scholarly journals Connecting Boolean Integrase Logic gates to a novel alkane control signal via engineered level matching.

2015 ◽  
Author(s):  
Thomas Folliard ◽  
Jerome Bonnet ◽  
John Ward ◽  
Frank Baganz ◽  
Christopher Grant ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Environmental Remediation ◽  
Transcriptional Control ◽  
Dna Recombination ◽  
Logic Gates ◽  
Logic Function ◽  
Control Signals ◽  
Phage Integrases ◽  
Logical Functions ◽  
Transcriptional Output

Boolean Integrase Logic gates use phage integrases that respond to transcriptional signals to implement logical functions within living cells via DNA recombination. Control of biological systems using these logic gates has many applications, including biomanufacturing, healthcare, or environmental remediation. Gates are highly sensitive to background transcriptional noise producing unwanted integrase expression and uncontrolled, permanent gate switching. Consequently, connecting gates to novel control signals requires time-consuming directed evolution of regions regulating integrase expression. Here we present an approach in which the activity of an alkane biosensor is tuned to match levels of existing integrase control signals. By adjusting AlkS expression, we tuned the transcriptional output of Palkb to match the output of existing integrase controllers. We successfully connected Palkb to two integrases with different transcriptional control requirements and demonstrated the original logic function was conserved. Our method complements directed evolution approaches to connect Boolean integrate logic gates to novel transcriptional sources and will ultimately facilitate the systematic in silico design of gates responding to various control signals.

Programmable Logic Gates Based on Tunable Multistable Mechanisms

2019 ◽  
Author(s):  
Mohamed Zanaty ◽  
Hubert Schneegans ◽  
Ilan Vardi ◽  
Simon Henein
Keyword(s):  
Logic Gate ◽  
Logic Gates ◽  
Building Blocks ◽  
Programmable Logic ◽  
Logic Device ◽  
Logic Function ◽  
Element Analysis ◽  
Stability Behavior ◽  
Binary Logic ◽  
Logical Operations

Abstract Binary logic operations are the building blocks of computing machines. In this paper, we present a new programmable binary logic gate based on programmable multistable mechanisms (PMM), which are multistable structures whose stability behavior depends on modifiable boundary conditions as defined and analyzed in our previous work. The logical state of a PMM is defined by its stability and logical operations are implemented by modifying the stability behavior of the mechanism. Our programmable logic device has two qualitatively different sets of inputs. The first set determines the logic function to be computed. The second set represents the logical inputs. The output is a single logical value, “true” if the mechanism changes state and “false” otherwise. In this way, we are able to mechanically implement a set of binary logical operations. This implementation is validated using an analytical model characterizing the qualitative stability behavior of the mechanism. This was further verified using finite element analysis and experimental demonstration.

scholarly journals The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control

2020 ◽  
Vol 117 (26) ◽  
pp. 15316-15321 ◽  
Author(s):  
Xiaofeng Fang ◽  
Zhe Wu ◽  
Oleg Raitskin ◽  
Kimberly Webb ◽  
Philipp Voigt ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Rna Binding ◽  
Antisense Transcription ◽  
Set Domain ◽  
Antisense Transcripts ◽  
Polycomb Repressive Complex 2 ◽  
Active Transcription ◽  
Transcriptional Output

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. AtArabidopsis thaliana FLC,antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3′ processing factors, reducesFLCtranscription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over theFLCgene body. SDG26 interacts with the RNA 3′ processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repressFLC. Overall, our work provides insights into RNA-mediated chromatin silencing.

