Variability of Microbiota under Diverse Conditions of Soil Moistening

Special study on microbiota in hydromorphic soils, which are formed with the participation of natural groundwater. А comparative assessment of the seasonal dynamics of the microbial numbers in communities under conditions of soil irrigation and formation of hydromorphic soils outside the irrigation system

Systematics and biology of some species of Micrurapteryx Spuler (Lepidoptera, Gracillariidae) from the Holarctic Region, with re-description of M. caraganella (Hering) from Siberia

During a DNA barcoding campaign of leaf-mining insects from Siberia, a genetically divergent lineage of a gracillariid belonging to the genus Micrurapteryx was discovered, whose larvae developed on Caragana Fabr. and Medicago L. (Fabaceae). Specimens from Siberia showed similar external morphology to the Palearctic Micrurapteryx gradatella and the Nearctic Parectopa occulta but differed in male genitalia, DNA barcodes, and nuclear genes histone H3 and 28S. Members of this lineage are re-described here as Micrurapteryx caraganella (Hering, 1957), comb. n., an available name published with only a brief description of its larva and leaf mine. Micrurapteryx caraganella is widely distributed throughout Siberia, from Tyumen oblast in the West to Transbaikalia in the East. Occasionally it may severely affect its main host, Caragana arborescens Lam. This species has been confused in the past with Micrurapreryx gradatella in Siberia, but field observations confirm that M. gradatella exists in Siberia and is sympatric with M. caraganella, at least in the Krasnoyarsk region, where it feeds on different host plants (Vicia amoena Fisch. and Vicia sp.). In addition, based on both morphological and molecular evidence as well as examination of type specimens, the North American Parectopa occulta Braun, 1922 and Parectopa albicostella Braun, 1925 are transferred to Micrurapteryx as M. occulta (Braun, 1922), comb. n. with albicostella as its junior synonym (syn. n.). Characters used to distinguish Micrurapteryx from Parectopa are presented and illustrated. These findings provide another example of the potential of DNA barcoding to reveal overlooked species and illuminate nomenclatural problems

Evolution of an Unconventional Superconducting State inside the Antiferromagnetic Phase of CeNiGe3_3 under Pressure: a 73^{73}Ge-Nuclear-Quadrupole-Resonance Study

We report a $^{73}$Ge nuclear-quadrupole-resonance (NQR) study on novel evolution of unconventional superconductivity in antiferromagnetic (AFM) CeNiGe$_3$. The measurements of the $^{73}$Ge-NQR spectrum and the nuclear spin-lattice relaxation rate ($1/T_1$) have revealed that the unconventional superconductivity evolves inside a commensurate AFM phase around the pressure ($P$) where N\'{e}el temperature $T_{\rm N}$ exhibits its maximum at 8.5 K. The superconducting transition temperature $T_{\rm SC}$ has been found to be enhanced with increasing $T_{\rm N}$, before reaching the quantum critical point at which the AFM order collapses. Above $T_{\rm SC}$, the AFM structure transits from an incommensurate spin-density-wave order to a commensurate AFM order at $T\sim 2$ K, accompanied by a longitudinal spin-density fluctuation. With regard to heavy-fermion compounds, these novel phenomena have hitherto never been reported in the $P$-$T$ phase diagram.Comment: 4 pages, 5 figure

Natural Diagonal Riemannian Almost Product and Para-Hermitian Cotangent Bundles

We obtain the natural diagonal almost product and locally product structures on the total space of the cotangent bundle of a Riemannian manifold. We find the Riemannian almost product (locally product) and the (almost) para-Hermitian cotangent bundles of natural diagonal lift type. We prove the characterization theorem for the natural diagonal (almost) para-K\"ahlerian structures on the total spaces of the cotangent bundle.Comment: 10 pages, will appear in Czechoslovak Mathematical Journa

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations

Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08 x 10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases

Шкала оценки сопутствующих заболеваний у ареактивных пациентов (CoCoS): лингвокультурная адаптация русскоязычной версии (сообщение)

