scholarly journals Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors

2021 ◽  
Vol 25 (5) ◽  
pp. 580-592
Author(s):  
P. S. Demenkov ◽  
E. A. Oshchepkova ◽  
T. V. Ivanisenko ◽  
V. A. Ivanisenko
Keyword(s):  
Environmental Factors ◽  
Ion Transport ◽  
Gene Networks ◽  
Crop Production ◽  
Molecular Genetic ◽  
Saline Stress ◽  
Cadmium Content ◽  
Biological Processes ◽  
Genetic Mechanisms ◽  
Associative Gene Networks

Methods for prioritizing or ranking candidate genes according to their importance based on specific criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been used in other fields, particularly in crop production. This is largely due to the development of technologies to solve problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, me tabolites, etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The prioritization results indicate that fundamental processes, such as gene expression, post-translational modifications, protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a group of processes related to the development of seeds (“seeding development”) was revealed to be drought specific, while processes associated with ion transport (“ion transport”) were included in the list of responses specific to salt stress and processes associated with the metabolism of lipids were found to be involved specifically in the response to cadmium.

scholarly journals QTL analysis and management of plant productivity in the precision agriculture

2020 ◽  
pp. 12-19
Author(s):  
Yu. V. Chesnokov
Keyword(s):  
Environmental Factors ◽  
Qtl Analysis ◽  
Precision Agriculture ◽  
Crop Production ◽  
Negative Impact ◽  
Molecular Genetic ◽  
Self Regulation ◽  
Agricultural Practices ◽  
Plant Productivity ◽  
Steady Increase

Modern crop cultivation technologies have reached the limits of “saturation” both in the ecological (environmental pollution, suppression of the mechanisms of its self-regulation), energy (exponential growth of irreplaceable energy costs for each additional unit of production), and in production. In this regard, environmental factors (air drought, frosts, active temperatures, etc.), which cannot be optimized, are becoming increasingly important in ensuring a steady increase in the yield of cultivated plant forms. In recent decades, more and more attention has been paid to technogenic and biological systems of agriculture, based on the ecologization and biologization of the intensification processes of adaptive crop production. Such approaches are the precision agriculture system (PA) and QTL analysis. Using these approaches allows not only to ensure a steady increase in productivity due to the combined use of the advantages of precision farming and molecular genetic assessment, including the creation of new forms and varieties that are responsive to РА agricultural practices, but also to level the negative impact of abiotic and biotic environmental factors that limit the size and quality of the crop as well as plant productivity. It is shown that the strategy of adaptive intensification of crop production through the use of the TK system and QTL analysis approaches is not alternative to existing farming systems, however, it focuses modern agriculture on the growth of knowledge-intensive agricultural production as a whole. An analysis of the causes under consideration, the current unfavorable trends in modern crop production and agriculture, clearly shows their scale and long-term nature, and therefore the inevitability of the search for new priorities for intensification of crop production and agriculture, providing a qualitatively new stage of their development in the interests of man.

scholarly journals Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Olga V. Saik ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
Elena Yu. Bragina ◽  
Maxim B. Freidin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Genetic Networks ◽  
Positive Sign ◽  
Phenotypic Traits ◽  
Protein Protein Interactions ◽  
Scientific Publications ◽  
Associative Gene Networks

AbstractComorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.

scholarly journals Identification and Functional Annotation of Genes Related to Horses’ Performance: From GWAS to Post-GWAS

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1173
Author(s):  
Thayssa O. Littiere ◽  
Gustavo H. F. Castro ◽  
Maria del Pilar R. Rodriguez ◽  
Cristina M. Bonafé ◽  
Ana F. B. Magalhães ◽  
...  
Keyword(s):  
Systematic Review ◽  
Transcription Factors ◽  
Candidate Genes ◽  
Gene Networks ◽  
Actin Polymerization ◽  
Biological Processes ◽  
Network Analyses ◽  
Arterial Blood ◽  
Gene Network Analysis ◽  
Genetic Mechanisms

Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene–TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene–TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene–TF network highlighting TFs and the most candidate genes for horse performance.

scholarly journals Reconstruction and Analysis of Gene Networks of Human Neurotransmitter Systems Reveal Genes with Contentious Manifestation for Anxiety, Depression, and Intellectual Disabilities

