scholarly journals Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement

Entropy ◽  
2021 ◽  
Vol 23 (5) ◽  
pp. 542
Author(s):  
Shi Yu ◽  
Jiaxin Wu ◽  
Xianliang Meng ◽  
Ruizhi Chu ◽  
Xiao Li ◽  
...  
Keyword(s):  
Cell Wall ◽  
Bacterial Chromosome ◽  
Dynamic Simulations ◽  
External Compression ◽  
Langevin Dynamic ◽  
Bacterial Chromosomes ◽  
Metabolic Reactions ◽  
Non Gaussian ◽  
Chromosome Segments ◽  
Cytoplasmic Particle

In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.

Effects of Cell-Wall Angle on the Mechanical Properties of Hexagonal Honeycombs

2013 ◽  
Vol 535-536 ◽  
pp. 377-380
Author(s):  
Ling Ling Hu ◽  
Tong Xi Yu
Keyword(s):  
Mechanical Properties ◽  
Cell Wall ◽  
Relative Density ◽  
Significant Influence ◽  
Absorption Capacity ◽  
Energy Absorption Capacity ◽  
Wall Angle ◽  
Dynamic Simulations ◽  
Crushing Strength ◽  
The Impact

The y-directional mechanical properties of hexagonal honeycombs with various cell-wall angles are explored. The results of both the quasi-static experiments and the dynamic simulations show that the cell-wall angle has a significant influence on the honeycombs’ mechanical properties, although the latter is dominated by the honeycombs’ relative density. This influence is weakened by the increase of the impact velocity. With retaining the honeycombs’ relative density as constant, the honeycomb with the cell-wall angle of about 45o exhibits the optimal crushing strength and energy absorption capacity.

scholarly journals Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in Brachypodium cesa1S830N

AoB Plants ◽  
2019 ◽  
Vol 11 (5) ◽  
Author(s):  
Chad Brabham ◽  
Abhishek Singh ◽  
Jozsef Stork ◽  
Ying Rong ◽  
Indrajit Kumar ◽  
...  
Keyword(s):  
Cell Wall ◽  
Molecular Dynamic ◽  
Missense Mutation ◽  
Primary Cell ◽  
Primary Cell Wall ◽  
Crystalline Cellulose ◽  
Molecular Dynamic Simulations ◽  
Cellulose Content ◽  
Cellulose Biosynthesis ◽  
Dynamic Simulations

Abstract Here, we present a study into the mechanisms of primary cell wall cellulose formation in grasses, using the model cereal grass Brachypodium distachyon. The exon found adjacent to the BdCESA1 glycosyltransferase QXXRW motif was targeted using Targeting Induced Local Lesions in Genomes (TILLING) and sequencing candidate amplicons in multiple parallel reactions (SCAMPRing) leading to the identification of the Bdcesa1S830N allele. Plants carrying this missense mutation exhibited a significant reduction in crystalline cellulose content in tissues that rely on the primary cell wall for biomechanical support. However, Bdcesa1S830N plants failed to exhibit the predicted reduction in plant height. In a mechanism unavailable to eudicotyledons, B. distachyon plants homozygous for the Bdcesa1S830N allele appear to overcome the loss of internode expansion anatomically by increasing the number of nodes along the stem. Stem biomechanics were resultantly compromised in Bdcesa1S830N. The Bdcesa1S830N missense mutation did not interfere with BdCESA1 gene expression. However, molecular dynamic simulations of the CELLULOSE SYNTHASE A (CESA) structure with modelled membrane interactions illustrated that Bdcesa1S830N exhibited structural changes in the translated gene product responsible for reduced cellulose biosynthesis. Molecular dynamic simulations showed that substituting S830N resulted in a stabilizing shift in the flexibility of the class specific region arm of the core catalytic domain of CESA, revealing the importance of this motion to protein function.

scholarly journals The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Enea Sancho-Vaello ◽  
David Gil-Carton ◽  
Patrice François ◽  
Eve-Julie Bonetti ◽  
Mohamed Kreir ◽  
...  
Keyword(s):  
Cell Death ◽  
Cell Wall ◽  
Bacterial Cell ◽  
Lipid Membranes ◽  
Bacterial Infections ◽  
Rational Design ◽  
Critical Role ◽  
Time Lapse ◽  
Dynamic Simulations ◽  
Bacterial Cell Death

Abstract The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.

scholarly journals Confinement and crowding control the morphology and dynamics of a model bacterial chromosome

