Stochastic modeling of aging cells reveals how damage accumulation, repair, and cell-division asymmetry affect clonal senescence and population fitness

BMC Bioinformatics, Journal Year: 2019, Volume and Issue: 20(1)

Published: July 15, 2019

Asymmetry during cellular division, both in the uneven partitioning of damaged components and cell volume, is a biological phenomenon experienced by many unicellular organisms. Previous work based on deterministic model claimed that such asymmetry volume aging-associated damage confers fitness benefit avoiding clonal senescence, primarily diversifying population. However, populations organisms are already naturally diversified due to inherent stochasticity processes.

Language: Английский

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Developing the genotype‐to‐phenotype relationship in evolutionary theory: A primer of developmental features

Evolution & Development, Journal Year: 2023, Volume and Issue: 25(6), P. 393 - 409

Published: April 7, 2023

Abstract For decades, there have been repeated calls for more integration across evolutionary and developmental biology. However, critiques in the literature recent funding initiatives suggest this remains incomplete. We one way forward is to consider how we elaborate most basic concept of development, relationship between genotype phenotype, traditional models processes. some questions, when complex features development are accounted for, predictions processes shift. present a primer on concepts clarify confusion fuel new questions approaches. The involve expanding base model genotype‐to‐phenotype include genome, space, time. A layer complexity added by incorporating systems, including signal‐response systems networks interactions. emergence function, which captures feedbacks phenotypic performance, offers further elaborations that explicitly link fitness with systems. Finally, such as plasticity niche construction conceptualize developing phenotype external environment, allowing fuller inclusion ecology models. Incorporating aspects into also accommodates pluralistic focus causal importance individual organisms, or agents generating patterns. Thus, laying out existing considering they used different fields, can gain clarity debates around extended synthesis pursue directions nesting evolution highlight areas biology need theoretical attention.

Language: Английский

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Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection

Cell Reports, Journal Year: 2020, Volume and Issue: 33(4), P. 108306 - 108306

Published: Oct. 1, 2020

How evolution can be facilitated by epigenetic mechanisms has received refreshed attention recently. To explore the role inheritance plays in evolution, we subject isogenic wild-type yeast cells expressing PGAL1-YFP (yellow fluorescent protein) to selection daily sorting based on reporter expression. We observe expression-level reductions multiple replicates sorted for lowest expression that persist several days, even after lifting pressure. Reduced is due factors galactose (GAL) network rather than global factors. Results using a constitutively active GAL are overall agreement with findings network. find local chromatin environment of significant effect observed phenotype. Genome sequencing, immunoprecipitation (ChIP)-qPCR, and sporulation analysis provide further insights into genetic contributors changes observed. Our work provides comprehensive example played gene evolution.

Language: Английский

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Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Journal Year: 2019, Volume and Issue: 1862(4), P. 457 - 471

Published: March 2, 2019

Language: Английский

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Phenotypic plasticity in the monoclonal marbled crayfish is associated with very low genetic diversity but pronounced epigenetic diversity

Current Zoology, Journal Year: 2022, Volume and Issue: 69(4), P. 426 - 441

Published: Dec. 2, 2022

Clonal organisms are particularly useful to investigate the contribution of epigenetics phenotypic plasticity, because confounding effects genetic variation negligible. In last decade, apomictic parthenogenetic marbled crayfish, Procambarus virginalis, has been developed as a model relationships between plasticity and epigenetic diversity in detail. This crayfish originated about 30 years ago by autotriploidy from single slough fallax. As result human releases active spreading, established numerous populations very diverse habitats 22 countries tropics cold temperate regions. Studies laboratory field revealed considerable coloration, spination, morphometric parameters, growth, food preference, population structure, trophic position, niche width. Illumina PacBio whole-genome sequencing representatives 19 Europe Madagascar demonstrated extremely low within among populations, indicating that observed ability live strikingly different environments not due adaptation selection on variation. contrast, differences were found DNA methylation patterns hundreds genes, suggesting environmentally induced is mediated mechanisms corresponding changes gene expression. Specific fingerprints persisted local over successive existence ecotypes, but there presently no information whether these signatures transgenerationally inherited or anew each generation recorded adaptive nonadaptive.

