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.

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

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

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

DOE PAGES

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.; ...

2016-06-08

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

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.

Variation to cause host injury between Russian wheat aphid (Homoptera: Aphididae) clones virulent to Dn4 wheat.

PubMed

Shufran, K A; Mornhinweg, D W; Baker, C A; Porter, D R

2007-10-01

Biotypes are infraspecific classifications based on biological rather than morphological characteristics. Cereal aphids are managed primarily by host plant resistance, and they often develop biotypes that injure or kill previously resistant plants. Although molecular genetic variation within aphid biotypes has been well documented, little is known about phenotypic variation, especially virulence or the biotype's ability to cause injury to cultivars with specific resistance genes. Five clones (single maternal lineages) of Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Homoptera: Aphididae), determined to be injurious to wheat, Triticum aestivum L., with the Dn4 gene, were evaluated on resistant and susceptible wheat and barley, Hordeum vulgare L., for their ability to cause chlorosis, reduction in plant height, and reduction in shoot dry weight. Variation to cause injury on resistant 'Halt' wheat, susceptible 'Jagger' wheat, and resistant 'STARS-9301B' barley was found among the Dn4 virulent clones. One clone caused up to 30.0 and 59.5% more reduction in plant height and shoot dry weight, respectively, on resistant Halt than other clones. It also caused up to 29.9 and 55.5% more reduction in plant height and shoot dry weight, respectively, on susceptible Jagger wheat. Although STARS-9301B barley exhibited an equal resistant response to feeding by all five clones based on chlorosis, two clones caused approximately 20% more reduction in plant height and shoot dry weight than three other clones. The most injurious clones on wheat were not the most injurious clones on barley. This is the first report of variation to cause varying degrees of plant damage within an aphid biotype virulent to a single host resistance gene. A single aphid clone may not accurately represent the true virulent nature of a biotype population in the field.

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

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

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...

Genetic structure and natural variation associated with host of origin in Penicillium expansum strains causing blue mould.

PubMed

Sanzani, S M; Montemurro, C; Di Rienzo, V; Solfrizzo, M; Ippolito, A

2013-07-15

Blue mould, caused by Penicillium expansum, is one of the most economically damaging postharvest diseases of pome fruits, although it may affect a wider host range, including sweet cherries and table grapes. Several reports on the role of mycotoxins in plant pathogenesis have been published, but few focussed on the influence of mycotoxins on the variation in host preference amongst producing fungi. In the present study the influence of the host on P. expansum pathogenicity/virulence was investigated, focussing mainly on the relationship with patulin production. Three P. expansum strain groups, originating from apples, sweet cherries, and table grapes (7 strains per host) were grown on their hosts of isolation and on artificial media derived from them. Strains within each P. expansum group proved to be more aggressive and produced more patulin than the other two groups under evaluation when grown on the host from which they originated. Table grape strains were the most aggressive (81% disease incidence) and strongest patulin producers (up to 554μg/g). The difference in aggressiveness amongst strains was appreciable only in the presence of a living host, suggesting that the complex pathogen-host interaction significantly influenced the ability of P. expansum to cause the disease. Incidence/severity of the disease and patulin production proved to be positively correlated, supporting the role of patulin as virulence/pathogenicity factor. The existence of genetic variation amongst isolates was confirmed by the High Resolution Melting method that was set up herein, which permitted discrimination of P. expansum from other species (P. chrysogenum and P. crustosum) and, within the same species, amongst the host of origin. Host effect on toxin production appeared to be exerted at a transcriptional level. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

PubMed Central

Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

2016-01-01

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

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.

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

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

Patterns and causes of geographic variation in bat echolocation pulses.

PubMed

Jiang, Tinglei; Wu, Hui; Feng, Jiang

2015-05-01

Evolutionary biologists have a long-standing interest in how acoustic signals in animals vary geographically, because divergent ecology and sensory perception play an important role in speciation. Geographic comparisons are valuable in determining the factors that influence divergence of acoustic signals. Bats are social mammals and they depend mainly on echolocation pulses to locate prey, to navigate and to communicate. Mounting evidence shows that geographic variation of bat echolocation pulses is common, with a mean 5-10 kHz differences in peak frequency, and a high level of individual variation may be nested in this geographical variation. However, understanding the geographic variation of echolocation pulses in bats is very difficult, because of differences in sample and statistical analysis techniques as well as the variety of factors shaping the vocal geographic evolution. Geographic differences in echolocation pulses of bats generally lack latitudinal, longitudinal and elevational patterns, and little is known about vocal dialects. Evidence is accumulating to support the fact that geographic variation in echolocation pulses of bats may be caused by genetic drift, cultural drift, ecological selection, sexual selection and social selection. Future studies could relate geographic differences in echolocation pulses to social adaptation, vocal learning strategies and patterns of dispersal. In addition, new statistical techniques and acoustic playback experiments may help to illustrate the causes and consequences of the geographic evolution of echolocation pulse in bats. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

[A brief history of the natural causes of human disease].

PubMed

Lips-Castro, Walter

2015-01-01

In the study of the causes of disease that have arisen during the development of humankind, one can distinguish three major perspectives: the natural, the supernatural, and the artificial. In this paper we distinguish the rational natural causes of disease from the irrational natural causes. Within the natural and rational causal approaches of disease, we can highlight the Egyptian theory of putrid intestinal materials called "wechdu", the humoral theory, the atomistic theory, the contagious theory, the cellular theory, the molecular (genetic) theory, and the ecogenetic theory. Regarding the irrational, esoteric, and mystic causal approaches to disease, we highlight the astrological, the alchemical, the iatrochemical, the iatromechanical, and others (irritability, solidism, brownism, and mesmerism).

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

Regional Variation in Causes of Injuries among Terrorism Victims for Mass Casualty Events

PubMed Central

Regens, James L.; Schultheiss, Amy; Mould, Nick

2015-01-01

The efficient allocation of medical resources to prepare for and respond to mass casualty events (MCEs) attributable to intentional acts of terrorism is a major challenge confronting disaster planners and emergency personnel. This research article examines variation in regional patterns in the causes of injures associated with 77,258 successful terrorist attacks that occurred between 1970 and 2013 involving the use of explosives, firearms, and/or incendiaries. The objective of this research is to estimate regional variation in the use of different conventional weapons in successful terrorist attacks in each world region on variation in injury cause distributions. Indeed, we find that the distributions of the number of injuries attributable to specific weapons types (i.e., by cause) vary greatly among the 13 world regions identified within the Global Terrorism Database. PMID:26347857

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.

Slope instability caused by small variations in hydraulic conductivity

USGS Publications Warehouse

Reid, M.E.

1997-01-01

Variations in hydraulic conductivity can greatly modify hillslope ground-water flow fields, effective-stress fields, and slope stability. In materials with uniform texture, hydraulic conductivities can vary over one to two orders of magnitude, yet small variations can be difficult to determine. The destabilizing effects caused by small (one order of magnitude or less) hydraulic conductivity variations using ground-water flow modeling, finite-element deformation analysis, and limit-equilibrium analysis are examined here. Low hydraulic conductivity materials that impede downslope ground-water flow can create unstable areas with locally elevated pore-water pressures. The destabilizing effects of small hydraulic heterogeneities can be as great as those induced by typical variations in the frictional strength (approximately 4??-8??) of texturally similar materials. Common "worst-case" assumptions about ground-water flow, such as a completely saturated "hydrostatic" pore-pressure distribution, do not account for locally elevated pore-water pressures and may not provide a conservative slope stability analysis. In site characterization, special attention should be paid to any materials that might impede downslope ground-water flow and create unstable regions.

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

PubMed Central

Cook, Daniel E.; Zdraljevic, Stefan; Tanny, Robyn E.; Seo, Beomseok; Riccardi, David D.; Noble, Luke M.; Rockman, Matthew V.; Alkema, Mark J.; Braendle, Christian; Kammenga, Jan E.; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C.

2016-01-01

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. PMID:27449056

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length.

PubMed

Cook, Daniel E; Zdraljevic, Stefan; Tanny, Robyn E; Seo, Beomseok; Riccardi, David D; Noble, Luke M; Rockman, Matthew V; Alkema, Mark J; Braendle, Christian; Kammenga, Jan E; Wang, John; Kruglyak, Leonid; Félix, Marie-Anne; Lee, Junho; Andersen, Erik C

2016-09-01

Telomeres are involved in the maintenance of chromosomes and the prevention of genome instability. Despite this central importance, significant variation in telomere length has been observed in a variety of organisms. The genetic determinants of telomere-length variation and their effects on organismal fitness are largely unexplored. Here, we describe natural variation in telomere length across the Caenorhabditis elegans species. We identify a large-effect variant that contributes to differences in telomere length. The variant alters the conserved oligonucleotide/oligosaccharide-binding fold of protection of telomeres 2 (POT-2), a homolog of a human telomere-capping shelterin complex subunit. Mutations within this domain likely reduce the ability of POT-2 to bind telomeric DNA, thereby increasing telomere length. We find that telomere-length variation does not correlate with offspring production or longevity in C. elegans wild isolates, suggesting that naturally long telomeres play a limited role in modifying fitness phenotypes in C. elegans. Copyright © 2016 by the Genetics Society of America.

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.

A review of the established and suspected causes of variations in human sex ratio at birth.

PubMed

James, William H; Grech, Victor

2017-06-01

The human sex ratio (proportion male) at birth (SRB) varies with many variables. Some of this variation has an established proximate cause. For instance, low SRB (more females) at birth are associated with various forms of stressful events or circumstances during or prior to pregnancy. These low SRB are almost certainly mainly caused by maternal-stress-induced male foetal loss. Other types of SRB variation are thought to be caused by hormonal variation in either or both parents around the time of conception. One or other of these two types of proximate cause seems to be responsible for most of the established variation of SRB. This will be illustrated here in respect of some selected forms of SRB variation. It seems likely that a clarification of the hormonal causes of SRB variation will also help explain the striking (apparent) inconsistencies in the results of reported tests of the influential Trivers-Willard hypothesis. It is further proposed that an appreciation of the evidence that parental hormones influence SRB may enhance understanding of several important pathologies (hepatitis B, toxoplasmosis, testicular cancer, prostate cancer and autism). Copyright © 2017 Elsevier B.V. All rights reserved.

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

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.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

PubMed

Hunter, Chad M; Huang, Wen; Mackay, Trudy F C; Singh, Nadia D

2016-04-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

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 of Model Mutant Phenotypes in Ciona intestinalis

PubMed Central

Brown, Euan R.; Leccia, Nicola I.; Squarzoni, Paola; Tarallo, Raffaella; Alfano, Christian; Caputi, Luigi; D'Ambrosio, Palmira; Daniele, Paola; D'Aniello, Enrico; D'Aniello, Salvatore; Maiella, Sylvie; Miraglia, Valentina; Russo, Monia Teresa; Sorrenti, Gerarda; Branno, Margherita; Cariello, Lucio; Cirino, Paola; Locascio, Annamaria; Spagnuolo, Antonietta; Zanetti, Laura; Ristoratore, Filomena

2008-01-01

Background The study of ascidians (Chordata, Tunicata) has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. Methodology/Principal Findings Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. Conclusions/Significance Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity. PMID:18523552

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster

PubMed Central

Hunter, Chad M.; Huang, Wen; Mackay, Trudy F. C.; Singh, Nadia D.

2016-01-01

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait. PMID:27035832

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris.

PubMed

Aw, Rochelle; Barton, Geraint R; Leak, David J

2017-06-01

Clonal variation, wherein a range of specific productivities of secreted proteins are observed from supposedly identical transformants, is an accepted aspect of working with Pichia pastoris. It means that a significant number of transformants need to be tested to obtain a representative sample, and in commercial protein production, companies regularly screen thousands of transformants to select for the highest secretor. Here, we have undertaken a detailed investigation of this phenomenon by characterising clones transformed with the human serum albumin gene. The titers of nine clones, each containing a single copy of the human serum albumin gene (identified by qPCR), were measured and the clones grouped into three categories, namely, high-, mid- and low-level secretors. Transcriptomic analysis, using microarrays, showed that no regulatory patterns consistently correlated with titer, suggesting that the causes of clonal variation are varied. However, a number of physiological changes appeared to underlie the differences in titer, suggesting there is more than one biochemical signature for a high-secreting strain. An anomalous low-secreting strain displaying high transcript levels that appeared to be nutritionally starved further emphasises the complicated nature of clonal variation.

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.

Satellite-based studies of maize yield spatial variations and their causes in China

NASA Astrophysics Data System (ADS)

Zhao, Y.

2013-12-01

Maize production in China has been expanding significantly in the past two decades, but yield has become relatively stagnant in the past few years, and needs to be improved to meet increasing demand. Multiple studies found that the gap between potential and actual yield of maize is as large as 40% to 60% of yield potential. Although a few major causes of yield gap have been qualitatively identified with surveys, there has not been spatial analysis aimed at quantifying relative importance of specific biophysical and socio-economic causes, information which would be useful for targeting interventions. This study analyzes the causes of yield variation at field and village level in Quzhou county of North China Plain (NCP). We combine remote sensing and crop modeling to estimate yields in 2009-2012, and identify fields that are consistently high or low yielding. To establish the relationship between yield and potential factors, we gather data on those factors through a household survey. We select targeted survey fields such that not only both extremes of yield distribution but also all soil texture categories in the county is covered. Our survey assesses management and biophysical factors as well as social factors such as farmers' access to agronomic knowledge, which is approximated by distance to the closest demonstration plot or 'Science and technology backyard'. Our survey covers 10 townships, 53 villages and 180 fields. Three to ten farmers are surveyed depending on the amount of variation present among sub pixels of each field. According to survey results, we extract the amount of variation within as well as between villages and or soil type. The higher within village or within field variation, the higher importance of management factors. Factors such as soil type and access to knowledge are more represented by between village variation. Through regression and analysis of variance, we gain more quantitative and thorough understanding of causes to yield variation at

All-Cause Hospital Admissions Among Older Adults After a Natural Disaster.

PubMed

Bell, Sue Anne; Abir, Mahshid; Choi, HwaJung; Cooke, Colin; Iwashyna, Theodore

2017-08-05

We characterize hospital admissions among older adults for any cause in the 30 days after a significant natural disaster in the United States. The main outcome was all-cause hospital admissions in the 30 days after natural disaster. Separate analyses were conducted to examine all-cause hospital admissions excluding the 72 hours after the disaster, ICU admissions, all-cause inhospital mortality, and admissions by state. A self-controlled case series analysis using the 2011 Medicare Provider and Analysis Review was conducted to examine exposure to natural disaster by elderly adults located in zip codes affected by tornadoes during the 2011 southeastern superstorm. Spatial data of tornado events were obtained from the National Oceanic and Atmospheric Administration's Severe Report database, and zip code data were obtained from the US Census Bureau. All-cause hospital admissions increased by 4% for older adults in the 30 days after the April 27, 2011, tornadoes (incidence rate ratio 1.04; 95% confidence interval 1.01 to 1.07). When the first 3 days after the disaster that may have been attributed to immediate injuries were excluded, hospitalizations for any cause also remained higher than when compared with the other 11 months of the year (incidence rate ratio 1.04; 95% confidence interval 1.01 to 1.07). There was no increase in ICU admissions or inhospital mortality associated with the natural disaster. When data were examined by individual states, Alabama, which had the highest number of persons affected, had a 9% increase in both hospitalizations and ICU admissions. When all time-invariant characteristics were controlled for, this natural disaster was associated with a significant increase in all-cause hospitalizations. This analysis quantifies acute care use after disasters through examining all-cause hospitalizations and represents an important contribution to building models of resilience-the ability to recover from a disaster-and hospital surge capacity

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

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

Seasonal variations of all-cause and cause-specific mortality by age, gender, and socioeconomic condition in urban and rural areas of Bangladesh.

PubMed

Burkart, Katrin; Khan, Mobarak H; Krämer, Alexander; Breitner, Susanne; Schneider, Alexandra; Endlicher, Wilfried R

2011-08-04

Mortality exhibits seasonal variations, which to a certain extent can be considered as mid-to long-term influences of meteorological conditions. In addition to atmospheric effects, the seasonal pattern of mortality is shaped by non-atmospheric determinants such as environmental conditions or socioeconomic status. Understanding the influence of season and other factors is essential when seeking to implement effective public health measures. The pressures of climate change make an understanding of the interdependencies between season, climate and health especially important. This study investigated daily death counts collected within the Sample Vital Registration System (VSRS) established by the Bangladesh Bureau of Statistics (BBS). The sample was stratified by location (urban vs. rural), gender and socioeconomic status. Furthermore, seasonality was analyzed for all-cause mortality, and several cause-specific mortalities. Daily deviation from average mortality was calculated and seasonal fluctuations were elaborated using non parametric spline smoothing. A seasonality index for each year of life was calculated in order to assess the age-dependency of seasonal effects. We found distinctive seasonal variations of mortality with generally higher levels during the cold season. To some extent, a rudimentary secondary summer maximum could be observed. The degree and shape of seasonality changed with the cause of death as well as with location, gender, and SES and was strongly age-dependent. Urban areas were seen to be facing an increased summer mortality peak, particularly in terms of cardiovascular mortality. Generally, children and the elderly faced stronger seasonal effects than youths and young adults. This study clearly demonstrated the complex and dynamic nature of seasonal impacts on mortality. The modifying effect of spatial and population characteristics were highlighted. While tropical regions have been, and still are, associated with a marked excess of

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.

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.

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.

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

Stress Variation Caused by the Terrestrial Water Storage Inferred from GRACE Data

NASA Astrophysics Data System (ADS)

Yi, H.; Wen, L.

2014-12-01

We estimate stress variation caused by the terrestrial water storage (TWS) change from 2003 to 2013. We first infer the TWS change from the monthly gravity field change in the Gravity Recovery and Climate Experiment (GRACE). We then estimate the stress change at the Earth's surface caused by elastic loading of mass change associated with the inferred TWS change.The monthly spherical harmonics of the GRACE gravity solutions are processed using a decorrelation filter and Gaussian smoothing, to suppress the noise in high degree and order, following the approach of Swenson and Wahr [2006] and Chen et al. [2007]. The gravity variation associated with the glacial isostatic adjustment (GIA) is further removed from the GRACE solutions based on a geodynamical model by Paulson et al. [2007]. The inferred TWS changes exhibit a trend of increase from 2003 to 2013 in Amazon basin, southern Africa, the northern United State America (USA) and Queen Maud Land of Antarctica, and a trend of decrease in the same period in central Argentina, southern Chile, northern India, northern Iran, Alaska of the USA, Greenland and Marie Byrd Land of Antarctica.Surface stress variation due to the TWS loading is calculated, assuming an incompressible and self-gravitating Earth, with an elastic crust and a viscoelastic mantle overlying an inviscid core based on PREM model. We will present the geographical distribution of the stress variation caused by the TWS loading and discuss its possible implications. Chen, J. L., C. R. Wilson, B. D. Tapley, and S. Grand (2007), GRACE detects coseismic and postseismic deformation from the Sumatra-Andaman earthquake, Geophys Res Lett, 34(13), doi:10.1029/2007GL030356. Paulson, A., S. J. Zhong, and J. Wahr (2007), Inference of mantle viscosity from GRACE and relative sea level data, Geophys J Int, 171(2), 497-508, doi:10.1111/j.1365-246X.2007.03556.x. Swenson, S., and J. Wahr (2006), Post-processing removal of correlated errors in GRACE data, Geophys Res Lett, 33

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

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.

Most common causes of natural and injury-related deaths in Addis Ababa, Ethiopia.

PubMed

Gemechu, Tufa; Tinsae, Mihrete; Ashenafi, Senait; Rodriguez, Victor Manuel; Lori, Alfredo; Collins, Michelle; Hurford, Rosemary; Haimanot, Rahel; Sandoval, Melissa; Mehari, Enawgaw; Langford, T Dianne

2009-01-01

In Ethiopia, like many developing countries, autopsy is rare unless conducted in the medico-legal arena, making vital statistics that include pathological diagnoses sparse. To determine the most common factors contributing to death among individuals who died from natural or injury-related events in Ethiopia 200 consecutive autopsies were conducted in 2006 at the Forensic Medico-legal Pathology Department, Menelik II Hospital, Addis Ababa, Ethiopia. The results describe significant pathological observations, putative cause of death, age distribution, and gender ratios. Eighty-one percent of the cases were male, and the mean age was 38.9 (+/-15.5 years). Fifty-two percent of the individuals died from natural causes, including infections, and 48% died from injury-related events. In the natural deaths group, as determined by gross examination at autopsy pulmonary complications were the most commonly reported cause of death, with suspected tuberculosis accounting for 12%. Tuberculosis (21, 8%) and liver disease (14, 5%) were the most common histopathological findings in the natural and injury-related causes groups, respectively. In the injury-related group, automobile accident was the most common cause of accidental death (80%), and homicide by beating was the most common cause of death in the intentional injury group (31%). These data provide valuable unbiased analyses of causes of death among individuals in Addis Ababa, Ethiopia.

Most common causes of natural and injury-related deaths in Addis Ababa, Ethiopia

PubMed Central

Gemechu, Tufa; Tinsae, Mihrete; Ashenafi, Senait; Rodriguez, Victor Manuel; Lori, Alfredo; Collins, Michelle; Hurford, Rosemary; Haimanot, Rahel; Sandoval, Melissa; Mehari, Enawgaw; Langford, T. Dianne

2009-01-01

SUMMARY In Ethopia, like many developing countries, autopsy is rare unless conducted in the medico-legal arena, making vital statistics that include sparse pathological diagnoses. To determine the most common factors contributing to death among individuals who died from natural or injury-related events in Ethiopia in 2006, 200 consecutive autopsies were conducted at the Forensic Medico-legal Pathology Department, Menelik II Hospital, Addis Ababa, Ethiopia. The results describe significant pathological observations, putative cause of death, age distribution, and gender ratios. Eighty-one percent of the cases were male, and the mean age was 38.9 (±15.5 years). Fifty-two percent of the individuals died from natural causes, including infections, and 48% died from injury-related events. In the natural deaths group, pulmonary complications were the most commonly reported cause of death by gross examination at autopsy, with suspected tuberculosis accounting for 12%. Tuberculosis (21, 8%) and liver disease (14, 5%) were the most common histopathological findings in the natural and injury-related causes groups, respectively. In the injury-related group, automobile accident was the most common cause of accidental death (80%), and homicide by beating was the most common cause of death in the intentional injury group (31%). These data provide valuable unbiased analyses of causes of death among individuals in Addis Ababa, Ethiopia. PMID:19321271

Causes of global mean surface temperature slowdowns, trends and variations from months to a century, 1891-2015

NASA Astrophysics Data System (ADS)

Folland, C. K.; Boucher, O.; Colman, A.; Parker, D. E.

2017-12-01

The recent slowdown in the warming of global mean surface temperature (GST) has highlighted the influences of natural variability. This talk discusses reconstructions of the variations of GST down to the monthly time scale since 1891 using monthly forcing data. We show that most of the variations in annual, and to some extent sub-annual, GST since 1891 can be reproduced skillfully from known forcing factors external and internal to the climate system. This includes the slowdown in warming over about 1998-2013 where reconstruction skill is particularly high down to the multi-monthly time scale. The relative contributions of the several key forcing factors to GST continually vary, but most of the net warming since 1891 is reconstructed to be attributable to the net forcing due to increasing greenhouse gases and anthropogenic aerosols. Separate analyses are carried out for three periods of GST slowdown:- 1896-1910, 1941-1976, together with 1998-2013 and some of its sub periods. We also study two periods where strong warming occurred, 1911-1940 and 1977-1997. Comparisons are made with the skill of average GST provided by 40 CMIP5 models. In the recent 1998-2013 slowdown, TSI forcing appears to have caused significant cooling, particularly over 2001-2010. This is additional to well documented cooling effects of an increased frequency of La Nina events, a negative Interdecadal Pacific Oscillation and some increases in volcanic forcing. Although there are short-term features of the GST curve since 1891 that cannot be fully explained, the most serious disagreements between the reconstructions and observations occur in the Second World War, especially in 1944-1945. Here observed near worldwide SSTs may be biased significantly too warm. Despite this, our generally high reconstruction skill is consistent with a good understanding of the multiple causes of observed GST variations and the general veracity of the GST record since 1891.

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

An interpretation of induced electric currents in long pipelines caused by natural geomagnetic sources of the upper atmosphere

USGS Publications Warehouse

Campbell, W.H.

1986-01-01

Electric currents in long pipelines can contribute to corrosion effects that limit the pipe's lifetime. One cause of such electric currents is the geomagnetic field variations that have sources in the Earth's upper atmosphere. Knowledge of the general behavior of the sources allows a prediction of the occurrence times, favorable locations for the pipeline effects, and long-term projections of corrosion contributions. The source spectral characteristics, the Earth's conductivity profile, and a corrosion-frequency dependence limit the period range of the natural field changes that affect the pipe. The corrosion contribution by induced currents from geomagnetic sources should be evaluated for pipelines that are located at high and at equatorial latitudes. At midlatitude locations, the times of these natural current maxima should be avoided for the necessary accurate monitoring of the pipe-to-soil potential. ?? 1986 D. Reidel Publishing Company.

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.

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

PubMed Central

Knights, Andrew J.; Abreu-Goodger, Cei; van de Bunt, Martijn; Guerra-Assunção, José Afonso; Bartonicek, Nenad; van Dongen, Stijn; Mägi, Reedik; Nisbet, James; Barrett, Amy; Rantalainen, Mattias; Nica, Alexandra C.; Quail, Michael A.; Small, Kerrin S.; Glass, Daniel; Enright, Anton J.; Winn, John; Deloukas, Panos; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Spector, Timothy D.; Durbin, Richard; Lindgren, Cecilia M.

2012-01-01

Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population. PMID:22589741

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

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.

[Advances in congenital vertebral malformation caused by genomic copy number variation].

PubMed

Liu, Zhenlei; Wu, Nan; Wu, Zhihong; Zuo, Yuzhi; Qiu, Guixing

2016-04-01

Congenital vertebral malformation (CVM) is a congenital vertebral structural deformity caused by abnormal somitogenesis during embryonic development, of which the reason lies in gene mutation or abnormal regulation of the genes that coordinate somitogenesis during embryonic period. ICVAS had proposed a new classification algorithm for CVM, which facilitated exploration for its genetic etiology. Genomic Copy Number Variation (CNV) is a kind of DNA mutation, which is important for human evolution, phenotype polymorphism and diseases. Series of advances have been made on genetic causes of CVM, especially on CVM caused by CNV. CNVs of chromosome 16p11.2, 10q24.31, 17p11.2, 20p11, 22q11.2 and a few other regions are associated with CVM, indicating that gene dosage may play important roles in the development of the spinal cord.

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 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.

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.

The causes of variation in learning and behavior: why individual differences matter

PubMed Central

Sauce, Bruno; Matzel, Louis D.

2013-01-01

In a seminal paper written five decades ago, Cronbach discussed the two highly distinct approaches to scientific psychology: experimental and correlational. Today, although these two approaches are fruitfully implemented and embraced across some fields of psychology, this synergy is largely absent from other areas, such as in the study of learning and behavior. Both Tolman and Hull, in a rare case of agreement, stated that the correlational approach held little promise for the understanding of behavior. Interestingly, this dismissal of the study of individual differences was absent in the biologically oriented branches of behavior analysis, namely, behavioral genetics and ethology. Here we propose that the distinction between “causation” and “causes of variation” (with its origins in the field of genetics) reveals the potential value of the correlational approach in understanding the full complexity of learning and behavior. Although the experimental approach can illuminate the causal variables that modulate learning, the analysis of individual differences can elucidate how much and in which way variables interact to support variations in learning in complex natural environments. For example, understanding that a past experience with a stimulus influences its “associability” provides little insight into how individual predispositions interact to modulate this influence on associability. In this “new” light, we discuss examples from studies of individual differences in animals’ performance in the Morris water maze and from our own work on individual differences in general intelligence in mice. These studies illustrate that, opposed to what Underwood famously suggested, studies of individual differences can do much more to psychology than merely providing preliminary indications of cause-effect relationships. PMID:23847569

Promoter difference of LcFT1 is a leading cause of natural variation of flowering timing in different litchi cultivars (Litchi chinensis Sonn.).