   Identification of complications and control of comorbidities are essential in monitoring the patients with chronic disorders of consciousness and predicting their outcomes. The researchers of the Department of Biotechnological and Applied Clinical Sciences of the University of L'Aquila (Italy) developed the Comorbidities Coma Scale (CoCoS) for a comprehensive assessment of such patients. Lack of an officially validated version of the scale hampers its use in Russia, while using versions which have not been completely validated prevents clinicians from obtaining reliable results when examining patients with chronic disorders of consciousness.   Aim. To develop the official Russian language version of the Comorbidities Coma Scale, considering various linguistic and cultural parameters, as a part of the 1st stage of the validation study.   Material and methods. The first stage of validation was completed: direct and reverse translation of the scale was performed by two independent medical translators. The translated version was assessed by an expert board including an expert translator, neurologists, and critical care specialists. Pilot test and two meetings of the expert board, before and after testing, were arranged to assess the results and approve the final Russian version of the scale.   Results. During the first meeting of the expert board, corrections were made in the Russian language version of the scale in terms of language and cultural adaptation. Pilot testing was carried out based on the inclusion and exclusion criteria. The researchers had no difficulties in understanding and interpreting the instructions for the scale. The second meeting of the expert board was held thereupon, and the final version of the Russian language version of the scale was adopted, which is available on the website of the Center for Validation of Health Status Questionnaires and Scales of the Research Center of Neurology.   Conclusion. The first stage of validation, i. e., linguistic and cultural adaptation, was carried out at the Research Center of Neurology (Moscow, Russia). For the first time, the Russian version of the scale for assessing comorbidities in patients with chronic disorders of consciousness was presented and approved for the practical use. The future publications will address the psychometric results of the scale such as sensitivity, validity, reliability.   Выявление осложнений и контроль над течением сопутствующих заболеваний является важнейшим этапом в отслеживании динамики и прогнозе исходов у пациентов с хроническими нарушениями сознания. Для проведения оценки состояния у данной категории пациентов сотрудниками департамента биотехнологических и прикладных клинических наук университета L'Aquila (Италия) была разработана шкала — Comorbidities Coma Scale (CoCoS). Отсутствие официально валидированной версии данной шкалы затрудняет ее применение в России, а использование версий, не прошедших все необходимые этапы валидации, препятствует получению достоверных результатов при обследовании пациентов с хроническими нарушениями сознания.   Цель. Разработка официальной русскоязычной версии Шкалы оценки сопутствующих заболеваний у ареактивных пациентов с учетом языковых и культурных особенностей ее пользователей в рамках проведения 1-го этапа валидационного исследования.   Материал и методы. Письменное разрешение на адаптацию шкалы CoCoS было получено сотрудниками группы валидации международных шкал и опросников Научного центра неврологии (ФГБНУ НЦН, г. Москва, Россия) у разработчика оригинальной версии Francesca Pistoia. Провели первый этап валидации: выполнен прямой и обратный перевод шкалы двумя независимыми медицинскими переводчиками. Произведена оценка разработанной версии экспертной комиссией с участием переводчика-эксперта, неврологов и анестезиологов-реаниматологов. Провели пилотное тестирование на 15 пациентах с диагнозом хронического нарушения сознания и два заседания экспертной комиссии до и после тестирования для оценки результатов и утверждения окончательной русскоязычной версии шкалы.   Результаты. В ходе первого заседания экспертной комиссии внесли поправки в русскоязычную версию шкалы в рамках языковой и культурной адаптации: были изменены единицы измерения лабораторных показателей с мг/дл на ммоль/л в 7-м и 14-м пунктах (оценка гликемии и концентрации креатинина, соответственно). Изменен термин «надаортальные сосуды» на «брахиоцефальные артерии» в 10-м пункте, сопоставлены предложенные варианты повреждения мягких тканей со стадиями развития пролежней согласно NPUAP — EPUAP [18] в 21-м пункте, добавлен параметр индекс массы тела (ИМТ) для оценки выраженности недостаточности питания. В ходе пилотного тестирования с учетом критериев включения и исключения сложностей при понимании и интерпретации инструкций шкалы у исследователей не возникло. По итогам состоялось второе заседание экспертной комиссии, на котором приняли окончательный вариант русскоязычной версии шкалы. Он доступен для ознакомления на сайте группы валидациимеждународных шкал и опросников ФГБНУ НЦН https://www.neurology.ru/reabilitaciya/centr-validacii-mezhdunarodnyh-shkal-i-oprosnikov, а также по QR-коду.   Заключение. На базе ФГБНУ НЦН выполнили первый этап валидации — лингвокультурную адаптацию. Впервые представили и рекомендовали к использованию русскоязычную версию Шкалы оценки сопутствующих заболеваний у ареактивных пациентов. В последующих публикациях будут представлены результаты оценки психометрических свойств (чувствительность, валидность, надежность) русскоязычной версии данной шкалы

