yeast to form biofilms contributes to better survival under stressful conditions. We see the impact of yeast biofilms and "flocs" (clumps) in human health and industry, where forming clumps enables yeast to act as a natural filter in brewing and forming biofilms enables yeast to remain virulent in cases of fungal infection. Despite the importance of biofilms in yeast natural isolates, the majority of our knowledge about yeast biofilm genetics comes from work with a few tractable laboratory strains. A new collection of sequenced natural isolates from the Saccharomyces Genome Resequencing Project enabled us to examine the breadth of biofilm-related phenotypes in geographically, ecologically, and genetically diverse strains of Saccharomyces cerevisiae. We present a panel of 31 haploid and 24 diploid strains for which we have characterized six biofilm-related phenotypes: complex colony morphology, complex mat formation, flocculation, agar invasion, polystyrene adhesion, and psuedohyphal growth. Our results show that there is extensive phenotypic variation between and within strains, and that these six phenotypes are primarily uncorrelated or weakly correlated, with the notable exception of complex colony and complex mat formation. We also show that the phenotypic strength of these strains varies significantly depending on ploidy, and the diploid strains demonstrate both decreased and increased phenotypic strength with respect to their haploid counterparts. This is a more complex view of the impact of ploidy on biofilm-related phenotypes than previous work with laboratory strains has suggested, demonstrating the importance and enormous potential of working with natural isolates of yeast. Copyright © 2014 Hope and Dunham.

Natural variation of root hydraulics in Arabidopsis grown in normal and salt-stressed conditions.

PubMed

Sutka, Moira; Li, Guowei; Boudet, Julie; Boursiac, Yann; Doumas, Patrick; Maurel, Christophe

2011-03-01

To gain insights into the natural variation of root hydraulics and its molecular components, genotypic differences related to root water transport and plasma membrane intrinsic protein (PIP) aquaporin expression were investigated in 13 natural accessions of Arabidopsis (Arabidopsis thaliana). The hydraulic conductivity of excised root systems (Lpr) showed a 2-fold variation among accessions. The contribution of aquaporins to water uptake was characterized using as inhibitors mercury, propionic acid, and azide. The aquaporin-dependent and -independent paths of water transport made variable contributions to the total hydraulic conductivity in the different accessions. The distinct suberization patterns observed among accessions were not correlated with their root hydraulic properties. Real-time reverse transcription-polymerase chain reaction revealed, by contrast, a positive overall correlation between Lpr and certain highly expressed PIP transcripts. Root hydraulic responses to salt stress were characterized in a subset of five accessions (Bulhary-1, Catania-1, Columbia-0, Dijon-M, and Monte-Tosso-0 [Mr-0]). Lpr was down-regulated in all accessions except Mr-0. In Mr-0 and Catania-1, cortical cell hydraulic conductivity was unresponsive to salt, whereas it was down-regulated in the three other accessions. By contrast, the five accessions showed qualitatively similar aquaporin transcriptional profiles in response to salt. The overall work provides clues on how hydraulic regulation allows plant adaptation to salt stress. It also shows that a wide range of root hydraulic profiles, as previously reported in various species, can be observed in a single model species. This work paves the way for a quantitative genetics analysis of root hydraulics.

Natural variation for a hybrid incompatibility between two species of Mimulus.

PubMed

Sweigart, Andrea L; Mason, Amanda R; Willis, John H

2007-01-01

Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky-Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1-hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1-hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection.

Metagenomic approaches to identify and isolate bioactive natural products from microbiota of marine sponges.

PubMed

Gurgui, Cristian; Piel, Jörn

2010-01-01

Many marine sponges harbor massive consortia of symbiotic bacteria belonging to diverse phyla. Sponges are also an unusually rich source of biologically active natural products, and evidence is accumulating that these compounds might often be synthesized by the symbionts. Since the study of sponge-associated bacteria is generally hampered by very low cultivation rates, cultivation-independent, metagenomic methods have recently been applied to sponges. These methods allow for the isolation of biosynthetic gene clusters that can ultimately be exploited to develop sustainable natural product sources by heterologous expression. However, general challenges encountered in sponge metagenomic research are the poor quality of the isolated DNA with respect to size and yield, the difficulty to identify genes of interest among numerous homologs, insufficient clone numbers in metagenomic libraries, and time-consuming screening procedures to identify and isolate rare positive clones. Here, we give an overview of methods that address these problems and can be used to streamline isolation of biosynthetic and other genes of interest.

Genetic variation in glia-neuron signalling modulates ageing rate.

PubMed

Yin, Jiang-An; Gao, Ge; Liu, Xi-Juan; Hao, Zi-Qian; Li, Kai; Kang, Xin-Lei; Li, Hong; Shan, Yuan-Hong; Hu, Wen-Li; Li, Hai-Peng; Cai, Shi-Qing

2017-11-08

The rate of behavioural decline in the ageing population is remarkably variable among individuals. Despite the considerable interest in studying natural variation in ageing rate to identify factors that control healthy ageing, no such factor has yet been found. Here we report a genetic basis for variation in ageing rates in Caenorhabditis elegans. We find that C. elegans isolates show diverse lifespan and age-related declines in virility, pharyngeal pumping, and locomotion. DNA polymorphisms in a novel peptide-coding gene, named regulatory-gene-for-behavioural-ageing-1 (rgba-1), and the neuropeptide receptor gene npr-28 influence the rate of age-related decline of worm mating behaviour; these two genes might have been subjected to recent selective sweeps. Glia-derived RGBA-1 activates NPR-28 signalling, which acts in serotonergic and dopaminergic neurons to accelerate behavioural deterioration. This signalling involves the SIR-2.1-dependent activation of the mitochondrial unfolded protein response, a pathway that modulates ageing. Thus, natural variation in neuropeptide-mediated glia-neuron signalling modulates the rate of ageing in C. elegans.

Natural Selection on Individual Variation in Tolerance of Gastrointestinal Nematode Infection

PubMed Central

Hayward, Adam D.; Nussey, Daniel H.; Wilson, Alastair J.; Berenos, Camillo; Pilkington, Jill G.; Watt, Kathryn A.; Pemberton, Josephine M.; Graham, Andrea L.

2014-01-01

Hosts may mitigate the impact of parasites by two broad strategies: resistance, which limits parasite burden, and tolerance, which limits the fitness or health cost of increasing parasite burden. The degree and causes of variation in both resistance and tolerance are expected to influence host–parasite evolutionary and epidemiological dynamics and inform disease management, yet very little empirical work has addressed tolerance in wild vertebrates. Here, we applied random regression models to longitudinal data from an unmanaged population of Soay sheep to estimate individual tolerance, defined as the rate of decline in body weight with increasing burden of highly prevalent gastrointestinal nematode parasites. On average, individuals lost weight as parasite burden increased, but whereas some lost weight slowly as burden increased (exhibiting high tolerance), other individuals lost weight significantly more rapidly (exhibiting low tolerance). We then investigated associations between tolerance and fitness using selection gradients that accounted for selection on correlated traits, including body weight. We found evidence for positive phenotypic selection on tolerance: on average, individuals who lost weight more slowly with increasing parasite burden had higher lifetime breeding success. This variation did not have an additive genetic basis. These results reveal that selection on tolerance operates under natural conditions. They also support theoretical predictions for the erosion of additive genetic variance of traits under strong directional selection and fixation of genes conferring tolerance. Our findings provide the first evidence of selection on individual tolerance of infection in animals and suggest practical applications in animal and human disease management in the face of highly prevalent parasites. PMID:25072883

Natural Variation of Epstein-Barr Virus Genes, Proteins, and Primary MicroRNA.

PubMed

Correia, Samantha; Palser, Anne; Elgueta Karstegl, Claudio; Middeldorp, Jaap M; Ramayanti, Octavia; Cohen, Jeffrey I; Hildesheim, Allan; Fellner, Maria Dolores; Wiels, Joelle; White, Robert E; Kellam, Paul; Farrell, Paul J

2017-08-01

Viral gene sequences from an enlarged set of about 200 Epstein-Barr virus (EBV) strains, including many primary isolates, have been used to investigate variation in key viral genetic regions, particularly LMP1, Zp, gp350, EBNA1, and the BART microRNA (miRNA) cluster 2. Determination of type 1 and type 2 EBV in saliva samples from people from a wide range of geographic and ethnic backgrounds demonstrates a small percentage of healthy white Caucasian British people carrying predominantly type 2 EBV. Linkage of Zp and gp350 variants to type 2 EBV is likely to be due to their genes being adjacent to the EBNA3 locus, which is one of the major determinants of the type 1/type 2 distinction. A novel classification of EBNA1 DNA binding domains, named QCIGP, results from phylogeny analysis of their protein sequences but is not linked to the type 1/type 2 classification. The BART cluster 2 miRNA region is classified into three major variants through single-nucleotide polymorphisms (SNPs) in the primary miRNA outside the mature miRNA sequences. These SNPs can result in altered levels of expression of some miRNAs from the BART variant frequently present in Chinese and Indonesian nasopharyngeal carcinoma (NPC) samples. The EBV genetic variants identified here provide a basis for future, more directed analysis of association of specific EBV variations with EBV biology and EBV-associated diseases. IMPORTANCE Incidence of diseases associated with EBV varies greatly in different parts of the world. Thus, relationships between EBV genome sequence variation and health, disease, geography, and ethnicity of the host may be important for understanding the role of EBV in diseases and for development of an effective EBV vaccine. This paper provides the most comprehensive analysis so far of variation in specific EBV genes relevant to these diseases and proposed EBV vaccines. By focusing on variation in LMP1, Zp, gp350, EBNA1, and the BART miRNA cluster 2, new relationships with the known

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.

PubMed

Heinig, Matthias; Adriaens, Michiel E; Schafer, Sebastian; van Deutekom, Hanneke W M; Lodder, Elisabeth M; Ware, James S; Schneider, Valentin; Felkin, Leanne E; Creemers, Esther E; Meder, Benjamin; Katus, Hugo A; Rühle, Frank; Stoll, Monika; Cambien, François; Villard, Eric; Charron, Philippe; Varro, Andras; Bishopric, Nanette H; George, Alfred L; Dos Remedios, Cristobal; Moreno-Moral, Aida; Pesce, Francesco; Bauerfeind, Anja; Rüschendorf, Franz; Rintisch, Carola; Petretto, Enrico; Barton, Paul J; Cook, Stuart A; Pinto, Yigal M; Bezzina, Connie R; Hubner, Norbert

2017-09-14

Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes. Moreover, we show a widespread effect of genetic variation on the regulation of transcription, isoform usage, and allele-specific expression. Systematic annotation of genome-wide association SNPs identifies 60 functional candidate genes for heart phenotypes, representing 20% of all published heart genome-wide association loci. Focusing on the dilated cardiomyopathy phenotype we found that eQTL variants are also enriched for dilated cardiomyopathy genome-wide association signals in two independent cohorts. RNA transcription, splicing, and allele-specific expression are each important determinants of the dilated cardiomyopathy phenotype and are controlled by genetic factors. Our results represent a powerful resource for the field of cardiovascular genetics.

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

PubMed Central

Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

PubMed

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

Heterochrony underpins natural variation in Cardamine hirsuta leaf form

PubMed Central

Cartolano, Maria; Pieper, Bjorn; Lempe, Janne; Tattersall, Alex; Huijser, Peter; Tresch, Achim; Darrah, Peter R.; Hay, Angela; Tsiantis, Miltos

2015-01-01

A key problem in biology is whether the same processes underlie morphological variation between and within species. Here, by using plant leaves as an example, we show that the causes of diversity at these two evolutionary scales can be divergent. Some species like the model plant Arabidopsis thaliana have simple leaves, whereas others like the A. thaliana relative Cardamine hirsuta bear complex leaves comprising leaflets. Previous work has shown that these interspecific differences result mostly from variation in local tissue growth and patterning. Now, by cloning and characterizing a quantitative trait locus (QTL) for C. hirsuta leaf shape, we find that a different process, age-dependent progression of leaf form, underlies variation in this trait within species. This QTL effect is caused by cis-regulatory variation in the floral repressor ChFLC, such that genotypes with low-expressing ChFLC alleles show both early flowering and accelerated age-dependent changes in leaf form, including faster leaflet production. We provide evidence that this mechanism coordinates leaf development with reproductive timing and may help to optimize resource allocation to the next generation. PMID:26243877

Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines.

PubMed

Ulvestad, Marte; Overland, Indra

2012-06-01

THIS ARTICLE DEVELOPS A FORMAL MODEL FOR COMPARING THE COST STRUCTURE OF THE TWO MAIN TRANSPORT OPTIONS FOR NATURAL GAS: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO 2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG.

Natural gas and CO2 price variation: impact on the relative cost-efficiency of LNG and pipelines

PubMed Central

Ulvestad, Marte; Overland, Indra

2012-01-01

This article develops a formal model for comparing the cost structure of the two main transport options for natural gas: liquefied natural gas (LNG) and pipelines. In particular, it evaluates how variations in the prices of natural gas and greenhouse gas emissions affect the relative cost-efficiency of these two options. Natural gas is often promoted as the most environmentally friendly of all fossil fuels, and LNG as a modern and efficient way of transporting it. Some research has been carried out into the local environmental impact of LNG facilities, but almost none into aspects related to climate change. This paper concludes that at current price levels for natural gas and CO2 emissions the distance from field to consumer and the volume of natural gas transported are the main determinants of transport costs. The pricing of natural gas and greenhouse emissions influence the relative cost-efficiency of LNG and pipeline transport, but only to a limited degree at current price levels. Because more energy is required for the LNG process (especially for fuelling the liquefaction process) than for pipelines at distances below 9100 km, LNG is more exposed to variability in the price of natural gas and greenhouse gas emissions up to this distance. If the prices of natural gas and/or greenhouse gas emission rise dramatically in the future, this will affect the choice between pipelines and LNG. Such a price increase will be favourable for pipelines relative to LNG. PMID:24683269

Natural genetic variation for morphological and molecular determinants of plant growth and yield.

PubMed

Nunes-Nesi, Adriano; Nascimento, Vitor de Laia; de Oliveira Silva, Franklin Magnum; Zsögön, Agustin; Araújo, Wagner L; Sulpice, Ronan

2016-05-01

The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Parameterization of aquatic ecosystem functioning and its natural variation: Hierarchical Bayesian modelling of plankton food web dynamics

NASA Astrophysics Data System (ADS)

Norros, Veera; Laine, Marko; Lignell, Risto; Thingstad, Frede

2017-10-01

Methods for extracting empirically and theoretically sound parameter values are urgently needed in aquatic ecosystem modelling to describe key flows and their variation in the system. Here, we compare three Bayesian formulations for mechanistic model parameterization that differ in their assumptions about the variation in parameter values between various datasets: 1) global analysis - no variation, 2) separate analysis - independent variation and 3) hierarchical analysis - variation arising from a shared distribution defined by hyperparameters. We tested these methods, using computer-generated and empirical data, coupled with simplified and reasonably realistic plankton food web models, respectively. While all methods were adequate, the simulated example demonstrated that a well-designed hierarchical analysis can result in the most accurate and precise parameter estimates and predictions, due to its ability to combine information across datasets. However, our results also highlighted sensitivity to hyperparameter prior distributions as an important caveat of hierarchical analysis. In the more complex empirical example, hierarchical analysis was able to combine precise identification of parameter values with reasonably good predictive performance, although the ranking of the methods was less straightforward. We conclude that hierarchical Bayesian analysis is a promising tool for identifying key ecosystem-functioning parameters and their variation from empirical datasets.

Tapping natural variation at functional level reveals allele specific molecular characteristics of potato invertase Pain-1.

PubMed

Draffehn, Astrid M; Durek, Pawel; Nunes-Nesi, Adriano; Stich, Benjamin; Fernie, Alisdair R; Gebhardt, Christiane

2012-12-01

Biochemical, molecular and genetic studies emphasize the role of the potato vacuolar invertase Pain-1 in the accumulation of reducing sugars in potato tubers upon cold storage, and thereby its influence on the quality of potato chips and French fries. Previous studies showed that natural Pain-1 cDNA alleles were associated with better chip quality and higher tuber starch content. In this study, we focused on the functional characterization of these alleles. A genotype-dependent transient increase of total Pain-1 transcript levels in cold-stored tubers of six different genotypes as well as allele-specific expression patterns were detected. 3D modelling revealed putative structural differences between allelic Pain-1 proteins at the molecule's surface and at the substrate binding site. Furthermore, the yeast SUC2 mutant was complemented with Pain-1 cDNA alleles and enzymatic parameters of the heterologous expressed proteins were measured at 30 and 4 °C. Significant differences between the alleles were detected. The observed functional differences between Pain-1 alleles did not permit final conclusions on the mechanism of their association with tuber quality traits. Our results show that natural allelic variation at the functional level is present in potato, and that the heterozygous genetic background influences the manifestation of this variation. © 2012 Blackwell Publishing Ltd.

Natural variation in chemosensation: lessons from an island nematode

PubMed Central

McGaughran, Angela; Morgan, Katy; Sommer, Ralf J

2013-01-01

All organisms must interact with their environment, responding in behavioral, chemical, and other ways to various stimuli throughout their life cycles. Characterizing traits that directly represent an organism's ability to sense and react to their environment provides useful insight into the evolution of life-history strategies. One such trait for the nematode Pristionchus pacificus, chemosensation, is involved in navigation to beetle hosts. Essential for the survival of the nematode, chemosensory behavior may be subject to variation as nematodes discriminate among chemical cues to complete their life cycle. We examine this hypothesis using natural isolates of P. pacificus from La Réunion Island. We select strains from a variety of La Réunion beetle hosts and geographic locations and examine their chemoattraction response toward organic compounds, beetle washes, and live beetles. We find that nematodes show significant differences in their response to various chemicals and are able to chemotax to live beetles in a novel assay. Further, strains can discriminate among different cues, showing more similar responses toward beetle washes than to organic compounds in cluster analyses. However, we find that variance in chemoattraction response is not significantly associated with temperature, location, or beetle host. Rather, strains show a more concerted response toward compounds they most likely directly encounter in the wild. We suggest that divergence in odor-guided behavior in P. pacificus may therefore have an important ecological component. PMID:24455150

Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans.

PubMed

Green, J W M; Snoek, L B; Kammenga, J E; Harvey, S C

2013-10-01

In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly investigated. Here, we report extensive natural genetic variation in dauer larvae development within growing populations across multiple wild isolates. Moreover, bin mapping of introgression lines (ILs) derived from the genetically divergent isolates N2 and CB4856 reveals 10 quantitative trait loci (QTLs) affecting dauer formation. Comparison of individual ILs to N2 identifies an additional eight QTLs, and sequential IL analysis reveals six more QTLs. Our results also show that a behavioural, laboratory-derived, mutation controlled by the neuropeptide Y receptor homolog npr-1 can affect dauer larvae development in growing populations. These findings illustrate the complex genetic architecture of variation in dauer larvae formation in C. elegans and may help to understand how the control of variation in dauer larvae development has evolved.

Riverine threat indices to assess watershed condition and identify primary management capacity of agriculture natural resource management agencies.

PubMed

Fore, Jeffrey D; Sowa, Scott P; Galat, David L; Annis, Gust M; Diamond, David D; Rewa, Charles

2014-03-01

Managers can improve conservation of lotic systems over large geographies if they have tools to assess total watershed conditions for individual stream segments and can identify segments where conservation practices are most likely to be successful (i.e., primary management capacity). The goal of this research was to develop a suite of threat indices to help agriculture resource management agencies select and prioritize watersheds across Missouri River basin in which to implement agriculture conservation practices. We quantified watershed percentages or densities of 17 threat metrics that represent major sources of ecological stress to stream communities into five threat indices: agriculture, urban, point-source pollution, infrastructure, and all non-agriculture threats. We identified stream segments where agriculture management agencies had primary management capacity. Agriculture watershed condition differed by ecoregion and considerable local variation was observed among stream segments in ecoregions of high agriculture threats. Stream segments with high non-agriculture threats were most concentrated near urban areas, but showed high local variability. 60 % of stream segments in the basin were classified as under U.S. Department of Agriculture's Natural Resources Conservation Service (NRCS) primary management capacity and most segments were in regions of high agricultural threats. NRCS primary management capacity was locally variable which highlights the importance of assessing total watershed condition for multiple threats. Our threat indices can be used by agriculture resource management agencies to prioritize conservation actions and investments based on: (a) relative severity of all threats, (b) relative severity of agricultural threats, and (c) and degree of primary management capacity.

Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake.

PubMed

Hou, Yali; Bickhart, Derek M; Chung, Hoyoung; Hutchison, Jana L; Norman, H Duane; Connor, Erin E; Liu, George E

2012-11-01

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. In this study, we performed an initial analysis of copy number variations (CNVs) using BovineHD SNP genotyping data from 147 Holstein cows identified as having high or low feed efficiency as estimated by residual feed intake (RFI). We detected 443 candidate CNV regions (CNVRs) that represent 18.4 Mb (0.6 %) of the genome. To investigate the functional impacts of CNVs, we created two groups of 30 individual animals with extremely low or high estimated breeding values (EBVs) for RFI, and referred to these groups as low intake (LI; more efficient) or high intake (HI; less efficient), respectively. We identified 240 (~9.0 Mb) and 274 (~10.2 Mb) CNVRs from LI and HI groups, respectively. Approximately 30-40 % of the CNVRs were specific to the LI group or HI group of animals. The 240 LI CNVRs overlapped with 137 Ensembl genes. Network analyses indicated that the LI-specific genes were predominantly enriched for those functioning in the inflammatory response and immunity. By contrast, the 274 HI CNVRs contained 177 Ensembl genes. Network analyses indicated that the HI-specific genes were particularly involved in the cell cycle, and organ and bone development. These results relate CNVs to two key variables, namely immune response and organ and bone development. The data indicate that greater feed efficiency relates more closely to immune response, whereas cattle with reduced feed efficiency may have a greater capacity for organ and bone development.

Genetic variation in heat-stress tolerance among South American Drosophila populations.

PubMed

Fallis, Lindsey C; Fanara, Juan Jose; Morgan, Theodore J

2011-10-01

Spatial or temporal differences in environmental variables, such as temperature, are ubiquitous in nature and impose stress on organisms. This is especially true for organisms that are isothermal with the environment, such as insects. Understanding the means by which insects respond to temperature and how they will react to novel changes in environmental temperature is important for understanding the adaptive capacity of populations and to predict future trajectories of evolutionary change. The organismal response to heat has been identified as an important environmental variable for insects that can dramatically influence life history characters and geographic range. In the current study we surveyed the amount of variation in heat tolerance among Drosophila melanogaster populations collected at diverse sites along a latitudinal gradient in Argentina (24°-38°S). This is the first study to quantify heat tolerance in South American populations and our work demonstrates that most of the populations surveyed have abundant within-population phenotypic variation, while still exhibiting significant variation among populations. The one exception was the most heat tolerant population that comes from a climate exhibiting the warmest annual mean temperature. All together our results suggest there is abundant genetic variation for heat-tolerance phenotypes within and among natural populations of Drosophila and this variation has likely been shaped by environmental temperature.

Fitness variation in response to artificial selection for reduced cell area, cell number and wing area in natural populations of Drosophila melanogaster.

PubMed

Trotta, Vincenzo; Calboli, Federico C F; Ziosi, Marcello; Cavicchi, Sandro

2007-08-16

Genetically based body size differences are naturally occurring in populations of Drosophila melanogaster, with bigger flies in the cold. Despite the cosmopolitan nature of body size clines in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of body size variation are not fully understood. In particular, it is not clear what the selective value of cell size and cell area variation exactly is. In the present work we determined variation in viability, developmental time and larval competitive ability in response to crowding at two temperatures after artificial selection for reduced cell area, cell number and wing area in four different natural populations of D. melanogaster. No correlated effect of selection on viability or developmental time was observed among all selected populations. An increase in competitive ability in one thermal environment (18 degrees C) under high larval crowding was observed as a correlated response to artificial selection for cell size. Viability and developmental time are not affected by selection for the cellular component of body size, suggesting that these traits only depend on the contingent genetic makeup of a population. The higher larval competitive ability shown by populations selected for reduced cell area seems to confirm the hypothesis that cell area mediated changes have a relationship with fitness, and might be the preferential way to change body size under specific circumstances.

Natural Variation of Drug Susceptibility in Wild-Type Human Immunodeficiency Virus Type 1

PubMed Central

Parkin, N. T.; Hellmann, N. S.; Whitcomb, J. M.; Kiss, L.; Chappey, C.; Petropoulos, C. J.

2004-01-01

Wild-type viruses from the ViroLogic phenotype-genotype database were evaluated to determine the upper confidence limit of the drug susceptibility distributions, or “biological cutoffs,” for the PhenoSense HIV phenotypic drug susceptibility assay. Definition of the natural variation in drug susceptibility in wild-type human immunodeficiency virus (HIV) type 1 isolates is necessary to determine the prevalence of innate drug resistance and to assess the capability of the PhenoSense assay to reliably measure subtle reductions in drug susceptibility. The biological cutoffs for each drug, defined by the 99th percentile of the fold change in the 50% inhibitory concentration distributions or the mean fold change plus 2 standard deviations, were lower than those previously reported for other phenotypic assays and lower than the clinically relevant cutoffs previously defined for the PhenoSense assay. The 99th percentile fold change values ranged from 1.2 (tenofovir) to 1.8 (zidovudine) for nucleoside reverse transcriptase RT inhibitors (RTIs), from 3.0 (efavirenz) to 6.2 (delavirdine) for nonnucleoside RTIs, and from 1.6 (lopinavir) to 3.6 (nelfinavir) for protease inhibitors. To evaluate the potential role of intrinsic assay variability in the observed variations in the drug susceptibilities of wild-type isolates, 10 reference viruses with different drug susceptibility patterns were tested 8 to 30 times each. The median coefficients of variation in fold change for the reference viruses ranged from 12 to 18% for all drugs except zidovudine (32%), strongly suggesting that the observed differences in wild-type virus susceptibility to the different drugs is related to intrinsic virus variability rather than assay variability. The low biological cutoffs and assay variability suggest that the PhenoSense HIV assay may assist in defining clinically relevant susceptibility cutoffs for resistance to antiretroviral drugs. PMID:14742192

Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.

PubMed

King, R A; Symondson, W O C; Thomas, R J

2015-06-01

Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.

Variation in Chemical Defense Among Natural Populations of Common Toad, Bufo bufo, Tadpoles: the Role of Environmental Factors.

PubMed

Bókony, Veronika; Móricz, Ágnes M; Tóth, Zsófia; Gál, Zoltán; Kurali, Anikó; Mikó, Zsanett; Pásztor, Katalin; Szederkényi, Márk; Tóth, Zoltán; Ujszegi, János; Üveges, Bálint; Krüzselyi, Dániel; Capon, Robert J; Hoi, Herbert; Hettyey, Attila

2016-04-01

Defensive toxins are widespread in nature, yet we know little about how various environmental factors shape the evolution of chemical defense, especially in vertebrates. In this study we investigated the natural variation in the amount and composition of bufadienolide toxins, and the relative importance of ecological factors in predicting that variation, in larvae of the common toad, Bufo bufo, an amphibian that produces toxins de novo. We found that tadpoles' toxin content varied markedly among populations, and the number of compounds per tadpole also differed between two geographical regions. The most consistent predictor of toxicity was the strength of competition, indicating that tadpoles produced more compounds and larger amounts of toxins when coexisting with more competitors. Additionally, tadpoles tended to contain larger concentrations of bufadienolides in ponds that were less prone to desiccation, suggesting that the costs of toxin production can only be afforded by tadpoles that do not need to drastically speed up their development. Interestingly, this trade-off was not alleviated by higher food abundance, as periphyton biomass had negligible effect on chemical defense. Even more surprisingly, we found no evidence that higher predation risk enhances chemical defenses, suggesting that low predictability of predation risk and high mortality cost of low toxicity might select for constitutive expression of chemical defense irrespective of the actual level of predation risk. Our findings highlight that the variation in chemical defense may be influenced by environmental heterogeneity in both the need for, and constraints on, toxicity as predicted by optimal defense theory.