Language: Английский

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Phenotypic plasticity as a facilitator of microbial evolution

Current Zoology, Journal Year: 2022, Volume and Issue: 8(1)

Published: Jan. 1, 2022

Abstract Tossed about by the tides of history, inheritance acquired characteristics has found a safe harbor at last in rapidly expanding field epigenetics. The slow pace genetic variation and high opportunity cost associated with maintaining diverse pool are well-matched flexibility epigenetic traits, which can enable low-cost exploration phenotypic space reactive tuning to environmental pressures. Aiding generation phenotypically plastic population, mechanisms often provide hotbed innovation for countering pressures, while potential fixation lead strong epigenetic–genetic evolutionary synergy. At level cells cellular populations, we begin this review exploring breadth storage intergenerational transmission information, followed brief common exotic epigenetically regulated phenotypes. We conclude offering an in-depth coverage recent papers centered around two critical issues: evolvability traits through Baldwinian adaptive plasticity synergy between evolution.

Language: Английский

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The Effect of Calorie Restriction on Protein Quality Control in Yeast

Biomolecules, Journal Year: 2023, Volume and Issue: 13(5), P. 841 - 841

Published: May 15, 2023

Initially, protein aggregates were regarded as a sign of pathological state the cell. Later, it was found that these assemblies are formed in response to stress, and some them serve signalling mechanisms. This review has particular focus on how intracellular related altered metabolism caused by different glucose concentrations extracellular environment. We summarise current knowledge role energy homeostasis pathways consequent effect aggregate accumulation removal. covers regulation at levels, including elevated degradation proteasome activity mediated Hxk2 protein, enhanced ubiquitination aberrant proteins through Torc1/Sch9 Msn2/Whi2, activation autophagy ATG genes. Finally, certain form reversible biomolecular stress reduced which used mechanism cell, controlling major primary sensing.

Language: Английский

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Ruminant Placental Adaptation in Early Maternal Undernutrition: An Overview

Frontiers in Veterinary Science, Journal Year: 2021, Volume and Issue: 8

Published: Oct. 20, 2021

Correct placental development during early gestation is considered the main determinant of fetal growth in late pregnancy. A reduction maternal nourishment occurring across developmental window has been linked to a wide range pregnancy disorders affecting transport capacity and consequently nutrient supply line, with long-term implications for offspring health productivity. In livestock, ruminant species specifically experience undernutrition extensive systems due seasonal changes food availability, significant economic losses farmer some situations. this review, we aim discuss effects reduced nutrition on specific focus placenta physiology. Different types adaptation strategies were examined, also considering potential epigenetic landscape, which known undergo reprogramming mammalian development. We discussed involvement autophagy as cellular degradation mechanism that may play key role response deficiency mediated by target rapamycin, named mTOR intracellular pathway.

Language: Английский

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Technological Approach to Mind Everywhere (TAME): an experimentally- grounded framework for understanding diverse bodies and minds

Published: Dec. 28, 2021

Synthetic biology and bioengineering provide the opportunity to create novel embodied cognitive systems (otherwise known as minds) in a very wide variety of chimeric architectures combining evolved designed material software. These advances are disrupting familiar concepts philosophy mind, require new ways thinking about comparing truly diverse intelligences, whose composition origin not like any available natural model species. In this Perspective, I introduce TAME - Technological Approach Mind Everywhere framework for understanding manipulating cognition unconventional substrates. formalizes non-binary (continuous), empirically-based approach strongly agency. When applied regenerating/developmental systems, suggests perspective on morphogenesis an example basal cognition. The deep symmetry between problem-solving anatomical, physiological, transcriptional, 3D (traditional behavioral) spaces drives specific hypotheses by which capacities can scale during evolution. An important medium exploited evolution joining active subunits into greater agents is developmental bioelectricity, implemented pre-neural use ion channels gap junctions cell-level feedback loops anatomical homeostasis. This architecture multi-scale competency biological has implications plasticity bodies minds, greatly potentiating evolvability. Considering classical recent data from perspectives computational science, evolutionary biology, cognition, reveals rich research program with many regenerative medicine, artificial intelligence.

Language: Английский

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Short heat shock has a long-term effect on mesenchymal stem cells’ transcriptome

iScience, Journal Year: 2023, Volume and Issue: 26(8), P. 107305 - 107305

Published: July 10, 2023

The adverse effects of heat stress (HS) on physiological systems are well documented, yet the underlying molecular mechanisms behind it remain poorly understood. To address this knowledge gap, we conducted a comprehensive investigation into impact HS mesenchymal stem cells (MSCs), focusing their morphology, phenotype, proliferative capacity, and fate determination. Our in-depth analysis MSCs' transcriptome revealed significant influence transcriptional landscape. Notably, even after short period stress, observed persistent alteration in cell identity, potentially mediated by activation bivalent genes. Furthermore, comparing differentially expressed genes following with state recovery, identified transient upregulation MLL other histone modifiers, providing potential mechanistic explanation for stable This could be used to predict modify long-term effect identity.

Language: Английский

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