scholarly journals The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes

2003 ◽  
Vol 358 (1429) ◽  
pp. 267-274 ◽  
Author(s):  
Frauke Baymann ◽  
Evelyne Lebrun ◽  
Myriam Brugna ◽  
Barbara Schoepp–Cothenet ◽  
Marie–Thérèse Giudici–Orticoni ◽  
...  
Keyword(s):  
Family Relationships ◽  
Three Dimensional ◽  
Building Blocks ◽  
Redox Enzyme ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Energy Conserving ◽  
Tree Topologies ◽  
Genome Analyses ◽  
Construction Kit

Genome analyses and the resolution of three–dimensional structures have provided evidence in recent years for hitherto unexpected family relationships between redox proteins of very diverse enzymes involved in bioenergetic electron transport. Many of these enzymes appear in fact to be constructed from only a limited set of building blocks. Phylogenetic analysis of selected units from this ‘redox enzyme construction kit’ indicates an origin for several prominent bioenergetic enzymes that is very early, lying before the divergence of Bacteria and Archaea. Possible scenarios for the early evolution of selected complexes are proposed based on the obtained tree topologies.

Evolution of the Cell

2021 ◽  
pp. 64-81
Author(s):  
Franklin M. Harold
Keyword(s):  
Genetic Information ◽  
Metabolic Networks ◽  
Building Blocks ◽  
Eukaryotic Cells ◽  
Evolutionary Relationships ◽  
Last Universal Common Ancestor ◽  
Living Things ◽  
Universal Common Ancestor ◽  
A Cell ◽  
P Cells

Cells are life’s basic building blocks, and there is no more profound question than how they came to be. What made this murky subject accessible is the invention of methods to sequence nucleic acids and proteins, and to infer evolutionary relationships from those sequences. It seems that all living things share a common ancestry in LUCA (the Last Universal Common Ancestor), a shadowy entity thought to have lived nearly 4 billion years ago. LUCA’s nature has been much debated, but she appears to have been a cell of sorts endowed with membranes, metabolic networks, a usable energy source and the machinery to express and reproduce genetic information. The earliest known event in cell history was the divergence of Archaea from Bacteria, about 3.5 billion years ago. Eukaryotic cells, more closely allied with Archaea than with Bacteria, appear much later, some 2 billion years ago. Their origin remains one of life’s mysteries, but the evidence currently favors a fusion or merger of an early archaeon with a bacterium; the latter became the ancestor of mitochondria, and played a major role in cell evolution. Eukaryotic cells of the contemporary kind emerged over hundreds of million years. Prominent events included a second instance of intracellular symbiosis, this time with a cyanobacterium, that introduced photosynthesis into the eukaryotic universe and initiated the plant lineage. Eukaryotic cells are the building blocks of all higher organisms. Just what has given the eukaryotic order an edge is yet another of life’s stubborn mysteries.

scholarly journals Lath Martensite Microstructure Modeling: A High-Resolution Crystal Plasticity Simulation Study

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 691
Author(s):  
Francisco-José Gallardo-Basile ◽  
Yannick Naunheim ◽  
Franz Roters ◽  
Martin Diehl
Keyword(s):  
High Resolution ◽  
Mechanical Behavior ◽  
Crystal Plasticity ◽  
Lath Martensite ◽  
Three Dimensional ◽  
Building Blocks ◽  
Quantitative Agreement ◽  
Carbon Steels ◽  
Plastic Behavior ◽  
Austenitic Phase