Transcriptional control signals in the genome of bovine papillomavirus type 1

Nature ◽  
1983 ◽  
Vol 303 (5912) ◽  
pp. 77-80 ◽  
Author(s):  
M. Saveria Campo ◽  
Demetrios A. Spandidos ◽  
Jas Lang ◽  
Neil M. Wilkie
Keyword(s):  
Transcriptional Control ◽  
Bovine Papillomavirus ◽  
Control Signals

Transcriptional control signals of a eukaryotic protein-coding gene

Science ◽  
1982 ◽  
Vol 217 (4557) ◽  
pp. 316-324 ◽  
Author(s):  
S. McKnight ◽  
R Kingsbury
Keyword(s):  
Transcriptional Control ◽  
Protein Coding ◽  
Eukaryotic Protein ◽  
Control Signals

scholarly journals All-Optical Reversible Logic Gates with Optically Controlled Bacteriorhodopsin Protein-Coated Microresonators

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Sukhdev Roy ◽  
Purnima Sethi ◽  
Juraj Topolancik ◽  
Frank Vollmer
Keyword(s):  
Low Power ◽  
Power Control ◽  
Near Infrared ◽  
Optical Switch ◽  
Logic Gates ◽  
Single Mode ◽  
Practical Applications ◽  
Control Signals ◽  
All Optical ◽  
Reversible Logic Gates

We present designs of all-optical reversible gates, namely, Feynman, Toffoli, Peres, and Feynman double gates, with optically controlled microresonators. To demonstrate the applicability, a bacteriorhodopsin protein-coated silica microcavity in contact between two tapered single-mode fibers has been used as an all-optical switch. Low-power control signals (<200 μW) at 532 nm and at 405 nm control the conformational states of the protein to switch a near infrared signal laser beam at 1310 or 1550 nm. This configuration has been used as a template to design four-port tunable resonant coupler logic gates. The proposed designs are general and can be implemented in both fiber-optic and integrated-optic formats and with any other coated photosensitive material. Advantages of directed logic, high Q-factor, tunability, compactness, low-power control signals, high fan-out, and flexibility of cascading switches in 2D/3D architectures to form circuits make the designs promising for practical applications.

scholarly journals Energy Efficient Tri-State CNFET Ternary Logic Gates

2018 ◽  
Author(s):  
Sepher Tabrizchi ◽  
Fazel Sharifi ◽  
Abdel-Hameed A. Badawy
Keyword(s):  
Carbon Nanotube ◽  
Field Effect Transistors ◽  
Logic Gates ◽  
Logic Circuits ◽  
Ternary Logic ◽  
Large Area ◽  
Logic Function ◽  
Correct Operation ◽  
Power Efficient ◽  
Simulation Results

Traditional silicon binary circuits continue to face challenges such as high leakage power dissipation and large area of interconnections. Multiple-Valued Logic (MVL) and nano-devices are two feasible solutions to overcome these problems. In this paper, we present a novel method to design ternary logic circuits based on Carbon Nanotube Field Effect Transistors (CNFETs). The proposed designs use the unique properties of CNFETs, e.g., adjusting the Carbon Nanotube&nbsp;(CNT)&nbsp;diameters to have the desired threshold voltage and have the&nbsp;same mobility of P-FET and N-FET transistors. Each of our designed logic circuits implements a logic function and its complementary via a control signal. Also, these circuits have a high impedance state which saves power while the circuits are not in use. We show a more detailed application of our approach by designing a two-digit adder-subtractor circuit. We simulate the proposed ternary circuits using HSPICE via standard 32nm CNFET technology. The simulation results indicate the correct operation of the designs under different process, voltage and temperature (PVT) variations. Moreover, we designed a two-digit adder/subtractor and a power efficient ternary logic ALU based on the proposed gates. Simulation results show that the two-digit adder/subtractor using our proposed gates has 12X and 5X lower power consumption and PDP (power delay product) respectively, compared to previous designs.

scholarly journals Antagonistic cotranscriptional regulation through ARGONAUTE1 and the THO/TREX complex orchestrates FLC transcriptional output

2021 ◽  
Vol 118 (47) ◽  
pp. e2113757118
Author(s):  
Congyao Xu ◽  
Xiaofeng Fang ◽  
Tiancong Lu ◽  
Caroline Dean
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Transcriptional Control ◽  
Antisense Transcript ◽  
Elongation Rate ◽  
Pol Ii ◽  
Alternative Processing ◽  
Floral Repressor ◽  
Related Proteins ◽  
Transcriptional Output

