Immune cell-specific and common molecular signatures in rheumatoid arthritis through molecular network approaches
In this study, transcriptomic data including synovial tissues, macrophages, blood, T cells, CD4+T cells, CD8+T cells, natural killer T (NKT), cells natural killer (NK) cells, neutrophils, and monocyte cells were analyzed with an integrative and comparative network biology perspective. Each dataset yielded a list of differentially expressed genes as well as a reconstruction of the tissue-specific protein-protein interaction (PPI) network. Molecular signatures were identified by a statistical test using the hypergeometric probability density function by employing the interactions of transcriptional regulators and PPI. Report...
Source: Biosystems - October 18, 2023 Category: Biotechnology Authors: Betul Comertpay Esra Gov Source Type: research
Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version
Biosystems. 2023 Oct 14:105060. doi: 10.1016/j.biosystems.2023.105060. Online ahead of print.ABSTRACTThe current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare m...
Source: Biosystems - October 16, 2023 Category: Biotechnology Authors: Marcos L ópez-Pérez F élix Aguirre-Garrido Leonardo Herrera-Z úñiga Francisco J Fern ández Source Type: research
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models
Biosystems. 2023 Oct 14:105062. doi: 10.1016/j.biosystems.2023.105062. Online ahead of print.ABSTRACTAchieving sustainable livestock management necessitates optimizing animal production while minimizing environmental impact. To achieve this, feed efficiency must be enhanced, and nutrition blueprints must be understood. In ruminant nutrition, this is of paramount importance, as it exposes degradation kinetics and nutritional benchmarks, allowing feed management and formulations to be more ecologically balanced. Previous research efforts have focused on exploring the relationship between a restricted set of nutrient paramete...
Source: Biosystems - October 16, 2023 Category: Biotechnology Authors: Selim Esen Source Type: research
Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version
Biosystems. 2023 Oct 14:105060. doi: 10.1016/j.biosystems.2023.105060. Online ahead of print.ABSTRACTThe current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare m...
Source: Biosystems - October 16, 2023 Category: Biotechnology Authors: Marcos L ópez-Pérez F élix Aguirre-Garrido Leonardo Herrera-Z úñiga Francisco J Fern ández Source Type: research
Optimizing ruminant nutrition: Insights from a comprehensive analysis of silage composition and in vitro gas production dynamics using nonlinear models
Biosystems. 2023 Oct 14:105062. doi: 10.1016/j.biosystems.2023.105062. Online ahead of print.ABSTRACTAchieving sustainable livestock management necessitates optimizing animal production while minimizing environmental impact. To achieve this, feed efficiency must be enhanced, and nutrition blueprints must be understood. In ruminant nutrition, this is of paramount importance, as it exposes degradation kinetics and nutritional benchmarks, allowing feed management and formulations to be more ecologically balanced. Previous research efforts have focused on exploring the relationship between a restricted set of nutrient paramete...
Source: Biosystems - October 16, 2023 Category: Biotechnology Authors: Selim Esen Source Type: research
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation
Biosystems. 2023 Oct 12:105038. doi: 10.1016/j.biosystems.2023.105038. Online ahead of print.ABSTRACTMetabolic Control Theory (MCT) and Metabolic Control Analysis (MCA) are the two sides, theoretical and experimental, of the measurement of the sensitivity of metabolic networks in the vicinity of a steady state. We will describe the birth and the development of this theory from the first analyses of linear pathways up to a global mathematical theory applicable to any metabolic network. We will describe how the theory, given the global nature of mitochondrial oxidative phosphorylation, solved the problem of what controls mit...
Source: Biosystems - October 14, 2023 Category: Biotechnology Authors: Jean-Pierre Mazat Source Type: research
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation
Biosystems. 2023 Oct 12:105038. doi: 10.1016/j.biosystems.2023.105038. Online ahead of print.ABSTRACTMetabolic Control Theory (MCT) and Metabolic Control Analysis (MCA) are the two sides, theoretical and experimental, of the measurement of the sensitivity of metabolic networks in the vicinity of a steady state. We will describe the birth and the development of this theory from the first analyses of linear pathways up to a global mathematical theory applicable to any metabolic network. We will describe how the theory, given the global nature of mitochondrial oxidative phosphorylation, solved the problem of what controls mit...
Source: Biosystems - October 14, 2023 Category: Biotechnology Authors: Jean-Pierre Mazat Source Type: research
The metabolic control theory: Its development and its application to mitochondrial oxidative phosphorylation
Biosystems. 2023 Oct 12:105038. doi: 10.1016/j.biosystems.2023.105038. Online ahead of print.ABSTRACTMetabolic Control Theory (MCT) and Metabolic Control Analysis (MCA) are the two sides, theoretical and experimental, of the measurement of the sensitivity of metabolic networks in the vicinity of a steady state. We will describe the birth and the development of this theory from the first analyses of linear pathways up to a global mathematical theory applicable to any metabolic network. We will describe how the theory, given the global nature of mitochondrial oxidative phosphorylation, solved the problem of what controls mit...