Mass-dependent cadmium isotopic variations in nature with emphasis on the marine environment

NASA Astrophysics Data System (ADS)

Schmitt, Anne-Désirée; Galer, Stephen J. G.; Abouchami, Wafa

2009-01-01

We report a survey of natural mass-dependent cadmium isotope fractionation measured by thermal ionization mass spectrometry using a double-spike technique (DS-TIMS). Over sixty samples of natural terrestrial Cd from diverse environments, including MORB, OIB, continental loess, hydrogenic and hydrothermal ferromanganese deposits, and sphalerites (both oceanic and from major continental ore deposits) were analysed. Our results are expressed in terms of ɛ 112/110Cd, which are deviations in 112Cd/ 110Cd from our in-house JMC Cd standard in parts per 10 4. The total ɛ 112/110Cd variation is relatively small, with a range of only 5 ɛ-units, and is one-to-two orders of magnitude smaller than that previously found in meteorites. The MORB, OIB and loess ɛ 112/110Cd values are similar and provide a good estimate for the bulk silicate Earth (BSE) value which is - 0.95 ± 0.12 relative to our Cd standard (ɛ 112/110Cd = + 0.16 relative to Münster JMC Cd). Taken together, these data suggest little Cd isotope fractionation takes place during crust-mantle segregation. Cd isotopic compositions of continental sphalerite (ZnS) deposits worldwide and high-temperature oceanic hydrothermal sulphides show remarkably similar ɛ 112/110Cd values, consistent with our estimate for the BSE. In contrast, mid-temperature oceanic sulphides from a single extinct hydrothermal chimney display over 4 ɛ-units variation — along with the most negative values. These variations are most probably caused by precipitation/redissolution of sulphide phases en route within the hydrothermal system. The ɛ 112/110Cd variability found in worldwide marine Fe-Mn deposits reflects the seawater Cd isotope signal upon precipitation from ambient seawater. A decrease in ɛ 112/110Cd is observed in passing from shallow-water Fe-Mn deposits to those from deeper waters (> 2000 m depth). This shift is explained by biological fractionation related to the uptake of dissolved seawater Cd by phytoplankton in the upper

Identifying Natural Alignments Between Ambulatory Surgery Centers and Local Health Systems: Building Broader Communities of Surgical Care.

PubMed

Funk, Russell J; Owen-Smith, Jason; Landon, Bruce E; Birkmeyer, John D; Hollingsworth, John M

2017-02-01

To develop and compare methods for identifying natural alignments between ambulatory surgery centers (ASCs) and hospitals that anchor local health systems. Using all-payer data from Florida's State Ambulatory Surgery and Inpatient Databases (2005-2009), we developed 3 methods for identifying alignments between ASCS and hospitals. The first, a geographic proximity approach, used spatial data to assign an ASC to its nearest hospital neighbor. The second, a predominant affiliation approach, assigned an ASC to the hospital with which it shared a plurality of surgeons. The third, a network community approach, linked an ASC with a larger group of hospitals held together by naturally occurring physician networks. We compared each method in terms of its ability to capture meaningful and stable affiliations and its administrative simplicity. Although the proximity approach was simplest to implement and produced the most durable alignments, ASC surgeon's loyalty to the assigned hospital was low with this method. The predominant affiliation and network community approaches performed better and nearly equivalently on these metrics, capturing more meaningful affiliations between ASCs and hospitals. However, the latter's alignments were least durable, and it was complex to administer. We describe 3 methods for identifying natural alignments between ASCs and hospitals, each with strengths and weaknesses. These methods will help health system managers identify ASCs with which to partner. Moreover, health services researchers and policy analysts can use them to study broader communities of surgical care.

Identifying QT prolongation from ECG impressions using a general-purpose Natural Language Processor

PubMed Central

Denny, Joshua C.; Miller, Randolph A.; Waitman, Lemuel Russell; Arrieta, Mark; Peterson, Joshua F.

2009-01-01

Objective Typically detected via electrocardiograms (ECGs), QT interval prolongation is a known risk factor for sudden cardiac death. Since medications can promote or exacerbate the condition, detection of QT interval prolongation is important for clinical decision support. We investigated the accuracy of natural language processing (NLP) for identifying QT prolongation from cardiologist-generated, free-text ECG impressions compared to corrected QT (QTc) thresholds reported by ECG machines. Methods After integrating negation detection to a locally-developed natural language processor, the KnowledgeMap concept identifier, we evaluated NLP-based detection of QT prolongation compared to the calculated QTc on a set of 44,318 ECGs obtained from hospitalized patients. We also created a string query using regular expressions to identify QT prolongation. We calculated sensitivity and specificity of the methods using manual physician review of the cardiologist-generated reports as the gold standard. To investigate causes of “false positive” calculated QTc, we manually reviewed randomly selected ECGs with a long calculated QTc but no mention of QT prolongation. Separately, we validated the performance of the negation detection algorithm on 5,000 manually-categorized ECG phrases for any medical concept (not limited to QT prolongation) prior to developing the NLP query for QT prolongation. Results The NLP query for QT prolongation correctly identified 2,364 of 2,373 ECGs with QT prolongation with a sensitivity of 0.996 and a positive predictive value of 1.000. There were no false positives. The regular expression query had a sensitivity of 0.999 and positive predictive value of 0.982. In contrast, the positive predictive value of common QTc thresholds derived from ECG machines was 0.07–0.25 with corresponding sensitivities of 0.994–0.046. The negation detection algorithm had a recall of 0.973 and precision of 0.982 for 10,490 concepts found within ECG impressions

Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae).

PubMed

Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

2014-11-01

The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution.

Immunological variation in Taenia solium porcine cysticercosis: measurement on the variation of the antibody immune response of naturally infected pigs against antigens extracted from their own cysticerci and from those of different pigs.

PubMed

Ostoa-Saloma, Pedro; Esquivel-Velázquez, Marcela; Larralde, Carlos

2013-10-18

Although it is widely assumed that both antigen and host immunological variability are involved in the variable intensity of natural porcine infections by Taenia solium (T. solium) cysticercis and success of immunodiagnostic tests vaccines, the magnitude of such combined variability has not been studied or measured at all. In this paper we report statistical data on the variability of the antibody response of naturally infected pigs against the antigens extracted from the vesicular fluids of their own infecting cysts (variance within pigs) and against antigen samples extracted from cysts of other cysticercotic pigs (variance among pigs). The variation between pigs was greater than the inter-pigs variations, which suggests that a concomitant immunity process prevents the establishment of cysts coming from a subsequent challenge. In so doing, we found that there is not a single antigenic band that was recognized by all hosts and that antigens varied among the cysts within the same pigs as well as among pigs. Our results may be valuable for the improvement of immunodiagnostic tests and of effective vaccines against naturally acquired porcine T. solium cysticercosis. Copyright © 2013 Elsevier B.V. All rights reserved.

Genome-wide association implicates numerous genes and pleiotropy underlying ecological trait variation in natural populations of Populus trichocarpa

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

McKown, Athena; Klapste, Jaroslav; Guy, Robert

2014-01-01

To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).

Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster.

PubMed

Cridland, Julie M; Thornton, Kevin R

2010-01-13

Several recent studies have focused on the evolution of recently duplicated genes in Drosophila. Currently, however, little is known about the evolutionary forces acting upon duplications that are segregating in natural populations. We used a high-throughput, paired-end sequencing platform (Illumina) to identify structural variants in a population sample of African D. melanogaster. Polymerase chain reaction and sequencing confirmation of duplications detected by multiple, independent paired-ends showed that paired-end sequencing reliably uncovered the break points of structural rearrangements and allowed us to identify a number of tandem duplications segregating within a natural population. Our confirmation experiments show that rates of confirmation are very high, even at modest coverage. Our results also compare well with previous studies using microarrays (Emerson J, Cardoso-Moreira M, Borevitz JO, Long M. 2008. Natural selection shapes genome wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 320:1629-1631. and Dopman EB, Hartl DL. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104:19920-19925.), which both gives us confidence in the results of this study as well as confirms previous microarray results.We were also able to identify whole-gene duplications, such as a novel duplication of Or22a, an olfactory receptor, and identify copy-number differences in genes previously known to be under positive selection, like Cyp6g1, which confers resistance to dichlorodiphenyltrichloroethane. Several "hot spots" of duplications were detected in this study, which indicate that particular regions of the genome may be more prone to generating duplications. Finally, population frequency analysis of confirmed events also showed an excess of rare variants in our population, which indicates that duplications segregating in the population may be deleterious and ultimately destined to be lost from the

Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster.

PubMed

Tatarenkov, Andrey; Ayala, Francisco J

2007-08-01

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.

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.

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

Evaluating intra- and inter-individual variation in the human placental transcriptome.

PubMed

Hughes, David A; Kircher, Martin; He, Zhisong; Guo, Song; Fairbrother, Genevieve L; Moreno, Carlos S; Khaitovich, Philipp; Stoneking, Mark

2015-03-19

Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. We estimate that on average, 33.2%, 58.9%, and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals, and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they each account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling, and metabolism. Many biological traits demonstrate correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection, directional selection, or diversifying selection. We apportion placental gene expression variation into individual, population, and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection.

Gravimetric phenotyping of whole plant transpiration responses to atmospheric vapour pressure deficit identifies genotypic variation in water use efficiency.

PubMed

Ryan, Annette C; Dodd, Ian C; Rothwell, Shane A; Jones, Ros; Tardieu, Francois; Draye, Xavier; Davies, William J

2016-10-01

There is increasing interest in rapidly identifying genotypes with improved water use efficiency, exemplified by the development of whole plant phenotyping platforms that automatically measure plant growth and water use. Transpirational responses to atmospheric vapour pressure deficit (VPD) and whole plant water use efficiency (WUE, defined as the accumulation of above ground biomass per unit of water used) were measured in 100 maize (Zea mays L.) genotypes. Using a glasshouse based phenotyping platform with naturally varying VPD (1.5-3.8kPa), a 2-fold variation in WUE was identified in well-watered plants. Regression analysis of transpiration versus VPD under these conditions, and subsequent whole plant gas exchange at imposed VPDs (0.8-3.4kPa) showed identical responses in specific genotypes. Genotype response of transpiration versus VPD fell into two categories: 1) a linear increase in transpiration rate with VPD with low (high WUE) or high (low WUE) transpiration rate at all VPDs, 2) a non-linear response with a pronounced change point at low VPD (high WUE) or high VPD (low WUE). In the latter group, high WUE genotypes required a significantly lower VPD before transpiration was restricted, and had a significantly lower rate of transpiration in response to VPD after this point, when compared to low WUE genotypes. Change point values were significantly positively correlated with stomatal sensitivity to VPD. A change point in stomatal response to VPD may explain why some genotypes show contradictory WUE rankings according to whether they are measured under glasshouse or field conditions. Furthermore, this novel use of a high throughput phenotyping platform successfully reproduced the gas exchange responses of individuals measured in whole plant chambers, accelerating the identification of plants with high WUE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Variational formulation of high performance finite elements: Parametrized variational principles

NASA Technical Reports Server (NTRS)

Felippa, Carlos A.; Militello, Carmello

1991-01-01

High performance elements are simple finite elements constructed to deliver engineering accuracy with coarse arbitrary grids. This is part of a series on the variational basis of high-performance elements, with emphasis on those constructed with the free formulation (FF) and assumed natural strain (ANS) methods. Parametrized variational principles that provide a foundation for the FF and ANS methods, as well as for a combination of both are presented.

Interindividual variability in the prevalence of OPRM1 and CYP2B6 gene variations may identify drug-susceptible populations.

PubMed

Bunten, H; Liang, W J; Pounder, D J; Seneviratne, C; Osselton, D

2011-09-01

Methadone is used worldwide for the treatment of heroin addiction; however, fatal poisonings are increasingly reported. The prevalence of CYP2B6 and μ-opioid receptor (OPRM1) gene variations were examined between a postmortem population where the deaths were associated with methadone and a live nondrug-using control population using Taqman™ SNP Genotyping assays. The CYP2B6*6 allele was higher in the postmortem population, but the difference was not significant (P = 0.92). The CYP2B6 T750C promoter variation was similar in frequency for both populations. Linkage between T750C and CYP2B6*6 was identified for both populations (P < 0.01). The prevalence of the OPRM1 A118G variation was significantly higher in the control population (P = 0.0046), which might indicate a protective mechanism against opioid toxicity. Individual susceptibility to methadone may be determined by screening for CYP2B6*6.

A Psychoevolutionary Approach to Identifying Preferred Nature Scenes With Potential to Provide Restoration From Stress.

PubMed

Thake, Carol L; Bambling, Matthew; Edirippulige, Sisira; Marx, Eric

2017-10-01

Research supports therapeutic use of nature scenes in healthcare settings, particularly to reduce stress. However, limited literature is available to provide a cohesive guide for selecting scenes that may provide optimal therapeutic effect. This study produced and tested a replicable process for selecting nature scenes with therapeutic potential. Psychoevolutionary theory informed the construction of the Importance for Survival Scale (IFSS), and its usefulness for identifying scenes that people generally prefer to view and that hold potential to reduce stress was tested. Relationships between Importance for Survival (IFS), preference, and restoration were tested. General community participants ( N = 20 males, 20 females; M age = 48 years) Q-sorted sets of landscape photographs (preranked by the researcher in terms of IFS using the IFSS) from most to least preferred, and then completed the Short-Version Revised Restoration Scale in response to viewing a selection of the scenes. Results showed significant positive relationships between IFS and each of scene preference (large effect), and restoration potential (medium effect), as well as between scene preference and restoration potential across the levels of IFS (medium effect), and for individual participants and scenes (large effect). IFS was supported as a framework for identifying nature scenes that people will generally prefer to view and that hold potential for restoration from emotional distress; however, greater therapeutic potential may be expected when people can choose which of the scenes they would prefer to view. Evidence for the effectiveness of the IFSS was produced.

US Vulnerability to Natural Disasters

NASA Astrophysics Data System (ADS)

van der Vink, G.; Apgar, S.; Batchelor, A.; Carter, C.; Gail, D.; Jarrett, A.; Levine, N.; Morgan, W.; Orlikowski, M.; Pray, T.; Raymar, M.; Siebert, A.; Shawa, T. W.; Wallace, C.

2002-05-01

Natural disasters result from the coincidence of natural events with the built environment. Our nation's infrastructure is growing at an exponential rate in many areas of high risk, and the Federal government's liability is increasing proportionally. By superimposing population density with predicted ground motion from earthquakes, historical hurricane tracks, historical tornado locations, and areas within the flood plain, we are able to identify locations of high vulnerability within the United States. We present a comprehensive map of disaster risk for the United States that is being produced for the Senate Natural Hazards Caucus. The map allows for the geographic comparison of natural disaster risk with past disaster declarations, the expenditure of Federal dollars for disaster relief, population increase, and variations of GDP. Every state is vulnerable to natural disasters. Although their frequency varies considerably, the annualized losses for disaster relief from hurricanes, earthquakes, and floods are approximately equivalent. While fast-growing states such as California and Florida remain highly vulnerable, changes in the occurrence of natural events combined with population increases are making areas such as Texas, North Carolina, and the East Coast increasingly vulnerable.

Frequency of mononuclear diploid cardiomyocytes underlies natural variation in heart regeneration.

PubMed

Patterson, Michaela; Barske, Lindsey; Van Handel, Ben; Rau, Christoph D; Gan, Peiheng; Sharma, Avneesh; Parikh, Shan; Denholtz, Matt; Huang, Ying; Yamaguchi, Yukiko; Shen, Hua; Allayee, Hooman; Crump, J Gage; Force, Thomas I; Lien, Ching-Ling; Makita, Takako; Lusis, Aldons J; Kumar, S Ram; Sucov, Henry M

2017-09-01

Adult mammalian cardiomyocyte regeneration after injury is thought to be minimal. Mononuclear diploid cardiomyocytes (MNDCMs), a relatively small subpopulation in the adult heart, may account for the observed degree of regeneration, but this has not been tested. We surveyed 120 inbred mouse strains and found that the frequency of adult mononuclear cardiomyocytes was surprisingly variable (>7-fold). Cardiomyocyte proliferation and heart functional recovery after coronary artery ligation both correlated with pre-injury MNDCM content. Using genome-wide association, we identified Tnni3k as one gene that influences variation in this composition and demonstrated that Tnni3k knockout resulted in elevated MNDCM content and increased cardiomyocyte proliferation after injury. Reciprocally, overexpression of Tnni3k in zebrafish promoted cardiomyocyte polyploidization and compromised heart regeneration. Our results corroborate the relevance of MNDCMs in heart regeneration. Moreover, they imply that intrinsic heart regeneration is not limited nor uniform in all individuals, but rather is a variable trait influenced by multiple genes.

Experimentally Identify the Effective Plume Chimney over a Natural Draft Chimney Model

NASA Astrophysics Data System (ADS)

Rahman, M. M.; Chu, C. M.; Tahir, A. M.; Ismail, M. A. bin; Misran, M. S. bin; Ling, L. S.

2017-07-01

The demands of energy are in increasing order due to rapid industrialization and urbanization. The researchers and scientists are working hard to improve the performance of the industry so that the energy consumption can be reduced significantly. Industries like power plant, timber processing plant, oil refinery, etc. performance mainly depend on the cooling tower chimney’s performance, either natural draft or forced draft. Chimney is used to create sufficient draft, so that air can flow through it. Cold inflow or flow reversal at chimney exit is one of the main identified problems that may alter the overall plant performance. The presence Effective Plume Chimney (EPC) is an indication of cold inflow free operation of natural draft chimney. Different mathematical model equations are used to estimate the EPC height over the heat exchanger or hot surface. In this paper, it is aim to identify the EPC experimentally. In order to do that, horizontal temperature profiling is done at the exit of the chimneys of face area 0.56m2, 1.00m2 and 2.25m2. A wire mesh screen is installed at chimneys exit to ensure cold inflow chimney operation. It is found that EPC exists in all modified chimney models and the heights of EPC varied from 1 cm to 9 cm. The mathematical models indicate that the estimated heights of EPC varied from 1 cm to 2.3 cm. Smoke test is also conducted to ensure the existence of EPC and cold inflow free option of chimney. Smoke test results confirmed the presence of EPC and cold inflow free operation of chimney. The performance of the cold inflow free chimney is increased by 50% to 90% than normal chimney.

Natural Variation in "Drosophila" Larval Reward Learning and Memory Due to a cGMP-Dependent Protein Kinase

ERIC Educational Resources Information Center

Kaun, Karla R.; Hendel, Thomas; Gerber, Bertram; Sokolowski, Marla B.

2007-01-01

Animals must be able to find and evaluate food to ensure survival. The ability to associate a cue with the presence of food is advantageous because it allows an animal to quickly identify a situation associated with a good, bad, or even harmful food. Identifying genes underlying these natural learned responses is essential to understanding this…

Determining the effects of dams on subdaily variation in river flows at a whole-basin scale

USGS Publications Warehouse

Zimmerman, J.K.H.; Letcher, B.H.; Nislow, K.H.; Lutz, K.A.; Magilligan, F.J.

2010-01-01

River regulation can alter the frequency and magnitude of subdaily flow variations causing major impacts on ecological structure and function. We developed an approach to quantify subdaily flow variation for multiple sites across a large watershed to assess the potential impacts of different dam operations (flood control, run-of-river hydropower and peaking hydropower) on natural communities. We used hourly flow data over a 9-year period from 30 stream gages throughout the Connecticut River basin to calculate four metrics of subdaily flow variation and to compare sites downstream of dams with unregulated sites. Our objectives were to (1) determine the temporal scale of data needed to characterize subdaily variability; (2) compare the frequency of days with high subdaily flow variation downstream of dams and unregulated sites; (3) analyse the magnitude of subdaily variation at all sites and (4) identify individual sites that had subdaily variation significantly higher than unregulated locations. We found that estimates of flow variability based on daily mean flow data were not sufficient to characterize subdaily flow patterns. Alteration of subdaily flows was evident in the number of days natural ranges of variability were exceeded, rather than in the magnitude of subdaily variation, suggesting that all rivers may exhibit highly variable subdaily flows, but altered rivers exhibit this variability more frequently. Peaking hydropower facilities had the most highly altered subdaily flows; however, we observed significantly altered ranges of subdaily variability downstream of some flood-control and run-of-river hydropower dams. Our analysis can be used to identify situations where dam operating procedures could be modified to reduce the level of hydrologic alteration. ?? 2009 John Wiley & Sons, Ltd.

Modeling, Modal Properties, and Mesh Stiffness Variation Instabilities of Planetary Gears

NASA Technical Reports Server (NTRS)

Parker, Robert G.; Lin, Jian; Krantz, Timothy L. (Technical Monitor)

2001-01-01

Planetary gear noise and vibration are primary concerns in their applications in helicopters, automobiles, aircraft engines, heavy machinery and marine vehicles. Dynamic analysis is essential to the noise and vibration reduction. This work analytically investigates some critical issues and advances the understanding of planetary gear dynamics. A lumped-parameter model is built for the dynamic analysis of general planetary gears. The unique properties of the natural frequency spectra and vibration modes are rigorously characterized. These special structures apply for general planetary gears with cyclic symmetry and, in practically important case, systems with diametrically opposed planets. The special vibration properties are useful for subsequent research. Taking advantage of the derived modal properties, the natural frequency and vibration mode sensitivities to design parameters are investigated. The key parameters include mesh stiffnesses, support/bearing stiffnesses, component masses, moments of inertia, and operating speed. The eigen-sensitivities are expressed in simple, closed-form formulae associated with modal strain and kinetic energies. As disorders (e.g., mesh stiffness variation. manufacturing and assembling errors) disturb the cyclic symmetry of planetary gears, their effects on the free vibration properties are quantitatively examined. Well-defined veering rules are derived to identify dramatic changes of natural frequencies and vibration modes under parameter variations. The knowledge of free vibration properties, eigen-sensitivities, and veering rules provide important information to effectively tune the natural frequencies and optimize structural design to minimize noise and vibration. Parametric instabilities excited by mesh stiffness variations are analytically studied for multi-mesh gear systems. The discrepancies of previous studies on parametric instability of two-stage gear chains are clarified using perturbation and numerical methods. The

Chemical and physical characteristics of natural ground waters in Michigan: A preliminary report

USGS Publications Warehouse

Cummings, T. Ray

1980-01-01

Wide variations occur in the chemical and physical characteristics of natural groundwaters in Michigan. Dissolved-solids concentrations range from 23 to 2,100 milligrams per liter. Waters having low dissolved-solids concentrations are calcium bicarbonate waters. Sodium, sulfate, and chloride increase as mineralization increases. Iron, aluminum, and titanium are higher at some locations than is common in most natural waters. Lead concentrations exceed those desirable in drinking water at some locations in the northern part of the Lower Peninsula. Generalized areal patterns of water quality variation suggest that geology is a primary cause of differences across the State. Examples of chemical associations in water suggest that chemical analyses may be valuable in tracing and identifying mineral deposits.

Comparing spatially explicit ecological and social values for natural areas to identify effective conservation strategies.

PubMed

Bryan, Brett Anthony; Raymond, Christopher Mark; Crossman, Neville David; King, Darran

2011-02-01

Consideration of the social values people assign to relatively undisturbed native ecosystems is critical for the success of science-based conservation plans. We used an interview process to identify and map social values assigned to 31 ecosystem services provided by natural areas in an agricultural landscape in southern Australia. We then modeled the spatial distribution of 12 components of ecological value commonly used in setting spatial conservation priorities. We used the analytical hierarchy process to weight these components and used multiattribute utility theory to combine them into a single spatial layer of ecological value. Social values assigned to natural areas were negatively correlated with ecological values overall, but were positively correlated with some components of ecological value. In terms of the spatial distribution of values, people valued protected areas, whereas those natural areas underrepresented in the reserve system were of higher ecological value. The habitats of threatened animal species were assigned both high ecological value and high social value. Only small areas were assigned both high ecological value and high social value in the study area, whereas large areas of high ecological value were of low social value, and vice versa. We used the assigned ecological and social values to identify different conservation strategies (e.g., information sharing, community engagement, incentive payments) that may be effective for specific areas. We suggest that consideration of both ecological and social values in selection of conservation strategies can enhance the success of science-based conservation planning. ©2010 Society for Conservation Biology.

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

PubMed Central

Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

2014-01-01

The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782

Natural variation in maternal care and cross-tissue patterns of oxytocin receptor gene methylation in rats

PubMed Central

Beery, Annaliese K.; McEwen, Lisa M.; MacIsaac, Julia L; Francis, Darlene D.; Kobor, Michael S.

2015-01-01

Since the first report of maternal care effects on DNA methylation in rats, epigenetic modifications of the genome in response to life experience have become the subject of intense focus across many disciplines. Oxytocin receptor expression varies in response to early experience, and both oxytocin signaling and methylation status of the oxytocin receptor gene (Oxtr) in blood have been related to disordered social behavior. It is unknown whether Oxtr methylation varies in response to early life experience, and whether currently employed peripheral measures of Oxtr methylation reflect variation in the brain. We examined the effects of early life rearing experience via natural variation in maternal licking and grooming during the first week of life on behavior, physiology, gene expression, and epigenetic regulation of Oxtr across blood and brain tissues (mononucleocytes, hippocampus, striatum, and hypothalamus). Rats reared by “high” licking-grooming (HL) and “low” licking-grooming (LL) rat dams exhibited differences across study outcomes: LL offspring were more active in behavioral arenas, exhibited lower body mass in adulthood, and showed reduced corticosterone responsivity to a stressor. Oxtr methylation was significantly lower at multiple CpGs in the blood of LL versus HL rats, but no differences were found in the brain. Across groups, Oxtr transcript levels in the hypothalamus were associated with reduced corticosterone secretion in response to stress, congruent with the role of oxytocin signaling in this region. Methylation of specific CpGs at a high or low level was consistent across tissues, especially within the brain. However, individual variation in methylation relative to these global patterns was not consistent across tissues. These results suggest that blood Oxtr methylation may reflect early experience of maternal care, and that Oxtr methylation across tissues is highly concordant for specific CpGs, but that inferences across tissues are not

Using natural language processing to identify problem usage of prescription opioids.

