scholarly journals Deep Gene Networks and Response to Stress

Mathematics ◽  
2021 ◽  
Vol 9 (23) ◽  
pp. 3028
Author(s):  
Sergey Vakulenko ◽  
Dmitry Grigoriev
Keyword(s):  
Gene Regulation ◽  
Genetic Code ◽  
Gene Networks ◽  
Environmental Changes ◽  
Immune Therapy ◽  
Genetic Regulation ◽  
Discrete Parameter ◽  
Response To Stress ◽  
The Stability ◽  
Random Fluctuations

We consider systems of differential equations with polynomial and rational nonlinearities and with a dependence on a discrete parameter. Such systems arise in biological and ecological applications, where the discrete parameter can be interpreted as a genetic code. The genetic code defines system responses to external perturbations. We suppose that these responses are defined by deep networks. We investigate the stability of attractors of our systems under sequences of perturbations (for example, stresses induced by environmental changes), and we introduce a new concept of biosystem stability via gene regulation. We show that if the gene regulation is absent, then biosystems sooner or later collapse under fluctuations. By a genetic regulation, one can provide attractor stability for large times. Therefore, in the framework of our model, we prove the Gromov–Carbone hypothesis that evolution by replication makes biosystems robust against random fluctuations. We apply these results to a model of cancer immune therapy.

scholarly journals Novel Gene Regulation in Normal and Abnormal Spermatogenesis

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 666
Author(s):  
Li Du ◽  
Wei Chen ◽  
Zixin Cheng ◽  
Si Wu ◽  
Jian He ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Leydig Cells ◽  
Molecular Mechanisms ◽  
New Technologies ◽  
Genetic Regulation ◽  
Myoid Cells ◽  
Epigenetic Factors ◽  
Future Directions ◽  
New Genes ◽  
Human Spermatogenesis

Spermatogenesis is a complex and dynamic process which is precisely controlledby genetic and epigenetic factors. With the development of new technologies (e.g., single-cell RNA sequencing), increasingly more regulatory genes related to spermatogenesis have been identified. In this review, we address the roles and mechanisms of novel genes in regulating the normal and abnormal spermatogenesis. Specifically, we discussed the functions and signaling pathways of key new genes in mediating the proliferation, differentiation, and apoptosis of rodent and human spermatogonial stem cells (SSCs), as well as in controlling the meiosis of spermatocytes and other germ cells. Additionally, we summarized the gene regulation in the abnormal testicular microenvironment or the niche by Sertoli cells, peritubular myoid cells, and Leydig cells. Finally, we pointed out the future directions for investigating the molecular mechanisms underlying human spermatogenesis. This review could offer novel insights into genetic regulation in the normal and abnormal spermatogenesis, and it provides new molecular targets for gene therapy of male infertility.

scholarly journals The collapse of genetic incompatibilities in a hybridizing population

2021 ◽  
Author(s):  
Tianzhu Xiong ◽  
James L MALLET
Keyword(s):  
Gene Regulation ◽  
Reproductive Isolation ◽  
Genetic Drift ◽  
Recombination Rate ◽  
Time Scale ◽  
Genetic Incompatibility ◽  
Genetic Process ◽  
Underlying Mechanisms ◽  
The Stability

Genetic incompatibility has long been considered to be a hallmark of speciation due to its role in reproductive isolation. Previous analyses of the stability of epistatic incompatibility show that it is subject to collapse upon hybridization. In the present work, we derive explicitly the distribution of the lifespan of two-locus incompatibilities, and show that genetic drift, along with recombination, is critical in determining the time scale of collapse. The first class of incompatibilities, where derived alleles separated in parental populations act antagonistically in hybrids, survive longer in smaller populations when incompatible alleles are (co)dominant and tightly linked, but collapse more quickly when they are recessive. The second class of incompatibilities, where fitness is reduced by disrupting co-evolved elements in gene regulation systems, collapse on a time scale proportional to the exponential of effective recombination rate. Overall, our result suggests that the effects of genetic drift and recombination on incompatibility's lifespan depend strongly on the underlying mechanisms of incompatibilities. As the time scale of collapse is usually shorter than the time scale of establishing a new incompatibility, the observed level of genetic incompatibilities in a particular hybridizing population may be shaped more by the collapse than by their initial accumulation. Therefore, a joint theory of accumulation-erosion of incompatibilities is in need to fully understand the genetic process under speciation with hybridization.

scholarly journals Experimental Study on Dynamic Resilient Modulus of Lime-Treated Expansive Soil

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Zheng Lu ◽  
Yang Zhao ◽  
Shaohua Xian ◽  
Hailin Yao
Keyword(s):  
Moisture Content ◽  
Environmental Changes ◽  
Resilient Modulus ◽  
Expansive Soils ◽  
Expansive Soil ◽  
Confining Pressure ◽  
Triaxial Tests ◽  
The Stability ◽  
Compaction Degree

