RNA-sequencing and Mathematical Modeling Identify Suite of Light-sensitive Circadian Genes in an Orb-web Weaving Spider

Abstract BackgroundMost organisms rely on a molecular circadian clock to orchestrate a wide range of physiological processes to match the 24-hour day. These molecular clocks are typically based on a negative feedback loop among a small set of proteins that govern the circadian output. Light or other environmental conditions can reset the circadian clock, but true circadian behaviors continue to cycle even in constant darkness, with an intrinsic period called the free-running period (FRP). Spiders have unusual FRPs, with some species having extremely short FRP (e.g. 18 hours for trashline orb weaver), and many having highly variable FRPs (intraspecific variation of up to 10 hours). In the absence of any genetic model of circadian rhythms in spiders, we developed a mathematical model to optimize experimental conditions for identifying circadian genes that also respond to light cues. ResultsOur mathematical model involved a single gene that encodes a protein that inhibits its own transcription. In our model, light degrades the circadian transcript, which allows a broad range of FRPs to be entrained to a 24-hour day. Our model predicted that exposing spiders to a pulse of light in the middle of the night would cause a pattern of expression between two later time points that was opposite the pattern exhibited by spiders who did not receive a pulse of light. RNA-sequencing of four groups of adult female orb weaving spiders, Metazygia wittfeldae, under these experimental conditions resulted in 528 significantly differentially expressed (DE) transcripts between the two collection times or between the light pulse and no light pulse. Consistent with our model, we found a cluster of transcripts with the flipped pattern of expression between the two collection times, dependent on the application of light.ConclusionsOur DE transcripts represent the first genetic evidence for circadian output in spiders. Furthermore, those transcripts with a flipped pattern of expression represent prime candidates for light-sensitive circadian genes, which may be involved in entraining the circadian clock to light. Functions of these genes varied from growth and development to reproduction to gene regulation, consistent with other circadian systems.

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Simulation of C1 fluxes in cyanobacteria: comparison between the carboxysome hypothesis and the equilibrium proposal

Canadian Journal of Botany ◽

10.1139/b97-923 ◽

1997 ◽

Vol 75 (12) ◽

pp. 2117-2130 ◽

Cited By ~ 1

Author(s):

Christophe Salon ◽

David Thomas Canvin

Keyword(s):

Mathematical Model ◽

Steady State ◽

Kinetic Constants ◽

Experimental Conditions ◽

Extracellular Medium ◽

Blue Green Algae ◽

Permeability Coefficients ◽

Inorganic Species ◽

Wide Range ◽

Entire Cell

Inorganic carbon fluxes were simulated by a mathematical model using an equilibrium hypothesis for a wide range of conditions in a closed system composed of air-grown cells of Synechococcus UTEX 625 in a reaction vessel connected to a mass spectrometer. The metabolic scheme took into account the input fluxes of CO2 and HCO3− transport into the cells, the output fluxes of CO2 and HCO3− efflux, the diversion of Q toward the formation of the internal C2 pool, and photosynthetic CO2 fixation. The equations expressed the variation in concentration of each inorganic species outside and inside the cell as a function of time. The input fluxes were previously characterized by their kinetic constants (K1/2 and Vm) both during initial uptake occurring upon illumination of the cells and under steady-state photosynthesis conditions. The efflux rates of the various Ci species from the cells were investigated under a wide variety of experimental conditions. Using these efflux rates, the permeability coefficients of the cell for CO2 and HCO3− were calculated previously. Using the kinetic constants for CO2 and HCO3− transport, the permeability coefficients of the cell for CO2 and HCO3− and the geometrical characteristics of the cells, the model simulated precisely the [HCO3−]/[CO2] ratio and the [CO2] and [O2] changes in the extracellular medium as well as the rate of filling of the internal Ci pool under various conditions. Accurate fitting of experimental data with calculated values were possible only when the intracellular Ci species were assumed to be in equilibrium throughout the entire cell volume. Results are discussed and compared with those given by previous hypotheses. Key words: Synechococcus UTEX 625, blue green algae, cyanobacteria, mathematical model, active CO2 transport, active HCO3− transport, steady state, photosynthesis, Ci concentrating mechanism.