PubMed

Carrell, David S; Cronkite, David; Palmer, Roy E; Saunders, Kathleen; Gross, David E; Masters, Elizabeth T; Hylan, Timothy R; Von Korff, Michael

2015-12-01

Accurate and scalable surveillance methods are critical to understand widespread problems associated with misuse and abuse of prescription opioids and for implementing effective prevention and control measures. Traditional diagnostic coding incompletely documents problem use. Relevant information for each patient is often obscured in vast amounts of clinical text. We developed and evaluated a method that combines natural language processing (NLP) and computer-assisted manual review of clinical notes to identify evidence of problem opioid use in electronic health records (EHRs). We used the EHR data and text of 22,142 patients receiving chronic opioid therapy (≥70 days' supply of opioids per calendar quarter) during 2006-2012 to develop and evaluate an NLP-based surveillance method and compare it to traditional methods based on International Classification of Disease, Ninth Edition (ICD-9) codes. We developed a 1288-term dictionary for clinician mentions of opioid addiction, abuse, misuse or overuse, and an NLP system to identify these mentions in unstructured text. The system distinguished affirmative mentions from those that were negated or otherwise qualified. We applied this system to 7336,445 electronic chart notes of the 22,142 patients. Trained abstractors using a custom computer-assisted software interface manually reviewed 7751 chart notes (from 3156 patients) selected by the NLP system and classified each note as to whether or not it contained textual evidence of problem opioid use. Traditional diagnostic codes for problem opioid use were found for 2240 (10.1%) patients. NLP-assisted manual review identified an additional 728 (3.1%) patients with evidence of clinically diagnosed problem opioid use in clinical notes. Inter-rater reliability among pairs of abstractors reviewing notes was high, with kappa=0.86 and 97% agreement for one pair, and kappa=0.71 and 88% agreement for another pair. Scalable, semi-automated NLP methods can efficiently and

Identifying Falls Risk Screenings Not Documented with Administrative Codes Using Natural Language Processing

PubMed Central

Zhu, Vivienne J; Walker, Tina D; Warren, Robert W; Jenny, Peggy B; Meystre, Stephane; Lenert, Leslie A

2017-01-01

Quality reporting that relies on coded administrative data alone may not completely and accurately depict providers’ performance. To assess this concern with a test case, we developed and evaluated a natural language processing (NLP) approach to identify falls risk screenings documented in clinical notes of patients without coded falls risk screening data. Extracting information from 1,558 clinical notes (mainly progress notes) from 144 eligible patients, we generated a lexicon of 38 keywords relevant to falls risk screening, 26 terms for pre-negation, and 35 terms for post-negation. The NLP algorithm identified 62 (out of the 144) patients who falls risk screening documented only in clinical notes and not coded. Manual review confirmed 59 patients as true positives and 77 patients as true negatives. Our NLP approach scored 0.92 for precision, 0.95 for recall, and 0.93 for F-measure. These results support the concept of utilizing NLP to enhance healthcare quality reporting. PMID:29854264

Simple Sequence Repeats Provide a Substrate for Phenotypic Variation in the Neurospora crassa Circadian Clock

PubMed Central

Michael, Todd P.; Park, Sohyun; Kim, Tae-Sung; Booth, Jim; Byer, Amanda; Sun, Qi; Chory, Joanne; Lee, Kwangwon

2007-01-01

Background WHITE COLLAR-1 (WC-1) mediates interactions between the circadian clock and the environment by acting as both a core clock component and as a blue light photoreceptor in Neurospora crassa. Loss of the amino-terminal polyglutamine (NpolyQ) domain in WC-1 results in an arrhythmic circadian clock; this data is consistent with this simple sequence repeat (SSR) being essential for clock function. Methodology/Principal Findings Since SSRs are often polymorphic in length across natural populations, we reasoned that investigating natural variation of the WC-1 NpolyQ may provide insight into its role in the circadian clock. We observed significant phenotypic variation in the period, phase and temperature compensation of circadian regulated asexual conidiation across 143 N. crassa accessions. In addition to the NpolyQ, we identified two other simple sequence repeats in WC-1. The sizes of all three WC-1 SSRs correlated with polymorphisms in other clock genes, latitude and circadian period length. Furthermore, in a cross between two N. crassa accessions, the WC-1 NpolyQ co-segregated with period length. Conclusions/Significance Natural variation of the WC-1 NpolyQ suggests a mechanism by which period length can be varied and selected for by the local environment that does not deleteriously affect WC-1 activity. Understanding natural variation in the N. crassa circadian clock will facilitate an understanding of how fungi exploit their environments. PMID:17726525

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

PubMed

Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske

2012-11-01

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

ESTIMATING WELFARE IN INSURANCE MARKETS USING VARIATION IN PRICES*

PubMed Central

Einav, Liran; Finkelstein, Amy; Cullen, Mark R.

2009-01-01

We provide a graphical illustration of how standard consumer and producer theory can be used to quantify the welfare loss associated with inefficient pricing in insurance markets with selection. We then show how this welfare loss can be estimated empirically using identifying variation in the price of insurance. Such variation, together with quantity data, allows us to estimate the demand for insurance. The same variation, together with cost data, allows us to estimate how insurer’s costs vary as market participants endogenously respond to price. The slope of this estimated cost curve provides a direct test for both the existence and nature of selection, and the combination of demand and cost curves can be used to estimate welfare. We illustrate our approach by applying it to data on employer-provided health insurance from one specific company. We detect adverse selection but estimate that the quantitative welfare implications associated with inefficient pricing in our particular application are small, in both absolute and relative terms. PMID:21218182

Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.

PubMed

Francisco, Marta; Joseph, Bindu; Caligagan, Hart; Li, Baohua; Corwin, Jason A; Lin, Catherine; Kerwin, Rachel E; Burow, Meike; Kliebenstein, Daniel J

2016-01-01

A key limitation in modern biology is the ability to rapidly identify genes underlying newly identified complex phenotypes. Genome wide association studies (GWAS) have become an increasingly important approach for dissecting natural variation by associating phenotypes with genotypes at a genome wide level. Recent work is showing that the Arabidopsis thaliana defense metabolite, allyl glucosinolate (GSL), may provide direct feedback regulation, linking defense metabolism outputs to the growth, and defense responses of the plant. However, there is still a need to identify genes that underlie this process. To start developing a deeper understanding of the mechanism(s) that modulate the ability of exogenous allyl GSL to alter growth and defense, we measured changes in plant biomass and defense metabolites in a collection of natural 96 A. thaliana accessions fed with 50 μM of allyl GSL. Exogenous allyl GSL was introduced exclusively to the roots and the compound transported to the leaf leading to a wide range of heritable effects upon plant biomass and endogenous GSL accumulation. Using natural variation we conducted GWAS to identify a number of new genes which potentially control allyl responses in various plant processes. This is one of the first instances in which this approach has been successfully utilized to begin dissecting a novel phenotype to the underlying molecular/polygenic basis.

Genetic Variation and Adaptation in Africa: Implications for Human Evolution and Disease

PubMed Central

Gomez, Felicia; Hirbo, Jibril; Tishkoff, Sarah A.

2014-01-01

Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent. PMID:24984772

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño

PubMed Central

González-Segovia, Eric; Ross-Ibarra, Jeffrey; Simpson, June K.

2017-01-01

Background Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions. Methods Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments. Results A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates. Discussion Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network

PubMed Central

Kozlov, Konstantin N.; Kulakovskiy, Ivan V.; Zubair, Asif; Marjoram, Paul; Lawrie, David S.; Nuzhdin, Sergey V.; Samsonova, Maria G.

2017-01-01

Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression. The analysis reveals that the sequence variants increase (decrease) gene expression if located within binding sites of repressors (activators). We show that the sign of SNP influence (activation or repression) may change in time and space and elucidate the origin of this change in specific examples. The thermodynamic modeling approach predicts non-local and non-linear effects arising from SNPs, and combinations of SNPs, in individual fly genotypes. Simulation of individual fly genotypes using our model reveals that this non-linearity reduces to almost additive inputs from multiple SNPs. Further, we see signatures of the action of purifying selection in the gap gene regulatory regions. To infer the specific targets of purifying selection, we analyze the patterns of polymorphism in the data at two phenotypic levels: the strengths of binding and expression. We find that combinations of SNPs show evidence of being under selective pressure, while individual SNPs do not. The model predicts that SNPs appear to accumulate in the genotypes of the natural population in a way biased towards small increases in activating action on the expression pattern. Taken together, these results provide a systems-level view of how genetic variation translates to the level of gene regulatory networks via combinatorial SNP effects. PMID:28898266

Identifying Potential Regions of Copy Number Variation for Bipolar Disorder

PubMed Central

Chen, Yi-Hsuan; Lu, Ru-Band; Hung, Hung; Kuo, Po-Hsiu

2014-01-01

Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions. PMID:27605030

Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation.

PubMed

Gao, Lexuan; Geng, Yupeng; Li, Bo; Chen, Jiakuan; Yang, Ji

2010-11-01

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome-wide methylation profiling using methylation-sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome-wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors. © 2010 Blackwell Publishing Ltd.

Natural Variation of Root Hydraulics in Arabidopsis Grown in Normal and Salt-Stressed Conditions1[C][W

PubMed Central

Sutka, Moira; Li, Guowei; Boudet, Julie; Boursiac, Yann; Doumas, Patrick; Maurel, Christophe

2011-01-01

To gain insights into the natural variation of root hydraulics and its molecular components, genotypic differences related to root water transport and plasma membrane intrinsic protein (PIP) aquaporin expression were investigated in 13 natural accessions of Arabidopsis (Arabidopsis thaliana). The hydraulic conductivity of excised root systems (Lpr) showed a 2-fold variation among accessions. The contribution of aquaporins to water uptake was characterized using as inhibitors mercury, propionic acid, and azide. The aquaporin-dependent and -independent paths of water transport made variable contributions to the total hydraulic conductivity in the different accessions. The distinct suberization patterns observed among accessions were not correlated with their root hydraulic properties. Real-time reverse transcription-polymerase chain reaction revealed, by contrast, a positive overall correlation between Lpr and certain highly expressed PIP transcripts. Root hydraulic responses to salt stress were characterized in a subset of five accessions (Bulhary-1, Catania-1, Columbia-0, Dijon-M, and Monte-Tosso-0 [Mr-0]). Lpr was down-regulated in all accessions except Mr-0. In Mr-0 and Catania-1, cortical cell hydraulic conductivity was unresponsive to salt, whereas it was down-regulated in the three other accessions. By contrast, the five accessions showed qualitatively similar aquaporin transcriptional profiles in response to salt. The overall work provides clues on how hydraulic regulation allows plant adaptation to salt stress. It also shows that a wide range of root hydraulic profiles, as previously reported in various species, can be observed in a single model species. This work paves the way for a quantitative genetics analysis of root hydraulics. PMID:21212301

Genomic regions controlling shape variation in the first upper molar of the house mouse

PubMed Central

Pantalacci, Sophie; Turner, Leslie M; Steingrimsson, Eirikur; Renaud, Sabrina

2017-01-01

Numerous loci of large effect have been shown to underlie phenotypic variation between species. However, loci with subtle effects are presumably more frequently involved in microevolutionary processes but have rarely been discovered. We explore the genetic basis of shape variation in the first upper molar of hybrid mice between Mus musculus musculus and M. m. domesticus. We performed the first genome-wide association study for molar shape and used 3D surface morphometrics to quantify subtle variation between individuals. We show that many loci of small effect underlie phenotypic variation, and identify five genomic regions associated with tooth shape; one region contained the gene microphthalmia-associated transcription factor Mitf that has previously been associated with tooth malformations. Using a panel of five mutant laboratory strains, we show the effect of the Mitf gene on tooth shape. This is the first report of a gene causing subtle but consistent variation in tooth shape resembling variation in nature. PMID:29091026

EPA's EnviroAtlas: Identifying Nature's benefits, deficits, and ...

EPA Pesticide Factsheets

Cities, towns, and Tribes rely on clean air, water and other natural resources for public health and well-being. Yet natural infrastructure and its benefits are not always fully understood or considered in local decisions. EnviroAtlas is a free, online, easy-to-use mapping toolkit designed for citizens, analysts, and decision-makers to assess the status of local and regional “green” assets, their relevance to society, current threats, and future opportunities. Research-based maps, analysis tools, and descriptive information address seven environmental benefit categories: - Clean air - Clean and plentiful water - Natural hazard mitigation - Climate stabilization - Recreation, culture, and aesthetics - Food, fuel, and materials - Biodiversity conservation More than 300 datasets for the coterminous U.S. summarize ecosystem processes, stressors, and end users at the spatial scale of sub-watersheds (n = ~90,000). A fine-scale component for selected communities features one-meter resolution landcover data and ~100 “green infrastructure” maps summarized by census block-group. Demographic data and built environment metrics are integrated into some of these maps, and are also provided by block group for overlays and other analyses. Numerous pixel-level maps are available as well. Map layers are consistent across EnviroAtlas communities; 18 of these are currently online, with six communities added annually. EnviroAtlas community maps and information addr

Sample preparation techniques for the determination of natural 15N/14N variations in amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS).

PubMed

Hofmann, D; Gehre, M; Jung, K

2003-09-01

In order to identify natural nitrogen isotope variations of biologically important amino acids four derivatization reactions (t-butylmethylsilylation, esterification with subsequent trifluoroacetylation, acetylation and pivaloylation) were tested with standard mixtures of 17 proteinogenic amino acids and plant (moss) samples using GC-C-IRMS. The possible fractionation of the nitrogen isotopes, caused for instance by the formation of multiple reaction products, was investigated. For biological samples, the esterification of the amino acids with subsequent trifluoroacetylation is recommended for nitrogen isotope ratio analysis. A sample preparation technique is described for the isotope ratio mass spectrometric analysis of amino acids from the non-protein (NPN) fraction of terrestrial moss. 14N/15N ratios from moss (Scleropodium spec.) samples from different anthropogenically polluted areas were studied with respect to ecotoxicologal bioindication.

Deep Resequencing Unveils Genetic Architecture of ADIPOQ and Identifies a Novel Low-Frequency Variant Strongly Associated With Adiponectin Variation

PubMed Central

Warren, Liling L.; Li, Li; Nelson, Matthew R.; Ehm, Margaret G.; Shen, Judong; Fraser, Dana J.; Aponte, Jennifer L.; Nangle, Keith L.; Slater, Andrew J.; Woollard, Peter M.; Hall, Matt D.; Topp, Simon D.; Yuan, Xin; Cardon, Lon R.; Chissoe, Stephanie L.; Mooser, Vincent; Morris, Andrew D.; Palmer, Colin N.A.; Perry, John R.; Frayling, Timothy M.; Whittaker, John C.; Waterworth, Dawn M.

2012-01-01

Increased adiponectin levels have been shown to be associated with a lower risk of type 2 diabetes. To understand the relations between genetic variation at the adiponectin-encoding gene, ADIPOQ, and adiponectin levels, and subsequently its role in disease, we conducted a deep resequencing experiment of ADIPOQ in 14,002 subjects, including 12,514 Europeans, 594 African Americans, and 567 Indian Asians. We identified 296 single nucleotide polymorphisms (SNPs), including 30 amino acid changes, and carried out association analyses in a subset of 3,665 subjects from two independent studies. We confirmed multiple genome-wide association study findings and identified a novel association between a low-frequency SNP (rs17366653) and adiponectin levels (P = 2.2E–17). We show that seven SNPs exert independent effects on adiponectin levels. Together, they explained 6% of adiponectin variation in our samples. We subsequently assessed association between these SNPs and type 2 diabetes in the Genetics of Diabetes Audit and Research in Tayside Scotland (GO-DARTS) study, comprised of 5,145 case and 6,374 control subjects. No evidence of association with type 2 diabetes was found, but we were also unable to exclude the possibility of substantial effects (e.g., odds ratio 95% CI for rs7366653 [0.91–1.58]). Further investigation by large-scale and well-powered Mendelian randomization studies is warranted. PMID:22403302

Genetic variation in California oaks

Treesearch

Constance I. Millar; Diane L. Delany; Lawrence A. Riggs

1990-01-01

In forestry the importance of genetic variation for successful reproduction, survival and growth has been widely documented for commercial conifers; until recently, little genetic work has been done on the California oaks. Even before the nature of genetic variation was scientifically investigated, its importance was suspected in operational forestry. Many failures of...

Novel quality indicators for metastatic colorectal cancer management identify significant variations in these measures across treatment centers in Australia.

PubMed

Turner, Natalie Heather; Wong, Hui-Li; Field, Kathryn; Wong, Rachel; Shapiro, Jeremy; Yip, Desmond; Nott, Louise; Tie, Jeanne; Kosmider, Suzanne; Tran, Ben; Desai, Jayesh; McKendrick, Joseph; Zimet, Allan; Richardson, Gary; Iddawela, Mahesh; Gibbs, Peter

2015-09-01

Defining multidisciplinary quality of care indicators (QCIs) for metastatic colorectal cancer (mCRC) could improve understanding of variations in routine practice care. This may identify areas of below-average performance, which could then be addressed by clinicians to improve the quality of care delivered. This study aimed to define a panel of QCIs in mCRC and, based on these QCIs, to evaluate quality of care across multiple Australian sites. A panel of clinicians with expertise in colorectal cancer defined evidence-based or best practice-based QCIs relevant to the routine multidisciplinary management of mCRC patients through structured consensus discussion. Related data were extracted from the Treatment of Recurrent and Advanced Colorectal Cancer (TRACC) registry, a prospectively maintained database recording comprehensive details on consecutive mCRC patients across multiple Australian hospitals. Variations in QCIs across sites were explored. Of 13 QCIs defined, data related to 10 were reliably extracted from TRACC. Analysis of data on 1276 patients across 10 sites demonstrated low rates of screening for hereditary nonpolyposis colorectal cancer in young patients and significant variation in surveillance-detected recurrences, lung resection rates and palliative chemotherapy use. Exploratory analyses suggested correlation between liver resection rates and survival. We have defined a novel set of mCRC QCIs and have demonstrated wide variation in the quality of care of mCRC across multiple Australian sites. With further validation to confirm a direct correlation between QCI and patient outcomes, these QCIs could be applied to improve the quality of care received by all mCRC patients. © 2015 Wiley Publishing Asia Pty Ltd.

Defining the consequences of genetic variation on a proteome–wide scale

PubMed Central

Chick, Joel M.; Munger, Steven C.; Simecek, Petr; Huttlin, Edward L.; Choi, Kwangbom; Gatti, Daniel M.; Raghupathy, Narayanan; Svenson, Karen L.; Churchill, Gary A.; Gygi, Steven P.

2016-01-01

Genetic variation modulates protein expression through both transcriptional and post-transcriptional mechanisms. To characterize the consequences of natural genetic diversity on the proteome, here we combine a multiplexed, mass spectrometry-based method for protein quantification with an emerging outbred mouse model containing extensive genetic variation from eight inbred founder strains. By measuring genome-wide transcript and protein expression in livers from 192 Diversity outbred mice, we identify 2,866 protein quantitative trait loci (pQTL) with twice as many local as distant genetic variants. These data support distinct transcriptional and post-transcriptional models underlying the observed pQTL effects. Using a sensitive approach to mediation analysis, we often identified a second protein or transcript as the causal mediator of distant pQTL. Our analysis reveals an extensive network of direct protein–protein interactions. Finally, we show that local genotype can provide accurate predictions of protein abundance in an independent cohort of collaborative cross mice. PMID:27309819

Identifying Repetitive Institutional Review Board Stipulations by Natural Language Processing and Network Analysis.

PubMed

Kury, Fabrício S P; Cimino, James J

2015-01-01

The corrections ("stipulations") to a proposed research study protocol produced by an institutional review board (IRB) can often be repetitive across many studies; however, there is no standard set of stipulations that could be used, for example, by researchers wishing to anticipate and correct problems in their research proposals prior to submitting to an IRB. The objective of the research was to computationally identify the most repetitive types of stipulations generated in the course of IRB deliberations. The text of each stipulation was normalized using the natural language processing techniques. An undirected weighted network was constructed in which each stipulation was represented by a node, and each link, if present, had weight corresponding to the TF-IDF Cosine Similarity of the stipulations. Network analysis software was then used to identify clusters in the network representing similar stipulations. The final results were correlated with additional data to produce further insights about the IRB workflow. From a corpus of 18,582 stipulations we identified 31 types of repetitive stipulations. Those types accounted for 3,870 stipulations (20.8% of the corpus) produced for 697 (88.7%) of all protocols in 392 (also 88.7%) of all the CNS IRB meetings with stipulations entered in our data source. A notable peroportion of the corrections produced by the IRB can be considered highly repetitive. Our shareable method relied on a minimal manual analysis and provides an intuitive exploration with theoretically unbounded granularity. Finer granularity allowed for the insight that is anticipated to prevent the need for identifying the IRB panel expertise or any human supervision.

Genetic variation affecting host-parasite interactions: major-effect quantitative trait loci affect the transmission of sigma virus in Drosophila melanogaster.

PubMed

Bangham, Jenny; Knott, Sara A; Kim, Kang-Wook; Young, Robert S; Jiggins, Francis M

2008-09-01

In natural populations, genetic variation affects resistance to disease. Whether that genetic variation comprises lots of small-effect polymorphisms or a small number of large-effect polymorphisms has implications for adaptation, selection and how genetic variation is maintained in populations. Furthermore, how much genetic variation there is, and the genes that underlie this variation, affects models of co-evolution between parasites and their hosts. We are studying the genetic variation that affects the resistance of Drosophila melanogaster to its natural pathogen--the vertically transmitted sigma virus. We have carried out three separate quantitative trait locus mapping analyses to map gene variants on the second chromosome that cause variation in the rate at which males transmit the infection to their offspring. All three crosses identified a locus in a similar chromosomal location that causes a large drop in the rate at which the virus is transmitted. We also found evidence for an additional smaller-effect quantitative trait locus elsewhere on the chromosome. Our data, together with previous experiments on the sigma virus and parasitoid wasps, indicate that the resistance of D. melanogaster to co-evolved pathogens is controlled by a limited number of major-effect polymorphisms.

3D-Analysis of a non-planispiral ammonoid from the Hunsrück Slate: natural or pathological variation?

PubMed Central

Stilkerich, Julia; Smrecak, Trisha A.

2017-01-01

We herein examine the only known non-planispirally coiled early Devonian ammonoid, the holotype specimen of Ivoites opitzi, to investigate if the host was encrusted in vivo and if these sclerobionts were responsible for the trochospiral coiling observed in this unique specimen. To test if the presence of runner-like sclerobionts infested the historically collected specimen of Ivoites opitzi during its life, we used microCT to produce a three-dimensional model of the surface of the specimen. Our results indicate that sclerobionts grew across the outer rim (venter) on both sides of the ammonoid conch at exactly the location where the deviation from the planispiral was recognized, and where subsequent ammonoid growth would likely preclude encrustation. This indicates in vivo encrustation of the I. opitzi specimen, and represents the earliest documentation of the phenomenon. Further, this suggests that non-planispiral coiling in I. opitzi was likely pathologically induced and does not represent natural morphological variation in the species. Despite the observed anomalies in coiling, the specimen reached adulthood and retains important identifying morphological features, suggesting the ammonoid was minimally impacted by encrustation in life. As such, appointing a new type specimen—as suggested by some authors—for the species is not necessary. In addition, we identify the sclerobionts responsible for modifying the coiling of this specimen as hederelloids, a peculiar group of sclerobionts likely related to phoronids. Hederelloids in the Devonian are commonly found encrusting on fossils collected in moderately deep environments within the photic zone and are rarely documented in dysphotic and aphotic samples. This indicates that when the ammonoid was encrusted it lived within the euphotic zone and supports the latest interpretations of the Hunsrück Slate depositional environment in the Bundenbach-Gemünden area. PMID:28674668

Investigating Variation, Teacher's Edition. Probing the Natural World/3.

ERIC Educational Resources Information Center

Florida State Univ., Tallahassee. Dept. of Science Education.

The teacher's edition for the unit entitled "Investigating Variation" in Intermediate Science Curriculum Study Level III, provides numerous suggestions for teaching specific activities included in the unit. The unit is aimed at selected aspects of measurement and analysis. The chapters included are "The Road…

Natural variation in maternal care and cross-tissue patterns of oxytocin receptor gene methylation in rats.

PubMed

Beery, Annaliese K; McEwen, Lisa M; MacIsaac, Julia L; Francis, Darlene D; Kobor, Michael S

2016-01-01

This article is part of a Special Issue "Parental Care". Since the first report of maternal care effects on DNA methylation in rats, epigenetic modifications of the genome in response to life experience have become the subject of intense focus across many disciplines. Oxytocin receptor expression varies in response to early experience, and both oxytocin signaling and methylation status of the oxytocin receptor gene (Oxtr) in blood have been related to disordered social behavior. It is unknown whether Oxtr DNA methylation varies in response to early life experience, and whether currently employed peripheral measures of Oxtr methylation reflect variation in the brain. We examined the effects of early life rearing experience via natural variation in maternal licking and grooming during the first week of life on behavior, physiology, gene expression, and epigenetic regulation of Oxtr across blood and brain tissues (mononucleocytes, hippocampus, striatum, and hypothalamus). Rats reared by "high" licking-grooming (HL) and "low" licking-grooming (LL) rat dams exhibited differences across study outcomes: LL offspring were more active in behavioral arenas, exhibited lower body mass in adulthood, and showed reduced corticosterone responsivity to a stressor. Oxtr DNA methylation was significantly lower at multiple CpGs in the blood of LL versus HL males, but no differences were found in the brain. Across groups, Oxtr transcript levels in the hypothalamus were associated with reduced corticosterone secretion in response to stress, congruent with the role of oxytocin signaling in this region. Methylation of specific CpGs at a high or low level was consistent across tissues, especially within the brain. However, individual variation in DNA methylation relative to these global patterns was not consistent across tissues. These results suggest that blood Oxtr DNA methylation may reflect early experience of maternal care, and that Oxtr methylation across tissues is highly concordant

Can natural variation in grain P concentrations be exploited in rice breeding to lower fertilizer requirements?

PubMed

Wang, Fanmiao; King, James Douglas Morrison; Rose, Terry; Kretzschmar, Tobias; Wissuwa, Matthias

2017-01-01

Agricultural usage of phosphorus (P) is largely driven by the amount of P removed from fields in harvested plant matter as offtake needs to be balanced by P fertilizer application. Reducing P concentration in grains is a way to decrease P offtake and reduce P fertilizer requirements or soil P mining where insufficient P is applied. Our objective was to assesses the genotypic variation for grain P concentration present within the rice gene pool and resolve to what extent it is affected by environment (P supply) or associated with genetic factors. About 2-fold variation in grain P concentrations were detected in two rice diversity panels, however, environmental effects were stronger than genotype effects. Genome wide association studies identified several putative loci associated with grain P concentrations. In most cases this was caused by minor haplotype associations with high grain P concentrations while associations with reduced P concentrations were identified on chromosomes 1, 6, 8, 11 and 12. Only the latter type of locus is of interest in breeding for reduced P concentrations and the most promising locus was at 20.7 Mb on chromosome 8, where a rare haplotype that was absent from all modern varieties studied reduced grain P concentration by 9.3%. This and all other loci were not consistently detected across environments or association panels, confirming that genetic effects were small compared to effects of environment. We conclude that the genetic effects detected were not sufficiently large or consistent to be of utility in plant breeding. Instead breeding efforts may have to rely on small to medium effect mutants already identified and attempt to achieve a more pronounced reduction in grain P concentration through the introgression of these mutants into a single genetic background.

