scholarly journals A Computational Design of a Programmable Biological Processor

2020 ◽  
Author(s):  
Miha Moškon ◽  
Žiga Pušnik ◽  
Lidija Magdevska ◽  
Nikolaj Zimic ◽  
Miha Mraz
Keyword(s):  
Information Processing ◽  
Host Cell ◽  
Dna Sequences ◽  
Logic Gates ◽  
Computational Design ◽  
Program Counter ◽  
Biological Oscillator ◽  
Living Organisms ◽  
Instruction Memory ◽  
Biological Program

AbstractBasic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures are, however, hardly scalable and are yet to be extended to more complex processing structures that would constitute a biological computer.Herein, we make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor, composed of an instruction memory containing a biological program, a program counter that is used to address this memory and a biological oscillator that triggers the execution of the next instruction in the memory. The described processor uses transcription and translation resources of the host cell to perform its operations and is able to sequentially execute a set of instructions written within the so-called instruction memory implemented with non-volatile DNA sequences. The addressing of the instruction memory is achieved with a biological implementation of the Johnson counter, which increases its state after an instruction is executed. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equations-based models. These models can be used to simulate the dynamics of the proposed processor.The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the proposed processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be written manually or can be generated automatically with the employment of the provided compiler.

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 Effects of Mycoplasmas on the Host Cell Signaling Pathways

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 308
Author(s):  
Sergei N. Borchsenius ◽  
Innokentii E. Vishnyakov ◽  
Olga A. Chernova ◽  
Vladislav M. Chernov ◽  
Nikolai A. Barlev
Keyword(s):  
Host Cell ◽  
Intracellular Signaling ◽  
Nuclear Translocation ◽  
Inflammatory Responses ◽  
Cell Interaction ◽  
Host Cells ◽  
Nuclear Factor ◽  
New Therapeutic Approaches ◽  
Anti Inflammatory ◽  
Living Organisms

Mycoplasmas are the smallest free-living organisms. Reduced sizes of their genomes put constraints on the ability of these bacteria to live autonomously and make them highly dependent on the nutrients produced by host cells. Importantly, at the organism level, mycoplasmal infections may cause pathological changes to the host, including cancer and severe immunological reactions. At the molecular level, mycoplasmas often activate the NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) inflammatory response and concomitantly inhibit the p53-mediated response, which normally triggers the cell cycle and apoptosis. Thus, mycoplasmal infections may be considered as cancer-associated factors. At the same time, mycoplasmas through their membrane lipoproteins (LAMPs) along with lipoprotein derivatives (lipopeptide MALP-2, macrophage-activating lipopeptide-2) are able to modulate anti-inflammatory responses via nuclear translocation and activation of Nrf2 (the nuclear factor-E2-related anti-inflammatory transcription factor 2). Thus, interactions between mycoplasmas and host cells are multifaceted and depend on the cellular context. In this review, we summarize the current information on the role of mycoplasmas in affecting the host’s intracellular signaling mediated by the interactions between transcriptional factors p53, Nrf2, and NF-κB. A better understanding of the mechanisms underlying pathologic processes associated with reprogramming eukaryotic cells that arise during the mycoplasma-host cell interaction should facilitate the development of new therapeutic approaches to treat oncogenic and inflammatory processes.

scholarly journals Nucleic Acid Computing and its Potential to Transform Silicon-Based Technology

2015 ◽  
Vol 2 (1) ◽  
Author(s):  
Seth G. Abels ◽  
Emil F. Khisamutdinov
Keyword(s):  
Nucleic Acid ◽  
Logic Gates ◽  
Rna Nanotechnology ◽  
Dna And Rna ◽  
Cellular Machinery ◽  
Living Organisms ◽  
Silicon Based ◽  
Molecular Computers

AbstractMolecular computers have existed on our planet for more than 3.5 billion years. Molecular computing devices, composed of biological substances such as nucleic acids, are responsible for the logical processing of a variety of inputs, creating viable outputs that are key components of the cellular machinery of all living organisms. We have begun to adopt some of the structural and functional knowledge of the cellular apparatus in order to fabricate nucleic-acid-based molecular computers in vitro and in vivo. Nucleic acid computing is directly dependent on advances in DNA and RNA nanotechnology. The field is still emerging and a number of challenges persist. Perhaps the most salient among these is how to translate a variety of nucleic-acid-based logic gates, developed by numerous research laboratories, into the realm of silicon-based computing. This mini-review provides some basic information on the advances in nucleic-acid-based computing and its potential to serve as an alternative that can revolutionize silicon-based technology.

scholarly journals Gate-Controlled Electron Quantum Interference Logic Devices

2021 ◽  
Author(s):  
Josef Weinbub ◽  
Mauro Ballicchia ◽  
Mihail Nedjalkov
Keyword(s):  
Information Processing ◽  
Integrated Circuits ◽  
Quantum Interference ◽  
Ballistic Transport ◽  
Logic Gates ◽  
Attractive Alternative ◽  
Logic Device ◽  
Wave Nature ◽  
New Type ◽  
Electron Quantum