Lath martensite is a complex hierarchical compound structure that forms during rapid cooling of carbon steels from the austenitic phase. At the smallest, i.e., ‘single crystal’ scale, individual, elongated domains, form the elemental microstructural building blocks: the name-giving laths. Several laths of nearly identical crystallographic orientation are grouped together to blocks, in which–depending on the exact material characteristics–clearly distinguishable subblocks might be observed. Several blocks with the same habit plane together form a packet of which typically three to four together finally make up the former parent austenitic grain. Here, a fully parametrized approach is presented which converts an austenitic polycrystal representation into martensitic microstructures incorporating all these details. Two-dimensional (2D) and three-dimensional (3D) Representative Volume Elements (RVEs) are generated based on prior austenite microstructure reconstructed from a 2D experimental martensitic microstructure. The RVEs are used for high-resolution crystal plasticity simulations with a fast spectral method-based solver and a phenomenological constitutive description. The comparison of the results obtained from the 2D experimental microstructure and the 2D RVEs reveals a high quantitative agreement. The stress and strain distributions and their characteristics change significantly if 3D microstructures are used. Further simulations are conducted to systematically investigate the influence of microstructural parameters, such as lath aspect ratio, lath volume, subblock thickness, orientation scatter, and prior austenitic grain shape on the global and local mechanical behavior. These microstructural features happen to change the local mechanical behavior, whereas the average stress–strain response is not significantly altered. Correlations between the microstructure and the plastic behavior are established.

scholarly journals SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nika Pende ◽  
Adrià Sogues ◽  
Daniela Megrian ◽  
Anna Sartori-Rupp ◽  
Patrick England ◽  
...  
Keyword(s):  
Cell Division ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Super Resolution ◽  
Binding Mode ◽  
Last Universal Common Ancestor ◽  
Division Plane ◽  
Multiple Factors ◽  
Universal Common Ancestor ◽  
Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

Design and Optimization of a Shape Memory Alloy-Based Self-Folding Sheet

2013 ◽  
Vol 135 (11) ◽  
Author(s):  
Edwin Peraza-Hernandez ◽  
Darren Hartl ◽  
Edgar Galvan ◽  
Richard Malak
Keyword(s):  
Shape Memory Alloy ◽  
Shape Memory ◽  
Three Dimensional ◽  
Building Blocks ◽  
Passive Layer ◽  
Von Mises Stress ◽  
Maximum Temperature ◽  
Radius Of Curvature ◽  
Folding Angle ◽  
The Impact

Origami engineering—the practice of creating useful three-dimensional structures through folding and fold-like operations on two-dimensional building-blocks—has the potential to impact several areas of design and manufacturing. In this article, we study a new concept for a self-folding system. It consists of an active, self-morphing laminate that includes two meshes of thermally-actuated shape memory alloy (SMA) wire separated by a compliant passive layer. The goal of this article is to analyze the folding behavior and examine key engineering tradeoffs associated with the proposed system. We consider the impact of several design variables including mesh wire thickness, mesh wire spacing, thickness of the insulating elastomer layer, and heating power. Response parameters of interest include effective folding angle, maximum von Mises stress in the SMA, maximum temperature in the SMA, maximum temperature in the elastomer, and radius of curvature at the fold line. We identify an optimized physical realization for maximizing folding capability under mechanical and thermal failure constraints. Furthermore, we conclude that the proposed self-folding system is capable of achieving folds of significant magnitude (as measured by the effective folding angle) as required to create useful 3D structures.

A new three-dimensional anionic cadmium(II) dicyanamide network

2014 ◽  
Vol 70 (11) ◽  
pp. 1054-1056 ◽  
Author(s):  
Qiang Li ◽  
Hui-Ting Wang
Keyword(s):  
Crystal Structure ◽  
Aqueous Solution ◽  
Unit Cell Volume ◽  
Three Dimensional ◽  
Building Blocks ◽  
The Other ◽  
Dimensional Structure ◽  
Cadmium Nitrate ◽  
Nitrate Tetrahydrate ◽  
Anionic Framework

A new cadmium dicyanamide complex, poly[tetramethylphosphonium [μ-chlorido-di-μ-dicyanamido-κ4N1:N5-cadmium(II)]], [(CH3)4P][Cd(NCNCN)2Cl], was synthesized by the reaction of tetramethylphosphonium chloride, cadmium nitrate tetrahydrate and sodium dicyanamide in aqueous solution. In the crystal structure, each CdIIatom is octahedrally coordinated by four terminal N atoms from four anionic dicyanamide (dca) ligands and by two chloride ligands. The dicyanamide ligands play two different roles in the building up of the structure; one role results in the formation of [Cd(dca)Cl]2building blocks, while the other links the building blocks into a three-dimensional structure. The anionic framework exhibits a solvent-accessible void of 673.8 Å3, amounting to 47.44% of the total unit-cell volume. The cavities in the network are occupied by pairs of tetramethylphosphonium cations.

