Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluating the Arrhenius equation for developmental processes.

ABSTRACT: The famous Arrhenius equation is well suited to describing the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multi-step biological processes, using frog and fruit fly embryogenesis as two canonical models. We find that the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental intervals scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multi-step reactions of idealized chemical networks, we are unable to generate comparable deviations from linearity. In contrast, we find the two enzymes GAPDH and β-galactosidase show non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius equation regardless of non-uniform developmental scaling and propose that the observed departure from this law likely results more from non-idealized individual steps rather than from the complexity of the system.

SUBMITTER: Crapse J

PROVIDER: S-EPMC8377445 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Decoupling the Arrhenius equation <i>via</i> mechanochemistry.

Project description:Mechanochemistry continues to reveal new possibilities in chemistry including the opportunity for "greening" reactions. Nevertheless, a clear understanding of the energetic transformations within mechanochemical systems remains elusive. We employed a uniquely modified ball mill and strategically chosen Diels-Alder reactions to evaluate the role of several ball-milling variables. This revealed three different energetic regions that we believe are defining characteristics of most, if not all, mechanochemical reactors. Relative to the locations of a given ball mill's regions, activation energy determines whether a reaction is energetically easy (Region I), challenging (Region II), or unreasonable (Region III) in a given timeframe. It is in Region II, that great sensitivity to mechanochemical conditions such as vial material and oscillation frequency emerge. Our unique modifications granted control of reaction vessel temperature, which in turn allowed control of the locations of Regions I, II, and III for our mill. Taken together, these results suggest envisioning vibratory mills (and likely other mechanochemical methodologies) as molecular-collision facilitating devices that act upon molecules occupying a thermally-derived energy distribution. This unifies ball-milling energetics with solution-reaction energetics via a common tie to the Arrhenius equation, but gives mechanochemistry the unique opportunity to influence either half of the equation. In light of this, we discuss a strategy for translating solvent-based reaction conditions to ball milling conditions. Lastly, we posit that the extra control via frequency factor grants mechanochemistry the potential for greater selectivity than conventional solution reactions.

| S-EPMC5609516 | biostudies-literature

Colistimethate Acidic Hydrolysis Revisited: Arrhenius Equation Modeling Using UPLC-QToF MS.

Project description:Colistimethate (CMS), the prodrug of polymyxin E (colistin), is an antibiotic widely used as a last-line therapy against multidrug resistant Gram-negative bacteria, but little is known about its pharmacokinetics as its administration has stopped as a result of high neuro- and nephro-toxicity. The measurement of CMS levels in patients' biological fluids is of great importance in order to find the optimal dose regimen reducing the drug toxicity. Until now, CMS assay methods are based on the indirect determination after its hydrolysis to colistin (CS). Herein, the aim is to find the optimal conditions for the complete hydrolysis of CMS to CS. The reaction was studied at accelerated conditions: 40 °C, 50 °C, and 60 °C, and the results were evaluated by assessing the Arrhenius equation and computation employing the Tenua software. A validated analytical methodology based on ultra-performance liquid chromatography (UPLC) coupled to a hybrid quadrupole time of flight (QToF) instrument is developed for the simultaneous measurement of CMS and CS. The current methodology resulted in complete hydrolysis, in contrast with the previously reported one.

| S-EPMC7830259 | biostudies-literature

Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.

Project description:Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.

| S-EPMC4629273 | biostudies-literature

Investigation of a Coupled Arrhenius-Type/Rossard Equation of AH36 Material.

Project description:High-temperature tensile testing of AH36 material in a wide range of temperatures (1173-1573 K) and strain rates (10-4-10-2 s-1) has been obtained by using a Gleeble system. These experimental stress-strain data have been adopted to develop the constitutive equation. The constitutive equation of AH36 material was suggested based on the modified Arrhenius-type equation and the modified Rossard equation respectively. The results indicate that the constitutive equation is strongly influenced by temperature and strain, especially strain. Moreover, there is a good agreement between the predicted data of the modified Arrhenius-type equation and the experimental results when the strain is greater than 0.02. There is also good agreement between the predicted data of the Rossard equation and the experimental results when the strain is less than 0.02. Therefore, a coupled equation where the modified Arrhenius-type equation and Rossard equation are combined has been proposed to describe the constitutive equation of AH36 material according to the different strain values in order to improve the accuracy. The correlation coefficient between the computed and experimental flow stress data was 0.998. The minimum value of the average absolute relative error shows the high accuracy of the coupled equation compared with the two modified equations.

| S-EPMC5507010 | biostudies-other

Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii.

Project description:Endogenous circadian rhythms allow living organisms to anticipate daily variations in their natural environment. Temperature regulation and entrainment mechanisms of circadian clocks are still poorly understood. To better understand the molecular basis of these processes, we built a mathematical model based on experimental data examining temperature regulation of the circadian RNA-binding protein CHLAMY1 from the unicellular green alga Chlamydomonas reinhardtii, simulating the effect of temperature on the rates by applying the Arrhenius equation. Using numerical simulations, we demonstrate that our model is temperature-compensated and can be entrained to temperature cycles of various length and amplitude. The range of periods that allow entrainment of the model depends on the shape of the temperature cycles and is larger for sinusoidal compared to rectangular temperature curves. We show that the response to temperature of protein (de)phosphorylation rates play a key role in facilitating temperature entrainment of the oscillator in Chlamydomonas reinhardtii. We systematically investigated the response of our model to single temperature pulses to explain experimentally observed phase response curves.

| S-EPMC3388193 | biostudies-literature

Evaluating Food Policy Councils Using Structural Equation Modeling.

