Single Track Performance of the Inner Detector New Track Reconstruction (NEWT)

In a previous series of documents we have presented the new ATLAS track reconstruction chain (NEWT) and several of the involved components. It has become the default reconstruction application for the Inner Detector. However, a large scale validation of the reconstruction performance in both efficiency and track resolutions has not been given yet. This documents presents the results of a systematic single track validation of the new track reconstruction and puts it in comparison with results obtained with different reconstruction applications

Nonlocal resistance and its fluctuations in microstructures of band-inverted HgTe/(Hg,Cd)Te quantum wells

We investigate experimentally transport in gated microsctructures containing a band-inverted HgTe/Hg_{0.3}Cd_{0.7}Te quantum well. Measurements of nonlocal resistances using many contacts prove that in the depletion regime the current is carried by the edge channels, as expected for a two-dimensional topological insulator. However, high and non-quantized values of channel resistances show that the topological protection length (i.e. the distance on which the carriers in helical edge channels propagate without backscattering) is much shorter than the channel length, which is ~100 micrometers. The weak temperature dependence of the resistance and the presence of temperature dependent reproducible quasi-periodic resistance fluctuations can be qualitatively explained by the presence of charge puddles in the well, to which the electrons from the edge channels are tunnel-coupled.Comment: 8 pages, 4 figures, published versio

Cytoplasmic male sterility and prospects for its utilization in breeding, genetic studies and seed production of potato

Increasing interest to cytoplasmic male sterility (CMS) and searching for restoration of pollen fertility (Rf) genes in potato is determined by a new way in the modern breeding of this important crop, the development of heterotic hybrids obtained after crosses of inbred diploid lines. The paper reviews the main results of studies on CMS-Rf genetic systems in different species of cultivated plants, the modern methods and approaches of investigating molecular mechanisms of CMS and pollen fertility restoration, and also the available literature data on the status of these studies in potato. The nature of chimeric mitochondrial genes accounting for cytoplasmic male sterility is considered; the peculiarities of the structure and functions of restoration of pollen fertility genes are discussed; examples of CMS-Rf genetic systems in cultivated plant species including representatives of the family Solanaceae are presented. The main results of research on molecular mechanisms of CMS and fertility restoration obtained in the post-genomic era for various plant species using methods of transcriptomic and proteomic analyses are provided. As in many plant species, cytoplasmic male sterility in potato is of hybrid origin. The results of investigating genetic control of male sterility in potato are presented that have been carried out using conventional approaches (hybridological analysis) and led to the formation of the concept of genic cytoplasmic male sterility in some species of section Petota of the genus Solanum. The characteristics of potato cytoplasms types which are associated with male sterility are given. According to classification of Hosaka, Sanetomo (2012), these types include: T/beta, W/gamma and D, each distinguished by the phenotypic appearance of male sterility traits and also by the frequency of occurrence in the breeding varieties gene pool and in various potato species. The results of studies on developing DNA markers for identification of various potato cytoplasm types are presented

Interspecific hybridization of potato: theoretical and applied aspects

The common potato Solanum tuberosum is the fourth most important crop in the world and like many other cultivated plants is characterized by low level of genetic diversity. The most effective approach to broaden genetic diversity of breeding varieties is based on the introgression of genetic material of wild and cultivated species belonging to section Petota Dumort. of the genus Solanum L. This section, according to estimates by different taxonomists, includes from 112 to 235 species. At the same time, because of the barriers of prezygotic and postzygotic incompatibility, only about 10 % of wild potato species have been actively involved into the breeding process and their genetic material has been introgressed into the gene pool of varieties. To date, molecular genetics, genomics, and biotechnology have accumulated a large amount of information, allowing the problems of extension of the genetic diversity of common potato to be addressed. The article presents a review of modern data about the genetic factors determining prezygotic and postzygotic incompatibility, about the features of involvement in the hybridization process of the self-compatible and self-incompatible species of section Petota and species with different values of the endosperm balance number (EBN), as well as possible mechanisms of interaction between the parental genomes during the formation of the endosperm of the hybrid seed. Data are provided on the value of the theory of EBN for the further development of applied research aimed at increasing the genetic diversity of the breeding gene pool. This review discusses the traditional and modern approaches and methods of overcoming interspecific incompatibility and gives examples of successful studies on introgressive hybridization of potato. The article is preceded by information about the genetic diversity of potato species belonging to section Petota of the genus Solanum

Nomenclatural standards of modern Russian potato cultivars preserved at the VIR herbarium (WIR): A new approach to cultivar genepool registration in a genebank

