scholarly journals Molecular adaptation response of Oenococcus oeni in non-Saccharomyces fermented wines: A comparative multi-omics approach

2021 ◽  
pp. 109490
Author(s):  
Aitor Balmaseda ◽  
Nicolas Rozès ◽  
Albert Bordons ◽  
Cristina Reguant
Keyword(s):  
Oenococcus Oeni ◽  
Molecular Adaptation ◽  
Adaptation Response

scholarly journals Effect of Adaptation to Ethanol on Cytoplasmic and Membrane Protein Profiles of Oenococcus oeni

2004 ◽  
Vol 70 (5) ◽  
pp. 2748-2755 ◽  
Author(s):  
M. Graça Silveira ◽  
Maja Baumgärtner ◽  
Frank M. Rombouts ◽  
Tjakko Abee
Keyword(s):  
Membrane Protein ◽  
Redox Balance ◽  
Oenococcus Oeni ◽  
Starter Cultures ◽  
Phosphotransferase System ◽  
Protein Patterns ◽  
Protein Levels ◽  
Proteomic Approach ◽  
Associated Proteins ◽  
Adaptation Response

ABSTRACT The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol adaptation, including cytoplasmic, membrane-associated, and integral membrane proteins, was investigated. Ethanol triggers alterations in protein patterns of O. oeni cells stressed with 12% ethanol for 1 h and those of cells grown in the presence of 8% ethanol. Levels of inosine-5′-monophosphate dehydrogenase and phosphogluconate dehydrogenase, which generate reduced nicotinamide nucleotides, were decreased during growth in the presence of ethanol, while glutathione reductase, which consumes NADPH, was induced, suggesting that maintenance of the redox balance plays an important role in ethanol adaptation. Phosphoenolpyruvate:mannose phosphotransferase system (PTS) components of mannose PTS, including the phosphocarrier protein HPr and EIIMan, were lacking in ethanol-adapted cells, providing strong evidence that mannose PTS is absent in ethanol-adapted cells, and this represents a metabolic advantage to O. oeni cells during malolactic fermentation. In cells grown in the presence of ethanol, a large increase in the number of membrane-associated proteins was observed. Interestingly, two of these proteins, dTDT-glucose-4,6-dehydratase and d-alanine:d-alanine ligase, are known to be involved in cell wall biosynthesis. Using a proteomic approach, we provide evidence for an active ethanol adaptation response of O. oeni at the cytoplasmic and membrane protein levels.

Exemplar Abstract for Oenococcus oeni (Garvie 1967) Dicks et al. 1995.

2003 ◽  
Author(s):  
Charles Thomas Parker ◽  
Dorothea Taylor ◽  
George M Garrity
Keyword(s):  
Oenococcus Oeni

Exemplar Abstract for Oenococcus oeni (Garvie 1967) Dicks et al. 1995.

2003 ◽  
Author(s):  
Charles Thomas Parker ◽  
Dorothea Taylor ◽  
George M Garrity
Keyword(s):  
Oenococcus Oeni

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

scholarly journals The Role of Fetal, Infant, and Childhood Nutrition in the Timing of Sexual Maturation

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 419
Author(s):  
Valeria Calcaterra ◽  
Hellas Cena ◽  
Corrado Regalbuto ◽  
Federica Vinci ◽  
Debora Porri ◽  
...  
Keyword(s):  
Sexual Maturation ◽  
Pubertal Development ◽  
Endocrine System ◽  
Metabolic Adaptation ◽  
Fetal Life ◽  
Critical Periods ◽  
Important Indicator ◽  
Prenatal Growth ◽  
Adaptation Response ◽  
Healthy Growth

Puberty is a crucial developmental stage in the life span, necessary to achieve reproductive and somatic maturity. Timing of puberty is modulated by and responds to central neurotransmitters, hormones, and environmental factors leading to hypothalamic-pituitary-gonadal axis maturation. The connection between hormones and nutrition during critical periods of growth, like fetal life or infancy, is fundamental for metabolic adaptation response and pubertal development control and prediction. Since birth weight is an important indicator of growth estimation during fetal life, restricted prenatal growth, such as intrauterine growth restriction (IUGR) and small for gestational age (SGA), may impact endocrine system, affecting pubertal development. Successively, lactation along with early life optimal nutrition during infancy and childhood may be important in order to set up timing of sexual maturation and provide successful reproduction at a later time. Sexual maturation and healthy growth are also influenced by nutrition requirements and diet composition. Early nutritional surveillance and monitoring of pubertal development is recommended in all children, particularly in those at risk, such as the ones born SGA and/or IUGR, as well as in the case of sudden weight gain during infancy. Adequate macro and micronutrient intake is essential for healthy growth and sexual maturity.

