Conformational changes in three-dimensional chromatin structure in Paulownia fortunei after phytoplasma infection

2021 ◽  
Author(s):  
Bingbing Li ◽  
Dan Lin ◽  
Xiaoqiao Zhai ◽  
Guoqiang Fan ◽  
Zhenli Zhao ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Chromatin Structure ◽  
Plant Disease Resistance ◽  
Transcriptional Activity ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Chromatin Conformation ◽  
Sequencing Data ◽  
Abiotic Stress Response ◽  
Paulownia Fortunei

Abstract Higher-order chromatin structures play important roles in regulating multiple biological processes, growth and development, biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia, or about whole-genome chromatin conformational changes that occur in response to Paulownia witches’ broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in healthy and phytoplasma-infected Paulownia fortunei genome. The heatmap results indicated that the strongest interactions between chromosomes were in the telomeres. We confirmed the main structural characteristics, such as A/B compartments, topologically associated domains, and chromatin loops were prominent in Paulownia genome and clearly altered in phytoplasma-infected plants. By combining chromatin Immunoprecipitation sequencing, Hi-C signals, and RNA sequencing data, we inferred that the chromatin structure changed and the modification levels of three histones (H3K4me3/K9ac/K36me3) increased in phytoplasma-infected P. fortunei, which was associated with changes of transcriptional activity. We concluded that epigenetic modifications, transcriptional activity might function in combination to shape chromatin packing in healthy and phytoplasm-infected Paulownia. Finally, 11 genes (such as RPN6, Sec61 subunit alpha), commonly located at specific TAD boundaries, A/B compartment switching, specific loops, and associated with histone marks, were identified and considered as closely related to PaWB stress. Our results provide new insights into the nexus between gene regulation and chromatin conformational alterations in non-model plants upon phytopathogen infection and plant disease resistance. Key words: Paulownia witches’ broom; chromatin conformation; histone modification; transcription regulation

scholarly journals Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

2014 ◽  
Vol 212 (1) ◽  
pp. 107-120 ◽  
Author(s):  
Kinjal Majumder ◽  
Olivia I. Koues ◽  
Elizabeth A.W. Chan ◽  
Katherine E. Kyle ◽  
Julie E. Horowitz ◽  
...  
Keyword(s):  
Long Range ◽  
Conformational Changes ◽  
Three Dimensional ◽  
Chromatin Conformation ◽  
Dynamic Changes ◽  
Architectural Elements ◽  
Receptor Locus ◽  
Long Range Interactions ◽  
Enhancer Function ◽  
Flanking Regions

Gene regulation relies on dynamic changes in three-dimensional chromatin conformation, which are shaped by composite regulatory and architectural elements. However, mechanisms that govern such conformational switches within chromosomal domains remain unknown. We identify a novel mechanism by which cis-elements promote long-range interactions, inducing conformational changes critical for diversification of the TCRβ antigen receptor locus (Tcrb). Association between distal Vβ gene segments and the highly expressed DβJβ clusters, termed the recombination center (RC), is independent of enhancer function and recruitment of V(D)J recombinase. Instead, we find that tissue-specific folding of Tcrb relies on two distinct architectural elements located upstream of the RC. The first, a CTCF-containing element, directly tethers distal portions of the Vβ array to the RC. The second element is a chromatin barrier that protects the tether from hyperactive RC chromatin. When the second element is removed, active RC chromatin spreads upstream, forcing the tether to serve as a new barrier. Acquisition of barrier function by the CTCF element disrupts contacts between distal Vβ gene segments and significantly alters Tcrb repertoires. Our findings reveal a separation of function for RC-flanking regions, in which anchors for long-range recombination must be cordoned off from hyperactive RC landscapes by chromatin barriers.

