scholarly journals Genetic code degeneracy is established by the decoding center of the ribosome

2021 ◽  
Author(s):  
Jean Lehmann ◽  
Shixin Ye
Keyword(s):  
Genetic Code ◽  
Base Pair ◽  
Significant Contribution ◽  
Kinetic Scheme ◽  
Evolutionary Models ◽  
Peptidyl Transferase ◽  
Early Appearance ◽  
Evolutionary Step ◽  
The Stability ◽  
Selection Of

The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson-Crick base pair at the second position of the anticodon-codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

Stabilization of networked switched affine systems with event-triggered strategy

2021 ◽  
pp. 014233122110213
Author(s):  
Dandan Li ◽  
Zhiqiang Zuo ◽  
Yijing Wang
Keyword(s):  
Affine Systems ◽  
Switching Law ◽  
Event Time ◽  
Sliding Motion ◽  
State Dependent ◽  
Event Triggering ◽  
Stability Issue ◽  
The Stability ◽  
Event Based ◽  
Selection Of

Using an event-based switching law, we address the stability issue for continuous-time switched affine systems in the network environment. The state-dependent switching law in terms of the region function is firstly developed. We combine the region function with the event-triggering mechanism to construct the switching law. This can provide more candidates for the selection of the next activated subsystem at each switching instant. As a result, it is possible for us to activate the appropriate subsystem to avoid the sliding motion. The Zeno behavior for the switched affine system can be naturally ruled out by guaranteeing a positive minimum inter-event time between two consecutive executions of the event-triggering threshold. Finally, two numerical examples are given to demonstrate the effectiveness of the proposed method.

The Weight of Fear of Violence in Household Budgets

2021 ◽  
pp. 073401682110383
Author(s):  
Bruno Truzzi ◽  
Marcelo Justus ◽  
Henrique C. Kawamura ◽  
Thomas V. Conti
Keyword(s):  
Instrumental Variables ◽  
Regularization Method ◽  
Household Level ◽  
Household Spending ◽  
Goods And Services ◽  
Level Ii ◽  
The Stability ◽  
The Relationship ◽  
Selection Of

This article investigates the relationship between the perception of violence and the spending on security goods and services in households. Individual microdata from a random national survey on family budget carried out in Brazil in 2008-2009 were used for modeling the household spending using two instrumental variables. The stability of results was checked by applying the Lasso-Gaussian regularization method in the selection of the statistically significant variables. Positive relationships were found between household spending on security goods and services and (i) the fear of insecurity at the household level, (ii) the neighbors’ spending on security, and (iii) the registered criminality, but no evidence was found on the relationship between the role of police on household spending on security goods and services.

scholarly journals SURVEYING IN THE STUDIES OF THE STABILITY OF EARTHY CONSTRUCTIONS, FOCUS ON SELECTED HISTORICAL MOUNDS IN KRAKOW (POLAND)

2016 ◽  
Vol 22 (2) ◽  
pp. 324-341
Author(s):  
Rafał Gawałkiewicz ◽  
Anna Szafarczyk
Keyword(s):  
Landslide Monitoring ◽  
Measurement Technology ◽  
Degree Of Deformation ◽  
Soil Creep ◽  
Measurement Series ◽  
Efficient Protection ◽  
The Stability ◽  
The Impact ◽  
Measurement Base ◽  
Selection Of

Mounds, as anthropogenic constructions of a very delicate structure, are subdued to constant changes, which, due to the impact of external factors (prolonged precipitation, tremors) are subdued to deformations in the form of mass movements. These phenomena usually have the character of mild soil creep in time and sometimes, as a result of rapid loss of stability, they are seriously damaged by landslide. This phenomenon causes temporary exclusion of the object from use. In the framework of the protection of these objects, the maintenance was carried out within the preventive measures referring to the construction and surveying monitoring of the geometry changes in time, as a result of phenomena taking place in the ground medium under the influence of environmental factors causing strains. The process of the deformation of mounds is similar to the characteristic, according to the Terzagie's theory. The application of surveying technologies of high precision allows the monitoring of changes in their geometry in time. The properly defined study area and the proper selection of measurement technology in the aspect of the accuracy of the prediction of changes, can efficiently help in defining the scale of deformations in the decisive process referring to the way of efficient protection of barrows. The article presents the results of point monitoring carried out with surveying technologies within 11 measurement series carried out on the selected measurement base of the Wanda Mound. The use of measurement technologies of integrated and specialist software, allows complex assessment of the degree of deformation and the trends of these changes in time, as well as identifying anomaly zones in the framework of the landslide monitoring.

