scholarly journals DNA-based long-lived reaction-diffusion patterning in a host hydrogel

2019 ◽  
Author(s):  
Georg Urtel ◽  
André Estevez-Torres ◽  
Jean-Christophe Galas
Keyword(s):  
Dna Sequences ◽  
Reaction Diffusion ◽  
Life Time ◽  
Side Reactions ◽  
Chemical Information ◽  
Living Matter ◽  
Synthetic Material ◽  
Synthetic Life ◽  
Three Stages ◽  
Living Organisms

AbstractThe development of living organisms is a source of inspiration for the creation of synthetic life-like materials. Embryo development is divided into three stages that are inextricably linked: patterning, differentiation and growth. During patterning, sustained out-of-equilibrium molecular programs interpret underlying molecular cues to create well-defined concentration profiles. Implementing this patterning stage in an autonomous synthetic material is a challenge that at least requires a programmable and long-lasting out-of-equilibrium chemistry compatible with a host material. Here we show that DNA/enzyme reactions can create reaction-diffusion patterns that are extraordinary long-lasting both in solution and inside an autonomous hydrogel. The life-time and stability of these patterns - here traveling fronts and two-band patterns - are significantly increased by blocking parasitic side reactions and by dramatically reducing the diffusion coefficient of specific DNA sequences. Immersed in oil, hydrogels pattern autonomously with limited evaporation, but can also exchange chemical information from other gels when brought in contact. Our primitive metabolic material thus recapitulates two important properties of living matter: a certain degree of autonomy that makes each piece of material an ‘individual’ with its own metabolism and, at the same time, the capacity to interact with other ‘individuals’.

scholarly journals Chemical computing with reaction–diffusion processes

2015 ◽  
Vol 373 (2046) ◽  
pp. 20140219 ◽  
Author(s):  
J. Gorecki ◽  
K. Gizynski ◽  
J. Guzowski ◽  
J. N. Gorecka ◽  
P. Garstecki ◽  
...  
Keyword(s):  
Information Processing ◽  
Diffusion Processes ◽  
Reaction Diffusion ◽  
Living Organism ◽  
Chemical Information ◽  
Bz Reaction ◽  
Living Organisms ◽  
Basic Features ◽  
Maximum Reliability ◽  
The Brain

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction–diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov–Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed.

scholarly journals Travelling colourful patterns in self-organized cellulose-based liquid crystalline structures

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Pedro E. S. Silva ◽  
Ricardo Chagas ◽  
Susete N. Fernandes ◽  
Pawel Pieranski ◽  
Robin L. B. Selinger ◽  
...  
Keyword(s):  
Simple Model ◽  
Temporal Variation ◽  
Liquid Crystalline ◽  
Diffusion Mechanism ◽  
Reaction Diffusion ◽  
Self Organization ◽  
Spatial And Temporal Variation ◽  
Living Matter ◽  
Equilibrium Conditions ◽  
Self Organized

AbstractCellulose-based systems are useful for many applications. However, the issue of self-organization under non-equilibrium conditions, which is ubiquitous in living matter, has scarcely been addressed in cellulose-based materials. Here, we show that quasi-2D preparations of a lyotropic cellulose-based cholesteric mesophase display travelling colourful patterns, which are generated by a chemical reaction-diffusion mechanism being simultaneous with the evaporation of solvents at the boundaries. These patterns involve spatial and temporal variation in the amplitude and sign of the helix´s pitch. We propose a simple model, based on a reaction-diffusion mechanism, which simulates the observed spatiotemporal colour behaviour.

scholarly journals A nanocrystalline monoclinic CaCO3precursor of metastable aragonite

2018 ◽  
Vol 4 (12) ◽  
pp. eaau6178 ◽  
Author(s):  
Péter Németh ◽  
Enrico Mugnaioli ◽  
Mauro Gemmi ◽  
György Czuppon ◽  
Attila Demény ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Structure Determination ◽  
Diffuse Scattering ◽  
Diffraction Tomography ◽  
Synthetic Material ◽  
Near Surface ◽  
Surface Conditions ◽  
Terrestrial Sediments ◽  
Living Organisms ◽  
New Phase

Despite its thermodynamical metastability at near-surface conditions, aragonite is widespread in marine and terrestrial sediments. It abundantly forms in living organisms, and its abiotic formation is favored in waters of a Mg2+/Ca2+ratio > 1.5. Here, we provide crystallographic evidence of a nanocrystalline CaCO3polymorph, which precipitates before aragonite in a cave. The new phase, which we term monoclinic aragonite (mAra), is crystallographically related to ordinary, orthorhombic aragonite. Electron diffraction tomography combined with structure determination demonstrates that mAra has a layered aragonite structure, in which some carbonates can be replaced by hydroxyls and up to 10 atomic % of Mg can be incorporated. The diagnostic electron diffraction features of mAra are diffuse scattering and satellite reflections along aragonite {110}. Similar features have previously been reported—although unrecognized—from biogenic aragonite formed in stromatolites, mollusks, and cyanobacteria as well as from synthetic material. We propose that mAra is a widespread crystalline CaCO3that plays a hitherto unrecognized key role in metastable aragonite formation.