Electron Microscopy and image reconstruction reveal the structural basis for spectrin's elastic properties

1992 ◽  
Vol 50 (1) ◽  
pp. 510-511
Author(s):  
Amy M. McGough ◽  
Robert Josephs
Keyword(s):  
Electron Microscopy ◽  
Elastic Properties ◽  
Conformational Changes ◽  
Quaternary Structure ◽  
Three Dimensional ◽  
Membrane Skeleton ◽  
Projection Algorithm ◽  
Structural Basis ◽  
Iterative Approximation ◽  
Membrane Skeletons

The remarkable deformability of the erythrocyte derives in large part from the elastic properties of spectrin, the major component of the membrane skeleton. It is generally accepted that spectrin's elasticity arises from marked conformational changes which include variations in its overall length (1). In this work the structure of spectrin in partially expanded membrane skeletons was studied by electron microscopy to determine the molecular basis for spectrin's elastic properties. Spectrin molecules were analysed with respect to three features: length, conformation, and quaternary structure. The results of these studies lead to a model of how spectrin mediates the elastic deformation of the erythrocyte.Membrane skeletons were isolated from erythrocyte membrane ghosts, negatively stained, and examined by transmission electron microscopy (2). Particle lengths and end-to-end distances were measured from enlarged prints using the computer program MACMEASURE. Spectrin conformation (straightness) was assessed by calculating the particles’ correlation length by iterative approximation (3). Digitised spectrin images were correlation averaged or Fourier filtered to improve their signal-to-noise ratios. Three-dimensional reconstructions were performed using a suite of programs which were based on the filtered back-projection algorithm and executed on a cluster of Microvax 3200 workstations (4).

scholarly journals Coupled Fluid–Solid Numerical Simulation for Flow Field Characteristics and Supporting Performance of Flexible Support Cylindrical Gas Film Seal

Aerospace ◽  
2021 ◽  
Vol 8 (4) ◽  
pp. 97
Author(s):  
Junfeng Sun ◽  
Meihong Liu ◽  
Zhen Xu ◽  
Taohong Liao ◽  
Xiangping Hu ◽  
...  
Keyword(s):  
Flow Field ◽  
Film Thickness ◽  
Fluid Dynamic ◽  
Structural Characteristics ◽  
Structural Parameters ◽  
Equivalent Stress ◽  
Three Dimensional ◽  
High Rotational Speed ◽  
Flexible Support ◽  
Flow Field Characteristics

A new type of cylindrical gas film seal (CGFS) with a flexible support is proposed according to the working characteristics of the fluid dynamic seal in high-rotational-speed fluid machinery, such as aero-engines and centrifuges. Compared with the CGFS without a flexible support, the CGFS with flexible support presents stronger radial floating characteristics since it absorbs vibration and reduces thermal deformation of the rotor system. Combined with the structural characteristics of a film seal, an analytical model of CGFS with a flexible wave foil is established. Based on the fluid-structure coupling analysis method, the three-dimensional flow field of a straight-groove CGFS model is simulated to study the effects of operating and structural parameters on the steady-state characteristics and the effects of gas film thickness, eccentricity, and the number of wave foils on the equivalent stress of the flexible support. Simulation results show that the film stiffness increases significantly when the depth of groove increases. When the gas film thickness increases, the average equivalent stress of the flexible support first decreases and then stabilizes. Furthermore, the number of wave foils affects the average foils thickness. Therefore, when selecting the number of wave foils, the support stiffness and buffer capacity should be considered simultaneously.

Retrovirus-induced interference with collagen I gene expression in Mov13 fibroblasts is maintained in the absence of DNA methylation

1991 ◽  
Vol 11 (1) ◽  
pp. 47-54
Author(s):  
H Chan ◽  
S Hartung ◽  
M Breindl
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chromatin Structure ◽  
Transcriptional Activity ◽  
Xenopus Laevis Oocytes ◽  
Regulatory Sequences ◽  
Type I ◽  
Wild Type ◽  
Col1a1 Gene

