scholarly journals Clamping of DNA shuts the condensin neck gate

2021 ◽  
Author(s):  
Byung-Gil Lee ◽  
James Rhodes ◽  
Jan Löwe
Keyword(s):  
The Other ◽  
Mechanistic Models ◽  
Complex Structures ◽  
Dna Compaction ◽  
Condensin Complex ◽  
Circular Dnas ◽  
Structural Maintenance Of Chromosomes

Condensin is a Structural Maintenance of Chromosomes (SMC) complex needed for the compaction of DNA into chromatids during mitosis. Lengthwise DNA compaction by condensin is facilitated by ATPase-driven loop extrusion, a process that is believed to be the fundamental activity of most, if not all SMC complexes. In order to obtain molecular insights, we obtained cryo-EM structures of yeast condensin in the presence of a slowly-hydrolysable ATP analogue and linear, as well as circular DNAs. The DNAs were shown to be clamped between the engaged heterodimeric SMC ATPase heads and the Ycs4 subunit, in a manner similar to previously reported DNA-bound SMC complex structures. Ycg1, the other non-SMC subunit was only flexibly bound to the complex, while also binding DNA tightly, and often remaining at a distance from the head module. In the clamped state, the DNA is encircled, or topologically entrapped, by the kleisin Brn1 and the two engaged head domains of Smc2 and Smc4, and this tripartite ring is closed at all interfaces, including at the neck of Smc2. We show that the neck gate opens upon head engagement in the absence of DNA, but it remains shut when DNA is present. Our work demonstrates that condensin and other SMC complexes go through similar conformations of the head modules during their ATPase cycle. In contrast, the behaviour of the Ycg1 subunit in the condensin complex might indicate differences in the implementation of the extrusion reactions and our findings will constrain further mechanistic models of loop extrusion by SMC complexes.

scholarly journals DNA sliding and loop formation by E. coli SMC complex: MukBEF

2021 ◽  
Author(s):  
man zhou
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Dna Interaction ◽  
Loop Formation ◽  
Unknown Mechanism ◽  
E Coli ◽  
Dna Compaction ◽  
And Function ◽  
Structural Maintenance Of Chromosomes

SMC (structural maintenance of chromosomes) complexes share conserved architectures and function in chromosome maintenance via an unknown mechanism. Here we have used single-molecule techniques to study MukBEF, the SMC complex in Escherichia coli. Real-time movies show MukB alone can compact DNA and ATP inhibits DNA compaction by MukB. We observed that DNA unidirectionally slides through MukB, potentially by a ratchet mechanism, and the sliding speed depends on the elastic energy stored in the DNA. MukE, MukF and ATP binding stabilize MukB and DNA interaction, and ATP hydrolysis regulates the loading/unloading of MukBEF from DNA. Our data suggests a new model for how MukBEF organizes the bacterial chromosome in vivo; and this model will be relevant for other SMC proteins.

The topological trapping of circular DNAs on agarose: Unexpected restrictions on DNA rotation

1978 ◽  
Vol 56 (6) ◽  
pp. 585-591 ◽  
Author(s):  
Jeremy S. Lee ◽  
A. Richard Morgan
Keyword(s):  
Secondary Structure ◽  
Binding Constant ◽  
Binding Assay ◽  
Sodium Perchlorate ◽  
Binding Constants ◽  
The Other ◽  
Calf Thymus ◽  
Potential Applications ◽  
Open Circular ◽  
Circular Dnas

DNA linked to an insoluble matrix has many potential applications. In some cases, it is highly desirable that the DNA be chemically unaltered, and for this reason, we have developed methods for topologically trapping circular DNAs on agarose. Open circular (oc) DNA containing at least one nick is readily trapped on agarose which has been heated or dissolved in sodium perchlorate to destroy secondary structure and then gelled by cooling or dialysis respectively. On the other hand, covalently closed circular (ccc) DNA of superhelix density −0.12 (PM2 DNA) is only poorly trapped unless first relaxed by topoisomerases or with the appropriate addition of an intercalating drug. When the oc DNA – agarose was used in a procedure for rapidly obtaining binding constants of drugs to DNA, the binding constant of ethidium was found to be considerably less than that expected. On addition of calf thymus topoisomerase to the binding-assay mixture, the ethidium-binding constant increased to the expected value. Thus, although free oc DNA is topologically unrestricted, oc DNA trapped in agarose must be rotationally constrained such that addition of ethidium introduced supercoils. The nature of these constraints is discussed with respect to the known structure of agarose bihelices.

scholarly journals DNA compaction in the early part of the SOS response is dependent on RecN and RecA

Microbiology ◽  
2014 ◽  
Vol 160 (5) ◽  
pp. 872-882 ◽  
Author(s):  
Ingvild Odsbu ◽  
Kirsten Skarstad
Keyword(s):  
Escherichia Coli ◽  
Fluorescence Microscopy ◽  
Growth Medium ◽  
Low Dose ◽  
Sos Response ◽  
Second Phase ◽  
Dna Compaction ◽  
Recombination Proteins ◽  
Structural Maintenance Of Chromosomes

