A general theory for temperature dependence in biology

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(30)

Published: July 18, 2022

At present, there is no simple, first principles–based, and general model for quantitatively describing the full range of observed biological temperature responses. Here we derive a theory dependence in biology based on Eyring–Evans–Polanyi’s chemical reaction rates. Assuming only that conformational entropy molecules changes with temperature, enzyme rates which takes form an exponential function modified by power law describes characteristic asymmetric curved response. Based few additional principles, our can be used to predict response above level, thus spanning quantum classical scales. Our provides analytical description shape curves demonstrates its generality showing convergence all responses onto universal relationships—a data collapse—under appropriate normalization identifying optimal around 25 ∘ C, characterizing curves. The good fit empirical wide variety rates, times, steady-state quantities, from molecular ecological scales across multiple taxonomic groups (from viruses mammals). This simple framework understand impact quantities principles thermodynamics, bridging

Language: Английский

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Theory and classification of mass extinction causation

National Science Review, Journal Year: 2023, Volume and Issue: 11(1)

Published: Sept. 8, 2023

Theory regarding the causation of mass extinctions is in need systematization, which focus this contribution. Every extinction has both an ultimate cause, i.e. trigger that leads to various climato-environmental changes, and one or more proximate cause(s), specific changes result elevated biotic mortality. With regard causes, strong cases can be made bolide (i.e. meteor) impacts, large igneous province (LIP) eruptions bioevolutionary events have each triggered Phanerozoic Big Five extinctions, tectono-oceanic some second-order events. Apart from other astronomical triggers (e.g. solar flares, gamma bursts supernova explosions) remain entirely realm speculation. mechanisms, most are related either carbon-release carbon-burial processes, former being associated with climatic warming, ocean acidification, reduced marine productivity lower carbonate δ13C values, latter cooling, increased higher values. Environmental parameters such as redox conditions terrestrial weathering intensity do not show consistent relationships carbon-cycle changes. In context, usefully classified using a matrix factors. Among end-Cretaceous biocrisis example bolide-triggered event, end-Permian end-Triassic biocrises examples LIP-triggered events, Late Ordovician Devonian bioevolution-triggered Whereas bolide-impact LIP-eruption mechanisms appear invariably cause carbon release, variable e.g. burial during release modern anthropogenic climate little no impact due certain types ecosystem change advent first predators around end-Ediacaran; appearance Paleolithic human hunters Australasia Americas). Broadly speaking, studies suffered insufficiently critical thinking-an impartial survey extant evidence shows (i) hypotheses common impacts LIP eruptions) for all suspect given manifest differences patterns environmental among them; (ii) were long-term inconsistent mechanism; (iii) claims periodicity depended critically on now-disproven idea they shared extrinsic impacts).

Language: Английский

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Abiotic selection of microbial genome size in the global ocean

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: March 13, 2023

Abstract Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little currently known about how size of prokaryotic evolves global ocean and whether patterns reflect shifts resource availability epipelagic relatively stable deep-sea environmental conditions. Using 364 marine metagenomes, we investigate average genome uncultured planktonic prokaryotes varies across tropical polar oceans to hadal realm. We find that highest perennially cold ocean, reflecting elongation coding genes gene dosage effects due duplications interior microbiome. Moreover, rate change temperature 16-fold higher than with depth up 200 m. Our results demonstrate factors can influence ecological strategies

Language: Английский

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Toward a cohesive understanding of ecological complexity

Science Advances, Journal Year: 2023, Volume and Issue: 9(25)

Published: June 21, 2023

Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of is, therefore, critical progress in ecology conservation amidst escalating global environmental change. However, myriad definitions complexity excessive reliance on conventional scientific approaches hamper conceptual advances synthesis. may be better understood by following the solid theoretical basis system science (CSS). We review features ecological described within CSS conduct bibliometric text mining analyses characterize articles that refer complexity. Our demonstrate study is a highly heterogeneous, endeavor only weakly related CSS. Current research trends typically organized around basic theory, scaling, macroecology. leverage our generalities identified suggest more coherent cohesive way forward ecology.

Language: Английский

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Temperature responses of ecosystem respiration

Nature Reviews Earth & Environment, Journal Year: 2024, Volume and Issue: 5(8), P. 559 - 571

Published: July 16, 2024

Language: Английский

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Trees have overlapping potential niches that extend beyond their realized niches

Science, Journal Year: 2024, Volume and Issue: 385(6704), P. 75 - 80

Published: July 4, 2024

Tree species appear to prefer distinct climatic conditions, but the true nature of these preferences is obscured by interactions and dispersal, which limit species' ranges. We quantified realized potential thermal niches 188 North American tree conduct a continental-scale test architecture niches. found strong consistent evidence that occurring at extremes occupy less than three-quarters their niches, overlap mean annual temperature ~12°C. These results clarify breadth tolerances temperate support centrifugal organization Accounting for nonrealized components ecological will advance theory prediction in global change ecology.

Language: Английский

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Hotter is not (always) better: Embracing unimodal scaling of biological rates with temperature

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(2)

Published: Feb. 1, 2024

Rate-temperature scaling relationships have fascinated biologists for nearly two centuries and are increasingly important in our era of global climate change. These hypothesized to originate from the temperature-dependent kinetics rate-limiting biochemical reactions metabolism. Several prominent theories formalized this hypothesis using Arrhenius model, which characterizes a monotonic temperature dependence an activation energy E. However, ubiquitous unimodal nature biological responses presents theoretical, methodological, conceptual challenges that restrict promise insight, prediction, progress. Here we review development key hypotheses methods temperature-scaling rates. Using simulations, examine constraints models, illustrating their sensitivity data nuances such as range noise, tendency yield variable underestimated E, with critical consequences change predictions. We also evaluate behaviour models when applied incomplete noisy datasets. conclude recommendations resolving these future research, advocate shift better characterize full responses.

Language: Английский

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DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 25(1)

Published: Nov. 22, 2023

Abstract The enzyme turnover rate, ${k}_{cat}$, quantifies kinetics by indicating the maximum efficiency of catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because cost experimental measurements. To predict and account strong temperature dependence, DLTKcat was developed this study demonstrated superior performance (log10-scale root mean squared error = 0.88, R-squared 0.66) than previously published models. Through two case studies, showed ability to effects protein sequence mutations changes on values. Although quantitative accuracy is not high enough yet model responses cellular metabolism changes, has potential eventually become a computational tool describe dependence biological systems.

Language: Английский

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Model-driven insights into the effects of temperature on metabolism

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 67, P. 108203 - 108203

Published: June 20, 2023

Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic molecular mechanisms underlying temperature responses paves way to develop approaches for mitigating effects of future climate scenarios. A systems view on physiology can be obtained by focusing metabolism since: (i) its functions depend transcription translation (ii) outcomes support organisms' development, growth, reproduction. Here we provide a systematic review modelling efforts directed investigating properties single biochemical reactions, system-level traits, metabolic subsystems, whole-cell across prokaryotes eukaryotes. We compare contrast computational theories that facilitate key enzymes their consideration in constraint-based as well kinetic models metabolism. In addition, summary insights from approaches, facilitating integration omics data temperature-modulated experiments with networks, resulting biotechnological applications. Lastly, perspective how types profit developments machine learning layers improve model-driven into relevant

Language: Английский

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Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers

Applied and Environmental Microbiology, Journal Year: 2023, Volume and Issue: 89(5)

Published: May 10, 2023

One of the largest uncertainties global warming is if microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades research effort, strength this to remains unknown.

Language: Английский

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