scholarly journals Assembly of multicomponent structures from hundreds of micron-scale building blocks using optical tweezers

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Jeffrey E. Melzer ◽  
Euan McLeod
Keyword(s):  
Optical Tweezers ◽  
Three Dimensional ◽  
Building Blocks ◽  
Optical Tweezer ◽  
Device Fabrication ◽  
Positional Accuracy ◽  
Component Structure ◽  
Material Development ◽  
Critical Process Parameters ◽  
Optical Positioning

AbstractThe fabrication of three-dimensional (3D) microscale structures is critical for many applications, including strong and lightweight material development, medical device fabrication, microrobotics, and photonic applications. While 3D microfabrication has seen progress over the past decades, complex multicomponent integration with small or hierarchical feature sizes is still a challenge. In this study, an optical positioning and linking (OPAL) platform based on optical tweezers is used to precisely fabricate 3D microstructures from two types of micron-scale building blocks linked by biochemical interactions. A computer-controlled interface with rapid on-the-fly automated recalibration routines maintains accuracy even after placing many building blocks. OPAL achieves a 60-nm positional accuracy by optimizing the molecular functionalization and laser power. A two-component structure consisting of 448 1-µm building blocks is assembled, representing the largest number of building blocks used to date in 3D optical tweezer microassembly. Although optical tweezers have previously been used for microfabrication, those results were generally restricted to single-material structures composed of a relatively small number of larger-sized building blocks, with little discussion of critical process parameters. It is anticipated that OPAL will enable the assembly, augmentation, and repair of microstructures composed of specialty micro/nanomaterial building blocks to be used in new photonic, microfluidic, and biomedical devices.

Construction of Three-Dimensional DNA Hydrogels from Linear Building Blocks

2014 ◽  
Vol 126 (32) ◽  
pp. 8468-8472 ◽  
Author(s):  
Tanja Nöll ◽  
Holger Schönherr ◽  
Daniel Wesner ◽  
Michael Schopferer ◽  
Thomas Paululat ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Building Blocks ◽  
Dna Hydrogels

A New POM-Based Supramolecular Compound: Synthesis, Structure and Adsorptive Property of [Cu(phen)2]3[W6O19]

2014 ◽  
Vol 919-921 ◽  
pp. 2013-2016 ◽  
Author(s):  
Ya Bing Liu ◽  
Hong Jie Wang ◽  
Hong Kai Zhao
Keyword(s):  
Three Dimensional ◽  
Building Blocks ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hybrid Compound ◽  
Adsorptive Property ◽  
X Ray ◽  
Hydrogen Bonding Interactions ◽  
Compound Synthesis ◽  
Metal Organic

A POM - based organice - inorganic hybrid compound with the chemical formula of[Cu (phen)2]3[W6O19] (phen = 1,10-phenanthroline) (1) has been hydrothermally synthesized andstructurally characterized by the elemental analysis, and single crystal X-ray diffraction. Compound 1 crystallizes in the monoclinic space groupC2/c witha=18.319(4) Å,b= 17.311(4) Å,c= 22.248(4) Å,β= 112.40(3) o,V= 6523(2) Å3,Z= 4, R1= 0.0448, andwR2=0.1218. Compound 1 consists of the [W6O19]3-building blocks and [Cu (phen)2]+metal organic cationic moieties, which are packed together via the extensive hydrogen-bonding interactions to form a three-dimensional supramolecular framework. The adsorption of methylene blue (MB) under UV irradiation with 1 as the heterogeneous adsorbent has been investigated, showing a good adsorptive property of 1 for MB degradation.

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