Can natural variation in grain P concentrations be exploited in rice breeding to lower fertilizer requirements?

PubMed Central

Wang, Fanmiao; King, James Douglas Morrison; Rose, Terry; Kretzschmar, Tobias

2017-01-01

Agricultural usage of phosphorus (P) is largely driven by the amount of P removed from fields in harvested plant matter as offtake needs to be balanced by P fertilizer application. Reducing P concentration in grains is a way to decrease P offtake and reduce P fertilizer requirements or soil P mining where insufficient P is applied. Our objective was to assesses the genotypic variation for grain P concentration present within the rice gene pool and resolve to what extent it is affected by environment (P supply) or associated with genetic factors. About 2-fold variation in grain P concentrations were detected in two rice diversity panels, however, environmental effects were stronger than genotype effects. Genome wide association studies identified several putative loci associated with grain P concentrations. In most cases this was caused by minor haplotype associations with high grain P concentrations while associations with reduced P concentrations were identified on chromosomes 1, 6, 8, 11 and 12. Only the latter type of locus is of interest in breeding for reduced P concentrations and the most promising locus was at 20.7 Mb on chromosome 8, where a rare haplotype that was absent from all modern varieties studied reduced grain P concentration by 9.3%. This and all other loci were not consistently detected across environments or association panels, confirming that genetic effects were small compared to effects of environment. We conclude that the genetic effects detected were not sufficiently large or consistent to be of utility in plant breeding. Instead breeding efforts may have to rely on small to medium effect mutants already identified and attempt to achieve a more pronounced reduction in grain P concentration through the introgression of these mutants into a single genetic background. PMID:28651022

Metabolomics identifies a biological response to chronic low-dose natural uranium contamination in urine samples.

PubMed

Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Eric; Banzet, Nathalie; Defoort, Catherine; Bott, Romain; Dublineau, Isabelle; Aigueperse, Jocelyne; Gourmelon, Patrick; Martin, Jean-Charles; Souidi, Maâmar

2013-01-01

Because uranium is a natural element present in the earth's crust, the population may be chronically exposed to low doses of it through drinking water. Additionally, the military and civil uses of uranium can also lead to environmental dispersion that can result in high or low doses of acute or chronic exposure. Recent experimental data suggest this might lead to relatively innocuous biological reactions. The aim of this study was to assess the biological changes in rats caused by ingestion of natural uranium in drinking water with a mean daily intake of 2.7 mg/kg for 9 months and to identify potential biomarkers related to such a contamination. Subsequently, we observed no pathology and standard clinical tests were unable to distinguish between treated and untreated animals. Conversely, LC-MS metabolomics identified urine as an appropriate biofluid for discriminating the experimental groups. Of the 1,376 features detected in urine, the most discriminant were metabolites involved in tryptophan, nicotinate, and nicotinamide metabolic pathways. In particular, N -methylnicotinamide, which was found at a level seven times higher in untreated than in contaminated rats, had the greatest discriminating power. These novel results establish a proof of principle for using metabolomics to address chronic low-dose uranium contamination. They open interesting perspectives for understanding the underlying biological mechanisms and designing a diagnostic test of exposure.

Copy Number Variations in Tilapia Genomes.

PubMed

Li, Bi Jun; Li, Hong Lian; Meng, Zining; Zhang, Yong; Lin, Haoran; Yue, Gen Hua; Xia, Jun Hong

2017-02-01

Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs. These CNVs account for 1.9% (12.411 Mb) of the used Nile tilapia reference genome. A total of 1100 predicted CNVs were found overlapping with exon regions of protein genes. Further association analysis based on linear model regression found 85 CNVs ranging between 300 and 27,000 base pairs significantly associated to population types (R 2  > 0.9 and P > 0.001). Our study sheds first insights on genome-wide CNVs in tilapia. These CNVs among and within tilapia populations may have functional effects on phenotypes and specific adaptation to particular environments.

Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance

PubMed Central

Li, Jian-Yong; Liu, Jiping; Dong, Dekun; Jia, Xiaomin; McCouch, Susan R.; Kochian, Leon V.

2014-01-01

Aluminum (Al) toxicity is a major constraint for crop production on acid soils which compose ∼40% of arable land in the tropics and subtropics. Rice is the most Al-tolerant cereal crop and offers a good model for identifying Al tolerance genes and mechanisms. Here we investigated natural variation in the rice Nramp aluminum transporter (NRAT1) gene encoding a root plasma membrane Al uptake transporter previously hypothesized to underlie a unique Al tolerance mechanism. DNA sequence variation in the NRAT1 coding and regulatory regions was associated with changes in NRAT1 expression and NRAT1 Al transport properties. These sequence changes resulted in significant differences in Al tolerance that were found to be associated with changes in the Al content of root cell wall and cell sap in 24 representative rice lines from a rice association panel. Expression of the tolerant OsNRAT1 allele in yeast resulted in higher Al uptake than did the sensitive allele and conferred greater Al tolerance when expressed in transgenic Arabidopsis. These findings indicate that NRAT1 plays an important role in rice Al tolerance by reducing the level of toxic Al in the root cell wall and transporting Al into the root cell, where it is ultimately sequestered in the vacuole. Given its ability to enhance Al tolerance in rice and Arabidopsis, this work suggests that the NRAT1 gene or its orthologs may be useful tools for enhancing Al tolerance in a wide range of plant species. PMID:24728832

Usefulness of natural regions for lake management: Analysis of variation among lakes in northwestern Wisconsin, USA

NASA Astrophysics Data System (ADS)

Omernik, James M.; Rohm, Christina M.; Lillie, Richard A.; Mesner, Nancy

1991-03-01

A map of summer total phosphorus in lakes was compiled recently for a three-state area of the upper Midwest for purposes of identifying regional patterns of total phosphorus in lakes and attainable lake trophic state. Spatial patterns in total phosphorus from approximately 3000 lakes were studied in conjunction with maps of geographic characteristics that tend to affect phosphorus balance in lakes to identify regions of similarity in phosphorus concentrations in lakes or similarity in the mosaic of values as compared to adjacent areas. While degrees of relative homogeneity are apparent at many scales, the map was designed at a scale that would yield regions with sufficient homogeneity to be useful for lake management throughout the area. In this study, data from 210 lakes in a 1560-mi2 area in northwestern Wisconsin, sampled by the Wisconsin Department of Natural Resources in the spring of 1988 (subsequent to the compilation of the phosphorus map), were examined to: (1) substantiate the existence of the regions depicted on the map in northwest Wisconsin, (2) determine the nature and relative precision of the regional boundaries, (3) determine the relative importance of natural and anthropogenic watershed characteristics, lake types, lake area, and lake depth in explaining within-region differences in lake phosphorus, and (4) demonstrate how the regions might be used by local lake managers.

Variation in Sulfur and Selenium Accumulation Is Controlled by Naturally Occurring Isoforms of the Key Sulfur Assimilation Enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 across the Arabidopsis Species Range1[W][OPEN

PubMed Central

Chao, Dai-Yin; Baraniecka, Patrycja; Danku, John; Koprivova, Anna; Lahner, Brett; Luo, Hongbing; Yakubova, Elena; Dilkes, Brian; Kopriva, Stanislav; Salt, David E.

2014-01-01

Natural variation allows the investigation of both the fundamental functions of genes and their role in local adaptation. As one of the essential macronutrients, sulfur is vital for plant growth and development and also for crop yield and quality. Selenium and sulfur are assimilated by the same process, and although plants do not require selenium, plant-based selenium is an important source of this essential element for animals. Here, we report the use of linkage mapping in synthetic F2 populations and complementation to investigate the genetic architecture of variation in total leaf sulfur and selenium concentrations in a diverse set of Arabidopsis (Arabidopsis thaliana) accessions. We identify in accessions collected from Sweden and the Czech Republic two variants of the enzyme ADENOSINE 5′-PHOSPHOSULFATE REDUCTASE2 (APR2) with strongly diminished catalytic capacity. APR2 is a key enzyme in both sulfate and selenate reduction, and its reduced activity in the loss-of-function allele apr2-1 and the two Arabidopsis accessions Hodonín and Shahdara leads to a lowering of sulfur flux from sulfate into the reduced sulfur compounds, cysteine and glutathione, and into proteins, concomitant with an increase in the accumulation of sulfate in leaves. We conclude from our observation, and the previously identified weak allele of APR2 from the Shahdara accession collected in Tadjikistan, that the catalytic capacity of APR2 varies by 4 orders of magnitude across the Arabidopsis species range, driving significant differences in sulfur and selenium metabolism. The selective benefit, if any, of this large variation remains to be explored. PMID:25245030

Seasonal variations of natural ventilation and radon-222 exhalation in a slightly rising dead-end tunnel.

PubMed

Perrier, Frédéric; Richon, Patrick; Gautam, Umesh; Tiwari, Dilli Ram; Shrestha, Prithvi; Sapkota, Soma Nath

2007-01-01

The concentration activity of radon-222 has been monitored, with some interruptions, from 1997 to 2005 in the end section of a slightly rising, dead-end, 38-m long tunnel located in the Phulchoki hill, near Kathmandu, Nepal. While a high concentration varying from 6 x 10(3) Bq m(-3) to 10 x 10(3) Bq m(-3) is observed from May to September (rainy summer season), the concentration remains at a low level of about 200 Bq m(-3) from October to March (dry winter season). This reduction of radon concentration is associated with natural ventilation of the tunnel, which, contrary to expectations for a rising tunnel, takes place mainly from October to March when the outside air temperature drops below the average tunnel temperature. This interpretation is supported by temperature measurements in the atmosphere of the tunnel, a few meters away from the entrance. The temporal variations of the diurnal amplitude of this temperature indeed follow the ventilation rate deduced from the radon measurements. In the absence of significant ventilation (summer season), the radon exhalation flux at the rock surface into the tunnel atmosphere can be inferred; it exhibits a yearly variation with additional transient reductions associated with heavy rainfall, likely to be due to water infiltration. No effect of atmospheric pressure variations on the radon concentration is observed in this tunnel. This experiment illustrates how small differences in the location and geometry of a tunnel can lead to vastly different behaviours of the radon concentration versus time. This observation has consequences for the estimation of the dose rate and the practicability of radon monitoring for tectonic purposes in underground environments.

Essential oil variation among natural populations of Lavandula multifida L. (Lamiaceae).

PubMed

Chograni, Hnia; Zaouali, Yosr; Rajeb, Chayma; Boussaid, Mohamed

2010-04-01

Volatiles from twelve wild Tunisian populations of Lavandula multifida L. growing in different bioclimatic zones were assessed by GC (RI) and GC/MS. Thirty-six constituents, representing 83.48% of the total oil were identified. The major components at the species level were carvacrol (31.81%), beta-bisabolene (14.89%), and acrylic acid dodecyl ester (11.43%). These volatiles, together with alpha-pinene, were also the main compounds discriminating the populations. According to these dominant compounds, one chemotype was revealed, a carvacrol/beta-bisabolene/acrylic acid dodecyl ester chemotype. However, a significant variation among the populations was observed for the majority of the constituents. A high chemical-population structure, estimated both by principal component analysis (PCA) and unweighted pair group method with averaging (UPGMA) cluster analysis based on Euclidean distances, was observed. Both methods allowed separation of the populations in three groups defined rather by minor than by major compounds. The population groups were not strictly concordant with their bioclimatic or geographic location. Conservation strategies should concern all populations, because of their low size and their high level of destruction. Populations exhibiting particular compounds other than the major ones should be protected first.

Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses.

PubMed

Koçer, Zeynep A; Fan, Yiping; Huether, Robert; Obenauer, John; Webby, Richard J; Zhang, Jinghui; Webster, Robert G; Wu, Gang

2014-12-12

Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.

Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs.

PubMed

Campoli, Chiara; Shtaya, Munqez; Davis, Seth J; von Korff, Maria

2012-06-21

The circadian clock is an endogenous mechanism that coordinates biological processes with daily changes in the environment. In plants, circadian rhythms contribute to both agricultural productivity and evolutionary fitness. In barley, the photoperiod response regulator and flowering-time gene Ppd-H1 is orthologous to the Arabidopsis core-clock gene PRR7. However, relatively little is known about the role of Ppd-H1 and other components of the circadian clock in temperate crop species. In this study, we identified barley clock orthologs and tested the effects of natural genetic variation at Ppd-H1 on diurnal and circadian expression of clock and output genes from the photoperiod-response pathway. Barley clock orthologs HvCCA1, HvGI, HvPRR1, HvPRR37 (Ppd-H1), HvPRR73, HvPRR59 and HvPRR95 showed a high level of sequence similarity and conservation of diurnal and circadian expression patterns, when compared to Arabidopsis. The natural mutation at Ppd-H1 did not affect diurnal or circadian cycling of barley clock genes. However, the Ppd-H1 mutant was found to be arrhythmic under free-running conditions for the photoperiod-response genes HvCO1, HvCO2, and the MADS-box transcription factor and vernalization responsive gene Vrn-H1. We suggest that the described eudicot clock is largely conserved in the monocot barley. However, genetic differentiation within gene families and differences in the function of Ppd-H1 suggest evolutionary modification in the angiosperm clock. Our data indicates that natural variation at Ppd-H1 does not affect the expression level of clock genes, but controls photoperiodic output genes. Circadian control of Vrn-H1 in barley suggests that this vernalization responsive gene is also controlled by the photoperiod-response pathway. Structural and functional characterization of the barley circadian clock will set the basis for future studies of the adaptive significance of the circadian clock in Triticeae species.

Epigenetic variation, inheritance, and parent-of-origin effects of cytosine methylation in maize (Zea mays).

PubMed

Lauria, Massimiliano; Piccinini, Sara; Pirona, Raul; Lund, Gertrud; Viotti, Angelo; Motto, Mario

2014-03-01

Pure epigenetic variation, or epigenetic variation that is independent of genetic context, may provide a mechanism for phenotypic variation in the absence of DNA mutations. To estimate the extent of pure epigenetic variation within and across generations and to identify the DNA regions targeted, a group of eight plants derived from a highly inbred line of maize (Zea mays) was analyzed by the methylation-sensitive amplified polymorphism (MSAP) technique. We found that cytosine methylation (mC) differences among individuals accounted for up to 7.4% of CCGG sites investigated by MSAP. Of the differentially methylated fragments (DMFs) identified in the S0 generation, ∼12% were meiotically inherited for at least six generations. We show that meiotically heritable mC variation was consistently generated for an average of 0.5% CCGG sites per generation and that it largely occurred somatically. We provide evidence that mC variation can be established and inherited in a parent-of-origin manner, given that the paternal lineage is more prone to both forward and reverse mC changes. The molecular characterization of selected DMFs revealed that the variation was largely determined by CG methylation changes that map within gene regions. The expression analysis of genes overlapping with DMFs did not reveal an obvious correlation between mC variation and transcription, reinforcing the idea that the primary function of gene-body methylation is not to control gene expression. Because this study focuses on epigenetic variation in field-grown plants, the data presented herein pertain to spontaneous epigenetic changes of the maize genome in a natural context.

Epigenetic Variation, Inheritance, and Parent-of-Origin Effects of Cytosine Methylation in Maize (Zea mays)

PubMed Central

Lauria, Massimiliano; Piccinini, Sara; Pirona, Raul; Lund, Gertrud; Viotti, Angelo; Motto, Mario

2014-01-01

Pure epigenetic variation, or epigenetic variation that is independent of genetic context, may provide a mechanism for phenotypic variation in the absence of DNA mutations. To estimate the extent of pure epigenetic variation within and across generations and to identify the DNA regions targeted, a group of eight plants derived from a highly inbred line of maize (Zea mays) was analyzed by the methylation-sensitive amplified polymorphism (MSAP) technique. We found that cytosine methylation (mC) differences among individuals accounted for up to 7.4% of CCGG sites investigated by MSAP. Of the differentially methylated fragments (DMFs) identified in the S0 generation, ∼12% were meiotically inherited for at least six generations. We show that meiotically heritable mC variation was consistently generated for an average of 0.5% CCGG sites per generation and that it largely occurred somatically. We provide evidence that mC variation can be established and inherited in a parent-of-origin manner, given that the paternal lineage is more prone to both forward and reverse mC changes. The molecular characterization of selected DMFs revealed that the variation was largely determined by CG methylation changes that map within gene regions. The expression analysis of genes overlapping with DMFs did not reveal an obvious correlation between mC variation and transcription, reinforcing the idea that the primary function of gene-body methylation is not to control gene expression. Because this study focuses on epigenetic variation in field-grown plants, the data presented herein pertain to spontaneous epigenetic changes of the maize genome in a natural context. PMID:24374354

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation.

PubMed

Mayer, Melanie G; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J

2015-06-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains' pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for

Genetic and epigenetic variation in the lineage specification of regulatory T cells

PubMed Central

Arvey, Aaron; van der Veeken, Joris; Plitas, George; Rich, Stephen S; Concannon, Patrick; Rudensky, Alexander Y

2015-01-01

Regulatory T (Treg) cells, which suppress autoimmunity and other inflammatory states, are characterized by a distinct set of genetic elements controlling their gene expression. However, the extent of genetic and associated epigenetic variation in the Treg cell lineage and its possible relation to disease states in humans remain unknown. We explored evolutionary conservation of regulatory elements and natural human inter-individual epigenetic variation in Treg cells to identify the core transcriptional control program of lineage specification. Analysis of single nucleotide polymorphisms in core lineage-specific enhancers revealed disease associations, which were further corroborated by high-resolution genotyping to fine map causal polymorphisms in lineage-specific enhancers. Our findings suggest that a small set of regulatory elements specify the Treg lineage and that genetic variation in Treg cell-specific enhancers may alter Treg cell function contributing to polygenic disease. DOI: http://dx.doi.org/10.7554/eLife.07571.001 PMID:26510014

Next-generation sequencing identifies the natural killer cell microRNA transcriptome

PubMed Central

Fehniger, Todd A.; Wylie, Todd; Germino, Elizabeth; Leong, Jeffrey W.; Magrini, Vincent J.; Koul, Sunita; Keppel, Catherine R.; Schneider, Stephanie E.; Koboldt, Daniel C.; Sullivan, Ryan P.; Heinz, Michael E.; Crosby, Seth D.; Nagarajan, Rakesh; Ramsingh, Giridharan; Link, Daniel C.; Ley, Timothy J.; Mardis, Elaine R.

2010-01-01

Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates for mediating this control process. While the expression and importance of miRNAs in T and B lymphocytes have been established, little is known about miRNAs in NK cells. Here, we used two next-generation sequencing (NGS) platforms to define the miRNA transcriptomes of resting and cytokine-activated primary murine NK cells, with confirmation by quantitative real-time PCR (qRT-PCR) and microarrays. We delineate a bioinformatics analysis pipeline that identified 302 known and 21 novel mature miRNAs from sequences obtained from NK cell small RNA libraries. These miRNAs are expressed over a broad range and exhibit isomiR complexity, and a subset is differentially expressed following cytokine activation. Using these miRNA NGS data, miR-223 was identified as a mature miRNA present in resting NK cells with decreased expression following cytokine activation. Furthermore, we demonstrate that miR-223 specifically targets the 3′ untranslated region of murine GzmB in vitro, indicating that this miRNA may contribute to control of GzmB translation in resting NK cells. Thus, the sequenced NK cell miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology. PMID:20935160

Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus).

PubMed

Galarza, Juan A; Sánchez-Fernández, Beatriz; Fandos, Paulino; Soriguer, Ramón

2017-07-01

The current magnitude of big-game hunting has outpaced the natural growth of populations, making artificial breeding necessary to rapidly boost hunted populations. In this study, we evaluated if the rapid increase of red deer (Cervus elaphus) abundance, caused by the growing popularity of big-game hunting, has impacted the natural genetic diversity of the species. We compared several genetic diversity metrics between 37 fenced populations subject to intensive management and 21 wild free-ranging populations. We also included a historically protected population from a national park as a baseline for comparisons. Contrary to expectations, our results showed no significant differences in genetic diversity between wild and fenced populations. Relatively lower genetic diversity was observed in the protected population, although differences were not significant in most cases. Bottlenecks were detected in both wild and fenced populations, as well as in the protected population. Assignment tests identified individuals that did not belong to their population of origin, indicating anthropogenic movement. We discuss the most likely processes, which could have led to the observed high levels of genetic variability and lack of differentiation between wild and fenced populations and suggest cautionary points for future conservation. We illustrate our comparative approach in red deer. However, our results and interpretations can be largely applicable to most ungulates subject to big-game hunting as most of them share a common exploitation-recovery history as well as many ecological traits. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Natural variation in PTB1 regulates rice seed setting rate by controlling pollen tube growth.

PubMed

Li, Shuangcheng; Li, Wenbo; Huang, Bin; Cao, Xuemei; Zhou, Xingyu; Ye, Shumei; Li, Chengbo; Gao, Fengyan; Zou, Ting; Xie, Kailong; Ren, Yun; Ai, Peng; Tang, Yangfan; Li, Xuemei; Deng, Qiming; Wang, Shiquan; Zheng, Aiping; Zhu, Jun; Liu, Huainian; Wang, Lingxia; Li, Ping

2013-01-01

Grain number, panicle seed setting rate, panicle number and grain weight are the most important components of rice grain yield. To date, several genes related to grain weight, grain number and panicle number have been described in rice. However, no genes regulating the panicle seed setting rate have been functionally characterized. Here we show that the domestication-related POLLEN TUBE BLOCKED 1 (PTB1), a RING-type E3 ubiquitin ligase, positively regulates the rice panicle seed setting rate by promoting pollen tube growth. The natural variation in expression of PTB1 which is affected by the promoter haplotype and the environmental temperature, correlates with the rice panicle seed setting rate. Our results support the hypothesis that PTB1 is an important maternal sporophytic factor of pollen tube growth and a key modulator of the rice panicle seed setting rate. This finding has implications for the improvement of rice yield.

Natural ground-water quality in Michigan, 1974-87

USGS Publications Warehouse

Cummings, T. Ray

1989-01-01

Wide variations occur in the chemical and physical characteristics of natural groundwaters in Michigan. Dissolved-solids concentrations range from 20 to 76,000 mg/L. Waters having low dissolved-solids concentrations are calcium bicarbonate-type waters. Sodium, sulfate, and chloride increase as mineralization increases. Iron, aluminum, and titanium concentrations are higher at some locations than is common in most natural waters. Lead concentrations exceed U.S. Environmental Protection Agency 's primary drinking-water regulations at some locations in the northern part of the lower Peninsula. Generalized areal patterns of water-quality variability indicate that geology is a primary cause of differences across the State. Examples of chemical associations in water indicate that chemical analyses may be valuable in tracing and identifying mineral deposits.

Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.

PubMed

Przytycki, Pawel F; Singh, Mona

2017-08-25

A major aim of cancer genomics is to pinpoint which somatically mutated genes are involved in tumor initiation and progression. We introduce a new framework for uncovering cancer genes, differential mutation analysis, which compares the mutational profiles of genes across cancer genomes with their natural germline variation across healthy individuals. We present DiffMut, a fast and simple approach for differential mutational analysis, and demonstrate that it is more effective in discovering cancer genes than considerably more sophisticated approaches. We conclude that germline variation across healthy human genomes provides a powerful means for characterizing somatic mutation frequency and identifying cancer driver genes. DiffMut is available at https://github.com/Singh-Lab/Differential-Mutation-Analysis .

Environmental Drivers of Benthic Flux Variation and Ecosystem Functioning in Salish Sea and Northeast Pacific Sediments.

PubMed

Belley, Rénald; Snelgrove, Paul V R; Archambault, Philippe; Juniper, S Kim

2016-01-01

The upwelling of deep waters from the oxygen minimum zone in the Northeast Pacific from the continental slope to the shelf and into the Salish Sea during spring and summer offers a unique opportunity to study ecosystem functioning in the form of benthic fluxes along natural gradients. Using the ROV ROPOS we collected sediment cores from 10 sites in May and July 2011, and September 2013 to perform shipboard incubations and flux measurements. Specifically, we measured benthic fluxes of oxygen and nutrients to evaluate potential environmental drivers of benthic flux variation and ecosystem functioning along natural gradients of temperature and bottom water dissolved oxygen concentrations. The range of temperature and dissolved oxygen encountered across our study sites allowed us to apply a suite of multivariate analyses rarely used in flux studies to identify bottom water temperature as the primary environmental driver of benthic flux variation and organic matter remineralization. Redundancy analysis revealed that bottom water characteristics (temperature and dissolved oxygen), quality of organic matter (chl a:phaeo and C:N ratios) and sediment characteristics (mean grain size and porosity) explained 51.5% of benthic flux variation. Multivariate analyses identified significant spatial and temporal variation in benthic fluxes, demonstrating key differences between the Northeast Pacific and Salish Sea. Moreover, Northeast Pacific slope fluxes were generally lower than shelf fluxes. Spatial and temporal variation in benthic fluxes in the Salish Sea were driven primarily by differences in temperature and quality of organic matter on the seafloor following phytoplankton blooms. These results demonstrate the utility of multivariate approaches in differentiating among potential drivers of seafloor ecosystem functioning, and indicate that current and future predictive models of organic matter remineralization and ecosystem functioning of soft-muddy shelf and slope seafloor

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors.

PubMed

Kim, Hee Ryung; Duc, Nguyen Minh; Chung, Ka Young

2018-03-01

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Identifying cross-cultural variations in psychostimulant use for attention deficit hyperactivity disorder using linked data.

PubMed

Ghosh, Manonita; Holman, C D'Arcy J; Preen, David B

2017-01-01

To validate the association between country-of-birth and disparities in the stimulant use for ADHD among individuals in Western Australia. Using linked data, a population-based retrospective cohort of individuals admitted to hospital before age 25 years was followed through to identify having stimulants for ADHD in 2003-2007. Multivariate logistic and linear regressions were used to characterise associations between stimulants and country-of-birth, geographical remoteness and socioeconomic status. Of 679,645 individuals, 14,122 (2.1%) had a record of having stimulants for ADHD. Of these, 205 (1.5%) were born in Africa, Asia, Middle-East or South America, while 13,664 (96.8%) were born in Australia/New Zealand, Europe or North America. Individuals with traditionally non-Anglophonic backgrounds were around one-half as likely to have stimulants as individuals with Anglophonic backgrounds (OR = 0.53, 95% CI 0.46-0.61, p < 0.001). Non-Anglophones were an average of 2.7 years older than Anglophones at onset of having stimulants. Individuals from remote and disadvantaged backgrounds had stimulants at younger ages than individuals living in metropolitan areas and with least disadvantage. The results highlight the importance of identifying factors underlying cultural differences in stimulant treatment for ADHD. Improving awareness of cultural variations may foster trust and rapport between patients and clinicians, and so better facilitate the appropriate and effective treatment of ADHD for each patient.

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

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

Woods, Daniel P.; Bednarek, Ryland; Bouché, Frédéric

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time.more » A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.« less

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

DOE PAGES

Woods, Daniel P.; Bednarek, Ryland; Bouché, Frédéric; ...