The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10–20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for ~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated ‘compact DNA’ stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.

scholarly journals Resizable Drone Designs: For Maneuvering through Paths of Varying Dimensions

2019 ◽  
Vol 8 (2) ◽  
pp. 3162-3166
Keyword(s):  
Embedded Systems ◽  
Unmanned Aerial Vehicle ◽  
Cost Effective ◽  
Search And Rescue ◽  
The Other ◽  
Complex Structures ◽  
Variable Size ◽  
Aerial Vehicle ◽  
Flying Robot ◽  
Flying Robots

An unmanned aerial vehicle, commonly known as a drone, is an aircraft without a human pilot aboard. Essentially, a drone is a flying robot that can be remotely controlled or fly autonomously through software-controlled flight plans in their embedded systems, Flying robots are increasingly adopted in search and rescue missions because of their capability to quickly collect and stream information from remote and dangerous areas. Their maneuverability and hovering capabilities allow them to navigate through complex structures, inspect damaged buildings, and even explore underground tunnels and caves. Since their size is fixed, maneuvering over the compact areas and tunnels of variable size becomes an issue. To overcome this issue, we propose a model of quadrotor design which has the capability to change its size. The arm length of the quadrotor is changed dynamically so that it can fly in areas of variable sizes that would be hard to reach with the quadrotor of fixed arm length. On the other hand, our model is cost-effective, since the arm of the drone is designed with PVC (Polyvinyl Chloride). Using this model, drones will be able to move over compact areas and passages of variable sizes, thus aiding in better exploration during search and rescue operations.

Cooperation and coercion

Linguistics ◽  
2016 ◽  
Vol 54 (4) ◽  
Author(s):  
Jenny Audring ◽  
Geert Booij
Keyword(s):  
Lexical Semantics ◽  
The Other ◽  
Complex Structures ◽  
Top Down ◽  
Broad Variety ◽  
The One ◽  
Semantic Flexibility

AbstractCoercion is a much-discussed topic in the linguistic literature. This article expands the usual range of cases at the most subtle and the extreme end: it demonstrates how coercion extends into semantic flexibility on the one hand and into idiomaticity on the other. After discussing a broad variety of coercion cases in syntax and morphology and briefly reviewing the equally diverse literature, we identify three mechanisms – selection, enrichment, and override – that have alternatively been proposed to account for coercion effects. We then present an approach that combines all three mechanisms, arguing that they can be unified along a single axis: the degree of top-down influence of complex structures on lexical semantics.

Comparative modular analysis of two complex sulfosalt structures: sterryite, Cu(Ag,Cu)3Pb19(Sb,As)22(As–As)S56, and parasterryite, Ag4Pb20(Sb,As)24S58

2012 ◽  
Vol 68 (5) ◽  
pp. 480-492 ◽  
Author(s):  
Yves Moëlo ◽  
Catherine Guillot-Deudon ◽  
Michel Evain ◽  
Paolo Orlandi ◽  
Cristian Biagioni
Keyword(s):  
Building Block ◽  
Driving Force ◽  
Three Dimensional ◽  
The Other ◽  
Complex Structures ◽  
Fundamental Building Block ◽  
Distinct Cell ◽  
Modular Analysis ◽  
Derivatives Of ◽  
Selection Of

The crystal structures of two very close, but distinct complex minerals of the lead sulfosalt group have been solved: sterryite, Cu(Ag,Cu)3Pb19(Sb,As)22(As–As)S56, and parasterryite, Ag4Pb20(Sb,As)24S58. They are analyzed and compared according to modular analysis. The fundamental building block is a complex column centred on a Pb6S12 triangular prismatic core, with two additional long and short arms. The main chemical and topological differences relate to the short arm, which induces a relative a/4 shift (∼ 2 Å along the elongation parameter) of the constitutive rod layers, as illustrated by distinct cell settings within the same space group (P21/n and P21/c, respectively). Selection of the shortest (i.e. strongest) (Sb,As)—S bonds permitted to enhance the polymeric organization of (Sb,As) atoms with triangular pyramidal coordination. These two quasi-homeotypic structures are expanded derivatives of owyheeite, Ag3Pb10Sb11S28. The hierarchy of organization levels from zero- to three-dimensional entities is subordinated to building operators, which appear as the driving force for the construction of such complex structures. Minor cations (Ag, Cu) or the As–As pair in sterryite secure the final locking, which favours the formation of one or the other compound.

scholarly journals Mixed (combined) phenotype of the late stage of age-related macular degeneration

2021 ◽  
Vol 14 (2) ◽  
pp. 69-75
Author(s):  
N. V. Neroeva ◽  
V. V. Neroev ◽  
M. V. Ryabina ◽  
A. G. Karmokova ◽  
O. A. Losanova
Keyword(s):  
Macular Degeneration ◽  
Late Stage ◽  
Geographic Atrophy ◽  
Accurate Diagnosis ◽  
The Other ◽  
Age Related Macular Degeneration ◽  
Complex Structures ◽  
Optimal Management ◽  
Age Related ◽  
Mixed Phenotype

