Statistical research of development of integration processes in Russian agriculture

The article is devoted to the main directions of improving the analysis of integration processes in Russian agriculture. By the integration processes, we mean the development of cooperation, agricultural holdings and agrarian clusters. The article describes the history of agricultural cooperation and the role of cooperatives in the development of integration processes. A key point is the study of integration from the perspective of agricultural holdings’ formation, as the largest vertically integrated structures specializing in the production and deep processing of agricultural raw materials and products. Based on analysis of materials published on the websites and information portals, investigated the activities of 82 existing Russian agricultural holdings. The geography of agricultural holdings, their structure and specialization, the amount of resources available to the agricultural holdings in their production activities was evaluated as a result of the study. Particular attention is given to the leaders of the production of basic agricultural products. The most complex integration system in Russian agriculture is an agrarian clusters based on such structures as cooperatives and agricultural holdings. The highlights five main approaches to the study of agricultural clusters, the main of which is the general improvement of the statistics of the agricultural sector, the development of the current statistical reporting and analysis, the improvement of sample survey of peasant farms’ and individual entrepreneurs’ activities, expanding the program All-Russian agricultural census and organization of sample surveys of agricultural holdings’ activity. To analyze the feasibility of agrarian clusters establishing, the program screening the prerequisites for the formation of clusters in the agricultural region is proposed. The implementation of the directions presented in this article, significantly enhance the objectivity of the analysis of integration processes in Russian agriculture

Анализ динамики воспроизводства экономики сельского хозяйства регионов России

The article deals with the dynamics of resources, factors and efficiency of agriculture for the period from 1991 to 2014, with the release of the individual sub-periods, taking into account the period of implementation of government programs. There have been analyzed the dynamics of resource reproduction and conditions of reproduction by groups of Russian regions. The question of price disparities in agriculture, commodity production and the dynamics of the structure by types of farms has been considered. There are some approaches to the analysis of the dynamics of reproduction of Agriculture of the Russian economy, including in the regional context in the article. According to the analysis it’s noted that there are positive trends in the economy of Agriculture of Russia. Extended reproduction occurs in several areas of production, and in some regions of the resource potential of agriculture has been increased considerably. Positive trends have continued in recent years, during the inter-state sanctions and conditions of import substitution. In comparison with other types of economic activity agriculture has stable growth. However, the accumulated negative trends of the past have not overcome. In most regions continue to shrink the crop area, the number of cattle. It is shows the great need of more detailed analysis of the efficiency of production, gross and net value added, wages, incomes of workers, profitability of production by region and by type of producers. In the methodical plan it was noted the need to pay particular attention to the results of the upcoming Russian Agricultural Census 2016, which will allow to trace the changes in the Russian agriculture in the last ten years since the 2006 All-Russia agricultural census

Сравнительная оценка регионов России с неблагоприятными условиями ведения сельского хозяйства

Joining the World Trade Organization (WTO) by the Russian Federation has caused the necessity of developing some measures for exit from WTO limitations in the field of state support for agriculture. In view of that, the Ministry of agriculture of Russia has assigned the group of Federation subjects with unfavorable conditions for development of agriculture. The authors have evaluated that group of regions in comparison with other areas according to a number of indicators. The conclusion is made about the necessity of differentiated approach to management of agroindustrial production with account for specific features of regions, deepening their specialization and shaping branchial regional clusters. Also stressed is the significance of expanding and deepening the statistical analysis of conditions and results of economic activities in subjects of the Russian Federatio

Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases. Keywords: biomarker discovery; data-independent acquisition; dynamic biological systems; gene annotation; precision medicine; proteomics

Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale.