Abstract Inspired by using the wave nature of electrons for electron quantum optics, we propose a new type of electron quantum interference logic device (eQILD), where an electron wave is coherently injected into a two-dimensional wave guide and controlled via two gates. Interference effects lead to different current levels in output channels and are utilized for classical logic gates. eQILDs can be reconfigured and support parallelism and multi-valued logic. The operating principle as well as realizations of a logic NAND and NOR gate is shown by means of dynamic quantum Wigner and classical simulations considering coherent/ballistic transport. Contrary to other advanced information processing approaches no magnetic or photonic mechanisms are required. The eQILD is inherently compatible with conventional integrated circuits and thus provides an attractive alternative towards advanced low-power information processing devices with the performance only limited by the single-electron source frequency, i.e., in the GHz regime.

scholarly journals Reinforcement Learning for Bio-Retrosynthesis

2019 ◽  
Author(s):  
Mathilde Koch ◽  
Thomas Duigou ◽  
Jean-Loup Faulon
Keyword(s):  
Reinforcement Learning ◽  
Metabolic Engineering ◽  
Development Process ◽  
Computational Design ◽  
Tree Search ◽  
Monte Carlo Tree Search ◽  
Command Line Tool ◽  
Living Organisms ◽  
Media Supplements ◽  
Engineering Projects

AbstractMetabolic engineering aims to produce chemicals of interest from living organisms, to advance towards greener chemistry. Despite efforts, the research and development process is still long and costly and efficient computational design tools are required to explore the chemical biosynthetic space. Here, we propose to explore the bio-retrosynthesis space using an Artificial Intelligence based approach relying on the Monte Carlo Tree Search reinforcement learning method, guided by chemical similarity. We implement this method in RetroPath RL, an open-source and modular command line tool. We validate it on a golden dataset of 20 manually curated experimental pathways as well as on a larger dataset of 152 successful metabolic engineering projects. Moreover, we provide a novel feature, that suggests potential media supplements to complement the enzymatic synthesis plan.

scholarly journals Tunable genetic devices through simultaneous control of transcription and translation

2019 ◽  
Author(s):  
Vittorio Bartoli ◽  
Grace A. Meaker ◽  
Mario di Bernardo ◽  
Thomas E. Gorochowski
Keyword(s):  
Host Cell ◽  
Environmental Conditions ◽  
Logic Gates ◽  
Living Cells ◽  
Fold Change ◽  
Response Functions ◽  
Genetic Circuits ◽  
Regulatory Motif ◽  
Trade Offs ◽  
Simultaneous Control

AbstractSynthetic genetic circuits allow us to modify the behavior of living cells. However, changes in environmental conditions and unforeseen interactions with the host cell can cause deviations from a desired function, resulting in the need for time-consuming reassembly to fix these issues. Here, we use a regulatory motif that controls transcription and translation to create genetic devices whose response functions can be dynamically tuned. This allows us, after construction, to shift the on and off states of a sensor by 4.5- and 28-fold, respectively, and modify genetic NOT and NOR logic gates to allow their transitions between states to be varied over a >6-fold range. In all cases, tuning leads to trade-offs in the fold-change and the ability to distinguish cellular states. This work lays the foundation for adaptive genetic circuits that can be tuned after their physical assembly to maintain functionality across diverse environments and design contexts.

scholarly journals A Novel Design and Implementation of New Double Feynman and Six-correction logic (DFSCL) gates in Quantum-dot Cellular Automata (QCA)

2017 ◽  
Vol 13 (15) ◽  
pp. 265
Author(s):  
Sajjad Waheed ◽  
Sharmin Aktar ◽  
Ali Newaz Bahar
Keyword(s):  
Information Processing ◽  
Cellular Automata ◽  
Power Consumption ◽  
Low Power ◽  
Logic Gate ◽  
Processing System ◽  
Logic Gates ◽  
Low Power Consumption ◽  
Switching Frequency ◽  
Promising Alternative

In recent years, quantum cellular automata (QCA) have been used widely to digital circuits and systems. QCA technology is a promising alternative to CMOS technology. It is attractive due to its fast speed, small area and low power consumption. The QCA offers a novel electronics paradigm for information processing and communication. It has the potential for attractive features such as faster speed, higher scale integration, higher switching frequency, smaller size and low power consumption than transistor based technology. In this paper, Double Feynman and Six-correction logic gate (DFSCL) is proposed based on QCA logic gates: MV gate and Inverter gate. The proposed circuit is a promising future in constructing of nano-scale low power consumption information processing system and can stimulate higher digital applications in QCA.

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.

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