We have studied the role of DNA methylation in repression of the murine alpha 1 type I collagen (COL1A1) gene in Mov13 fibroblasts. In Mov13 mice, a retroviral provirus has inserted into the first intron of the COL1A1 gene and blocks its expression at the level of transcriptional initiation. We found that regulatory sequences in the COL1A1 promoter region that are involved in the tissue-specific regulation of the gene are unmethylated in collagen-expressing wild-type fibroblasts and methylated in Mov13 fibroblasts, confirming and extending earlier observations. To directly assess the role of DNA methylation in the repression of COL1A1 gene transcription, we treated Mov13 fibroblasts with the demethylating agent 5-azacytidine. This treatment resulted in a demethylation of the COL1A1 regulatory sequences but failed to activate transcription of the COL1A1 gene. Moreover, the 5-azacytidine treatment induced a transcription-competent chromatin structure in the retroviral sequences but not in the COL1A1 promoter. In DNA transfection and microinjection experiments, we found that the provirus interfered with transcriptional activity of the COL1A1 promoter in Mov13 fibroblasts but not in Xenopus laevis oocytes. In contrast, the wild-type COL1A1 promoter was transcriptionally active in Mov13 fibroblasts. These experiments showed that the COL1A1 promoter is potentially transcriptionally active in the presence of proviral sequences and that Mov13 fibroblasts contain the trans-acting factors required for efficient COL1A1 gene expression. Our results indicate that the provirus insertion in Mov13 can inactivate COL1A1 gene expression at several levels. It prevents the developmentally regulated establishment of a transcription-competent methylation pattern and chromatin structure of the COL1A1 domain and, in the absence of DNA methylation, appears to suppress the COL1A1 promoter in a cell-specific manner, presumably by assuming a dominant chromatin structure that may be incompatible with transcriptional activity of flanking cellular sequences.

scholarly journals The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis

2018 ◽  
Vol 201 (4) ◽  
Author(s):  
Tomáš Kouba ◽  
Jiří Pospíšil ◽  
Jarmila Hnilicová ◽  
Hana Šanderová ◽  
Ivan Barvík ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Mycobacterium Smegmatis ◽  
Drug Target ◽  
Conformational Dynamics ◽  
Three Dimensional ◽  
Cryo Electron Microscopy ◽  
Bacterial Rna ◽  
High Degree

ABSTRACT Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σA but no other factors. Each form was detected by cryo-electron microscopy in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme and confirm that region 1.1 of σA is directed into the primary channel of RNAP. Taken together, we describe the conformational changes of unrestrained mycobacterial RNAP. IMPORTANCE We describe here three-dimensional structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-electron microscopy. These structures fill the thus-far-empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.

Novel Ultrasonic Technology for Devulcanization of Waste Rubbers

1995 ◽  
Vol 68 (2) ◽  
pp. 267-280 ◽  
Author(s):  
A. I. Isayev ◽  
J. Chen ◽  
A. Tukachinsky
Keyword(s):  
Mechanical Properties ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Ultrasonic Waves ◽  
Styrene Butadiene Rubber ◽  
Butadiene Rubber ◽  
Processing Conditions ◽  
Laboratory Reactor ◽  
Plant Level ◽  
Theological Properties

Abstract A novel patented process and several reactors have been developed for devulcanization of waste rubbers. The technology is based on the use of the high power ultrasonics. The ultrasonic waves of certain levels in the presence of pressure and heat rapidly break up the three-dimensional network in crosslinked rubbers. The devulcanized rubber can be reprocessed, shaped and revulcanized in much the same way as a virgin rubber. The first laboratory reactor has been scaled up to pilot-plant level by the National Feedscrew and Machining, Inc. Various devulcanization experiments were carried out with model styrene-butadiene rubber (SBR) and with ground rubber tire (GRT). Curing behavior, Theological properties, and structural characteristics of rubbers devulcanized at various processing conditions were studied, as well as mechanical properties of revulcanized rubber samples. A possible mechanism of the devulcanization is discussed. The performed measurements indicate that the rubbers are partially devulcanized, and the devulcanization process is accompanied by certain degradation of the macromolecular chains. In spite of these observations, the processing conditions are identified at which the retention of the mechanical properties is found to be good. A further work is in progress to find the optimal conditions of devulcanization and to improve the selectivity of the process towards breaking up the chemical network only.