Project description:At least 282 Food Policy Councils (FPCs) are currently working to improve access to healthy foods in their communities by connecting food system sectors, gathering community input, and advising food policy. Empirical research on FPCs is limited. This study empirically evaluates FPCs to better understand the relationships between Organizational Capacity, Social Capital, and Council Effectiveness by testing a FPC Framework adapted from Allen and colleagues (2012). Members of all FPCs in the U.S., Canada, and Native American Tribes and First Nations were invited to complete the Food Policy Council Self-Assessment Tool (FPC-SAT). Structural equation modeling was used to test the FPC Framework. Three hundred and fifty-four FPC members from 95 councils completed the FPC-SAT. After slight modification, a revised FPC Framework was a good fit with the data (?2 = 40.085, df = 24, p-value = .021, comparative fit index = 0.988, Tucker Lewis index = 0.982, root mean squared error of approximation = 0.044, p-close = .650). A moderation analysis revealed that community context influences the relationship between Social Capital and Council Effectiveness within the FPC Framework. The FPC Framework can guide capacity building interventions and FPC evaluations. The empirically tested framework can help FPCs efficiently work toward achieving their missions and improving their local food system.

| S-EPMC7262635 | biostudies-literature

Developmental processes in face perception.

Project description:Understanding the developmental origins of face recognition has been the goal of many studies of various approaches. Contributions of experience-expectant mechanisms (early component), like perceptual narrowing, and lifetime experience (late component) to face processing remain elusive. By investigating captive chimpanzees of varying age, a rare case of a species with lifelong exposure to non-conspecific faces at distinctive levels of experience, we can disentangle developmental components in face recognition. We found an advantage in discriminating chimpanzee above human faces in young chimpanzees, reflecting a predominant contribution of an early component that drives the perceptual system towards the conspecific morphology, and an advantage for human above chimpanzee faces in old chimpanzees, reflecting a predominant late component that shapes the perceptual system along the critical dimensions of the face exposed to. We simulate the contribution of early and late components using computational modeling and mathematically describe the underlying functions.

| S-EPMC3540399 | biostudies-literature

Developmental processes in Ediacara macrofossils.

Project description:The Ediacara Biota preserves the oldest fossil evidence of abundant, complex metazoans. Despite their significance, assigning individual taxa to specific phylogenetic groups has proved problematic. To better understand these forms, we identify developmentally controlled characters in representative taxa from the Ediacaran White Sea assemblage and compare them with the regulatory tools underlying similar traits in modern organisms. This analysis demonstrates that the genetic pathways for multicellularity, axial polarity, musculature, and a nervous system were likely present in some of these early animals. Equally meaningful is the absence of evidence for major differentiation of macroscopic body units, including distinct organs, localized sensory machinery or appendages. Together these traits help to better constrain the phylogenetic position of several key Ediacara taxa and inform our views of early metazoan evolution. An apparent lack of heads with concentrated sensory machinery or ventral nerve cords in such taxa supports the hypothesis that these evolved independently in disparate bilaterian clades.

| S-EPMC7934905 | biostudies-literature

Erroneous Arrhenius: modified arrhenius model best explains the temperature dependence of ectotherm fitness.

Project description:The initial rise of fitness that occurs with increasing temperature is attributed to Arrhenius kinetics, in which rates of reaction increase exponentially with increasing temperature. Models based on Arrhenius typically assume single rate-limiting reactions over some physiological temperature range for which all the rate-limiting enzymes are in 100% active conformation. We test this assumption using data sets for microbes that have measurements of fitness (intrinsic rate of population growth) at many temperatures and over a broad temperature range and for diverse ectotherms that have measurements at fewer temperatures. When measurements are available at many temperatures, strictly Arrhenius kinetics are rejected over the physiological temperature range. However, over a narrower temperature range, we cannot reject strictly Arrhenius kinetics. The temperature range also affects estimates of the temperature dependence of fitness. These results indicate that Arrhenius kinetics only apply over a narrow range of temperatures for ectotherms, complicating attempts to identify general patterns of temperature dependence.

| S-EPMC4629913 | biostudies-literature

Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes.

Project description:The chemical master equation and its continuum approximations are indispensable tools in the modeling of chemical reaction networks. These are routinely used to capture complex nonlinear phenomena such as multimodality as well as transient events such as first-passage times, that accurately characterise a plethora of biological and chemical processes. However, some mechanisms, such as heterogeneous cellular growth or phenotypic selection at the population level, cannot be represented by the master equation and thus have been tackled separately. In this work, we propose a unifying framework that augments the chemical master equation to capture such auxiliary dynamics, and we develop and analyse a numerical solver that accurately simulates the system dynamics. We showcase these contributions by casting a diverse array of examples from the literature within this framework and applying the solver to both match and extend previous studies. Analytical calculations performed for each example validate our numerical results and benchmark the solver implementation.

| S-EPMC8352075 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data