Mass spectrometry (MS)-based ubiquitinomics provides system-level understanding of ubiquitin signaling. Here we present a scalable workflow for deep and precise in vivo ubiquitinome profiling, coupling an improved sample preparation protocol with data-independent acquisition (DIA)-MS and neural network-based data processing specifically optimized for ubiquitinomics. Compared to data-dependent acquisition (DDA), our method more than triples identification numbers to 70,000 ubiquitinated peptides in single MS runs, while significantly improving robustness and quantification precision. Upon inhibition of the oncology target USP7, we simultaneously record ubiquitination and consequent changes in abundance of more than 8,000 proteins at high temporal resolution. While ubiquitination of hundreds of proteins increases within minutes of USP7 inhibition, we find that only a small fraction of those are ever degraded, thereby dissecting the scope of USP7 action. Our method enables rapid mode-of-action profiling of candidate drugs targeting DUBs or ubiquitin ligases at high precision and throughput

Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC

Genetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such phenotypic heterogeneity, but detection of metabolically divergent subpopulations remains technically challenging. We developed a proteomics-based technology, termed differential isotope labelling by amino acids (DILAC), that can detect producer and consumer subpopulations of a particular amino acid within an isogenic cell population by monitoring peptides with multiple occurrences of the amino acid. We reveal that young, morphologically undifferentiated yeast colonies contain subpopulations of lysine producers and consumers that emerge due to nutrient gradients. Deconvoluting their proteomes using DILAC, we find evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. Finally, by combining DILAC with fluorescence-activated cell sorting, we show that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B. Overall, DILAC captures previously unnoticed metabolic heterogeneity and provides experimental evidence for the role of metabolic specialization and cross-feeding interactions as a source of phenotypic heterogeneity in isogenic cell populations

Cystatin C is associated with adverse COVID-19 outcomes in diverse populations

COVID-19 has highly variable clinical courses. The search for prognostic host factors for COVID-19 outcome is a priority. We performed logistic regression for ICU admission against a polygenic score (PGS) for Cystatin C (CyC) production in patients with COVID-19. We analyzed the predictive value of longitudinal plasma CyC levels in an independent cohort of patients hospitalized with COVID-19. In four cohorts spanning European and African ancestry populations, we identified a significant association between CyC-production PGS and odds of critical illness (n cases=2,319), with the strongest association captured in the UKB cohort (OR 2.13, 95% CI 1.58-2.87, p=7.12e-7). Plasma proteomics from an independent cohort of hospitalized COVID-19 patients ( n cases = 131) demonstrated that CyC production was associated with COVID-specific mortality (p=0.0007). Our findings suggest that CyC may be useful for stratification of patients and it has functional role in the host response to COVID-19.Peer reviewe

Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening

The mechanisms linking systemic infection to hyperinflammation and immune dysfunction in sepsis are poorly understood. Extracellular histones promote sepsis pathology, but their source and mechanism of action remain unclear. Here, we show that by controlling fungi and bacteria captured by splenic macrophages, neutrophil-derived myeloperoxidase attenuates sepsis by suppressing histone release. In systemic candidiasis, microbial capture via the phagocytic receptor SIGNR1 neutralizes myeloperoxidase by facilitating marginal zone infiltration and T cell death-dependent histone release. Histones and hyphae induce cytokines in adjacent CD169 macrophages including G-CSF that selectively depletes mature Ly6G$^{high}$ neutrophils by shortening their lifespan in favour of immature Ly6G$^{low}$ neutrophils with a defective oxidative burst. In sepsis patient plasma, these mediators shorten mature neutrophil lifespan and correlate with neutrophil mortality markers. Consequently, high G-CSF levels and neutrophil lifespan shortening activity are associated with sepsis patient mortality. Hence, by exploiting phagocytic receptors, pathogens degrade innate and adaptive immunity through the detrimental impact of downstream effectors on neutrophil lifespan

Oxonium ion scanning mass spectrometry for large-scale plasma glycoproteomics

Protein glycosylation, a complex and heterogeneous post-translational modification that is frequently dysregulated in disease, has been difficult to analyse at scale. Here we report a data-independent acquisition technique for the large-scale mass-spectrometric quantification of glycopeptides in plasma samples. The technique, which we named ‘OxoScan-MS’, identifies oxonium ions as glycopeptide fragments and exploits a sliding-quadrupole dimension to generate comprehensive and untargeted oxonium ion maps of precursor masses assigned to fragment ions from non-enriched plasma samples. By applying OxoScan-MS to quantify 1,002 glycopeptide features in the plasma glycoproteomes from patients with COVID-19 and healthy controls, we found that severe COVID-19 induces differential glycosylation in IgA, haptoglobin, transferrin and other disease-relevant plasma glycoproteins. OxoScan-MS may allow for the quantitative mapping of glycoproteomes at the scale of hundreds to thousands of samples