scholarly journals Influence of Environmental Parameters on the Stability of the DNA Molecule

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1446
Author(s):  
Alexander Svidlov ◽  
Mikhail Drobotenko ◽  
Alexander Basov ◽  
Eugeny Gerasimenko ◽  
Anna Elkina ◽  
...  

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

2021 ◽  
Vol 13 (3) ◽  
pp. 1326
Author(s):  
Hongfang Li ◽  
Huixiao Wang ◽  
Yaxue Yang ◽  
Ruxin Zhao

The interactions of water, energy, and food, which are essential resources for human survival, livelihoods, production, and development, constitute a water–energy–food (WEF) nexus. Applying symbiosis theory, the economic, social, and natural factors were considered at the same time in the WEF system, and we conducted a micro-level investigation focusing on the stability, coordination, and sustainability of the symbiotic units (water, energy, and food), and external environment of the WEF system in 36 prefecture-level cities across three northeastern provinces of China. Finally, we analyzed the synergistic safety and coupling coordination degree of the WEF system by the combination of stability, coordination, and sustainability, attending to the coordination relationship and influences of the external environment. The results indicated that the synergistic safety of the WEF system in three northeastern provinces need to equally pay attention to the stability, coordination, and sustainability of the WEF system, since their weights were 0.32, 0.36 and 0.32, respectively. During 2010–2016, the synergistic safety indexes of the WEF system ranged between 0.40 and 0.60, which was a state of boundary safety. In the current study, the coupling coordination degree of the WEF system fluctuated around a value of 0.6, maintaining a primary coordination level; while in the future of 2021–2026, it will decline to 0.57–0.60, dropping to a weak coordinated level. The conclusion could provide effective information for decision-makers to take suitable measures for the security development of a WEF system.


2021 ◽  
Vol 7 (3) ◽  
pp. 166
Author(s):  
Dmitriy Rodionov ◽  
Andrey Zaytsev ◽  
Evgeniy Konnikov ◽  
Nikolay Dmitriev ◽  
Yulia Dubolazova

The global COVID-19 pandemic has led to the self-isolation of people and the transformation of many economic and social processes into an electronic version thus contributing to the digitalization of all spheres. Being part of this environment, enterprises generate information resources to develop their desired image, which may vary according to the factors characterizing the information environment. Information capital is a comprehensive characteristic of an enterprise and determines its effectiveness and sustainability. The purpose of this study is to develop a toolkit that allows one to assess the information capital of an enterprise, reflecting its perception within the digital information environment. It is necessary to develop the methodology for the formation of such tools. As a result, a fuzzy-plural approach has been developed to evaluate the index of external information capital. This model allows us to assess the external information capital and to simulate its changes caused by various kinds of information events. The study of key elements, for example, the stability and tonality indices, index of target perception made it possible to systematize chaotic changes in the external environment and describe them using the Chen–Lee attractor model. The results of this study can be useful for researchers in the field of digital information analysis, in particular for the comparative analysis of enterprises and the assessment of their information capital.


2021 ◽  
Vol 9 (7) ◽  
pp. 772
Author(s):  
Huixuan Fu ◽  
Shichuan Wang ◽  
Yan Ji ◽  
Yuchao Wang

This paper addressed the formation control problem of surface unmanned vessels with model uncertainty, parameter perturbation, and unknown environmental disturbances. A formation control method based on the control force saturation constraint and the extended state observer (ESO) was proposed. Compared with the control methods which only consider the disturbances from external environment, the method proposed in this paper took model uncertainties, parameter perturbation, and external environment disturbances as the compound disturbances, and the ESO was used to estimate and compensate for the disturbances, which improved the anti-disturbance performance of the controller. The formation controller was designed with the virtual leader strategy, and backstepping technique was designed with saturation constraint (SC) function to avoid the lack of force of the actuator. The stability of the closed-loop system was analyzed with the Lyapunov method, and it was proved that the whole system is uniformly and ultimately bounded. The tracking error can converge to arbitrarily small by choosing reasonable controller parameters. The comparison and analysis of simulation experiments showed that the controller designed in this paper had strong anti-disturbance and anti-saturation performance to the compound disturbances of vessels and can effectively complete the formation control.


Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 960
Author(s):  
Meagan Archer ◽  
Jianping Xu

Aspergillus is a genus of filamentous fungi with vast geographic and ecological distributions. Species within this genus are clinically, agriculturally and biotechnologically relevant, leading to increasing interest in elucidating gene expression dynamics of key metabolic and physiological processes. Reverse-transcription quantitative Polymerase Chain Reaction (RT-qPCR) is a sensitive and specific method of quantifying gene expression. A crucial step for comparing RT-qPCR results between strains and experimental conditions is normalisation to experimentally validated reference gene(s). In this review, we provide a critical analysis of current reference gene selection and validation practices for RT-qPCR gene expression analyses of Aspergillus. Of 90 primary research articles obtained through our PubMed query, 17 experimentally validated the reference gene(s) used. Twenty reference genes were used across the 90 studies, with beta-tubulin being the most used reference gene, followed by actin, 18S rRNA and glyceraldehyde 3-phosphate dehydrogenase. Sixteen of the 90 studies used multiple reference genes for normalisation. Failing to experimentally validate the stability of reference genes can lead to conflicting results, as was the case for four studies. Overall, our review highlights the need to experimentally validate reference genes in RT-qPCR studies of Aspergillus.