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Characterization of induction methods for Drosophila seizure mutations

10.1101/2021.03.01.433313 ◽

2021 ◽

Author(s):

Jurga Mituzaite ◽

Rasmus Petersen ◽

Adam Claridge-Chang ◽

Richard A. Baines

Keyword(s):

Drosophila Melanogaster ◽

Motor Neurons ◽

Genetic Model ◽

Single Gene ◽

Underlying Disease ◽

New Drugs ◽

Seizure Susceptibility ◽

Systematic Analysis ◽

Heat Induction ◽

Wide Range

AbstractEpilepsy is one of the most common neurological disorders. Around one third of patients do not respond to current medications. This lack of treatment indicates a need for better understanding of the underlying mechanisms and, importantly, the identification of novel targets for drug manipulation. The fruitfly Drosophila melanogaster has a fast reproduction time, powerful genetics, and facilitates large sample sizes, making it a strong model of seizure mechanisms. However, there has not yet been a systematic analysis of the wide range of behavioral and physiological phenotypes observed across major fly seizure genotypes. To understand this, we systematically measured seizure severity and secondary behavioral phenotypes at both the larval and adult stage. Comparison of several seizure-induction methods; specifically electrical, mechanical and heat-induction, show that larval electroshock is the most effective at inducing seizures across a wide range of seizure-prone mutants. Locomotion in adults and larvae was found to be non-predictive of seizure susceptibility. Recording activity in identified larval motor neurons revealed variations in action potential patterns, across different genotypes, but these patterns did not correlate with seizure susceptibility. To conclude, while there is wide variation in mechanical induction, heat induction, and secondary phenotypes, electroshock is the most consistent method of seizure induction across known major seizure genotypes in Drosophila.Significance StatementEpilepsy is a neurological disorder affecting 1 in 130 people globally, with a significant impact on patients, families, and society. Approximately one third of epileptics do not respond to currently available medication. Thus, better insights into underlying disease mechanisms and identification of new drugs are needed. Fruit flies (Drosophila melanogaster) are a powerful genetic model: a number of single gene mutant flies exhibit seizures, phenotypes that have been shown to respond to established antiepileptic drugs. We compare methods of seizure induction and their utility, to establish which induction method is the most consistent across a range of different seizure-inducing genetic backgrounds. Adopting a common method for seizure analysis in this model will, we predict, speed identification of novel anti-convulsive treatments.

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Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

10.26434/chemrxiv.9461462 ◽

2019 ◽

Author(s):

Christopher John ◽

Greg M. Swain ◽

Robert P. Hausinger ◽

Denis A. Proshlyakov

Keyword(s):

Active Site ◽

Structural Model ◽

Heme Iron ◽

Chemical Transformations ◽

Experimental Conditions ◽

Strongly Coupled ◽

Non Heme Iron ◽

Reversible Redox ◽

Wide Range ◽

Complex Structural

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semi-empirical computational methods, demonstrating that the Fe (III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and 171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

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Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

International Journal of Molecular Sciences ◽

10.3390/ijms22157879 ◽

2021 ◽

Vol 22 (15) ◽

pp. 7879

Author(s):

Yingxia Gao ◽

Yi Zheng ◽

Léon Sanche

Keyword(s):

Condensed Phase ◽

Genetic Material ◽

High Energy ◽

Dna Lesions ◽

Low Energy ◽

Experimental Investigations ◽

Experimental Conditions ◽

Strand Breaks ◽

Sequence Of Events ◽

Wide Range

The complex physical and chemical reactions between the large number of low-energy (0–30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.

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Review of the Upright Balance Assessment Based on the Force Plate

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18052696 ◽

2021 ◽

Vol 18 (5) ◽

pp. 2696

Author(s):

Baoliang Chen ◽

Peng Liu ◽

Feiyun Xiao ◽

Zhengshi Liu ◽

Yong Wang

Keyword(s):

Postural Balance ◽

Force Plate ◽

Assessment Method ◽

Balance Assessment ◽

Experimental Conditions ◽

Methodological Research ◽

Assessment Tests ◽

Wide Range ◽

Foot Posture ◽

Plate System

Quantitative assessment is crucial for the evaluation of human postural balance. The force plate system is the key quantitative balance assessment method. The purpose of this study is to review the important concepts in balance assessment and analyze the experimental conditions, parameter variables, and application scope based on force plate technology. As there is a wide range of balance assessment tests and a variety of commercial force plate systems to choose from, there is room for further improvement of the test details and evaluation variables of the balance assessment. The recommendations presented in this article are the foundation and key part of the postural balance assessment; these recommendations focus on the type of force plate, the subject’s foot posture, and the choice of assessment variables, which further enriches the content of posturography. In order to promote a more reasonable balance assessment method based on force plates, further methodological research and a stronger consensus are still needed.

