Associations Between Inverted Repeats and the Structural Evolution of Bacterial Genomes

Abstract The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong underrepresentation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

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M. BOVIS BCG-1 (RUSSIA) SUB-STRAIN GENOME STABILITY INVESTIGATION WITHIN THE ENTIRE PRODUCTION PROCESS

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-2018-2-58-67 ◽

2018 ◽

pp. 58-67

Author(s):

E. V. Otrashevskaya ◽

V. N. Vinokurova ◽

E. A. Shilikov ◽

E. A. Sotnikova ◽

T. A. Perevyshina ◽

...

Keyword(s):

Production Process ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Stability ◽

Genome Structure ◽

Whole Genome Sequence ◽

Whole Genome ◽

Vaccine Production ◽

The Stability ◽

Strain Genome

Aim. The aim of the current study was to analyze the genome structure of the M. bovis BCG-1 (Russia) sub-strain, used for the vaccine production, as well as its genome stability within the entire production process. Materials and methods. Whole genome sequencing and M. bovis BCG-1 (Russia) working seed lot and for the last production passage of the sub-strain cultivation from a number of the vaccine batches. Additionally, VNTR sequences of 24 locus analyses, RD patterns comparison, as well as spoligotyping were performed. Results. The whole genome sequence of the M. bovis BCG-1 (Russia) working seed lot was assembled, annotated and deposited to GenBank. On the basis of DU2- and RD-regions analyzes M. bovis BCG-1 (Russia) sub-strain was confirmed to be belonged to BCG Russia strains of DU2-I group. Whole genome sequencing followed by comparative analysis of RD patterns and SNPs confirmed the stability of the vaccine sub-strain genome from the working seed lot to a number of the vaccine batches obtained within the two-years period. VNTR profile and spoligopattern exactly matched the M. bovis BCG-1 (Russia). Conclusion. Thus the M. bovis BCG-1 (Russia) sub-strain genome identity and stability have been studied and demonstrated. The obtained result confirmed the vaccine production process consistency.

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Forward Rate Bias in Developed and Developing Countries: More Risky Not Less Rational

Econometrics ◽

10.3390/econometrics8040043 ◽

2020 ◽

Vol 8 (4) ◽

pp. 43

Author(s):

Michael D. Goldberg ◽

Olesia Kozlova ◽

Deniz Ozabaci

Keyword(s):

Developing Countries ◽

Forward Rate ◽

Currency Markets ◽

Developed Country ◽

Slope Coefficient ◽

Break Points ◽

Time Periods ◽

The Stability ◽

Widespread View ◽

Shed Light

This paper examines the stability of the Bilson–Fama regression for a panel of 55 developed and developing countries. We find multiple break points for nearly every country in our panel. Subperiod estimates of the slope coefficient show a negative bias during some time periods and a positive bias during other time periods in nearly every country. The subperiod biases display two key patterns that shed light on the literature’s linear regression findings. The results point toward the importance of risk in currency markets. We find that risk is greater for developed country markets. The evidence undercuts the widespread view that currency returns are predictable or that developed country markets are less rational.

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Structural Evolution Upon Annealing of Multi-Layer Si/Fe Thin Films Prepared by Magnetron Sputtering

Materials Science Forum ◽

10.4028/www.scientific.net/msf.561-565.1161 ◽

2007 ◽

Vol 561-565 ◽

pp. 1161-1164

Author(s):

Xiao Na Li ◽

Bing Hu ◽

Chuang Dong ◽

Xin Jiang

Keyword(s):

Thin Films ◽

Magnetron Sputtering ◽

Room Temperature ◽

Structural Evolution ◽

Radio Frequency Magnetron Sputtering ◽

Transmission Electron ◽

Direct Band ◽

The Stability ◽

Sputtering System

Fe/Si multi-layer films were fabricated on Si (100) substrates utilizing radio frequency magnetron sputtering system. Si/β-FeSi2 structure was found in the films after the deposition. Structural characterization of Fe-silicide sample was performed by transmission electron microscopy, to explore the dependence of the microstructure of β-FeSi2 film on the preparation parameters. It was found that β-FeSi2 particles were formed after the deposition without annealing, whose size is less than 20nm ,with a direct band-gap of 0.94eV in room temperature. After annealing at 850°C, particles grow lager, however the stability of thin films was still good.

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New molecular insights into the stability of Ni–Pd hollow nanoparticles

Inorganic Chemistry Frontiers ◽

10.1039/c7qi00370f ◽

2017 ◽

Vol 4 (10) ◽

pp. 1679-1690 ◽

Cited By ~ 10

Author(s):

Hamed Akbarzadeh ◽

Esmat Mehrjouei ◽

Amir Nasser Shamkhali ◽

Mohsen Abbaspour ◽

Sirous Salemi ◽

...

Keyword(s):

Molecular Dynamics ◽

Thermal Behavior ◽

Molecular Dynamics Simulations ◽

Structural Evolution ◽

Hollow Nanoparticles ◽

The Stability ◽

Dynamics Simulations

Molecular dynamics simulations were used to investigate the structural evolution and thermal behavior of Ni–Pd hollow nanoparticles.

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In Situ SEM Observation of Structured Si/C Anodes Reactions in an Ionic-Liquid-Based Lithium-Ion Battery

Applied Sciences ◽

10.3390/app9050956 ◽

2019 ◽

Vol 9 (5) ◽

pp. 956 ◽

Cited By ~ 4

Author(s):

Huifeng Shi ◽

Xianqiang Liu ◽

Rui Wu ◽

Yijing Zheng ◽

Yonghe Li ◽

...