Dynamic resilient modulus is the design index of highway subgrade design code in China, which is significantly affected by the traffic loads and environmental changes. In this study, dynamic triaxial tests were conducted to investigate the influence of moisture content, compaction degree, cyclic deviator stress, and confining pressure on lime-treated expansive soil. The suitability of UT-Austin model to lime-treated expansive soils was verified. The results indicate that the dynamic resilient modulus of lime-treated expansive soils increases nonlinearly with the increase of compaction degree, while decreases nonlinearly with the increase of dynamic stress level. The dynamic resilient modulus decreases linearly with the increase of moisture content and increases linearly with the increase of confining pressure. Moreover, the moisture content has a more significant effect on the dynamic resilient modulus of lime-treated expansive soil. Therefore, it is necessary to ensure the stability of soil humidity state and its excellent mechanical properties under long-term cyclic loading for the course of subgrade filling and service. Finally, the calculated results of the UT-Austin model for dynamic resilient modulus show a good agreement with the test results.

scholarly journals Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

2020 ◽  
Vol 48 (14) ◽  
pp. 8146-8164 ◽  
Author(s):  
Griffin M Schroeder ◽  
Debapratim Dutta ◽  
Chapin E Cavender ◽  
Jermaine L Jenkins ◽  
Elizabeth M Pritchett ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Bound States ◽  
Environmental Changes ◽  
Bound State ◽  
Yellow Mosaic Virus ◽  
Elastic Band ◽  
Rna Motifs ◽  
Shine Dalgarno Sequence ◽  
Effector Recognition ◽  
Molecular Framework

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

scholarly journals Computational modelling unravels the precise clockwork of cyanobacteria

2018 ◽  
Vol 8 (6) ◽  
pp. 20180038 ◽  
Author(s):  
Nicolas M. Schmelling ◽  
Ilka M. Axmann
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Circadian Clock ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Computational Modelling ◽  
Circadian Clocks ◽  
Fitness Advantage ◽  
Fundamental Part ◽  
Global Gene Regulation

Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.

Studies on the carbohydrate metabolism of sheep. XIV. The adrenal response to psychological stress

1962 ◽  
Vol 13 (2) ◽  
pp. 282 ◽  
Author(s):  
RL Reid ◽  
SC Mills
Keyword(s):  
Blood Glucose ◽  
Plasma Cortisol ◽  
Environmental Changes ◽  
Road Transport ◽  
Plasma Cortisol Level ◽  
Stressful Situation ◽  
Glucose Levels ◽  
Short Period ◽  
Adrenaline Release ◽  
Response To Stress

The effect of change in environment on plasma cortisol and blood glucose levels in sheep has been studied in the following situations: movement from grazing paddock to small enclosed yards, movement from grazing paddock to indoor animal quarters, and short periods of transport. Consistent large increases in plasma cortisol values were recorded in previously grazing animals, but the degree of elevation during road transport was usually less in "trained" animals housed indoors. Previous undernourishment or fasting increased the changes in plasma cortisol level in response to stress. Individual variation in plasma cortisol response between animals was considerable. Pronounced, but variable, increases in blood glucose occurred in all experiments except those in which exercise (walking) was associated with the brief stressful situation created by moving animals from the paddock into an enclosed yard. It is concluded that movement to an unfamiliar environment is an emotionally stressful situation, but that there are important differences in the quantitative adrenal cortical response between the grazing animal and experimental animals housed indoors and already subjected to a series of novel environmental changes. It is further suggested that exercise during a short period of stress may modify or prevent the normal hyperglycaemic response to adrenaline release. These experiments provide further support for the conclusion that the elevated plasma cortisol levels observed in the "stress syndrome" of pregnancy toxaemia are primarily a response to physical or emotional stress, rather than to the nutritional stress of fasting or severe undernutrition.

scholarly journals Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinyi Wan ◽  
Filipe Pinto ◽  
Luyang Yu ◽  
Baojun Wang
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Protein Binding ◽  
Gene Networks ◽  
Dynamic Range ◽  
Gene Expression Regulation ◽  
Single Layer ◽  
Regulation Mechanism ◽  
Gene Circuits ◽  
Synthetic Dna

AbstractVersatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

scholarly journals Dynamics Analysis and Prediction of Genetic Regulation in Glycerol Metabolic Network via Structural Kinetic Modelling

2015 ◽  
Vol 2015 ◽  
pp. 1-9
Author(s):  
Jianxiong Ye ◽  
Honglei Xu ◽  
Xueying Huang ◽  
Chongrong Ke ◽  
Enmin Feng
Keyword(s):  
Klebsiella Pneumoniae ◽  
Dynamic System ◽  
Genetic Manipulation ◽  
Kinetic Modelling ◽  
Formation Rate ◽  
Genetic Regulation ◽  
Stable State ◽  
Intermediary Metabolite ◽  
The Stability ◽  
Nonlinear Regulation