PubMed

Ding, Feng; Zhang, Shuwei; Chen, Houbin; Su, Zuanxian; Zhang, Rong; Xiao, Qiusheng; Li, Hongli

2015-12-01

Litchi (Litchi chinensis) is an important subtropical evergreen fruit crop with high commercial value due to its high nutritional values and favorable tastes. However, irregular bearing attributed to unstable flowering is a major ongoing problem for litchi producers. There is a need to better understand the genetic and molecular mechanisms underlying the reproductive process in litchi. In a previous study, our laboratory had analyzed the transcriptome of litchi leaves before and after low-temperature treatment with RNA-seq technology. Herein, we demonstrated that litchi flowering was induced by low-temperature and identified two FLOWERING LOCUS T (FT) homologue genes named LcFT1 and LcFT2, respectively. We found that low-temperature could only induce LcFT1 expression in leaves, but could not induce LcFT2 expression. Heterologous expression of LcFT1 in transgenic tobacco and Arabidopsis plants induced their precocious flowering. These results indicate that LcFT1 plays a pivotal role in litchi floral induction by low-temperature. In addition, we found that two types of LcFT1 promoter existed in different litchi cultivars. The LcFT1 promoters in the early-flowering cultivars belonged to one type whereas LcFT1 promoters in the late-flowering belonged to another one. LcFT1 promoter in the early-flowering cultivars was more sensitive to low-temperature than that of the late-flowering cultivars was, which may be caused by the different cis-acting elements, including MYC, MYB, ABRE, and WRKY cis-acting elements, which were found to be present in the LcFT1 promoter sequences of the early-flowering cultivars. This difference may be responsible for the different requirements of low-temperature for floral induction in the early- and late-flowering cultivars of litchi. Taken together, the difference in LcFT1 promoter sequences may be one of the leading cause for the natural variation of flowering timing in different litchi cultivars. Our study has provided valuable genetic

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

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.

Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

PubMed Central

Chao, Dai-Yin; Silva, Adriano; Baxter, Ivan; Huang, Yu S.; Nordborg, Magnus; Danku, John; Lahner, Brett; Yakubova, Elena; Salt, David E.

2012-01-01

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 on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids. PMID:22969436

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.

Nonconsumptive predator-driven mortality causes natural selection on prey.

PubMed

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

2014-03-01

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

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 variation in floral nectar proteins of two Nicotiana attenuata accessions.

PubMed

Seo, Pil Joon; Wielsch, Natalie; Kessler, Danny; Svatos, Ales; Park, Chung-Mo; Baldwin, Ian T; Kim, Sang-Gyu

2013-07-13

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. 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. 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.

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

Individual variation in prey selection by sea otters: Patterns, causes and implications

USGS Publications Warehouse

Estes, J.A.; Riedman, M.L.; Staedler, M.M.; Tinker, M.T.; Lyon, B.E.

2003-01-01

1. Longitudinal records of prey selection by 10 adult female sea otters on the Monterey Peninsula, California, from 1983 to 1990 demonstrate extreme inter-individual variation in diet. Variation in prey availability cannot explain these differences as the data were obtained from a common spatial-temporal area. 2. Individual dietary patterns persisted throughout our study, thus indicating that they are life-long characteristics. 3. Individual dietary patterns in sea otters appear to be transmitted along matrilines, probably by way of learning during the period of mother-young association. 4. Efficient utilization of different prey types probably requires radically different sensory/motor skills, each of which is difficult to acquire and all of which may exceed the learning and performance capacities of any single individual. This would explain the absence of generalists and inertia against switching, but not the existence of alternative specialists. 5. Such individual variation might arise in a constant environment from frequency-dependent effects, whereby the relative benefit of a given prey specialization depends on the number of other individuals utilizing that prey. Additionally, many of the sea otter's prey fluctuate substantially in abundance through time. This temporal variation, in conjunction with matrilineal transmission of foraging skills, may act to mediate the temporal dynamics of prey specializations. 6. Regardless of the exact cause, such extreme individual variation in diet has broad ramifications for population and community ecology. 7. The published literature indicates that similar patterns occur in many other species.

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.

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.

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.

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.

Use of natural variation to identify loci associated with relevant agronomic phenotypic traits

USDA-ARS?s Scientific Manuscript database

Analysis of natural allelic variation is a useful discovery tool to identify novel alleles in genes and pathways that are consistent with agronomic productivity and environmental stability. Switchgrass, a native perennial North American prairie grass and emerging biofuel feedstock species, is divide...

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.

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

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.

River pollution caused by natural stone industry

NASA Astrophysics Data System (ADS)

Oktriani, Ani; Darmajanti, Linda; Soesilo, Tri Edhi Budhi

2017-03-01

The natural stone industry is classified as small industry. Current wastewater treatment still causes pollution in the river. This thesis aims to analyze the performance of wastewater treatment in natural stones industry. The data was collected from water quality test (parameters: temperature, pH, DO, and TSS). The wastewater treatment performance was in a slightly higher position compared to the 2nd class quality standards of Government Regulation No. 82/2001. The parameter that exceeded quality standards was the concentration of TSS, which was up to 240.8 mg/l. The high concentration of TSS was affected by the absence of sludge management schedule, which resulted in non-optimal precipitation. Besides that, the design of sedimentation basin was still not adapted with wastewater debit. Referring to the results, this study suggests the government of Cirebon District to provide wastewater treatment development through the village staff. Furthermore, the government also needs to give strict punishment to business owner who does not treat waste correctly and does not have a business license. Moreover, the sale value of sludge as byproduct of wastewater treatment needs to be increased.

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.

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.

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.

Subject Reaction to Human-Caused and Naturally-Occurring Radioactive Threat.

ERIC Educational Resources Information Center

Belford, Susan; Gibbs, Margaret

While research has shown that people are adversely psychologically affected by knowledge that their communities have been toxically contaminated, it has been suggested that those who see a disaster as naturally occurring tend to be less adversely affected than those who see a disaster as caused by human acts. To examine this issue, questionnaires…

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.

Errors in Site Index Determination Caused by Tree Age Variation in Even-Aged Oak Stands

Treesearch

Robert A. McQuilkin

1975-01-01

Age deviations of individual trees in even-aged oak stands in Missouri caused variations in the height growth patterns and site index estimates of these younger or older trees. A correction factor for site index estimates on these age-deviant trees is given.

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

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.

Dry-wet variations and cause analysis in Northeast China at multi-time scales

NASA Astrophysics Data System (ADS)

Hu, Qi; Pan, Feifei; Pan, Xuebiao; Hu, Liting; Wang, Xiaoxiao; Yang, Pengyu; Wei, Pei; Pan, Zhihua

2017-07-01

Global warming has caused unevenly distributed changes in precipitation and evapotranspiration, which has and will certainly impact on the wet-dry variations. Based on daily meteorological data collected at 91 weather stations in Northeast China (NEC), the spatiotemporal characteristics of dry and wet climatic variables (precipitation, crop reference evapotranspiration (ET0), and humid index (HI)) are analyzed, and the probable reasons causing the changes in these variables are discussed during the period of 1961-2014. Precipitation showed non-significant trend over the period of 1961-2014, while ET0 showed a significant decreasing trend, which led to climate wetting in NEC. The period of 2001-2012 exhibited smaller semiarid area and larger humid area compared to the period of 1961-1980, indicating NEC has experienced wetting process at decadal scale. ET0 was most sensitive to relative humidity, and wind speed was the second most sensitive variable. Sunshine hours and temperature were found to be less influential to ET0 in the study area. The changes in wind speed in the recent 54 years have caused the greatest influence on ET0, followed by temperature. For each month, wind speed was the most significant variable causing ET0 reduction in all months except July. Temperature, as a dominant factor, made a positive contribution to ET0 in February and March, as well as sunshine hours in June and July, and relative humidity in August and September. In summary, NEC has experienced noticeable climate wetting due to the significantly decreasing ET0, and the decrease in wind speed was the biggest contributor for the ET0 reduction. Although agricultural drought crisis is expected to be partly alleviated, regional water resources management and planning in Northeast China should consider the potential water shortage and water conflict in the future because of spatiotemporal dry-wet variations in NEC.

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

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.

Analyses of natural variation indicates that the absence of RPS4/RRS1 and amino acid change in RPS4 cause loss of their functions and resistance to pathogens.

PubMed

Narusaka, Mari; Iuchi, Satoshi; Narusaka, Yoshihiro

2017-03-04

A pair of Arabidopsis thaliana resistance proteins, RPS4 and RRS1, recognizes the cognate Avr effector from the bacterial pathogens Pseudomonas syringae pv. tomato expressing avrRps4 (Pst-avrRps4), Ralstonia solanacearum, and the fungal pathogen Colletotrichum higginsianum and leads to defense signaling activation against the pathogens. In the present study, we analyzed 14 A. thaliana accessions for natural variation in Pst-avrRps4 and C. higginsianum susceptibility, and found new compatible and incompatible Arabidopsis-pathogen interactions. We first found that A. thaliana accession Cvi-0 is susceptible to Pst-avrRps4. Interestingly, the genome sequence assembly indicated that Cvi-0 lost both RPS4 and RRS1, but not RPS4B and RRS1B, compared to the reference genome sequence from A. thaliana accession Col-0. On the other hand, the natural variation analysis of RPS4 alleles from various Arabidopsis accessions revealed that one amino-acid change, Y950H, is responsible for the loss of resistance to Pst-avrRps4 and C. higginsianum in RLD-0. Our data indicate that the amino acid change, Y950H, in RPS4 resulted in the loss of both RPS4 and RRS1 functions and resistance to pathogens.

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

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.

Strong intensity variations of laser feedback interferometer caused by atmospheric turbulence

NASA Astrophysics Data System (ADS)

Sun, Yiyi; Li, Zhiping

2003-05-01

The significant variation of the laser output can be caused by feedback of a small part of laser beam, which is reflected or backscattered by a target at a long distance from laser source, into the laser cavity. This paper describes and analyzes theoretically and experimentally the influence of atmospheric turbulence on interference caused by laser feedback. The influence depends upon both the energy of feedback into the laser cavity and the strength of turbulence over a laser propagation path in the atmosphere. In the case of stronger energy of feedback and weak turbulence variance of fluctuation of the laser output can be enhanced by hundreds to thousands times. From our measurements and theoretical analysis it shows thatthese significant enhancements can result from the change of laser-cavity-modes which can be stimulated simultaneously and from beat oscillations between a variety of frequencies of laser modes. This also can result from optical chaos inside the laser resonator because a non-separable distorted external cavity can become a prerequisite for optical chaos.

Orthopyroxenes as Recorders of Diogenite Petrogenesis: Nature and Causes of Intragrain Chemical Variability

NASA Astrophysics Data System (ADS)

Papike, J. J.; Spilde, M. N.

1993-07-01

Diogenites can as a first approximation be considered as orthopyroxene cumulates in differentiated asteroids [1]. Orthopyroxene is a very powerful mineral recorder in mafic cumulates as demonstrated by Lambert and Simmons [2], who "inverted" REE data from cores of orthopyroxene crystals to estimate the melt compositions parental to the various cumulate horizons in the Stillwater Complex, Montana. These authors demonstrated that the rims of orthopyroxene grains are enriched in REE relative to cores, most likely because of subsolidus orthopyroxene/trapped melt exchange. These authors also noted the importance of working with elements with slow diffusion rates (e.g., REE) relative to those with rapid diffusion rates (e.g., Fe^2+, Mg). In most diogenites, the primary pyroxene is orthopyroxene, while in Fe- enriched diogenites (e.g., some assemblages in Garland and Yamato 75032 [3]) the primary pyroxene phase is pigeonite. In slowly cooled cumulate assemblages, monoclinic pigeonite inverts to orthopyroxene with complex augite exsolution lamellae, and the trace-element records of the parental magmas are essentially lost. Our recent SIMS studies indicate a strong fractionation of REE into the augite lamellae. Most of the orthopyroxene grains that we examined in our original suite of 13 diogenites have fine (100) augite lamellae. These lamellae can easily be reintegrated with the host orthopyroxene by using a relatively broad EMP or SIMS beam of 15-20 micrometers. In this study, we consider the nature and causes of OPX intragrain chemical variations. Our previous studies [4] showed that Cr and Al showed significant variations among the different diogenites and that specific diogenites trend toward one of several different trajectories on a Cr-Al plot. We also found significant chemical variability in individual OPX grains. To date, we have identified three types of intragrain chemical variations: (1) smooth trends from core to rim, (2) periodic linear variations [e

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

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.

Apparent pollution of groundwater caused by natural formation of chloroform in forest soils

NASA Astrophysics Data System (ADS)

Jacobsen, O.; Laier, T.; Albers, C. N.; Hunkeler, D.

2011-12-01

Halogenated compounds are known to be formed in natural environments. Many of these compounds are similar to industrially produced compounds and are toxic or carcinogenic. High concentration of chloroform in groundwater is usually attributed to anthropogenic input, but we have found that the groundwater beneath some pristine areas contained chloroform exceeding 1 μg/L. We investigated four coniferous forests over a period of several years in order to measure the net-formation of chloroform. Field measurements of atmospheric and soil air concentrations of chloroform were monitored. Analyses of soil air at 40 cm depth in different parts of the forests and adjacent areas revealed an extremely large variation in chloroform concentration exceeding two orders of magnitude. Up to 100 ppbv was found in soil air under the spruce forest, to be compared to an ambient atmospheric concentration of 0.02 ppbv. The concentration of chloroform in soil air showed seasonal variation similar to that of CO2. Chloroform formation during incubation of undisturbed top-soil samples was found to be largest in soils from dense conifers stands with well-developed humus layers, while low chloroform formation occurred in soils from beech forest and agricultural grassland. We suggest that the mechanism behind the formation of chloroform is an unspecific chlorination of organic matter, caused by microbial activity in the soil. The aquifers are in fluvio-glacial sands with few layers of silt and a groundwater table from 4 to 7 m below the surface. In the shallowest parts of the aquifer, the groundwater has chloroform concentrations of 0.1 to 5 μg/L, and the groundwater is oxic with an age from 5 to 45 years using CFC-dating. Analyses of oxic groundwater > 40 years showed that it still contained chloroform at concentrations of 1 μg/L. Stable carbon isotopic analyses of chloroform from the uppermost groundwater in different parts of the forests and from soil water showed values from δ13C = -13

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

Variation for epicuticular waxes and thrips resistance in onion

USDA-ARS?s Scientific Manuscript database

Onion thrips (Thrips tabaci) and thrips-vectored Iris Yellow Spot Virus (IYSV) routinely cause significant losses to the bulb and seed crops of onion. Both pests have become more problematic as global temperatures rise. Natural variation exists in onion for amounts and types of epicuticular waxes on...

Sex ratio variation shapes the ecological effects of a globally introduced freshwater fish

PubMed Central

Fryxell, David C.; Arnett, Heather A.; Apgar, Travis M.; Kinnison, Michael T.; Palkovacs, Eric P.

2015-01-01

Sex ratio and sexual dimorphism have long been of interest in population and evolutionary ecology, but consequences for communities and ecosystems remain untested. Sex ratio could influence ecological conditions whenever sexual dimorphism is associated with ecological dimorphism in species with strong ecological interactions. We tested for ecological implications of sex ratio variation in the sexually dimorphic western mosquitofish, Gambusia affinis. This species causes strong pelagic trophic cascades and exhibits substantial variation in adult sex ratios. We found that female-biased populations induced stronger pelagic trophic cascades compared with male-biased populations, causing larger changes to key community and ecosystem responses, including zooplankton abundance, phytoplankton abundance, productivity, pH and temperature. The magnitude of such effects indicates that sex ratio is important for mediating the ecological role of mosquitofish. Because both sex ratio variation and sexual dimorphism are common features of natural populations, our findings should encourage broader consideration of the ecological significance of sex ratio variation in nature, including the relative contributions of various sexually dimorphic traits to these effects. PMID:26490793

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

An Estimate of Changes in the Sun's Total Irradiance Caused by UV Irradiance Variations from 1874 to 1988

NASA Technical Reports Server (NTRS)

Lean, J.

1990-01-01

Enhanced emission from bright solar faculae is a source of significant variation in the sun's total irradiance. Relative to the emission from the quiet sun, facular emission is known to be considerably greater at UV wavelengths than at visible wavelengths. Determining the spectral dependence of facular emission is of interest for the physical insight this may provide to the origin of the sun's irradiance variations. It is also of interest because solar radiation at lambda less than 300 nm is almost totally absorbed in the Earth's atmosphere. Depending on the magnitude of the UV irradiance variations, changes in the sun's irradiance that penetrates to the Earth's surface may not be equivalent to total irradiance variations measured above the Earth's atmosphere. Using an empirical model of total irradiance variations which accounts separately for changes caused by bright faculae from those associated with dark sunspots, the contribution of UV irradiance variations to changes in the sun's total irradiance is estimated during solar cycles 12 to 21.

Super-emitters in natural gas infrastructure are caused by abnormal process conditions

NASA Astrophysics Data System (ADS)

Zavala-Araiza, Daniel; Alvarez, Ramón A.; Lyon, David R.; Allen, David T.; Marchese, Anthony J.; Zimmerle, Daniel J.; Hamburg, Steven P.

2017-01-01

Effectively mitigating methane emissions from the natural gas supply chain requires addressing the disproportionate influence of high-emitting sources. Here we use a Monte Carlo simulation to aggregate methane emissions from all components on natural gas production sites in the Barnett Shale production region (Texas). Our total emission estimates are two-thirds of those derived from independent site-based measurements. Although some high-emitting operations occur by design (condensate flashing and liquid unloadings), they occur more than an order of magnitude less frequently than required to explain the reported frequency at which high site-based emissions are observed. We conclude that the occurrence of abnormal process conditions (for example, malfunctions upstream of the point of emissions; equipment issues) cause additional emissions that explain the gap between component-based and site-based emissions. Such abnormal conditions can cause a substantial proportion of a site's gas production to be emitted to the atmosphere and are the defining attribute of super-emitting sites.

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

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.

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.

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.

Young Children's Ideas about the Nature, Causes, Justification, and Alleviation of Poverty

ERIC Educational Resources Information Center

Chafel, Judith A.; Neitzel, Carin

2005-01-01

Sixty-four 8-year-old boys and girls from urban and rural settings and representing different races and socioeconomic status backgrounds responded to questions about the nature, causes, justification, and alleviation of poverty. Much of what the children said indicated that they had not yet internalized prevailing adult norms and values about the…

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

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.

Spatiotemporal variations in the b-value of earthquake magnitude-frequency distributions: Classification and causes

NASA Astrophysics Data System (ADS)

El-Isa, Z. H.; Eaton, David W.

2014-03-01

Interpretation of the b-value of earthquake frequency-magnitude distributions has received considerable attention in recent decades. This paper provides a comprehensive review of previous investigations of spatial and temporal variations in b-value, including their classification and possible causes. Based on least-squares regression of seismicity data compiled from the NEIC, IRIS and ISC catalogs, we find an average value of 1.02 ± 0.03 for the whole Earth and its two hemispheres, consistent with the general view that in seismically active regions the long-term average value is close to unity. Nevertheless, wide-ranging b-variations (0.3 ≤ b ≤ 2.5) have been reported in the literature. This variability has been interpreted to arise from one or more of the following factors: prevailing stress state, crustal heterogeneity, focal depth, pore pressure, geothermal gradient, tectonic setting, petrological/environmental/geophysical characteristics, clustering of events, incomplete catalog data, and/or method of calculation. Excluding the latter, all of these factors appear to be linked, directly or indirectly, with the effective state of stress. Although time-dependent changes in b-value are well documented, conflicting observations reveal either a precursory increase or decrease in b value before major earthquakes. Our compilation of published analyses suggests that statistically significant b-variations occur globally on various timescales, including annual, monthly and perhaps diurnal. Taken together, our review suggests that b-variations are most plausibly linked with changes in effective stress.

Arsenic: Association of regional concentrations in drinking water with suicide and natural causes of death in Italy.

PubMed

Pompili, Maurizio; Vichi, Monica; Dinelli, Enrico; Erbuto, Denise; Pycha, Roger; Serafini, Gianluca; Giordano, Gloria; Valera, Paolo; Albanese, Stefano; Lima, Annamaria; De Vivo, Benedetto; Cicchella, Domenico; Rihmer, Zoltan; Fiorillo, Andrea; Amore, Mario; Girardi, Paolo; Baldessarini, Ross J

2017-03-01

Arsenic, as a toxin, may be associated with higher mortality rates, although its relationship to suicide is not clear. Given this uncertainty, we evaluated associations between local arsenic concentrations in tapwater and mortality in regions of Italy, to test the hypothesis that both natural-cause and suicide death rates would be higher with greater trace concentrations of arsenic. Arsenic concentrations in drinking-water samples from 145 sites were assayed by mass spectrometry, and correlated with local rates of mortality due to suicide and natural causes between 1980 and 2011, using weighted, least-squares univariate and multivariate regression modeling. Arsenic concentrations averaged 0.969 (CI: 0.543-1.396) µg/L, well below an accepted safe maximum of 10µg/L. Arsenic levels were negatively associated with corresponding suicide rates, consistently among both men and women in all three study-decades, whereas mortality from natural causes increased with arsenic levels. Contrary to an hypothesized greater risk of suicide with higher concentrations of arsenic, we found a negative association, suggesting a possible protective effect, whereas mortality from natural causes was increased, in accord with known toxic effects of arsenic. The unexpected inverse association between arsenic and suicide requires further study. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Anomalies of natural gas compositions and carbon isotope ratios caused by gas diffusion - A case from the Donghe Sandstone reservoir in the Hadexun Oilfield, Tarim Basin, northwest China

NASA Astrophysics Data System (ADS)

Wang, Yangyang; Chen, Jianfa; Pang, Xiongqi; Zhang, Baoshou; Wang, Yifan; He, Liwen; Chen, Zeya; Zhang, Guoqiang

2018-05-01

Natural gases in the Carboniferous Donghe Sandstone reservoir within the Block HD4 of the Hadexun Oilfield, Tarim Basin are characterized by abnormally low total hydrocarbon gas contents (<65%), low methane contents (<10%) and low dryness coefficients (<0.5), and a reversal of the normal trend of carbon isotope ratios, showing δ13C methane (C1) > δ13C ethane (C2) < δ13C propane (C3) < δ13C butane (C4). Specifically, methane is enriched in 13C with the variations in δ13C1 values between gases from Block HD4 and gases from its neighboring blocks reaching 10‰. This type of abnormal gas has never been reported previously in the Tarim Basin and such large variations in δ13C have rarely been observed in other basins globally. Based on a comprehensive analysis of gas geochemical data and the geological setting of the Carboniferous reservoirs in the Hadexun Oilfield, we reveal that the anomalies of the gas compositions and carbon isotope ratios in the Donghe Sandstone reservoir are caused by gas diffusion through the poorly-sealed caprock rather than by pathways such as gas mixing, microorganism degradation, different kerogen types or thermal maturity degrees of source rocks. The documentation of an in-reservoir gas diffusion during the post entrapment process as a major cause for gas geochemical anomalies may offer important insight into exploring natural gas resources in deeply buried sedimentary basins.

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.

Systematic and random variations in digital Thematic Mapper data

NASA Technical Reports Server (NTRS)

Duggin, M. J. (Principal Investigator); Sakhavat, H.

1985-01-01

Radiance recorded by any remote sensing instrument will contain noise which will consist of both systematic and random variations. Systematic variations may be due to sun-target-sensor geometry, atmospheric conditions, and the interaction of the spectral characteristics of the sensor with those of upwelling radiance. Random variations in the data may be caused by variations in the nature and in the heterogeneity of the ground cover, by variations in atmospheric transmission, and by the interaction of these variations with the sensing device. It is important to be aware of the extent of random and systematic errors in recorded radiance data across ostensibly uniform ground areas in order to assess the impact on quantative image analysis procedures for both the single date and the multidate cases. It is the intention here to examine the systematic and the random variations in digital radiance data recorded in each band by the thematic mapper over crop areas which are ostensibly uniform and which are free from visible cloud.

What causes amyotrophic lateral sclerosis?

PubMed Central

Martin, Sarah; Al Khleifat, Ahmad; Al-Chalabi, Ammar

2017-01-01

Amyotrophic lateral sclerosis is a neurodegenerative disease predominantly affecting upper and lower motor neurons, resulting in progressive paralysis and death from respiratory failure within 2 to 3 years. The peak age of onset is 55 to 70 years, with a male predominance. The causes of amyotrophic lateral sclerosis are only partly known, but they include some environmental risk factors as well as several genes that have been identified as harbouring disease-associated variation. Here we review the nature, epidemiology, genetic associations, and environmental exposures associated with amyotrophic lateral sclerosis. PMID:28408982

Environmental Variation Generates Environmental Opportunist Pathogen Outbreaks.

PubMed

Anttila, Jani; Kaitala, Veijo; Laakso, Jouni; Ruokolainen, Lasse

2015-01-01

Many socio-economically important pathogens persist and grow in the outside host environment and opportunistically invade host individuals. The environmental growth and opportunistic nature of these pathogens has received only little attention in epidemiology. Environmental reservoirs are, however, an important source of novel diseases. Thus, attempts to control these diseases require different approaches than in traditional epidemiology focusing on obligatory parasites. Conditions in the outside-host environment are prone to fluctuate over time. This variation is a potentially important driver of epidemiological dynamics and affect the evolution of novel diseases. Using a modelling approach combining the traditional SIRS models to environmental opportunist pathogens and environmental variability, we show that epidemiological dynamics of opportunist diseases are profoundly driven by the quality of environmental variability, such as the long-term predictability and magnitude of fluctuations. When comparing periodic and stochastic environmental factors, for a given variance, stochastic variation is more likely to cause outbreaks than periodic variation. This is due to the extreme values being further away from the mean. Moreover, the effects of variability depend on the underlying biology of the epidemiological system, and which part of the system is being affected. Variation in host susceptibility leads to more severe pathogen outbreaks than variation in pathogen growth rate in the environment. Positive correlation in variation on both targets can cancel the effect of variation altogether. Moreover, the severity of outbreaks is significantly reduced by increase in the duration of immunity. Uncovering these issues helps in understanding and controlling diseases caused by environmental pathogens.

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

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.

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...

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.

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

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

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

Nature and results of treatment of war wounds caused by cluster bombs.

PubMed

Mitković, Milorad; Bumbasirević, Marko; Grubor, Predrag; Milenković, Sasa; Micić, Ivan; Stojiljković, Predrag; Kostić, Igor; Karaleić, Sasa; Stamenić, Sonja; Pavlović, Predrag; Stanojlović, Milos; Jovanović, Vladimir; Radovanović, Zoran; Cirić, Tamara; Kutlesić-Stojanović, Katarina; Mitković, Milan

2013-01-01

The aim of this study is to describe the nature of war wounds with fracture caused by cluster bombs and to suggest treatment options for such injuries. The nature of wounds caused by cluster bombs differs from those caused by conventional arms (they are more severe). The sides of the wounds are represented by conquasated soft tissues (such as fat and muscle) with thick dead tissues, ordinarily with a thickness of 0.5-4.5 cm. Another main characteristic of such injuries is the high percentage of amputations needed due to the high rate of neurovascular damage. This paper investigates the cases of 81 patients who sustained a total of 99 war wounds with fractures. The average age of the patients was 32.7 years while the youngest was 20 and the oldest, 77. According to The International Committee of the Red Cross (ICRC) classification of war wounds, 14 patients had grade I injuries, 48 patients grade II, and 29 patients, grade III. Mitkovic external fixation system, known also as the "War Fixator" was used for all fractures fixation. One protocol, which was a modification of the ICRC's protocol adapted to our specific conditions, was used throughout the study. For solving soft tissue defects, a rotator fasciocutan flap was the most frequently used. For solving of bones defect Mitkovic reconstructive external fixation device was used. All fractures we treated healed. We concluded that shortening the procedural time and being a very simple, immediate using of Mitkovic versatile external fixator ("War Fixator") is, leads to desirable results.