Soft Matter ◽  
2019 ◽  
Vol 15 (12) ◽  
pp. 2677-2687 ◽  
Author(s):  
Pinaki Swain ◽  
Bela M. Mulder ◽  
Debasish Chaudhuri
Keyword(s):  
Bacterial Chromosome ◽  
Cylindrical Cell ◽  
Bacterial Chromosomes

Motivated by recent experiments probing the shape, size and dynamics of bacterial chromosomes in growing cells, we consider a circular polymer attached to side-loops to model the chromosome confined to a cylindrical cell, in the presence of cytoplasmic crowders.

scholarly journals Structure of bacterial chromosome: An analysis of DNA-protein interactions in vivo

2017 ◽  
Vol 71 (0) ◽  
pp. 0-0
Author(s):  
Joanna Hołówka ◽  
Małgorzata Płachetka
Keyword(s):  
Protein Interactions ◽  
Global Scale ◽  
Hierarchical Organization ◽  
Bacterial Chromosome ◽  
Precise Analysis ◽  
Bacterial Chromosomes ◽  
High Throughput Dna Sequencing ◽  
In Vivo Footprinting ◽  
Microscopy Techniques

According to recent reports, bacterial chromosomes exhibit a hierarchical organization. The number of proteins that bind DNA are responsible for local and global organization of the DNA ensuring proper chromosome compaction. Advanced molecular biology techniques combined with high-throughput DNA sequencing methods allow a precise analysis of bacterial chromosome structures on a local and global scale. Methods such as in vivo footprinting and ChIP-seq allow to map binding sites of analyzed proteins in certain chromosomal regions or along the whole chromosome while analysis of the spatial interactions on global scale could be performed by 3C techniques. Additional insight into complex structures created by chromosome-organizing proteins is provided by high-resolution fluorescence microscopy techniques.

scholarly journals circHiC: circular visualization of Hi-C data and integration of genomic data

2020 ◽  
Author(s):  
Ivan Junier ◽  
Nelle Varoquaux
Keyword(s):  
Genomic Data ◽  
Bacterial Chromosome ◽  
Link Type ◽  
Genome Wide ◽  
Bacterial Chromosomes ◽  
Wide Contact ◽  
Linear Chromosomes

SummaryGenome wide contact frequencies obtained using Hi-C-like experiments have raised novel challenges in terms of visualization and rationalization of chromosome structuring phenomena. In bacteria, display of Hi-C data should be congruent with the circularity of chromosomes. However, standard representations under the form of square matrices or horizontal bands are not adapted to periodic conditions as those imposed by (most) bacterial chromosomes. Here, we fill this gap and propose a Python library, built upon the widely used Matplotlib library, to display Hi-C data in circular strips, together with the possibility to overlay genomic data. The proposed tools are light and fast, aiming to facilitate the exploration and understanding of bacterial chromosome structuring data. The library further includes the possibility to handle linear chromosomes, providing a fresh way to display and explore eukaryotic data.Availability and implementationThe package runs under Python 3 and is freely available at https://github.com/TrEE-TIMC/circHiC. The documentation can be found at https://tree-timc.github.io/circhic/; images obtained in different organisms are provided in the gallery section and are accompanied with [email protected], [email protected]

scholarly journals Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Wenjun Jiang ◽  
Xuejin Zhao ◽  
Tslil Gabrieli ◽  
Chunbo Lou ◽  
Yuval Ebenstein ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Single Step ◽  
Gene Synthesis ◽  
Gibson Assembly ◽  
Large Gene ◽  
Cas9 Nuclease ◽  
Bacterial Chromosomes ◽  
One Step ◽  
Chromosome Segments

Abstract The cloning of long DNA segments, especially those containing large gene clusters, is of particular importance to synthetic and chemical biology efforts for engineering organisms. While cloning has been a defining tool in molecular biology, the cloning of long genome segments has been challenging. Here we describe a technique that allows the targeted cloning of near-arbitrary, long bacterial genomic sequences of up to 100 kb to be accomplished in a single step. The target genome segment is excised from bacterial chromosomes in vitro by the RNA-guided Cas9 nuclease at two designated loci, and ligated to the cloning vector by Gibson assembly. This technique can be an effective molecular tool for the targeted cloning of large gene clusters that are often expensive to synthesize by gene synthesis or difficult to obtain directly by traditional PCR and restriction-enzyme-based methods.

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