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

Macrophage population state and proliferative activity of spleen cells under liver regeneration conditions

Relevance. Currently, the participation of immune system cells in the regulation of reparative processes is attracting more and more attention of researchers. There is an anatomical connection between the liver and spleen by means of portal vein. Thus, cytokines and other biologically active substances can enter the liver from the spleen through the portal vein, as well as cells can migrate to the liver. However, the specific mechanisms of mutual influence of the mentioned organs, including in reparative processes, remain poorly studied. The aim of our work was to study the state of spleen monocyte-macrophage population after liver resection, as well as the proliferative activity of spleen cells during liver regeneration . Materials and Methods . The model of liver regeneration after 70 % resection in mouse was reproduced in this work. The animals were taken out of the experiment after 1, 3 and 7 days. The marker of cell proliferation Ki67 was immunohistochemically detected, the state of spleen monocyte-macrophage population was evaluated by markers CD68, CD115, CD206, F4/80 by methods of immunohistochemistry and flow cytometry. Results and Discussion . The liver regeneration had a pronounced effect on the cytoarchitectonics of the spleen. In 1 day after liver resection in the spleen there was observed a decrease in the share of Ki67+cells, according to the flow cytometry data there was a decrease in the number of CD115+cells, in 3 and 7 days there was a decrease in the number of F4/80+ macrophages. Conclusion . Liver resection causes changes in the state of cell populations of the spleen as well. First of all, to the decrease in the activity of proliferative processes in it, as well as to the changes in the state of the monocyte-macrophage system. A decrease in the content of CD115+ and F4/80+ cells in the spleen was found, which indirectly indicates the migration of monocytes/macrophages after liver resection, which can also influence the course of reparative processes in the liver

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

On the nature of citrate-derived surface species on Ag nanoparticles: insights from X-ray photoelectron spectroscopy

Citrate is an important stabilizing, reducing, and complexing reagent in the wet chemical synthesis of nanoparticles of silver and other metals, however, the exact nature of adsorbates, and its mechanism of action are still uncertain. Here, we applied X-ray photoelectron spectroscopy, soft X-ray absorption near-edge spectroscopy, and other techniques in order to determine the surface composition and to specify the citrate-related species at Ag nanoparticles 3 immobilized from the dense hydrosol prepared using room-temperature reduction of aqueous Ag+ ions with ferrous ions and citrate as stabilizer (Carey Lea method). It was found that, contrary to the common view, the species adsorbed on the Ag nanoparticles are, in large part, products of citrate decomposition comprising an alcohol group and one or two carboxylate bound to the surface Ag, and minor unbound carboxylate group; these may also be mixtures of citrate with lower molecular weight anions. No ketone groups were specified, and very minor surface Ag(I) and Fe (mainly, ferric oxyhydroxides) species were detected. Moreover, the adsorbates were different at AgNPs having various size and shape. The relation between the capping and the particle growth, colloidal stability of the high-concentration sol and properties of AgNPs is briefly considered

On the nature of citrate-derived surface species on Ag nanoparticles: insights from X-ray photoelectron spectroscopy

Citrate is an important stabilizing, reducing, and complexing reagent in the wet chemical synthesis of nanoparticles of silver and other metals, however, the exact nature of adsorbates, and its mechanism of action are still uncertain. Here, we applied X-ray photoelectron spectroscopy, soft X-ray absorption near-edge spectroscopy, and other techniques in order to determine the surface composition and to specify the citrate-related species at Ag nanoparticles 3 immobilized from the dense hydrosol prepared using room-temperature reduction of aqueous Ag+ ions with ferrous ions and citrate as stabilizer (Carey Lea method). It was found that, contrary to the common view, the species adsorbed on the Ag nanoparticles are, in large part, products of citrate decomposition comprising an alcohol group and one or two carboxylate bound to the surface Ag, and minor unbound carboxylate group; these may also be mixtures of citrate with lower molecular weight anions. No ketone groups were specified, and very minor surface Ag(I) and Fe (mainly, ferric oxyhydroxides) species were detected. Moreover, the adsorbates were different at AgNPs having various size and shape. The relation between the capping and the particle growth, colloidal stability of the high-concentration sol and properties of AgNPs is briefly considered