Source: Biosystems - October 14, 2023 Category: Biotechnology Authors: Jean-Pierre Mazat Source Type: research
Revisiting Carl Jung's archetype theory a psychobiological approach
Biosystems. 2023 Oct 11:105059. doi: 10.1016/j.biosystems.2023.105059. Online ahead of print.ABSTRACTThis paper delves into the concept of archetypes, universal patterns of behavior and cognition, and proposes a novel tripartite model distinguishing between structural, regulatory, and representational archetypes. Drawing on insights from code biology, neuroscience, genetics, and epigenetics, the model provides a nuanced framework for understanding archetypes and their role in shaping cognition and behavior. The paper also explores the interplay between these elements to express representational archetypes. Furthermore, it ...
Source: Biosystems - October 13, 2023 Category: Biotechnology Authors: Jo ão Ereiras Vedor Source Type: research
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects
Biosystems. 2023 Oct 7;234:105045. doi: 10.1016/j.biosystems.2023.105045. Online ahead of print.ABSTRACTCollective cell migration is essential for a wide range of biological processes such as: morphogenesis, wound healing, and cancer spreading. However, it is well known that migrating epithelial collectives frequently undergo jamming, stay trapped some period of time, and then start migration again. Consequently, only a part of epithelial cells actively contributes to the tissue development. In contrast to epithelial cells, migrating mesenchymal collectives successfully avoid the jamming. It has been confirmed that the epi...
Source: Biosystems - October 9, 2023 Category: Biotechnology Authors: Ivana Pajic-Lijakovic Milan Milivojevic Source Type: research
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects
Biosystems. 2023 Oct 7:105045. doi: 10.1016/j.biosystems.2023.105045. Online ahead of print.ABSTRACTCollective cell migration is essential for a wide range of biological processes such as: morphogenesis, wound healing, and cancer spreading. However, it is well known that migrating epithelial collectives frequently undergo jamming, stay trapped some period of time, and then start migration again. Consequently, only a part of epithelial cells actively contributes to the tissue development. In contrast to epithelial cells, migrating mesenchymal collectives successfully avoid the jamming. It has been confirmed that the epithel...
Source: Biosystems - October 9, 2023 Category: Biotechnology Authors: Ivana Pajic-Lijakovic Milan Milivojevic Source Type: research
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects
Biosystems. 2023 Oct 7:105045. doi: 10.1016/j.biosystems.2023.105045. Online ahead of print.ABSTRACTCollective cell migration is essential for a wide range of biological processes such as: morphogenesis, wound healing, and cancer spreading. However, it is well known that migrating epithelial collectives frequently undergo jamming, stay trapped some period of time, and then start migration again. Consequently, only a part of epithelial cells actively contributes to the tissue development. In contrast to epithelial cells, migrating mesenchymal collectives successfully avoid the jamming. It has been confirmed that the epithel...
Source: Biosystems - October 9, 2023 Category: Biotechnology Authors: Ivana Pajic-Lijakovic Milan Milivojevic Source Type: research
Cell jamming-to-unjamming transitions and vice versa in development: Physical aspects
Biosystems. 2023 Oct 7:105045. doi: 10.1016/j.biosystems.2023.105045. Online ahead of print.ABSTRACTCollective cell migration is essential for a wide range of biological processes such as: morphogenesis, wound healing, and cancer spreading. However, it is well known that migrating epithelial collectives frequently undergo jamming, stay trapped some period of time, and then start migration again. Consequently, only a part of epithelial cells actively contributes to the tissue development. In contrast to epithelial cells, migrating mesenchymal collectives successfully avoid the jamming. It has been confirmed that the epithel...
Source: Biosystems - October 9, 2023 Category: Biotechnology Authors: Ivana Pajic-Lijakovic Milan Milivojevic Source Type: research
Discovering ecoacoustic codes in beehives: First evidence and perspectives
Biosystems. 2023 Oct 6:105041. doi: 10.1016/j.biosystems.2023.105041. Online ahead of print.ABSTRACTThe sounds present inside a beehive originate from the overlap of honeybee buzzes with external sounds. They reveal patterns that support the hypothesis that the sonic context of the beehive may be utilized by honeybees as a source of ecoacoustic codes for communication and the coordination of social activity. Patterns were observed in a data series of acoustic files sampled at a frequency of 48 kHz during the period May-July 2023 in a beehive of Apis mellifera ligustica (Spinola, 1806). The acoustic information was extracte...
Source: Biosystems - October 8, 2023 Category: Biotechnology Authors: Almo Farina Source Type: research
Discovering ecoacoustic codes in beehives: First evidence and perspectives
Biosystems. 2023 Oct 6:105041. doi: 10.1016/j.biosystems.2023.105041. Online ahead of print.ABSTRACTThe sounds present inside a beehive originate from the overlap of honeybee buzzes with external sounds. They reveal patterns that support the hypothesis that the sonic context of the beehive may be utilized by honeybees as a source of ecoacoustic codes for communication and the coordination of social activity. Patterns were observed in a data series of acoustic files sampled at a frequency of 48 kHz during the period May-July 2023 in a beehive of Apis mellifera ligustica (Spinola, 1806). The acoustic information was extracte...
Source: Biosystems - October 8, 2023 Category: Biotechnology Authors: Almo Farina Source Type: research
