scholarly journals A de novo matrix for macroscopic living materials from bacteria

2021 ◽  
Author(s):  
Sara Molinari ◽  
Robert F. Tesoriero ◽  
Dong Li ◽  
Swetha Sridhar ◽  
Rong Cai ◽  
...  
Keyword(s):  
De Novo ◽  
Caulobacter Crescentus ◽  
Living Cells ◽  
Structure And Function ◽  
Self Organization ◽  
Morphological Properties ◽  
Interacting Protein ◽  
And Function ◽  
Assembly Principles ◽  
Living Materials

Engineered living materials (ELMs) embed living cells in a biopolymer matrix to create novel materials with tailored functions. While bottom-up assembly of macroscopic ELMs with a de novo matrix would offer the greatest control over material properties, we lack the ability to genetically encode a protein matrix that leads to collective self-organization. Here we report growth of ELMs from Caulobacter crescentus cells that display and secrete a self-interacting protein. This protein formed a de novo matrix and assembled cells into centimeter-scale ELMs. Discovery of design and assembly principles allowed us to tune the mechanical, catalytic, and morphological properties of these ELMs. This work provides novel tools, design and assembly rules, and a platform for growing ELMs with control over matrix and cellular structure and function.

scholarly journals GENETIC MAPPING OF GENES REQUIRED FOR MOTILITY IN CAULOBACTER CRESCENTUS

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 523-532
Author(s):  
Bert Ely ◽  
Ronda H Croft ◽  
Connie J Gerardot
Keyword(s):  
Genetic Mapping ◽  
Caulobacter Crescentus ◽  
Pleiotropic Effect ◽  
Structure And Function ◽  
Bacteriophage Resistance ◽  
And Function ◽  
Chromosomal Map ◽  
Bacterial Systems

ABSTRACT Mutations in more than 30 genes affect motility in Caulobacter crescentus. We have determined the chromosomal map locations for 27 genes involved in flagellar morphogenesis (fla), three genes involved in flagellar function (mot), and three genes that have a pleiotropic effect on both motility and bacteriophage resistance (ple). Three multigene clusters have been detected at widely separated chromosomal locations, but in addition, there are 12 fla and mot genes that are found at eight additional sites scattered around the C. cresentus chromosome. Thus, there is more scatter of genes involved in flagellar structure and function than has been observed in other bacterial systems.

scholarly journals riboCIRC: a comprehensive database of translatable circRNAs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huihui Li ◽  
Mingzhe Xie ◽  
Yan Wang ◽  
Ludong Yang ◽  
Zhi Xie ◽  
...  
Keyword(s):  
De Novo ◽  
Species Conservation ◽  
Structure And Function ◽  
Research Community ◽  
Genome Browser ◽  
Valuable Resource ◽  
Sequence Structure ◽  
A Genome ◽  
Context Specific ◽  
And Function

AbstractriboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com.

New Approach for Researching Forest Ecosystem

2012 ◽  
Vol 472-475 ◽  
pp. 3384-3389
Author(s):  
Zai Qiang Huo ◽  
Xue Qun Zhu
Keyword(s):  
Complex System ◽  
Forest Ecosystem ◽  
Driving Force ◽  
Structure And Function ◽  
The Self ◽  
Self Organization ◽  
New Approach ◽  
Edge Of Chaos ◽  
And Function ◽  
Research Frontiers

It is valuable to be researched in the application of science of complexity to the forest ecosystem. Forest ecosystem is an adaptive complex system which is suggested to be at the edge of chaos or at the criticality. The inner interaction of a forest ecosystem is the main driving force for the self-organization, complexity and order in the forest ecosystem. Forest ecosystem complexity is one of the research frontiers of ecological and evolutionary problems presently. The application of science of complexity to the forest ecosystem complexity studies, its concept, background, methodology and theory are briefly introduced. The forest ecosystem complexity is defined as the structure and function diversity, self-organization and the order of an ecosystem. Its main methods include the cellular automaton, genetic algorithm, game theory, complex network, etc. This paper has discussed mechanism and development of forest ecosystem complexity, by applying the principle and methods of science of complexity, which is a new approach for understanding ecological and evolutionary problems.

Illuminating cellular structure and function in the early secretory pathway by multispectral 3D imaging in living cells

2000 ◽  
Author(s):  
Jens Rietdorf ◽  
David J. Stephens ◽  
Anthony Squire ◽  
Jeremy Simpson ◽  
David T. Shima ◽  
...  
Keyword(s):  
Cellular Structure ◽  
3D Imaging ◽  
Secretory Pathway ◽  
Living Cells ◽  
Structure And Function ◽  
Early Secretory Pathway ◽  
And Function

Probing the Structure and Function of Human Glutaminase-Interacting Protein: A Possible Target for Drug Design†‡

Biochemistry ◽  
2008 ◽  
Vol 47 (35) ◽  
pp. 9208-9219 ◽  
Author(s):  
Monimoy Banerjee ◽  
Chengdong Huang ◽  
Javier Marquez ◽  
Smita Mohanty
Keyword(s):  
Drug Design ◽  
Protein A ◽  
Structure And Function ◽  
Interacting Protein ◽  
And Function

scholarly journals MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

2020 ◽  
Vol 48 (9) ◽  
pp. 5135-5146 ◽  
Author(s):  
Christopher Maffeo ◽  
Aleksei Aksimentiev
Keyword(s):  
Self Assembly ◽  
De Novo ◽  
Dna Nanotechnology ◽  
Equilibrium Structure ◽  
Molecular Graphics ◽  
Structure And Dynamics ◽  
Self Assembled ◽  
Actual Shape ◽  
And Function ◽  
Assembly Principles

Abstract Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

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