Stability of a tokamak plasma with diffuse toroidal rotation

2020 ◽  
Vol 86 (5) ◽  
Author(s):  
O. E. López ◽  
L. Guazzotto
Keyword(s):  
Shooting Method ◽  
Tokamak Plasma ◽  
Solution Technique ◽  
Large Aspect Ratio ◽  
Internal Resonances ◽  
Flow Shear ◽  
Magnetic Shear ◽  
The Stability ◽  
External Kink ◽  
Selection Of

The present work considers the stability of a high- $\beta$ , large aspect ratio, circular plasma with diffuse profiles for the safety factor and the angular toroidal frequency (López & Guazzotto, Phys. Plasmas, vol. 24, 032501). An application of the Frieman–Rotenberg formalism results in a system of scalar eigenmode equations whose coupling is retained at the plasma–vacuum transition but is disregarded across the plasma column, which is a standard practice. The solution technique consists of a multidimensional shooting method for the poloidal harmonics; robust initial guesses are constructed by solving the dispersion relation in the static scenario with vanishing magnetic shear. Flow shear appears as a high- $\beta$ toroidal contribution, and we illustrate its destabilizing influence on $n=1$ external kink modes in the presence of ideal and resistive walls. Internal resonances are avoided by means of the selection of appropriate equilibrium parameters. The stabilizing influence of a finite positive average magnetic shear is also exemplified.

A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome

Nature ◽  
1995 ◽  
Vol 377 (6547) ◽  
pp. 309-314 ◽  
Author(s):  
Raymond R. Samaha ◽  
Rachel Green ◽  
Harry F. Noller
Keyword(s):  
Base Pair ◽  
23S Rrna ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Centre

scholarly journals Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Dorota M. Krzyżanowska ◽  
Anna Supernat ◽  
Tomasz Maciąg ◽  
Marta Matuszewska ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Reference Genes ◽  
Significance Threshold ◽  
Expression Studies ◽  
Reverse Transcription Quantitative Pcr ◽  
Gene Expression Studies ◽  
The Stability ◽  
Selection Of

Abstract Reverse transcription quantitative PCR (RT-qPCR), a method of choice for quantification of gene expression changes, requires stably expressed reference genes for normalization of data. So far, no reference genes were established for the Alphaproteobacteria of the genus Ochrobactrum. Here, we determined reference genes for gene expression studies in O. quorumnocens A44. Strain A44 was cultured under 10 different conditions and the stability of expression of 11 candidate genes was evaluated using geNorm, NormFinder and BestKeeper. Most stably expressed genes were found to be rho, gyrB and rpoD. Our results can facilitate the choice of reference genes in the related Ochrobactrum strains. O. quorumnocens A44 is able to inactivate a broad spectrum of N-acyl homoserine lactones (AHLs) – the quorum sensing molecules of many Gram-negative bacteria. This activity is attributed to AiiO hydrolase, yet it remains unclear whether AHLs are the primary substrate of this enzyme. Using the established RT-qPCR setup, we found that the expression of the aiiO gene upon exposure to two AHLs, C6-HLS and 3OC12-HSL, does not change above the 1-fold significance threshold. The implications of this finding are discussed in the light of the role of quorum sensing-interfering enzymes in the host strains.

scholarly journals Development of protocol for screening of formulation attributes and the assessment of common quality problems in oleuropein loaded nanostructured lipid carriers

2019 ◽  
Vol 10 (2) ◽  
pp. 1382-1391 ◽  
Author(s):  
Sucharitha P ◽  
Satyanarayana SV ◽  
Bhaskar Reddy K
Keyword(s):  
Thermal Analysis ◽  
Nanostructured Lipid Carriers ◽  
Solid Lipid ◽  
Minimum Particle Size ◽  
Lipid Particles ◽  
Quality Issues ◽  
Relative Solubility ◽  
The Stability ◽  
Selection Of

