scholarly journals Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root

2014 ◽  
Vol 5 ◽  
Author(s):  
Natalie M. Clark ◽  
Maria A. de Luis Balaguer ◽  
Rosangela Sozzani
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Arabidopsis Root ◽  
Auxin Gradient

Circadian clocks and phosphorylation: Insights from computational modeling

2009 ◽  
Vol 4 (3) ◽  
pp. 290-303 ◽  
Author(s):  
Jean-Christophe Leloup
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Regulatory Mechanism ◽  
Circadian Clocks ◽  
Recent Experimental Data ◽  
Sleep Phase ◽  
Clock Proteins ◽  
High Degree ◽  
Clock Protein

AbstractCircadian clocks are based on a molecular mechanism regulated at the transcriptional, translational and post-translational levels. Recent experimental data unravel a complex role of the phosphorylations in these clocks. In mammals, several kinases play differential roles in the regulation of circadian rhythmicity. A dysfunction in the phosphorylation of one clock protein could lead to sleep disorders such as the Familial Advanced Sleep Phase Disorder, FASPS. Moreover, several drugs are targeting kinases of the circadian clocks and can be used in cancer chronotherapy or to treat mood disorders. In Drosophila, recent experimental observations also revealed a complex role of the phosphorylations. Because of its high degree of homology with mammals, the Drosophila system is of particular interest. In the circadian clock of cyanobacteria, an atypical regulatory mechanism is based only on three clock proteins (KaiA, KaiB, KaiC) and ATP and is sufficient to produce robust temperature-compensated circadian oscillations of KaiC phosphorylation. This review will show how computational modeling has become a powerful and useful tool in investigating the regulatory mechanism of circadian clocks, but also how models can give rise to testable predictions or reveal unexpected results.

scholarly journals Fixation durations in scene viewing: Experimental data and computational modeling

2010 ◽  
Vol 8 (6) ◽  
pp. 1107-1107 ◽  
Author(s):  
A. Nuthmann ◽  
T. J. Smith ◽  
J. M. Henderson
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Fixation Durations ◽  
Scene Viewing

scholarly journals An Auxin Gradient and Maximum in the Arabidopsis Root Apex Shown by High-Resolution Cell-Specific Analysis of IAA Distribution and Synthesis

2009 ◽  
Vol 21 (6) ◽  
pp. 1659-1668 ◽  
Author(s):  
Sara V. Petersson ◽  
Annika I. Johansson ◽  
Mariusz Kowalczyk ◽  
Alexander Makoveychuk ◽  
Jean Y. Wang ◽  
...  
Keyword(s):  
High Resolution ◽  
Root Apex ◽  
Arabidopsis Root ◽  
Specific Analysis ◽  
Resolution Cell ◽  
Auxin Gradient

Computational Modeling to Predict Mechanical Function of Joints: Application to the Lower Leg With Simulation of Two Cadaver Studies

2007 ◽  
Vol 129 (6) ◽  
pp. 811-817 ◽  
Author(s):  
Peter C. Liacouras ◽  
Jennifer S. Wayne
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Computational Models ◽  
Three Dimensional ◽  
Lower Leg ◽  
Joint Kinematics ◽  
Syndesmotic Injury ◽  
Joint Function ◽  
Calcaneofibular Ligament ◽  
Cadaver Studies

