scholarly journals Nucleosome induced homology recognition in chromatin

2021 ◽  
Author(s):  
Jonathan G. Hedley ◽  
Vladimir B. Teif ◽  
Alexei A. Kornyshev
Keyword(s):  
Dna Sequences ◽  
Electrostatic Interactions ◽  
Genetic Recombination ◽  
Weak Interactions ◽  
Helical Structure ◽  
Potential Well ◽  
Sequence Recognition ◽  
Chromatin Fibers ◽  
The One ◽  
Nucleosome Arrays

ABSTRACTOne of the least understood properties of chromatin is the ability of its similar regions to recognise each other through weak interactions. Theories based on electrostatic interactions between helical macromolecules suggest that the ability to recognize sequence homology is an innate property of the non-ideal helical structure of DNA. However, this theory does not account for nucleosomal packing of DNA. Can homologous DNA sequences recognize each other while wrapped up in the nucleosomes? Can structural homology arise at the level of nucleosome arrays? Here we present a theoretical investigation of the recognition-potential-well between chromatin fibers sliding against each other. This well is different to the one predicted and observed for bare DNA; the minima in energy do not correspond to literal juxtaposition, but are shifted by approximately half the nucleosome repeat length. The presence of this potential-well suggests that nucleosome positioning may induce mutual sequence recognition between chromatin fibers and facilitate formation of chromatin nanodomains. This has implications for nucleosome arrays enclosed between CTCF-cohesin boundaries, which may form stiffer stem-like structures instead of flexible entropically favourable loops. We also consider switches between chromatin states, e.g., through acetylation/deacetylation of histones, and discuss nucleosome-induced recognition as a precursory stage of genetic recombination.

scholarly journals Nucleosome-induced homology recognition in chromatin

2021 ◽  
Vol 18 (179) ◽  
pp. 20210147
Author(s):  
Jonathan G. Hedley ◽  
Vladimir B. Teif ◽  
Alexei A. Kornyshev
Keyword(s):  
Dna Sequences ◽  
Electrostatic Interactions ◽  
Genetic Recombination ◽  
Weak Interactions ◽  
Helical Structure ◽  
Potential Well ◽  
Structural Homology ◽  
Sequence Recognition ◽  
The One ◽  
Nucleosome Arrays

One of the least understood properties of chromatin is the ability of its similar regions to recognize each other through weak interactions. Theories based on electrostatic interactions between helical macromolecules suggest that the ability to recognize sequence homology is an innate property of the non-ideal helical structure of DNA. However, this theory does not account for the nucleosomal packing of DNA. Can homologous DNA sequences recognize each other while wrapped up in the nucleosomes? Can structural homology arise at the level of nucleosome arrays? Here, we present a theoretical model for the recognition potential well between chromatin fibres sliding against each other. This well is different from the one predicted for bare DNA; the minima in energy do not correspond to literal juxtaposition, but are shifted by approximately half the nucleosome repeat length. The presence of this potential well suggests that nucleosome positioning may induce mutual sequence recognition between chromatin fibres and facilitate the formation of chromatin nanodomains. This has implications for nucleosome arrays enclosed between CTCF–cohesin boundaries, which may form stiffer stem-like structures instead of flexible entropically favourable loops. We also consider switches between chromatin states, e.g. through acetylation/deacetylation of histones, and discuss nucleosome-induced recognition as a precursory stage of genetic recombination.

Quantum Tunneling

2017 ◽  
Author(s):  
Frank S. Levin
Keyword(s):  
Quantum Tunneling ◽  
Alpha Particles ◽  
Attractive Potential ◽  
Scanning Tunneling ◽  
Finite Width ◽  
Potential Well ◽  
Surface Molecules ◽  
Repulsive Coulomb ◽  
The Subject ◽  
The One

Quantum tunneling, wherein a quanject has a non-zero probability of tunneling into and then exiting a barrier of finite width and height, is the subject of Chapter 13. The description for the one-dimensional case is extended to the barrier being inverted, which forms an attractive potential well. The first application of this analysis is to the emission of alpha particles from the decay of radioactive nuclei, where the alpha-nucleus attraction is modeled by a potential well and the barrier is the repulsive Coulomb potential. Excellent results are obtained. Ditto for the similar analysis of proton burning in stars and yet a different analysis that explains tunneling through a Josephson junction, the connector between two superconductors. The final application is to the scanning tunneling microscope, a device that allows the microscopic surfaces of solids to be mapped via electrons from the surface molecules tunneling into the tip of the STM probe.