scholarly journals Modified HuffBit Compress Algorithm – An Application of R

2018 ◽  
Vol 15 (3) ◽  
Author(s):  
Nahida Habib ◽  
Kawsar Ahmed ◽  
Iffat Jabin ◽  
Mohammad Motiur Rahman
Keyword(s):  
Dna Sequences ◽  
Binary Tree ◽  
Deoxyribonucleic Acid ◽  
Repetitive Sequences ◽  
Huffman Codes ◽  
R Language ◽  
Living Organisms ◽  
Encoding Method ◽  
Dna Sequence Compression ◽  
Sequence Compression

Abstract The databases of genomic sequences are growing at an explicative rate because of the increasing growth of living organisms. Compressing deoxyribonucleic acid (DNA) sequences is a momentous task as the databases are getting closest to its threshold. Various compression algorithms are developed for DNA sequence compression. An efficient DNA compression algorithm that works on both repetitive and non-repetitive sequences known as “HuffBit Compress” is based on the concept of Extended Binary Tree. In this paper, here is proposed and developed a modified version of “HuffBit Compress” algorithm to compress and decompress DNA sequences using the R language which will always give the Best Case of the compression ratio but it uses extra 6 bits to compress than best case of “HuffBit Compress” algorithm and can be named as the “Modified HuffBit Compress Algorithm”. The algorithm makes an extended binary tree based on the Huffman Codes and the maximum occurring bases (A, C, G, T). Experimenting with 6 sequences the proposed algorithm gives approximately 16.18 % improvement in compression ration over the “HuffBit Compress” algorithm and 11.12 % improvement in compression ration over the “2-Bits Encoding Method”.

scholarly journals Study of a Li-Ion Cell Kinetics in Five Regions to Predict Li Plating Using a Pseudo Two-Dimensional Model

2019 ◽  
Vol 11 (22) ◽  
pp. 6392 ◽  
Author(s):  
Sanaz Momeni Boroujeni ◽  
Kai Peter Birke
Keyword(s):  
Cell Model ◽  
Simulated Data ◽  
Ionic Conductivities ◽  
Life Time ◽  
Einstein Relation ◽  
Side Reactions ◽  
Two Dimensional ◽  
Calculation Results ◽  
Li Ion ◽  
Aging Mechanisms

Detecting or predicting lithium plating in Li-ion cells and subsequently suppressing or preventing it have been the aim of many researches as it directly contributes to the aging, safety, and life-time of the cell. Although abundant influencing parameters on lithium deposition are already known, more information is still needed in order to predict this phenomenon and prevent it in time. It is observed that balancing in a Li-ion cell can play an important role in controlling lithium plating. In this work, five regions are defined with the intention of covering all the zones participating in the charge transfer from one electrode to the other during cell cycling. We employ a pseudo two-dimensional (P2D) cell model including two irreversible side reactions of solid electrolyte interface (SEI) formation and lithium plating (Li-P) as the anode aging mechanisms. With the help of simulated data and the Nernst–Einstein relation, ionic conductivities of the regions are calculated separately. Calculation results show that by aging the cell, more deviation between ionic conductivities of cathode and anode takes place which leads to the start of Li plating.

New horizons in organic chemistry

1961 ◽  
Vol 16 (1) ◽  
pp. 77-80
Keyword(s):  
Organic Chemistry ◽  
Modern Concept ◽  
Living Matter ◽  
Large Area ◽  
Tartaric Acids ◽  
Inorganic Substances ◽  
Original Definition ◽  
Dynamic Stereochemistry ◽  
Carbon Compounds ◽  
Living Organisms

Tercentenary Lecture delivered by Sir Alexander Todd, F.R.S., at 2.30 p.m.on Wednesday 20 July at the Royal There have been two definitions of organic chemistry. The original definition, due to Berzelius ( ca . 1800), was ‘the chemistry of substances found in living matter.’ The second, commonly ascribed to Gmelin, appeared first about fifty years later, when more was known about the peculiarities of the substances found in living matter—the ‘organic’ substances as distinct from the ‘inorganic’ substances—and was simply ‘the chemistry of the carbon compounds. ’ Each of these definitions is defensible, but neither is wholly satisfactory, since the first is too restricted and the second is, in certain respects, too general. A very large number of known carbon compounds are of purely synthetic origin and do not, as far as we are aware, occur in living matter, but it is undoubtedly true that the study of substances which are found in living organisms has provided most of the major stimuli to the advance of organic chemistry for almost a hundred years, and there is little reason to believe that this will not continue to be the case in the future. After all, it was Pasteur’s work on the tartaric acids from wine that led to the van’t Hoff-Le Bel theory of the tetrahedral carbon atom, the anthraquinone dyestuffs stem from Graebe and Liebermann’s work on alizarin from madder root, and work on polymerization and plastics goes back to the studies of Harries on natural rubber. Many other examples could be quoted, but I shall mention only one more because it is less well known than it should be. It was the work of Windaus on the natural sterols which caused Hiickel to develop his theoretical studies on stereoisomerism in fused ring systems; through these studies, important enough in themselves, developed in due course the modern concept of dynamic stereochemistry of cyclic structures which has had such a profound influence over a very large area of organic chemistry.