The current study aims to explore and identify the screening of formulation components and evaluates the quality issues of nanostructured lipid carriers (NLCs) for the phenolic secoirodoid Oleuropein. The stepwise screening of the components for preparation of NLCs includes the selection of solid lipid, liquid lipid based on the relative solubility of Oleuropein in different lipids. Polaxomer 188 was selected as the main surfactant for the preparation of NLCs because of its good emulsification efficacy for the solid lipid liquid mix. Lecithin was used to enhance the stability of NLC. The optimized formulation was also evaluated for different quality issues. Thermal analysis by DSC revealed that the lipid particles maintained sufficiently good melting point even after nanonization. Absence of gelation and resilience for the stress provided by autoclaving further established the quality of the developed NLCs. In a nutshell, a systematic protocol was developed for designing of Oleuropein NLC with good particulate parameters of minimum particle size and maximum zeta potential with narrow polydispersity index.

scholarly journals Spectrophotometric indicators of the stability of anthocyanin-containing extracts depending on the color of plant materials

2020 ◽  
Vol 31 (2) ◽  
pp. 88-92
Author(s):  
Vladimir Mikhailovich Koldaev ◽  
Artem Yurevich Manyakhin ◽  
Petr Semenovich Zorikov
Keyword(s):  
Hydrochloric Acid ◽  
Stability Factor ◽  
Plant Materials ◽  
Herbal Preparations ◽  
Violet Color ◽  
The Stability ◽  
Selection Of ◽  
Factor Coefficient ◽  
Anthocyanin Degradation

AbstractThis paper aims at spectrophotometric determination of changes in stability of extractable anthocyanins during drying of plant materials depending on their color. Raw and dried colored parts of 50 plant species from 25 families were used for the study. The extracts were prepared over 95% ethanol acidified with hydrochloric acid (pH ~ 1). The absorption spectra were registered within the range of 210 to 680 nm. The extinction variability factor, coefficient of intensity absorption relative and generalized stability factor were used to determine the anthocyanin degradation. The highest values of the stability factor were obtained for the extracts from fruit shells of burgundy or violet color within the range of 0.934±0.024 to 0.973±0.024, while the extracts from flower petals of the same care featured the stability factor that was 1.19 to 1.44 times less. The values of the stability factor of the extracts from black, red and blue materials are 1.15 to 1.19 times, 1.74 to 2.48 times and 4.65 to 4.84 times less respectively than those of the extracts from violet-burgundy materials. It is appropriate to apply the spectrophotometric factors of anthocyanins stability used in this study to selection of promising plants for industrial cultivation as material of anthocyanin-containing herbal preparations. The most stable anthocyanins are those of burgundy-purple and black fruits.

scholarly journals Stability of Wheat Genotypes by AMMI and Yield Evaluated under Peninsular Zone of India

2021 ◽  
Author(s):  
Ajay Verma ◽  
G.P. Singh
Keyword(s):  
Weighted Average ◽  
Principal Component ◽  
Efficient Estimation ◽  
High Yield ◽  
First Year ◽  
Wheat Genotypes ◽  
Stability Measure ◽  
Linear Behaviour ◽  
The Stability ◽  
Selection Of

Background: Efficient estimation of main and interaction effects under multi environment trials had been carried out by AMMI. Studies with low proportion of the variance explained by first interaction principal component IPCA1 under AMMI analysis had been reported biased interpretation for the stability of the genotypes.Methods: Weighted Average of Absolute scores (WAASB), quantitative stability measure had been recommended for selection of productive genotypes with broad adaptation. The selection of promising genotypes had been assisted by use of superiority index (WAASBY) that considered simultaneous use of yield and stability by allowing variable weighting mechanism for yield and stability.Result: Wheat GW509 and HI1633 genotypes had been identified by stability measure WAASB for the first year. While Superiority index considered stability and high yield settled for HI1633 and Raj4083 genotypes. Analytic measures of adaptability PRVG and MHPRVG observed suitability of HI1633 and Raj 4083. SI expressed positive linear behaviour with yield, MHPRVG and PRVG measures. While stability measure WAASB maintained moderate negative correlation with yield, SI, MHPRVG and PRVG. Wheat genotypes HI1633, HI1641 and HI1646 identified by stability measure for the next year of study. Superiority index selected HI1641, HI1633 and MACS6752 genotypes. SI expressed direct linear relation with yield, MHPRVG and PRVG. Stability measure exhibited indirect relationships with SI, MHPRVG, PRVG and yield Wheat genotypes HI1633, Raj 4083 for first year and HI1641, MACS6752 for the second year of study.

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