scholarly journals IIMLP: integrated information-entropy-based method for LncRNA prediction

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Junyi Li ◽  
Huinian Li ◽  
Xiao Ye ◽  
Li Zhang ◽  
Qingzhe Xu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Information Entropy ◽  
Area Under The Curve ◽  
Prediction Method ◽  
Machine Learning Algorithms ◽  
Reading Frame ◽  
Non Coding Rna ◽  
The One ◽  
Long Non Coding Rna

Abstract Background The prediction of long non-coding RNA (lncRNA) has attracted great attention from researchers, as more and more evidence indicate that various complex human diseases are closely related to lncRNAs. In the era of bio-med big data, in addition to the prediction of lncRNAs by biological experimental methods, many computational methods based on machine learning have been proposed to make better use of the sequence resources of lncRNAs. Results We developed the lncRNA prediction method by integrating information-entropy-based features and machine learning algorithms. We calculate generalized topological entropy and generate 6 novel features for lncRNA sequences. By employing these 6 features and other features such as open reading frame, we apply supporting vector machine, XGBoost and random forest algorithms to distinguish human lncRNAs. We compare our method with the one which has more K-mer features and results show that our method has higher area under the curve up to 99.7905%. Conclusions We develop an accurate and efficient method which has novel information entropy features to analyze and classify lncRNAs. Our method is also extendable for research on the other functional elements in DNA sequences.

scholarly journals Bound states of a Klein–Gordon particle in the presence of a smooth potential well

2020 ◽  
Vol 35 (23) ◽  
pp. 2050140
Author(s):  
Eduardo López ◽  
Clara Rojas
Keyword(s):  
Bound States ◽  
Gordon Equation ◽  
Bound State ◽  
Potential Well ◽  
One Dimensional ◽  
Smooth Potential ◽  
Klein Gordon ◽  
The One ◽  
Potential Parameters ◽  
Klein Gordon Equation

We solve the one-dimensional time-independent Klein–Gordon equation in the presence of a smooth potential well. The bound state solutions are given in terms of the Whittaker [Formula: see text] function, and the antiparticle bound state is discussed in terms of potential parameters.

Approximate approaches to the one-dimensional finite potential well

2011 ◽  
Vol 32 (6) ◽  
pp. 1701-1710 ◽  
Author(s):  
Shilpi Singh ◽  
Praveen Pathak ◽  
Vijay A Singh
Keyword(s):  
Potential Well ◽  
One Dimensional ◽  
The One

CLASSICAL DIFFUSION AND QUANTAL LOCALIZATION OF A KICKED PARTICLE IN A WELL

1988 ◽  
Vol 02 (01) ◽  
pp. 103-120 ◽  
Author(s):  
AVRAHAM COHEN ◽  
SHMUEL FISHMAN
Keyword(s):  
Diffusion Coefficient ◽  
Classical Limit ◽  
Approximate Formula ◽  
Quantum Systems ◽  
Potential Well ◽  
Diffusive Growth ◽  
Classical Chaos ◽  
The One ◽  
Short Time ◽  
Infinite Potential Well

The classical and quantal behavior of a particle in an infinite potential well, that is periodically kicked is studied. The kicking potential is K|q|α, where q is the coordinate, while K and α are constants. Classically, it is found that for α > 2 the energy of the particle increases diffusively, for α < 2 it is bounded and for α = 2 the result depends on K. An approximate formula for the diffusion coefficient is presented and compared with numerical results. For quantum systems that are chaotic in the classical limit, diffusive growth of energy takes place for a short time and then it is suppressed by quantal effects. For the systems that are studied in this work the origin of the quantal localization in energy is related to the one of classical chaos.

scholarly journals Meiosis-Based Laboratory Evolution of the Thermal Tolerance in Kluyveromyces marxianus

2022 ◽  
Vol 9 ◽  
Author(s):  
Li Wu ◽  
Yilin Lyu ◽  
Pingping Wu ◽  
Tongyu Luo ◽  
Junyuan Zeng ◽  
...  
Keyword(s):  
Kluyveromyces Marxianus ◽  
Thermal Tolerance ◽  
Genetic Recombination ◽  
Original Strain ◽  
Heterologous Proteins ◽  
Diploid Strain ◽  
Nonsense Mutations ◽  
Laboratory Evolution ◽  
The One ◽  
Selection Of