VIR is creating a collection of nomenclature standards for cultivars of different crops in line with the provisions of the International Code of Nomenclature for Cultivated Plants (ICNCP). The nomenclatural standards are designed in the form of a herbarium sample in cooperation with the authors of cultivars, who select plant material for each cultivar in the experimental field of their organization and forward it to the scientific herbarium together with the accompanying documents. Registering of herbarium specimen in the scientific herbarium is followed by the publication of nomenclatural standards. The article presents a new VIR genebank strategy for registering plant material of domestic cultivars received from breeders, which includes the design of nomenclatural standards; the development of a genetic passport of a cultivar using DNA samples from the plant delivered to the scientific herbarium; and application of biotechnological methods for keeping explants (isolated from the acquired plant material as buds or meristems) alive. The proposed integrated approach makes it possible to document cultivars not only with the help of nomenclatural standards, but also with the use of molecular-genetic methods, as well as to save genotyped specimens, transferred to herbarium, in in vitro and in cryo collections. This approach is applicable to any vegetatively propagated crop. The article summarizes the first results of our proposed strategy using modern domestic potato cultivars as an example. Collection, transfer and preparation of plant material for nomenclatural standards of potato varieties are specific; this article explains our protocol for this work. The implementation of this strategy in 2018-2020 led to the designation of nomenclatural standards for 66 Russian potato varieties and elaboration of their genetic passports, which are presented in a series of articles included into issues Nos.3 and 4, Volume 3, of the journal “Plant Biotechnology and Breeding”, containing an overview of methodological approaches to registration of modern domestic cultivars in the VIR collection. DNA samples obtained from the plant material provided by the cultivar authors for nomenclatural standard designation will continue to be used as a source of information on the genetic potential of a cultivar through the expansion of the list of DNA markers and the application of new genetic technologies

ОПРЕДЕЛЕНИЕ СИНТЕТИЧЕСКИХ КРАСИТЕЛЕЙ Е102, Е110, Е124, Е131 В ЙОГУРТЕ МЕТОДОМ ТВЕРДОФАЗНОЙ СПЕКТРОФОТОМЕТРИИ

Tartrazine E102, Yellow "Sunset" E110, Ponso 4R E124 and the Patented Blue E131 food synthetic dyes solid-phase extraction from yoghurts and biokefirs in a transparent polymethylmethacrylate matrix as a solid extractant was studied. The analytical signal was formed due to the accumulation of the dye in the volume of the polymer matrix without violating the transparency, and this corresponded to the wavelength of the maximum absorption of the corresponding dye. The sorption mechanism was based on the protonization of the carbonyl groups of PMM in the acidic media, and, as a result, the optode surface became positively charged. Therefore, the sorption of the R± form of the E131 dye and the azo dye anions occurred by the positively charged PMM surface. The effectiveness of the proposed approach was shown for the identification and determination of the 2 food-grade synthetic dyes content using the visual and spectrophotometric methods. The optimal conditions for the analysis corresponded to pH 3, the duration of dye extraction into the polymer matrix was 20 min, the range of the detected concentrations was 0.2–40.0  mg / kg with the detection limit of 0.05 mg/kg, and an excess of sweeteners and preservatives did not significantly affect the results of the analysis. The results of the determination of the listed dyes were demonstrated in the current work for the case of individual and group presence of dyes in biokefirs and yogurts. The proposed technique is simple in execution and could be carried out using the standard spectrophotometric equipment. The advantage of the developed method for the determination of artificial dyes in comparison with the method of spectrophotometric determination with liquid extraction is a significant increase in the sensitivity of determination due to the accumulation of analyte, the exclusion of turbidity of an aliquot and the absence of dye loss due to its transition into the supernatant, and then into the solid phase of the matrix.Keywords: colorimetric sensor, solid-phase spectrophotometry, polymethylmethacrylate matrix, synthetic food colorant, dairy productDOI: http://dx.doi.org/10.15826/analitika.2020.24.1.002  A.A. Dudkina1, N.V. Saranchina1, T.N. Volgina1, N.A. Gavrilenko2, M.A. Gavrilenko11Tomsk Polytechnic University, 30 Lenin Ave, Tomsk, 634050, Russian Federation2Tomsk State University, 36 Lenin Ave, Tomsk, 634050, Russian FederationИзучена твердофазная экстракция пищевых синтетических красителей тартразин Е102, желтый «солнечный закат» Е110, понсо 4R Е124 и патентованный синий Е131 из йогуртов и биокефиров в прозрачную полиметилметакрилатную матрицу в качестве твердого экстрагента. Аналитический сигнал формируется вследствие накопления красителя в объеме полимерной матрицы без нарушения прозрачности и соответствует длине волны максимума поглощения соответствующего красителя. Механизм сорбции основан на том, что в кислых средах карбонильные группы ПММ способны подвергаться протонизации, за счет этого поверхность оптода становится положительно заряженной. Таким образом, происходит сорбция R± формы красителя Е131 и  анионов азокрасителей положительно заряженной поверхностью ПММ. Показана эффективность предложенного подхода для идентификации и определения содержания двух пищевых синтетических красителей визуальным и спектрофотометрическим методом. Найдены оптимальные условия проведения анализа: рН 3, продолжительность экстракции красителей в полимерную матрицу 20 минут, диапазон определяемых концентраций 0.2–40.0 мг/кг с пределом обнаружения 0.05 мг/кг, избыток подсластителей и консервантов не оказывает существенного влияния на результаты анализа. Приведены результаты определения перечисленных красителей, в том числе при их совместном присутствии в образцах биокефиров и йогуртов. Методика осуществляется на спектрофотометрическом оборудовании, либо простой полуколичественной визуальной оценкой. Преимуществом разработанной методики определения искусственных красителей по сравнению с методом спектрофотометрического определения с жидкостной экстракцией является значительное повышение чувствительности определения вследствие накопления аналита и исключения мутности аликвоты, а также отсутствие потерь красителя вследствие его перехода в надосадочную жидкость и, затем, в твердую фазу матрицы.Ключевые слова: колориметрический сенсор, твердофазная спектрофотометрия, полиметилметакрилатная матрица, синтетический пищевой краситель, молочный продуктDOI: http://dx.doi.org/10.15826/analitika.2020.24.1.00