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Analysis of Dynamic Response of a Two Degrees of Freedom (2-DOF) Ball Bearing Nonlinear Model

Applied Sciences ◽

10.3390/app11020787 ◽

2021 ◽

Vol 11 (2) ◽

pp. 787

Author(s):

Bartłomiej Ambrożkiewicz ◽

Grzegorz Litak ◽

Anthimos Georgiadis ◽

Nicolas Meier ◽

Alexander Gassner

Keyword(s):

Mathematical Model ◽

Degrees Of Freedom ◽

Ball Bearing ◽

Hertzian Contact ◽

Two Degrees Of Freedom ◽

Wide Range ◽

Shape Errors ◽

Nonlinear Features ◽

Fourier Transform Phase ◽

Hertzian Contact Theory

Often the input values used in mathematical models for rolling bearings are in a wide range, i.e., very small values of deformation and damping are confronted with big values of stiffness in the governing equations, which leads to miscalculations. This paper presents a two degrees of freedom (2-DOF) dimensionless mathematical model for ball bearings describing a procedure, which helps to scale the problem and reveal the relationships between dimensionless terms and their influence on the system’s response. The derived mathematical model considers nonlinear features as stiffness, damping, and radial internal clearance referring to the Hertzian contact theory. Further, important features are also taken into account including an external load, the eccentricity of the shaft-bearing system, and shape errors on the raceway investigating variable dynamics of the ball bearing. Analysis of obtained responses with Fast Fourier Transform, phase plots, orbit plots, and recurrences provide a rich source of information about the dynamics of the system and it helped to find the transition between the periodic and chaotic response and how it affects the topology of RPs and recurrence quantificators.

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Towards Reduced CNNs for De-Noising Phase Images Corrupted with Speckle Noise

Photonics ◽

10.3390/photonics8070255 ◽

2021 ◽

Vol 8 (7) ◽

pp. 255

Author(s):

Marie Tahon ◽

Silvio Montresor ◽

Pascal Picart

Keyword(s):

Phase Error ◽

Speckle Noise ◽

Experimental Conditions ◽

Benchmark Data ◽

Wide Range ◽

Phase Images ◽

Different Depths ◽

Phase Data ◽

Do So

Digital holography is a very efficient technique for 3D imaging and the characterization of changes at the surfaces of objects. However, during the process of holographic interferometry, the reconstructed phase images suffer from speckle noise. In this paper, de-noising is addressed with phase images corrupted with speckle noise. To do so, DnCNN residual networks with different depths were built and trained with various holographic noisy phase data. The possibility of using a network pre-trained on natural images with Gaussian noise is also investigated. All models are evaluated in terms of phase error with HOLODEEP benchmark data and with three unseen images corresponding to different experimental conditions. The best results are obtained using a network with only four convolutional blocks and trained with a wide range of noisy phase patterns.

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Insights into mammalian biology from the wild house mouse Mus musculus

eLife ◽

10.7554/elife.05959 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 45

Author(s):

Megan Phifer-Rixey ◽

Michael W Nachman

Keyword(s):

House Mouse ◽

Mus Musculus ◽

Genetic Model ◽

Inbred Strains ◽

Mendelian Inheritance ◽

Model Organisms ◽

House Mice ◽

Small Subset ◽

Wild Mice ◽

Wide Range

The house mouse, Mus musculus, was established in the early 1900s as one of the first genetic model organisms owing to its short generation time, comparatively large litters, ease of husbandry, and visible phenotypic variants. For these reasons and because they are mammals, house mice are well suited to serve as models for human phenotypes and disease. House mice in the wild consist of at least three distinct subspecies and harbor extensive genetic and phenotypic variation both within and between these subspecies. Wild mice have been used to study a wide range of biological processes, including immunity, cancer, male sterility, adaptive evolution, and non-Mendelian inheritance. Despite the extensive variation that exists among wild mice, classical laboratory strains are derived from a limited set of founders and thus contain only a small subset of this variation. Continued efforts to study wild house mice and to create new inbred strains from wild populations have the potential to strengthen house mice as a model system.