2016-10-14

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time.more » A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.« less

Characteristic variations in reflectance of surface soils

NASA Technical Reports Server (NTRS)

Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

1982-01-01

Surface soil samples from a wide range of naturally occurring soils were obtained for the purpose of studying the characteristic variations in soil reflectance as these variations relate to other soil properties and soil classification. A total 485 soil samples from the U.S. and Brazil representing 30 suborders of the 10 orders of 'Soil Taxonomy' was examined. The spectral bidirectional reflectance factor was measured on uniformly moist soils over the 0.52 to 2.32 micron wavelength range with a spectroradiometer adapted for indoor use. Five distinct soil spectral reflectance curve forms were identified according to curve shape, the presence or absence of absorption bands, and the predominance of soil organic matter and iron oxide composition. These curve forms were further characterized according to generically homogeneous soil properties in a manner similar to the subdivisions at the suborder level of 'Soil Taxonomy'. Results indicate that spectroradiometric measurements of soil spectral bidirectional reflectance factor can be used to characterize soil reflectance in terms that are meaningful to soil classification, genesis, and survey.

NATURALIZATION OF U.S. IMMIGRANTS

PubMed Central

Woodrow-Lafield, Karen A.; Xu, Xiaohe; Kersen, Thomas; Poch, Bunnak

2008-01-01

The saga of U.S. immigrant naturalization is merely sketched for about 25 million immigrants entered in three decades of renewed immigration. This study documents naturalization outcomes for immigrants from ten major countries of origin, using administrative records on immigrants and naturalizations. Following the 1978-1987 admission cohorts for the first decade or more of permanent residence, this study finds significant covariate effects on the timing of naturalization by origin, mode of entry, and immigrant visa class, net other influences of demographic and background characteristics. Immigrants from the Philippines, Vietnam, and China, naturalized more quickly than immigrants from India, Korea, Cuba, Colombia, Jamaica, the Dominican Republic, and Mexico. Those who adjusted from statuses as nonimmigrants, refugees, or asylees became naturalized citizens more quickly. Those immigrants with employment-sponsorship naturalized faster than family-sponsored immigrants. Spouses of citizens, spouses of permanent residents, spouses of siblings of citizens, and spouses of sons and daughters of citizens naturalized faster than some other immigrants. Gender was not significant in the multivariate analysis but further research will more fully explore sex-specific variation in the timing of naturalization given likely variation in women’s representation by origin and admission categories. PMID:19122767

In situ monitoring of tracer tests: how to distinguish tracer recovery from natural background

NASA Astrophysics Data System (ADS)

Bailly-Comte, V.; Durepaire, X.; Batiot-Guilhe, C.; Schnegg, P.-A.

2018-03-01

Hydrogeological tracer tests are primarily conducted with fluorescent tracers. Field fluorometers make it possible to monitor tracers at very low concentrations (<1 ppb) and at high frequency. However, changes in natural fluorescence at a site resulting from variations of dissolved and suspended inorganic and organic material may compromise the measurement of useful signals, thereby limiting the chances of identifying or quantifying the real tracer recovery. An elevated natural signal can mask small concentrations of the tracer while its variability can give the impression of a false recovery. This article shows how the use of a combination of several continuous measurements at different wavelengths allows a better extraction of the natural signal. Field multispectral fluorometers were installed at two Mediterranean karst outlets; both drain carbonate systems but have different environmental conditions. The fluorometers functioned over several hydrologic cycles, in periods affected or not by artificial tracers, making it possible to observe natural signal variations at these sites. The optical properties of this type of field fluorometer were used to calculate the spectral response of the different optics of the measuring probe. These responses, superimposed on three-dimensional excitation/emission matrices produced from laboratory fluorescence measurements, allowed an understanding of what the fluorometer sees under natural flow conditions. The result is an innovative method for correcting artificial tracer results. This type of correction makes it possible to fine-tune the effect of natural background variation on tracer recovery curves for a clear identification of the tracer presence and a more precise quantification of its recovery.

Nature and causes of Quaternary climate variation of tropical South America

NASA Astrophysics Data System (ADS)

Baker, Paul A.; Fritz, Sherilyn C.

2015-09-01

This selective review of the Quaternary paleoclimate of the South American summer monsoon (SASM) domain presents viewpoints regarding a range of key issues in the field, many of which are unresolved and some of which are controversial. (1) El Niño-Southern Oscillation variability, while the most important global-scale mode of interannual climate variation, is insufficient to explain most of the variation of tropical South American climate observed in both the instrumental and the paleoclimate records. (2) Significant climate variation in tropical South America occurs on seasonal to orbital (i.e. multi-millennial) time scales as a result of sea-surface temperature (SST) variation and ocean-atmosphere interactions of the tropical Atlantic. (3) Decadal-scale climate variability, linked with this tropical Atlantic variability, has been a persistent characteristic of climate in tropical South America for at least the past half millennium, and likely, far beyond. (4) Centennial-to-millennial climate events in tropical South America were of longer duration and, perhaps, larger amplitude than any observed in the instrumental period, which is little more than a century long in tropical South America. These were superimposed upon both precession-paced insolation changes that caused significant variation in SASM precipitation and eccentricity-paced global glacial boundary conditions that caused significant changes in the tropical South American moisture balance. As a result, river sediment and water discharge increased and decreased across tropical South America, lake levels rose and fell, paleolakes arose and disappeared on the Altiplano, glaciers waxed and waned in the tropical Andes, and the tropical rainforest underwent significant changes in composition and extent. To further evaluate climate forcing over the last glacial cycle (˜125 ka), we developed a climate forcing model that combines summer insolation forcing and a proxy for North Atlantic SST forcing to

Type 2 diabetes mellitus disease risk genes identified by genome wide copy number variation scan in normal populations.

PubMed

Prabhanjan, Manasa; Suresh, Raviraj V; Murthy, Megha N; Ramachandra, Nallur B

2016-03-01

To identify the role of copy number variations (CNVs) on disease risk genes and its effect on disease phenotypes in type 2 diabetes mellitus (T2DM) in 12 random populations using high throughput arrays. CNV analysis was carried out on a total of 1715 individuals from 12 populations, from ArrayExpress Archive of the European Bioinformatics Institute along with our subjects using Affymetrix Genome Wide SNP 6.0 array. CNV effect on T2DM genes were analyzed using several bioinformatics tools and a molecular protein interaction network was constructed to identify the disease mechanism altered by the CNVs. Analysis showed 34.4% of the total population to be under CNV burden for T2DM, with 83 disease causal and associated genes being under CNV influence. Hotspots were identified on chromosomes 22, 12, 6, 19 and 11.Overlap studies with case cohorts revealed significant disease risk genes such as EGFR, E2F1, PPP1R3A, HLA and TSPAN8. CNVs play a significant role in predisposing T2DM in normal cohorts and contribute to the phenotypic effects. Thus, CNVs should be considered as one of the major contributors in predisposition of the disease. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Synthesis of Cycloprodigiosin Identifies the Natural Isolate as a Scalemic Mixture

DOE PAGES

Johnson, Rebecca E.; de Rond, Tristan; Lindsay, Vincent N. G.; ...

2015-07-17

We prepared the enantiomers of the natural product cycloprodigiosin using an expedient five-step synthetic sequence that takes advantage of a Schöllkopf–Barton–Zard (SBZ) pyrrole annulation with a chiral isocyanoacetate and a nitrocyclohexene derivative. Using chiral HPLC and X-ray crystallographic analyses of the synthetically prepared material and natural isolate (isolated from the marine bacterium Pseudoalteromonas rubra), naturally occurring cycloprodigiosin was determined to be a scalemic mixture occurring in an enantiomeric ratio of 83:17 (R)/(S) at C4'.

Synthesis of Cycloprodigiosin Identifies the Natural Isolate as a Scalemic Mixture

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

Johnson, Rebecca E.; de Rond, Tristan; Lindsay, Vincent N. G.

We prepared the enantiomers of the natural product cycloprodigiosin using an expedient five-step synthetic sequence that takes advantage of a Schöllkopf–Barton–Zard (SBZ) pyrrole annulation with a chiral isocyanoacetate and a nitrocyclohexene derivative. Using chiral HPLC and X-ray crystallographic analyses of the synthetically prepared material and natural isolate (isolated from the marine bacterium Pseudoalteromonas rubra), naturally occurring cycloprodigiosin was determined to be a scalemic mixture occurring in an enantiomeric ratio of 83:17 (R)/(S) at C4'.

Maize HapMap2 identifies extant variation from a genome in flux

USDA-ARS?s Scientific Manuscript database

The maize genome is the largest, most diverse and complex plant genome sequenced to date. Using high-throughput sequencing to access genetic variation and a population genetics model to score the polymorphisms, we characterize and unite the diversity of the world’s key breeding germplasm, wild rela...

Daily variation in natural disaster casualties: information flows, safety, and opportunity costs in tornado versus hurricane strikes.

PubMed

Zahran, Sammy; Tavani, Daniele; Weiler, Stephan

2013-07-01

Casualties from natural disasters may depend on the day of the week they strike. With data from the Spatial Hazard Events and Losses Database for the United States (SHELDUS), daily variation in hurricane and tornado casualties from 5,043 tornado and 2,455 hurricane time/place events is analyzed. Hurricane forecasts provide at-risk populations with considerable lead time. Such lead time allows strategic behavior in choosing protective measures under hurricane threat; opportunity costs in terms of lost income are higher during weekdays than during weekends. On the other hand, the lead time provided by tornadoes is near zero; hence tornados generate no opportunity costs. Tornado casualties are related to risk information flows, which are higher during workdays than during leisure periods, and are related to sheltering-in-place opportunities, which are better in permanent buildings like businesses and schools. Consistent with theoretical expectations, random effects negative binomial regression results indicate that tornado events occurring on the workdays of Monday through Thursday are significantly less lethal than tornados that occur on weekends. In direct contrast, and also consistent with theory, the expected count of hurricane casualties increases significantly with weekday occurrences. The policy implications of observed daily variation in tornado and hurricane events are considered. © 2012 Society for Risk Analysis.

Condition dependence and the nature of genetic variation for male sex comb bristle number in Drosophila melanogaster.

PubMed

Ahuja, Abha; De Vito, Scott; Singh, Rama S

2011-04-01

Genetic architecture of variation underlying male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila, was examined. First, in order to test for condition dependence, diet was manipulated in a set of ten Drosophila melanogaster full-sib families. We confirmed heightened condition dependent expression of sex comb bristle number and its female homologue (distal transverse row bristles) as compared to non-sex sternopleural bristles. Significant genotype by environment effects were detected for the sex traits indicating a genetic basis for condition dependence. Next we measured sex comb bristle number and sternopleural bristle number, as well as residual mass, a commonly used condition index, in a set of thirty half-sib families. Sire effect was not significant for sex comb and sternopleural bristle number, and we detected a strong dominance and/or maternal effect or X chromosome effect for both traits. A strong sire effect was detected for condition and its heritability was the highest as compared to sex comb and sternopleural bristles. We discuss our results in light of the rapid response to divergent artificial selection for sex comb bristle number reported previously. The nature of genetic variation for male sex traits continues to be an important unresolved issue in evolutionary biology.

Multigenic Natural Variation Underlies Caenorhabditis elegans Olfactory Preference for the Bacterial Pathogen Serratia marcescens

PubMed Central

Glater, Elizabeth E.; Rockman, Matthew V.; Bargmann, Cornelia I.

2013-01-01

The nematode Caenorhabditis elegans can use olfaction to discriminate among different kinds of bacteria, its major food source. We asked how natural genetic variation contributes to choice behavior, focusing on differences in olfactory preference behavior between two wild-type C. elegans strains. The laboratory strain N2 strongly prefers the odor of Serratia marcescens, a soil bacterium that is pathogenic to C. elegans, to the odor of Escherichia coli, a commonly used laboratory food source. The divergent Hawaiian strain CB4856 has a weaker attraction to Serratia than the N2 strain, and this behavioral difference has a complex genetic basis. At least three quantitative trait loci (QTLs) from the CB4856 Hawaii strain (HW) with large effect sizes lead to reduced Serratia preference when introgressed into an N2 genetic background. These loci interact and have epistatic interactions with at least two antagonistic QTLs from HW that increase Serratia preference. The complex genetic architecture of this C. elegans trait is reminiscent of the architecture of mammalian metabolic and behavioral traits. PMID:24347628

Spatial variation of natural radiation and childhood leukaemia incidence in Great Britain.

PubMed

Richardson, S; Monfort, C; Green, M; Draper, G; Muirhead, C

This paper describes an analysis of the geographical variation of childhood leukaemia incidence in Great Britain over a 15 year period in relation to natural radiation (gamma and radon). Data at the level of the 459 district level local authorities in England, Wales and regional districts in Scotland are analysed in two complementary ways: first, by Poisson regressions with the inclusion of environmental covariates and a smooth spatial structure; secondly, by a hierarchical Bayesian model in which extra-Poisson variability is modelled explicitly in terms of spatial and non-spatial components. From this analysis, we deduce a strong indication that a main part of the variability is accounted for by a local neighbourhood 'clustering' structure. This structure is furthermore relatively stable over the 15 year period for the lymphocytic leukaemias which make up the majority of observed cases. We found no evidence of a positive association of childhood leukaemia incidence with outdoor or indoor gamma radiation levels. There is no consistent evidence of any association with radon levels. Indeed, in the Poisson regressions, a significant positive association was only observed for one 5-year period, a result which is not compatible with a stable environmental effect. Moreover, this positive association became clearly non-significant when over-dispersion relative to the Poisson distribution was taken into account.

Adaptive potential of genomic structural variation in human and mammalian evolution.

PubMed

Radke, David W; Lee, Charles

2015-09-01

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenza.

PubMed

Mell, Joshua Chang; Viadas, Cristina; Moleres, Javier; Sinha, Sunita; Fernández-Calvet, Ariadna; Porsch, Eric A; St Geme, Joseph W; Nislow, Corey; Redfield, Rosemary J; Garmendia, Junkal

2016-04-01

Many bacterial species actively take up and recombine homologous DNA into their genomes, called natural competence, a trait that offers a means to identify the genetic basis of naturally occurring phenotypic variation. Here, we describe "transformed recombinant enrichment profiling" (TREP), in which natural transformation is used to generate complex pools of recombinants, phenotypic selection is used to enrich for specific recombinants, and deep sequencing is used to survey for the genetic variation responsible. We applied TREP to investigate the genetic architecture of intracellular invasion by the human pathogen Haemophilus influenzae, a trait implicated in persistence during chronic infection. TREP identified the HMW1 adhesin as a crucial factor. Natural transformation of the hmw1 operon from a clinical isolate (86-028NP) into a laboratory isolate that lacks it (Rd KW20) resulted in ~1,000-fold increased invasion into airway epithelial cells. When a distinct recipient (Hi375, already possessing hmw1 and its paralog hmw2) was transformed by the same donor, allelic replacement of hmw2AHi375 by hmw1A86-028NP resulted in a ~100-fold increased intracellular invasion rate. The specific role of hmw1A86-028NP was confirmed by mutant and western blot analyses. Bacterial self-aggregation and adherence to airway cells were also increased in recombinants, suggesting that the high invasiveness induced by hmw1A86-028NP might be a consequence of these phenotypes. However, immunofluorescence results found that intracellular hmw1A86-028NP bacteria likely invaded as groups, instead of as individual bacterial cells, indicating an emergent invasion-specific consequence of hmw1A-mediated self-aggregation.

Identifying financial crises in real time

NASA Astrophysics Data System (ADS)

da Fonseca, Eder Lucio; Ferreira, Fernando F.; Muruganandam, Paulsamy; Cerdeira, Hilda A.

2013-03-01

Following the thermodynamic formulation of a multifractal measure that was shown to enable the detection of large fluctuations at an early stage, here we propose a new index which permits us to distinguish events like financial crises in real time. We calculate the partition function from which we can obtain thermodynamic quantities analogous to the free energy and specific heat. The index is defined as the normalized energy variation and it can be used to study the behavior of stochastic time series, such as financial market daily data. Famous financial market crashes-Black Thursday (1929), Black Monday (1987) and the subprime crisis (2008)-are identified with clear and robust results. The method is also applied to the market fluctuations of 2011. From these results it appears as if the apparent crisis of 2011 is of a different nature to the other three. We also show that the analysis has forecasting capabilities.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

PubMed

Charlesworth, Brian; Charlesworth, Deborah; Coyne, Jerry A; Langley, Charles H

2016-08-01

The 1966 GENETICS papers by John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity. These papers stimulated a large research program that found similarly high electrophoretic variability in many different species and led to statistical tools for interpreting the data in terms of population genetics processes such as genetic drift, balancing and purifying selection, and the effects of selection on linked variants. The current use of whole-genome sequences in studies of variation is the direct descendant of this pioneering work. Copyright © 2016 by the Genetics Society of America.

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.

PubMed

Meslamani, Jamel; Rognan, Didier; Kellenberger, Esther

2011-05-01

The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class. The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme). SCOPE AND APPLICATIONS: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure). The sc-PDB database is freely available at: http://bioinfo-pharma.u-strasbg.fr/scPDB.

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

PubMed

Wallberg, Andreas; Han, Fan; Wellhagen, Gustaf; Dahle, Bjørn; Kawata, Masakado; Haddad, Nizar; Simões, Zilá Luz Paulino; Allsopp, Mike H; Kandemir, Irfan; De la Rúa, Pilar; Pirk, Christian W; Webster, Matthew T

2014-10-01

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system- and sperm motility-related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.

Trait Variation in Yeast Is Defined by Population History

PubMed Central

Warringer, Jonas; Zörgö, Enikö; Cubillos, Francisco A.; Zia, Amin; Gjuvsland, Arne; Simpson, Jared T.; Forsmark, Annabelle; Durbin, Richard; Omholt, Stig W.; Louis, Edward J.; Liti, Gianni; Moses, Alan; Blomberg, Anders

2011-01-01

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism. PMID:21698134

Trait variation in yeast is defined by population history.

PubMed

Warringer, Jonas; Zörgö, Enikö; Cubillos, Francisco A; Zia, Amin; Gjuvsland, Arne; Simpson, Jared T; Forsmark, Annabelle; Durbin, Richard; Omholt, Stig W; Louis, Edward J; Liti, Gianni; Moses, Alan; Blomberg, Anders

2011-06-01

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.

On the Use of Biomineral Oxygen Isotope Data to Identify Human Migrants in the Archaeological Record: Intra-Sample Variation, Statistical Methods and Geographical Considerations

PubMed Central

Lightfoot, Emma; O’Connell, Tamsin C.

2016-01-01

Oxygen isotope analysis of archaeological skeletal remains is an increasingly popular tool to study past human migrations. It is based on the assumption that human body chemistry preserves the δ18O of precipitation in such a way as to be a useful technique for identifying migrants and, potentially, their homelands. In this study, the first such global survey, we draw on published human tooth enamel and bone bioapatite data to explore the validity of using oxygen isotope analyses to identify migrants in the archaeological record. We use human δ18O results to show that there are large variations in human oxygen isotope values within a population sample. This may relate to physiological factors influencing the preservation of the primary isotope signal, or due to human activities (such as brewing, boiling, stewing, differential access to water sources and so on) causing variation in ingested water and food isotope values. We compare the number of outliers identified using various statistical methods. We determine that the most appropriate method for identifying migrants is dependent on the data but is likely to be the IQR or median absolute deviation from the median under most archaeological circumstances. Finally, through a spatial assessment of the dataset, we show that the degree of overlap in human isotope values from different locations across Europe is such that identifying individuals’ homelands on the basis of oxygen isotope analysis alone is not possible for the regions analysed to date. Oxygen isotope analysis is a valid method for identifying first-generation migrants from an archaeological site when used appropriately, however it is difficult to identify migrants using statistical methods for a sample size of less than c. 25 individuals. In the absence of local previous analyses, each sample should be treated as an individual dataset and statistical techniques can be used to identify migrants, but in most cases pinpointing a specific homeland should

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair.

PubMed

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pospiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-02-01

Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62-0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. © The Author(s) 2017. Published by Oxford University Press.

Meta-analysis of genome-wide association studies identifies 8 novel loci involved in shape variation of human head hair

PubMed Central

Liu, Fan; Chen, Yan; Zhu, Gu; Hysi, Pirro G; Wu, Sijie; Adhikari, Kaustubh; Breslin, Krystal; Pośpiech, Ewelina; Hamer, Merel A; Peng, Fuduan; Muralidharan, Charanya; Acuna-Alonzo, Victor; Canizales-Quinteros, Samuel; Bedoya, Gabriel; Gallo, Carla; Poletti, Giovanni; Rothhammer, Francisco; Bortolini, Maria Catira; Gonzalez-Jose, Rolando; Zeng, Changqing; Xu, Shuhua; Jin, Li; Uitterlinden, André G; Ikram, M Arfan; van Duijn, Cornelia M; Nijsten, Tamar; Walsh, Susan; Branicki, Wojciech; Wang, Sijia; Ruiz-Linares, Andrés; Spector, Timothy D; Martin, Nicholas G; Medland, Sarah E; Kayser, Manfred

2018-01-01

Abstract Shape variation of human head hair shows striking variation within and between human populations, while its genetic basis is far from being understood. We performed a series of genome-wide association studies (GWASs) and replication studies in a total of 28 964 subjects from 9 cohorts from multiple geographic origins. A meta-analysis of three European GWASs identified 8 novel loci (1p36.23 ERRFI1/SLC45A1, 1p36.22 PEX14, 1p36.13 PADI3, 2p13.3 TGFA, 11p14.1 LGR4, 12q13.13 HOXC13, 17q21.2 KRTAP, and 20q13.33 PTK6), and confirmed 4 previously known ones (1q21.3 TCHH/TCHHL1/LCE3E, 2q35 WNT10A, 4q21.21 FRAS1, and 10p14 LINC00708/GATA3), all showing genome-wide significant association with hair shape (P < 5e-8). All except one (1p36.22 PEX14) were replicated with nominal significance in at least one of the 6 additional cohorts of European, Native American and East Asian origins. Three additional previously known genes (EDAR, OFCC1, and PRSS53) were confirmed at the nominal significance level. A multivariable regression model revealed that 14 SNPs from different genes significantly and independently contribute to hair shape variation, reaching a cross-validated AUC value of 0.66 (95% CI: 0.62–0.70) and an AUC value of 0.64 in an independent validation cohort, providing an improved accuracy compared with a previous model. Prediction outcomes of 2504 individuals from a multiethnic sample were largely consistent with general knowledge on the global distribution of hair shape variation. Our study thus delivers target genes and DNA variants for future functional studies to further evaluate the molecular basis of hair shape in humans. PMID:29220522

Interdependency Assessment of Coupled Natural Gas and Power Systems in Energy Market

NASA Astrophysics Data System (ADS)

Yang, Hongzhao; Qiu, Jing; Zhang, Sanhua; Lai, Mingyong; Dong, Zhao Yang

2015-12-01

Owing to the technological development of natural gas exploration and the increasing penetration of gas-fired power generation, gas and power systems inevitably interact with each other from both physical and economic points of view. In order to effectively assess the two systems' interdependency, this paper proposes a systematic modeling framework and constructs simulation platforms for coupled gas and power systems in an energy market environment. By applying the proposed approach to the Australian national electricity market (NEM) and gas market, the impacts of six types of market and system factors are quantitatively analyzed, including power transmission limits, gas pipeline contingencies, gas pipeline flow constraints, carbon emission constraints, power load variations, and non-electric gas load variations. The important interdependency and infrastructure weakness for the two systems are well studied and identified. Our work provides a quantitative basis for grid operators and policy makers to support and guide operation and investment decisions for electric power and natural gas industries.

The Educational Nature of Different Ways Teachers Communicate with Children about Natural Phenomena

ERIC Educational Resources Information Center

Gustavsson, Laila; Pramling, Niklas

2014-01-01

This empirical study analyses the qualitatively different ways in which teachers approach children's learning in and about nature. The empirical data consists of video observations of children and teachers communicating with one another around natural phenomena found during excursions into a forest. Variation theory is presented as a framework for…

Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

PubMed

Popovsky-Sarid, Sigal; Borovsky, Yelena; Faigenboim, Adi; Parsons, Eugene P; Lohrey, Gregory T; Alkalai-Tuvia, Sharon; Fallik, Elazar; Jenks, Matthew A; Paran, Ilan

2017-02-01

Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.

An investigation of natural genetic variation in the circadian system of Drosophila melanogaster: rhythm characteristics and methods of quantification.

PubMed

Emery, P T; Morgan, E; Birley, A J

1994-04-01

Variation in four characteristics of the circadian locomotor activity rhythm was investigated in 24 true-breeding strains of Drosophila melanogaster with a view to establishing methods of phenotypic measurement sufficiently robust to allow subsequent biometric analysis. Between them, these strains formed a representative sample of the genetic variability of a natural population. Period, phase, definition (the degree to which a rhythmic signal was obscured by noise), and rhythm waveform were all found to vary continuously among the strains, although within each strain the rhythm phenotype was remarkably consistent. Each characteristic was found to be sufficiently robust to permit objective measurement using several different methods of quantification, which were then compared.

Identifying natural and anthropogenically-induced geohazards from satellite ground motion and geospatial data: Stoke-on-Trent, UK

NASA Astrophysics Data System (ADS)

Jordan, Hannah; Cigna, Francesca; Bateson, Luke

2017-12-01

Determining the location and nature of hazardous ground motion resulting from natural and anthropogenic processes such as landslides, tectonic movement and mining is essential for hazard mitigation and sustainable resource use. Ground motion estimates from satellite ERS-1/2 persistent scatterer interferometry (PSI) were combined with geospatial data to identify areas of observed geohazards in Stoke-on-Trent, UK. This investigation was performed within the framework of the EC FP7-SPACE PanGeo project which aimed to provide free and open access to geohazard information for 52 urban areas across Europe. Geohazards identified within the city of Stoke-on-Trent and neighbouring rural areas are presented here alongside an examination of the PanGeo methodology. A total of 14 areas experiencing ground instability caused by natural and anthropogenic processes have been defined, covering 122.35 km2. These are attributed to a range of geohazards, including landslides, ground dissolution, made ground and mining activities. The dominant geohazard (by area) is ground movement caused by post-mining groundwater recharge and mining-related subsidence (93.19% of total geohazard area), followed by landsliding (5.81%). Observed ground motions along the satellite line-of-sight reach maxima of +35.23 mm/yr and -22.57 mm/yr. A combination of uplift, subsidence and downslope movement is displayed. 'Construction sites' and 'continuous urban fabric' (European Urban Atlas land use types) form the land uses most affected (by area) by ground motion and 'discontinuous very low density urban fabric' the least. Areas of 'continuous urban fabric' also show the highest average velocity towards the satellite (5.08 mm/yr) and the highest PS densities (1262.92 points/km2) along with one of the lowest standard deviations. Rural land uses tend to result in lower PS densities and higher standard deviations, a consequence of fewer suitable reflectors in these regions. PSI is also limited in its ability to

Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis.

PubMed

Huang, Xueqing; Ding, Jia; Effgen, Sigi; Turck, Franziska; Koornneef, Maarten

2013-08-01

Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

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.

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

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.

Modelling categorical data to identify factors influencing concern for the natural environment in Iran.