Quantitative transcriptional control is essential for physiological and developmental processes in many organisms. Transcriptional output is influenced by cotranscriptional processes interconnected to chromatin regulation, but how the functions of different cotranscriptional regulators are integrated is poorly understood. The Arabidopsis floral repressor locus FLOWERING LOCUS C (FLC) is cotranscriptionally repressed by alternative processing of the antisense transcript COOLAIR. Proximal 3′-end processing of COOLAIR resolves a cotranscriptionally formed R-loop, and this process physically links to a histone-modifying complex FLD/SDG26/LD. This induces a chromatin environment locally that determines low transcription initiation and a slow elongation rate to both sense and antisense strands. Here, we show that ARGONAUTE1 (AGO1) genetically functions in this cotranscriptional repression mechanism. AGO1 associates with COOLAIR and influences COOLAIR splicing dynamics to promote proximal COOLAIR, R-loop resolution, and chromatin silencing. Proteomic analyses revealed physical associations between AGO1, subunits of RNA Polymerase II (Pol II), the splicing-related proteins—the spliceosome NineTeen Complex (NTC) and related proteins (NTR)—and the THO/TREX complex. We connect these activities by demonstrating that the THO/TREX complex activates FLC expression acting antagonistically to AGO1 in COOLAIR processing. Together these data reveal that antagonistic cotranscriptional regulation through AGO1 or THO/TREX influences COOLAIR processing to deliver a local chromatin environment that determines FLC transcriptional output. The involvement of these conserved cotranscriptional regulators suggests similar mechanisms may underpin quantitative transcriptional regulation generally.

Resettable and enzyme-free molecular logic devices for the intelligent amplification detection of multiple miRNAs via catalyzed hairpin assembly

Nanoscale ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 5048-5057 ◽  
Author(s):  
Siqi Zhang ◽  
Kai-Bin Li ◽  
Wei Shi ◽  
Jie Zhang ◽  
De-Man Han ◽  
...  
Keyword(s):  
Detection System ◽  
Logic Gates ◽  
Magnetic Bead ◽  
Multiplex Detection ◽  
Logic Function ◽  
Logic Devices ◽  
Molecular Logic ◽  
Catalyzed Hairpin Assembly

In this work, we developed a magnetic bead/DNA system to construct a library of logic gates, enabling the sensing of multiplex target miRNAs. The CHA-based multiplex detection system can distinguish individual target miRNAs under a logic function control.

Enhanced prompt trigger optical switching using nonlinear photonic crystal ring resonator for application on all-optical AND/NAND and OR/NOR logic function

Frequenz ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mohamed Salah Bouaouina ◽  
Mohamed Redha Lebbal ◽  
Mohamed Bouchemat ◽  
Touraya Bouchemat
Keyword(s):  
Optical Switching ◽  
Ring Resonator ◽  
Optical Switch ◽  
Logic Gates ◽  
Threshold Power ◽  
Logic Function ◽  
Optical Elements ◽  
High Data ◽  
Nonlinear Photonic Crystal ◽  
All Optical

Abstract Nowadays, the development of optical telecommunication systems requires more efficient all-optical elements appreciation to their high data transmission speeds and reduced electromagnetic interferences. In this work, our objective is to attest by simulation a design of an optical switch using 2D photonic crystals from polystyrene, an organic polymeric material with high Kerr non-linearity. This excellent ultra-fast switching leads us to the exploited in the construction of two new structures of all-optical AND/NAND and OR/NOR logic gates. These structures based on non-linear ring resonator NRR of different radius in order to operate a telecom wavelength of 1550.3 µm using RSoft (Full-Wave) software. The average contrast intensity is between 15.52 and 23.42 dB and low delay time varied from 20 fs to 5.0 ps. Hence, resulting a very high output signal for ON-switching (82–130% of P in) and a weak signal for OFF-switching (0.2–7% of P in) through a minimum threshold power around of 1.2 mW/μm2.

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