Kluyveromyces marxianus is the fastest-growing eukaryote and a promising host for producing bioethanol and heterologous proteins. To perform a laboratory evolution of thermal tolerance in K. marxianus, diploid, triploid and tetraploid strains were constructed, respectively. Considering the genetic diversity caused by genetic recombination in meiosis, we established an iterative cycle of “diploid/polyploid - meiosis - selection of spores at high temperature” to screen thermotolerant strains. Results showed that the evolution of thermal tolerance in diploid strain was more efficient than that in triploid and tetraploid strains. The thermal tolerance of the progenies of diploid and triploid strains after a two-round screen was significantly improved than that after a one-round screen, while the thermal tolerance of the progenies after the one-round screen was better than that of the initial strain. After a two-round screen, the maximum tolerable temperature of Dip2-8, a progeny of diploid strain, was 3°C higher than that of the original strain. Whole-genome sequencing revealed nonsense mutations of PSR1 and PDE2 in the thermotolerant progenies. Deletion of either PSR1 or PDE2 in the original strain improved thermotolerance and two deletions displayed additive effects, suggesting PSR1 and PDE2 negatively regulated the thermotolerance of K. marxianus in parallel pathways. Therefore, the iterative cycle of “meiosis - spore screening” developed in this study provides an efficient way to perform the laboratory evolution of heat resistance in yeast.

scholarly journals Relativistic quantum heat engine from uncertainty relation standpoint

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Pritam Chattopadhyay ◽  
Goutam Paul
Keyword(s):  
Uncertainty Relation ◽  
Relativistic Quantum ◽  
Heat Engine ◽  
Potential Well ◽  
Relativistic Case ◽  
Heat Engines ◽  
Quantum Heat Engine ◽  
Thermodynamic Variables ◽  
The One ◽  
Work Done

AbstractEstablished heat engines in quantum regime can be modeled with various quantum systems as working substances. For example, in the non-relativistic case, we can model the heat engine using infinite potential well as a working substance to evaluate the efficiency and work done of the engine. Here, we propose quantum heat engine with a relativistic particle confined in the one-dimensional potential well as working substance. The cycle comprises of two isothermal processes and two potential well processes of equal width, which forms the quantum counterpart of the known isochoric process in classical nature. For a concrete interpretation about the relation between the quantum observables with the physically measurable parameters (like the efficiency and work done), we develop a link between the thermodynamic variables and the uncertainty relation. We have used this model to explore the work extraction and the efficiency of the heat engine for a relativistic case from the standpoint of uncertainty relation, where the incompatible observables are the position and the momentum operators. We are able to determine the bounds (the upper and the lower bounds) of the efficiency of the heat engine through the thermal uncertainty relation.

scholarly journals Cytotaxonomic considerations on the sex chromosome variation observed within Acomys ngurui Verheyen et al. 2011 (Rodentia Muridae)

Zootaxa ◽  
2012 ◽  
Vol 3493 (1) ◽  
pp. 35 ◽  
Author(s):  
RICCARDO CASTIGLIA ◽  
FLAVIA ANNESI
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
East African ◽  
Chromosome Variation ◽  
Mtdna Sequence ◽  
Two New Species ◽  
Morphologic Analysis ◽  
The One ◽  
Future Work

The taxonomy of the East African Muridae belonging to the Acomys spinosissimus Peters 1852 species complex has been recently revised (Verheyen et al., 2011). Two new species have been described by means of external morphologic analysis, craniometry, enzymes, mitochondrial DNA sequences and karyological information. For one of the two new species, Acomys ngurui Verheyen et al. 2011, a polymorphic karyotype has been observed. In fact, for 19 of the 22 karyotyped individuals, the karyotype is identical to the one described for A. spinosissimus s. s. (2n = 60, aFN = 68), characterized by a sex chromosome constitution of the XX/XY type, with an acrocentric X and a submetacentric Y (Dippenaar and Rautenbach, 1986). The remaining three females possess a karyotype that resembles the one reported by Matthey (1965) and Barome et al. (2001) characterized by a unique giant metacentric X chromosome (Xg), and by a variable diploid number (2n = 59–62). These females were found in the three localities in Tanzania together with specimens with the typical ‘spinosissimus’ karyotype. Specimens carrying the Xg were not distinguishable on the basis of their mtDNA sequence or morphology from the other specimens with XY karyotype (Verheyen et al., 2011). The authors concluded that the available evidence did not allow one to give taxonomic value to this chromosomal configuration, characterized by a particular sex determination, hoping for future work that will study the animals bearing this typical karyotype in more detail.

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