PERSPECTIVES ON LARGE-SCALE NATURAL RESOURCES SURVEYS WHEN CAUSE-EFFECT IS A POTENTIAL ISSUE

EPA Science Inventory

Our objective is to present a perspective on large-scale natural resource monitoring when cause-effect is a potential issue. We believe that the approach of designing a survey to meet traditional commodity production and resource state descriptive objectives is too restrictive an...

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.

Natural selection stops the evolution of male attractiveness

PubMed Central

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

2011-01-01

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

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.

The Nature, Causes and Effects of School Violence in South African High Schools

ERIC Educational Resources Information Center

Ncontsa, Vusumzi Nelson; Shumba, Almon

2013-01-01

We sought to investigate the nature, causes and effects of school violence in four South African high schools. A purposive sample of five principals, 80 learners and 20 educators was selected from the four schools used in the study. A sequential mixed method approach was used in this study; both questionnaires and interviews were used. The design…

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.

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

Intraseasonal variation in survival and probable causes of mortality in greater sage-grouse Centrocercus urophasianus

USGS Publications Warehouse

Blomberg, Erik J.; Gibson, Daniel; Sedinger, James S.; Casazza, Michael L.; Coates, Peter S.

2013-01-01

The mortality process is a key component of avian population dynamics, and understanding factors that affect mortality is central to grouse conservation. Populations of greater sage-grouse Centrocercus urophasianus have declined across their range in western North America. We studied cause-specific mortality of radio-marked sage-grouse in Eureka County, Nevada, USA, during two seasons, nesting (2008-2012) and fall (2008-2010), when survival was known to be lower compared to other times of the year. We used known-fate and cumulative incidence function models to estimate weekly survival rates and cumulative risk of cause-specific mortalities, respectively. These methods allowed us to account for temporal variation in sample size and staggered entry of marked individuals into the sample to obtain robust estimates of survival and cause-specific mortality. We monitored 376 individual sage-grouse during the course of our study, and investigated 87 deaths. Predation was the major source of mortality, and accounted for 90% of all mortalities during our study. During the nesting season (1 April - 31 May), the cumulative risk of predation by raptors (0.10; 95% CI: 0.05-0.16) and mammals (0.08; 95% CI: 0.03-013) was relatively equal. In the fall (15 August - 31 October), the cumulative risk of mammal predation was greater (M(mam) = 0.12; 95% CI: 0.04-0.19) than either predation by raptors (M(rap) = 0.05; 95% CI: 0.00-0.10) or hunting harvest (M(hunt) = 0.02; 95% CI: 0.0-0.06). During both seasons, we observed relatively few additional sources of mortality (e.g. collision) and observed no evidence of disease-related mortality (e.g. West Nile Virus). In general, we found little evidence for intraseasonal temporal variation in survival, suggesting that the nesting and fall seasons represent biologically meaningful time intervals with respect to sage-grouse survival.

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.

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

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.

Magnetic field variation caused by rotational speed change in a magnetohydrodynamic dynamo.

PubMed

Miyagoshi, Takehiro; Hamano, Yozo

2013-09-20

We have performed numerical magnetohydrodynamic dynamo simulations in a spherical shell with rotational speed or length-of-day (LOD) variation, which is motivated by correlations between geomagnetic field and climatic variations with ice and non-ice ages. The results show that LOD variation leads to magnetic field variation whose amplitude is considerably larger than that of LOD variation. The heat flux at the outer sphere and the zonal flow also change. The mechanism of the magnetic field variation due to LOD variation is also found. The keys are changes of dynamo activity and Joule heating.

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.

Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus.

PubMed

Grunert, Steffen; Labudde, Dirk

2015-01-01

The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations.

Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus

PubMed Central

Labudde, Dirk

2015-01-01

The importance of short membrane sequence motifs has been shown in many works and emphasizes the related sequence motif analysis. Together with specific transmembrane helix-helix interactions, the analysis of interacting sequence parts is helpful for understanding the process during membrane protein folding and in retaining the three-dimensional fold. Here we present a simple high-throughput analysis method for deriving mutational information of interacting sequence parts. Applied on aquaporin water channel proteins, our approach supports the analysis of mutational variants within different interacting subsequences and finally the investigation of natural variants which cause diseases like, for example, nephrogenic diabetes insipidus. In this work we demonstrate a simple method for massive membrane protein data analysis. As shown, the presented in silico analyses provide information about interacting sequence parts which are constrained by protein evolution. We present a simple graphical visualization medium for the representation of evolutionary influenced interaction pattern pairs (EIPPs) adapted to mutagen investigations of aquaporin-2, a protein whose mutants are involved in the rare endocrine disorder known as nephrogenic diabetes insipidus, and membrane proteins in general. Furthermore, we present a new method to derive new evolutionary variations within EIPPs which can be used for further mutagen laboratory investigations. PMID:26180540

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

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

On the Cause of Eastern Equatorial Pacific Ocean T-S Variations Associated with El Nino

NASA Technical Reports Server (NTRS)

Wang, Ou; Fukumori, Ichiro; Lee, Tong; Cheng, Benny

2004-01-01

The nature of observed variations in temperature-salinity (T-S) relationship between El Nino and non-El Nino years in the pycnocline of the eastern equatorial Pacific Ocean (NINO3 region, 5(deg)S-5(deg)N, 150(deg)W-90(deg)W) is investigated using an ocean general circulation model. The origin of the subject water mass is identified using the adjoint of a simulated passive tracer. The higher salinity during El Nino is attributed to larger convergence of saltier water from the Southern Hemisphere and smaller convergence of fresher water from the Northern Hemisphere.

Glaciers. Attribution of global glacier mass loss to anthropogenic and natural causes.

PubMed

Marzeion, Ben; Cogley, J Graham; Richter, Kristin; Parkes, David

2014-08-22

The ongoing global glacier retreat is affecting human societies by causing sea-level rise, changing seasonal water availability, and increasing geohazards. Melting glaciers are an icon of anthropogenic climate change. However, glacier response times are typically decades or longer, which implies that the present-day glacier retreat is a mixed response to past and current natural climate variability and current anthropogenic forcing. Here we show that only 25 ± 35% of the global glacier mass loss during the period from 1851 to 2010 is attributable to anthropogenic causes. Nevertheless, the anthropogenic signal is detectable with high confidence in glacier mass balance observations during 1991 to 2010, and the anthropogenic fraction of global glacier mass loss during that period has increased to 69 ± 24%. Copyright © 2014, American Association for the Advancement of Science.

[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...

Natural variation in a single amino acid substitution underlies physiological responses to topoisomerase II poisons.

PubMed

Zdraljevic, Stefan; Strand, Christine; Seidel, Hannah S; Cook, Daniel E; Doench, John G; Andersen, Erik C

2017-07-01

Many chemotherapeutic drugs are differentially effective from one patient to the next. Understanding the causes of this variability is a critical step towards the development of personalized treatments and improvements to existing medications. Here, we investigate sensitivity to a group of anti-neoplastic drugs that target topoisomerase II using the model organism Caenorhabditis elegans. We show that wild strains of C. elegans vary in their sensitivity to these drugs, and we use an unbiased genetic approach to demonstrate that this natural variation is explained by a methionine-to-glutamine substitution in topoisomerase II (TOP-2). The presence of a non-polar methionine at this residue increases hydrophobic interactions between TOP-2 and its poison etoposide, as compared to a polar glutamine. We hypothesize that this stabilizing interaction results in increased genomic instability in strains that contain a methionine residue. The residue affected by this substitution is conserved from yeast to humans and is one of the few differences between the two human topoisomerase II isoforms (methionine in hTOPIIα and glutamine in hTOPIIβ). We go on to show that this amino acid difference between the two human topoisomerase isoforms influences cytotoxicity of topoisomerase II poisons in human cell lines. These results explain why hTOPIIα and hTOPIIβ are differentially affected by various poisons and demonstrate the utility of C. elegans in understanding the genetics of drug responses.

Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes.

PubMed

Katsumura, Takafumi; Oda, Shoji; Nakagome, Shigeki; Hanihara, Tsunehiko; Kataoka, Hiroshi; Mitani, Hiroshi; Kawamura, Shoji; Oota, Hiroki

2014-12-22

Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection. Interestingly, sexually selected traits show geographical variations within species despite strong directional selective pressures. This paradox has eluded many evolutionary biologists for some time, and several models have been proposed (e.g. 'indicator model' and 'trade-off model'). However, disentangling which of these theories explains empirical patterns remains difficult, because genetic polymorphisms that cause variation in sexual differences are still unknown. In this study, we show that polymorphisms in cytochrome P450 (CYP) 1B1, which encodes a xenobiotic-metabolizing enzyme, are associated with geographical differences in sexual dimorphism in the anal fin morphology of medaka fish (Oryzias latipes). Biochemical assays and genetic cross experiments show that high- and low-activity CYP1B1 alleles enhanced and declined sex differences in anal fin shapes, respectively. Behavioural and phylogenetic analyses suggest maintenance of the high-activity allele by sexual selection, whereas the low-activity allele possibly has experienced positive selection due to by-product effects of CYP1B1 in inferred ancestral populations. The present data can elucidate evolutionary mechanisms behind genetic variations in sexual dimorphism and indicate trade-off interactions between two distinct mechanisms acting on the two alleles with pleiotropic effects of xenobiotic-metabolizing enzymes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

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

Genetic variation affecting host-parasite interactions: different genes affect different aspects of sigma virus replication and transmission in Drosophila melanogaster.

PubMed

Bangham, Jenny; Kim, Kang-Wook; Webster, Claire L; Jiggins, Francis M

2008-04-01

In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.

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

Institutional Capacity for Natural Disasters: Methodology for Case Studies in Africa

DTIC Science & Technology

2013-03-01

Politician’s Dilemma (Berkeley: University of California Press, 1994); Haggard, Stephan, “Reform of the State in Latin America ” in Shahid Javed...Burki, et al., eds., Development in Latin America and the Caribbean (Washington: World Bank, 1997). 30 Cohen and Werker 2008: 797. 31 Keefer 2009: 21...capacity for natural disasters examines the causes of variation in government policies to reduce the risk of, prepare for, and respond to natural

Causes of 142Nd Variation in Earth

NASA Astrophysics Data System (ADS)

Boyet, M.; Bouvier, A.; Gannoun, A.; Carlson, R.

2015-12-01

Variability of the 142Nd/144Nd ratio can reflect Sm/Nd fractionation during the lifetime of 146Sm, i.e. the first 500 Ma of Solar System history1 and nucleosynthetic heterogeneity inherited from the solar nebula. Deciphering the message carried by 142Nd variability requires a detailed examination of the data for Earth and meteorites. The elevated 142Nd/144Nd in terrestrial samples relative to average chondrites suggests that all terrestrial rocks sampled by volcanism over the Earth's history come from a geochemical reservoir characterized by a superchondritic Sm/Nd ratio. The chemical compliment to this reservoir, however, has never been seen, so it either was lost during Earth's accretion2,3, or is preserved in a deep hidden reservoir 1,4. These models are based on a comparison of Earth rocks and O-chondrites because they do not show any variation in stable Sm and Nd isotopic composition compared to Earth6-8. The first analyzed E-chondrites with terrestrial 142Nd/144Nd showed 144Sm excesses that reflect an excess p-process contribution. Although 142Nd is mainly produced by s-process, there is a direct p-process component estimated to be lower than 4 %. We will present new Sm and Nd isotopic data on meteoritic materials. CAIs show deficits in both r- and p-process isotopes that would lead to elevated 142Nd, yet the bulk C-chondrites in which they are contained show excesses in r-process isotopes and hence 142Nd/144Nd lower than terrestrial. The new E-chondrites data do not confirm the 142Nd-144Sm correlation observed in bulk chondrites In light of these results and using 146Sm-142Nd isochrons for constraining the bulk 142Nd/144Nd ratio of planetary bodies, we will discuss the 142Nd signature of terrestrial samples (from Hadean to present). 1Boyet & Carlson, Science 2005; 2O'Neill & Palme, Phil. Trans. R. Soc 2008; 3Caro et al. Nature 2008; 4Andreasen et al. EPSL 2008; 6Andreasen & Sharma, Science 2006; 7Carlson et al., Science 2007; 8Gannoun et al. PNAS 2011.

Effects of increased alcohol availability during adolescence on the risk of all-cause and cause-specific disability pension: a natural experiment.

PubMed

Thern, Emelie; de Munter, Jeroen; Hemmingsson, Tomas; Davey Smith, George; Ramstedt, Mats; Tynelius, Per; Rasmussen, Finn

2017-06-01

To test if being exposed to increased alcohol availability during adolescence is associated with an increased risk of receiving disability pension due to all-cause, alcohol use disorders and mental disorders. Register-based population-based study using a natural experiment setting, the alcohol policy change in Sweden (1967-68), with increased access to strong beer in a narrow time window and geographical area. The individuals exposed to the policy change were compared with non-exposed individuals living in the rest of Sweden, excluding a border area. Sweden. A total of 518 810 individuals (70 761 in the intervention group; 448 049 in the control group) born 1948-1953, aged 14-20 years during the policy change. Date and diagnosis of the outcome variable of disability pension due to all-cause, alcohol use disorders and mental disorders were obtained from the Swedish National Social Insurance Agency database from 1971 to 2013. Individual and family level socio-demographic and health-related covariates, as well as a regional level covariate, were included. Compared with the control group, adolescents exposed to the alcohol policy change were at an increased risk of receiving disability pension due to all-causes [hazard ratio (HR) = 1.09, 95% confidence interval (CI) = 1.07-1.11], alcohol use disorders (HR = 1.17, 95% CI = 1.05-1.30) and mental disorders (HR = 1.19, 95% CI = 1.15-1.23). In Sweden, a natural experiment with a 43-year follow-up suggests that exposure to increased alcohol availability during adolescence is associated with an increased risk of receiving a disability pension due to all-cause, alcohol use disorder and mental disorder diagnoses. © 2017 The Authors. Addiction published by John Wiley & Sons Ltd on behalf of Society for the Study of Addiction.

The global tobacco disease pandemic: nature, causes, and cures.

PubMed

Warner, K E; Mackay, J

2006-01-01

Tobacco use kills 5 million citizens globally every year. The World Health Organization (WHO) projects that the number of deaths will double just 15 years from now. Tobacco will then constitute the leading cause of death in the developing world, as it already is in developed countries today. This paper describes the nature and extent of the tobacco pandemic, characteristics of the global tobacco industry, and national and international efforts to diminish the toll of tobacco. The review includes examination of the economic and political strategies employed by the multinational tobacco industry to increase cigarette consumption, as well as the policies that governments have adopted to combat smoking. The most promising development is the new Framework Convention on Tobacco Control, WHO's first-ever international health treaty. While aggressive tobacco control policies can and will diminish the toll of tobacco, the prospects for the foreseeable future appear grim.

Fast Oxidation Processes in a Naturally Reduced Aquifer Zone Caused by Dissolved Oxygen

NASA Astrophysics Data System (ADS)

Davis, J. A.; Jemison, N. E.; Williams, K. H.; Hobson, C.; Bush, R. P.

2014-12-01

The occurrence of naturally reduced zones is quite common in alluvial aquifers in the western U.S.A. due to the burial of woody debris in flood plains. The naturally reduced zones are heterogeneously dispersed in such aquifers and are characterized by high concentrations of organic carbon and reduced phases, including iron sulfides and reduced forms of metals, including uranium(IV). The persistence of high concentrations of dissolved uranium(VI) at uranium-contaminated aquifers on the Colorado Plateau has been attributed to slow oxidation of insoluble uranium(IV) mineral phases that are found in association with these natural reducing zones, although there is little understanding of the relative importance of various potential oxidants. Three field experiments were conducted within an alluvial aquifer adjacent to the Colorado River near Rifle, CO wherein groundwater associated with naturally reduced zones was pumped into a gas-impermeable tank, mixed with a conservative tracer (Br-), bubbled with a gas phase composed of 97% O2 and 3% CO2, and then returned to the subsurface in the same well from which it was withdrawn. Within minutes of re-injection of the oxygenated groundwater, dissolved uranium(VI) concentrations increased from less than 1 μM to greater than 2.5 μM, demonstrating that oxygen can be an important oxidant for uranium in these field systems if supplied to the naturally reduced zones. Small concentrations of nitrate were also observed in the previously nitrate-free groundwater, and Fe(II) decreased to the detection limit. These results contrast with other laboratory and field results in which oxygen was introduced to systems containing high concentrations of mackinawite (FeS) rather than the more crystalline iron sulfides found in aged, naturally reduced zones. The flux of oxygen to the naturally reduced zones in the alluvial aquifers occurs mainly through interactions between groundwater and gas phases at the water table, and seasonal variations

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...

Causes of forbush decreases and other cosmic ray variations

NASA Technical Reports Server (NTRS)

Barouch, E.; Burlaga, L. F.

1974-01-01

The relationship between neutron monitor variations and the intensity variations of the interplanetary magnetic field is studied, using Deep River data and IMP-series satellite data. In over 80% of the cases studied, identifiable depressions of the cosmic ray intensity are associated with magnetic field enhancements of several hours duration and intensity above 10 gamma. Conversely, each magnetic field enhancement has an identifiable effect (though not necessarily a marked depression) on the cosmic ray intensity. Long lasting Forbush decreases are found to be the consequence of the successive action of several such features. An explanation is presented and discussed.

Causes of variation among rice models in yield response to CO2 examined with Free-Air CO2 Enrichment and growth chamber experiments.

PubMed

Hasegawa, Toshihiro; Li, Tao; Yin, Xinyou; Zhu, Yan; Boote, Kenneth; Baker, Jeffrey; Bregaglio, Simone; Buis, Samuel; Confalonieri, Roberto; Fugice, Job; Fumoto, Tamon; Gaydon, Donald; Kumar, Soora Naresh; Lafarge, Tanguy; Marcaida Iii, Manuel; Masutomi, Yuji; Nakagawa, Hiroshi; Oriol, Philippe; Ruget, Françoise; Singh, Upendra; Tang, Liang; Tao, Fulu; Wakatsuki, Hitomi; Wallach, Daniel; Wang, Yulong; Wilson, Lloyd Ted; Yang, Lianxin; Yang, Yubin; Yoshida, Hiroe; Zhang, Zhao; Zhu, Jianguo

2017-11-01

The CO 2 fertilization effect is a major source of uncertainty in crop models for future yield forecasts, but coordinated efforts to determine the mechanisms of this uncertainty have been lacking. Here, we studied causes of uncertainty among 16 crop models in predicting rice yield in response to elevated [CO 2 ] (E-[CO 2 ]) by comparison to free-air CO 2 enrichment (FACE) and chamber experiments. The model ensemble reproduced the experimental results well. However, yield prediction in response to E-[CO 2 ] varied significantly among the rice models. The variation was not random: models that overestimated at one experiment simulated greater yield enhancements at the others. The variation was not associated with model structure or magnitude of photosynthetic response to E-[CO 2 ] but was significantly associated with the predictions of leaf area. This suggests that modelled secondary effects of E-[CO 2 ] on morphological development, primarily leaf area, are the sources of model uncertainty. Rice morphological development is conservative to carbon acquisition. Uncertainty will be reduced by incorporating this conservative nature of the morphological response to E-[CO 2 ] into the models. Nitrogen levels, particularly under limited situations, make the prediction more uncertain. Improving models to account for [CO 2 ] × N interactions is necessary to better evaluate management practices under climate change.

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.

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.

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.

Variation in genotype and higher virulence of a strain of Sporothrix schenckii causing disseminated cutaneous sporotrichosis.

PubMed

Zhang, Zhenying; Liu, Xiaoming; Lv, Xuelian; Lin, Jingrong

2011-12-01

Sporotrichosis is usually a localized, lymphocutaneous disease, but its disseminated type was rarely reported. The main objective of this study was to identify specific DNA sequence variation and virulence of a strain of Sporothrix schenckii isolated from the lesion of disseminated cutaneous sporotrichosis. We confirmed this strain to be S. schenckii by(®) tubulin and chitin synthase gene sequence analysis in addition to the routine mycological and partial ITS and NTS sequencing. We found a 10-bp deletion in the ribosomal NTS region of this strain, in reference to the sequence of control strains isolated from fixed cutaneous sporotrichosis. After inoculated into immunosuppressed mice, this strain caused more extensive system involvement and showed stronger virulence than the control strain isolated from a fixed cutaneous sporotrichosis. Our study thus suggests that different clinical manifestation of sporotrichosis may be associated with variation in genotype and virulence of the strain, independent of effects due to the immune status of the host.

Variations of iron flux and organic carbon remineralization in a subterranean estuary caused by interannual variations in recharge

USGS Publications Warehouse

Roy, Moutusi; Martin, Jonathan B.; Cable, Jaye E.; Smith, Christopher G.

2013-01-01

We determine the inter-annual variations in diagenetic reaction rates of sedimentary iron (Fe ) in an east Florida subterranean estuary and evaluate the connection between metal fluxes and recharge to the coastal aquifer. Over the three-year study period (from 2004 to 2007), the amount of Fe-oxides reduced at the study site decreased from 192 g/yr to 153 g/yr and associated organic carbon (OC) remineralization decreased from 48 g/yr to 38 g/yr. These reductions occurred although the Fe-oxide reduction rates remained constant around 1 mg/cm2/yr. These results suggest that changes in flow rates of submarine groundwater discharge (SGD) related to changes in precipitation may be important to fluxes of the diagenetic reaction products. Rainfall at a weather station approximately 5 km from the field area decreased from 12.6 cm/month to 8.4 cm/month from 2004 to 2007. Monthly potential evapotranspiration (PET) calculated from Thornthwaite’s method indicated potential evapotranspiration cycled from about 3 cm/month in the winter to about 15 cm/month in the summer so that net annual recharge to the aquifer decreased from 40 cm in 2004 to -10 cm in 2007. Simultaneously, with the decrease in recharge of groundwater, freshwater SGD decreased by around 20% and caused the originally 25 m wide freshwater seepage face to decrease in width by about 5 m. The smaller seepage face reduced the area under which Fe-oxides were undergoing reductive dissolution. Consequently, the observed decrease in Fe flux is controlled by hydrology of the subterranean estuary. These results point out the need to better understand linkages between temporal variations in diagenetic reactions and changes in flow within subterranean estuaries in order to accurately constrain their contribution to oceanic fluxes of solutes from subterranean estuaries.

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

Natural Products: Key Prototypes to Drug Discovery Against Neglected Diseases Caused by Trypanosomatids.

PubMed

Varela, Marina Themoteo; Fernandes, Joao Paulo S

2018-04-30

Neglected tropical diseases are a group of infections caused by microorganisms and viruses that affect mainly poor regions of the world. In addition, most available drugs are associated with long periods of treatment and high toxicity which limits the application and patient compliance. Investment in research and development is not seen as an attractive deal by the pharmaceutical industry since the final product must ideally be cheap, not returning the amount invested. Natural products have always played an important source for bioactive compounds and are advantageous over synthetic compounds when considering the unique structural variety and biological activities. On the other hand, isolation difficulties and low yields, environmental impact and high cost usually limit their application as drug per se. In this review, the use of natural products as prototypes for the semi-synthesis or total synthesis, as well as natural products as promising hits are covered, specifically regarding compounds with activities against trypanosomatids such as Trypanosoma spp. and Leishmania spp. Selected reports from literature with this approach were retrieved. As summary, it can be concluded that natural products are an underestimated source for designing novel agents against these parasites. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

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.

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

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

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.

Partial nephrogenic diabetes insipidus caused by a novel AQP2 variation impairing trafficking of the aquaporin-2 water channel.

PubMed

Dollerup, Pia; Thomsen, Troels Møller; Nejsum, Lene N; Færch, Mia; Österbrand, Martin; Gregersen, Niels; Rittig, Søren; Christensen, Jane H; Corydon, Thomas J

2015-12-29

Autosomal dominant inheritance of congenital nephrogenic diabetes insipidus (CNDI) is rare and usually caused by variations in the AQP2 gene. We have investigated the genetic and molecular background underlying symptoms of diabetes insipidus (DI) in a Swedish family with autosomal dominant inheritance of the condition. The proband and her father were subjected to water deprivation testing and direct DNA sequencing of the coding regions of the AQP2 and AVP genes. Madin-Darby canine kidney (MDCK) cells stably expressing AQP2 variant proteins were generated by lentiviral gene delivery. Localization of AQP2 variant proteins in the cells under stimulated and unstimulated conditions was analyzed by means of immunostaining and confocal laser scanning microscopy. Intracellular trafficking of AQP2 variant proteins was studied using transient expression of mutant dynamin2-K44A-GFP protein and AQP2 variant protein phosphorylation levels were assessed by Western blotting analysis. Clinical and genetic data suggest that the proband and her father suffer from partial nephrogenic DI due to a variation (g.4807C > T) in the AQP2 gene. The variation results in substitution of arginine-254 to tryptophan (p.R254W) in AQP2. Analysis of MDCK cells stably expressing AQP2 variant proteins revealed disabled phosphorylation, impaired trafficking and intracellular accumulation of AQP2-R254W protein. Notably, blocking of the endocytic pathway demonstrated impairment of AQP2-R254W to reach the cell surface. Partial CNDI in the Swedish family is caused by an AQP2 variation that seems to disable the encoded AQP2-R254W protein to reach the subapical vesicle population as well as impairing its phosphorylation at S256. The AQP2-R254W protein is thus unable to reach the plasma membrane to facilitate AVP mediated urine concentration.

Colonizing the world in spite of reduced MHC variation

USGS Publications Warehouse

Gangoso, L.; Alcaide, M.; Grande, J.M.; Muñoz, J.; Talbot, Sandra L.; Sonsthagen, Sarah A.; Sage, Kevin; Figuerola, J.

2012-01-01

Reduced immune gene diversity is thought to negatively affect the capacity of organisms to adapt to pathogen challenges, which represent a major force in natural selection. Genes of the Major Histocompatibility Complex (MHC) are the most widely invoked adaptive loci in conservation biology, and have become the most popular genetic markers to investigate pathogen-host interactions in vertebrates. Although MHC genes are the most polymorphic genes described in the vertebrate genome, the extent to which MHC diversity determines the long-term persistence of populations is, unclear and often debated, as recent studies have documented the occurrence of natural populations thriving even after a depletion of MHC diversity caused by genetic drift. Here, we show that some phylogenetically related species belonging to the Falco genus (Aves: Falconidae) present a dramatically low MHC variability that has not precluded, nevertheless, the successful colonization of almost all existing regions and habitats worldwide. We found evidence for two remarkably different patterns of MHC variation within the genus. While kestrels show a high MHC variation according to the general theory, falcons exhibit an ancestrally low intra- and inter-specific MHC allelic diversity. We provide compelling evidence that this pattern is not caused by the degeneration of functional genes into pseudogenes, the inadvertent analyses of paralogous MHC genes, or the devastating action of genetic drift. Instead, our results strongly support the idea of an evolutionary transition driven and maintained by natural selection from primarily highly variable towards low polymorphic, but functional and expressed, MHC genes with species-specific pathogen-recognition capabilities.

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.

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

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.

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.

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

Geographic variation in forest composition and precipitation predict the synchrony of forest insect outbreaks

Treesearch

Kyle J. Haynes; Andrew M. Liebhold; Ottar N. Bjørnstad; Andrew J. Allstadt; Randall S. Morin

2018-01-01

Evaluating the causes of spatial synchrony in population dynamics in nature is notoriously difficult due to a lack of data and appropriate statistical methods. Here, we use a recently developed method, a multivariate extension of the local indicators of spatial autocorrelation statistic, to map geographic variation in the synchrony of gypsy moth outbreaks. Regression...

Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice.

PubMed

Shen, Rongxin; Wang, Lan; Liu, Xupeng; Wu, Jiang; Jin, Weiwei; Zhao, Xiucai; Xie, Xianrong; Zhu, Qinlong; Tang, Huiwu; Li, Qing; Chen, Letian; Liu, Yao-Guang

2017-11-03

Hybrids between divergent populations commonly show hybrid sterility; this reproductive barrier hinders hybrid breeding of the japonica and indica rice (Oryza sativa L.) subspecies. Here we show that structural changes and copy number variation at the Sc locus confer japonica-indica hybrid male sterility. The japonica allele, Sc-j, contains a pollen-essential gene encoding a DUF1618-domain protein; the indica allele, Sc-i, contains two or three tandem-duplicated ~ 28-kb segments, each carrying an Sc-j-homolog with a distinct promoter. In Sc-j/Sc-i hybrids, the high-expression of Sc-i in sporophytic cells causes suppression of Sc-j expression in pollen and selective abortion of Sc-j-pollen, leading to transmission ratio distortion. Knocking out one or two of the three Sc-i copies by CRISPR/Cas9 rescues Sc-j expression and male fertility. Our results reveal the gene dosage-dependent allelic suppression as a mechanism of hybrid incompatibility, and provide an effective approach to overcome the reproductive barrier for hybrid breeding.