scholarly journals Global evidence of constraints and limits to human adaptation

2021 ◽  
Vol 21 (3) ◽  
Author(s):  
Adelle Thomas ◽  
Emily Theokritoff ◽  
Alexandra Lesnikowski ◽  
Diana Reckien ◽  
Kripa Jagannathan ◽  
...  
Keyword(s):  
Climate Change ◽  
Systematic Review ◽  
Behavioral Adaptation ◽  
Human Adaptation ◽  
Small Islands ◽  
Intergovernmental Panel ◽  
Natural Systems ◽  
Adaptation Response ◽  
Cultural Constraints ◽  
Global Evidence

AbstractConstraints and limits to adaptation are critical to understanding the extent to which human and natural systems can successfully adapt to climate change. We conduct a systematic review of 1,682 academic studies on human adaptation responses to identify patterns in constraints and limits to adaptation for different regions, sectors, hazards, adaptation response types, and actors. Using definitions of constraints and limits provided by the Intergovernmental Panel on Climate Change (IPCC), we find that most literature identifies constraints to adaptation but that there is limited literature focused on limits to adaptation. Central and South America and Small Islands generally report greater constraints and both hard and soft limits to adaptation. Technological, infrastructural, and ecosystem-based adaptation suggest more evidence of constraints and hard limits than other types of responses. Individuals and households face economic and socio-cultural constraints which also inhibit behavioral adaptation responses and may lead to limits. Finance, governance, institutional, and policy constraints are most prevalent globally. These findings provide early signposts for boundaries of human adaptation and are of high relevance for guiding proactive adaptation financing and governance from local to global scales.

scholarly journals The Effects of Hill-Robertson Interference Between Weakly Selected Mutations on Patterns of Molecular Evolution and Variation

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 929-944 ◽  
Author(s):  
Gilean A T McVean ◽  
Brian Charlesworth
Keyword(s):  
Codon Bias ◽  
Molecular Adaptation ◽  
Weak Selection ◽  
Multiple Loci ◽  
Locus Model ◽  
Fitness Consequences ◽  
Novel Variants ◽  
Population Sizes ◽  
The Hill ◽  
Reversible Mutation

Abstract Associations between selected alleles and the genetic backgrounds on which they are found can reduce the efficacy of selection. We consider the extent to which such interference, known as the Hill-Robertson effect, acting between weakly selected alleles, can restrict molecular adaptation and affect patterns of polymorphism and divergence. In particular, we focus on synonymous-site mutations, considering the fate of novel variants in a two-locus model and the equilibrium effects of interference with multiple loci and reversible mutation. We find that weak selection Hill-Robertson (wsHR) interference can considerably reduce adaptation, e.g., codon bias, and, to a lesser extent, levels of polymorphism, particularly in regions of low recombination. Interference causes the frequency distribution of segregating sites to resemble that expected from more weakly selected mutations and also generates specific patterns of linkage disequilibrium. While the selection coefficients involved are small, the fitness consequences of wsHR interference across the genome can be considerable. We suggest that wsHR interference is an important force in the evolution of nonrecombining genomes and may explain the unexpected constancy of codon bias across species of very different census population sizes, as well as several unusual features of codon usage in Drosophila.

scholarly journals Increased Response to Altered Auditory Feedback in Dyslexia: A Weaker Sensorimotor Magnet Implied in the Phonological Deficit

2017 ◽  
Vol 60 (3) ◽  
pp. 654-667 ◽  
Author(s):  
Mark R. van den Bunt ◽  
Margriet A. Groen ◽  
Takayuki Ito ◽  
Ana A. Francisco ◽  
Vincent L. Gracco ◽  
...  
Keyword(s):  
Native Speakers ◽  
Reading Group ◽  
Linear Mixed Effects Model ◽  
Phonological Representations ◽  
Linear Mixed Effects ◽  
Phonological Deficit ◽  
Adaptation Response ◽  
After Effect ◽  
Effect Phase ◽  
Phonological Abilities

Purpose The purpose of this study was to examine whether developmental dyslexia (DD) is characterized by deficiencies in speech sensory and motor feedforward and feedback mechanisms, which are involved in the modulation of phonological representations. Method A total of 42 adult native speakers of Dutch (22 adults with DD; 20 participants who were typically reading controls) were asked to produce /bep/ while the first formant (F1) of the /e/ was not altered (baseline), increased (ramp), held at maximal perturbation (hold), and not altered again (after-effect). The F1 of the produced utterance was measured for each trial and used for statistical analyses. The measured F1s produced during each phase were entered in a linear mixed-effects model. Results Participants with DD adapted more strongly during the ramp phase and returned to baseline to a lesser extent when feedback was back to normal (after-effect phase) when compared with the typically reading group. In this study, a faster deviation from baseline during the ramp phase, a stronger adaptation response during the hold phase, and a slower return to baseline during the after-effect phase were associated with poorer reading and phonological abilities. Conclusion The data of the current study are consistent with the notion that the phonological deficit in DD is associated with a weaker sensorimotor magnet for phonological representations.

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