PubMed

Parizanganeh, Abdolhossein; Lakhan, V Chris; Yazdani, Mahmoud; Ahmad, Sajid R

2011-10-01

Loglinear modelling techniques were used to identify the interactions and interrelationships underlying categorical environmental concern data collected from 9062 respondents in Iran. After fitting various loglinear models to the data, the most parsimonious model highlighted that a combination of interacting factors, namely educational attainment, age, gender, and residential location were responsible for influencing personal concern for the environment. Although high educational attainment had a close correspondence with high concern for the environment the loglinear results, when visualized with a geographical information system, demonstrated wide spatial variations in educational attainment and concern for the environment. Nearly two-thirds of the respondents were not highly educated, and were therefore not highly concerned for the environment. The finding that both rural and urban male and female respondents in the 15-24 years age category, with 10-12 years of education, had the strongest interaction with personal concern for the environment could be beneficial for policy planners to utilize education as the primary instrument to enhance environmental governance and prospects for sustainable development. Copyright © 2011 Elsevier Ltd. All rights reserved.

Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations - a next generation sequencing approach in the gopher tortoise.

PubMed

Elbers, Jean P; Brown, Mary B; Taylor, Sabrina S

2018-01-19

Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i.e., the immunomes) in 16 Florida gopher tortoises, Gopherus polyphemus. All tortoises produced antibodies against Mycoplasma agassizii (an etiologic agent of infectious upper respiratory tract disease; URTD) and, at the time of sampling, either had (n = 10) or lacked (n = 6) clinical signs. We found several variants associated with URTD clinical status in complement and lectin genes, which may play a role in Mycoplasma immunity. Thirty-five genes deviated from neutrality according to Tajima's D. These genes were enriched in functions relating to macromolecule and protein modifications, which are vital to immune system functioning. These results are suggestive of genetic differences that might contribute to disease severity, a finding that is consistent with other mycoplasmal diseases. This has implications for management because tortoises across their range may possess genetic variation associated with a more severe response to URTD. More generally: 1) this approach demonstrates that a broader consideration of immune genes is better able to identify important variants, and; 2) this data pipeline can be adopted to identify alleles associated with disease susceptibility or resistance in other taxa, and therefore provide information on a population's risk of succumbing to disease, inform translocations to increase genetic variation for disease resistance

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

PubMed Central

Mayer, Melanie G.; Rödelsperger, Christian; Witte, Hanh; Riebesell, Metta; Sommer, Ralf J.

2015-01-01

Many nematodes form dauer larvae when exposed to unfavorable conditions, representing an example of phenotypic plasticity and a major survival and dispersal strategy. In Caenorhabditis elegans, the regulation of dauer induction is a model for pheromone, insulin, and steroid-hormone signaling. Recent studies in Pristionchus pacificus revealed substantial natural variation in various aspects of dauer development, i.e. pheromone production and sensing and dauer longevity and fitness. One intriguing example is a strain from Ohio, having extremely long-lived dauers associated with very high fitness and often forming the most dauers in response to other strains´ pheromones, including the reference strain from California. While such examples have been suggested to represent intraspecific competition among strains, the molecular mechanisms underlying these dauer-associated patterns are currently unknown. We generated recombinant-inbred-lines between the Californian and Ohioan strains and used quantitative-trait-loci analysis to investigate the molecular mechanism determining natural variation in dauer development. Surprisingly, we discovered that the orphan gene dauerless controls dauer formation by copy number variation. The Ohioan strain has one dauerless copy causing high dauer formation, whereas the Californian strain has two copies, resulting in strongly reduced dauer formation. Transgenic animals expressing multiple copies do not form dauers. dauerless is exclusively expressed in CAN neurons, and both CAN ablation and dauerless mutations increase dauer formation. Strikingly, dauerless underwent several duplications and acts in parallel or downstream of steroid-hormone signaling but upstream of the nuclear-hormone-receptor daf-12. We identified the novel or fast-evolving gene dauerless as inhibitor of dauer development. Our findings reveal the importance of gene duplications and copy number variations for orphan gene function and suggest daf-12 as major target for

Variation in flooding-induced morphological traits in natural populations of white clover (Trifolium repens) and their effects on plant performance during soil flooding

PubMed Central

Huber, Heidrun; Jacobs, Elke; Visser, Eric J. W.

2009-01-01

Background and Aims Soil flooding leads to low soil oxygen concentrations and thereby negatively affects plant growth. Differences in flooding tolerance have been explained by the variation among species in the extent to which traits related to acclimation were expressed. However, our knowledge of variation within natural species (i.e. among individual genotypes) in traits related to flooding tolerance is very limited. Such data could tell us on which traits selection might have taken place, and will take place in future. The aim of the present study was to show that variation in flooding-tolerance-related traits is present among genotypes of the same species, and that both the constitutive variation and the plastic variation in flooding-induced changes in trait expression affect the performance of genotypes during soil flooding. Methods Clones of Trifolium repens originating from a river foreland were subjected to either drained, control conditions or to soil flooding. Constitutive expression of morphological traits was recorded on control plants, and flooding-induced changes in expression were compared with these constitutive expression levels. Moreover, the effect of both constitutive and flooding-induced trait expression on plant performance was determined. Key Results Constitutive and plastic variation of several morphological traits significantly affected plant performance. Even relatively small increases in root porosity and petiole length contributed to better performance during soil flooding. High specific leaf area, by contrast, was negatively correlated with performance during flooding. Conclusions The data show that different genotypes responded differently to soil flooding, which could be linked to variation in morphological trait expression. As flooded and drained conditions exerted different selection pressures on trait expression, the optimal value for constitutive and plastic traits will depend on the frequency and duration of flooding. These data

The Space-Time Variation of Global Crop Yields, Detecting Simultaneous Outliers and Identifying the Teleconnections with Climatic Patterns

NASA Astrophysics Data System (ADS)

Najafi, E.; Devineni, N.; Pal, I.; Khanbilvardi, R.

2017-12-01

An understanding of the climate factors that influence the space-time variability of crop yields is important for food security purposes and can help us predict global food availability. In this study, we address how the crop yield trends of countries globally were related to each other during the last several decades and the main climatic variables that triggered high/low crop yields simultaneously across the world. Robust Principal Component Analysis (rPCA) is used to identify the primary modes of variation in wheat, maize, sorghum, rice, soybeans, and barley yields. Relations between these modes of variability and important climatic variables, especially anomalous sea surface temperature (SSTa), are examined from 1964 to 2010. rPCA is also used to identify simultaneous outliers in each year, i.e. systematic high/low crop yields across the globe. The results demonstrated spatiotemporal patterns of these crop yields and the climate-related events that caused them as well as the connection of outliers with weather extremes. We find that among climatic variables, SST has had the most impact on creating simultaneous crop yields variability and yield outliers in many countries. An understanding of this phenomenon can benefit global crop trade networks.

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

PubMed Central

Hsieh, PingHsun; Veeramah, Krishna R.; Lachance, Joseph; Tishkoff, Sarah A.; Wall, Jeffrey D.; Hammer, Michael F.; Gutenkunst, Ryan N.

2016-01-01

African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due to their unique lifestyle in the Central African rainforest. To identify genomic targets of adaptation, we sequenced the genomes of four Biaka Pygmies from the Central African Republic and jointly analyzed these data with the genome sequences of three Baka Pygmies from Cameroon and nine Yoruba famers. To account for the complex demographic history of these populations that includes both isolation and gene flow, we fit models using the joint allele frequency spectrum and validated them using independent approaches. Our two best-fit models both suggest ancient divergence between the ancestors of the farmers and Pygmies, 90,000 or 150,000 yr ago. We also find that bidirectional asymmetric gene flow is statistically better supported than a single pulse of unidirectional gene flow from farmers to Pygmies, as previously suggested. We then applied complementary statistics to scan the genome for evidence of selective sweeps and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P-values for candidates using whole-genome simulations incorporating demography and variation in both recombination and mutation rates. We found that genes and gene sets involved in muscle development, bone synthesis, immunity, reproduction, cell signaling and development, and energy metabolism are likely to be targets of positive natural selection in Western African Pygmies or their recent ancestors. PMID:26888263

Genome-wide association studies reveal a simple genetic basis of resistance to naturally coevolving viruses in Drosophila melanogaster.

PubMed

Magwire, Michael M; Fabian, Daniel K; Schweyen, Hannah; Cao, Chuan; Longdon, Ben; Bayer, Florian; Jiggins, Francis M

2012-01-01

Variation in susceptibility to infectious disease often has a substantial genetic component in animal and plant populations. We have used genome-wide association studies (GWAS) in Drosophila melanogaster to identify the genetic basis of variation in susceptibility to viral infection. We found that there is substantially more genetic variation in susceptibility to two viruses that naturally infect D. melanogaster (DCV and DMelSV) than to two viruses isolated from other insects (FHV and DAffSV). Furthermore, this increased variation is caused by a small number of common polymorphisms that have a major effect on resistance and can individually explain up to 47% of the heritability in disease susceptibility. For two of these polymorphisms, it has previously been shown that they have been driven to a high frequency by natural selection. An advantage of GWAS in Drosophila is that the results can be confirmed experimentally. We verified that a gene called pastrel--which was previously not known to have an antiviral function--is associated with DCV-resistance by knocking down its expression by RNAi. Our data suggest that selection for resistance to infectious disease can increase genetic variation by increasing the frequency of major-effect alleles, and this has resulted in a simple genetic basis to variation in virus resistance.

DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA.

PubMed

Bhaskar, Anand; Song, Yun S

2014-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the "folded" SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes' rule of signs for polynomials to the Laplace transform of piecewise continuous functions.

Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development

PubMed Central

Pires, Nuno D.; Bemer, Marian; Müller, Lena M.; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

2016-01-01

Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict. PMID:26811909

Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

PubMed

Pires, Nuno D; Bemer, Marian; Müller, Lena M; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

2016-01-01

Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

Towards identifying novel anti-Eimeria agents: trace elements, vitamins, and plant-based natural products.

PubMed

Wunderlich, Frank; Al-Quraishy, Saleh; Steinbrenner, Holger; Sies, Helmut; Dkhil, Mohamed A

2014-10-01

Eimeriosis, a widespread infectious disease of livestock, is caused by coccidian protozoans of the genus Eimeria. These obligate intracellular parasites strike the digestive tract of their hosts and give rise to enormous economic losses, particularly in poultry, ruminants including cattle, and rabbit farming. Vaccination, though a rational prophylactic measure, has not yet been as successful as initially thought. Numerous broad-spectrum anti-coccidial drugs are currently in use for treatment and prophylactic control of eimeriosis. However, increasing concerns about parasite resistance, consumer health, and environmental safety of the commercial drugs warrant efforts to search for novel agents with anti-Eimeria activity. This review summarizes current approaches to prevent and treat eimeriosis such as vaccination and commercial drugs, as well as recent attempts to use dietary antioxidants as novel anti-Eimeria agents. In particular, the trace elements selenium and zinc, the vitamins A and E, and natural products extracted from garlic, barberry, pomegranate, sweet wormwood, and other plants are discussed. Several of these novel anti-Eimeria agents exhibit a protective role against oxidative stress that occurs not only in the intestine of Eimeria-infected animals, but also in their non-parasitized tissues, in particular, in the first-pass organ liver. Currently, it appears to be promising to identify safe combinations of low-cost natural products with high anti-Eimeria efficacy for a potential use as feed supplementation in animal farming.

Variational nature, integration, and properties of Newton reaction path

NASA Astrophysics Data System (ADS)

Bofill, Josep Maria; Quapp, Wolfgang

2011-02-01

The distinguished coordinate path and the reduced gradient following path or its equivalent formulation, the Newton trajectory, are analyzed and unified using the theory of calculus of variations. It is shown that their minimum character is related to the fact that the curve is located in a valley region. In this case, we say that the Newton trajectory is a reaction path with the category of minimum energy path. In addition to these findings a Runge-Kutta-Fehlberg algorithm to integrate these curves is also proposed.

Variational nature, integration, and properties of Newton reaction path.

PubMed

Bofill, Josep Maria; Quapp, Wolfgang

2011-02-21

The distinguished coordinate path and the reduced gradient following path or its equivalent formulation, the Newton trajectory, are analyzed and unified using the theory of calculus of variations. It is shown that their minimum character is related to the fact that the curve is located in a valley region. In this case, we say that the Newton trajectory is a reaction path with the category of minimum energy path. In addition to these findings a Runge-Kutta-Fehlberg algorithm to integrate these curves is also proposed.

NCR1 Expression Identifies Canine Natural Killer Cell Subsets with Phenotypic Similarity to Human Natural Killer Cells

PubMed Central

Foltz, Jennifer A.; Somanchi, Srinivas S.; Yang, Yanwen; Aquino-Lopez, Arianexys; Bishop, Erin E.; Lee, Dean A.

2016-01-01

Canines spontaneously develop many cancers similar to humans – including osteosarcoma, leukemia, and lymphoma – offering the opportunity to study immune therapies in a genetically heterogeneous and immunocompetent environment. However, a lack of antibodies recognizing canine NK cell markers has resulted in suboptimal characterization and unknown purity of NK cell products, hindering the development of canine models of NK cell adoptive immunotherapy. To this end, we generated a novel antibody to canine NCR1 (NKp46), the putative species-wide marker of NK cells, enabling purification of NK cells for further characterization. We demonstrate that CD3−/NKp46+ cells in healthy and osteosarcoma-bearing canines have phenotypic similarity to human CD3−/NKp46+ NK cells, expressing mRNA for CD16 and the natural cytotoxicity receptors NKp30, NKp44, and NKp80. Functionally, we demonstrate with the calcein release assay that canine CD3−/NKp46+ cells kill canine tumor cell lines without prior sensitization and secrete IFN-γ, TNF-α, IL-8, IL-10, and granulocyte-macrophage colony-stimulating factor as measured by Luminex. Similar to human NK cells, CD3−/NKp46+ cells expand rapidly on feeder cells expressing 4-1BBL and membrane-bound IL-21 (median = 20,283-fold in 21 days). Furthermore, we identify a minor Null population (CD3−/CD21−/CD14−/NKp46−) with reduced cytotoxicity against osteosarcoma cells, but similar cytokine secretion as CD3−/NKp46+ cells. Null cells in canines and humans have reduced expression of NKG2D, NKp44, and CD16 compared to NKp46+ NK cells and can be induced to express NKp46 with further expansion on feeder cells. In conclusion, we have identified and characterized canine NK cells, including an NKp46− subset of canine and human NK cells, using a novel anti-canine NKp46 antibody, and report robust ex vivo expansion of canine NK cells sufficient for adoptive immunotherapy. PMID:27933061

Natural Variation in the Carbon Oxidation State and Oxidative Ratio of a Deciduous Forest

NASA Astrophysics Data System (ADS)

Masiello, C. A.; Calligan, L. J.; Gallagher, M. E.; Hockaday, W. C.; Robertson, G. P.

2007-12-01

Here we report natural variability in the oxidative ratio (OR) and carbon oxidation state (Cox) of a temperate, deciduous forest measured on an annual basis via elemental analysis of leaf litter. The OR of the terrestrial biosphere is a key component in O2 -based calculations of the biosphere's uptake of fossil fuel CO2 (eg [ Keeling, et al., 1996]). Ecosystem OR has been assumed to be invariant; however, small OR variations may cause significant shifts in the calculated size of the terrestrial biospheric C sink [ Randerson, et al., 2006]. Accurate measurements of OR are necessary for the accurate apportionment of fossil fuel CO2 between the atmosphere, oceans, and terrestrial biosphere. Ecosystem OR is linearly related to Cox, a parameter which can be easily measured via elemental analysis, calorimetry, or solid state nuclear magnetic resonance [ Masiello, et al., 2007]. We are measuring Cox and OR at the three deciduous forest sites within the Kellogg Biological Station NSF LTER (lter.kbs.msu.edu). We report OR from litter collected from three forest sites from 1998-2003, a time series which covers periods of both normal and low precipitation. We also report error introduced in the Cox to OR conversion via a range of plausible assumptions about ecosystem N cycling. Keeling, R. F., et al. (1996), Global and hemispheric CO2 sinks deduced from changes in atmospheric O2 concentration, Nature, 381, 218-221. Masiello, C.A. et al. (in review 2007) Two new approaches for measuring ecosystem carbon oxidation state and oxidative ratio. J.G.R. Biogeosciences. Randerson, J. T., et al. (2006), Is carbon within the global terrestrial biosphere becoming more oxidized? Implications for trends in atmospheric O2, Global Change Biology, 12, 260-271.

Phenotypic Screening Identifies Synergistically Acting Natural Product Enhancing the Performance of Biomaterial Based Wound Healing.

PubMed

Sivasubramanian, Srinivasan; Chandrasekar, Gayathri; Svensson Akusjärvi, Sara; Thangam, Ramar; Sathuvan, Malairaj; Kumar, R B S; Hussein, Hawraa; Vincent, Savariar; Madhan, Balaraman; Gunasekaran, Palani; Kitambi, Satish S

2017-01-01

The potential of multifunctional wound heal biomaterial relies on the optimal content of therapeutic constituents as well as the desirable physical, chemical, and biological properties to accelerate the healing process. Formulating biomaterials such as amnion or collagen based scaffolds with natural products offer an affordable strategy to develop dressing material with high efficiency in healing wounds. Using image based phenotyping and quantification, we screened natural product derived bioactive compounds for modulators of types I and III collagen production from human foreskin derived fibroblast cells. The identified hit was then formulated with amnion to develop a biomaterial, and its biophysical properties, in vitro and in vivo effects were characterized. In addition, we performed functional profiling analyses by PCR array to understand the effect of individual components of these materials on various genes such as inflammatory mediators including chemokines and cytokines, growth factors, fibroblast stimulating markers for collagen secretion, matrix metalloproteinases, etc., associated with wound healing. FACS based cell cycle analyses were carried out to evaluate the potential of biomaterials for induction of proliferation of fibroblasts. Western blot analyses was done to examine the effect of biomaterial on collagen synthesis by cells and compared to cells grown in the presence of growth factors. This work demonstrated an uncomplicated way of identifying components that synergistically promote healing. Besides, we demonstrated that modulating local wound environment using biomaterials with bioactive compounds could enhance healing. This study finds that the developed biomaterials offer immense scope for healing wounds by means of their skin regenerative features such as anti-inflammatory, fibroblast stimulation for collagen secretion as well as inhibition of enzymes and markers impeding the healing, hydrodynamic properties complemented with other features

Phenotypic Screening Identifies Synergistically Acting Natural Product Enhancing the Performance of Biomaterial Based Wound Healing

PubMed Central

Sivasubramanian, Srinivasan; Chandrasekar, Gayathri; Svensson Akusjärvi, Sara; Thangam, Ramar; Sathuvan, Malairaj; Kumar, R. B. S.; Hussein, Hawraa; Vincent, Savariar; Madhan, Balaraman; Gunasekaran, Palani; Kitambi, Satish S.

2017-01-01

The potential of multifunctional wound heal biomaterial relies on the optimal content of therapeutic constituents as well as the desirable physical, chemical, and biological properties to accelerate the healing process. Formulating biomaterials such as amnion or collagen based scaffolds with natural products offer an affordable strategy to develop dressing material with high efficiency in healing wounds. Using image based phenotyping and quantification, we screened natural product derived bioactive compounds for modulators of types I and III collagen production from human foreskin derived fibroblast cells. The identified hit was then formulated with amnion to develop a biomaterial, and its biophysical properties, in vitro and in vivo effects were characterized. In addition, we performed functional profiling analyses by PCR array to understand the effect of individual components of these materials on various genes such as inflammatory mediators including chemokines and cytokines, growth factors, fibroblast stimulating markers for collagen secretion, matrix metalloproteinases, etc., associated with wound healing. FACS based cell cycle analyses were carried out to evaluate the potential of biomaterials for induction of proliferation of fibroblasts. Western blot analyses was done to examine the effect of biomaterial on collagen synthesis by cells and compared to cells grown in the presence of growth factors. This work demonstrated an uncomplicated way of identifying components that synergistically promote healing. Besides, we demonstrated that modulating local wound environment using biomaterials with bioactive compounds could enhance healing. This study finds that the developed biomaterials offer immense scope for healing wounds by means of their skin regenerative features such as anti-inflammatory, fibroblast stimulation for collagen secretion as well as inhibition of enzymes and markers impeding the healing, hydrodynamic properties complemented with other features

Contribution of vertical land motions to coastal sea level variations: a global synthesis of multisatellite altimetry, tide gauge and GPS measurements

NASA Astrophysics Data System (ADS)

Pfeffer, Julia; Allemand, Pascal

2016-04-01

Coastal sea level variations result from a complex mix of climatic, oceanic and geodynamical processes driven by natural and anthropogenic constraints. Combining data from multiple sources is one solution to identify particular processes and progress towards a better understanding of the sea level variations and the assessment of their impacts at coast. Here, we present a global database merging multisatellite altimetry with tide gauges and Global Positioning System (GPS) measurements. Vertical land motions and sea level variations are estimated simultaneously for a network of 886 ground stations with median errors lower than 1 mm/yr. The contribution of vertical land motions to relative sea level variations is explored to better understand the natural hazards associated with sea level rise in coastal areas. Worldwide, vertical land motions dominate 30 % of observed coastal trends. The role of the crust is highly heterogeneous: it can amplify, restrict or counter the effects of climate-induced sea level change. A set of 182 potential vulnerable localities are identified by large coastal subsidence which increases by several times the effects of sea level rise. Though regional behaviours exist, principally caused by GIA (Glacial Isostatic Adjustment), the local variability in vertical land motion prevails. An accurate determination of the vertical motions observed at the coast is fundamental to understand the local processes which contribute to sea level rise, to appraise its impacts on coastal populations and make future predictions.

Ethnic variations in pathways into early intervention services for psychosis.

PubMed

Ghali, Sharif; Fisher, Helen L; Joyce, John; Major, Barnaby; Hobbs, Lorna; Soni, Sujata; Chisholm, Brock; Rahaman, Nikola; Papada, Peggy; Lawrence, Jo; Bloy, Sally; Marlowe, Karl; Aitchison, Katherine J; Power, Paddy; Johnson, Sonia

2013-04-01

Ethnic variations have previously been identified in the duration of untreated psychosis (DUP) and pathways into psychiatric services. These have not been examined in the context of early intervention services, which may alter these trajectories. To explore ethnic differences in the nature and duration of pathways into early intervention services. In a naturalistic cohort study, data were collected for 1024 individuals with psychotic disorders accepted for case management by eight London early intervention services. Duration of untreated psychosis was prolonged in the White British group compared with most other ethnic groups. White British individuals were more likely to make contact with their general practitioner and less likely to be seen within emergency medical services. All Black patient groups were more likely than their White British counterparts to experience involvement of criminal justice agencies. Variations continue to exist in how and when individuals from different ethnic groups access early intervention services. These may account for disparities in DUP.

Changes in snoring during natural sleep identified by acoustic crest factor analysis at different times of night.

PubMed

Hill, P D; Osman, E Z; Osborne, J E; Lee, B W

2000-12-01

Sleep nasendoscopy can be used to identify the site of snoring but questions remain about how well a short assessment during drug-induced sleep reflects the natural condition. To investigate the uniformity of snoring during natural sleep we studied five patients (three men, two women) referred by their GPs for treatment of their snoring. A digital audio tape recorder captured the free-field snore sound at different times of night in hospital. Acoustic Crest Factor values were calculated on the 15 recordings made, having previously demonstrated that high crest factor values distinguish palatal from non-palatal snoring at sleep nasendoscopy. Some recordings showed reproducibility, but others showed substantial changes between recordings an hour apart. We infer that the snoring mechanism may change in some individuals during the night, with or without a change of snore site. We conclude a single recording, as in sleep nasendoscopy, may not be representative.

Natural and Unanticipated Modifiers of RNAi Activity in Caenorhabditis elegans

PubMed Central

Asad, Nadeem; Aw, Wen Yih; Timmons, Lisa

2012-01-01

Organisms used as model genomics systems are maintained as isogenic strains, yet evidence of sequence differences between independently maintained wild-type stocks has been substantiated by whole-genome resequencing data and strain-specific phenotypes. Sequence differences may arise from replication errors, transposon mobilization, meiotic gene conversion, or environmental or chemical assault on the genome. Low frequency alleles or mutations with modest effects on phenotypes can contribute to natural variation, and it has proven possible for such sequences to become fixed by adapted evolutionary enrichment and identified by resequencing. Our objective was to identify and analyze single locus genetic defects leading to RNAi resistance in isogenic strains of Caenorhabditis elegans. In so doing, we uncovered a mutation that arose de novo in an existing strain, which initially frustrated our phenotypic analysis. We also report experimental, environmental, and genetic conditions that can complicate phenotypic analysis of RNAi pathway defects. These observations highlight the potential for unanticipated mutations, coupled with genetic and environmental phenomena, to enhance or suppress the effects of known mutations and cause variation between wild-type strains. PMID:23209671

Naturally Occurring Variations in the Human Cholinesterase Genes: Heritability and Association with Cardiovascular and Metabolic Traits

PubMed Central

Valle, Anne M.; Radić, Zoran; Rana, Brinda K.; Mahboubi, Vafa; Wessel, Jennifer; Shih, Pei-an Betty; Rao, Fangwen; O'Connor, Daniel T.

2011-01-01

Cholinergic neurotransmission in the central and autonomic nervous systems regulates immediate variations in and longer-term maintenance of cardiovascular function with acetylcholinesterase (AChE) activity that is critical to temporal responsiveness. Butyrylcholinesterase (BChE), largely confined to the liver and plasma, subserves metabolic functions. AChE and BChE are found in hematopoietic cells and plasma, enabling one to correlate enzyme levels in whole blood with hereditary traits in twins. Using both twin and unrelated subjects, we found certain single nucleotide polymorphisms (SNPs) in the ACHE gene correlated with catalytic properties and general cardiovascular functions. SNP discovery from ACHE resequencing identified 19 SNPs: 7 coding SNPs (cSNPs), of which 4 are nonsynonymous, and 12 SNPs in untranslated regions, of which 3 are in a conserved sequence of an upstream intron. Both AChE and BChE activity traits in blood were heritable: AChE at 48.8 ± 6.1% and BChE at 81.4 ± 2.8%. Allelic and haplotype variations in the ACHE and BCHE genes were associated with changes in blood AChE and BChE activities. AChE activity was associated with BP status and SBP, whereas BChE activity was associated with features of the metabolic syndrome (especially body weight and BMI). Gene products from cDNAs with nonsynonymous cSNPs were expressed and purified. Protein expression of ACHE nonsynonymous variant D134H (SNP6) is impaired: this variant shows compromised stability and altered rates of organophosphate inhibition and oxime-assisted reactivation. A substantial fraction of the D134H instability could be reversed in the D134H/R136Q mutant. Hence, common genetic variations at ACHE and BCHE loci were associated with changes in corresponding enzymatic activities in blood. PMID:21493754

Biosynthetic Potential-Based Strain Prioritization for Natural Product Discovery: A Showcase for Diterpenoid-Producing Actinomycetes

PubMed Central

2015-01-01

Natural products remain the best sources of drugs and drug leads and serve as outstanding small-molecule probes to dissect fundamental biological processes. A great challenge for the natural product community is to discover novel natural products efficiently and cost effectively. Here we report the development of a practical method to survey biosynthetic potential in microorganisms, thereby identifying the most promising strains and prioritizing them for natural product discovery. Central to our approach is the innovative preparation, by a two-tiered PCR method, of a pool of pathway-specific probes, thereby allowing the survey of all variants of the biosynthetic machineries for the targeted class of natural products. The utility of the method was demonstrated by surveying 100 strains, randomly selected from our actinomycete collection, for their biosynthetic potential of four classes of natural products, aromatic polyketides, reduced polyketides, nonribosomal peptides, and diterpenoids, identifying 16 talented strains. One of the talented strains, Streptomyces griseus CB00830, was finally chosen to showcase the discovery of the targeted classes of natural products, resulting in the isolation of three diterpenoids, six nonribosomal peptides and related metabolites, and three polyketides. Variations of this method should be applicable to the discovery of other classes of natural products. PMID:24484381

Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses.