Assessment of infrastructure functional damages caused by natural-technological disasters

NASA Astrophysics Data System (ADS)

Massabò, Marco; Trasforini, Eva; Traverso, Stefania; Rudari, Roberto; De Angeli, Silvia; Cecinati, Francesca; Cerruti, Valentina

2013-04-01

The assessment of infrastructure damages caused by technological disaster poses several challenges, from gathering needed information on the territorial system to the definition of functionality curves for infrastructures elements (such as, buildings, road school) that are exposed to both natural and technological event. Moreover, areas affected by natural or natech (technological disasters triggered by natural events) disasters have often very large extensions and a rapid survey of them to gather all the needed information is a very difficult task, for many reasons, not least the difficult access to the existing databases and resources. We use multispectral optical imagery with other geographical and unconventional data to identify and characterize exposed elements. Our efforts in the virtual survey and during the investigation steps have different aims: to identify the vulnerability of infrastructures, buildings or activities; to execute calculations of exposition to risk; to estimate physical and functional damages. Subsequently, we apply specific algorithms to estimate values of acting forces and physical and functional damages. The updated picture of target areas in terms of risk-prone people, infrastructures and their connections is very important. It is possible to develop algorithms providing values of systemic functionality for each network element. The methodology is here applied to a natech disaster, arising from the combination of a flood event (specifically, the January 2010 flooding of Drin and Buna rivers, with a worsening in the road safety levels in the Shkoder area) with and the subsequent overturning of a truck transporting hazardous material. The accident causes the loss of containment and the total material release. Once the release has taken place, the evolution will depend on the physical state of the substance spilled (liquid, gas or dust). As a specific case we consider the rupture of a trucks transporting liquid fuels such as gasoline

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.

Variations of iron flux and organic carbon remineralization in a subterranean estuary caused by inter-annual variations in recharge

NASA Astrophysics Data System (ADS)

Roy, Moutusi; Martin, Jonathan B.; Cable, Jaye E.; Smith, Christopher G.

2013-02-01

We determine the inter-annual variations in diagenetic reaction rates of sedimentary iron (Fe) in an east Florida subterranean estuary and evaluate the connection between metal fluxes and recharge to the coastal aquifer. Over the three years study period (from 2004 to 2007), the amount of Fe-oxides reduced at the study site decreased from 192 to 153 g/yr and associated organic carbon (OC) remineralization decreased from 48 to 38 g/yr. These reductions occurred although the Fe-oxide reduction rates remained constant around 1 mg/cm2/yr. These results suggest that changes in flow rates of submarine groundwater discharge (SGD) related to changes in precipitation may be important to fluxes of the diagenetic reaction products. Rainfall at a weather station approximately 5 km from the field area decreased from 12.6 to 8.4 cm/month from 2004 to 2007. Monthly potential evapotranspiration (PET) calculated from Thornthwaite's method indicated potential evapotranspiration cycled from about 3 cm/month in the winter to about 15 cm/month in the summer so that net annual recharge to the aquifer decreased from 40 cm in 2004 to -10 cm in 2007. Simultaneously with the decrease in recharge of groundwater, freshwater SGD decreased by around 20% and caused the originally 25 m wide freshwater seepage face to decrease in width by about 5 m. The smaller seepage face reduced the area under which Fe-oxides were undergoing reductive dissolution. Consequently, the observed decrease in Fe flux is controlled by hydrology of the subterranean estuary. These results point out the need to better understand linkages between temporal variations in diagenetic reactions and changes in flow within subterranean estuaries in order to accurately constrain their contribution to oceanic fluxes of solutes from subterranean estuaries.

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.

Intraspecific Variation among Social Insect Colonies: Persistent Regional and Colony-Level Differences in Fire Ant Foraging Behavior

PubMed Central

Bockoven, Alison A.; Wilder, Shawn M.; Eubanks, Micky D.

2015-01-01

Individuals vary within a species in many ecologically important ways, but the causes and consequences of such variation are often poorly understood. Foraging behavior is among the most profitable and risky activities in which organisms engage and is expected to be under strong selection. Among social insects there is evidence that within-colony variation in traits such as foraging behavior can increase colony fitness, but variation between colonies and the potential consequences of such variation are poorly documented. In this study, we tested natural populations of the red imported fire ant, Solenopsis invicta, for the existence of colony and regional variation in foraging behavior and tested the persistence of this variation over time and across foraging habitats. We also reared single-lineage colonies in standardized environments to explore the contribution of colony lineage. Fire ants from natural populations exhibited significant and persistent colony and regional-level variation in foraging behaviors such as extra-nest activity, exploration, and discovery of and recruitment to resources. Moreover, colony-level variation in extra-nest activity was significantly correlated with colony growth, suggesting that this variation has fitness consequences. Lineage of the colony had a significant effect on extra-nest activity and exploratory activity and explained approximately half of the variation observed in foraging behaviors, suggesting a heritable component to colony-level variation in behavior. PMID:26197456

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

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.

Genetic variation in arthropod vectors of disease-causing organisms: obstacles and opportunities.

PubMed Central

Gooding, R H

1996-01-01

An overview of the genetic variation in arthropods that transmit pathogens to vertebrates is presented, emphasizing the genetics of vector-pathogen relationships and the biochemical genetics of vectors. Vector-pathogen interactions are reviewed briefly as a prelude to a discussion of the genetics of susceptibility and refractoriness in vectors. Susceptibility to pathogens is controlled by maternally inherited factors, sex-linked dominant alleles, and dominant and recessive autosomal genes. There is widespread interpopulation (including intercolony) and temporal variation in susceptibility to pathogens. The amount of biochemical genetic variation in vectors is similar to that found in other invertebrates. However, the amount varies widely among species, among populations within species, and temporally within populations. Biochemical genetic studies show that there is considerable genetic structuring of many vectors at the local, regional, and global levels. It is argued that genetic variation in vectors is critical in understanding vector-pathogen interactions and that genetic variation in vectors creates both obstacles to and opportunities for application of genetic techniques to the control of vectors. PMID:8809462

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.

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

Numerical simulation of scouring-deposition variations caused by rainfall-induced landslides in the upstream of Zengwun River, Taiwan

NASA Astrophysics Data System (ADS)

Lee, Ming-Hsi; Liao, Yi-Wen; Tsai, Kuang-Jung

2017-04-01

In recent years, the increasing sediment disasters of severe rainfall-induced landslides on human lives and lifeline facilities worldwide have advanced the necessity to find out both economically acceptable and useful techniques to predict the occurrence and destructive power of the disasters. In August 2009, Typhoon Morakot brought a large amount of rainfall with both high intensity and long duration to a vast area of Taiwan. Unfortunately, this resulted in a catastrophic landslide in watershed of Zengwun-River reservoir, southern Taiwan. Meanwhile, large amounts of landslides were formed in the upstream of Zengwun River. The major scope of this study is to apply numerical model to simulate the scouring-deposition variations caused by rainfall-induced landslides that occurred in the upstream of Zengwun River during Typhoon Morakot. This study proposed the relation diagrams of the intermediate diameter (d50), recurrence interval (T) and scouring-deposition depth (D), and applied the diagrams to understand the impacts of the scouring-deposition variations on the structures for water and soil conservation and their measurements. Based on the simulation of scouring-deposition variation at the Da-Bu dam and Da-Bang dam, this study also discussed the scouring-deposition variations of different sections under different scenarios (including flow rate, intermediate diameters and structures). In summary, the result suggested that the diagrams of the intermediate diameter, recurrence interval and scouring-deposition depth could be used as the reference for designing the check dams, ground sills and lateral constructions.

Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes

PubMed Central

Blundell, John E.; Baker, Jennifer Lyn; Boyland, Emma; Blaak, Ellen; Charzewska, Jadwiga; de Henauw, Stefaan; Frühbeck, Gema; Gonzalez-Gross, Marcela; Hebebrand, Johannes; Holm, Lotte; Kriaucioniene, Vilma; Lissner, Lauren; Oppert, Jean-Michel; Schindler, Karin; Silva, Analiza Mónica; Woodward, Euan

2017-01-01

Over the last 10 years the prevalence of obesity across the European continent has in general been rising. With the exception of a few countries where a levelling-off can be perceived, albeit at a high level, this upward trend seems likely to continue. However, considerable country to country variation is noticeable, with the proportion of people with obesity varying by 10% or more. This variation is intriguing and suggests the existence of different profiles of risk or protection factors operating in different countries. The identification of such protection factors could indicate suitable targets for interventions to help manage the obesity epidemic in Europe. This report is the output of a 2-day workshop on the ‘Diversity of Obesity in Europe’. The workshop included 14 delegates from 12 different European countries. This report contains the contributions and discussions of the materials and viewpoints provided by these 14 experts; it is not the output of a single mind. However, such is the nature of scientific analysis regarding obesity that it is possible that a different set of 14 experts may have come to a different set of conclusions. Therefore the report should not be seen as a definitive statement of a stable situation. Rather it is a focus for discussion and comment, and a vehicle to drive forward further understanding and management of obesity in Europe. PMID:28190010

Variation of haemoglobin extinction coefficients can cause errors in the determination of haemoglobin concentration measured by near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Kim, J. G.; Liu, H.

2007-10-01

Near-infrared spectroscopy or imaging has been extensively applied to various biomedical applications since it can detect the concentrations of oxyhaemoglobin (HbO2), deoxyhaemoglobin (Hb) and total haemoglobin (Hbtotal) from deep tissues. To quantify concentrations of these haemoglobin derivatives, the extinction coefficient values of HbO2 and Hb have to be employed. However, it was not well recognized among researchers that small differences in extinction coefficients could cause significant errors in quantifying the concentrations of haemoglobin derivatives. In this study, we derived equations to estimate errors of haemoglobin derivatives caused by the variation of haemoglobin extinction coefficients. To prove our error analysis, we performed experiments using liquid-tissue phantoms containing 1% Intralipid in a phosphate-buffered saline solution. The gas intervention of pure oxygen was given in the solution to examine the oxygenation changes in the phantom, and 3 mL of human blood was added twice to show the changes in [Hbtotal]. The error calculation has shown that even a small variation (0.01 cm-1 mM-1) in extinction coefficients can produce appreciable relative errors in quantification of Δ[HbO2], Δ[Hb] and Δ[Hbtotal]. We have also observed that the error of Δ[Hbtotal] is not always larger than those of Δ[HbO2] and Δ[Hb]. This study concludes that we need to be aware of any variation in haemoglobin extinction coefficients, which could result from changes in temperature, and to utilize corresponding animal's haemoglobin extinction coefficients for the animal experiments, in order to obtain more accurate values of Δ[HbO2], Δ[Hb] and Δ[Hbtotal] from in vivo tissue measurements.

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).

Differences in monthly variation, cause, and place of injury between femoral neck and trochanteric fractures: 6-year survey (2008–2013) in Kyoto prefecture, Japan

PubMed Central

Horii, Motoyuki; Fujiwara, Hiroyoshi; Mikami, Yasuo; Ikeda, Takumi; Ueshima, Keiichiro; Ikoma, Kazuya; Shirai, Toshiharu; Nagae, Masateru; Oka, Yoshinobu; Sawada, Koshiro; Kuriyama, Nagato; Kubo, Toshikazu

2016-01-01

Summary Background The incidence of femoral neck and trochanteric fractures reportedly differ by age and regionality. We investigated differences in monthly variations of the occurrence of femoral neck and trochanteric fractures as well as place and cause of injury in the Kyoto prefecture over a 6-year period. Methods Fracture type (neck or trochanteric fracture), age, sex, place of injury, and cause of injury were surveyed among patients aged ≥ 65 years with hip fractures that occurred between 2008 and 2013 who were treated in 1 of 13 participating hospitals (5 in an urban area and 8 in a rural area). The proportion of sick beds in the participating hospitals was 24.7% (4,151/16,781). Monthly variations in the number of patients were investigated in urban and rural areas in addition to the entire Kyoto prefecture. Place of injury was classified as indoors or outdoors, and cause of injury was categorized as simple fall, accident, or uncertain. Results There were 2,826 patients with neck fractures (mean age, 82.1 years) and 3,305 patients with trochanteric fractures (mean age, 85.0 years). There were similarities in the monthly variation of the number of fractures in addition to the place and cause of injury between neck and trochanteric fractures. Indoors (approximately 74%) and simple falls (approximately 78%) were the primary place and cause of injury, respectively. The place of injury was not significantly different by fracture type with each age group. Significantly more patients with neck fracture had “uncertain” as the cause of injury than trochanteric fracture in all age groups. Conclusions Based on the results of the present study, the injury pattern might not have a great effect on the susceptibility difference between neck and trochanteric fractures. PMID:27252738

The influence of ENSO, PDO and PNA on secular rainfall variations in Hawai‘i

Treesearch

Abby G. Frazier; Oliver Elison Timm; Thomas W. Giambelluca; Henry F. Diaz

2017-01-01

Over the last century, significant declines in rainfall across the state of Hawai‘i have been observed, and it is unknown whether these declines are due to natural variations in climate, or manifestations of human-induced climate change. Here, a statistical analysis of the observed rainfall variability was applied as first step towards better understanding causes for...

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

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.

Natural variance in pH as a complication in detecting acidification of lakes

USGS Publications Warehouse

Turk, J.T.

1988-01-01

Natural variance in the pH of three dilute lakes in the Flat Tops Wilderness Area, Colorado, complicates the detection of acidification. Variations in pH during July-September of 1983 were: 0.95 (Ned Wilson Lake), 1.36 (Upper Island Lake), and 1.53 (Oyster Lake). Mean diurnal variations in pH during 1983 were: 0.37 (Ned Wilson Lake), 0.54 (Upper Island Lake), and 0.39 (Oyster Lake). Replicate pH measurements indicate that pH can be measured with a mean variance due to measurement error of ?? 0.005. Regression analysis indicates that samples collected on the same day of different years may differ because of time of day and percentage of cloud cover. Differences in wind duration and intensity and primary productivity also may cause the pH to differ between years. Such differences can be either random or systematic. Comparisons of pH among 3 yr of data from Ned Wilson Lake indicate that natural variations in pH are much larger than variations in Colorado Lakes previously attributed to acidification by precipitation.

The Myth of Community Differences as the Cause of Variations Among IRBs

PubMed Central

Klitzman, Robert

2013-01-01

Background Although variations among institutional review boards (IRBs) have been documented for 30 years, they continue, raising crucial questions as to why they persist as well as how IRBs view and respond to these variations. Methods In-depth, 2-hour interviews were conducted with 46 IRB chairs, administrators, and members. The leadership of 60 U.S. IRBs were contacted (every fourth one in the list of the top 240 institutions by NIH funding). IRB leaders from 34 of these institutions were interviewed (response rate = 55%). Results The interviewees suggest that differences often persist because IRBs think these are legitimate, and regulations permit variations due to differing “community values.” Yet, these variations frequently appear to stem more from differences in institutional and subjective personality factors, and from “more eyes” examining protocols, trying to foresee all potential future logistical problems, than from the values of the communities from which research participants are drawn. However, IRBs generally appear to defend these variations as reflecting underlying differences in community norms. Conclusions These data pose critical questions for policy and practice. Attitudinal changes and education among IRBs, principal investigators (PIs), policymakers, and others and research concerning these issues are needed. PMID:25285236

Does variation in mineral composition alter the short-wave light scattering properties of desert dust aerosol?

NASA Astrophysics Data System (ADS)

Smith, Andrew J. A.; Grainger, Roy G.

2014-01-01

Mineral dust aerosol is a major component of natural airborne particulates. Using satellite measurements from the visible and near-infrared, there is insufficient information to retrieve a full microphysical and chemical description of an aerosol distribution. As such, refractive index is one of many parameters that must be implicitly assumed in order to obtain an optical depth retrieval. This is essentially a proxy for the dust mineralogy. Using a global soil map, it is shown that as long as a reasonable refractive index for dust is assumed, global dust variability is unlikely to cause significant variation in the optical properties of a dust aerosol distribution in the short-wave, and so should not greatly affect retrievals of mineral dust aerosol from space by visible and near-infrared radiometers. Errors in aerosol optical depth due to this variation are expected to be ≲ 1 %. The work is framed around the ORAC AATSR aerosol retrieval, but is equally applicable to similar satellite retrievals. In this case, variations in the top-of-atmosphere reflectance caused by mineral variation are within the noise limits of the instrument.

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.

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

Signal, noise, and variation in neural and sensory-motor latency

PubMed Central

Lee, Joonyeol; Joshua, Mati; Medina, Javier F.; Lisberger, Stephen G.

2016-01-01

Analysis of the neural code for sensory-motor latency in smooth pursuit eye movements reveals general principles of neural variation and the specific origin of motor latency. The trial-by-trial variation in neural latency in MT comprises: a shared component expressed as neuron-neuron latency correlations; and an independent component that is local to each neuron. The independent component arises heavily from fluctuations in the underlying probability of spiking with an unexpectedly small contribution from the stochastic nature of spiking itself. The shared component causes the latency of single neuron responses in MT to be weakly predictive of the behavioral latency of pursuit. Neural latency deeper in the motor system is more strongly predictive of behavioral latency. A model reproduces both the variance of behavioral latency and the neuron-behavior latency correlations in MT if it includes realistic neural latency variation, neuron-neuron latency correlations in MT, and noisy gain control downstream from MT. PMID:26971946

Dissolved organic carbon and unimodal variation in sexual signal coloration in mosquitofish: a role for light limitation?

PubMed Central

Layman, Craig A.

2017-01-01

Natural selection plays an important role in the evolution of sexual communication systems. Here, we assess the effect of two well-known selection agents, transmission environment and predation, on interpopulation variation in sexual signals. Our model system is a series of 21 populations of Bahamian mosquitofish subjected to independent variation in optical conditions and predation risk. We show that optically diverse environments, caused by locally variable dissolved organic carbon concentrations, rather than spatial variation in predation, drove divergence in fin coloration (fin redness). We found a unimodal pattern of phenotypic variation along the optical gradient indicating a threshold-type response of visual signals to broad variation in optical conditions. We discuss evolutionary and ecological mechanisms that may drive such a pattern as well as the implications of non-monotonic clines for evolutionary differentiation. PMID:28381625

GF-1 and Landsat observed a 40-year wetland spatiotemporal variation and its coupled environmental factors in Yangtze River estuary

NASA Astrophysics Data System (ADS)

Sun, Nan; Zhu, Weining; Cheng, Qian

2018-07-01

Wetlands are health indicators of aquatic ecosystems and also vulnerable to regional environmental and socio-economic changes. For exploring wetland spatiotemporal variations in estuarine and coastal regions of the Yangtze River, we extracted wetland information from 40-year time-series images of Landsat, GF-1, and other satellites, using the classification method of decision tree. Potential environmental and socio-economic factors which may drive wetland variations were analyzed. Results show that the wetland area in Yangtze River estuary has increased 663 km2, but it was only contributed by the increasing of human-made wetlands (767 km2), which were mostly caused by economic growth and constructions of human-made hydro-projects in Yangtze Delta. In comparison, natural wetlands, such as tidal flats and marshes, have decreased 163 km2. Land reclamation has changed these natural wetlands into reservoirs, aquaculture ponds and paddy fields. Wetlands in Shanghai and Qidong urban regions were mainly affected by human activities, while wetland variations in Chongming Island were mainly controlled by natural factors such as the upstream discharge, precipitation, diurnal variation of tidal level and long-term sea level rising. The general trend is that the natural wetland was transformed into the human-made wetland, and the human-made wetland was transformed into construction land.

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.

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-...

Biology and Genetics of Prions Causing Neurodegeneration

PubMed Central

Prusiner, Stanley B.

2014-01-01

Prions are proteins that acquire alternative conformations that become self-propagating. Transformation of proteins into prions is generally accompanied by an increase in β-sheet structure and a propensity to aggregate into oligomers. Some prions are beneficial and perform cellular functions, whereas others cause neurodegeneration. In mammals, more than a dozen proteins that become prions have been identified and a similar number has been found in fungi. In both mammals and fungi, variations in the prion conformation encipher the biological properties of distinct prion strains. Increasing evidence argues that prions cause many neurodegenerative diseases (NDs), including Alzheimer’s, Parkinson’s, Creutzfeldt-Jakob, and Lou Gehrig’s diseases, as well as the tauopathies. The majority of NDs are sporadic, and 10% to 20% are inherited. The late onset of heritable NDs, like their sporadic counterparts, may reflect the stochastic nature of prion formation; the pathogenesis of such illnesses seems to require prion accumulation to exceed some critical threshold before neurological dysfunction manifests. PMID:24274755

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

Prosperity as a cause of death.

PubMed

Eyer, J

1977-01-01

The general death rate rises during business booms and falls during depressions. The causes of death involved in this variation range from infectious diseases through accidents to heart disease, cancer, and cirrhosis of the liver, and include the great majority of all causes of death. Less than 2 percent of the death rate-that for suicide and homicide-varies directly with unemployment. In the older historical data, deterioration of housing and rise of alcohol consumption on the boom may account for part of this variation. In twentieth-century cycles, the role of social stress is probably predominant. Overwork and fragmentation of community through migration are two important sources of stress which rise with the boom, and they are demonstrably related to the causes of death which show this variation.

Studies on the Origins and Nature of Critical Current Variations in Rare Earth Barium Copper Oxide Coated Conductors

NASA Astrophysics Data System (ADS)

Hu, Xinbo

REBCO (REBa2Cu3O7-delta, RE=rare earth elements) coated conductor (CC) is one of the best candidates for building high-field magnets and it has been improved greatly in recent years. CC overcome the grain boundary problem by using either a rolling assisted biaxially textured substrate (RABiTS) or ion beam assisted deposition (IBAD) of a template for the REBCO. Artificial pinning centers were also introduced to increase critical current density. Despite all these improvements, one significant residual problem is lengthwise critical current (Ic) variations of the CCs. Characterizations of CCs can not only identify the variations, but also provide insight that can help improve the manufacturing process. This study focuses on cross-sectional and vortex pinning variations in CCs. With the reel-to-reel Ic and magnetization measurement system (YateStar), a systematic study has been carried out for CCs made in the last 5-6 years as this technology has rapidly developed. We found that cross-section variations exist for almost all conductors because of width variations. But this contribution to the total Ic variation is small. Vortex pinning variations are found to be the main reason for Ic variations, especially for conductors from different production runs. Even for conductors from the same run, pinning variations are often present. Microscopy studies show that the density and length of BaZrO3 (BZO) nanorods vary between different conductors even though they have nominally the same specifications. Pinning variations in one single tape are mostly attributed to the size variations of BZO nanorods and the configurations of RE2O3 precipitates. Deconstruction of magnet coils and cables were carried out to understand the reasons for in-service degradation. The prototype coil for the 32 T project was safely quenched more than 100 times but it degraded in 3 spontaneous quenches (conducted in an accelerated fatigue testing campaign at ramp rates much larger than service

A mobile tool about causes and distribution of dramatic natural phenomena

NASA Astrophysics Data System (ADS)

Boppidi, Ravikanth Reddy

Most Research suggests that tablet computers could aid the study of many scientific concepts that are difficult to grasp, such as places, time and statistics. These occur especially in the study of geology, chemistry, biology and so on. Tapping the technology will soon become critical career training for future generations. Teaching through mobile is more interactive and helps students to grasp quickly. In this thesis an interactive mobile tool is developed which explains about the causes and distribution of natural disasters like Earthquakes, Tsunami, Tropical Cyclones, Volcanic Eruptions and Tornadoes. The application shows the places of disasters on an interactive map and it also contains YouTube embedded videos, which explain the disasters visually. The advantage of this tool is, it can be deployed onto major mobile operating systems like Android and IOS. The application's user interface (UI) is made very responsive using D3 JavaScript, JQuery, Java Script, HTML, CSS so that it can adapt to mobiles, tablets, and desktop screens.

A behavioral ecology approach to traffic accidents: interspecific variation in causes of traffic casualties among birds.

PubMed

Møller, Anders Pape; Erritzøe, Helga; Erritzøe, Johannes

2011-04-01

Birds and other animals are frequently killed by cars, causing the death of many million individuals per year. Why some species are killed more often than others has never been investigated. In this work hypothesized that risk taking behavior may affect the probability of certain kinds of individuals being killed disproportionately often. Furthermore, behavior of individuals on roads, abundance, habitat preferences, breeding sociality, and health status may all potentially affect the risk of being killed on roads. We used information on the abundance of road kills and the abundance in the surrounding environment of 50 species of birds obtained during regular censuses in 2001-2006 in a rural site in Denmark to test these predictions. The frequency of road kills increased linearly with abundance, while the proportion of individuals sitting on the road or flying low across the road only explained little additional variation in frequency of road casualties. After having accounted for abundance, we found that species with a short flight distance and hence taking greater risks when approached by a potential cause of danger were killed disproportionately often. In addition, solitary species, species with a high prevalence of Plasmodium infection, and species with a large bursa of Fabricius for their body size had a high susceptibility to being killed by cars. These findings suggest that a range of different factors indicative of risk-taking behavior, visual acuity and health status cause certain bird species to be susceptible to casualties due to cars.

Natural and anthropogenic variations in the N cycle - A perspective provided by nitrogen isotopes in trees near oil-sand developments

NASA Astrophysics Data System (ADS)

Savard, M. M.; Bégin, C.; Marion, J.; Smirnoff, A.

2011-12-01

Nitrogen stable isotopes of tree-ring series have been recently used to detect past air pollution effects on forests in the contexts of point sources, highways or peri-urban regions. Here, we want to assess their potential to understand changes in soil processes and reveal perturbations of the N cycle. Our approach involves combining tree-ring N, C and O stable isotope series with statistical modelling to distinguish the responses of trees due to natural (climatic) conditions from the ones potentially caused by emissions from the Athabasca oil-sand developments where truck fleets, oil upgraders, desulphurization and hydrogen plants, boilers, heaters and turbines have been active since 1967. Three white spruce trees [Picea glauca (Moench)] 165 years or older, were selected in a well drained brunisolic site, at 55 km from the heart of the development operations (white and black spruce trees from other sites are currently being investigated). Their growth rings were dated and separated at a time resolution of 1 or 2 years for the 1880-2009 period. The average oxygen isotope ratios of cellulose do not show long-term anomalies and reflect climatic conditions. The average C isotope ratios of cellulose covering the 1880-1965 period show short-term variations mostly explained by local climatic conditions, whereas the 1966-1995 series presents similar short-term variations superimposed on a long-term isotopic increase significantly departing from the oxygen isotope curve. Most importantly, the nitrogen isotope series of treated wood shows an average decrease of 1.0% during the 1970-2009 period. The statistical links between the variations of the regional drought index and the isotopic C and N responses during the pre-operation period allows to develop predictive climatic models. When we apply these models to predict the natural isotopic behaviour of the recent period, the measured isotopic trends of the operation period depart from the modelled curves. In contrast, using

Dissolved organic carbon and unimodal variation in sexual signal coloration in mosquitofish: a role for light limitation?

PubMed

Giery, Sean T; Layman, Craig A

2017-04-12

Natural selection plays an important role in the evolution of sexual communication systems. Here, we assess the effect of two well-known selection agents, transmission environment and predation, on interpopulation variation in sexual signals. Our model system is a series of 21 populations of Bahamian mosquitofish subjected to independent variation in optical conditions and predation risk. We show that optically diverse environments, caused by locally variable dissolved organic carbon concentrations, rather than spatial variation in predation, drove divergence in fin coloration (fin redness). We found a unimodal pattern of phenotypic variation along the optical gradient indicating a threshold-type response of visual signals to broad variation in optical conditions. We discuss evolutionary and ecological mechanisms that may drive such a pattern as well as the implications of non-monotonic clines for evolutionary differentiation. © 2017 The Author(s).