Silver Nanoparticles Formation by Glucose Reduction in Aqueous Solutions

В статье рассматривается простой метод получения в водных растворах наночастиц серебра, которые могут использоваться в качестве зародышей при синтезе несферических наночастиц и композитов на основе серебра. Процесс является экологически безопасным и представляет собой восстановление нитрата серебра глюкозой при микроволновой обработке. Изучено влияние таких условий протекания реакции, как природа восстановителя (глюкоза, аскорбиновая кислота или их смесь), начальная концентрация глюкозы и нитрата серебра, рН, время реакции, найдены оптимальные параметры синтеза. Полученные частицы охарактеризованы методами оптической спектроскопии, просвечивающей электронной микроскопии, атомно-силовой микроскопии и рентгеновской фотоэлектронной спектроскопии.This article describes a facile, solution-based preparation of stable uniform nanoparticles of silver, which can be used as seeds for the synthesis of non-spherical nanoparticles and composite structures. The environment-friendly procedure involves the reduction of aqueous AgNO3 with glucose under microwave irradiation. The effects of a reducing-agent nature (glucose, ascorbic acid, or their mixtures), initial concentrations of glucose and AgNO3, pH, time of reaction have been investigated, and optimal synthesis conditions have been found. The products obtained were characterized by UV-viz absorption spectroscopy, transmission electron microscopy (TEM), atomic-force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS)

Silver Nanoparticles Formation by Glucose Reduction in Aqueous Solutions

В статье рассматривается простой метод получения в водных растворах наночастиц серебра, которые могут использоваться в качестве зародышей при синтезе несферических наночастиц и композитов на основе серебра. Процесс является экологически безопасным и представляет собой восстановление нитрата серебра глюкозой при микроволновой обработке. Изучено влияние таких условий протекания реакции, как природа восстановителя (глюкоза, аскорбиновая кислота или их смесь), начальная концентрация глюкозы и нитрата серебра, рН, время реакции, найдены оптимальные параметры синтеза. Полученные частицы охарактеризованы методами оптической спектроскопии, просвечивающей электронной микроскопии, атомно-силовой микроскопии и рентгеновской фотоэлектронной спектроскопии.This article describes a facile, solution-based preparation of stable uniform nanoparticles of silver, which can be used as seeds for the synthesis of non-spherical nanoparticles and composite structures. The environment-friendly procedure involves the reduction of aqueous AgNO3 with glucose under microwave irradiation. The effects of a reducing-agent nature (glucose, ascorbic acid, or their mixtures), initial concentrations of glucose and AgNO3, pH, time of reaction have been investigated, and optimal synthesis conditions have been found. The products obtained were characterized by UV-viz absorption spectroscopy, transmission electron microscopy (TEM), atomic-force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS)

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

Preparation of Composite Materials with Antibacterial Properties Based on Ultra-High Molecular Weight Polyethylene

Изучено влияние способа введения серебра в сверхвысокомолекулярный полиэтилен (СВМПЭ) на состояние серебра, морфологию композита, его антимикробную активность и механические свойства с использованием растровой электронной микроскопии, рентгеновской фотоэлектронной спектроскопии. Бактерицидная активность относительно E. Coli оценена для ряда коллоидных растворов наночастиц и растворов солей серебра, порошка СВМПЭ после нанесения на него металлов и пластин, полученных при высокотемпературном прессовании порошка. Активность зависит от природы раствора металла и обычно снижается после прессования. Наибольшим антимикробным действием обладают компактные образцы с достаточной пористостью, пропитанные водно-спиртовым раствором нитрата серебра после формования; серебро в них находится преимущественно в металлической форме в области микрометровых пор. Истираемость такого композита примерно вдвое выше, чем непористых образцов, в том числе полученных прессованием порошков с нанесенными металламиIncorporation of nanosilver in ultrahigh molecular weight polyethylene (UHMWPE) matrix, and the morphology, state of silver, antimicrobial activity and wearing of the composite materials produced have been studied employing scanning electron microscopy and X-ray photoelectron spectroscopy. Antibacterial activity of a series of Ag nanoparticle hydrosols and aqueous solutions of salts, UHMWPE powders with deposited metal and composites prepared by pressure molding of the powders or impregnation of porous compact polymer were tested against E. Coli. The activity, which depends upon the nature of the metal solution, commonly decreased after the molding. The composites with high activity were obtained by impregnation of porous enough UHMWPE compacts with aqueous – ethanol solution of AgNO3, which contain preferentially elemental silver in micrometer scale voids. The wearability of the composite material is only two times lower than that of compact UHMWPE and the samples prepared using metal impregnated polymer granule