CAD Software for Cable Design: A Three-Dimensional Visualization Tool

2010 ◽  
Author(s):  
Rodrigo Provasi ◽  
Christiano Odir Cardoso Meirelles ◽  
Clo´vis de Arruda Martins
Keyword(s):  
Computer Aided Design ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Axial Stiffness ◽  
General Description ◽  
Post Processing ◽  
Cad System ◽  
Processing Resources ◽  
Definition Of ◽  
Electrical Cables

The concept and project of umbilical cables and flexible pipes are not simple tasks, due to the great variety of components and possible arrangements. The design of those elements is based on the functions they are intended to perform. Also, some structural characteristics determine which component will be selected, including electrical cables and hydraulic hoses, to control underwater equipment, protective sheaths, helically wounded tensile armors, anti-wear layers, interlocked carcasses; pressure armors and so on. The modeling process consists on defining the cable features and selecting the elements that will compose it. The process should take into account the desired structural characteristics, such as axial stiffness, and must respect some constraints, such as weight. To have an operational cable, one must follow a number of steps from definition to validation of the cable and any tool that provides a easier way to deal with this process is highly desired. In this scenario, Computer Aided Design software was conceived. It enables the definition of cable elements and set its relative arrangements in a cross-section view. Post-processing features are also part of the program, enabling users to visualize the geometry, determining possible interferences only visible in a three-dimensional visualization module. Although a solver is also available to determine stress and displacements and, as a sub-product, the cable weight and equivalent stiffness, the CAD software can be easily integrated to other solvers, to provide pre and post processing resources. This paper gives a general description of the whole CAD system but focus on the three-dimensional module. Through the paper, an overview of the software is shown, pointing out the system requirements. Next, the user interface is described, showing its features and, to conclude, modeled cables geometries and some results are shown.

scholarly journals Improved scFv Anti-LOX-1 Binding Activity by Fusion with LOX-1-Binding Peptides

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Wei Hu ◽  
Qiuhong Xie ◽  
Hongyu Xiang
Keyword(s):  
Targeted Delivery ◽  
Structural Characteristics ◽  
Low Density Lipoprotein ◽  
Three Dimensional ◽  
Density Lipoprotein ◽  
Binding Activity ◽  
Single Chain ◽  
C Terminus ◽  
Density Lipoprotein Receptor ◽  
Therapeutic Molecules

The oxidized low-density lipoprotein receptor-1 (LOX-1) targeted single-chain variable fragment (scFvs) is a promising molecule for the targeted delivery of imaging and therapeutic molecules of atherosclerotic diseases; however, its applications are limited by the inherent low antigen affinity. In this study, the three-dimensional (3D) model of the anti-LOX-1 scFv was constructed and its docking with the LOX-1 protein was developed. To improve the LOX-1-binding activity, the anti-LOX-1 scFv was designed to fuse with one of three LOX-1-binding heptapeptides, LTPATAI, FQTPPQL, and LSIPPKA, at its N-terminus and C-terminus and in the linker region, which have different LOX-1-binding interfaces with the anti-LOX-1 scFv analyzed by an array of computational approaches. These scFv/peptide fusions were constructed, successfully expressed in Brevibacillus choshinensis hosts, and purified by a two-step column purification process. The antigen binding activity, structural characteristics, thermal stability, and stability in serum of these fusion proteins were examined. Results showed that the scFv with N-terminal fusing peptides proteins demonstrated increased LOX-1-binding activity without decrease in stability. These findings will help increase the application efficacy of LOX-1 targeting scFv in LOX-1-based therapy.

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