With multimodal visualization of the chorioretinal complex structures using modern research methods, it was possible to isolatea mixed, or combined, phenotype of the late stage of age-related macular degeneration (AMD). Early detection of this AMD form is of vital importance not only for accurate diagnosis, but for choosing optimal management tactics for patients. The paper presents two clinical cases with different variants of the development of the mixed phenotype of the late AMD stage. In one case, the long-lasting “geographic atrophy” (GA) was complicated by the development of choroidal neovascularization, while in the other case GA appeared during the treatment of wetAMD.

scholarly journals Analysis of Periodic Structures Made of Pins Inside a Parallel Plate Waveguide

Symmetry ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 582 ◽  
Author(s):  
Nafsika Memeletzoglou ◽  
Carlos Sanchez-Cabello ◽  
Francisco Pizarro-Torres ◽  
Eva Rajo-Iglesias
Keyword(s):  
Parallel Plate ◽  
Periodic Structures ◽  
The Other ◽  
Refractive Indices ◽  
Complex Structures ◽  
Reference Case ◽  
Electromagnetic Mode ◽  
Parallel Plate Waveguide ◽  
Transverse Electromagnetic ◽  
Mode Tem

In this work, we have analyzed different versions of periodic structures made with metallic pins located inside a parallel plate waveguide (PPWG), varying the symmetry and disposition of the pins. The analysis focuses on two main parameters related to wave propagation. On one hand, we have studied how the different proposed structures can create a stopband so that the parallel plate modes can be used in gap waveguide technology or filtering structures. On the other hand, we have analyzed the dispersion and equivalent refractive index of the first propagating transverse electromagnetic mode (TEM). The results show how the use of complex structures made with pins in the top and bottom plates of a PPWG have no advantages in terms of the achieved stopband size. However, for the case of the propagating mode, it is possible to find less dispersive modes and a higher range of equivalent refractive indices when using double-pin structures compared to a reference case with single pins.

scholarly journals The structure of topaz [Al (F, OH)] 2 SiO 4

1928 ◽  
Vol 121 (787) ◽  
pp. 358-367 ◽  
Keyword(s):  
Close Packing ◽  
The Other ◽  
Complex Structures ◽  
General Outline ◽  
Full Account ◽  
Large Size ◽  
New Type ◽  
Quantitative Examination ◽  
Considerable Detail ◽  
Oxygen Atoms

1. In a recent paper on the structure of certain silicates, Prof. W. L. Bragg and one of the authors discussed in considerable detail the role which the oxygen atoms—due to their relatively large size—played in these compounds. The structures examined fell roughly into two classes: one in which the O atoms were throughout packed as closely together as possible, the other in which close packing was local only. Many examples of structures which had actually been worked out were given, and it was suggested that topaz might possibly prove a further example of a close-packed arrangement of large ions. An attempt to solve the structure of topaz on these lines proved unexpectedly difficult, and a detailed general quantitative examination was therefore carried out. A full account of this examination, which has now been completed, will be published later in the 'Zeitschrift für Kristallographie.’ We propose here to give but a general outline of the structure, desiring rather to draw attention to an interesting new type or variant of close packing which the study has revealed, and which suggests important considerations in the elucidation of complex structures still awaiting analysis.

scholarly journals Three-dimensional-printing for microfluidics or the other way around?

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Yi Zhang
Keyword(s):  
3D Printing ◽  
Social Impact ◽  
Three Dimensional ◽  
The Other ◽  
Complex Structures ◽  
Three Dimensional Printing ◽  
Strong Focus ◽  
3D Printed ◽  
Near Net Shape ◽  
Dimensional Printing

As microfluidic devices are designed to tackle more intricate tasks, the architecture of microfluidic devicesbecomes more complex, and more sophisticated fabrication techniques are in demand. Therefore, it is sensible to fabricatemicrofluidic devices by three-dimensional (3D)-printing, which is well-recognized for its unique ability to monolithicallyfabricate complex structures using a near-net-shape additive manufacturing process. Many 3D-printed microfluidic platformshave been demonstrated but can 3D-printed microfluidics meet the demanding requirements in today’s context, and hasmicrofluidics truly benefited from 3D-printing? In contrast to 3D-printed microfluidics, some go the other way around andexploit microfluidics for 3D-printing. Many innovative printing strategies have been made possible with microfluidicsenabled3D-printing, although the limitations are also largely evident. In this perspective article, we take a look at the currentdevelopment in 3D-printed microfluidics and microfluidics-enabled 3D printing with a strong focus on the limitations of thetwo technologies. More importantly, we attempt to identify the innovations required to overcome these limitations and todevelop new high-value applications that would make a scientific and social impact in the future.

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