PubMed

Byrd-Leotis, Lauren; Liu, Renpeng; Bradley, Konrad C; Lasanajak, Yi; Cummings, Sandra F; Song, Xuezheng; Heimburg-Molinaro, Jamie; Galloway, Summer E; Culhane, Marie R; Smith, David F; Steinhauer, David A; Cummings, Richard D

2014-06-03

Influenza viruses bind to host cell surface glycans containing terminal sialic acids, but as studies on influenza binding become more sophisticated, it is becoming evident that although sialic acid may be necessary, it is not sufficient for productive binding. To better define endogenous glycans that serve as viral receptors, we have explored glycan recognition in the pig lung, because influenza is broadly disseminated in swine, and swine have been postulated as an intermediary host for the emergence of pandemic strains. For these studies, we used the technology of "shotgun glycomics" to identify natural receptor glycans. The total released N- and O-glycans from pig lung glycoproteins and glycolipid-derived glycans were fluorescently tagged and separated by multidimensional HPLC, and individual glycans were covalently printed to generate pig lung shotgun glycan microarrays. All viruses tested interacted with one or more sialylated N-glycans but not O-glycans or glycolipid-derived glycans, and each virus demonstrated novel and unexpected differences in endogenous N-glycan recognition. The results illustrate the repertoire of specific, endogenous N-glycans of pig lung glycoproteins for virus recognition and offer a new direction for studying endogenous glycan functions in viral pathogenesis.

Infrared spectroscopic study of natural hydrotalcites carrboydite and hydrohonessite.

PubMed

Frost, Ray L; Weier, Matt L; Clissold, Meagan E; Williams, Peter A

2003-12-01

Infrared spectroscopy has proven most useful for the study of anions in the interlayer of natural hydrotalcites. A suite of naturally occurring hydrotalcites including carrboydite, hydrohonessite, reevesite, motukoreaite and takovite were analysed. Variation in the hydroxyl stretching region was observed and the band profile is a continuum of states resulting from the OH stretching of the hydroxyl and water units. Infrared spectroscopy identifies some isomorphic substitution of sulphate for carbonate through an anion exchange mechanism for the minerals carrboydite and hydrohonessite. The infrared spectra of the CO3 and SO4 stretching region of takovite is complex because of band overlap. For this mineral some sulphate has replaced the carbonate in the structure. In the spectra of takovites, a band is observed at 1346 cm(-1) and is attributed to the carbonate anion hydrogen bonded to water in the interlayer. Infrared spectroscopy has proven most useful for the study of the interlayer structure of these natural hydrotalcites.

A national assessment of underground natural gas storage: identifying wells with designs likely vulnerable to a single-point-of-failure

NASA Astrophysics Data System (ADS)

Michanowicz, Drew R.; Buonocore, Jonathan J.; Rowland, Sebastian T.; Konschnik, Katherine E.; Goho, Shaun A.; Bernstein, Aaron S.

2017-05-01

The leak of processed natural gas (PNG) from October 2015 to February 2016 from the Aliso Canyon storage facility, near Los Angeles, California, was the largest single accidental release of greenhouse gases in US history. The Interagency Task Force on Natural Gas Storage Safety and California regulators recently recommended operators phase out single-point-of-failure (SPF) well designs. Here, we develop a national dataset of UGS well activity in the continental US to assess regulatory data availability and uncertainty, and to assess the prevalence of certain well design deficiencies including single-point-of-failure designs. We identified 14 138 active UGS wells associated with 317 active UGS facilities in 29 states using regulatory and company data. State-level wellbore datasets contained numerous reporting inconsistencies that limited data concatenation. We identified 2715 active UGS wells across 160 facilities that, like the failed well at Aliso Canyon, predated the storage facility, and therefore were not originally designed for gas storage. The majority (88%) of these repurposed wells are located in OH, MI, PA, NY, and WV. Repurposed wells have a median age of 74 years, and the 2694 repurposed wells constructed prior to 1979 are particularly likely to exhibit design-related deficiencies. An estimated 210 active repurposed wells were constructed before 1917—before cement zonal isolation methods were utilized. These wells are located in OH, PA, NY, and WV and represent the highest priority related to potential design deficiencies that could lead to containment loss. This national baseline assessment identifies regulatory data uncertainties, highlights a potentially widespread vulnerability of the natural gas supply chain, and can aid in prioritization and oversight for high-risk wells and facilities.

Novel genetic capacitors and potentiators for the natural genetic variation of sensory bristles and their trait specificity in Drosophila melanogaster.

PubMed

Takahashi, Kazuo H

2015-11-01

Cryptic genetic variation (CGV) is defined as the genetic variation that has little effect on phenotypic variation under a normal condition, but contributes to heritable variation under environmental or genetic perturbations. Genetic buffering systems that suppress the expression of CGV and store it in a population are called genetic capacitors, and the opposite systems are called genetic potentiators. One of the best-known candidates for a genetic capacitor and potentiator is the molecular chaperone protein, HSP90, and one of its characteristics is that it affects the genetic variation in various morphological traits. However, it remains unclear whether the wide-ranging effects of HSP90 on a broad range of traits are a general feature of genetic capacitors and potentiators. In the current study, I searched for novel genetic capacitors and potentiators for quantitative bristle traits of Drosophila melanogaster and then investigated the trait specificity of their genetic buffering effect. Three bristle traits of D. melanogaster were used as the target traits, and the genomic regions with genetic buffering effects were screened using the 61 genomic deficiencies examined previously for genetic buffering effects in wing shape. As a result, four and six deficiencies with significant effects on increasing and decreasing the broad-sense heritability of the bristle traits were identified, respectively. Of the 18 deficiencies with significant effects detected in the current study and/or by the previous study, 14 showed trait-specific effects, and four affected the genetic buffering of both bristle traits and wing shape. This suggests that most genetic capacitors and potentiators exert trait-specific effects, but that general capacitors and potentiators with effects on multiple traits also exist. © 2015 John Wiley & Sons Ltd.

Variations on seepage water geochemistry induced by natural and anthropogenic microclimatic changes: Implications for the speleothems growth conditions

NASA Astrophysics Data System (ADS)

Fernandez-Cortes, A.; Sanchez-Moral, S.; Canaveras, J. C.; Cuevas, J.; Cuezva, S.; Andreu, J. M.; Abella, R.

2009-04-01

During an annual cycle the effect of microclimatic changes (natural and anthropogenic origin) on the geochemical characteristics of seepage water and mineral precipitation rates was analyzed, for two karstic caves under opposing environmental stability and energy exchange with exterior. On the one hand Castañar cave (Caceres, Spain), an extremely controlled show cave with limited visitation showing a minimum exchange rate of energy with the outer atmosphere and, secondly, Canelobre cave (Alicante, Spain), a widely visited cave where the anthropogenic impact generates both high-speed and high-energy environmental changes. Microclimatic variations play a key role in CO2-dessgasing caused by the imbalance of pCO2 between the karstic water and the cave air, favoring the slow processes of mineral precipitation. Thus, a pCO2-range of seepage water have been detected for each cave (from 10-2.30/-2.35 to 10-2.47/-2.52 bar for Castañar cave, and from 10-2.8/-2.85 to 10-2.95/-3.0 bar for Canelobre cave) where the mineral oversaturation prevails, determining the type and rate of mineral precipitation in each cave. Finally, it analyzes how the changes on the oversaturation/ precipitation states are controlled by microclimatic variations, such as: 1) natural underground air renewal through the porous system of upper soil and the network of host-rock fissures (isolating membranes), or else through the cave entrance, 2) cumulative disruptions in the pCO2 levels of cave air due to the presence of visitors, and 3) forced ventilation of the subterranean atmosphere due to the uncontrolled opening of cave entrances. The obtained results reinforce the significance of the microclimatic fluctuations on short time scales in the dynamic and evolution of the subterranean karst system, in terms of rates of mineral precipitation and growth of speleothems. Likewise the interpretations are useful in order to ensure the constant climate required for the conservation of caves.

Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation

PubMed Central

Blake, Jonathon; Riddell, Andrew; Theiss, Susanne; Gonzalez, Alexis Perez; Haase, Bettina; Jauch, Anna; Janssen, Johannes W. G.; Ibberson, David; Pavlinic, Dinko; Moog, Ute; Benes, Vladimir; Runz, Heiko

2014-01-01

Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception. PMID:24625750

Nuclear field shift in natural environments

NASA Astrophysics Data System (ADS)

Moynier, Frédéric; Fujii, Toshiyuki; Brennecka, Gregory A.; Nielsen, Sune G.

2013-03-01

The nuclear field shift (NFS) is an isotope shift in atomic energy levels caused by a combination of differences in nuclear size and shape and electron densities at the nucleus. The effect of NFS in isotope fractionation was theoretically established by Bigeleisen in 1996 [Bigeleisen J. (1996) J. Am. Chem. Soc. 118:3676-3680] and has been analytically measured in laboratory chemical exchange reactions. More recently, some isotopic variations of heavy elements (Hg, Tl, U) measured in natural systems as well as isotopic anomalies measured for lower-mass elements in meteorites have been attributed to the NFS effect. These isotopic variations open up new and exciting fields of investigations in Earth sciences. In this paper, we review the different natural systems in which NFS has been proposed to be the origin of isotopic variations.

Sources of floral scent variation

PubMed Central

Raguso, Robert A; Ashman, Tia-Lynn

2009-01-01

Studies of floral scent generally assume that genetic adaptation due to pollinator-mediated natural selection explains a significant amount of phenotypic variance, ignoring the potential for phenotypic plasticity in this trait. In this paper, we assess this latter possibility, looking first at previous studies of floral scent variation in relation to abiotic environmental factors. We then present data from our own research that suggests among-population floral scent variation is determined, in part, by environmental conditions and thus displays phenotypic plasticity. Such an outcome has strong ramifications for the study of floral scent variation; we conclude by presenting some fundamental questions that should lead to greater insight into our understanding of the evolution of this trait, which is important to plant-animal interactions. PMID:19649189

Natural products that reduce rotavirus infectivity identified by a cell-based moderate-throughput screening assay.

PubMed

Shaneyfelt, Mark E; Burke, Anna D; Graff, Joel W; Jutila, Mark A; Hardy, Michele E

2006-09-01

There is widespread interest in the use of innate immune modulators as a defense strategy against infectious pathogens. Using rotavirus as a model system, we developed a cell-based, moderate-throughput screening (MTS) assay to identify compounds that reduce rotavirus infectivity in vitro, toward a long-term goal of discovering immunomodulatory agents that enhance innate responses to viral infection. A natural product library consisting of 280 compounds was screened in the assay and 15 compounds that significantly reduced infectivity without cytotoxicity were identified. Time course analysis of four compounds with previously characterized effects on inflammatory gene expression inhibited replication with pre-treatment times as minimal as 2 hours. Two of these four compounds, alpha-mangostin and 18-beta-glycyrrhetinic acid, activated NFkappaB and induced IL-8 secretion. The assay is adaptable to other virus systems, and amenable to full automation and adaptation to a high-throughput format. Identification of several compounds with known effects on inflammatory and antiviral gene expression that confer resistance to rotavirus infection in vitro suggests the assay is an appropriate platform for discovery of compounds with potential to amplify innate antiviral responses.

Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja.

PubMed

Duarte-Delgado, Diana; Juyó, Deissy; Gebhardt, Christiane; Sarmiento, Felipe; Mosquera-Vásquez, Teresa

2017-03-09

Potato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, which is mainly diploid and represents an important genetic resource for potato breeding. The objective of this research was to identify novel genetic variants related with frying quality in loci with key functions in carbohydrate metabolism, with the purpose of discovering genetic variability useful in breeding programs. Therefore, an association analysis was implemented with 109 SNP markers identified in ten candidate genes. The analyses revealed four associations in the locus InvGE coding for an apoplastic invertase and one association in the locus SssI coding for a soluble starch synthase. The SNPs SssI-C 45711901 T and InvGE-C 2475454 T were associated with sucrose content and frying color, respectively, and were not found previously in tetraploid genotypes. The rare haplotype InvGE-A 2475187 C 2475295 A 2475344 was associated with higher fructose contents. Our study allowed a more detailed analysis of the sequence variation of exon 3 from InvGE, which was not possible in previous studies because of the high frequency of insertion-deletion polymorphisms in tetraploid potatoes. The association mapping strategy using a candidate gene approach in Group Phureja allowed the identification of novel SNP markers in InvGE and SssI associated with frying color and the tuber sugar content measured by High Performance Liquid Chromatography (HPLC). These novel associations might be useful in potato breeding programs for improving quality traits and to increase crop genetic variability. The results suggest that some genes involved in the natural variation of tuber sugar content and frying color are conserved in both Phureja and tetraploid germplasm. Nevertheless, the associated variants in both types of germplasm were present in different regions of these genes. This

Variation in Essential Oil and Bioactive Compounds of Curcuma kwangsiensis Collected from Natural Habitats.

PubMed

Zhang, Lanyue; Yang, Zhiwen; Huang, Zebin; Zhao, Mincong; Li, Penghui; Zhou, Wei; Zhang, Kun; Zheng, Xi; Lin, Li; Tang, Jian; Fang, Yanxiong; Du, Zhiyun

2017-07-01

The chemical compositions of essential oils (EOs) extracted from Curcuma kwangsiensis rhizomes collected from six natural habitats in P. R. China were evaluated using gas chromatography/mass spectrometry (GC/MS). Fifty-seven components were identified from the six EOs, and their main constituents were 8,9-dehydro-9-formyl-cycloisolongifolene (2.37 - 42.59%), germacrone (6.53 - 22.20%), and l-camphor (0.19 - 6.12%). The six EOs exhibited different DPPH radical-scavenging activities (IC 50 , 2.24 - 31.03 μg/ml), with the activity of most of EOs being much higher than that of Trolox C (IC 50 , 10.49 μg/ml) and BHT (IC 50 , 54.13 μg/ml). Most EOs had potent antimicrobial effects against the tested bacteria and fungus. They also exhibited cytotoxicity against B16 (IC 50 , 4.44 - 147.4 μg/ml) and LNCaP cells (IC 50 , 73.94 - 429.25 μg/ml). The EOs showed excellent anti-inflammatory action by significantly downregulating expression of pro-inflammatory cytokines, cyclooxygenase-2, and tumor necrosis factor-α. This study provides insight into the interrelation among growth location, phytoconstituents, and bioactivities, and the results indicate the potential of C. kwangsiensis as natural nutrients, medicines, and others additives. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Spatiotemporal Variations and Driving Factors of Air Pollution in China.

PubMed

Zhan, Dongsheng; Kwan, Mei-Po; Zhang, Wenzhong; Wang, Shaojian; Yu, Jianhui

2017-12-08

In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP) witness the strongest and most significant positive effects on air pollution ratio.

Spatiotemporal Variations and Driving Factors of Air Pollution in China

PubMed Central

Zhan, Dongsheng; Zhang, Wenzhong; Wang, Shaojian; Yu, Jianhui

2017-01-01

In recent years, severe and persistent air pollution episodes in China have drawn wide public concern. Based on ground monitoring air quality data collected in 2015 in Chinese cities above the prefectural level, this study identifies the spatiotemporal variations of air pollution and its associated driving factors in China using descriptive statistics and geographical detector methods. The results show that the average air pollution ratio and continuous air pollution ratio across Chinese cities in 2015 were 23.1 ± 16.9% and 16.2 ± 14.8%. The highest levels of air pollution ratio and continuous air pollution ratio were observed in northern China, especially in the Bohai Rim region and Xinjiang province, and the lowest levels were found in southern China. The average and maximum levels of continuous air pollution show distinct spatial variations when compared with those of the continuous air pollution ratio. Monthly changes in both air pollution ratio and continuous air pollution ratio have a U-shaped variation, indicating that the highest levels of air pollution occurred in winter and the lowest levels happened in summer. The results of the geographical detector model further reveal that the effect intensity of natural factors on the spatial disparity of the air pollution ratio is greater than that of human-related factors. Specifically, among natural factors, the annual average temperature, land relief, and relative humidity have the greatest and most significant negative effects on the air pollution ratio, whereas human factors such as population density, the number of vehicles, and Gross Domestic Product (GDP) witness the strongest and most significant positive effects on air pollution ratio. PMID:29292783

Functional variation in the gut microbiome of wild Drosophila populations.

PubMed

Bost, Alyssa; Martinson, Vincent G; Franzenburg, Soeren; Adair, Karen L; Albasi, Alice; Wells, Martin T; Douglas, Angela E

2018-05-26

Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Variation and evolution of male sex combs in Drosophila: nature of selection response and theories of genetic variation for sexual traits.

PubMed

Ahuja, Abha; Singh, Rama S

2008-05-01

We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.

Gender variations in the optical properties of skin in murine animal models

NASA Astrophysics Data System (ADS)

Calabro, Katherine; Curtis, Allison; Galarneau, Jean-Rene; Krucker, Thomas; Bigio, Irving J.

2011-01-01

Gender is identified as a significant source of variation in optical reflectance measurements on mouse skin, with variation in the thickness of the dermal layer being the key explanatory variable. For three different mouse strains, the thickness values of the epidermis, dermis, and hypodermis layers, as measured by histology, are correlated to optical reflectance measurements collected with elastic scattering spectroscopy (ESS). In all three strains, males are found to have up to a 50% increase in dermal thickness, resulting in increases of up to 80% in reflectance values and higher observed scattering coefficients, as compared to females. Collagen in the dermis is identified as the primary source of these differences due to its strong scattering nature; increased dermal thickness leads to a greater photon path length through the collagen, as compared to other layers, resulting in a larger scattering signal. A related increase in the observed absorption coefficient in females is also observed. These results emphasize the importance of considering gender during experimental design in studies that involve photon interaction with mouse skin. The results also elucidate the significant impact that relatively small thickness changes can have on observed optical measurements in layered tissue.

Statistics, Uncertainty, and Transmitted Variation

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

Wendelberger, Joanne Roth

2014-11-05

The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

A variational approach to niche construction

PubMed Central

Ramstead, Maxwell J. D.; Veissière, Samuel P. L.; Campbell, John O.; Friston, Karl J.

2018-01-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. PMID:29643221

Fluctuations in food supply drive recruitment variation in a marine fish.

PubMed

Okamoto, Daniel K; Schmitt, Russell J; Holbrook, Sally J; Reed, Daniel C

2012-11-22

Reproductive rates and survival of young in animal populations figure centrally in generating management and conservation strategies. Model systems suggest that food supply can drive these often highly variable properties, yet for many wild species, quantifying such effects and assessing their implications have been challenging. We used spatially explicit time series of a well-studied marine reef fish (black surfperch Embiotoca jacksoni) and its known prey resources to evaluate the extent to which fluctuations in food supply influenced production of young by adults and survival of young to subadulthood. Our analyses reveal: (i) variable food available to both adults and to their offspring directly produced an order of magnitude variation in the number of young-of-year (YOY) produced per adult and (ii) food available to YOY produced a similar magnitude of variation in their subsequent survival. We also show that such large natural variation in vital rates can significantly alter decision thresholds (biological reference points) important for precautionary management. These findings reveal how knowledge of food resources can improve understanding of population dynamics and reduce risk of overharvest by more accurately identifying periods of low recruitment.

Identifying genes affectng stress response in rainbow trout

USDA-ARS?s Scientific Manuscript database

Genomic analyses have the potential to impact aquaculture production traits by identifying markers as proxies for traits which are expensive or difficult to measure and characterizing genetic variation and biochemical mechanisms underlying phenotypic variation. One such set of traits are the respon...

Natural variations in the rhenium isotopic composition of meteorites

NASA Astrophysics Data System (ADS)

Liu, R.; Hu, L.; Humayun, M.

2017-03-01

Rhenium is an important element with which to test hypotheses of isotope variation. Historically, it has been difficult to precisely correct the instrumental mass bias in thermal ionization mass spectrometry. We used W as an internal standard to correct mass bias on the MC-ICP-MS, and obtained the first precise δ187Re values ( ±0.02‰, 2SE) for iron meteorites and chondritic metal. Relative to metal from H chondrites, IVB irons are systematically higher in δ187Re by 0.14 ‰. δ187Re for other irons are similar to H chondritic metal, although some individual samples show significant isotope fractionation. Since 185Re has a high neutron capture cross section, the effect of galactic cosmic-ray (GCR) irradiation on δ187Re was examined using correlations with Pt isotopes. The pre-GCR irradiation δ187Re for IVB irons is lower, but the difference in δ187Re between IVB irons and other meteoritic metal remains. Nuclear volume-dependent fractionation for Re is about the right magnitude near the melting point of iron, but because of the refractory and compatible character of Re, a compelling explanation in terms of mass-dependent fractionation is elusive. The magnitude of a nucleosynthetic s-process deficit for Re estimated from Mo and Ru isotopes is essentially unresolvable. Since thermal processing reduced nucleosynthetic effects in Pd, it is conceivable that Re isotopic variations larger than those in Mo and Ru may be present in IVBs since Re is more refractory than Mo and Ru. Thus, the Re isotopic difference between IVBs and other irons or chondritic metal remains unexplained.

Modeling Modern Methane Emissions from Natural Wetlands. 2; Interannual Variations 1982-1993

NASA Technical Reports Server (NTRS)

Walter, Bernadette P.; Heimann, Martin; Mattews, Elaine; Hansen, James E. (Technical Monitor)

2001-01-01

A global run of a process-based methane model [Walter et al., this issue] is performed using high-frequency atmospheric forcing fields from ECMWF reanalyses of the period from 1982 to 1993. We calculate global annual methane emissions to be 260 Tg/ yr. 25% of methane emissions originate from wetlands north of 30 deg. N. Only 60% of the produced methane is emitted, while the rest is re-oxidized. A comparison of zonal integrals of simulated global wetland emissions and results obtained by an inverse modeling approach shows good agreement. In a test with data from two wetlands, the seasonality of simulated and observed methane emissions agrees well. The effects of sub-grid scale variations in model parameters and input data are examined. Modeled methane emissions show high regional, seasonal and interannual variability. Seasonal cycles of methane emissions are dominated by temperature in high latitude wetlands, and by changes in the water table in tropical wetlands. Sensitivity tests show that +/- 1 C changes in temperature lead to +/- 20 % changes in methane emissions from wetlands. Uniform changes of +/- 20% in precipitation alter methane emissions by about +/- 18%. Limitations in the model are analyzed. Simulated interannual variations in methane emissions from wetlands are compared to observed atmospheric growth rate anomalies. Our model simulation results suggest that contributions from other sources than wetlands and/or the sinks are more important in the tropics than north-of 30 deg. N. In higher northern latitudes, it seems that a large part, of the observed interannual variations can be explained by variations in wetland emissions. Our results also suggest that reduced wetland emissions played an important role in the observed negative methane growth rate anomaly in 1992.

The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention

PubMed Central

Akhund-Zade, Jamilla; Bergland, Alan O.; Crowe, Sarah O.; Unckless, Robert L.

2017-01-01

Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A. Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention. PMID:28042107

Identifying Interacting Genetic Variations by Fish-Swarm Logic Regression

PubMed Central

Yang, Aiyuan; Yan, Chunxia; Zhu, Feng; Zhao, Zhongmeng; Cao, Zhi

2013-01-01

Understanding associations between genotypes and complex traits is a fundamental problem in human genetics. A major open problem in mapping phenotypes is that of identifying a set of interacting genetic variants, which might contribute to complex traits. Logic regression (LR) is a powerful multivariant association tool. Several LR-based approaches have been successfully applied to different datasets. However, these approaches are not adequate with regard to accuracy and efficiency. In this paper, we propose a new LR-based approach, called fish-swarm logic regression (FSLR), which improves the logic regression process by incorporating swarm optimization. In our approach, a school of fish agents are conducted in parallel. Each fish agent holds a regression model, while the school searches for better models through various preset behaviors. A swarm algorithm improves the accuracy and the efficiency by speeding up the convergence and preventing it from dropping into local optimums. We apply our approach on a real screening dataset and a series of simulation scenarios. Compared to three existing LR-based approaches, our approach outperforms them by having lower type I and type II error rates, being able to identify more preset causal sites, and performing at faster speeds. PMID:23984382

Geographic and phenotypic variation in heartwood and essential-oil characters in natural populations of Santalum austrocaledonicum in Vanuatu.

PubMed

Page, Tony; Southwell, Ian; Russell, Mike; Tate, Hanington; Tungon, Joseph; Sam, Chanel; Dickinson, Geoff; Robson, Ken; Leakey, Roger R B

2010-08-01

Phenotypic variation in heartwood and essential-oil characters of Santalum austrocaledonicum was assessed across eleven populations on seven islands of Vanuatu. Trees differed significantly in their percentage heartwood cross-sectional area and this varied independently of stem diameter. The concentrations of the four major essential-oil constituents (alpha-santalol, beta-santalol, (Z)-beta-curcumen-12-ol, and cis-nuciferol) of alcohol-extracted heartwood exhibited at least tenfold and continuous tree-to-tree variation. Commercially important components alpha- and beta-santalol found in individual trees ranged from 0.8-47% and 0-24.1%, respectively, across all populations, and significant (P<0.05) differences for each were found between individual populations. The Erromango population was unique in that the mean concentrations of its monocyclic ((Z)-beta-curcumen-12-ol and cis-nuciferol) sesquiterpenes exceeded those of its bi- and tricyclic (alpha- and beta-santalol) sesquiterpenes. Heartwood colour varied between trees and spanned 65 colour categories, but no identifiable relationships were found between heartwood colour and alpha- and beta-santalol, although a weak relationship was evident between colour saturation and total oil concentration. These results indicate that the heartwood colour is not a reliable predictive trait for oil quality. The results of this study highlight the knowledge gaps in fundamental understanding of heartwood biology in Santalum genus. The intraspecific variation in heartwood cross-sectional area, oil concentration, and oil quality traits is of considerable importance to the domestication of sandalwood and present opportunities for the development of highly superior S. austrocaledonicum cultivars that conform to the industry's International Standards used for S. album.

Effects of source and seasonal variations of natural organic matters on the fate and transport of CeO2 nanoparticles in the environment.