Keyword(s):

Morphological Evolution ◽

Structural Evolution ◽

Lithium Ion ◽

Composite Electrodes ◽

Charge Capacity ◽

Shed Light ◽

3D Electrode ◽

Large Charge ◽

Scanning Electron

In situ scanning electron microscopy (SEM) offers a good way to investigate the structural evolution during lithiation and delithiation processes. In this paper, the dynamical morphological evolution of 3D-line-structured/unstructured Si/C composite electrodes was observed by in situ SEM. The investigation revealed the microstructural origin of large charge capacity for 3D-line-structured anodes. Based on this proposed mechanism, a coarse optimization of 3D-line-structured anodes was proposed. These results shed light on the unique advantages of using an in situ SEM technique when studying realistic bulk batteries and designing 3D electrode structures.

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Ab Initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries

10.26434/chemrxiv.13720888.v2 ◽

2021 ◽

Author(s):

David Carrasco-Busturia ◽

Steen Lysgaard ◽

Piotr Jankowski ◽

Tejs Vegge ◽

Arghya Bhowmik ◽

...

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Deep Eutectic Solvents ◽

Ionic Species ◽

Electrochemical Activity ◽

Molecular Composition ◽

Ab Initio Molecular Dynamics ◽

The Stability ◽

Shed Light ◽

Battery Anode

Deep eutectic solvents (DES) have emerged as an alternative for conventional ionic liquids in aluminum batteries. Elucidating DES composition is fundamental to understand aluminum electrodeposition in the battery anode. Despite numerous experiemental efforts, the speciation of these DES remains elusive. This work shows how \textit{Ab initio} molecular dynamics (AIMD) simulations can shed light on the molecular composition of DES. For the particular example of AlCl$_{3}$:urea, one of the most popular DES, we carried out a systematic AIMD study, showing how an excess of AlCl$_{3}$ in the AlCl$_{3}$:urea mixture promotes the stability of ionic species vs neutral ones and also favors the reactivity in the system. These two facts explain the experimentally observed enhanced electrochemical activity in salt-rich DES. We also observe the transfer of simple $[$AlCl$_{x}$(urea)$_{y}]$ clusters between different species in the liquid, giving rise to free $[$AlCl$_{4}]^{-}$ units. The small size of these $[$AlCl$_{4}]^{-}$ units favors the transport of ionic species towards the anode, facilitating the electrodeposition of aluminum.

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Universal modesty in signal-burying games

10.31234/osf.io/j6a7h ◽

2018 ◽

Author(s):

Tadeg Quillien

Keyword(s):

Simple Model ◽

Evolutionary Game ◽

Costly Signaling ◽

Positive Information ◽

Probabilistic Information ◽

Signaling Dynamics ◽

The Stability ◽

Positive Traits ◽

Shed Light

Why would people hide positive information about themselves? Evolutionary game theorists have recently developed the signal-burying game as a simple model to shed light on this puzzle; they have shown that the game has an equilibrium where some agents are better off deliberately reducing the visibility of the signal by which they broadcast their positive traits. However, their explanation falls short of explaining all modesty norms, since this equilibrium also features individuals who openly brag. This leaves modesty norms that everyone adheres to in want of an explanation. Here we show that the signal-burying framework actually affords such an explanation: the game contains an equilibrium where all agents who send a signal voluntarily reduce its conspicuousness. Surprisingly, the stability of the two kinds of equilibria rely on very different principles. The equilibrium where some agents brag is stable because of costly signaling dynamics. By contrast, the universal modesty equilibrium exists because buried signals contain probabilistic information about a sender's type, and receivers make optimal use of this information. In the latter equilibrium, burying a signal can be understood as a handicap which makes the signal more honest, but honesty is not achieved through standard costly signaling dynamics.

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Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants

Genome Biology and Evolution ◽

10.1093/gbe/evz256 ◽

2019 ◽

Cited By ~ 1

Author(s):

Weiwen Wang ◽

Robert Lanfear

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Single Copy ◽

Land Plant ◽

Inverted Repeats ◽

Individual Plant ◽

Single Individual ◽

Equal Frequency ◽

Flip Flop ◽

Chloroplast Genomes

Abstract The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labour-intensive, and this phenomenon remains understudied. Here we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.

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Divalent Cations Affect the Stability and Structure of Dad2p, a Subunit of the Candida Albicans Kinetochore Dam1 Complex

Journal of Molecular Biology Research ◽

10.5539/jmbr.v6n1p26 ◽

2016 ◽

Vol 6 (1) ◽

pp. 26

Author(s):

Jennifer Turner Waldo ◽

Tsering Dolma ◽

Emily Rouse

Keyword(s):

Candida Albicans ◽

Mitotic Spindle ◽

Divalent Cations ◽

Dynamic Structure ◽

Biochemical Properties ◽

Differential Scanning Fluorimetry ◽

A Subunit ◽

Dam1 Complex ◽

The Stability ◽

Shed Light

The heterodecameric Dam1 complex is involved in establishing and maintaining the connection between the kinetochore and the mitotic spindle during mitosis. Biochemical studies of the reconstituted complex have shed light upon how it interacts with microtubules. However, little information about the biochemical properties of the isolated subunits has been available. This report examines the stability and structure of Dad2p, one of the Dam1 complex subunits isolated from Candida albicans. By employing differential scanning fluorimetry, protease protection and hydrodynamic analyses, we show that Dad2p is specifically responsive to the presence of divalent cations. This observation may be important for understanding the dynamic structure and regulation of the Dam1 complex in fungal cells.

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