2013 ◽  
Vol 860-863 ◽  
pp. 1073-1077 ◽  
Author(s):  
Zhi Guo Kong ◽  
Hong Wei Zhang ◽  
Zi Ning Tang

In order to improve the performance of a new type of full hybrid electric bus, this paper puts forward a set of coordinated control method to adjust the operation of the engine and two motors. In the engine start-stop logic control, comprehensive consideration of SOC, the speed of the bus and the accelerator pedal stroke are performed, while hysteresis control is introduced to improve the stability of the control; In the engine working point adjusting control, not only the engine speed command rate of change was optimized, but also the output torque rate was optimized to match the air injection and exhaust, etc. Further, the method based on dynamic constraints was used to optimize the working point adjustment process. At present, there are hundreds of busses operates in route. Results verify the feasibility and effectiveness of the control method. The vehicle has good fuel economy, and the dynamic performance and driving comfort are also greatly improved.


Author(s):  
S.S. Dzhimak ◽  
M.I. Drobotenko ◽  
A.A. Basov ◽  
A.A. Svidlov ◽  
M.G. Baryshev

The evaluation results of the possible deuterium atoms effect on the DNA base pair opening are presented in the article. The cause of these processes is the replacement of protium with deuterium atom due to the increase of energy required to break the hydrogen bond. These processes can be studied by method of mathematical modeling, with account of open states between base pairs being the key condition of the adequacy of the mathematical model of the DNA. The experiment data show that the presence of deuterium in a chain of nucleotides can cause - depending on the value of hydrogen bond disruption energy - both increase and decrease in probability of open states occurrence. For example: hydrogen bond disruption energy of 0.358·10-22 n·m, non-zero probability of open states occurrence is observed in case of the absence of deuterium in the molecule, and with hydrogen bond disruption energy of 0.359·10-22 n·m or more such probability equals zero. Also, when one deuterium atom is present in a molecule, non-zero probability is observed even with hydrogen bond disruption energy equal to 0.368·10-22 n·m (i.e. more than 0.358·10-22 n·m). Thus participation of deuterium atoms in the formation of hydrogen bonds of double helixes of a DNA molecule can cause the changes in the time required for transfer of genetic information, which can explain the effect of even minor deviations in deuterium concentration in a medium on metabolic processes in a living system.


Author(s):  
Yev. ZAIATS ◽  
V. KOVALIOV ◽  
A. KOSOLAPOV

Raising of problem. Today, the task of creating the toolkit for estimating the duration and cost of the reconstruction of industrial buildings with a change in their functional purpose is important, taking into account the probabilistic impact of the changing external environment, the resource restrictions of the project and compliance with modern requirements for construction objects intended primarily for the needs of the customer, investor. Purpose of the article. Statement of the main provisions of the methods for assessing the conditions for the reconstruction of industrial buildings with a change in their functional appointment and the substantiation for the effective organizational and technological decisions for the production of building work. Conclusion. The choice of effective organizational and technological decisions for building work is based on the assessment of the conditions for the reconstruction of industrial buildings with a change in their functional purposes, taking into account the existing resource restrictions, the requirements for energy efficiency, safety, quality and environmental friendliness of objects, acceptable risk levels, the conditions for the stability of the slopes and the sustainability of buildings, located on the slopes. The substantiation and the choice of rational organizational and technological decisions are based on determining the duration and cost of reconstruction of industrial buildings with a change in functional purpose, when calculating which it is necessary to take into account the systemic effect of determining factors and probabilistic nature of this impact, as well as the possibility of adjusting the decisions considered in order to ensure the specified resource restrictions. The main feature of the developed approach is that, changing the values of determining factors, within the existing resource restrictions, we obtain various solutions with the corresponding values of the duration and cost of the reconstruction of industrial buildings with a change in functional purpose. The choice of the most rational decision from the options received is carried out by the customer (investor), depending on the possibilities and wishes.


2021 ◽  
Vol 235 ◽  
pp. 02017
Author(s):  
Yingrui Liu

Family business plays an important role in the world’s economic activities, and has made great contributions to the stability and development of the economy of various countries. Innovation is an important but inexplicable part of the strategic focus of family business. Based on the existing literature, this paper discusses the factors that influence the innovation behavior of enterprises from the perspective of family involvement and external environment.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
E Mestres ◽  
Q Matia-Algué ◽  
A Villamar ◽  
M García-Jiménez ◽  
A Casals ◽  
...  