Ab initio optical properties of Si(100)

We compute the linear optical properties of different reconstructions of the clean and hydrogenated Si(100) surface within DFT-LDA, using norm-conserving pseudopotentials. The equilibrium atomic geometries of the surfaces, determined from self-consistent total energy calculations within the Car-Parrinello scheme, strongly influence Reflectance Anisotropy Spectra (RAS), showing differences between the p(2x2) and c(4x2)reconstructions. The Differential Reflectivity spectrum for the c(4x2) reconstruction shows a positive peak at energies < 1 eV, in agreement with experimental results.Comment: fig. 2 correcte

Long-term preservation of modern Russian potato cultivars in the VIR cryobank

Cryopreservation of shoot-tips (apexes) excised from in vitro plants is used for long-term preservation of potato cultivars. The most widely used method for creating potato cryo-collections is droplet-vitrification of shoot-tips which, together with its numerous modifications, is widely used in genebanks. A modified protocol of droplet vitrification method is used at VIR for cryopreservation of shoot tips from in vitro potato plants. This paper presents the results of cryopreservation of modern cultivars which were released by seven Russian breeding centers. In vitro clones used in the cryopreservation experiments were genetically identical to the cultivars’ nomenclatural standards and herbarium vouchers.The frequency of post-thaw regeneration in control experiments after short-term cryopreservation varied from 23.3 to 53.3%, depending on the genotype. Five out of 16 accessions (‘Varâg’, ‘Gusar’, ‘Evpatij’, ‘Solnečnyj’, ‘Tango’)* had low post-cryogenic regenerative capacity from 20 to 30%; the regeneration rate exceeded 30% in 11 accessions, and 8 cultivars (‘Grand’, ‘Zlatka’, ‘Lina’, ‘Safo’, ‘Siverskij’, ‘Signal’, ‘Utro’, ‘Ûna’) and ‘Аlyj Parus’ breeding clone had regeneration rate above 40%. The regeneration rate in the studied subset was genotype independent according to the ANOVA results (p=0.711). Viability and regeneration rate were significantly correlated (r=0.86). As a result of the experiments, explants of 14 modern cultivars and two breeding clones with the known post-thaw regeneration rate were successfully cryopreserved in the VIR cryobank. Four cultivars (‘Grand’, ‘Gusar’, ‘Signal’, ‘Utro’) were monitored for their regeneration capacity after the long-term (seven months) preservation in the VIR cryobank. On an average, these four cultivars demonstrated a post-thaw regeneration capacity of 41.8%. It can be concluded that the use of the modified method of droplet vitrification is relevant for increasing the VIR potato cryo-collection