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 699
Author(s):  
Roman Ivanov ◽  
Vladimir Zamyatin ◽  
Aleksandra Klimenko ◽  
Yury Matushkin ◽  
Alexander Savostyanov ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Intellectual Disabilities ◽  
Protein Interactions ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Phenotypic Traits ◽  
Electrophysiological Properties ◽  
Complex Interactions ◽  
Anxiety Depression

Background: The study of the biological basis of anxiety, depression, and intellectual disabilities in humans is one of the most actual problems of modern neurophysiology. Of particular interest is the study of complex interactions between molecular genetic factors, electrophysiological properties of the nervous system, and the behavioral characteristics of people. The neurobiological understanding of neuropsychiatric disorders requires not only the identification of genes that play a role in the molecular mechanisms of the occurrence and course of diseases, but also the understanding of complex interactions that occur between these genes. A systematic study of such interactions obviously contributes to the development of new methods of diagnosis, prevention, and treatment of disorders, as the orientation to allele variants of individual loci is not reliable enough, because the literature describes a number of genes, the same alleles of which can be associated with different, sometimes extremely different variants of phenotypic traits, depending on the genetic background, of their carriers, habitat, and other factors. Results: In our study, we have reconstructed a series of gene networks (in the form of protein–protein interactions networks, as well as networks of transcription regulation) to build a model of the influence of complex interactions of environmental factors and genetic risk factors for intellectual disability, depression, and other disorders in human behavior. Conclusion: A list of candidate genes whose expression is presumably associated with environmental factors and has potentially contentious manifestation for behavioral and neurological traits is identified for further experimental verification.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

scholarly journals Drought and Saline Stress Tolerance Induced in Somatic Hybrids of Solanum chacoense and Potato Cultivars by Using Mismatch Repair Deficiency

Agriculture ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 696
Author(s):  
Imola Molnár ◽  
Lavinia Cozma ◽  
Tünde-Éva Dénes ◽  
Imre Vass ◽  
István-Zoltán Vass ◽  
...  
Keyword(s):  
Climate Change ◽  
Mismatch Repair ◽  
Crop Production ◽  
Somatic Hybrids ◽  
Potato Cultivars ◽  
Solanum Chacoense ◽  
Saline Stress ◽  
Severe Drought ◽  
Mismatch Repair Deficiency ◽  
Repair Deficiency

Global climate change, especially when involving drought and salinity, poses a major challenge to sustainable crop production, causing severe yield losses. The environmental conditions are expected to further aggravate crop production in the future as a result of continuous greenhouse gas emissions, causing further temperature rise and leading to increased evapotranspiration, severe drought, soil salinity, as well as insect and disease threats. These suboptimal growth conditions have negative impact on plant growth, survival, and crop yield. Potato is well known as a crop extremely susceptible to drought, which is primarily attributed to its shallow root system. With potato being the fourth major food crop, increasing potato productivity is thus important for food security and for feeding global population. To maintain a sustainable potato production, it is necessary to develop stress tolerant potato cultivars that cope with the already ongoing climate change. The aim of our study is to analyze the response of potato somatic hybrids to drought and salt stress under in vitro conditions; the somatic hybrids studied are the wild relative Solanum chacoense (+) Solanum tuberosum, with or without mismatch repair deficiency (MMR). Upon this selection of drought and salt tolerant genotypes, somatic hybrids and their parents were phenotyped on a semi-automated platform, and lines tolerant to medium water scarcity (20% compared to 60% soil water capacity) were identified. Although none of the parental species were tolerant to drought, some of the MMR-deficient somatic hybrids showed tolerance to drought and salt as a new trait.

scholarly journals Educational Attainment and Personality Are Genetically Intertwined

2017 ◽  
Vol 28 (11) ◽  
pp. 1631-1639 ◽  
Author(s):  
René Mõttus ◽  
Anu Realo ◽  
Uku Vainik ◽  
Jüri Allik ◽  
Tõnu Esko
Keyword(s):  
Educational Attainment ◽  
Personality Traits ◽  
Personality Trait ◽  
Factor Model ◽  
Five Factor Model ◽  
Molecular Genetic ◽  
Maximum Amount ◽  
Biological Processes ◽  
Psychological Traits ◽  
Polygenic Scores