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics.

PubMed

Bo, Tao; Shao, Shanshan; Wu, Dongming; Niu, Shaona; Zhao, Jiajun; Gao, Ling

2017-08-01

Recent studies performed provide mechanistic insight into effects of the microbiota on cholesterol metabolism, but less focus was given to how cholesterol impacts the gut microbiota. In this study, ApoE -/- Sprague Dawley (SD) rats and their wild-type counterparts (n = 12) were, respectively, allocated for two dietary condition groups (normal chow and high-cholesterol diet). Total 16S rDNA of fecal samples were extracted and sequenced by high-throughput sequencing to determine differences in microbiome composition. Data were collected and performed diversity analysis and phylogenetic analysis. The influence of cholesterol on gut microbiota was discussed by using cholesterol dietary treatment as exogenous cholesterol disorder factor and genetic modification as endogenous metabolic disorder factor. Relative microbial variations were compared to illustrate the causality and correlation of cholesterol and gut microbiota. It turned out comparing to genetically modified rats, exogenous cholesterol intake may play more effective role in changing gut microbiota profile, although the serum cholesterol level of genetically modified rats was even higher. Relative abundance of some representative species showed that the discrepancies due to dietary variation were more obvious, whereas some low abundance species changed because of genetic disorders. Our results partially demonstrated that gut microbiota are relatively more sensitive to dietary variation. Nevertheless, considering the important effect of bacteria in cholesterol metabolism, the influence to gut flora by "genetically caused cholesterol disorder" cannot be overlooked. Manipulation of gut microbiota might be an effective target for preventing cholesterol-related metabolic disorders. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Anthocyanin inhibits propidium iodide DNA fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry.

PubMed

Bennett, Michael D; Price, H James; Johnston, J Spencer

2008-04-01

Measuring genome size by flow cytometry assumes direct proportionality between nuclear DNA staining and DNA amount. By 1997 it was recognized that secondary metabolites may affect DNA staining, thereby causing inaccuracy. Here experiments are reported with poinsettia (Euphorbia pulcherrima) with green leaves and red bracts rich in phenolics. DNA content was estimated as fluorescence of propidium iodide (PI)-stained nuclei of poinsettia and/or pea (Pisum sativum) using flow cytometry. Tissue was chopped, or two tissues co-chopped, in Galbraith buffer alone or with six concentrations of cyanidin-3-rutinoside (a cyanidin-3-rhamnoglucoside contributing to red coloration in poinsettia). There were large differences in PI staining (35-70 %) between 2C nuclei from green leaf and red bract tissue in poinsettia. These largely disappeared when pea leaflets were co-chopped with poinsettia tissue as an internal standard. However, smaller (2.8-6.9 %) differences remained, and red bracts gave significantly lower 1C genome size estimates (1.69-1.76 pg) than green leaves (1.81 pg). Chopping pea or poinsettia tissue in buffer with 0-200 microm cyanidin-3-rutinoside showed that the effects of natural inhibitors in red bracts of poinsettia on PI staining were largely reproduced in a dose-dependent way by this anthocyanin. Given their near-ubiquitous distribution, many suspected roles and known affects on DNA staining, anthocyanins are a potent, potential cause of significant error variation in genome size estimations for many plant tissues and taxa. This has important implications of wide practical and theoretical significance. When choosing genome size calibration standards it seems prudent to select materials producing little or no anthocyanin. Reviewing the literature identifies clear examples in which claims of intraspecific variation in genome size are probably artefacts caused by natural variation in anthocyanin levels or correlated with environmental factors known to induce

Solar UV radiation variations and their stratospheric and climatic effects

NASA Technical Reports Server (NTRS)

Donnelly, R. F.; Heath, D. F.

1985-01-01

Nimbus-7 SBUV measurements of the short-term solar UV variations caused by solar rotation and active-region evolution have determined the amplitude and wavelength dependence for the active-region component of solar UV variations. Intermediate-term variations lasting several months are associated with rounds of major new active regions. The UV flux stays near the peak value during the current solar cycle variation for more than two years and peaks about two years later than the sunspot number. Nimbus-7 measurements have observed the concurrent stratospheric ozone variations caused by solar UV variations. There is now no doubt that solar UV variations are an important cause of short- and long-term stratospheric variations, but the strength of the coupling to the troposphere and to climate has not yet been proven.

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

The Nature, Causes and Practices of Academic Dishonesty/Cheating in Higher Education: The Case of Hawassa University

ERIC Educational Resources Information Center

Bachore, Mebratu Mulatu

2016-01-01

The main objective of the study was to assess the perception of teachers and learners on the nature of practice, the type and the causes of academic cheating (dishonesty) in Hawassa University. The study was basically a survey which employed both qualitative and quantitative approaches to gather data. The subjects were 20 instructors and 60…

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 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.

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

Does infectious disease cause global variation in the frequency of intrastate armed conflict and civil war?

PubMed

Letendre, Kenneth; Fincher, Corey L; Thornhill, Randy

2010-08-01

Geographic and cross-national variation in the frequency of intrastate armed conflict and civil war is a subject of great interest. Previous theory on this variation has focused on the influence on human behaviour of climate, resource competition, national wealth, and cultural characteristics. We present the parasite-stress model of intrastate conflict, which unites previous work on the correlates of intrastate conflict by linking frequency of the outbreak of such conflict, including civil war, to the intensity of infectious disease across countries of the world. High intensity of infectious disease leads to the emergence of xenophobic and ethnocentric cultural norms. These cultures suffer greater poverty and deprivation due to the morbidity and mortality caused by disease, and as a result of decreased investment in public health and welfare. Resource competition among xenophobic and ethnocentric groups within a nation leads to increased frequency of civil war. We present support for the parasite-stress model with regression analyses. We find support for a direct effect of infectious disease on intrastate armed conflict, and support for an indirect effect of infectious disease on the incidence of civil war via its negative effect on national wealth. We consider the entanglements of feedback of conflict into further reduced wealth and increased incidence of disease, and discuss implications for international warfare and global patterns of wealth and imperialism.

Spatiotemporal variations in vegetation cover on the Loess Plateau, China, between 1982 and 2013: possible causes and potential impacts.

PubMed

Kong, Dongxian; Miao, Chiyuan; Borthwick, Alistair G L; Lei, Xiaohui; Li, Hu

2018-05-01

Vegetation is a key component of the ecosystem and plays an important role in water retention and resistance to soil erosion. In this study, we used a multiyear normalized difference vegetation index (NDVI) dataset (1982-2013) and corresponding datasets for observed climatic variables to analyze changes in the NDVI at both temporal and spatial scales. The relationships between NDVI, climate change, and human activities were also investigated. The annual average NDVI showed an upward trend over the 32-year study period, especially in the center of the Loess Plateau. NDVI variations lagged behind monthly temperature changes by approximately 1 month. The contribution of human activities to variations in NDVI has become increasingly significant in recent years, with human activities responsible for 30.4% of the change in NDVI during the period 2001-2013. The increased vegetation coverage has reduced soil erosion on the Loess Plateau in recent years. It is suggested that natural restoration of vegetation is the most effective measure for control of erosion; engineering measures that promote this should feature in the future governance of the Loess Plateau.

Host-parasite coevolution: genetic variation in a virus population and the interaction with a host gene.

PubMed

Wilfert, L; Jiggins, F M

2010-07-01

Host-parasite coevolution is considered to be an important factor in maintaining genetic variation in resistance to pathogens. Drosophila melanogaster is naturally infected by the sigma virus, a vertically transmitted and host-specific pathogen. In fly populations, there is a large amount of genetic variation in the transmission rate from parent to offspring, much of which is caused by major-effect resistance polymorphisms. We have found that there are similarly high levels of genetic variation in the rate of paternal transmission among 95 different isolates of the virus as in the host. However, when we examined a transmission-blocking gene in the host, we found that it was effective across virus isolates. Therefore, the high levels of genetic variation observed in this system do not appear to be maintained because of coevolution resulting from interactions between this host gene and parasite genes.

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 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.

Microsatellites as targets of natural selection.

PubMed

Haasl, Ryan J; Payseur, Bret A

2013-02-01

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

Microsatellites as Targets of Natural Selection

PubMed Central

Haasl, Ryan J.; Payseur, Bret A.

2013-01-01

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

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.

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

Race, common genetic variation, and therapeutic response disparities in heart failure.

PubMed

Taylor, Mathew R; Sun, Albert Y; Davis, Gordon; Fiuzat, Mona; Liggett, Stephen B; Bristow, Michael R

2014-12-01

Because of its comparatively recent evolution, Homo sapiens exhibit relatively little within-species genomic diversity. However, because of genome size, a proportionately small amount of variation creates ample opportunities for both rare mutations that may cause disease as well as more common genetic variations that may be important in disease modification or pharmacogenetics. Primarily because of the East African origin of modern humans, individuals of African ancestry (AA) exhibit greater degrees of genetic diversity than more recently established populations, such as those of European ancestry (EA) or Asian ancestry. Those population effects extend to differences in frequency of common gene variants that may be important in heart failure natural history or therapy. For cell-signaling mechanisms important in heart failure, we review and present new data for genetic variation between AA and EA populations. Data indicate that: 1) neurohormonal signaling mechanisms frequently (16 of the 19 investigated polymorphisms) exhibit racial differences in the allele frequencies of variants comprising key constituents; 2) some of these differences in allele frequency may differentially affect the natural history of heart failure in AA compared with EA individuals; and 3) in many cases, these differences likely play a role in observed racial differences in drug or device response. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

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...

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.

Ethane C-C clumping in natural gas : a proxy for cracking processes ?

NASA Astrophysics Data System (ADS)

Clog, M. D.; Ferreira, A. A.; Santos Neto, E. V.; Eiler, J. M.

2014-12-01

Ethane (C2H6) is the second-most abundant alkane in most natural gas reservoirs, and is used to produce ethylene for petrochemical industries. It is arguably the simplest molecule that can manifest multiple 13C substitutions. There are several plausible controls on Δ13C2H6in natural gas: thermodynamically controlled homogeneous isotope exchange reactions analogous to those behind carbonate clumped isotope thermometry; inheritance from larger biomolecules that undergo thermal degradation to produce natural gas; mixing of natural gases that differ markedly in bulk isotopic composition; diffusive fractionation; or combinations of these and/or other, less expected fractionations. There is little basis for predicting which of these will control isotopic variations among natural ethanes, but we think it likely that addition of this new isotopic proxy will reveal new insights into the natural chemistry of ethane. We have developed a method to measure the abundance of 13C2H6 in natural samples, using high-resolution mass spectrometry. We define Δ13C2H6 as 1000 . ((13C2H6/12C2H6)measured/(13C2H6/12C2H6)stochastic -1). We studied several suites of natural gas samples and experimentally produced or modified ethane. Natural ethanes, including closely related samples from a single natural gas field, exhibit surprisingly large ranges in Δ13C2H6 (4 ‰ overall; up to 3 ‰ in one gas field). Such ranges cannot be explained by thermodynamic equilibrium at a range of different temperatures, or by diffusive fractionation. Kinetic isotope effects associated with 'cracking' reactions, and/or inheritance of non-equilibrium carbon isotope structures from source organics are more likely causes. We observe a correlation between Δ13C2H6 and the concentration of alkanes other than methane in several suites of natural gases, suggesting the causes of clumped isotope variations are tied to the controls on gas wetness. An experiment examining ethane residual to high-temperature pyrolysis

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

Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

NASA Astrophysics Data System (ADS)

Maier, E.; Buckenmaier, A.; Tollrian, R.; Nürnberger, B.

2012-06-01

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.

Adult sex ratio variation: implications for breeding system evolution.

PubMed

Székely, T; Weissing, F J; Komdeur, J

2014-08-01

Adult sex ratio (ASR) exhibits immense variation in nature, although neither the causes nor the implications of this variation are fully understood. According to theory, the ASR is expected to influence sex roles and breeding systems, as the rarer sex in the population has more potential partners to mate with than the more common sex. Changes in mate choice, mating systems and parental care suggest that the ASR does influence breeding behaviour, although there is a need for more tests, especially experimental ones. In the context of breeding system evolution, the focus is currently on operational sex ratios (OSRs). We argue that the ASR plays a role of similar importance and urge researchers to study the ASR and the OSR side by side. Finally, we plead for a dynamic view of breeding system evolution with feedbacks between mating, parenting, OSR and ASR on both ecological and evolutionary time scales. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological?

PubMed

Richards, Emilie J; Brown, Jeremy M; Barley, Anthony J; Chong, Rebecca A; Thomson, Robert C

2018-02-19

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

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.

Fast Variations In Spectrum of Comet Halley

NASA Astrophysics Data System (ADS)

Borysenko, S. A.

The goal of this work is to research fast variations of spectral lines intensities in spectra of comet Halley. The present research was made on the basis of more then 500 high- resolution spectrogram obtained by L.M. Shulman and H.K. Nazarchuk in November- December, 1985 at the 6-m telescope (SAO, Russia). Some fast variations with different quasiperiods were detected in all the spectrograms. Quasiperiods of these variations were from 15 - 40 min to 1.5 - 2 hours. As data from spacecraft "Vega-2" show, more fast variations with quasiperiods 5 - 10 min are obviously present in cometary time variations. Only the most important lines so as C2, C3, CN, CH and NH2 were analyzed. False periods were checked by comparison of the power spectra of the variations with the computed spectral window of the data. Only false periods about 400 sec (the avarage period of exposition) were detected. An algorithm for analysis of locally Poisson's time series was proposed. Two types of fast variations are detected: 1)high amplitude variations with more long quasiperiods (1.5 - 2 hours) and the coefficient of crosscorrelations between line intensities about 0.9 - 0.95; 2)low amplitude variations with short periods (15 - 40 min), which look like white noise and have the coefficient of crosscorrelations about 0.1 - 0.3. This difference may be caused by nature of variations. The first type variations may be an effect of both active processes in cometary nucleus and streams of solar protons. Analysis of solar proton flux variation with energies >1 MeV in November - Decem- ber 1985 confirms the above-mentioned version. In the second case it may by only inner processes in the nucleus that generate the observed variations. For determination of general parameters of cometary atmosphere, such as the produc- tion rates of radicals C2, C3, CN, CH, and NH2 it was necessary to estimate the contri- bution of dust grains luminiscence into the continuum of the comet. Space and wave- length distribution

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.

Stochastic variation in telomere shortening rate causes heterogeneity of human fibroblast replicative life span.

PubMed

Martin-Ruiz, Carmen; Saretzki, Gabriele; Petrie, Joanne; Ladhoff, Juliane; Jeyapalan, Jessie; Wei, Wenyi; Sedivy, John; von Zglinicki, Thomas

2004-04-23

The replicative life span of human fibroblasts is heterogeneous, with a fraction of cells senescing at every population doubling. To find out whether this heterogeneity is due to premature senescence, i.e. driven by a nontelomeric mechanism, fibroblasts with a senescent phenotype were isolated from growing cultures and clones by flow cytometry. These senescent cells had shorter telomeres than their cycling counterparts at all population doubling levels and both in mass cultures and in individual subclones, indicating heterogeneity in the rate of telomere shortening. Ectopic expression of telomerase stabilized telomere length in the majority of cells and rescued them from early senescence, suggesting a causal role of telomere shortening. Under standard cell culture conditions, there was a minor fraction of cells that showed a senescent phenotype and short telomeres despite active telomerase. This fraction increased under chronic mild oxidative stress, which is known to accelerate telomere shortening. It is possible that even high telomerase activity cannot fully compensate for telomere shortening in all cells. The data show that heterogeneity of the human fibroblast replicative life span can be caused by significant stochastic cell-to-cell variation in telomere shortening.

Pathogenesis of autism: a patchwork of genetic causes

PubMed Central

Grigorenko, Elena L

2009-01-01

Autism spectrum disorders (ASDs) are relatively infrequent but are devastating developmental conditions characterized by marked deficiencies in social, communicative and other behavioral domains. It has been known for a substantial period of time that these disorders are genetic in nature. However, elucidating the specific mechanisms of these disorders has been difficult. A major reason for such difficulty is the recognized genetic heterogeneity of ASDs. Specifically, many genetic mechanisms related to structural variations in the genome have been reported as possible genetic causes of these disorders. This review briefly exemplifies these genetic mechanisms, presents a concise overview of the evidence for the genetic basis of ASDs and provides an appraisal of the specific structural genetic variants thought to contribute to the pathogenesis of these complex disorders. PMID:19953194

Solar Cycle Variations and Equatorial Oscillations: Modeling Study

NASA Technical Reports Server (NTRS)

Mayr, H. G.; Mengel, J. G.; Drob, D. P.; Chan, K. L.; Porter, H. S.; Bhartia, P. K. (Technical Monitor)

2001-01-01

Solar cycle activity effects (SCAE) in the lower and middle atmosphere, reported in several studies, are difficult to explain on the basis of the small changes in solar radiation that accompany the 11-year cycle, It is therefore natural to speculate that dynamical processes may come into play to produce a leverage. Such a leverage may be provided by the Quasi-Biennial Oscillation (QBO) in the zonal circulation of the stratosphere, which has been linked to solar activity variations. Driven primarily by wave mean flow interaction, the QBO period and its amplitude are variable but are also strongly influenced by the seasonal cycle in the solar radiation. This influence extends to low altitudes referred to as "downward control". Relatively small changes in solar radiative forcing can produce small changes in the period and phase of the QBO, but this in turn can produce measurable differences in the wind field. Thus, the QBO may be an amplifier of solar activity variations and a natural conduit of these variations to lower altitudes. To test this hypothesis, we conducted experiments with a 2D (two-dimensional) version of our Numerical Spectral Model that incorporates Hines' Doppler Spread Parameterization for small-scale gravity waves (GW). Solar cycle radiance variations (SCRV) are accounted for by changing the radiative heating rate on a logarithmic scale from 0.1 % at the surface to 1 % at 50 km to 10% at 100 km. With and without SCRV, but with the same GW flux, we then conduct numerical experiments to evaluate the magnitude of the SCAE in the zonal circulation. The numerical results indicate that, under certain conditions, the SCAE is significant and can extend to lower altitudes where the SCRV is inconsequential. At 20-km the differences in the modeled wind velocities are as large as 5 m/s. For a modeled QBO period of 30 months, we find that the seasonal cycle in the solar forcing (through the Semi-annual Oscillation (SAO)) acts as a strong pacemaker to lockup the

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

Spatial and temporal demographic variation drives within-season fluctuations in sexual selection.

PubMed

Kasumovic, Michael M; Bruce, Matthew J; Andrade, Maydianne C B; Herberstein, Marie E

2008-09-01

Our understanding of selection in nature stems mainly from whole-season and cross-sectional estimates of selection gradients. These estimates suggest that selection is relatively constant within, but fluctuates between seasons. However, the strength of selection depends on demographics, and because demographics can vary within seasons, there is a gap in our understanding regarding the extent to which seasonal fluctuations in demographics may cause variation in selection. Here we use two populations of the golden orb-web spider (Nephila plumipes) that differ in density to examine how demographics change within a season and whether there are correlated shifts in selection. We demonstrate that there is within-season variation in sex ratio and density at multiple spatial and temporal scales. This variation led to changes in the competitive challenges that males encountered at different times of the season and was correlated with significant variation in selection gradients on male size and weight between sampling periods. We highlight the importance of understanding the biology of the organism under study to correctly determine the relevant scale in which to examine selection. We also argue that studies may underestimate the true variation in selection by averaging values, leading to misinterpretation of the effect of selection on phenotypic evolution.

Determinants of all cause mortality in Poland.

PubMed

Genowska, Agnieszka; Jamiołkowski, Jacek; Szpak, Andrzej; Pajak, Andrzej

2012-01-01

The study objective was to evaluate quantitatively the relationship between demographic characteristics, socio-economic status and medical care resources with all cause mortality in Poland. Ecological study was performed using data for the population of 66 subregions of Poland, obtained from the Central Statistical Office of Poland. The information on the determinants of health and all cause mortality covered the period from 1st January 2005 to 31st December 2010. Results for the repeated measures were analyzed using Generalized Estimating Equations GEE model. In the model 16 independent variables describing health determinants were used, including 6 demographic variables, 6 socio-economic variables, 4 medical care variables. The dependent variable, was age standardized all cause mortality rate. There was a large variation in all cause mortality, demographic features, socio-economic characteristics, and medical care resources by subregion. All cause mortality showed weak associations with demographic features, among which only the increased divorce rate was associated with higher mortality rate. Increased education level, salaries, gross domestic product (GDP) per capita, local government expenditures per capita and the number of non-governmental organizations per 10 thousand population was associated with decrease in all cause mortality. The increase of unemployment rate was related with a decrease of all cause mortality. Beneficial relationship between employment of medical staff and mortality was observed. Variation in mortality from all causes in Poland was explained partly by variation in socio-economic determinants and health care resources.

Comparative analyses across cattle genders and breeds reveal the pitfalls caused by false positive and lineage-differential copy number variations.

PubMed

Zhou, Yang; Utsunomiya, Yuri T; Xu, Lingyang; Hay, El Hamidi Abdel; Bickhart, Derek M; Sonstegard, Tad S; Van Tassell, Curtis P; Garcia, Jose Fernando; Liu, George E

2016-07-06

We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle.

Soils: man-caused radioactivity and radiation forecast

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

Gablin, Vassily

2007-07-01

Available in abstract form only. Full text of publication follows: One of the main tasks of the radiation safety guarantee is non-admission of the excess over critical radiation levels. In Russia they are man-caused radiation levels. Meanwhile any radiation measurement represents total radioactivity. That is why it is hard to assess natural and man-caused contributions to total radioactivity. It is shown that soil radioactivity depends on natural factors including radioactivity of rocks and cosmic radiation as well as man-caused factors including nuclear and non-nuclear technologies. Whole totality of these factors includes unpredictable (non-deterministic) factors - nuclear explosions and radiation accidents,more » and predictable ones (deterministic) - all the rest. Deterministic factors represent background radioactivity whose trends is the base of the radiation forecast. Non-deterministic factors represent man-caused radiation treatment contribution which is to be controlled. This contribution is equal to the difference in measured radioactivity and radiation background. The way of calculation of background radioactivity is proposed. Contemporary soils are complicated technologically influenced systems with multi-leveled spatial and temporary inhomogeneity of radionuclides distribution. Generally analysis area can be characterized by any set of factors of soil radioactivity including natural and man-caused factors. Natural factors are cosmic radiation and radioactivity of rocks. Man-caused factors are shown on Fig. 1. It is obvious that man-caused radioactivity is due to both artificial and natural emitters. Any result of radiation measurement represents total radioactivity i.e. the sum of activities resulting from natural and man-caused emitters. There is no gauge which could separately measure natural and man-caused radioactivity. That is why it is so hard to assess natural and man-caused contributions to soil radioactivity. It would have been possible if

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

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.

Missense SLC25A38 variations play an important role in autosomal recessive inherited sideroblastic anemia

PubMed Central

Kannengiesser, Caroline; Sanchez, Mayka; Sweeney, Marion; Hetet, Gilles; Kerr, Briedgeen; Moran, Erica; Fuster Soler, Jose L.; Maloum, Karim; Matthes, Thomas; Oudot, Caroline; Lascaux, Axelle; Pondarré, Corinne; Sevilla Navarro, Julian; Vidyatilake, Sudharma; Beaumont, Carole; Grandchamp, Bernard; May, Alison

2011-01-01

Background Congenital sideroblastic anemias are rare disorders with several genetic causes; they are characterized by erythroblast mitochondrial iron overload, differ greatly in severity and some occur within a syndrome. The most common cause of non-syndromic, microcytic sideroblastic anemia is a defect in the X-linked 5-aminolevulinate synthase 2 gene but this is not always present. Recently, variations in the gene for the mitochondrial carrier SLC25A38 were reported to cause a non-syndromic, severe type of autosomal-recessive sideroblastic anemia. Further evaluation of the importance of this gene was required to estimate the proportion of patients affected and to gain further insight into the range and types of variations involved. Design and Methods In three European diagnostic laboratories sequence analysis of SLC25A38 was performed on DNA from patients affected by congenital sideroblastic anemia of a non-syndromic nature not caused by variations in the 5-aminolevulinate synthase 2 gene. Results Eleven patients whose ancestral origins spread across several continents were homozygous or compound heterozygous for ten different SLC25A38 variations causing premature termination of translation (p.Arg117X, p.Tyr109LeufsX43), predicted splicing alteration (c.625G>C; p.Asp209His) or missense substitution (p.Gln56Lys, p.Arg134Cys, p.Ile147Asn, p.Arg187Gln, p.Pro190Arg, p.Gly228Val, p.Arg278Gly). Only three of these variations have been described previously (p.Arg117X, p.Tyr109LeufsX43 and p.Asp209His). All new variants reported here are missense and affect conserved amino acids. Structure modeling suggests that these variants may influence different aspects of transport as described for mutations in other mitochondrial carrier disorders. Conclusions Mutations in the SLC25A38 gene cause severe, non-syndromic, microcytic/hypochromic sideroblastic anemia in many populations. Missense mutations are shown to be of importance as are mutations that affect protein production

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.

Catalogue of UBVRI photometry of T Tauri stars and analysis of the causes of their variability

NASA Astrophysics Data System (ADS)

Herbst, W.; Herbst, D. K.; Grossman, E. J.; Weinstein, D.

1994-11-01

A computer-based catalogue of UBVRI photoelectric photometry of T Tauri stars and their earlier type analogs has been compiled. It presently includes over 10 000 entries on 80 stars and will be updated on a regular basis; it is available on Internet. The catalogue is used to analyze the sometimes bizarre light variations of pre-main-sequence stars on time scales of days to months in an attempt to illuminate the nature and causes of the phenomenon. It is useful in discussing their light variations to divide the stars into three groups according to their spectra. These are: weak T Tauri stars (WTTS; spectral class later than K0 and WH-alpha less than 10 A, classical T Tauri stars (CTTS; spectral class later than K0 and WH-alpha greater than 10 A), and early type T Tauri stars (ETTS; spectral class of K0 or earlier). Three distinct types of variability are displayed by stars in the catalogue. Type I variations are periodic in VRI and undoubtedly caused by rotational modulation of a star with an asymmetric distribution of cool spots on its surface. Irregular flare activity is sometimes seen on such stars in U and B. Type I variations are easiest to see on WTTS but are clearly present on CTTS and ETTS as well. Type II variations are caused by hot 'spots' or zones and, it is argued, result from changes in the excess or 'veiling' continuum commonly attributed to an accretion boundary layer or impact zone of a magnetically channeled accretion flow. This type of variation is seen predominantly or solely in CTTS. A sub-category, designated Type IIp, consists of stars which display periodic variations caused by hot spots. Whereas cool spots may last for hundreds or thousands of rotations, hot spots appear to come and go on a much shorter time scale. This suggests that both unsteady accretion and rotation of the star contribute to Type II variations. It is shown that a third type of variation exists among ETTS, including stars as early as A type. UX Ori is a typical example

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.

Obliquity variation in a Mars climate evolution model

NASA Technical Reports Server (NTRS)

Tyler, D.; Haberle, Robert M.

1993-01-01

The existence of layered terrain in both polar regions of Mars is strong evidence supporting a cyclic variation in climate. It has been suggested that periods of net deposition have alternated with periods of net erosion in creating the layered structure that is seen today. The cause for this cyclic climatic behavior is variation in the annually averaged latitudinal distribution of solar insolation in response to obliquity cycles. For Mars, obliquity variation leads to major climatological excursion due to the condensation and sublimation of the major atmospheric constituent, CO2. The atmosphere will collapse into the polar caps, or existing caps will rapidly sublimate into the atmosphere, dependent upon the polar surface heat balance and the direction of the change in obliquity. It has been argued that variations in the obliquity of Mars cause substantial departures from the current climatological values of the surface pressure and the amount of CO2 stored in both the planetary regolith and polar caps. In this new work we have modified the Haberle et al. model to incorporate variable obliquity by allowing the polar and equatorial insolation to become functions of obliquity, which we assume to vary sinusoidally in time. As obliquity varies in the model, there can be discontinuities in the time evolution of the model equilibrium values for surface pressure, regolith, and polar cap storage. The time constant, tau r, for the regolith to find equilibrium with the climate is estimated--depending on the depth, thermal conductivity, and porosity of the regolith--between 10(exp 4) and 10(exp 6) yr. Thus, using 2000-yr timesteps to move smoothly through the 0.1250 m.y. obliquity cycles, we have an atmosphere/regolith system that cannot be assumed in equilibrium. We have dealt with this problem by limiting the rate at which CO2, can move between the atmosphere and regolith, mimicking the diffusive nature and effects of the temperature and pressure waves, by setting the time

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.