scholarly journals The proneural wave in the Drosophila optic lobe is driven by an excitable reaction-diffusion mechanism

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
David J Jörg ◽  
Elizabeth E Caygill ◽  
Anna E Hakes ◽  
Esteban G Contreras ◽  
Andrea H Brand ◽  
...  
Keyword(s):  
Visual Processing ◽  
Optic Lobe ◽  
Diffusion Mechanism ◽  
Growth Factor Receptor ◽  
Reaction Diffusion ◽  
Travelling Wave ◽  
Proneural Gene ◽  
Spatiotemporal Information ◽  
Drosophila Brain ◽  
Living Organisms

In living organisms, self-organised waves of signalling activity propagate spatiotemporal information within tissues. During the development of the largest component of the visual processing centre of the Drosophila brain, a travelling wave of proneural gene expression initiates neurogenesis in the larval optic lobe primordium and drives the sequential transition of neuroepithelial cells into neuroblasts. Here, we propose that this ‘proneural wave’ is driven by an excitable reaction-diffusion system involving epidermal growth factor receptor (EGFR) signalling interacting with the proneural gene l’sc. Within this framework, a propagating transition zone emerges from molecular feedback and diffusion. Ectopic activation of EGFR signalling in clones within the neuroepithelium demonstrates that a transition wave can be excited anywhere in the tissue by inducing signalling activity, consistent with a key prediction of the model. Our model illuminates the physical and molecular underpinnings of proneural wave progression and suggests a generic mechanism for regulating the sequential differentiation of tissues.

Genomics and homeostasis

2003 ◽  
Vol 284 (3) ◽  
pp. R611-R627 ◽  
Author(s):  
Allen W. Cowley
Keyword(s):  
Dna Sequences ◽  
Positional Cloning ◽  
Regulatory Pathways ◽  
Complex Functions ◽  
Challenges And Opportunities ◽  
The Galaxy ◽  
Systems Physiology ◽  
Living Organisms ◽  
New Hypothesis ◽  
Statistical Results

The Cannon lecture this year illustrates how knowledge of DNA sequences of complex living organisms is beginning to shape the landscape of physiology in the 21st century. Enormous challenges and opportunities now exist for physiologists to relate the galaxy of genes to normal and pathological functions. The first extensive genomic systems biology map for cardiovascular and renal function was completed last year as well as a new hypothesis-generating tool (“physiological profiling”) that enables us to hypothesize relationships between specific genes responsible for the regulation of regulatory pathways. Techniques of chromosomal substitution (consomic and congenic rats) are beginning to confirm statistical results from linkage analysis studies, narrow the regions of genetic interest for positional cloning, and provide genetically well-defined control strains for physiological studies. Patterns of gene expression identified by microarray and mapping of expressed genes to chromosomal sites are adding to the understanding of systems physiology. The previously unimaginable goal of connecting ∼36,000 genes to the complex functions of mammalian systems is indeed well underway.

scholarly journals Synthetic Life with Alternative Nucleic Acids as Genetic Materials

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3483
Author(s):  
Peng Nie ◽  
Yanfen Bai ◽  
Hui Mei
Keyword(s):  
Nucleic Acids ◽  
Genetic Information ◽  
Structural Parameters ◽  
Living Cells ◽  
Information Storage ◽  
Chemically Modified ◽  
Synthetic Life ◽  
Living Organisms

DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.

Chemoinformatics on Metabolic Pathways

2011 ◽  
pp. 318-339
Author(s):  
Masahiro Hattori ◽  
Masaaki Kotera
Keyword(s):  
Metabolic Pathway ◽  
Chemical Space ◽  
Research Area ◽  
Chemical Information ◽  
Prediction System ◽  
Future Directions ◽  
Heterogeneous Information ◽  
Research Areas ◽  
Living Organisms ◽  
Product Pair

Chemical genomics is one of the cutting-edge research areas in the post-genomic era, which requires a sophisticated integration of heterogeneous information, i.e., genomic and chemical information. Enzymes play key roles for dynamic behavior of living organisms, linking information in the chemical space and genomic space. In this chapter, the authors report our recent efforts in this area, including the development of a similarity measure between two chemical compounds, a prediction system of a plausible enzyme for a given substrate and product pair, and two different approaches to predict the fate of a given compound in a metabolic pathway. General problems and possible future directions are also discussed, in hope to attract more activities from many researchers in this research area.

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