Heritable variance in psychological traits may reflect genetic and biological processes that are not necessarily specific to these particular traits but pertain to a broader range of phenotypes. We tested the possibility that the personality domains of the five-factor model and their 30 facets, as rated by people themselves and their knowledgeable informants, reflect polygenic influences that have been previously associated with educational attainment. In a sample of more than 3,000 adult Estonians, education polygenic scores (EPSs), which are interpretable as estimates of molecular-genetic propensity for education, were correlated with various personality traits, particularly from the neuroticism and openness domains. The correlations of personality traits with phenotypic educational attainment closely mirrored their correlations with EPS. Moreover, EPS predicted an aggregate personality trait tailored to capture the maximum amount of variance in educational attainment almost as strongly as it predicted the attainment itself. We discuss possible interpretations and implications of these findings.

Manganese as a Micronutrient in Agriculture: Crop Requirement and Management

2021 ◽  
Vol 12 (1-2) ◽  
pp. 225-242
Author(s):  
MH Rashed ◽  
TS Hoque ◽  
MMR Jahangir ◽  
MA Hashem
Keyword(s):  
Growth And Development ◽  
Crop Production ◽  
Nutrient Elements ◽  
Biological Processes ◽  
Critical Levels ◽  
Plant Growth And Development ◽  
Safe Environment ◽  
Body Of Knowledge ◽  
Cell Compartments ◽  
Manganese Uptake

Manganese (Mn) as an essential plant micronutrient affects plant development, when at deficient or toxic levels. Manganese is used in several biological processes as an important contributor in plant growth and development. Manganese uptake depends on forms of Mn in soil solution, crop characteristics including growth rate, and ineteractions with other environmental factors. Its distribution in soils and requirement for crops vary from location to location, depending on soil type and reactions. Despite the metabolic roles of Mn in different plant cell compartments, the importance of Mn requirement in plants, distribution in soils and application to crops has been understated. As a micronutrient, judicious Mn management requires to critically evaluating its concentration in soils, biochemical functions, critical levels, soil availability and interactions with other nutrient elements is essential. This review has critically analysed the existing body of knowledge on Mn distribution in soils, dynamics, functions and management towards better crop production and safe environment. Environ. Sci. & Natural Resources, 12(1&2): 225-242, 2019

scholarly journals The Molecular-Genetic Basis of Functional Hyperandrogenism and the Polycystic Ovary Syndrome

2005 ◽  
Vol 26 (2) ◽  
pp. 251-282 ◽  
Author(s):  
Héctor F. Escobar-Morreale ◽  
Manuel Luque-Ramírez ◽  
José L. San Millán
Keyword(s):  
Environmental Factors ◽  
Polycystic Ovary Syndrome ◽  
Diagnostic Criteria ◽  
Genetic Basis ◽  
Polycystic Ovary ◽  
Molecular Genetic ◽  
Ovary Syndrome ◽  
The Metabolic Syndrome ◽  
Molecular Genetic Basis ◽  
Functional Hyperandrogenism

The genetic mechanisms underlying functional hyperandrogenism and the polycystic ovary syndrome (PCOS) remain largely unknown. Given the large number of genetic variants found in association with these disorders, the emerging picture is that of a complex multigenic trait in which environmental influences play an important role in the expression of the hyperandrogenic phenotype. Among others, genomic variants in genes related to the regulation of androgen biosynthesis and function, insulin resistance, and the metabolic syndrome, and proinflammatory genotypes may be involved in the genetic predisposition to functional hyperandrogenism and PCOS. The elucidation of the molecular genetic basis of these disorders has been burdened by the heterogeneity in the diagnostic criteria used to define PCOS, the limited sample size of the studies conducted to date, and the lack of precision in the identification of ethnic and environmental factors that trigger the development of hyperandrogenic disorders. Progress in this area requires adequately sized multicenter collaborative studies after standardization of the diagnostic criteria used to classify hyperandrogenic patients, in whom modifying environmental factors such as ethnicity, diet, and lifestyle are identified with precision. In addition to classic molecular genetic techniques such as linkage analysis in the form of a whole-genome scan and large case-control studies, promising genomic and proteomic approaches will be paramount to our understanding of the pathogenesis of functional hyperandrogenism and PCOS, allowing a more precise prevention, diagnosis, and treatment of these prevalent disorders.

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