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

Accidental introductions of natural enemies: causes and implications

USDA-ARS?s Scientific Manuscript database

Accidental introductions of natural enemies, including parasitoid and predatory groups, may exceed species introduced intentionally. Several factors favor this: a general surge in international trade; lack of surveillance for species that are not associated with live plants or animals; inability to ...

Relations of Tualatin River water temperatures to natural and human-caused factors

USGS Publications Warehouse

Risley, John C.

1997-01-01

Aquatic research has long shown that the survival of cold-water fish, such as salmon and trout, decreases markedly as water temperatures increase above a critical threshold, particularly during sensitive life stages of the fish. In an effort to improve the overall health of aquatic ecosystems, the State of Oregon in 1996 adopted a maximum water-temperature standard of 17.8 degrees Celsius (68 degrees Fahrenheit), based on a 7-day moving average of daily maximum temperatures, for most water bodies in the State. Anthropogenic activities are not permitted to raise the temperature of a water body above this level. In the Tualatin River, a tributary of the Willamette River located in northwestern Oregon, water temperatures periodically surpass this threshold during the low-flow summer and fall months.An investigation by the U.S. Geological Survey quantified existing seasonal, diel, and spatial patterns of water temperatures in the main stem of the river, assessed the relation of water temperatures to natural climatic conditions and anthropogenic factors (such as wastewater-treatment-plant effluent and modification of riparian shading), and assessed the impact of various flow management practices on stream temperatures. Half-hourly temperature measurements were recorded at 13 monitoring sites from river mile (RM) 63.9 to RM 3.4 from May to November of 1994. Four synoptic water- temperature surveys also were conducted in the upstream and downstream vicinities of two wastewater-treatment-plant outfalls. Temperature and streamflow time-series data were used to calibrate two dynamic-flow heat-transfer models, DAFLOW-BLTM (RM 63.9-38.4) and CE-QUAL-W2 (RM 38.4-3.4). Simulations from the models provided a basis for approximating 'natural' historical temperature patterns, performing effluent and riparian-shading sensitivity analyses, and evaluating mitigation management scenarios under 1994 climatic conditions. Findings from the investigation included (1) under 'natural

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.

Genetic variants associated with neurodegenerative Alzheimer disease in natural models.

PubMed

Salazar, Claudia; Valdivia, Gonzalo; Ardiles, Álvaro O; Ewer, John; Palacios, Adrián G

2016-02-26

The use of transgenic models for the study of neurodegenerative diseases has made valuable contributions to the field. However, some important limitations, including protein overexpression and general systemic compensation for the missing genes, has caused researchers to seek natural models that show the main biomarkers of neurodegenerative diseases during aging. Here we review some of these models-most of them rodents, focusing especially on the genetic variations in biomarkers for Alzheimer diseases, in order to explain their relationships with variants associated with the occurrence of the disease in humans.

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

Individuals in food webs: the relationships between trophic position, omnivory and among-individual diet variation.

PubMed

Svanbäck, Richard; Quevedo, Mario; Olsson, Jens; Eklöv, Peter

2015-05-01

Among-individual diet variation is common in natural populations and may occur at any trophic level within a food web. Yet, little is known about its variation among trophic levels and how such variation could affect phenotypic divergence within populations. In this study we investigate the relationships between trophic position (the population's range and average) and among-individual diet variation. We test for diet variation among individuals and across size classes of Eurasian perch (Perca fluviatilis), a widespread predatory freshwater fish that undergoes ontogenetic niche shifts. Second, we investigate among-individual diet variation within fish and invertebrate populations in two different lake communities using stable isotopes. Third, we test potential evolutionary implications of population trophic position by assessing the relationship between the proportion of piscivorous perch (populations of higher trophic position) and the degree of phenotypic divergence between littoral and pelagic perch sub-populations. We show that among-individual diet variation is highest at intermediate trophic positions, and that this high degree of among-individual variation likely causes an increase in the range of trophic positions among individuals. We also found that phenotypic divergence was negatively related to trophic position in a population. This study thus shows that trophic position is related to and may be important for among-individual diet variation as well as to phenotypic divergence within populations.

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

Can natural gas save lives? Evidence from the deployment of a fuel delivery system in a developing country.

PubMed

Cesur, Resul; Tekin, Erdal; Ulker, Aydogan

2018-05-01

There has been a widespread displacement of coal by natural gas as space heating and cooking technology in Turkey in the last two decades, triggered by the deployment of natural gas networks. We examine the impact of this development on mortality among adults and the elderly by exploiting the variation in the timing of the deployment and the intensity of expansion of gas networks across provinces using data from 2001 to 2016. The results indicate that the expansion of natural gas has caused significant reductions in mortality among both adults and the elderly. These findings are supported by our auxiliary analysis, which demonstrates that the expansion of natural gas networks might have led to a significant improvement in air quality. Furthermore, we show that the mortality gains are primarily driven by reductions in cardio-respiratory deaths, which are more likely to be due to conditions caused or exacerbated by air pollution. Copyright © 2018 Elsevier B.V. All rights reserved.

Variation of mechanical and thermal properties of the thermoplastics reinforced with natural fibers by electron beam processing

NASA Astrophysics Data System (ADS)

Kim, Sok Won; Oh, Seungmin; Lee, Kyuse

2007-11-01

With restrictions for environmental protection being strengthened, the thermoplastics reinforced with natural fibers (NFs) such as jute, kenaf, flax, etc., appeared as an automobile interior material instead of the chemical plastics. Regardless of many advantages, one shortcoming is the deformation after being formed in high temperature of about 200 °C, caused by the poor adhesion between the natural fibers and thermoplastics. Also, the energy saving in connection with car air-conditioning becomes very important. In this study, the thermal conductivity, tensile strength, and deformation of several kinds of thermoplastic composites composing of 50% polypropylene (PP) and 50% natural fiber irradiated by the electron beam (energy: 0.5 MeV, dose: 0-20 kGy) were measured. The length and thickness of PP and NF are 80±10 mm and 40-120 μm, respectively. The results show that the thermal conductivity and the tensile strength changed and became minimum when the dose of electron beam is 10 kGy, and the deformation after the thermal cycle were reduced by the electron beam.

The impact of a 2 X CO2 climate on lightning-caused fires

NASA Technical Reports Server (NTRS)

Price, Colin; Rind, David

1994-01-01

Future climate change could have significant repercussions for lightning-caused wildfires. Two empirical fire models are presented relating the frequency of lightning fires and the area burned by these fires to the effective precipitation and the frequency of thunderstorm activity. One model deals with the seasonal variations in lightning fires, while the second model deals with the interannual variations of lightning fires. These fire models are then used with the Goddard Institute for Space Studies General Circulation Model to investigate possible changes in fire frequency and area burned in a 2 X CO2 climate. In the United States, the annual mean number of lightning fires increases by 44%, while the area burned increases by 78%. On a global scale, the largest increase in lightning fires can be expected in untouched tropical ecosystems where few natural fires occur today.

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

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

Structurally diverse natural products that cause potassium leakage trigger multicellularity in Bacillus subtilis.

PubMed

López, Daniel; Fischbach, Michael A; Chu, Frances; Losick, Richard; Kolter, Roberto

2009-01-06

We report a previously undescribed quorum-sensing mechanism for triggering multicellularity in Bacillus subtilis. B. subtilis forms communities of cells known as biofilms in response to an unknown signal. We discovered that biofilm formation is stimulated by a variety of small molecules produced by bacteria--including the B. subtilis nonribosomal peptide surfactin--that share the ability to induce potassium leakage. Natural products that do not cause potassium leakage failed to induce multicellularity. Small-molecule-induced multicellularity was prevented by the addition of potassium, but not sodium or lithium. Evidence is presented that potassium leakage stimulates the activity of a membrane protein kinase, KinC, which governs the expression of genes involved in biofilm formation. We propose that KinC responds to lowered intracellular potassium concentration and that this is a quorum-sensing mechanism that enables B. subtilis to respond to related and unrelated bacteria.

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.

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.

Rate variation and estimation of divergence times using strict and relaxed clocks.

PubMed

Brown, Richard P; Yang, Ziheng

2011-09-26

Understanding causes of biological diversity may be greatly enhanced by knowledge of divergence times. Strict and relaxed clock models are used in Bayesian estimation of divergence times. We examined whether: i) strict clock models are generally more appropriate in shallow phylogenies where rate variation is expected to be low, ii) the likelihood ratio test of the clock (LRT) reliably informs which model is appropriate for dating divergence times. Strict and relaxed models were used to analyse sequences simulated under different levels of rate variation. Published shallow phylogenies (Black bass, Primate-sucking lice, Podarcis lizards, Gallotiinae lizards, and Caprinae mammals) were also analysed to determine natural levels of rate variation relative to the performance of the different models. Strict clock analyses performed well on data simulated under the independent rates model when the standard deviation of log rate on branches, σ, was low (≤ 0.1), but were inappropriate when σ>0.1 (95% of rates fall within 0.0082-0.0121 subs/site/Ma when σ = 0.1, for a mean rate of 0.01). The independent rates relaxed clock model performed well at all levels of rate variation, although posterior intervals on times were significantly wider than for the strict clock. The strict clock is therefore superior when rate variation is low. The performance of a correlated rates relaxed clock model was similar to the strict clock. Increased numbers of independent loci led to slightly narrower posteriors under the relaxed clock while older root ages provided proportionately narrower posteriors. The LRT had low power for σ = 0.01-0.1, but high power for σ = 0.5-2.0. Posterior means of σ2 were useful for assessing rate variation in published datasets. Estimates of natural levels of rate variation ranged from 0.05-3.38 for different partitions. Differences in divergence times between relaxed and strict clock analyses were greater in two datasets with higher σ2 for one or more

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.

Time variations in the Earth's gravity field

NASA Astrophysics Data System (ADS)

Shum, C. K.; Eanes, R. J.

1992-01-01

At the present time, the causes and consequences of changes in the Earth's gravity field due to geophysical and meteorological phenomena are not well understood. The Earth's gravity field represents the complicated distribution of all of the matter that makes up our planet. Its variations are caused by the motions of the solid Earth interacting with the gravitational attraction of the Sun and the Moon (tides) and with the Earth's atmosphere, oceans, polar ice caps and groundwater due to changing weather patterns. These variations influence the rotation of the Earth, alter the orbits of Earth satellites, cause sea level fluctuations, and indirectly affect the global climate pattern.

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

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

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

Blindness caused by cosmetic filler injection: a review of cause and therapy.

PubMed

Carruthers, Jean D A; Fagien, Steve; Rohrich, Rod J; Weinkle, Susan; Carruthers, Alastair

2014-12-01

Vascular occlusion causing blindness is a rare yet greatly feared complication of the use of facial aesthetic fillers. The authors performed a review of the aesthetic literature to ascertain the reported cases of blindness and the literature reporting variations in the vascular anatomy of the human face. The authors suggest a small but potentially helpful addition to the accepted management of the acute case. Cases of blindness, mostly irreversible, from aesthetic filler injections have been reported from Asia, Europe, and North America. Autologous fat appears to be the most frequent filler causing blindness. Some cases of partial visual recovery have been reported with hyaluronic acid and calcium hydroxylapatite fillers. The sudden profusion of new medical and nonmedical aesthetic filler injectors raises a new cause for alarm about patient safety. The published reports in the medical literature are made by experienced aesthetic surgeons and thus the actual incidence may be even higher. Also, newer injectors may not be aware of the variations in the pattern of facial vascular arborization. The authors present a summary of the relevant literature to date and a suggested helpful addition to the protocols for urgent management.

A systematic review of the extent, nature and likely causes of preventable adverse events arising from hospital care.

PubMed

Sari, A Akbari; Doshmangir, L; Sheldon, T

2010-01-01

Understanding the nature and causes of medical adverse events may help their prevention. This systematic review explores the types, risk factors, and likely causes of preventable adverse events in the hospital sector. MEDLINE (1970-2008), EMBASE, CINAHL (1970-2005) and the reference lists were used to identify the studies and a structured narrative method used to synthesise the data. Operative adverse events were more common but less preventable and diagnostic adverse events less common but more preventable than other adverse events. Preventable adverse events were often associated with more than one contributory factor. The majority of adverse events were linked to individual human error, and a significant proportion of these caused serious patient harm. Equipment failure was involved in a small proportion of adverse events and rarely caused patient harm. The proportion of system failures varied widely ranging from 3% to 85% depending on the data collection and classification methods used. Operative adverse events are more common but less preventable than diagnostic adverse events. Adverse events are usually associated with more than one contributory factor, the majority are linked to individual human error, and a proportion of these with system failure.

Use of a doxycycline-enrofloxacin-metronidazole combination with/without diminazene diaceturate to treat naturally occurring canine babesiosis caused by Babesia gibsoni

PubMed Central

2010-01-01

Canine babesiosis is an important worldwide, tick-borne disease caused by hemoprotozoan parasites of the genus Babesia. Babesia gibsoni is the predominant species that causes canine babesiosis in Taipei, Taiwan. It is a small pleomorphic intraerythrocytic parasite that can cause erythrocyte destruction and hemolytic anemia. Efficacy of oral administration of a doxycycline-enrofloxacin-metronidazole combination with and without injections of diminazene diaceturate in the management of naturally occurring canine babesiosis caused by B. gibsoni was evaluated retrospectively. The overall efficacy of this combination of doxycycline-enrofloxacin-metronidazole in conjunction with and without administration of diminazene diaceturate was 85.7% and 83.3%, respectively; with a mean recovery time of 24.2 and 23.5 days, respectively. Concomitant use of intramuscular diminazene diaceturate may not improve the efficacy of a doxycycline-enrofloxacin-metronidazole combination in management of canine babesiosis caused by B. gibsoni. PMID:20416095

Human and natural influences on the changing thermal structure of the atmosphere

PubMed Central

Santer, Benjamin D.; Painter, Jeffrey F.; Bonfils, Céline; Mears, Carl A.; Solomon, Susan; Wigley, Tom M. L.; Gleckler, Peter J.; Schmidt, Gavin A.; Doutriaux, Charles; Gillett, Nathan P.; Taylor, Karl E.; Thorne, Peter W.; Wentz, Frank J.

2013-01-01

Since the late 1970s, satellite-based instruments have monitored global changes in atmospheric temperature. These measurements reveal multidecadal tropospheric warming and stratospheric cooling, punctuated by short-term volcanic signals of reverse sign. Similar long- and short-term temperature signals occur in model simulations driven by human-caused changes in atmospheric composition and natural variations in volcanic aerosols. Most previous comparisons of modeled and observed atmospheric temperature changes have used results from individual models and individual observational records. In contrast, we rely on a large multimodel archive and multiple observational datasets. We show that a human-caused latitude/altitude pattern of atmospheric temperature change can be identified with high statistical confidence in satellite data. Results are robust to current uncertainties in models and observations. Virtually all previous research in this area has attempted to discriminate an anthropogenic signal from internal variability. Here, we present evidence that a human-caused signal can also be identified relative to the larger “total” natural variability arising from sources internal to the climate system, solar irradiance changes, and volcanic forcing. Consistent signal identification occurs because both internal and total natural variability (as simulated by state-of-the-art models) cannot produce sustained global-scale tropospheric warming and stratospheric cooling. Our results provide clear evidence for a discernible human influence on the thermal structure of the atmosphere. PMID:24043789

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....

The Rules of Variation Expanded, Implications for the Research on Compatible Genomics.

PubMed

Castro-Chavez, Fernando

2011-05-12

The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable of homologous recombination is explored by using examples of human polymorphisms in the LDLRAP1 gene, and by the production of fertile offspring by crossbreeding. Examples of dogs, llamas and finches will be presented by a rational control of: natural crossbreeding of organisms with compatible genomes (something already happening in nature), the current work focuses on the generation of new varieties after a careful plan. This study is presented within the context of biosemiotics, which studies the processing of information, signaling and signs by living systems. I define a group of organisms having compatible genomes as a single theme: the genomic species or population, able to speak the same molecular language through different accents, with each variety within a theme being a different version of the same book. These studies have a molecular, compatible genetics context. Population and ecosystem biosemiotics will be exemplified by a possible genetic damage capable of causing mutations by breaking the rules of variation through the coordinated patterns of atoms present in the 9/11 World Trade Center contaminated dust (U, Ba, La, Ce, Sr, Rb, K, Mn, Mg, etc.), combination that may be able to overload the molecular quality control mechanisms of the human body. I introduce here the balance of codons in the circular genetic code: 2[1(1)+1(3)+1(4)+4(2)]=2[2(2)+3(4)].

The Rules of Variation Expanded, Implications for the Research on Compatible Genomics

PubMed Central

Castro-Chavez, Fernando

2011-01-01

The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable of homologous recombination is explored by using examples of human polymorphisms in the LDLRAP1 gene, and by the production of fertile offspring by crossbreeding. Examples of dogs, llamas and finches will be presented by a rational control of: natural crossbreeding of organisms with compatible genomes (something already happening in nature), the current work focuses on the generation of new varieties after a careful plan. This study is presented within the context of biosemiotics, which studies the processing of information, signaling and signs by living systems. I define a group of organisms having compatible genomes as a single theme: the genomic species or population, able to speak the same molecular language through different accents, with each variety within a theme being a different version of the same book. These studies have a molecular, compatible genetics context. Population and ecosystem biosemiotics will be exemplified by a possible genetic damage capable of causing mutations by breaking the rules of variation through the coordinated patterns of atoms present in the 9/11 World Trade Center contaminated dust (U, Ba, La, Ce, Sr, Rb, K, Mn, Mg, etc.), combination that may be able to overload the molecular quality control mechanisms of the human body. I introduce here the balance of codons in the circular genetic code: 2[1(1)+1(3)+1(4)+4(2)]=2[2(2)+3(4)]. PMID:21743816

Causes of skill in seasonal predictions of the Arctic Oscillation

NASA Astrophysics Data System (ADS)

Kumar, Arun; Chen, Mingyue

2017-11-01

Based on an analysis of hindcasts from a seasonal forecast system, complemented by the analysis of a large ensemble of AMIP simulations, possible causes for skillful prediction of the winter Arctic Oscillation (AO) on a seasonal time-scale are analyzed. The possibility that the recent increase in AO skill could be due to model improvements, or due to changes in the persistence characteristics of the AO, is first discounted. The analysis then focuses on exploring the possibility that the recent increase in prediction skill in AO may be due to sampling variations or could have physical causes. Temporal variations in AO skill due entirely to sampling alone cannot be discounted as this is a fundamental constraint on verifications over a short time-series. This notion is supported from theoretical considerations, and from the analysis of the temporal variations in the perfect model skill where substantial variations in skill due to sampling alone are documented. As for the physical causes, the analysis indicates possible links in the prediction skill of AO with the SST forcing from the tropics, particularly related to the SST variations associated with the Trans-Niño Index (TNI). Interannual and low frequency variations in the TNI could have contributed to similar temporal variations in AO skill. For example, a dominance of central Pacific El Niño events after 2000 (a reflection of low-frequency variations in TNI) coincided with an increase in the prediction skill of AO. The analysis approach and results provide an avenue for further investigations; for example, model simulations forced with the SST pattern associated with the TNI, to establish or reaffirm causes for AO skill.

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.

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.

Habitat fragmentation causes bottlenecks and inbreeding in the European tree frog (Hyla arborea).

PubMed Central

Andersen, Liselotte W.; Fog, Kåre; Damgaard, Christian

2004-01-01

A genetic study of the European tree frog, Hyla arborea, in Denmark was undertaken to examine the population structure on mainland Jutland and the island of Lolland after a period of reduction in suitable habitat and population sizes. The two regions have experienced the same rate of habitat loss but fragmentation has been more severe on Lolland. Genetic variation based on 12 polymorphic DNA microsatellites was analysed in 494 tree frogs sampled from two ponds in Jutland and 10 ponds on Lolland. A significant overall deviation from Hardy-Weinberg expectations could be attributed to three ponds, all on Lolland. This was most probably caused by an inbreeding effect reducing fitness, which was supported by the observed significant negative correlation between larva survival and mean F(IS) value and mean individual inbreeding coefficient. A significant reduction in genetic variation (bottleneck) was detected in most of the ponds on Lolland. Population-structure analysis suggested the existence of at least 11 genetically different populations, corresponding to most of the sampled population units. The results indicated that the populations were unique genetic units and could be used to illustrate the migration pattern between newly established ponds arisen either by natural colonization of tree frogs or by artificial introduction. A high degree of pond fidelity in the tree frogs was suggested. A severe fragmentation process reducing population size and fitness within some of the populations probably caused the significant reduction in genetic variation of tree frog populations on Lolland. PMID:15306354

Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes.

PubMed

Zeng, Qian-Qian; He, Ke; Sun, Dan-Dan; Ma, Mei-Ying; Ge, Yun-Fa; Fang, Sheng-Guo; Wan, Qiu-Hong

2016-02-18

pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.

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.

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.

High Resolution Directional Variation And Time Variation Of Sporadic Meteors

NASA Astrophysics Data System (ADS)

Campbell-Brown, Margaret

2007-10-01

The directional dependence of the flux and orbits of sporadic meteoroids is of great importance to understanding the origin and nature of this population of small solar system bodies. The Canadian Meteor Orbit Radar (CMOR) has recorded over 5 million meteoroid orbits from 2002 to the present. This dataset, larger than any previously available, makes it possible to study the sporadic meteor distribution at much greater spatial resolution than previously possible. The rates of meteor orbits with radiants occurring in two degree bins over the whole sky have been calculated from five years of data. The rates have been corrected for observing biases, such as initial trail radius and the collecting area for each radiant, and weighted to a constant limiting mass and a constant limiting energy. The variation of the rates with solar longitude is also examined. The directional variation of geocentric speed, semimajor axis, eccentricity, inclination and other orbital parameters has been calculated, as have the collision probabilities of each meteoroid with the Earth, and the average collisional lifetime for the observed meteoroids. The majority of meteoroids in the mass range observed by CMOR originate in the helion and antihelion sporadic sources. In addition to the north and south apex sources and the north toroidal source, the CMOR data shows a ring of radiants approximately 55 degrees from the apex, with a significant depletion of radiants immediately inside the ring. The depletion of radiants appears to be caused by removal of meteoroids through collisions, as the collisional lifetimes of meteoroids inside the ring are significantly shorter than those observed outside the ring. Further study of the sporadic meteoroid distribution may reveal whether the complex is in a steady state, and the approximate number and orbital characteristics of the parent bodies. Thanks to the NASA MSFC MEO Office.

Quantifying the Variation in the Effective Population Size Within a Genome

PubMed Central

Gossmann, Toni I.; Woolfit, Megan; Eyre-Walker, Adam

2011-01-01

The effective population size (Ne) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in Ne is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that Ne is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species—most genes have an Ne that is within a few fold of all other genes. Nonetheless we show that this modest variation in Ne is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of Ne, even taking into account the obvious nonindependence between these measures. PMID:21954163

Alternative approaches used to assess structural changes of natural zircon caused by heat treatment

NASA Astrophysics Data System (ADS)

Huong, L. T. T.; Thuyet, N. T. M.; Phan, T. L.; Tran, N.; Toan, D. N.; Thang, P. D.; Huy, B. T.

2018-03-01

It is known that large changes in the crystal structure of zircon (ZrSiO4) can be assessed through the linewidth of the characteristic Raman mode (Δν3) at 1008 cm-1. However, the use of Δν3 to assess small changes caused by heat treatment at temperatures below its decomposition temperature of 1670 °C is difficult. The present work points out that the combination of X-ray diffraction (XRD) analyses, and photoluminescence (PL) and Raman (RS) measurements with different excitation wavelengths is an effective approach to solve the above problem. In this context, we have selected natural zircon containing some rare-earth (RE) impurities, and then studied the changes in its crystal structure caused by heat treatment at temperatures Tan=400-1600 °C. XRD analyses reveal that small modifications of the unit-cell parameters occur as Tan>600 °C. Taking the intensity ratios of the ν3 mode to RE-related emissions (Iν3/IRE) or the PL intensity ratios between RE-related emissions into consideration, the similar results in good agreement with the XRD analyses are also found. We believe that the small structural changes are related to the migration and redistribution of defects and impurities, and re-crystallization of zircon. This could be further confirmed though the relation between paramagnetic and ferromagnetic signals when Tan changes.

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

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

Constraining the Methane Budget Variations after the Pinatubo Eruption using a Combined Forward and Inverse Modeling Approach

NASA Astrophysics Data System (ADS)

Banda, N.; Krol, M. C.; van Weele, M.; van Noije, T.; Dlugokencky, E. J.; Röckmann, T.

2015-12-01

The eruption of Pinatubo in 1991 caused global scale changes in climate and radiation. Large perturbations in the methane growth rate were observed after the eruption, caused by variations in either methane sources or methane sinks. Natural methane emissions from wetlands are influenced by changes in temperature and precipitation, having a significant contribution to methane variability. The main removal of methane from the atmosphere is the reaction with the hydroxyl radical (OH). OH concentrations are in turn sensitive to temperature, humidity and the amount of UV radiation. In Bândă et al. (2015), we quantified the variability in methane sources and sinks in the 5 years following the eruption, using the 3D chemistry and transport model TM5. We derived an OH inter-annual variability of 1.6% during this period. A 4.5% increase in OH levels from 1992 to 1993, caused by enhanced stratospheric ozone depletion, a recovery of stratospheric aerosols and decreased NMVOC emissions, was found to contribute to the observed drop in methane growth rate. However, using bottom-up inventories of methane emissions, the exact timing and magnitude of the observed methane growth rate variations could not be matched by our simulations. The variability in natural wetland emissions and in biomass burning emissions is quite uncertain in this period. Emission reductions in the Former Soviet Union were also proposed as a reason for the observed decrease in methane growth rate. Based on the OH variability from our previous chemistry forward model simulations, we infer methane emissions after the Pinatubo eruption using a linearized inverse modeling setup. We can therefore quantify the variability in the methane emissions needed to match the methane variations observed in weekly air samples collected in NOAA's Cooperative Global Air Sampling Network and to identify the emission categories that contributed to these variations. Reference: Bândă, N., Krol, M., van Weele, M., van Noije, T

Electrical and Electrorheological Properties of Alumina/Natural Rubber (STR XL) Composites

PubMed Central

Tangboriboon, Nuchnapa; Uttanawanit, Nuttapot; Longtong, Mean; Wongpinthong, Piraya; Sirivat, Anuvat; Kunanuruksapong, Ruksapong

2010-01-01

The electrorheological properties (ER) of natural rubber (XL)/alumina (Al2O3) composites were investigated in oscillatory shear mode under DC electrical field strengths between 0 to 2 kV/mm. SEM micrographs indicate a mean particle size of 9.873 ± 0.034 µm and particles that are moderately dispersed in the matrix. The XRD patterns indicate Al2O3 is of the β-phase polytype which possesses high ionic conductivity. The storage modulus (G′) of the composites, or the rigidity, increases by nearly two orders of magnitude, with variations in particle volume fraction and electrical field strength. The increase in the storage modulus is caused the ionic polarization of the alumina particles and the induced dipole moments set up in the natural rubber matrix.

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.

Tracking Down the Causes of Recent Induced and Natural Intraplate Earthquakes with 3D Seismological Analyses in Northwest Germany

NASA Astrophysics Data System (ADS)

Uta, P.; Brandes, C.; Boennemann, C.; Plenefisch, T.; Winsemann, J.