Comorbidities Coma Scale (CoCoS): Linguistic and Cultural Adaptation of the Russian-Language Version

Identification of complications and control of comorbidities are essential in monitoring the patients with chronic disorders of consciousness and predicting their outcomes. The researchers of the Department of Biotechnological and Applied Clinical Sciences of the University of L'Aquila (Italy) developed the Comorbidities Coma Scale (CoCoS) for a comprehensive assessment of such patients. Lack of an officially validated version of the scale hampers its use in Russia, while using versions which have not been completely validated prevents clinicians from obtaining reliable results when examining patients with chronic disorders of consciousness.   Aim. To develop the official Russian language version of the Comorbidities Coma Scale, considering various linguistic and cultural parameters, as a part of the 1st stage of the validation study.   Material and methods. The first stage of validation was completed: direct and reverse translation of the scale was performed by two independent medical translators. The translated version was assessed by an expert board including an expert translator, neurologists, and critical care specialists. Pilot test and two meetings of the expert board, before and after testing, were arranged to assess the results and approve the final Russian version of the scale.   Results. During the first meeting of the expert board, corrections were made in the Russian language version of the scale in terms of language and cultural adaptation. Pilot testing was carried out based on the inclusion and exclusion criteria. The researchers had no difficulties in understanding and interpreting the instructions for the scale. The second meeting of the expert board was held thereupon, and the final version of the Russian language version of the scale was adopted, which is available on the website of the Center for Validation of Health Status Questionnaires and Scales of the Research Center of Neurology.   Conclusion. The first stage of validation, i. e., linguistic and cultural adaptation, was carried out at the Research Center of Neurology (Moscow, Russia). For the first time, the Russian version of the scale for assessing comorbidities in patients with chronic disorders of consciousness was presented and approved for the practical use. The future publications will address the psychometric results of the scale such as sensitivity, validity, reliability

Worldwide diversity of endophytic fungi and insects associated with dormant tree twigs

International trade in plants and climate change are two of the main factors causing damaging tree pests (i.e. fungi and insects) to spread into new areas. To mitigate these risks, a large-scale assessment of tree-associated fungi and insects is needed. We present records of endophytic fungi and insects in twigs of 17 angiosperm and gymnosperm genera, from 51 locations in 32 countries worldwide. Endophytic fungi were characterized by high-throughput sequencing of 352 samples from 145 tree species in 28 countries. Insects were reared from 227 samples of 109 tree species in 18 countries and sorted into taxonomic orders and feeding guilds. Herbivorous insects were grouped into morphospecies and were identified using molecular and morphological approaches. This dataset reveals the diversity of tree-associated taxa, as it contains 12,721 fungal Amplicon Sequence Variants and 208 herbivorous insect morphospecies, sampled across broad geographic and climatic gradients and for many tree species. This dataset will facilitate applied and fundamental studies on the distribution of fungal endophytes and insects in trees

Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

Background: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets. Results: Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression. Conclusions: We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS datasets of metabolomic phenotypes. We report novel loci and potential biochemical mechanisms that contribute to our understanding of the genetic basis of metabolic variation and its relationship to disease development and progression