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FEMS Microbiology Ecology Mar 2023Efforts to isolate uncultured microorganisms over the last century and a half, as well as the advanced 'omics' technologies developed over the last three decades, have... (Review)
Review
Efforts to isolate uncultured microorganisms over the last century and a half, as well as the advanced 'omics' technologies developed over the last three decades, have greatly increased the knowledge and resources of microbiology. However, many cellular functions such as growth remain unknown in most of the microbial diversity identified through genomic sequences from environmental samples, as evidenced by the increasingly precise observations of the phenomenon known as the 'great plate count anomaly'. Faced with the many microbial cells recalcitrant to cultivation present in environmental samples, Epstein proposed the 'scout' model, characterised by a dominance of dormant cells whose awakening would be strictly stochastic. Unfortunately, this hypothesis leaves few exploitable possibilities for microbial cultivation. This review proposes that many microorganisms follow the 'comfort timing' strategy, characterised by an exit from dormancy responding to a set of environmental conditions close to optimal for growth. This 'comfort timing' strategy offers the possibility of designing culture processes that could isolate a larger proportion of uncultured microorganisms. Two methods are briefly proposed in this article. In addition, the advantages of dormancy, of the 'scout' model and of the 'comfort timing' strategy for survival under difficult conditions, but also for colonisation of environments, are discussed.
Topics: Genomics; Adaptation, Physiological; Acclimatization
PubMed: 36921985
DOI: 10.1093/femsec/fiad026 -
PloS One 2014Reef managers cannot fight global warming through mitigation at local scale, but they can use information on thermal patterns to plan for reserve networks that maximize...
Reef managers cannot fight global warming through mitigation at local scale, but they can use information on thermal patterns to plan for reserve networks that maximize the probability of persistence of their reef system. Here we assess previous methods for the design of reserves for climate change and present a new approach to prioritize areas for conservation that leverages the most desirable properties of previous approaches. The new method moves the science of reserve design for climate change a step forwards by: (1) recognizing the role of seasonal acclimation in increasing the limits of environmental tolerance of corals and ameliorating the bleaching response; (2) using the best proxy for acclimatization currently available; (3) including information from several bleaching events, which frequency is likely to increase in the future; (4) assessing relevant variability at country scales, where most management plans are carried out. We demonstrate the method in Honduras, where a reassessment of the marine spatial plan is in progress.
Topics: Acclimatization; Animals; Anthozoa; Climate Change; Conservation of Natural Resources; Coral Reefs; Environmental Monitoring; Seawater; Temperature
PubMed: 25333380
DOI: 10.1371/journal.pone.0110634 -
American Journal of Physiology.... Jan 2005During the past several decades, many risk factors for cerebrovascular and cardiovascular disease have been identified. More recently, it has been appreciated that... (Review)
Review
During the past several decades, many risk factors for cerebrovascular and cardiovascular disease have been identified. More recently, it has been appreciated that inadequate nutrition and/or other intrauterine factors during fetal development may play an important role in the genesis of these conditions. An additional stress factor that may "program" the fetus for disease later in life is chronic hypoxia. In studies originally designed to examine the function of developing cerebral arterial function in response to long-term hypoxia (LTH), it has become clear that many cellular and subcellular changes may have important implications for later life. Here we review some of the significant alterations in fetal cerebral artery structure and function induced by high-altitude (3,820 m, 12,470 ft) LTH ( approximately 110 days). LTH is associated with augmentation or upregulation of presynaptic functions, including responses to perivascular (i.e., sympathetic) nerve stimulation, and structural maturational changes. In contrast, many postsynaptic functions related to the Ca(2+)-dependent contractile pathway tend to be downregulated, whereas elements of the Ca(2+)-independent contraction pathway are upregulated. The results emphasize the role of high-altitude LTH in modulating many aspects of electromechanical and pharmacomechanical coupling in the developing cerebral vasculature. A complicating factor is that the regulation of cerebrovascular tone by Ca(2+)-dependent and Ca(2+)-independent pathways changes significantly as a function of maturational age. In addition to highlighting independent regulation of various elements of the signal transduction cascade, the studies demonstrate the potential for LTH to program the fetus for cerebrovascular and other disease as an adult.