PubMed

Li, Zhen; Sahle-Demessie, Endalkachew; Aly Hassan, Ashraf; Pressman, Jonathan G; Sorial, George A; Han, Changseok

2017-12-31

Natural organic matter (NOM) affects the stability and transport of nanoparticles (NPs) in natural waters by modifying their physiochemical properties. Source location, and seasonal variations, influence their molecular, physical and electrical charge properties. To understand the variations of NOM on the mobilization of NPs, large volumes of water were collected from the Ohio River (OR) over winter and summer seasons and dissolved NOMs were concentrated. The chemical and structural differences of these NOMs were compared with the Suwannee River humic acid (SRHA) SRHA using 1 H and 13 C nuclear magnetic resonance spectroscopy, and Fourier transforms infrared (FTIR) spectroscopy. Thermal analysis and FTIR confirmed that differences in composition, structure, and functional groups are a result of SRHA fractionation compared to whole molecule OR-NOM. The influence of OR-NOMs on the surface charge of CeO 2 NPs and the effects on the transport and retention in a three-phase (deposition-rinse-re-entrainment) sand-packed columns were investigated at CeO 2 NPs initial concertation of 10ppm, pH6.8, increasing ionic strength (3, 5, and 10mM), retention time of 1min, and increasing NOM concentration (1, 5, and 10ppm). The summer OR-NOM showed higher stabilization and mobilization effect on the CeO 2 than the winter NOM; while their effect was very different form the SRHA. The stabilization of NPs is attributed to both electrostatic and steric effects. The differences in the chemical structure of the complex and heterogeneous NOMs showed disparate reactivity and direct impact on CeO 2 -NPs stability. Using SRHA to study the effect of NOM for drinking water related assessment does not sufficiently represent the natural conditions of the environment. Published by Elsevier B.V.

A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)

PubMed Central

Li, M-H; Tiirikka, T; Kantanen, J

2014-01-01

In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10−11 for all the colours; P=2.3 × 10−11 for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding. PMID:24022497

Use of natural pH variation to increase the flocculation of the marine microalgae Nannochloropsis oculata.

PubMed

Sales, Rafael; Abreu, Paulo Cesar

2015-02-01

Microalgae is largely used in aquaculture as feed. More recently, these microorganisms have been considered as an important feedstock for biodiesel production. However, the concentration of produced biomass represents a large parcel of production costs. In this study, we have evaluated the influence of natural pH variation of culture medium, caused by photosynthetic activity, on the flocculation of the marine microalgae Nannochloropsis oculata. Experiments were conducted with the same culture with different pH values (8.5 and 9.6), obtained after exposing the cells to different light conditions. For each pH value, different treatments were composed by adding 0, 5, 10, and 30 mM of NaOH and the flocculant Flopam® (FO4800 SH) at concentrations of 0, 0.5, 1, and 5 ppm. Higher flocculation efficiencies were obtained for the culture with pH 9.6 in comparison to 8.5 for the same NaOH and Flopam concentrations. Lower concentrations of base and flocculant were needed for flocculating the culture in higher pH, representing an economy of 20 % in the costs of crop harvesting.

A variational approach to niche construction.

PubMed

Constant, Axel; Ramstead, Maxwell J D; Veissière, Samuel P L; Campbell, John O; Friston, Karl J

2018-04-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. © 2018 The Authors.

mRNA Expression Signatures of Human Skeletal Muscle Atrophy Identify a Natural Compound that Increases Muscle Mass

PubMed Central

Kunkel, Steven D.; Suneja, Manish; Ebert, Scott M.; Bongers, Kale S.; Fox, Daniel K.; Malmberg, Sharon E.; Alipour, Fariborz; Shields, Richard K.; Adams, Christopher M.

2011-01-01

SUMMARY Skeletal muscle atrophy is a common and debilitating condition that lacks a pharmacologic therapy. To develop a potential therapy, we identified 63 mRNAs that were regulated by fasting in both human and mouse muscle, and 29 mRNAs that were regulated by both fasting and spinal cord injury in human muscle. We used these two unbiased mRNA expression signatures of muscle atrophy to query the Connectivity Map, which singled out ursolic acid as a compound whose signature was opposite to those of atrophy-inducing stresses. A natural compound enriched in apples, ursolic acid reduced muscle atrophy and stimulated muscle hypertrophy in mice. It did so by enhancing skeletal muscle insulin/IGF-I signaling, and inhibiting atrophy-associated skeletal muscle mRNA expression. Importantly, ursolic acid’s effects on muscle were accompanied by reductions in adiposity, fasting blood glucose and plasma cholesterol and triglycerides. These findings identify a potential therapy for muscle atrophy and perhaps other metabolic diseases. PMID:21641545

Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains.

PubMed

Steenwyk, Jacob; Rokas, Antonis

2017-05-05

Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S. cerevisiae wine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance ( CUP ), flocculation ( FLO ), and glucose metabolism ( HXT ), as well as the SNO gene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation. Copyright © 2017 Steenwyk and Rokas.

Effects of a Changing Climate on Seasonal Variation in Natural Recharge of Unconfined Coastal Aquifers

NASA Astrophysics Data System (ADS)

Antonellini, Marco; Nella Mollema, Pauline

2013-04-01

Irregular rainfall patterns throughout the year result in the discontinuous natural recharge of coastal aquifers, which has an effect on the size of freshwater lenses present in sandy deposits. The thickness of the freshwater lenses is important in the context of farmland salinization and coastal ecosystems survival. This study presents numerical models that simulate continuous and discontinuous recharge in sandy coastal aquifers and the thickness of resulting fresh water lenses under current and future climate scenarios. Temperature data for the period 1960-1990 from LOCCLIM FAO and from the IPCC SRES A1b scenario for 2070-2100, have been used to calculate the potential evapotranspiration. Potential recharge was defined as the difference between the precipitation and potential evapotranspiration in twelve locations around the world: Ameland (The Netherlands), Auckland and Wellington (New Zealand), Hong Kong, Ravenna (Italy), Mekong (Vietnam), Mumbai (India), New Jersey (USA), Nile Delta (Egypt), Kobe and Tokyo (Japan), and Singapore. These locations have shallow coastal aquifers along low lying coasts and comparable aquifer structure, which is the result of similar sediment supply and deposition in the Holocene as well as by the sea level changes from the last ice age to the present time. Particular attention has been paid to temporal variations of natural recharge that can vary from continuous recharge throughout the year to discontinuous recharge. The most dramatic reduction in the magnitude of potential annual recharge by the end of this century will occur at lower latitudes (Mumbai, Singapore, Hong Kong and Mekong). The most pronounced change in length of the dry period occurs for Kobe (Japan) and Singapore even though the total annual amount of recharge remains practically the same. The Influence of variable recharge on the size of freshwater lenses surrounded by saline water is simulated with the SEAWAT model. Models where the recharge is applied

A Simple Test Identifies Selection on Complex Traits.

PubMed

Beissinger, Tim; Kruppa, Jochen; Cavero, David; Ha, Ngoc-Thuy; Erbe, Malena; Simianer, Henner

2018-05-01

Important traits in agricultural, natural, and human populations are increasingly being shown to be under the control of many genes that individually contribute only a small proportion of genetic variation. However, the majority of modern tools in quantitative and population genetics, including genome-wide association studies and selection-mapping protocols, are designed to identify individual genes with large effects. We have developed an approach to identify traits that have been under selection and are controlled by large numbers of loci. In contrast to existing methods, our technique uses additive-effects estimates from all available markers, and relates these estimates to allele-frequency change over time. Using this information, we generate a composite statistic, denoted [Formula: see text] which can be used to test for significant evidence of selection on a trait. Our test requires pre- and postselection genotypic data but only a single time point with phenotypic information. Simulations demonstrate that [Formula: see text] is powerful for identifying selection, particularly in situations where the trait being tested is controlled by many genes, which is precisely the scenario where classical approaches for selection mapping are least powerful. We apply this test to breeding populations of maize and chickens, where we demonstrate the successful identification of selection on traits that are documented to have been under selection. Copyright © 2018 Beissinger et al.

Maximizing vegetation response on management burns by identifying fire regimes

Treesearch

V. Thomas Parker

1989-01-01

Maintenance of vegetation is a central goal of watershed management. When prescribed burning of chaparral is included in management practice, then it is important for managers to understand and use the natural chaparral fire regime to maximize vegetation response. Variations from the natural fire regime in intensity, frequency, season, and environmental conditions at...

Evolutionary biology: variation isn't always sexy.

PubMed

Safran, Rebecca J; Hauber, Mark E

2007-05-15

A recent study has found that differences in a male trait, considered a textbook example of sexual selection, are in fact due to naturally selected variation in the aerodynamic optimum for each individual.

Testing the niche variation hypothesis with a measure of body condition

EPA Science Inventory

Individual variation and fitness are cornerstones of evolution by natural selection. The niche variation hypothesis (NVH) posits that when interspecific competition is relaxed, intraspecific competition should drive niche expansion by selection favoring use of novel resources. Po...

Sperm Competitive Ability in Drosophila melanogaster Associated With Variation in Male Reproductive Proteins

PubMed Central

Fiumera, Anthony C.; Dumont, Bethany L.; Clark, Andrew G.

2005-01-01

Multiple mating by females establishes the opportunity for postcopulatory sexual selection favoring males whose sperm is preferentially employed in fertilizations. Here we use natural variation in a wild population of Drosophila melanogaster to investigate the genetic basis of sperm competitive ability. Approximately 101 chromosome 2 substitution lines were scored for components of sperm competitive ability (P1′, P2′, fecundity, remating rate, and refractoriness), genotyped at 70 polymorphic markers in 10 male reproductive genes, and measured for transcript abundance of those genes. Permutation tests were applied to quantify the statistical significance of associations between genotype and phenotype. Nine significant associations were identified between polymorphisms in the male reproductive genes and sperm competitive ability and 13 were identified between genotype and transcript abundance, but no significant associations were found between transcript abundance and sperm competitive ability. Pleiotropy was evident in two genes: a polymorphism in Acp33A associated with both P1′ and P2′ and a polymorphism in CG17331 associated with both elevated P2′ and reduced refractoriness. The latter case is consistent with antagonistic pleiotropy and may serve as a mechanism maintaining genetic variation. PMID:15466425

Dopa decarboxylase (Ddc) affects variation in Drosophila longevity.

PubMed

De Luca, Maria; Roshina, Nataliya V; Geiger-Thornsberry, Gretchen L; Lyman, Richard F; Pasyukova, Elena G; Mackay, Trudy F C

2003-08-01

Mutational analyses in model organisms have shown that genes affecting metabolism and stress resistance regulate life span, but the genes responsible for variation in longevity in natural populations are largely unidentified. Previously, we mapped quantitative trait loci (QTLs) affecting variation in longevity between two Drosophila melanogaster strains. Here, we show that the longevity QTL in the 36E;38B cytogenetic interval on chromosome 2 contains multiple closely linked QTLs, including the Dopa decarboxylase (Ddc) locus. Complementation tests to mutations show that Ddc is a positional candidate gene for life span in these strains. Linkage disequilibrium (LD) mapping in a sample of 173 alleles from a single population shows that three common molecular polymorphisms in Ddc account for 15.5% of the genetic contribution to variance in life span from chromosome 2. The polymorphisms are in strong LD, and the effects of the haplotypes on longevity suggest that the polymorphisms are maintained by balancing selection. DDC catalyzes the final step in the synthesis of the neurotransmitters, dopamine and serotonin. Thus, these data implicate variation in the synthesis of bioamines as a factor contributing to natural variation in individual life span.

Molecular Darwinism: The Contingency of Spontaneous Genetic Variation

PubMed Central

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions. PMID:21979160

Molecular Darwinism: the contingency of spontaneous genetic variation.

PubMed

Arber, Werner

2011-01-01

The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

Strain Prioritization for Natural Product Discovery by a High-Throughput Real-Time PCR Method

PubMed Central

2015-01-01

Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered. PMID:25238028

Heterotaxy in Caenorhabditis: widespread natural variation in left–right arrangement of the major organs

PubMed Central

Callander, Davon C.; López-Santos, Agustín; Torres Cleuren, Yamila N.; Santure, Anna W.

2016-01-01

Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness, we found that L/R asymmetry of the major organs, the gut and gonad, varies among natural isolates of the species in both males and hermaphrodites. In hermaphrodites, heterotaxy can involve one or both bilaterally asymmetric gonad arms. Male heterotaxy is probably not attributable to relaxed selection in this hermaphroditic species, as it is also seen in gonochoristic Caenorhabditis species. Heterotaxy increases in many isolates at elevated temperature, with one showing a pregastrulation temperature-sensitive period, suggesting a very early embryonic or germline effect on this much later developmental outcome. A genome-wide association study of 100 isolates showed that male heterotaxy is associated with three genomic regions. Analysis of recombinant inbred lines suggests that a small number of loci are responsible for the observed variation. These findings reveal that heterotaxy is a widely varying quantitative trait in an animal with an otherwise highly stereotyped anatomy, demonstrating unexpected plasticity in an L/R arrangement of the major organs even in a simple animal. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821534

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

Segregating Variation in the Polycomb Group Gene cramped Alters the Effect of Temperature on Multiple Traits

PubMed Central

Gibert, Jean-Michel; Karch, François; Schlötterer, Christian

2011-01-01

The phenotype produced by a given genotype can be strongly modulated by environmental conditions. Therefore, natural populations continuously adapt to environment heterogeneity to maintain optimal phenotypes. It generates a high genetic variation in environment-sensitive gene networks, which is thought to facilitate evolution. Here we analyze the chromatin regulator crm, identified as a candidate for adaptation of Drosophila melanogaster to northern latitudes. We show that crm contributes to environmental canalization. In particular, crm modulates the effect of temperature on a genomic region encoding Hedgehog and Wingless signaling effectors. crm affects this region through both constitutive heterochromatin and Polycomb silencing. Furthermore, we show that crm European and African natural variants shift the reaction norms of plastic traits. Interestingly, traits modulated by crm natural variants can differ markedly between Drosophila species, suggesting that temperature adaptation facilitates their evolution. PMID:21283785

The Evolution of Personality Variation in Humans and Other Animals

ERIC Educational Resources Information Center

Nettle, Daniel

2006-01-01

A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article…

Continuous flow analysis combined with a light-absorption ratio variation approach for determination of copper at ng/ml level in natural water.

PubMed

Gao, Hong-Wen; Wang, Chun-Lei; Jia, Jiang-Yan; Zhang, Ya-Lei

2007-06-01

The complexation between Cu(II) and naphthochrome green (NG) is very sensitive at pH 4.09 with the formation of complex ion [Cu(NG)2(H2O)2](2-). It can thus used for the determination of Cu(II) by the light-absorption ratio variation approach (LARVA) with a good selectivity. Both the ordinary detection procedure and continuous flow analysis (CFA) were carried out, where the latter is fit for continuous and rapid analysis of samples. The limit of detection (LOD) of Cu(II) is only 1 ng/ml, which is favorable for direct monitoring of natural water. About 30 samples could be analyzed per hour by CFA. Cu(II) contents in Yangtze River, West Lake, Taihu Lake of China and seawater near Shanghai were determined with satisfactory results. The CFA-LARVA spectrophotometry was the first to be coupled and it will play an important role in the in-situ analysis of natural water quality.

An Evaluation of a Natural Language Processing Tool for Identifying and Encoding Allergy Information in Emergency Department Clinical Notes

PubMed Central

Goss, Foster R.; Plasek, Joseph M.; Lau, Jason J.; Seger, Diane L.; Chang, Frank Y.; Zhou, Li

2014-01-01

Emergency department (ED) visits due to allergic reactions are common. Allergy information is often recorded in free-text provider notes; however, this domain has not yet been widely studied by the natural language processing (NLP) community. We developed an allergy module built on the MTERMS NLP system to identify and encode food, drug, and environmental allergies and allergic reactions. The module included updates to our lexicon using standard terminologies, and novel disambiguation algorithms. We developed an annotation schema and annotated 400 ED notes that served as a gold standard for comparison to MTERMS output. MTERMS achieved an F-measure of 87.6% for the detection of allergen names and no known allergies, 90% for identifying true reactions in each allergy statement where true allergens were also identified, and 69% for linking reactions to their allergen. These preliminary results demonstrate the feasibility using NLP to extract and encode allergy information from clinical notes. PMID:25954363

Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression.

PubMed

Chen, Carla Chia-Ming; Schwender, Holger; Keith, Jonathan; Nunkesser, Robin; Mengersen, Kerrie; Macrossan, Paula

2011-01-01

Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.

Identify and Quantify the Mechanistic Sources of Sensor Performance Variation Between Individual Sensors SN1 and SN2

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

Diaz, Aaron A.; Baldwin, David L.; Cinson, Anthony D.

2014-08-06

This Technical Letter Report satisfies the M3AR-14PN2301022 milestone, and is focused on identifying and quantifying the mechanistic sources of sensor performance variation between individual 22-element, linear phased-array sensor prototypes, SN1 and SN2. This effort constitutes an iterative evolution that supports the longer term goal of producing and demonstrating a pre-manufacturing prototype ultrasonic probe that possesses the fundamental performance characteristics necessary to enable the development of a high-temperature sodium-cooled fast reactor inspection system. The scope of the work for this portion of the PNNL effort conducted in FY14 includes performing a comparative evaluation and assessment of the performance characteristics of themore » SN1 and SN2 22 element PA-UT probes manufactured at PNNL. Key transducer performance parameters, such as sound field dimensions, resolution capabilities, frequency response, and bandwidth are used as a metric for the comparative evaluation and assessment of the SN1 and SN2 engineering test units.« less

Evaluation of aging and hydration in natural volcanic glass: magnetic property variations during artificial aging and hydration experiments

NASA Astrophysics Data System (ADS)

Bowles, J. A.; Patiman, A.

2017-12-01

The recorded geomagnetic field intensity is a function of magnetic mineralogy, grain size, and mineral concentration as well as material stability in nature and during laboratory experiments. Fresh, unhydrated, volcanic glasses are recognized as a nearly ideal natural material for use in paleointensity experiments because they contain the requisite single domain to pseudo-single-domain magnetic particles. Although alteration of magnetic mineralogy can be monitored during the experiments, it is unclear how mineralogy and hence magnetization might change with age as the metastable glass structure relaxes and/or the glass becomes hydrated. Bulk magnetic properties as a function of age show no clear trend, even over hundreds of millions of years. This may be due to the fact that even in fresh, unhydrated glass, there are small-scale differences in magnetic properties due to variation cooling rate or composition variations. Therefore, in order to better understand how magnetic mineralogy evolves with time and hydration, we conducted artificial aging and hydration experiments on fresh, unhydrated rhyolitic (South Deadman Creek, California, 650-yr) and basaltic (Axial Seamount, 2011) end-member glasses. Here, we present the results of artificial aging and hydration experiments. Elevated temperatures accelerate the glass relaxation process in a way that relaxation time decreases with increasing temperature. Aged samples are dry-annealed at 200, 300 and 400 °C for up to 240 days. A second set of samples are hydrated under pressure at 300°C and 450°C. In all cases, isothermal remanent magnetization (IRM) acquisition is monitored to assess changes in the coercivity spectrum and saturation IRM. Preliminary aging results show that in basaltic and rhyolitic glass there is one main peak coercivity at 150 mT and 35 mT, respectively. An increasing sIRM and decreasing peak coercivity trend is observed in basaltic glass whereas no trend is shown in the rhyolitic glass in both

Temporal variations in natural attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediments impacted by a contaminated groundwater plume.

PubMed

Hamonts, Kelly; Kuhn, Thomas; Vos, Johan; Maesen, Miranda; Kalka, Harald; Smidt, Hauke; Springael, Dirk; Meckenstock, Rainer U; Dejonghe, Winnie

2012-04-15

Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. Biotransformation, sorption and dilution of CAHs in the impacted river sediments have been reported to reduce discharge, but the effect of temporal variations in environmental conditions on the occurrence and extent of those processes in river sediments is largely unknown. We monitored the reduction of CAH discharge into the Zenne River during a 21-month period. Despite a relatively stable influx of CAHs from the groundwater, the total reduction in CAH discharge from 120 to 20 cm depth in the river sediments, on average 74 ± 21%, showed moderate to large temporal variations, depending on the riverbed location. High organic carbon and anaerobic conditions in the river sediments allowed microbial reductive dechlorination of both chlorinated ethenes and chlorinated ethanes. δ(13)C values of the CAHs showed that this biotransformation was remarkably stable over time, despite fluctuating pore water temperatures. Daughter products of the CAHs, however, were not detected in stoichiometric amounts and suggested the co-occurrence of a physical process reducing the concentrations of CAHs in the riverbed. This process was the main process causing temporal variations in natural attenuation of the CAHs and was most likely dilution by surface water-mixing. However, higher spatial resolution monitoring of flow transients in the riverbed is required to prove dilution contributions due to dynamic surface water-groundwater flow exchanges. δ(13)C values and a site-specific isotope enrichment factor for reductive dechlorination of the main groundwater pollutant vinyl chloride (VC) allowed assessment of changes over time in the extent of both biotransformation and dilution of VC for different scenarios in which those processes either occurred consecutively or simultaneously between 120 and 20 cm depth in the riverbed. The extent of reductive dechlorination of VC ranged from 27

New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18.

PubMed

Paulus, Constanze; Rebets, Yuriy; Tokovenko, Bogdan; Nadmid, Suvd; Terekhova, Larisa P; Myronovskyi, Maksym; Zotchev, Sergey B; Rückert, Christian; Braig, Simone; Zahler, Stefan; Kalinowski, Jörn; Luzhetskyy, Andriy

2017-02-10

Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual α-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family - lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites.

New natural products identified by combined genomics-metabolomics profiling of marine Streptomyces sp. MP131-18

PubMed Central

Paulus, Constanze; Rebets, Yuriy; Tokovenko, Bogdan; Nadmid, Suvd; Terekhova, Larisa P.; Myronovskyi, Maksym; Zotchev, Sergey B.; Rückert, Christian; Braig, Simone; Zahler, Stefan; Kalinowski, Jörn; Luzhetskyy, Andriy

2017-01-01

Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis. The combined genomics-metabolics profiling of the strain led to the identification of several new biologically active compounds. As a result, the family of bisindole pyrroles spiroindimicins was extended with two new members, spiroindimicins E and F. Furthermore, prediction of the biosynthetic pathway for unusual α-pyrone lagunapyrone isolated from MP131-18 resulted in foresight and identification of two new compounds of this family – lagunapyrones D and E. The diversity of identified and predicted compounds from Streptomyces sp. MP131-18 demonstrates that marine-derived actinomycetes are not only a promising source of new natural products, but also represent a valuable pool of genes for combinatorial biosynthesis of secondary metabolites. PMID:28186197

The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention.

PubMed

Akhund-Zade, Jamilla; Bergland, Alan O; Crowe, Sarah O; Unckless, Robert L

2017-01-01

Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention. © The Author 2017. Published by Oxford University Press on behalf of the Entomological Society of America.

DESCARTES’ RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA1

PubMed Central

Bhaskar, Anand; Song, Yun S.

2016-01-01

The sample frequency spectrum (SFS) is a widely-used summary statistic of genomic variation in a sample of homologous DNA sequences. It provides a highly efficient dimensional reduction of large-scale population genomic data and its mathematical dependence on the underlying population demography is well understood, thus enabling the development of efficient inference algorithms. However, it has been recently shown that very different population demographies can actually generate the same SFS for arbitrarily large sample sizes. Although in principle this nonidentifiability issue poses a thorny challenge to statistical inference, the population size functions involved in the counterexamples are arguably not so biologically realistic. Here, we revisit this problem and examine the identifiability of demographic models under the restriction that the population sizes are piecewise-defined where each piece belongs to some family of biologically-motivated functions. Under this assumption, we prove that the expected SFS of a sample uniquely determines the underlying demographic model, provided that the sample is sufficiently large. We obtain a general bound on the sample size sufficient for identifiability; the bound depends on the number of pieces in the demographic model and also on the type of population size function in each piece. In the cases of piecewise-constant, piecewise-exponential and piecewise-generalized-exponential models, which are often assumed in population genomic inferences, we provide explicit formulas for the bounds as simple functions of the number of pieces. Lastly, we obtain analogous results for the “folded” SFS, which is often used when there is ambiguity as to which allelic type is ancestral. Our results are proved using a generalization of Descartes’ rule of signs for polynomials to the Laplace transform of piecewise continuous functions. PMID:28018011

Per-service supervised learning for identifying desired WoT apps from user requests in natural language

PubMed Central

2017-01-01

Web of Things (WoT) platforms are growing fast so as the needs for composing WoT apps more easily and efficiently. We have recently commenced the campaign to develop an interface where users can issue requests for WoT apps entirely in natural language. This requires an effort to build a system that can learn to identify relevant WoT functions that fulfill user’s requests. In our preceding work, we trained a supervised learning system with thousands of publicly-available IFTTT app recipes based on conditional random fields (CRF). However, the sub-par accuracy and excessive training time motivated us to devise a better approach. In this paper, we present a novel solution that creates a separate learning engine for each trigger service. With this approach, parallel and incremental learning becomes possible. For inference, our system first identifies the most relevant trigger service for a given user request by using an information retrieval technique. Then, the learning engine associated with the trigger service predicts the most likely pair of trigger and action functions. We expect that such two-phase inference method given parallel learning engines would improve the accuracy of identifying related WoT functions. We verify our new solution through the empirical evaluation with training and test sets sampled from a pool of refined IFTTT app recipes. We also meticulously analyze the characteristics of the recipes to find future research directions. PMID:29149217

Per-service supervised learning for identifying desired WoT apps from user requests in natural language.

PubMed

Yoon, Young

2017-01-01

Web of Things (WoT) platforms are growing fast so as the needs for composing WoT apps more easily and efficiently. We have recently commenced the campaign to develop an interface where users can issue requests for WoT apps entirely in natural language. This requires an effort to build a system that can learn to identify relevant WoT functions that fulfill user's requests. In our preceding work, we trained a supervised learning system with thousands of publicly-available IFTTT app recipes based on conditional random fields (CRF). However, the sub-par accuracy and excessive training time motivated us to devise a better approach. In this paper, we present a novel solution that creates a separate learning engine for each trigger service. With this approach, parallel and incremental learning becomes possible. For inference, our system first identifies the most relevant trigger service for a given user request by using an information retrieval technique. Then, the learning engine associated with the trigger service predicts the most likely pair of trigger and action functions. We expect that such two-phase inference method given parallel learning engines would improve the accuracy of identifying related WoT functions. We verify our new solution through the empirical evaluation with training and test sets sampled from a pool of refined IFTTT app recipes. We also meticulously analyze the characteristics of the recipes to find future research directions.

DOG1 expression is predicted by the seed-maturation environment and contributes to geographical variation in germination in Arabidopsis thaliana.

PubMed

Chiang, George C K; Bartsch, Melanie; Barua, Deepak; Nakabayashi, Kazumi; Debieu, Marilyne; Kronholm, Ilkka; Koornneef, Maarten; Soppe, Wim J J; Donohue, Kathleen; De Meaux, Juliette

2011-08-01

Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in A. thaliana. Here, we report interaccession variation in DOG1 expression and document that DOG1 expression is associated with seed-maturation temperature effects on germination; DOG1 expression increased when seeds were matured at low temperature, and this increased expression was associated with increased dormancy of those seeds. Variation in DOG1 expression suggests a geographical structure such that southern accessions, which are more dormant, tend to initiate DOG1 expression earlier during seed maturation and achieved higher expression levels at the end of silique development than did northern accessions. Although elimination of the synthesis of phytohormone abscisic acid (ABA) results in the elimination of maternal temperature effects on dormancy, DOG1 expression predicted dormancy better than expression of genes involved in ABA metabolism. © 2011 Blackwell Publishing Ltd.

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

PubMed Central

Veltsos, P; Gregson, E; Morrissey, B; Slate, J; Hoikkala, A; Butlin, R K; Ritchie, M G

2015-01-01