Glycerol can be biologically converted to 1,3-propanediol (1,3-PD) byKlebsiella pneumoniae. In the synthesis pathway of 1,3-PD, the accumulation of an intermediary metabolite 3-hydroxypropionaldehyde (3-HPA) would cause an irreversible cessation of the dynamic system. Genetic manipulation on the key enzymes which control the formation rate and consumption rate of 3-HPA would decrease the accumulation of 3-HPA, resulting in nonlinear regulation on the dynamic system. The interest of this work is to focus on analyzing the influence of 3-HPA inhibition on the stability of the dynamic system. Due to the lack of intracellular knowledge, structural kinetic modelling is applied. On the basis of statistical account of the dynamical capabilities of the system in the parameter space, we conclude that, under weak or no inhibition to the reaction of 3-HPA consumption, the system is much easier to obtain a stable state, whereas strong inhibition to its formation is in favor of stabilizing the system. In addition, the existence of Hopf bifurcation in this system is also verified. The obtained results are helpful for deeply understanding the metabolic and genetic regulations of glycerol fermentation byKlebsiella pneumoniae.

scholarly journals A medium-spatial scale distribution pattern of Pseudoscorpionida (Arachnida) in a gradient of topography (altitude and inclination), soil factors, and litter in a central Amazonia forest reserve, Brazil

2006 ◽  
Vol 66 (3) ◽  
pp. 791-802 ◽  
Author(s):  
N. O. Aguiar ◽  
T. L. Gualberto ◽  
E. Franklin
Keyword(s):  
Spatial Scale ◽  
Environmental Changes ◽  
Biological Indicators ◽  
Predictor Variables ◽  
Generalist Predators ◽  
Soil Factors ◽  
Abundance And Diversity ◽  
The Stability ◽  
Clay Percentage ◽  
Trail System

In Amazonia, nothing is known about the distribution of the invertebrates on a medium-spatial scale pattern. In a trail system of 64 km² at Ducke Reserve, we sampled 72 transects using the hand-sorting method and Berlese-Tullgren extraction. The reserve possesses ecosystems of "terra-firme" forest and the trail system represents a gradient of topographic soil factors and vegetation, avoiding categorizations. Considering the abundance and diversity of Pseudoscorpionida, we investigated the relation of the community to environmental factors tested (topography, clay percentage, litter, and soil pH), to the two major drainage basins of the reserve, and if these invertebrates can be used as biological indicators to monitor changes. We registered two species for the first time in the reserve, increasing the known diversity to 17 species. The lack of correlation with the predictor variables and the large home range, indicate that pseudoscorpions are not good biological indicators in the reserve. As the eastern and western watersheds are not separate management units for the community, our results show that they are generalist predators. In spite of our results and lack of knowledge concerning their biology, life history and taxonomy, pseudoscorpions are cosmopolitan and easy to find and measure. Compared with previous studies in the reserve, they have a consistent pattern of abundance and diversity throughout the years showing the stability of the community which can be checked mainly by comparison with environmental changes that would occur in the reserve. An investigation on a medium-spatial scale pattern and over a long-term period including other habitats, and also other predictor variables, like humidity, the structure of the vegetation and canopy closure, will be necessary to reinforce the observed tendencies.

Improved Stability Using Environmental Adaptive Yaw Control for Autonomous Unmanned Helicopter and Bifurcation of Maneuvering in Turning

2011 ◽  
Vol 23 (6) ◽  
pp. 1091-1099 ◽  
Author(s):  
Hiroaki Nakanishi ◽  
◽  
Sayaka Kanata ◽  
Tetsuo Sawaragi ◽  
Keyword(s):  
Feedback Loop ◽  
Environmental Changes ◽  
Angular Rate ◽  
Unmanned Helicopter ◽  
Yaw Control ◽  
Heading Control ◽  
Improved Stability ◽  
The Stability ◽  
Turning Maneuver ◽  
Autonomous Helicopter

Adaptation to environmental changes, such as wind, plays a very important role in improving the reliability of autonomous unmanned helicopters. Adaptive yaw (heading) control for an autonomous helicopter is discussed in this paper. The control structure is based on a hierarchal scheme that utilizes an inner yaw feedback control loop plus an outer feedback loop. The outer loop estimates the direction of the airspeed using roll angle and roll angular rate. Stable coupling in yaw and roll motion is induced by the proposed controller to improve the stability of the helicopter’s flight. Turning utilizing the proposed adaptive control system is discussed in particular. Results of flight experiments show that bifurcation of the helicopter’smaneuvering in turning occurs depending on airspeed. The results indicate that the autonomous unmanned helicopter can select a turning maneuver that is suitable for the environmental conditions, thus stabilizing its flight.

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