Abstract Study question Do commercial mineral oil brands differ in their capacity to stabilize the human embryo culture system, and is this related to the oil’s viscosity? Summary answer While the oils’ viscosity only had minor effects on temperature maintenance, it showed a direct correlation with the stability of pH and osmolality during culture. What is known already Mineral oil is a key component of the in vitro embryo culture system, which stabilizes temperature, pH and osmolality of the media during culture. Its use has been implemented worldwide for several decades and many manufacturers currently produce and commercialize oil intended for human embryo culture. Unfortunately, oil remains as one of the less characterized products in the IVF laboratory due to a lack of standardized nomenclature, production and testing. With differing physico-chemical properties, such as viscosity, oils produced by various manufacturers could behave differently to the same culture conditions and, thus, its use may need to be adjusted accordingly. Study design, size, duration Viscosity was quantified in three high-viscosity (H-V) and three low-viscosity (L-V) oils with a viscosity-meter. The required time for media’s pH to equilibrate using each oil was studied, as well as its subsequent stability outside the incubator for 30min. In-drop temperature was assessed during 15min when taking a dish outside the incubator, and again when putting it back. Additionally, each oil’s capacity to avoid media evaporation was studied with daily osmolality measurements during 7 days. Participants/materials, setting, methods pH equilibration was measured with a continuous pHmeter (Log&Guard, Vitrolife) in 4-well dishes prepared with 600µl of medium and 500µl of oil. For the other experiments, 35mm dishes with 4ml of oil and 20µl media droplets were used. pH stability was assessed after 0, 15 and 30min outside the incubator with a blood-gas-analyzer (epoc,SiemensHelthineers). A fine-gauge thermocouple was used to measure in-drop temperature loss/recovery. Daily osmolality readings were taken with a vapor pressure osmometer (Vapro5600,Wescor). Main results and the role of chance The selected oil samples had a viscosity of 115, 111, 52, 22, 18, and 12cP. The medium’s pH took approximately 12h to completely equilibrate under H-V oils, while it took less than 4h in L-V. Similarly, the rise in pH after 30min on a heated stage outside of the incubator with room atmosphere was 0.03, 0.04, 0.06, 0.13, 0.17, and 0.26, respectively. Dishes were taken out of the incubator and placed on a heated surface. In the first five minutes, the in-drop temperature loss ranged between –0.22 and –0.13oC/min, with no significant differences observed between oil types. However, temperature plateaued at a significantly higher value in L-V oils (36.5oC), compared to H-V brands (36.25–36.1oC; p = 0.0005). By contrast, all samples followed a similar pattern when the dishes were returned to the benchtop incubator, with temperature taking around 7 minutes to completely recover. Some media evaporated in all oil groups during the 7-day culture in a dry benchtop incubator. The linear regression performed to compare the evaporation rate between groups showed a statistically significant correlation between oil viscosity and the rate of evaporation (p < 0.0001), with an osmolality rise ranging between +2.55mmol/kg/day in the most viscous oil and +6.29mmol/kg/day in the least viscous. Limitations, reasons for caution While the selected oils for this study represent a wide range of options in the market, future projects could widen this selection and include additional tests, such as optimized bioassays. Results may vary between centers, and thus each laboratory should test and optimize their culture system with their own settings. Wider implications of the findings: Different oil brands have shown differing physico-chemical properties that have a direct effect on the culture system and the stability of several culture conditions. These results may be of major importance to adapt the settings and methodologies followed in each IVF laboratory according to the type of oil being used. Trial registration number Not applicable


Author(s):  
Robert B. Macgregor Jr ◽  
John Q. Wu

The effect of pressure on the helix-coil transition temperature (Tm) is reported for the double-stranded polymers poly(dA)poly(dT), poly[d(A-T)], poly[d(l-C], and poly[d(G-C] and triple-stranded poly(dA)2poly(dT). The Tm increases as a function of pressure, implying a positive volume change for the transition and leading to the conclusion that the molar volume of the coil form is larger than the molar volume of the helix. From the change in Tm as a function of pressure, molar volume changes of the transition (ΔVt) are calculated using the Clapeyron equation and calorimetrically determined enthalpies. For the doublestranded polymers, ΔVt, increases in the order poly[d(l-C] < polyt[d(A-T)] < poly(dA)-poly(dT) < polylcl(G-C)]. The value of ΔVt, for the triple-stranded to single-stranded transition of poly(dA) 2poly(dT) is larger than that of poly[d(G-C)I. The magnitude of ΔVt increases with salt concentration in all cases studied; however, the change of ΔVt with salt concentration depends on the sequence of the DNA and the number of strands involved in the transition. In the model proposed to explain the results, the overall molar volume change of the transition is a function of a negative volume change arising from changes in the electrostatic interactions of the DNA strands, and a positive volume change due to unstacking the bases. The model predicted the direction of the change in the ΔVt for several experiments. The magnitude of AVJ increases with counter ion radius, thus for polyld(A-T)], ΔVt, increases in the series Na+ , K+, Cs+, The ΔVt also increases if the charge on the phosphodiester groups is removed. The kinetics of the formation of double-stranded (dA)19(dT)19 in 50 mM NaCI are slowed approximately 14-fold at 200 MPa relative to atmospheric pressure. The implied volume of activation of +37 ml mol−l in the direction of this change is also in agreement with the proposed model. The stability of double- and triple-stranded DNA helices in water around neutral pH depends on the base composition and sequence, as well as on the ionic strength of the solution. Each of these dependencies also defines how DNA interacts with water.


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