2015-12-01

Northwest Germany is a typical low strain intraplate region with a low seismic activity. Nevertheless, 58 well documented earthquakes with magnitudes of 0.5 - 4.3 affected the area in the last 40 years. Most of the epicenters were located in the vicinity of active natural gas fields and some inside. Accordingly, the earthquakes were interpreted as a consequence of hydrocarbon recovery (e.g. Dahm et al. 2007, Bischoff et al. 2013) and classified as induced events in the bulletins of the Federal Institute for Geosciences and Natural Resources (BGR). The two major ones have magnitudes of 4.3 and 4.0. They are the strongest earthquakes ever recorded in Northern Germany. Consequently, these events raise the question whether the ongoing extraction itself can cause them or if other natural tectonic processes like glacial isostatic adjustment may considerably contribute to their initiation. Recent studies of Brandes et al. (2012) imply that lithospheric stress changes due to post glacial isostatic adjustment might be also a potential natural cause for earthquakes in Central Europe. In order to better analyse the earthquakes and to test this latter hypothesis we performed a relocalization of the events with the NonLinLoc (Lomax et al. 2000) program package and two differently scaled 3D P-wave velocity models. Depending on the station coverage for a distinct event, either a fine gridded local model (88 x 73 x 15 km, WEG-model, made available by the industry) or a coarse regional model (1600 x 1600 x 45 km, data from CRUST1.0, Laske et al. 2013) and for some cases a combination of both models was used for the relocalization. The results confirm the trend of the older routine analysis: The majority of the events are located at the margins of the natural gas fields, some of them are now located closer to them. Focal depths mostly vary between 3.5 km and 10 km. However, for some of the events, especially for the older events with relatively bad station coverage, the error bars

Investigation of priorities in water quality management based on correlations and variations.

PubMed

Boyacıoğlu, Hülya; Gündogdu, Vildan; Boyacıoğlu, Hayal

2013-04-15

The development of water quality assessment strategies investigating spatial and temporal changes caused by natural and anthropogenic phenomena is an important tool in management practices. This paper used cluster analysis, water quality index method, sensitivity analysis and canonical correlation analysis to investigate priorities in pollution control activities. Data sets representing 22 surface water quality parameters were subject to analysis. Results revealed that organic pollution was serious threat for overall water quality in the region. Besides, oil and grease, lead and mercury were the critical variables violating the standard. In contrast to inorganic variables, organic and physical-inorganic chemical parameters were influenced by variations in physical conditions (discharge, temperature). This study showed that information produced based on the variations and correlations in water quality data sets can be helpful to investigate priorities in water management activities. Moreover statistical techniques and index methods are useful tools in data - information transformation process. Copyright © 2013 Elsevier Ltd. All rights reserved.

Towards Comprehensive Variation Models for Designing Vehicle Monitoring Systems

NASA Technical Reports Server (NTRS)

McAdams, Daniel A.; Tumer, Irem Y.; Clancy, Daniel (Technical Monitor)

2002-01-01

When designing vehicle vibration monitoring systems for aerospace devices, it is common to use well-established models of vibration features to determine whether failures or defects exist. Most of the algorithms used for failure detection rely on these models to detect significant changes in a flight environment. In actual practice, however, most vehicle vibration monitoring systems are corrupted by high rates of false alarms and missed detections. This crucial roadblock makes their implementation in real vehicles (e.g., helicopter transmissions and aircraft engines) difficult, making their operation costly and unreliable. Research conducted at the NASA Ames Research Center has determined that a major reason for the high rates of false alarms and missed detections is the numerous sources of statistical variations that are not taken into account in the modeling assumptions. In this paper, we address one such source of variations, namely, those caused during the design and manufacturing of rotating machinery components that make up aerospace systems. We present a novel way of modeling the vibration response by including design variations via probabilistic methods. Using such models, we develop a methodology to account for design and manufacturing variations, and explore the changes in the vibration response to determine its stochastic nature. We explore the potential of the methodology using a nonlinear cam-follower model, where the spring stiffness values are assumed to follow a normal distribution. The results demonstrate initial feasibility of the method, showing great promise in developing a general methodology for designing more accurate aerospace vehicle monitoring systems.

Secular bathymetric variations of the North Channel in the Changjiang (Yangtze) Estuary, China, 1880-2013: Causes and effects

NASA Astrophysics Data System (ADS)

Mei, Xuefei; Dai, Zhijun; Wei, Wen; Li, Weihua; Wang, Jie; Sheng, Hao

2018-02-01

As the interface between the fluvial upland system and the open coast, global estuaries are facing serious challenges owing to various anthropogenic activities, especially to the Changjiang Estuary. Since the establishment of the Three Gorges Dam (TGD), currently the world's largest hydraulic structure, and certain other local hydraulic engineering structures, the Changjiang Estuary has experienced severe bathymetric variations. It is urgent to analyze the estuarine morphological response to the basin-wide disturbance to enable a better management of estuarine environments. North Channel (NC), the largest anabranched estuary in the Changjiang Estuary, is the focus of this study. Based on the analysis of bathymetric data between 1880 and 2013 and related hydrological data, we developed the first study on the centennial bathymetric variations of the NC. It is found that the bathymetric changes of NC include two main modes, with the first mode representing 64% of the NC variability, which indicates observable deposition in the mouth bar and its outer side area (lower reach); the second mode representing 11% of the NC variability, which further demonstrates channel deepening along the inner side of the mouth bar (upper reach) during 1970-2013. Further, recent erosion observed along the inner side of the mouth bar is caused by riverine sediment decrease, especially in relation to TGD induced sediment trapping since 2003, while the deposition along the lower reach since 2003 can be explained by the landward sediment transport because of flood-tide force strengthen under the joint action of TGD induced seasonal flood discharge decrease and land reclamation induced lower reach narrowing. Generally, the upper and lower NC reach are respectively dominated by fluvial and tidal discharge, however, episodic extreme floods can completely alter the channel morphology by smoothing the entire channel. The results presented herein for the NC enrich our understanding of bathymetric

Variations in embodied energy and carbon emission intensities of construction materials

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

Wan Omar, Wan-Mohd-Sabki; School of Environmental Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis; Doh, Jeung-Hwan, E-mail: j.doh@griffith.edu.au

2014-11-15

Identification of parameter variation allows us to conduct more detailed life cycle assessment (LCA) of energy and carbon emission material over their lifecycle. Previous research studies have demonstrated that hybrid LCA (HLCA) can generally overcome the problems of incompleteness and accuracy of embodied energy (EE) and carbon (EC) emission assessment. Unfortunately, the current interpretation and quantification procedure has not been extensively and empirically studied in a qualitative manner, especially in hybridising between the process LCA and I-O LCA. To determine this weakness, this study empirically demonstrates the changes in EE and EC intensities caused by variations to key parameters inmore » material production. Using Australia and Malaysia as a case study, the results are compared with previous hybrid models to identify key parameters and issues. The parameters considered in this study are technological changes, energy tariffs, primary energy factors, disaggregation constant, emission factors, and material price fluctuation. It was found that changes in technological efficiency, energy tariffs and material prices caused significant variations in the model. Finally, the comparison of hybrid models revealed that non-energy intensive materials greatly influence the variations due to high indirect energy and carbon emission in upstream boundary of material production, and as such, any decision related to these materials should be considered carefully. - Highlights: • We investigate the EE and EC intensity variation in Australia and Malaysia. • The influences of parameter variations on hybrid LCA model were evaluated. • Key significant contribution to the EE and EC intensity variation were identified. • High indirect EE and EC content caused significant variation in hybrid LCA models. • Non-energy intensive material caused variation between hybrid LCA models.« less

The long-term trend in the diurnal temperature range over Asia and its natural and anthropogenic causes

NASA Astrophysics Data System (ADS)

Liu, Lin; Li, Zhanqing; Yang, Xin; Gong, Hainan; Li, Chao; Xiong, Anyuan

2016-04-01

Understanding the causes of long-term temperature trends is at the core of climate change studies. Any observed trend can result from natural variability or anthropogenic influences or both. In the present study, we evaluated the performance of 18 climate models from the Coupled Model Intercomparison Project Phase 5 on simulating the Asian diurnal temperature range (DTR) and explored the potential causes of the long-term trend in the DTR by examining the response of the DTR to natural forcing (volcanic aerosols and solar variability) and anthropogenic forcing (anthropogenic greenhouse gases (GHG) and aerosols) in the historical period of 1961-2005. For the climatology, the multimodel ensemble mean reproduced the geographical distribution and amplitude of the DTR over eastern China and India but underestimated the magnitudes of the DTR over the Tibetan Plateau and the high-latitude regions of the Asian continent. These negative biases in the DTR over frigid zones existed in most models. Seasonal biases in the DTR pattern from models were similar to the bias in the annual mean DTR pattern. Based on three selected state-of-the-art models, the observed decreasing trend in the DTR over Asia was reasonably reproduced in the all-forcing run. A comparison of separate forcing experiments revealed that anthropogenic forcing plays the dominant role in the declining trend in the DTR. Observations and model simulations showed that GHG forcing is mainly responsible for the negative trends in the DTR over Asia but that anthropogenic aerosol forcing was also behind the decreasing trend in the DTR over China and especially over eastern China.

Earth orbital variations and vertebrate bioevolution

NASA Technical Reports Server (NTRS)

Mclean, Dewey M.

1988-01-01

Cause of the Pleistocene-Holocene transition mammalian extinctions at the end of the last age is the subject of debate between those advocating human predation and climate change. Identification of an ambient air temperature (AAT)-uterine blood flow (UBF) coupling phenomenon supports climate change as a factor in the extinctions, and couples the extinctions to earth orbital variations that drive ice age climatology. The AAT-UBF phenomenon couples mammalian bioevolution directly to climate change via effects of environmental heat upon blood flow to the female uterus and damage to developing embryos. Extinctions were in progress during climatic warming before the Younger Dryas event, and after, at times when the AAT-UBF couple would have been operative; however, impact of a sudden short-term cooling on mammals in the process of adapting to smaller size and relatively larger S/V would have been severe. Variations in earth's orbit, and orbital forcing of atmospheric CO2 concentrations, were causes of the succession of Pleistocene ice ages. Coincidence of mammalian extinctions with terminations of the more intense cold stages links mammalian bioevolution to variations in earth's orbit. Earth orbital variations are a driving source of vertebrate bioevolution.

Are Solar Activity Variations Amplified by the QBO: A Modeling Study

NASA Technical Reports Server (NTRS)

Mengel, J. G.; Mayr, H. G.; Drob, D. P.; Porter, H. S.; Bhartia, P. K. (Technical Monitor)

2002-01-01

Solar cycle activity effects (SCAE) in the lower and middle atmosphere, reported in several studies, are difficult to explain on the basis of the small changes in solar radiation that accompany the 11-year cycle. It is therefore natural to speculate that dynamical processes may come into play to produce a leverage. Such a leverage may be provided by the Quasi-Biennial Oscillation (QBO) in the zonal circulation of the stratosphere, which has been linked to solar activity variations. Driven primarily by wave mean flow interaction, the QBO period and its amplitude are variable but are also strongly influenced by the seasonal cycle in the solar radiation. This influence extends to low altitudes and is referred to as 'downward control'. Small changes in the solar radiative forcing may produce small changes in the period and phase of the QBO, but these in turn may produce measurable differences in the wind field. Thus, the QBO may be an amplifier of solar activity variations and a natural conduit of these variations to lower altitudes. To test this hypothesis, we conducted experiments with a 2D version of our Numerical Spectral Model that incorporates Hines' Doppler Spread Parameterization for small-scale gravity waves (GW). Solar cycle radiance variations (SCRV) are accounted for by changing the radiative heating rate on a logarithmic scale from 0.1% at the surface to 1% at 50 km to 10% at 100 km. With and without SCRV, but with the same GW flux, we then conduct numerical experiments to evaluate the magnitude of the SCAE in the zonal circulation. The numerical results indicate that, under certain conditions, the SCAE is significant and can extend to lower altitudes where the SCRV is small. For a modeled QBO period of 30 months, we find that the seasonal cycle in the solar forcing acts as a strong pacemaker to lock up the phase and period of the QBO. The SCAE then shows up primarily as a distinct but relatively weak amplitude modulation. But with a different QBO period

Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases

PubMed Central

Naz, Mufassra; Kodamullil, Alpha Tom

2016-01-01

The work we present here is based on the recent extension of the syntax of the Biological Expression Language (BEL), which now allows for the representation of genetic variation information in cause-and-effect models. In our article, we describe, how genetic variation information can be used to identify candidate disease mechanisms in diseases with complex aetiology such as Alzheimer’s disease and Parkinson’s disease. In those diseases, we have to assume that many genetic variants contribute moderately to the overall dysregulation that in the case of neurodegenerative diseases has such a long incubation time until the first clinical symptoms are detectable. Owing to the multilevel nature of dysregulation events, systems biomedicine modelling approaches need to combine mechanistic information from various levels, including gene expression, microRNA (miRNA) expression, protein–protein interaction, genetic variation and pathway. OpenBEL, the open source version of BEL, has recently been extended to match this requirement, and we demonstrate in our article, how candidate mechanisms for early dysregulation events in Alzheimer’s disease can be identified based on an integrative mining approach that identifies ‘chains of causation’ that include single nucleotide polymorphism information in BEL models. PMID:26249223

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

Variation with interplanetary sector of the total magnetic field measured at the OGO 2, 4, and 6 satellites

NASA Technical Reports Server (NTRS)

Langel, R. A.

1973-01-01

Variations in the scalar magnetic field (delta B) from the polar orbiting OGO 2, 4, and 6 spacecraft are examined as a function of altitude for times when the interplanetary magnetic field is toward the sun and for times when the interplanetary magnetic field away from the sun. This morphology is basically the same as that found when all data, irrespective of interplanetary magnetic sector, are averaged together. Differences in delta B occur, both between sectors and between seasons, which are similar in nature to variations in the surface delta Z found by Langel (1973c). The altitude variation of delta B at sunlit local times, together with delta Z at the earth's surface, demonstrates that the delta Z and delta B which varies with sector has an ionospheric source. Langel (1973b) showed that the positive delta B region in the dark portion of the hemisphere is due to at least two sources, the westward electrojet and an unidentified non-ionospheric source(s). Comparison of magnetic variations between season/sector at the surface and at the satellite, in the dark portion of the hemisphere, indicates that these variations are caused by variations in the latitudinally narrow electrojet currents and not by variations in the non-ionospheric source of delta B.

Pelage Variation and Distribution of the Black Lion Tamarin, Leontopithecus chrysopygus.

PubMed

Garbino, Guilherme Siniciato Terra; Rezende, Gabriela Cabral; Valladares-Padua, Claudio

2016-01-01

The black lion tamarin, Leontopithecus chrysopygus, is endemic to the Atlantic Forest of the interior of the state of São Paulo in Brazil. Since the discovery of the species, authors have described variations in the pelage of L. chrysopygus, but the nature of this variation has remained unknown. We examined museum specimens and living animals to see if the pelage of L. chrysopygus varies individually, geographically or ontogenetically. We reviewed all known locality records of the species, and concluded that the pelage of L. chrysopygus varies individually and ontogenetically, but not geographically. The extent of the golden chromogenetic fields is larger in younger individuals, and the pelage becomes darker after successive moults. We examined 2 juveniles that presented a pelage similar to adult L. caissara. Geographically, there is a clear break in the phenotypes attributed to L. caissara and L. chrysopygus, precluding clinal variation and corroborating the specific status of the former. The separation between these 2 species is coincident with a tectonic fault known as the 'Guapiara lineament', and may have been caused by a recent activation of this geological formation. We also suggest a historical contact zone between L. chrysopygus and the marmoset Callithrix aurita in the upper Rio Tietê region. © 2016 S. Karger AG, Basel.

Seasonal, synoptic and diurnal variation of atmospheric water-isotopologues in the boundary layer of Southwestern Germany caused by plant transpiration, cold-front passages and dewfall.

NASA Astrophysics Data System (ADS)

Christner, Emanuel; Dyroff, Christoph; Kohler, Martin; Zahn, Andreas; Gonzales, Yenny; Schneider, Matthias

2013-04-01

Atmospheric water is an enormously crucial trace gas. It is responsible for ~70 % of the natural greenhouse effect (Schmidt et al., JGR, 2010) and carries huge amounts of latent heat. The isotopic composition of water vapor is an elegant tracer for a better understanding and quantification of the extremely complex and variable hydrological cycle in Earth's atmosphere (evaporation, cloud condensation, rainout, re-evaporation, snow), which in turn is a prerequisite to improve climate modeling and predictions. As H216O, H218O and HDO differ in vapor pressure and mass, isotope fractionation occurs due to condensation, evaporation and diffusion processes. In contrast to that, plants are able to transpire water with almost no isotope fractionation. For that reason the ratio of isotopologue concentrations in the boundary layer (BL) provides, compared to humidity measurements alone, independent and additional constraints for quantifying the strength of evaporation and transpiration. Furthermore the isotope ratios contain information about transport history of an air mass and microphysical processes, that is not accessible by humidity measurements. Within the project MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water) a commercial Picarro Analyzer L2120-i is operated at Karlsruhe in Southwestern Germany, which is continuously measuring the isotopologues H216O, HDO and H218O of atmospheric water vapor since January 2012. A one year record of H216O, HDO and H218O shows clear seasonal, synoptic and diurnal characteristics and reveals the main driving processes affecting the isotopic composition of water vapor in the Middle European BL. Changes in continental plant transpiration and evaporation throughout the year lead to a slow seasonal HDO/H216O-variation, that cannot be explained by pure Rayleigh condensation. Furthermore, cold-front passages from NW lead to fast and pronounced depletion of the HDO/H216O-ratio within

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

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

Optical turbulence on underwater image degradation in natural environments.

PubMed

Hou, Weilin; Woods, Sarah; Jarosz, Ewa; Goode, Wesley; Weidemann, Alan

2012-05-10

It is a well-known fact that the major degradation source on electro-optical imaging underwater is from scattering by particles of various origins and sizes. Recent research indicates that, under certain conditions, the apparent degradation could also be caused by the variations of index of refraction associated with temperature and salinity microstructures in the ocean and lakes. The combined impact has been modeled previously through the simple underwater imaging model. The current study presents the first attempts in quantifying the level of image degradation due to optical turbulence in natural waters in terms of modulation transfer functions using measured turbulence dissipation rates. Image data collected from natural environments during the Skaneateles Optical Turbulence Exercise are presented. Accurate assessments of the turbulence conditions are critical to the model validation and were measured by two instruments to ensure consistency and accuracy. Optical properties of the water column in the field were also measured in coordination with temperature, conductivity, and depth. The results show that optical turbulence degrades the image quality as predicted and on a level comparable to that caused by the particle scattering just above the thermocline. Other contributing elements involving model closure, including temporal and spatial measurement scale differences among sensors and mitigation efforts, are discussed.

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.

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

How much better are females? The occurrence of female advantage, its proximal causes and its variation within and among gynodioecious species

PubMed Central

Dufay, Mathilde; Billard, Emmanuelle

2012-01-01

Background Gynodioecy is a reproductive system of interest for evolutionary biologists, as it poses the question of how females can be maintained while competing with hermaphrodites that possess both male and female functions. One necessary condition for the maintenance of this polymorphism is the occurrence of a female advantage, i.e. a better seed production or quality by females compared with hermaphrodites. Theoretically, its magnitude can be low when sterility mutations are cytoplasmic, while a 2-fold advantage is needed in the case of nuclear sterility. Such a difference is often thought to be due to reduced inbreeding depression in obligatory outcrossed females. Finally, variation in sex ratio and female advantage occur among populations of some gynodioecious species, though the prevalence of such variation is unknown. Scope By reviewing and analysing the data published on 48 gynodioecious species, we examined three important issues about female advantage. (1) Are reduced selfing and inbreeding depression likely to be the major cause of female advantage? (2) What is the magnitude of female advantage and does it fit theoretical predictions? (3) Does the occurrence or the magnitude of female advantage vary among populations within species and why? Conclusions It was found that a female advantage occurred in 40 species, with a magnitude comprised between 1 and 2 in the majority of cases. In many species, reduced selfing may not be a necessary cause of this advantage. Finally, female advantage varied among populations in some species, but both positive and negative correlations were found with female frequency. The role of reduced selfing in females for the evolution of gynodioecy, as well as the various processes that affect sex ratios and female advantage in populations are discussed. PMID:21459860

Temporal Trends in Geographical Variation in Breast Cancer Mortality in China, 1973-2005: An Analysis of Nationwide Surveys on Cause of Death.

PubMed

Xia, Changfa; Kahn, Clare; Wang, Jinfeng; Liao, Yilan; Chen, Wanqing; Yu, Xue Qin

2016-09-28

To describe geographical variation in breast cancer mortality over time, we analysed breast cancer mortality data from three retrospective national surveys on causes of death in recent decades in China. We first calculated the age-standardized mortality rate (ASMR) for each of the 31 provinces in mainland China stratified by survey period (1973-1975, 1990-1992 and 2004-2005). To test whether the geographical variation in breast cancer mortality changed over time, we then estimated the rate ratio (RR) for the aggregated data for seven regions and three economic zones using generalized linear models. Finally, we examined the correlation between mortality rate and several macro-economic measures at the provincial level. We found that the overall ASMR increased from 2.98 per 100,000 in 1973-1975 to 3.08 per 100,000 in 1990-1992, and to 3.85 per 100,000 in 2004-2005. Geographical variation in breast cancer mortality also increased significantly over time at the regional level ( p = 0.002) but not at the economic zone ( p = 0.089) level, with RR being generally lower for Western China (Northwest and Southwest) and higher in Northeast China over the three survey periods. These temporal and spatial trends in breast cancer mortality were found to be correlated with per capita gross domestic product, number of hospitals and health centres' beds per 10,000 population and number of practicing doctors per 10,000 population, and average number of live births for women aged 15-64. It may be necessary to target public health policies in China to address the widening geographic variation in breast cancer mortality, and to take steps to ensure that the ease of access and the quality of cancer care across the country is improved for all residents.

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 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.

Influence of Sub-Daily Variation on Multi-Fractal Detrended Fluctuation Analysis of Wind Speed Time Series

PubMed Central

Li, Weinan; Kong, Yanjun; Cong, Xiangyu

2016-01-01

Using multi-fractal detrended fluctuation analysis (MF-DFA), the scaling features of wind speed time series (WSTS) could be explored. In this paper, we discuss the influence of sub-daily variation, which is a natural feature of wind, in MF-DFA of WSTS. First, the choice of the lower bound of the segment length, a significant parameter of MF-DFA, was studied. The results of expanding the lower bound into sub-daily scope shows that an abrupt declination and discrepancy of scaling exponents is caused by the inability to keep the whole diel process of wind in one single segment. Additionally, the specific value, which is effected by the sub-daily feature of local meteo-climatic, might be different. Second, the intra-day temporal order of wind was shuffled to determine the impact of diel variation on scaling exponents of MF-DFA. The results illustrate that disregarding diel variation leads to errors in scaling. We propose that during the MF-DFA of WSTS, the segment length should be longer than 1 day and the diel variation of wind should be maintained to avoid abnormal phenomena and discrepancy in scaling exponents. PMID:26741491

Population genomics and the causes of local differentiation.

PubMed

Tonsor, Stephen J

2012-11-01

Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock-full of genetic variation. This variation was a surprise that required a re-thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range-wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high-throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.

Genomic Conflicts that Cause Pollen Mortality and Raise Reproductive Barriers in Arabidopsis thaliana

PubMed Central

Simon, Matthieu; Durand, Stéphanie; Pluta, Natacha; Gobron, Nicolas; Botran, Lucy; Ricou, Anthony; Camilleri, Christine; Budar, Françoise

2016-01-01

Species differentiation and the underlying genetics of reproductive isolation are central topics in evolutionary biology. Hybrid sterility is one kind of reproductive barrier that can lead to differentiation between species. Here, we analyze the complex genetic basis of the intraspecific hybrid male sterility that occurs in the offspring of two distant natural strains of Arabidopsis thaliana, Shahdara and Mr-0, with Shahdara as the female parent. Using both classical and quantitative genetic approaches as well as cytological observation of pollen viability, we demonstrate that this particular hybrid sterility results from two causes of pollen mortality. First, the Shahdara cytoplasm induces gametophytic cytoplasmic male sterility (CMS) controlled by several nuclear loci. Second, several segregation distorters leading to allele-specific pollen abortion (pollen killers) operate in hybrids with either cytoplasm. The complete sterility of the hybrid with the Shahdara cytoplasm results from the genetic linkage of the two causes of pollen mortality, i.e., CMS nuclear determinants and pollen killers. Furthermore, natural variation at these loci in A. thaliana is associated with different male-sterility phenotypes in intraspecific hybrids. Our results suggest that the genomic conflicts that underlie segregation distorters and CMS can concurrently lead to reproductive barriers between distant strains within a species. This study provides a new framework for identifying molecular mechanisms and the evolutionary history of loci that contribute to reproductive isolation, and possibly to speciation. It also suggests that two types of genomic conflicts, CMS and segregation distorters, may coevolve in natural populations. PMID:27182945

A discussion of plausible solar irradiance variations, 1700-1992

NASA Technical Reports Server (NTRS)

Hoyt, Douglas V.; Schatten, Kenneth H.

1993-01-01

From satellite observations the solar total irradiance is known to vary. Sunspot blocking, facular emission, and network emission are three identified causes for the variations. In this paper we examine several different solar indices measured over the past century that are potential proxy measures for the Sun's irradiance. These indices are (1) the equatorial solar rotation rate, (2) the sunspot structure, the decay rate of individual sunspots, and the number of sunspots without umbrae, and (3) the length and decay rate of the sunspot cycle. Each index can be used to develop a model for the Sun's total irradiance as seen at the Earth. Three solar indices allow the irradiance to be modeled back to the mid-1700s. The indices are (1) the length of the solar cycle, (2) the normalized decay rate of the solar cycle, and (3) the mean level of solar activity. All the indices are well correlated, and one possible explanation for their nearly simultaneous variations is changes in the Sun's convective energy transport. Although changes in the Sun's convective energy transport are outside the realm of normal stellar structure theory (e.g., mixing length theory), one can imagine variations arising from even the simplest view of sunspots as vertical tubes of magnetic flux, which would serve as rigid pillas affecting the energy flow patterns by ensuring larger-scale eddies. A composite solar irradiance model, based upon these proxies, is compared to the northern hemisphere temperature depatures for 1700-1992. Approximately 71% of the decadal variance in the last century can be modeled with these solar indices, although this analysis does not include anthropogenic or other variations which would affect the results. Over the entire three centuries, approx. 50% of the variance is modeled. Both this analysis and previous similar analyses have correlations of model solar irradiances and measured Earth surface temperatures that are significant at better than the 95% confidence level

Heritability of Two Morphological Characters within and among Natural Populations of Drosophila melanogaster

PubMed Central

Coyne, Jerry A.; Beecham, Edward

1987-01-01

Heritabilities of wing length and abdominal bristle number, as well as genetic correlations between these characters, were determined within and among populations of Drosophila melanogaster in nature. Substantial "natural" heritabilities were found when wild-caught flies from one population were compared to their laboratory-reared offspring. Natural heritabilities of bristle number approximated those derived from laboratory-raised parents and offspring, but wing length heritability was significantly lower in nature than in the laboratory. Among-population heritabilities, estimated by regressing population means of wild-caught flies against those of their laboratory-reared descendants, were close to 0.5. The genetic differentiation of populations was clinal with latitude, and was accompanied by significant geographic differences in the norms of reaction to temperature. These clines are similar to those reported on other continents and in other Drosophila species, and are almost certainly caused by natural selection. Genetic regressions between the characters reveal that the cline in bristle number may be a correlated response to geographic selection on wing length, but not vice versa. Our results indicate that there is a sizable genetic component to phenotypic variation within and among populations of D. melanogaster in nature. PMID:3123311

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

A systematic review of medical practice variation in OECD countries.