Topics: Acclimatization; Adaptation, Physiological; Altitude; Animals; Brain; Cerebrovascular Circulation; Fetal Hypoxia; Fetus; Oxygen; Signal Transduction
PubMed: 15590993
DOI: 10.1152/ajpregu.00462.2004 -
Methods in Molecular Biology (Clifton,... 2023The ATG8 family of proteins regulates the autophagy process from the autophagosome maturation and cargo recruitment up to degradation. Autophagy dysfunction is involved...
The ATG8 family of proteins regulates the autophagy process from the autophagosome maturation and cargo recruitment up to degradation. Autophagy dysfunction is involved in the development of multiple diseases. The LC3 interacting region (LIR)-based molecular traps have been designed to isolate endogenous ATG8 proteins and their interactors in order to facilitate the study of selective autophagy events. Here, we summarize protocols describing LC3 traps and sample preparation as well as adaptations for the analysis of ATG8 proteins in different biological models. This protocol was optimized to prepare affinity columns, reduce background, and improve the protein recovery to be analyzed by immunodetection with antibodies recognizing proteins of interest.
Topics: Autophagy-Related Protein 8 Family; Macroautophagy; Acclimatization; Antibodies; Autophagy
PubMed: 36446976
DOI: 10.1007/978-1-0716-2859-1_14 -
Molecular Ecology Jan 2023Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive...
Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.
Topics: Genetic Variation; Selection, Genetic; Bayes Theorem; Adaptation, Physiological; Acclimatization
PubMed: 36301304
DOI: 10.1111/mec.16750 -
The Journal of Experimental Biology May 2023Multiple variables determine the success of an escape response of an animal, and the rapidity of the escape manoeuvre is often the most important. Fan worms (Annelida:...
Multiple variables determine the success of an escape response of an animal, and the rapidity of the escape manoeuvre is often the most important. Fan worms (Annelida: Sabellidae) can rapidly withdraw their tentacles, which are covered in heavily ciliated ramifications called pinnules, into their tubes to protect them from approaching threats. Here, we explore the dynamic and mechanistic features behind this escape manoeuvre. The escape responses of fan worms were recorded by high-speed videography and quantified by computerized motion analysis, showing an ultrahigh retraction speed of 272±135 mm s-1 (8±4 body lengths s-1). We found that fan worms possess powerful muscle-driven systems, which can generate contractive forces up to 36 times their body weight. In order to achieve these rapid, forceful movements through seawater without damaging their tentacles, fan worms have developed functional morphological adaptations to reduce fluidic drag, including the flattening of their radiolar pinnules and the deformation of bodily segmental ridges. Our hydrodynamic models indicate that these mechanical processes can decrease fluidic drag by 47%, trapped mass by 75% and friction coefficient by 89%. These strategies allow fan worms to execute rapid escape responses and could inspire the design of fast in-pipe robots.
Topics: Animals; Annelida; Polychaeta; Body Weight; Movement; Acclimatization
PubMed: 37073720
DOI: 10.1242/jeb.245731 -
Communications Biology Aug 2023Insect wings are adaptive structures that automatically respond to flight forces, surpassing even cutting-edge engineering shape-morphing systems. A widely accepted but...
Insect wings are adaptive structures that automatically respond to flight forces, surpassing even cutting-edge engineering shape-morphing systems. A widely accepted but not yet explicitly tested hypothesis is that a 3D component in the wing's proximal region, known as basal complex, determines the quality of wing shape changes in flight. Through our study, we validate this hypothesis, demonstrating that the basal complex plays a crucial role in both the quality and quantity of wing deformations. Systematic variations of geometric parameters of the basal complex in a set of numerical models suggest that the wings have undergone adaptations to reach maximum camber under loading. Inspired by the design of the basal complex, we develop a shape-morphing mechanism that can facilitate the shape change of morphing blades for wind turbines. This research enhances our understanding of insect wing biomechanics and provides insights for the development of simplified engineering shape-morphing systems.
Topics: Animals; Acclimatization; Biomechanical Phenomena; Engineering
PubMed: 37591993
DOI: 10.1038/s42003-023-05206-1 -
Current Biology : CB Jan 2023In many plants, flowering time is influenced by daylength as an adaptive response. In soybean (Glycine max) cultivars, however, photoperiodic flowering reduces crop...