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Robust sideslip angle observer of commercial vehicles based on cornering stiffness estimation using neural network

Proceedings of the Institution of Mechanical Engineers Part D Journal of Automobile Engineering ◽

10.1177/09544070211072401 ◽

2022 ◽

pp. 095440702110724

Author(s):

Chenyu Zhou ◽

Liangyao Yu ◽

Yong Li ◽

Jian Song

Keyword(s):

Neural Network ◽

Mathematical Model ◽

Stability Control ◽

Estimation Accuracy ◽

Accurate Estimation ◽

Commercial Vehicles ◽

Sideslip Angle ◽

The Neural Network ◽

Wide Range ◽

The Mathematical Model

Accurate estimation of sideslip angle is essential for vehicle stability control. For commercial vehicles, the estimation of sideslip angle is challenging due to severe load transfer and tire nonlinearity. This paper presents a robust sideslip angle observer of commercial vehicles based on identification of tire cornering stiffness. Since tire cornering stiffness of commercial vehicles is greatly affected by tire force and road adhesion coefficient, it cannot be treated as a constant. To estimate the cornering stiffness in real time, the neural network model constructed by Levenberg-Marquardt backpropagation (LMBP) algorithm is employed. LMBP is a fast convergent supervised learning algorithm, which combines the steepest descent method and gauss-newton method, and is widely used in system parameter estimation. LMBP does not rely on the mathematical model of the actual system when building the neural network. Therefore, when the mathematical model is difficult to establish, LMBP can play a very good role. Considering the complexity of tire modeling, this study adopted LMBP algorithm to estimate tire cornering stiffness, which have simplified the tire model and improved the estimation accuracy. Combined with neural network, A time-varying Kalman filter (TVKF) is designed to observe the sideslip angle of commercial vehicles. To validate the feasibility of the proposed estimation algorithm, multiple driving maneuvers under different road surface friction have been carried out. The test results show that the proposed method has better accuracy than the existing algorithm, and it’s robust over a wide range of driving conditions.

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Probabilistic Model of the Reflectivity of Construction Materials of the Agroindustrial Complex

Elektrotekhnologii i elektrooborudovanie v APK ◽

10.22314/2658-4859-2021-68-3-111-115 ◽

2021 ◽

Vol 3 (44) ◽

pp. 111-115

Author(s):

Tat’yana R. Gallyamova ◽

Keyword(s):

Mathematical Model ◽

Energy Consumption ◽

Reflection Coefficient ◽

Probabilistic Method ◽

Construction Materials ◽

Research Purpose ◽

Visible Range ◽

Industrial Complex ◽

Large Area ◽

Wide Range

When developing modern lighting technologies for objects of the agro-industrial complex, the problem arises of assessing the contribution of reflected light to the normalized illumination. The reflective properties of the surfaces of materials are characterized by a reflection coeﬃcient ρ, which reaches a value of 0.7. This allows us to consider the reflective surfaces as an additional light source and the possibility of reducing energy consumption costs. (Research purpose) The research purpose is in developing a mathematical model that allows us to estimate the spectral reflection coeﬃcient ρ(λ) of materials of construction technologies of the agro-industrial complex in the ultraviolet and visible spectral regions. (Materials and methods) That the disadvantage of various models is the lack of an analytical method for calculating the reflection coeﬃcient in a wide range of wavelengths. We used a probabilistic method to overcome this disadvantage. (Results and discussion) The developed mathematical model makes it possible to estimate the reflection coeﬃcient of the rough surface of materials in a wide range of the spectrum. For concrete, the area of agreement between theory and experiment is in the wavelength range from 250 to 1000 nm. The saturation mode predicted by the theory (the independence of the reflection coeﬃcient from the wavelength) at a reflection coeﬃcient of 0.4 is consistent with the experimental values in the visible range of the spectrum for construction materials of the agro-industrial complex, in particular, gray textured concrete, gray facade paint, light wood, gray silicate brick, new plaster without whitewash. (Conclusions) In the case of normal light incidence, the developed mathematical model allows us to theoretically estimate the reflection coeﬃcient of the rough surfaces of construction technologies of the agro-industrial complex. The proposed model can be used in the development and design of a system of technological lighting of large-area premises (for example, when keeping birds on the floor), as well as for developing recommendations for reducing the energy consumption of existing lighting systems.

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