Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum

<p>Abstract</p> <p>Background</p> <p>The pea aphid, <it>Acyrthosiphon pisum</it>, is an emerging genomic model system for studies of polyphenisms, bacterial symbioses, host-plant specialization, and the vectoring of plant viruses. Here we provide estimates of nucleotide diversity and linkage disequilibrium (LD) in native (European) and introduced (United States) populations of the pea aphid. Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations.</p> <p>Results</p> <p>We sampled four non-coding loci from 24 unique aphid clones from the U. S. (12 from New York and 12 from California) and 24 clones from Europe (12 alfalfa and 12 clover specialists). For each locus, we sequenced approximately 1 kb from two amplicons spaced ~10 kb apart to estimate both short range and longer range LD. We sequenced over 250 kb in total. Nucleotide diversity averaged 0.6% across all loci and all populations. LD decayed slowly within ~1 kb but reached much lower levels over ~10 kb. Contrary to our expectations, neither LD nor nucleotide diversity were significantly different between native and introduced populations.</p> <p>Conclusion</p> <p>Both introduced and native populations of pea aphids exhibit low levels of nucleotide diversity and moderate levels of LD. The introduction of pea aphids to North America has not led to a detectable reduction of nucleotide diversity or increase in LD relative to native populations.</p

Laser annealing of metal nanoparticles implanted in dielectrics

The interaction of excimer laser pulses with silica consisting ion-synthesized copper nanoparticles is studied. Using optical reflectance of composite layers it is established that at the initial stage laser annealing leads to the fragmentation of the nanoparticles to smaller ones. After continuous irradiation by several pulses, the nanoparticles become larger due to the heating of the surrounding glass. The laser treatment for a longer time (more than several tens pulses) results in the dissociation of nanoparticles into small clusters and individual atoms. The mechanisms responsible for the modification of the composite material under high power laser radiation are discussed. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE)

A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants

The impact of deleterious variation on both plant fitness and crop productivity is not completely understood and is a hot topic of debates. The deleterious mutations in plants have been solely predicted using sequence conservation methods rather than function-based classifiers due to lack of well-annotated mutational datasets in these organisms. Here, we developed a machine learning classifier based on a dataset of deleterious and neutral mutations in Arabidopsis thaliana by extracting 18 informative features that discriminate deleterious mutations from neutral, including 9 novel features not used in previous studies. We examined linear SVM, Gaussian SVM, and Random Forest classifiers, with the latter performing best. Random Forest classifiers exhibited a markedly higher accuracy than the popular PolyPhen-2 tool in the Arabidopsis dataset. Additionally, we tested whether the Random Forest, trained on the Arabidopsis dataset, accurately predicts deleterious mutations in Orýza sativa and Pisum sativum and observed satisfactory levels of performance accuracy (87% and 93%, respectively) higher than obtained by the PolyPhen-2. Application of Transfer learning in classifiers did not improve their performance. To additionally test the performance of the Random Forest classifier across different angiosperm species, we applied it to annotate deleterious mutations in Cicer arietinum and validated them using population frequency data. Overall, we devised a classifier with the potential to improve the annotation of putative functional mutations in QTL and GWAS hit regions, as well as for the evolutionary analysis of proliferation of deleterious mutations during plant domestication; thus optimizing breeding improvement and development of new cultivars

New approach to the synthesis of porous silicon with silver nanoparticles using ion implantation technique

A new technique for the synthesis of porous silicon layers with silver nanoparticles has been proposed which is based on the high-dose low-energy implantation of crystalline silicon with metal ions. In order to demonstrate this technique, in this work we implanted a polished wafer of monocrystalline silicon Ag+-ions with an energy of 30 keV at a dose of 1.5 × 1017 ion/cm2 and a current density in the ion beam of 4 μA/cm2. Using high-resolution scanning electron and atomic force microscopy, as well as X-ray spectral microprobe analysis and Raman scattering, it is shown that an amorphous layer of a porous silicon is formed at the surface of silicon as a result of implantation with average sizes of pore holes on the order of 150-180 nm; depth of about 100 nm; and thickness of the walls of 30-60 nm, in whose structure silver nanoparticles are located with a diameter of 5-10 nm. In addition, it is shown that the formation of pores by implantation with silver ions is accompanied by sputtering the surface of silicon. © 2014 Pleiades Publishing, Ltd