In many plants, flowering time is influenced by daylength as an adaptive response. In soybean (Glycine max) cultivars, however, photoperiodic flowering reduces crop yield and quality in high-latitude regions. Understanding the genetic basis of wild soybean (Glycine soja) adaptation to high latitudes could aid breeding of improved cultivars. Here, we identify the Tof4 (Time of flowering 4) locus, which encodes by an E1-like protein, E1La, that represses flowering and enhances adaptation to high latitudes in wild soybean. Moreover, we found that Tof4 physically associates with the promoters of two important FLOWERING LOCUS T (FT2a and FT5a) and with Tof5 to inhibit their transcription under long photoperiods. The effect of Tof4 on flowering and maturity is mediated by FT2a and FT5a proteins. Intriguingly, Tof4 and the key flowering repressor E1 independently but additively regulate flowering time, maturity, and grain yield in soybean. We determined that weak alleles of Tof4 have undergone natural selection, facilitating adaptation to high latitudes in wild soybean. Notably, over 71.5% of wild soybean accessions harbor the mutated alleles of Tof4 or a previously reported gain-of-function allele Tof5, suggesting that these two loci are the genetic basis of wild soybean adaptation to high latitudes. Almost no cultivated soybean carries the mutated tof4 allele. Introgression of the tof4-1 and Tof5 alleles into modern soybean or editing E1 family genes thus represents promising avenues to obtain early-maturity soybean, thereby improving productivity in high latitudes.
Topics: Glycine max; Plant Proteins; Plant Breeding; Adaptation, Physiological; Acclimatization; Photoperiod; Flowers; Gene Expression Regulation, Plant
PubMed: 36538932
DOI: 10.1016/j.cub.2022.11.061 -
Journal of Phycology Apr 2019Temperate kelp forests (Laminarians) are threatened by temperature stress due to ocean warming and photoinhibition due to increased light associated with canopy loss....
Temperate kelp forests (Laminarians) are threatened by temperature stress due to ocean warming and photoinhibition due to increased light associated with canopy loss. However, the potential for evolutionary adaptation in kelp to rapid climate change is not well known. This study examined family-level variation in physiological and photosynthetic traits in the early life-cycle stages of the ecologically important Australasian kelp Ecklonia radiata and the response of E. radiata families to different temperature and light environments using a family × environment design. There was strong family-level variation in traits relating to morphology (surface area measures, branch length, branch count) and photosynthetic performance (F /F ) in both haploid (gametophyte) and diploid (sporophyte) stages of the life-cycle. Additionally, the presence of family × environment interactions showed that offspring from different families respond differently to temperature and light in the branch length of male gametophytes and oogonia surface area of female gametophytes. Negative responses to high temperatures were stronger for females vs. males. Our findings suggest E. radiata may be able to respond adaptively to climate change but studies partitioning the narrow vs. broad sense components of heritable variation are needed to establish the evolutionary potential of E. radiata to adapt under climate change.
Topics: Acclimatization; Animals; Climate Change; Ecosystem; Female; Kelp; Life Cycle Stages; Male
PubMed: 30506918
DOI: 10.1111/jpy.12820 -
Nature Genetics Dec 2020Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. The genetic mechanisms of this remarkable...
Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. The genetic mechanisms of this remarkable evolutionary success are not well understood. By whole-genome sequencing of populations from 25 subspecies within the genera Triticum and Aegilops, we identified composite introgression from wild populations contributing to a substantial portion (4-32%) of the bread wheat genome, which increased the genetic diversity of bread wheat and allowed its divergent adaptation. Meanwhile, convergent adaptation to human selection showed 2- to 16-fold enrichment relative to random expectation-a certain set of genes were repeatedly selected in Triticum species despite their drastic differences in ploidy levels and growing zones, indicating the important role of evolutionary constraints in shaping the adaptive landscape of bread wheat. These results showed the genetic necessities of wheat as a global crop and provided new perspectives on transferring adaptive success across species for crop improvement.
Topics: Acclimatization; Biological Evolution; Bread; Crops, Agricultural; Evolution, Molecular; Genetic Variation; Genome, Plant; Phylogeny; Triticum; Whole Genome Sequencing
PubMed: 33106631
DOI: 10.1038/s41588-020-00722-w