Computational models of musculoskeletal joints and limbs can provide useful information about joint mechanics. Validated models can be used as predictive devices for understanding joint function and serve as clinical tools for predicting the outcome of surgical procedures. A new computational modeling approach was developed for simulating joint kinematics that are dictated by bone/joint anatomy, ligamentous constraints, and applied loading. Three-dimensional computational models of the lower leg were created to illustrate the application of this new approach. Model development began with generating three-dimensional surfaces of each bone from CT images and then importing into the three-dimensional solid modeling software SOLIDWORKS and motion simulation package COSMOSMOTION. Through SOLIDWORKS and COSMOSMOTION, each bone surface file was filled to create a solid object and positioned necessary components added, and simulations executed. Three-dimensional contacts were added to inhibit intersection of the bones during motion. Ligaments were represented as linear springs. Model predictions were then validated by comparison to two different cadaver studies, syndesmotic injury and repair and ankle inversion following ligament transection. The syndesmotic injury model was able to predict tibial rotation, fibular rotation, and anterior/posterior displacement. In the inversion simulation, calcaneofibular ligament extension and angles of inversion compared well. Some experimental data proved harder to simulate accurately, due to certain software limitations and lack of complete experimental data. Other parameters that could not be easily obtained experimentally can be predicted and analyzed by the computational simulations. In the syndesmotic injury study, the force generated in the tibionavicular and calcaneofibular ligaments reduced with the insertion of the staple, indicating how this repair technique changes joint function. After transection of the calcaneofibular ligament in the inversion stability study, a major increase in force was seen in several of the ligaments on the lateral aspect of the foot and ankle, indicating the recruitment of other structures to permit function after injury. Overall, the computational models were able to predict joint kinematics of the lower leg with particular focus on the ankle complex. This same approach can be taken to create models of other limb segments such as the elbow and wrist. Additional parameters can be calculated in the models that are not easily obtained experimentally such as ligament forces, force transmission across joints, and three-dimensional movement of all bones. Muscle activation can be incorporated in the model through the action of applied forces within the software for future studies.

scholarly journals Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching

2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Samuel E. Jackson ◽  
Ian Vernon ◽  
Junli Liu ◽  
Keith Lindsey
Keyword(s):  
Experimental Data ◽  
Mathematical Model ◽  
Parameter Space ◽  
History Matching ◽  
Parameter Spaces ◽  
Arabidopsis Root ◽  
Biologically Relevant ◽  
Hormonal Crosstalk ◽  
The Mathematical Model ◽  
Insight Into

AbstractA major challenge in plant developmental biology is to understand how plant growth is coordinated by interacting hormones and genes. To meet this challenge, it is important to not only use experimental data, but also formulate a mathematical model. For the mathematical model to best describe the true biological system, it is necessary to understand the parameter space of the model, along with the links between the model, the parameter space and experimental observations. We develop sequential history matching methodology, using Bayesian emulation, to gain substantial insight into biological model parameter spaces. This is achieved by finding sets of acceptable parameters in accordance with successive sets of physical observations. These methods are then applied to a complex hormonal crosstalk model for Arabidopsis root growth. In this application, we demonstrate how an initial set of 22 observed trends reduce the volume of the set of acceptable inputs to a proportion of 6.1 × 10−7 of the original space. Additional sets of biologically relevant experimental data, each of size 5, reduce the size of this space by a further three and two orders of magnitude respectively. Hence, we provide insight into the constraints placed upon the model structure by, and the biological consequences of, measuring subsets of observations.

scholarly journals Ten simple rules for the computational modeling of behavioral data

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Robert C Wilson ◽  
Anne GE Collins
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Neural Correlates ◽  
Behavioral Data ◽  
Great Power ◽  
Great Responsibility ◽  
Simple Rules ◽  
Modeling Techniques ◽  
The Mind

Computational modeling of behavior has revolutionized psychology and neuroscience. By fitting models to experimental data we can probe the algorithms underlying behavior, find neural correlates of computational variables and better understand the effects of drugs, illness and interventions. But with great power comes great responsibility. Here, we offer ten simple rules to ensure that computational modeling is used with care and yields meaningful insights. In particular, we present a beginner-friendly, pragmatic and details-oriented introduction on how to relate models to data. What, exactly, can a model tell us about the mind? To answer this, we apply our rules to the simplest modeling techniques most accessible to beginning modelers and illustrate them with examples and code available online. However, most rules apply to more advanced techniques. Our hope is that by following our guidelines, researchers will avoid many pitfalls and unleash the power of computational modeling on their own data.

scholarly journals Mechanism of Consistent Gyrus Formation: an Experimental and Computational Study

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tuo Zhang ◽  
Mir Jalil Razavi ◽  
Xiao Li ◽  
Hanbo Chen ◽  
Tianming Liu ◽  
...  
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Computational Study ◽  
Regional Growth ◽  
Cortical Plate ◽  
Joint Analysis ◽  
Growth Speed ◽  
Differential Growth ◽  
Analysis Scheme ◽  
Special Area