New way for synthesis of porous silicon using ion implantation

A novel idea to create a porous silicon layers by low-energy high-dose metal-ion implantation was realized. To demonstrate a possibility for this technique Ag-ion implantation into monocrystalline silicone substrate was provided. Silicon plates were implanted at energy 30 keV with doses of 7.5 × 1016 - 1.5 × 1017 ion/cm2 at room temperature. Surface porous structures were analyzed by scanning electron microscope images and energy-dispersive X-ray data. It is shown that the average sizes of porous are increasing approximately from 70 to 120 μm with an increasing of ion doses. The formation of silver nanoparticles inside porous silicon walls was also observed. Novel developed technology based on ion implantation is suggested to give a new way for using of porous layer structures combined with the silicon matrix for various applications

Identification of co-regulated transcripts affecting male body size in Drosophila

Factor analysis is an analytic approach that describes the covariation among a set of genes through the estimation of 'factors', which may be, for example, transcription factors, microRNAs (miRNAs), and so on, by which the genes are co-regulated. Factor analysis gives a direct mechanism by which to relate gene networks to complex traits. Using simulated data, we found that factor analysis clearly identifies the number and structure of factors and outperforms hierarchical cluster analysis. Noise genes, genes that are not correlated with any factor, can be distinguished even when factor structure is complex. Applied to body size in Drosophila simulans, an evolutionarily important complex trait, a factor was directly associated with body size

Copper nanoparticles synthesized in polymers by ion implantation: Surface morphology and optical properties of the nanocomposites

Copyright © Materials Research Society 2014. Polymethylmethacrylate (PMMA) and polyimide (PI) samples are implanted by 40 keV Cu+ ions with high fluences to synthesize copper nanoparticles in shallow polymer layers. The produced metal/polymer nanocomposites are studied using atomic force and scanning electron microscopies as well as optical transmission spectroscopy. It is found that nucleation and growth of copper nanoparticles are strongly fluence-dependent as well as they are affected by the polymer properties, in particular, by radiation stability yielding different nanostructures for the implanted PI and PMMA. Shallow synthesized nanoparticles are observed to partly tower above the sample surface due to a side effect of high-fluence irradiation leading to considerable sputtering of polymers. Implantation and particle formation significantly change optical properties of both polymers reducing transmittance in the UV-visible range due to structural and compositional change as well as causing an absorption band related to localized surface plasmon resonance (LSPR) of the nanoparticles. The role of polymer type and its degradation under the implantation on LSPR is studied to optimize conditions for the formation of nanoplasmonic materials

Copper nanoparticles synthesized in polymers by ion implantation: Surface morphology and optical properties of the nanocomposites

© Materials Research Society 2015. Polymethylmethacrylate (PMMA) and polyimide (PI) samples are implanted by 40 keV Cu+ ions with high fluences to synthesize copper nanoparticles in shallow polymer layers. The produced metal/polymer nanocomposites are studied using atomic force and scanning electron microscopies as well as optical transmission spectroscopy. It is found that nucleation and growth of copper nanoparticles are strongly fluence-dependent as well as they are affected by the polymer properties, in particular, by radiation stability yielding different nanostructures for the implanted PI and PMMA. Shallow synthesized nanoparticles are observed to partly tower above the sample surface due to a side effect of high-fluence irradiation leading to considerable sputtering of polymers. Implantation and particle formation significantly change optical properties of both polymers reducing transmittance in the UV-visible range due to structural and compositional change as well as causing an absorption band related to localized surface plasmon resonance (LSPR) of the nanoparticles. The role of polymer type and its degradation under the implantation on LSPR is studied to optimize conditions for the formation of nanoplasmonic materials

Specificity of silver nanoparticle synthesis in quartz glass upon low-energy ion implantation

Silica-based composite materials with silver nanoparticles (NPs) were studied. Synthesis of the NPs was carried out using a low-energy (30 keV) implantation of Ag + ions to high fluences. After the implantation, the samples were thermally annealed at 300°C for 1 hour in argon atmosphere. Synthesized NPs demonstrated an absorption band related to surface plasmon resonance (SPR). Shift of the SPR maximum towards longer wavelengths was found with an increase of ion fluence. This shift correlates with an enlargement of the hemispherical protrusions observed on the sample surface using atomic force microscopy. The obtained results were interpreted as increase of the NPs in size. It was shown that the post-implantation thermal annealing leads to change of size of the NPs thus allowing to develop a technological approach for controlled synthesis of NPs in shallow dielectric layers. © 2011 Pleiades Publishing, Ltd

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy