scholarly journals Combinatorial engineering of bulk-assembled monodisperse coacervate droplets towards logically integrated protocells

2021 ◽  
Author(s):  
Qingchuan Li ◽  
Qingchun Song ◽  
Jing Wei ◽  
Yang Cao ◽  
Dairong Chen ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Colloidal Particles ◽  
Extreme Environments ◽  
Lipid Vesicles ◽  
Building Blocks ◽  
Cellular Systems ◽  
Integrative Approach ◽  
Size Uniformity ◽  
Inanimate Matter ◽  
High Diversity

AbstractThe emergence of life requires the appropriate integration of protometabolisms, compartments, and protogenomes from an intricate interplay of non-living constituents. Unveiling the mechanism of how life-related building blocks are logically integrated towards life from a high diversity of inanimate matter is an ongoing challenging task of current science. Various compartments such as lipid vesicles and coacervates have been proposed as possible microcontainers to hold prebiotic genetic materials and metabolic reactions for the construction of integrated systems. However, the spontaneous assembly of these compartments allows no selective and logical integration from a high diversity of inanimate matter, thus making the appropriate integration of the inanimate towards membranous life more a coincident and low probability event. Herein, we show that the assembly of colloidal particles with coacervate-forming molecules provides a combinatorial approach for the regularization of matter of chaos towards protocells with cellular hallmarks of size uniformity, logical integration, and unilamellar membransation. Monodisperse coacervate droplets coated by colloidal particles are assembled through hydrodynamic forcing-promoted coalescence. Using these coacervates as platform, a combinatorially integrative approach is developed to engineer the complexity of coacervates, from coacervate entities with programmable spatial loading to diverse interconnected coacervate consortia with collective morphology evolution. A fluidic unilamellar membrane is assembled on coacervate via freeze-thaw treatment of coacervates coated by liposome particles, including liposome particles with heterogenous lamellarity, resulting in coacervate-supported monodisperse giant unilamellar vesicles with gated permeability to polar molecules and remarkable structural and functional stability at extreme environments. This work provides an integrative approach to process crude building blocks towards disciplined and integrated cellular systems, which might have mediated the transition from the inanimate to life. This approach is promisingly utilized for high throughput screening of possible integrated form of primitive life from a high diversity of inanimate matter as well as on demand bulk-generation of monodisperse hierarchical microdroplets with flexibly integrated functions.

scholarly journals Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1004
Author(s):  
Salvatore Esposito ◽  
Riccardo Aversano ◽  
Pasquale Tripodi ◽  
Domenico Carputo
Keyword(s):  
Dna Repair ◽  
Mirna Expression ◽  
Building Blocks ◽  
Nucleotide Metabolism ◽  
Integrative Approach ◽  
Whole Genome ◽  
Solanum Commersonii ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Micro Rnas

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.

scholarly journals Self-Assembly of Shape-Tunable Oblate Colloidal Particles into Orientationally Ordered Crystals, Glassy Crystals and Plastic Crystals

Soft Matter ◽  
2021 ◽  
Author(s):  
Jiawei Lu ◽  
Xiangyu Bu ◽  
Xinghua Zhang ◽  
Bing Liu
Keyword(s):  
Crystal Structures ◽  
Self Assembly ◽  
Colloidal Particles ◽  
Building Blocks ◽  
Fundamental Question ◽  
The Self ◽  
Plastic Crystals ◽  
Self Assembled ◽  
Glassy Crystals ◽  
The Relationship

The shapes of colloidal particles are crucial to the self-assembled superstructures. Understanding the relationship between the shapes of building blocks and the resulting crystal structures is an important fundamental question....

scholarly journals Actuation of synthetic cells with proton gradients generated by light-harvesting E. coli

2020 ◽  
Author(s):  
Kevin Jahnke ◽  
Noah Ritzmann ◽  
Julius Fichtler ◽  
Anna Nitschke ◽  
Yannik Dreher ◽  
...  
Keyword(s):  
Lipid Vesicles ◽  
Cellular Systems ◽  
Top Down ◽  
Ph Gradients ◽  
Proton Gradients ◽  
Bottom Up ◽  
E Coli ◽  
Genetically Engineer ◽  
Synthetic Cells ◽  
Dna Triplex

Abstract Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness new types of living systems. Both approaches, however, face their own challenges towards biotechnological and biomedical applications. Here, we realize a strategic merger to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them as organelle mimics in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we can reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. By attaching a polymerized DNA origami plate to the DNA triplex motif, we obtain a cytoskeleton mimic that considerably deforms lipid vesicles in a pH-responsive manner. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells as potent microreactors.

scholarly journals Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

2015 ◽  
Vol 11 ◽  
pp. 2355-2364 ◽  
Author(s):  
Shintaro Kawano ◽  
Toshiyuki Kida ◽  
Mitsuru Akashi ◽  
Hirofumi Sato ◽  
Motohiro Shizuma ◽  
...  
Keyword(s):  
Colloidal Particles ◽  
Adsorption Property ◽  
Building Blocks ◽  
Pickering Emulsion ◽  
Surface Active Property ◽  
Water Interface ◽  
Pickering Emulsions ◽  
Surface Active ◽  
Oil Water ◽  
Interfacial Adsorption

Background: Emulsions stabilized by colloidal particles are known as Pickering emulsions. To date, soft microgel particles as well as inorganic and organic particles have been utilized as Pickering emulsifiers. Although cyclodextrin (CD) works as an attractive emulsion stabilizer through the formation of a CD–oil complex at the oil–water interface, a high concentration of CD is normally required. Our research focuses on an effective Pickering emulsifier based on a soft colloidal CD polymer (CD nanogel) with a unique surface-active property. Results: CD nanogels were prepared by crosslinking heptakis(2,6-di-O-methyl)-β-cyclodextrin with phenyl diisocyanate and subsequent immersion of the resulting polymer in water. A dynamic light scattering study shows that primary CD nanogels with 30–50 nm diameter assemble into larger CD nanogels with 120 nm diameter by an increase in the concentration of CD nanogel from 0.01 to 0.1 wt %. The CD nanogel has a surface-active property at the air–water interface, which reduces the surface tension of water. The CD nanogel works as an effective Pickering emulsion stabilizer even at a low concentration (0.1 wt %), forming stable oil-in-water emulsions through interfacial adsorption by the CD nanogels. Conclusion: Soft CD nanogel particles adsorb at the oil–water interface with an effective coverage by forming a strong interconnected network and form a stable Pickering emulsion. The adsorption property of CD nanogels on the droplet surface has great potential to become new microcapsule building blocks with porous surfaces. These microcapsules may act as stimuli-responsive nanocarriers and nanocontainers.

A design path for the hierarchical self-assembly of patchy colloidal particles

Soft Matter ◽  
2015 ◽  
Vol 11 (19) ◽  
pp. 3913-3919 ◽  
Author(s):  
E. Edlund ◽  
O. Lindgren ◽  
M. Nilsson Jacobi
Keyword(s):  
Self Assembly ◽  
Colloidal Particles ◽  
Building Blocks

Patchy colloidal particles are promising candidates for building blocks in directed self-assembly.

PTFE-PMMA core-shell colloidal particles as building blocks for self-assembled opals: synthesis, properties and optical response

2012 ◽  
Vol 61 (8) ◽  
pp. 1294-1301 ◽  
Author(s):  
Diego Antonioli ◽  
Simone Deregibus ◽  
Guido Panzarasa ◽  
Katia Sparnacci ◽  
Michele Laus ◽  
...  
Keyword(s):  
Colloidal Particles ◽  
Optical Response ◽  
Building Blocks ◽  
Core Shell ◽  
Synthesis Properties ◽  
Self Assembled

Evolution of glycolytic enzymes

1981 ◽  
Vol 293 (1063) ◽  
pp. 191-203 ◽  
Keyword(s):  
Structure Function ◽  
Quaternary Structure ◽  
Extreme Environments ◽  
Building Blocks ◽  
Binding Domain ◽  
Glycolytic Enzymes ◽  
Nucleotide Binding Domain ◽  
Structural Adaptation ◽  
Convergence And Divergence ◽  
Complex Enzymes

The requirements for glycolysis are examined in relation to other essential metabolic processes in the most primitive organisms. The construction of more complex enzymes from primitive domain building blocks is assessed with respect to glycolytic enzymes. Special attention is given to the evolution of the NAD binding domain in dehydrogenases and the related, frequently observed nucleotide binding domain. An attempt is made to differentiate between convergence and divergence of frequently observed domains. Consideration is given to the structure-function relation of these domains and the development of quaternary structure in later stages of evolution. Some attention is also given to the evolution of structural adaptation to extreme environments as a means of differentiating between essential functions and specific modifications.

From the de Broglie to Visible Wavelengths: Manipulating Electrons and Photons With Colloids

MRS Bulletin ◽  
1998 ◽  
Vol 23 (10) ◽  
pp. 39-43 ◽  
Author(s):  
Alfons van Blaaderen
Keyword(s):  
Brownian Motion ◽  
Colloidal Particles ◽  
Three Dimensional ◽  
Building Blocks ◽  
Extensive Literature ◽  
Gas Molecules ◽  
Visible Wavelengths ◽  
Solvent Molecules ◽  
Shell Particles ◽  
Lower Size

Because of their size and ability to selforganize, colloidal particles are ideal building blocks for the creation of three-dimensional (3D) structures that can have feature sizes of the order of the wavelength of electrons, photons, or both. This article is too short to provide an extensive literature survey but instead will give some illustrative examples, based on work of the author and co-workers, of how specially developed core-shell particles might be organized on a 3D lattice. These examples are only intended to give an impression of how colloidal-particle systems can be used in the design of new materials with interesting photonic properties.Generally particles are considered colloidal if their size is between several nm and several μm. This range is more or less defined by the importance of Brownian motion—that is, the irregular, overdamped, random displacements the particles make as a result of the not completely averaged-out bombardment of solvent (or gas) molecules. Consequently the lower size range is determined by the size of the solvent molecules. Compared to the particle size, the solvent molecules need to be so small that the time scales of the solvent molecules and particles are so far apart that the solvent molecules can be “integrated out” in a description of the particles. If such a description holds, the solvent can be approximated well by a continuum. The upper size limit is determined by the size at which external fields, like gravity, start to overshadow the effects of Brownian motion.

scholarly journals Interpretable Retrosynthesis Prediction in Two Steps

2020 ◽  
Author(s):  
Chaochao Yan ◽  
Qianggang Ding ◽  
Shuangjia Zheng ◽  
Jinyu Yang ◽  
Yang Yu ◽  
...  
Keyword(s):  
State Of The Art ◽  
Building Blocks ◽  
Computer Aided ◽  
Free Model ◽  
Benchmark Datasets ◽  
Previous State ◽  
Target Molecules ◽  
Template Free ◽  
Synthetic Routes ◽  
High Diversity

Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. Computer-aided retrosynthesis can potentially assist chemists in designing synthetic routes; however, at present, it is cumbersome and lacks interpretability behind their predictions. In this study, we devise a novel template-free model for retrosynthetic expansion by automating the procedure that chemistsusedtodo. Our method plans synthesis in two steps, by first identifying the potential disconnection bonds of the molecule graph with a graph neural network and thereafter generating synthons according to the identified disconnection bonds of the target molecule graph, and then predicting the associated reactants SMILES based on the obtained synthons with a reactant prediction model. While outperforming previous state-of-the-art baselines by a significant margin on the benchmark datasets, our model also provides predictions with high diversity and chemically reasonable interpretation.

scholarly journals Molecular Transport across Lipid Membranes Controls Cell-Free Expression Level and Dynamics

2019 ◽  
Author(s):  
Patrick M. Caveney ◽  
Rosemary M. Dabbs ◽  
William T. McClintic ◽  
C. Patrick Collier ◽  
Michael L. Simpson
Keyword(s):  
Gene Expression ◽  
Membrane Transport ◽  
Molecular Species ◽  
Lipid Membranes ◽  
Molecular Transport ◽  
Lipid Vesicles ◽  
Cellular Systems ◽  
Control Of Gene Expression ◽  
External Resources ◽  
Synthetic Cell

SummaryEssential steps toward synthetic cell-like systems require controlled transport of molecular species across the boundary between encapsulated expression and the external environment. When molecular species (e.g. small ions, amino acids) required for expression (i.e. expression resources) may cross this boundary, this transport process plays an important role in gene expression dynamics and expression variability. Here we show how the location (encapsulated or external) of the expression resources controls the level and the dynamics of cell-free protein expression confined in permeable lipid vesicles. Regardless of the concentration of encapsulated resources, external resources were essential for protein production. Compared to resource poor external environments, plentiful external resources increased expression by ~7-fold, and rescued expression when internal resources were lacking. Intriguingly, the location of resources and the membrane transport properties dictated expression dynamics in a manner well predicted by a simple transport-expression model. These results suggest membrane engineering as a means for spatio-temporal control of gene expression in cell-free synthetic biology applications and demonstrate a flexible experimental platform to understand the interplay between membrane transport and expression in cellular systems.

Sign in / Sign up

Export Citation Format

Share Document