Abstract As a significant type of cerebral cortical convolution pattern, the gyrus is widely preserved across species. Although many hypotheses have been proposed to study the underlying mechanisms of gyrus formation, it is currently still far from clear which factors contribute to the regulation of consistent gyrus formation. In this paper, we employ a joint analysis scheme of experimental data and computational modeling to investigate the fundamental mechanism of gyrus formation. Experimental data on mature human brains and fetal brains show that thicker cortices are consistently found in gyral regions and gyral cortices have higher growth rates. We hypothesize that gyral convolution patterns might stem from heterogeneous regional growth in the cortex. Our computational simulations show that gyral convex patterns may occur in locations where the cortical plate grows faster than the cortex of the brain. Global differential growth can only produce a random gyrification pattern, but it cannot guarantee gyrus formation at certain locations. Based on extensive computational modeling and simulations, it is suggested that a special area in the cerebral cortex with a relatively faster growth speed could consistently engender gyri.

scholarly journals Combined changes in Wnt signaling response and contact inhibition induce altered proliferation in radiation-treated intestinal crypts

2016 ◽  
Vol 27 (11) ◽  
pp. 1863-1874 ◽  
Author(s):  
S.-J. Dunn ◽  
J. M. Osborne ◽  
P. L. Appleton ◽  
I. Näthke
Keyword(s):  
Experimental Data ◽  
Computational Modeling ◽  
Wnt Signaling ◽  
Recovery Period ◽  
Control Cell ◽  
Contact Inhibition ◽  
Driving Mechanism ◽  
Cycle Duration ◽  
Proliferation Zone ◽  
Proliferative Zone

Curative intervention is possible if colorectal cancer is identified early, underscoring the need to detect the earliest stages of malignant transformation. A candidate biomarker is the expanded proliferative zone observed in crypts before adenoma formation, also found in irradiated crypts. However, the underlying driving mechanism for this is not known. Wnt signaling is a key regulator of proliferation, and elevated Wnt signaling is implicated in cancer. Nonetheless, how cells differentiate Wnt signals of varying strengths is not understood. We use computational modeling to compare alternative hypotheses about how Wnt signaling and contact inhibition affect proliferation. Direct comparison of simulations with published experimental data revealed that the model that best reproduces proliferation patterns in normal crypts stipulates that proliferative fate and cell cycle duration are set by the Wnt stimulus experienced at birth. The model also showed that the broadened proliferation zone induced by tumorigenic radiation can be attributed to cells responding to lower Wnt concentrations and dividing at smaller volumes. Application of the model to data from irradiated crypts after an extended recovery period permitted deductions about the extent of the initial insult. Application of computational modeling to experimental data revealed how mechanisms that control cell dynamics are altered at the earliest stages of carcinogenesis.

scholarly journals A 1000-year-old mystery solved: Unlocking the molecular structure for the medieval blue from Chrozophora tinctoria, also known as folium

2020 ◽  
Vol 6 (16) ◽  
pp. eaaz7772 ◽  
Author(s):  
P. Nabais ◽  
J. Oliveira ◽  
F. Pina ◽  
N. Teixeira ◽  
V. de Freitas ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Experimental Data ◽  
Cultural Heritage ◽  
Computational Modeling ◽  
21St Century ◽  
Interdisciplinary Approach ◽  
Computational Studies ◽  
Analytical Characterization ◽  
Medieval Manuscript

The molecular structure of the medieval watercolor known as folium has finally been solved in the 21st century. The interdisciplinary approach taken was the key to producing extracts that had been prepared following medieval instructions, and shows the blue/purple chromophore as the major dye in Chrozophora tinctoria fruits (shell). A multi-analytical characterization of its structure was made using HPLC-DAD-MS, GC-MS, NMR (1H, 13C, COSY, HSQC, HMBC, INADEQUATE), and computational studies. The results demonstrate that the blue compound corresponds to 6′-hydroxy-4,4′-dimethoxy-1,1′-dimethyl-5′-{[3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}-[3,3′-bipyridine]-2,2′,5,6(1H,1′H)-tetraone, a hermidin derivative, which we named chrozophoridin. Experimental data and computational modeling studies show that this mono-glycosylated dimer is represented by two stable isomers (atropisomers). This is an indispensable piece of knowledge for the characterization of this medieval dye in works of art such as medieval manuscript illuminations and for testing its stability and contributes to the preservation of our cultural heritage.

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