Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version

López-Pérez, Marcos; Aguirre-Garrido, Félix; Herrera-Zúñiga, Leonardo; Fernández, Francisco J.

doi:10.1016/j.biosystems.2023.105060

Cited by 3 publications

(2 citation statements)

References 79 publications

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“…Last but not least, it is worth highlighting that the molecular techniques employed in the included papers in the review also allow for identifying antibiotic resistance genes, focusing on those directly associated with resistance or previously linked to such processes in research or available in databases. By targeting specific genes or genomic regions known to confer resistance, researchers can elucidate the underlying mechanisms driving resistance development in pathogens [56]. Notably, many pathogens regulate their pathogenicity and virulence via a resistance phenotype, sometimes covertly.…”

Section: Discussionmentioning

confidence: 99%

A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review

Matys,

Kensy,

Gedrange

et al. 2024

IJMS

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Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.

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Section: Discussionmentioning

confidence: 99%

A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review

Matys,

Kensy,

Gedrange

et al. 2024

IJMS

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“…Many studies have focused on the impact of environmental change on the growth of plant biomass allocation [18][19][20] and have linked it with gene regulation, such as determining that different genotypes of specific genes affect biomass allocation [21], cultivating crop varieties with excellent resistance, and using biomass-allocation patterns with technical means to induce genetic variation [22,23]. Several research studies have shown that specific environments can profoundly affect gene networks and circuits [24]. However, few research studies have focused on the genetic-regulation mechanism behind the covariation of phenotypic traits responding to different environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

The Genetic Architecture of the Root System during Seedling Emergence in Populus euphratica under Salt Stress and Control Environments

Liang,

Gong,

et al. 2024

Applied Sciences

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The growth of the Populus euphratica root system is of great significance for its survival under adverse environmental stress. In harsh saline-stress environments, the proportion, morphology, and functionality of the taproots and lateral roots and how they manifest specific adaptive structures, growth strategies, and potential genetic controls are still subjects for further exploration. In this study, we delve into the fundamental patterns and trade-offs of root morphology and functionality by constructing an environment-induced differential interaction equation (EDIE) to model the independent and interactive growth of the root system while considering the influence of environmental conditions. We identify 93 key QTLs in the control group and 44 key QTLs in the salt-stress group, of which 2 QTLs are significant in both environments. By constructing ODE-based QTL networks, we explore in depth how these loci regulate the growth of the root system under different environmental conditions while considering their independent direct effects and epistatic effects among loci. This study elucidates the intrinsic factors that influence the variations in taproots and lateral roots, providing crucial insights into the relationship between root morphology and functionality.

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Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida

Sun,

Lv,

Lei

et al. 2024

Microorganisms

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Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon’s gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon’s defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b.

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Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version

Cited by 3 publications

References 79 publications

A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review

A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review

The Genetic Architecture of the Root System during Seedling Emergence in Populus euphratica under Salt Stress and Control Environments

Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida

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