PubMed

Corallo, Ashley N; Croxford, Ruth; Goodman, David C; Bryan, Elisabeth L; Srivastava, Divya; Stukel, Therese A

2014-01-01

Major variations in medical practice have been documented internationally. Variations raise questions about the quality, equity, and efficiency of resource allocation and use, and have important implications for health care and health policy. To perform a systematic review of the peer-reviewed literature on medical practice variations in OECD countries. We searched MEDLINE to find publications on medical practice variations in OECD countries published between 2000 and 2011. We present an overview of the characteristics of published studies as well as the magnitude of variations for select high impact conditions. A total of 836 studies were included. Consistent with the gray literature, there were large variations across regions, hospitals and physician practices for almost every condition and procedure studied. Many studies focused on high-impact conditions, but very few looked at the causes or outcomes of medical practice variations. While there were an overwhelming number of publications on medical practice variations the coverage was broad and not often based on a theoretical construct. Future studies should focus on conditions and procedures that are clinically important, policy relevant, resource intensive, and have high levels of public awareness. Further study of the causes and consequences of variations is important. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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.

Identified Natural Hazards May Cause Adverse Impact on Sustainability of Desalination Plants in Red Sea

NASA Astrophysics Data System (ADS)

Aburizaiza, O. S.; Zaigham, N. A.; Nayyar, Z. A.; Mahar, G. A.; Siddique, A.; Eusufi, S. N.

2011-12-01

The Red Sea and its surrounding countries have harsh arid climatic conditions where fast growth of the socio-economic activities and rapid change of lifestyle have caused tremendous stress on water to the level of acute crisis. To meet the water demands, the Red Sea countries have adopted seawater desalination giving priority against their land-based resources. Saudi Arabia is the largest desalinated-water producers in the Red Sea and has practically no adequate backup plan in case of sudden unforeseen emergency. Out of about 3.64 million m3/day, Saudi Arabia is alone being desalinated about 3.29 m3/day seawater from Red Sea and more projects are in progress. Present integrated research study has identified some of natural and anthropogenic hazards, which may be major threats to the quality of the seawater as well as to the desalination plants themselves. Results of present study reveal that the submarine complex morphologic features may cause the isolation of Red Sea from any of the open sea, the increase in the seismicity trends, the active volcanism causing unique longitudinal as well as transverse deformations of the axial trough particularly in the southern part of the Red Sea, the consistently generating enormous hot-brine tectonic-factory all along the deeper parts of the Red Sea rifting trough and other related issues. Considering the identified odd conditions, the total dependence on seawater desalination may not be worthwhile for sustainable water management strategy and consequent socio-economic developments in future. It is recommended that the priority should also be given mainly in three main disciplines to meet the future water challenges - one, developing reliable backup water management; second, alternate options for the supplementary resources of water; and third, the development and immediate implementation of the water-use conservation strategy plan.

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 ...

Use of primary diagnosis during hospitalization in the Unified Health System (Sistema Único de Saúde) to qualify information regarding the underlying cause of natural deaths among the elderly.

PubMed

Cascão, Angela Maria; Jorge, Maria Helena Prado de Mello; Costa, Antonio José Leal; Kale, Pauline Lorena

2016-01-01

Ill-defined causes of death are common among the elderly owing to the high frequency of comorbidities and, consequently, to the difficulty in defining the underlying cause of death. To analyze the validity and reliability of the "primary diagnosis" in hospitalization to recover the information on the underlying cause of death in natural deaths among the elderly whose deaths were originally assigned to "ill-defined cause" in their Death Certificate. The hospitalizations occurred in the state of Rio de Janeiro, in 2006. The databases obtained in the Information Systems on Mortality and Hospitalization were probabilistically linked. The following data were calculated for hospitalizations of the elderly that evolved into deaths with a natural cause: concordance percentages, Kappa coefficient, sensitivity, specificity, and the positive predictive value of the primary diagnosis. Deaths related to "ill-defined causes" were assigned to a new cause, which was defined based on the primary diagnosis. The reliability of the primary diagnosis was good, according to the total percentage of consistency (50.2%), and fair, according to the Kappa coefficient (k = 0.4; p < 0.0001). Diseases related to the circulatory system and neoplasia occurred with the highest frequency among the deaths and the hospitalizations and presented a higher consistency of positive predictive values per chapter and grouping of the International Classification of Diseases. The recovery of the information on the primary cause occurred in 22.6% of the deaths with ill-defined causes (n = 14). The methodology developed and applied for the recovery of the information on the natural cause of death among the elderly in this study had the advantage of effectiveness and the reduction of costs compared to an investigation of the death that is recommended in situations of non-linked and low positive predictive values. Monitoring the mortality profile by the cause of death is necessary to periodically update the

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.

Effects of increased alcohol availability during adolescence on the risk of all‐cause and cause‐specific disability pension: a natural experiment

PubMed Central

de Munter, Jeroen; Hemmingsson, Tomas; Davey Smith, George; Ramstedt, Mats; Tynelius, Per; Rasmussen, Finn

2017-01-01

Abstract Aim To test if being exposed to increased alcohol availability during adolescence is associated with an increased risk of receiving disability pension due to all‐cause, alcohol use disorders and mental disorders. Design Register‐based population‐based study using a natural experiment setting, the alcohol policy change in Sweden (1967–68), with increased access to strong beer in a narrow time window and geographical area. The individuals exposed to the policy change were compared with non‐exposed individuals living in the rest of Sweden, excluding a border area. Setting Sweden. Participants A total of 518 810 individuals (70 761 in the intervention group; 448 049 in the control group) born 1948–1953, aged 14–20 years during the policy change. Measurements Date and diagnosis of the outcome variable of disability pension due to all‐cause, alcohol use disorders and mental disorders were obtained from the Swedish National Social Insurance Agency database from 1971 to 2013. Individual and family level socio‐demographic and health‐related covariates, as well as a regional level covariate, were included. Findings Compared with the control group, adolescents exposed to the alcohol policy change were at an increased risk of receiving disability pension due to all‐causes [hazard ratio (HR) = 1.09, 95% confidence interval (CI) = 1.07–1.11], alcohol use disorders (HR = 1.17, 95% CI = 1.05–1.30) and mental disorders (HR = 1.19, 95% CI = 1.15–1.23). Conclusion In Sweden, a natural experiment with a 43‐year follow‐up suggests that exposure to increased alcohol availability during adolescence is associated with an increased risk of receiving a disability pension due to all‐cause, alcohol use disorder and mental disorder diagnoses. PMID:28060450

Sources of Variation in Sweat Chloride Measurements in Cystic Fibrosis.

PubMed

Collaco, Joseph M; Blackman, Scott M; Raraigh, Karen S; Corvol, Harriet; Rommens, Johanna M; Pace, Rhonda G; Boelle, Pierre-Yves; McGready, John; Sosnay, Patrick R; Strug, Lisa J; Knowles, Michael R; Cutting, Garry R

2016-12-01

Expanding the use of cystic fibrosis transmembrane conductance regulator (CFTR) potentiators and correctors for the treatment of cystic fibrosis (CF) requires precise and accurate biomarkers. Sweat chloride concentration provides an in vivo assessment of CFTR function, but it is unknown the degree to which CFTR mutations account for sweat chloride variation. To estimate potential sources of variation for sweat chloride measurements, including demographic factors, testing variability, recording biases, and CFTR genotype itself. A total of 2,639 sweat chloride measurements were obtained in 1,761 twins/siblings from the CF Twin-Sibling Study, French CF Modifier Gene Study, and Canadian Consortium for Genetic Studies. Variance component estimation was performed by nested mixed modeling. Across the tested CF population as a whole, CFTR gene mutations were found to be the primary determinant of sweat chloride variability (56.1% of variation) with contributions from variation over time (e.g., factors related to testing on different days; 13.8%), environmental factors (e.g., climate, family diet; 13.5%), other residual factors (e.g., test variability; 9.9%), and unique individual factors (e.g., modifier genes, unique exposures; 6.8%) (likelihood ratio test, P < 0.001). Twin analysis suggested that modifier genes did not play a significant role because the heritability estimate was negligible (H 2  = 0; 95% confidence interval, 0.0-0.35). For an individual with CF, variation in sweat chloride was primarily caused by variation over time (58.1%) with the remainder attributable to residual/random factors (41.9%). Variation in the CFTR gene is the predominant cause of sweat chloride variation; most of the non-CFTR variation is caused by testing variability and unique environmental factors. If test precision and accuracy can be improved, sweat chloride measurement could be a valuable biomarker for assessing response to therapies directed at mutant CFTR.

Fault geometric complexity and how it may cause temporal slip-rate variation within an interacting fault system

NASA Astrophysics Data System (ADS)

Zielke, Olaf; Arrowsmith, Ramon

2010-05-01

Slip-rates along individual faults may differ as a function of measurement time scale. Short-term slip-rates may be higher than the long term rate and vice versa. For example, vertical slip-rates along the Wasatch Fault, Utah are 1.7+/-0.5 mm/yr since 6ka, <0.6 mm/yr since 130ka, and 0.5-0.7 mm/yr since 10Ma (Friedrich et al., 2003). Following conventional earthquake recurrence models like the characteristic earthquake model, this observation implies that the driving strain accumulation rates may have changed over the respective time scales as well. While potential explanations for such slip-rate variations may be found for example in the reorganization of plate tectonic motion or mantle flow dynamics, causing changes in the crustal velocity field over long spatial wavelengths, no single geophysical explanation exists. Temporal changes in earthquake rate (i.e., event clustering) due to elastic interactions within a complex fault system may present an alternative explanation that requires neither variations in strain accumulation rate or nor changes in fault constitutive behavior for frictional sliding. In the presented study, we explore this scenario and investigate how fault geometric complexity, fault segmentation and fault (segment) interaction affect the seismic behavior and slip-rate along individual faults while keeping tectonic stressing-rate and frictional behavior constant in time. For that, we used FIMozFric--a physics-based numerical earthquake simulator, based on Okada's (1992) formulations for internal displacements and strains due to shear and tensile faults in a half-space. Faults are divided into a large number of equal-sized fault patches which communicate via elastic interaction, allowing implementation of geometrically complex, non-planar faults. Each patch has assigned a static and dynamic friction coefficient. The difference between those values is a function of depth--corresponding to the temperature-dependence of velocity-weakening that is

Natural selection on immune defense: A field experiment.

PubMed

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

2017-02-01

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

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

Decreased necrotizing fasciitis capacity caused by a single nucleotide mutation that alters a multiple gene virulence axis

PubMed Central

Olsen, Randall J.; Sitkiewicz, Izabela; Ayeras, Ara A.; Gonulal, Vedia E.; Cantu, Concepcion; Beres, Stephen B.; Green, Nicole M.; Lei, Benfang; Humbird, Tammy; Greaver, Jamieson; Chang, Ellen; Ragasa, Willie P.; Montgomery, Charles A.; Cartwright, Joiner; McGeer, Allison; Low, Donald E.; Whitney, Adeline R.; Cagle, Philip T.; Blasdel, Terry L.; DeLeo, Frank R.; Musser, James M.

2010-01-01

Single-nucleotide changes are the most common cause of natural genetic variation among members of the same species, but there is remarkably little information bearing on how they alter bacterial virulence. We recently discovered a single-nucleotide mutation in the group A Streptococcus genome that is epidemiologically associated with decreased human necrotizing fasciitis (“flesh-eating disease”). Working from this clinical observation, we find that wild-type mtsR function is required for group A Streptococcus to cause necrotizing fasciitis in mice and nonhuman primates. Expression microarray analysis revealed that mtsR inactivation results in overexpression of PrsA, a chaperonin involved in posttranslational maturation of SpeB, an extracellular cysteine protease. Isogenic mutant strains that overexpress prsA or lack speB had decreased secreted protease activity in vivo and recapitulated the necrotizing fasciitis-negative phenotype of the ΔmtsR mutant strain in mice and monkeys. mtsR inactivation results in increased PrsA expression, which in turn causes decreased SpeB secreted protease activity and reduced necrotizing fasciitis capacity. Thus, a naturally occurring single-nucleotide mutation dramatically alters virulence by dysregulating a multiple gene virulence axis. Our discovery has broad implications for the confluence of population genomics and molecular pathogenesis research. PMID:20080771

Decreased necrotizing fasciitis capacity caused by a single nucleotide mutation that alters a multiple gene virulence axis.

PubMed

Olsen, Randall J; Sitkiewicz, Izabela; Ayeras, Ara A; Gonulal, Vedia E; Cantu, Concepcion; Beres, Stephen B; Green, Nicole M; Lei, Benfang; Humbird, Tammy; Greaver, Jamieson; Chang, Ellen; Ragasa, Willie P; Montgomery, Charles A; Cartwright, Joiner; McGeer, Allison; Low, Donald E; Whitney, Adeline R; Cagle, Philip T; Blasdel, Terry L; DeLeo, Frank R; Musser, James M

2010-01-12

Single-nucleotide changes are the most common cause of natural genetic variation among members of the same species, but there is remarkably little information bearing on how they alter bacterial virulence. We recently discovered a single-nucleotide mutation in the group A Streptococcus genome that is epidemiologically associated with decreased human necrotizing fasciitis ("flesh-eating disease"). Working from this clinical observation, we find that wild-type mtsR function is required for group A Streptococcus to cause necrotizing fasciitis in mice and nonhuman primates. Expression microarray analysis revealed that mtsR inactivation results in overexpression of PrsA, a chaperonin involved in posttranslational maturation of SpeB, an extracellular cysteine protease. Isogenic mutant strains that overexpress prsA or lack speB had decreased secreted protease activity in vivo and recapitulated the necrotizing fasciitis-negative phenotype of the DeltamtsR mutant strain in mice and monkeys. mtsR inactivation results in increased PrsA expression, which in turn causes decreased SpeB secreted protease activity and reduced necrotizing fasciitis capacity. Thus, a naturally occurring single-nucleotide mutation dramatically alters virulence by dysregulating a multiple gene virulence axis. Our discovery has broad implications for the confluence of population genomics and molecular pathogenesis research.

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...

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.

Large-scale causes of variation in the serpentine vegetation of California

USGS Publications Warehouse

Grace, J.B.; Safford, H.D.; Harrison, S.

2007-01-01

Serpentine vegetation in California ranges from forest to shrubland and grassland, harbors many rare and endemic species, and is only moderately altered by invasive exotic species at the present time. To better understand the factors regulating the distribution of common/representative species, endemic/rare species, and the threat of exotics in this important flora, we analyzed broad-scale community patterns and environmental conditions in a geographically stratified set of samples from across the state. We considered three major classes of environmental influences: climate (especially precipitation), soils (especially the Mg2+/Ca2+ ratio), and the indirect influences of climate on soils. We used ordination to identify the major axes of variation in common species abundances, structural equation models to analyze the relationship of community axes and endemic and exotic species richness to the environment, and group analysis techniques to identify consistent groupings of species and characterize their properties. We found that community variation could be explained by a two-axis ordination. One axis ranged from conifer forest to grassland and was strongly related to precipitation. The second axis ranged from chaparral to grassland and had little relationship to current environmental conditions, suggesting a possible role for successional history. Precipitation and elevation were respectively the largest influences on endemic and exotic richness, followed by Mg 2+/Ca2+. The results also support the idea that long-term precipitation patterns have altered the Mg2+/Ca2+ ratio via selective leaching, resulting in indirect influences on endemics (positive) and exotics (negative) but not affecting the abundances of common species. We discuss implications of these findings for the conservation of the California serpentine flora. ?? 2007 Springer Science+Business Media B.V.

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

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.

Temporal Trends in Geographical Variation in Breast Cancer Mortality in China, 1973–2005: An Analysis of Nationwide Surveys on Cause of Death

PubMed Central

Xia, Changfa; Kahn, Clare; Wang, Jinfeng; Liao, Yilan; Chen, Wanqing; Yu, Xue Qin

2016-01-01

To describe geographical variation in breast cancer mortality over time, we analysed breast cancer mortality data from three retrospective national surveys on causes of death in recent decades in China. We first calculated the age-standardized mortality rate (ASMR) for each of the 31 provinces in mainland China stratified by survey period (1973–1975, 1990–1992 and 2004–2005). To test whether the geographical variation in breast cancer mortality changed over time, we then estimated the rate ratio (RR) for the aggregated data for seven regions and three economic zones using generalized linear models. Finally, we examined the correlation between mortality rate and several macro-economic measures at the provincial level. We found that the overall ASMR increased from 2.98 per 100,000 in 1973–1975 to 3.08 per 100,000 in 1990–1992, and to 3.85 per 100,000 in 2004–2005. Geographical variation in breast cancer mortality also increased significantly over time at the regional level (p = 0.002) but not at the economic zone (p = 0.089) level, with RR being generally lower for Western China (Northwest and Southwest) and higher in Northeast China over the three survey periods. These temporal and spatial trends in breast cancer mortality were found to be correlated with per capita gross domestic product, number of hospitals and health centres’ beds per 10,000 population and number of practicing doctors per 10,000 population, and average number of live births for women aged 15–64. It may be necessary to target public health policies in China to address the widening geographic variation in breast cancer mortality, and to take steps to ensure that the ease of access and the quality of cancer care across the country is improved for all residents. PMID:27690073

Proteomics insight into the biological safety of transgenic modification of rice as compared with conventional genetic breeding and spontaneous genotypic variation.

PubMed

Gong, Chun Yan; Li, Qi; Yu, Hua Tao; Wang, Zizhang; Wang, Tai

2012-05-04

The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM indica rice, herbicide-resistant Bar68-1 carrying bar and insect-resistant 2036-1a carrying cry1Ac/sck, and their respective controls D68 and MH86, as well as indica variety MH63, a parental line for breeding MH86, and japonica variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between indica and japonica cultivars, second among indica varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating japonica and indica cultivars, as well as indica varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties.

Air pollution exposure, cause-specific deaths and hospitalizations in a highly polluted Italian region.

PubMed

Carugno, Michele; Consonni, Dario; Randi, Giorgia; Catelan, Dolores; Grisotto, Laura; Bertazzi, Pier Alberto; Biggeri, Annibale; Baccini, Michela

2016-05-01

The Lombardy region in northern Italy ranks among the most air polluted areas of Europe. Previous studies showed air pollution short-term effects on all-cause mortality. We examine here the effects of particulate matter with aerodynamic diameter ≤10µm (PM10) and nitrogen dioxide (NO2) exposure on deaths and hospitalizations from specific causes, including cardiac, cerebrovascular and respiratory diseases. We considered air pollution, mortality and hospitalization data for a non-opportunistic sample of 18 highly polluted and most densely populated areas of the region in the years 2003-2006. We obtained area-specific effect estimates for PM10 and NO2 from a Poisson regression model on the daily number of total deaths or cause-specific hospitalizations and then combined them in a Bayesian random-effects meta-analysis. For cause-specific mortality, we applied a case-crossover analysis. Age- and season-specific analyses were also performed. Effect estimates were expressed as percent variation in mortality or hospitalizations associated with a 10µg/m(3) increase in PM10 or NO2 concentration. Natural mortality was positively associated with both pollutants (0.30%, 90% Credibility Interval [CrI]: -0.31; 0.78 for PM10; 0.70%, 90%CrI: 0.10; 1.27 for NO2). Cardiovascular deaths showed a higher percent variation in association with NO2 (1.12%, 90% Confidence Interval [CI]: 0.14; 2.11), while the percent variation for respiratory mortality was highest in association with PM10 (1.64%, 90%CI: 0.35; 2.93). The effect of both pollutants was more evident in the summer season. Air pollution was also associated to hospitalizations, the highest variations being 0.77% (90%CrI: 0.22; 1.43) for PM10 and respiratory diseases, and 1.70% (90%CrI: 0.39; 2.84) for NO2 and cerebrovascular diseases. The effect of PM10 on respiratory hospital admissions appeared to increase with age. For both pollutants, effects on cerebrovascular hospitalizations were more evident in subjects aged less than

Variation, "evolution", immortality and genetic instabilities in tumour cells.

PubMed

Bignold, L P

2007-08-18

The pathological characteristics of tumour cells often include variation of their histopathological features (i.e. "degrees of de-differentiation") between cases of the same tumour type and between different foci within individual tumours. Usually, only a few cell lines from tumours are immortal. Currently, somatic mutation, replicative infidelity of DNA and aneuploidy are suggested as alternative mechanisms of genomic disturbance underlying tumours. Nevertheless, apart from Hansemann's ideas of "anaplasia" and "de-differentiation" (proposed in the 1890s), and supposed "evolutionary themes" in cancer cell biology, little has been published concerning how histopathologic variation and immortality in tumour cells might arise. This paper reviews applications of the concepts of "variation" to tumours, including concepts of "evolution" and "cellular Darwinism". It is proposed that combinations of somatic mutation, DNA replicative infidelity and aneuploidy may explain the variabilities in tumours, and provide immortality in occasional tumour cells. A possible model involves (i) an initial somatic mutation causing reduced replicative fidelity of DNA, which could be variable in intensity, and thus give rise to variations between cases; (ii) a phase of replicative infidelity of DNA causing daughter cells lines to develop various abnormalities to different degrees, and hence provide for variation between areas of the same tumour. As a last event (iii) occasional asymmetric chromosomal distributions (aneuploidy) might "refresh" the ability of a daughter cell to replicate DNA faithfully causing them to become immortal. Thus extensively mutant and variable, hyperploid, and occasionally immortal cells might arise.

Strain rate dependent calcite microfabric evolution - An experiment carried out by nature

NASA Astrophysics Data System (ADS)

Rogowitz, Anna; Grasemann, Bernhard; Huet, Benjamin; Habler, Gerlinde

2014-12-01

A flanking structure developed along a secondary shear zone in calcite marbles, on Syros (Cyclades, Greece), provides a natural laboratory for directly studying the effects of strain rate variations on calcite deformation at identical pressure and temperature conditions. The presence and rotation of a fracture during progressive deformation caused extreme variations in finite strain and strain rate, forming a localized ductile shear zone that shows different microstructures and textures. Textures and the degree of intracrystalline deformation were measured by electron backscattered diffraction. Marbles from the host rocks and the shear zone, which deformed at various strain rates, display crystal-preferred orientation, suggesting that the calcite preferentially deformed by intracrystalline-plastic deformation. Increasing strain rate results in a switch from subgrain rotation to bulging recrystallization in the dislocation-creep regime. With increasing strain rate, we observe in fine-grained (3 μm) ultramylonitic zones a change in deformation regime from grain-size insensitive to grain-size sensitive. Paleowattmeter and the paleopiezometer suggest strain rates for the localized shear zone around 10-10 s-1 and for the marble host rock around 10-12 s-1. We conclude that varying natural strain rates can have a first-order effect on the microstructures and textures that developed under the same metamorphic conditions.

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.

The Effect of Cause of Death on Responses to the Bereaved: Suicide Compared to Accident and Natural Causes.

ERIC Educational Resources Information Center

Allen, Breon G.; And Others

1994-01-01

Examined impact of cause of death on responses to bereaved individual. Sixty adults listened to audiotape of recently bereaved widow. There were three versions of tape, each identical except for stated cause of death: suicide, accident, or heart attack. Found that respondents were more anxious after interaction than before. Perceptions of person…

Annual Variation in Flowering Phenology, Pollination, Mating System, and Pollen Yield in Two Natural Populations of Schima wallichii (DC.) Korth

PubMed Central

Khanduri, Vinod Prasad; Sharma, C. M.; Kumar, K. S.; Ghildiyal, S. K.

2013-01-01

Background. Schima wallichii is a highly valuable tree of tropical forest in north-east Himalaya region that grows naturally in a wide range of altitudes between 750 and 2400 m asl with varying environments. Flowering phenology of tropical tree species at population level is generally ignored and therefore a detailed knowledge of flowering and fruiting patterns of important multipurpose tree species is critical to the successful management of forest genetic resources. Materials and Methods. The study was conducted at two different altitudes (i.e., 750 m and 900 m asl) in the tropical semideciduous forest of north-east Himalaya. The floral phenology including flowering synchrony in the populations, anthesis, anther dehiscence, stigma receptivity, pollinators visitation frequency, and mating system including index of self-incompatibility were worked out in Schima wallichii according to the ear-marked standard methods given by various scientists for each parameter. Results. The flowering period in Schima wallichii varied from 33 to 42 days with mean synchrony of 0.54 to 0.68 between the populations. The stigma was receptive up to 2.5 days only and showed slightly protandrous type of dichogamy. Average pollen production ranged between 6.90 × 107 pollen per tree in 2007 and 15.49 × 108 pollen per tree in 2011. A three-year masting cycle was noticed in this species. The frequency of visitation of honey bees was fairly high (5.2 ± 1.12 visits/flower/hour) as compared to other pollinators. The hand pollination revealed maximum fruit (74.2 ± 5.72%) and seed (70.8 ± 7.46%) settings. Conclusions. The variation in flowering phenology and pollen yield individually and annually along with temporal separation in anther dehiscence and pollinator's visitation cause pollen limited reproduction, which ultimately influences the reproductive success in Schima wallichii. PMID:24501577

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.

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

What constitutes a nesting attempt? Variation in criteria causes bias and hinders comparisons across studies

USGS Publications Warehouse

Garcia, V.; Conway, C.J.

2009-01-01

Because reliable estimates of nesting success are very important to avian studies, the defnition of a “successful nest” and the use of different analytical methods to estimate success have received much attention. By contrast, variation in the criteria used to determine whether an occupied site that did not produce offspring contained a nesting attempt is a source of bias that has been largely ignored. This problem is especially severe in studies that deal with species whose nest contents are relatively inaccessible because observers cannot determine whether or not an egg was laid for a large proportion of occupied sites. Burrowing Owls (Athene cunicularia) often lay their eggs ≥3 m below ground, so past Burrowing Owl studies have used a variety of criteria to determine whether a nesting attempt was initiated. We searched the literature to document the extent of that variation and examined how that variation influenced estimates of daily nest survival. We found 13 different sets of criteria used by previous authors and applied each criterion to our data set of 1,300 occupied burrows. We found significant variation in estimates of daily nest survival depending on the criteria used. Moreover, differences in daily nest survival among populations were apparent using some sets of criteria but not others. These inconsistencies may lead to incorrect conclusions and invalidate comparisons of the productivity and relative site quality among populations. We encourage future authors working on cavity-, canopy-, or burrow-nesting birds to provide specific details on the criteria they used to identify a nesting attempt.

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

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power. PMID:26198076

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

A comprehensive review of the prevalence of beta globin gene variations and the co-inheritance of related gene variants in Saudi Arabians with beta-thalassemia

PubMed Central

Alaithan, Mousa A.; AbdulAzeez, Sayed; Borgio, J. Francis

2018-01-01

Beta-thalassemia is a genetic disorder that is caused by variations in the beta-hemoglobin (HBB) gene. Saudi Arabia is among the countries most affected by beta-thalassemia, and this is particularly problematic in the Eastern regions. This review article is an attempt to compile all the reported mutations to facilitate further national-level studies to prepare a Saudi repository of HBB gene variations. In Saudi Arabians, IVSI-5 (G>C) and Cd 39 (C>T) are the most prevalent HBB gene variations out of 42 variations. The coinheritance of HBB gene variations with ATRX, HBA1, HBA2, HBA12, AHSP, and KLF1 gene variations were observed to be common in the Saudi population. National surveys on the molecular nature of hemoglobinopathies should be set up through collaborations between research centers from various regions to create a well-documented molecular data bank. This data bank can be used to develop a premarital screening program and lead to the best treatment and prevention strategies for beta-thalassemia. PMID:29619482

Intraspecific variation in social organization by genetic variation, developmental plasticity, social flexibility or entirely extrinsic factors.

PubMed

Schradin, Carsten

2013-05-19

Previously, it was widely believed that each species has a specific social organization, but we know now that many species show intraspecific variation in their social organization. Four different processes can lead to intraspecific variation in social organization: (i) genetic variation between individuals owing to local adaptation (between populations) or evolutionarily stable strategies within populations; (ii) developmental plasticity evolved in long-term (more than one generation) unpredictable and short-term (one generation) predictable environments, which is mediated by organizational physiological effects during early ontogeny; (iii) social flexibility evolved in highly unpredictable environments, which is mediated by activational physiological effects in adults; (iv) entirely extrinsic factors such as the death of a dominant breeder. Variation in social behaviour occurs between individuals in the case of genetic variation and developmental plasticity, but within individuals in the case of social flexibility. It is important to study intraspecific variation in social organization to understand the social systems of species because it reveals the mechanisms by which species can adapt to changing environments, offers a useful tool to study the ultimate and proximate causes of sociality, and is an interesting phenomenon by itself that needs scientific explanation.

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