Multiple Input Sensing and Signal Integration Using a Split Cas12a System.

The ability to integrate biological signals and execute a functional response when appropriate is critical for sophisticated cell engineering using synthetic biology. Although the CRISPR-Cas system has been harnessed for synthetic manipulation of the genome, it has not been fully utilized for complex environmental signal sensing, integration, and actuation. Here, we develop a split dCas12a platform and show that it allows for the construction of multi-input, multi-output logic circuits in mammalian cells. The system is highly programmable and can generate expandable AND gates with two, three, and four inputs. It can also incorporate NOT logic by using anti-CRISPR proteins as an OFF switch. By coupling the split dCas12a design to multiple tumor-relevant promoters, we provide a proof of concept that the system can implement logic gating to specifically detect breast cancer cells and execute therapeutic immunomodulatory responses.

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.

There is a growing interest in inferring context specific gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data. This involves identifying the regulatory relationships between transcription factors (TFs) and genes in individual cells, and then characterizing these relationships at the level of specific cell types or cell states. In this study, we introduce scGATE (single-cell gene regulatory gate) as a novel computational tool for inferring TF-gene interaction networks and reconstructing Boolean logic gates involving regulatory TFs using scRNA-seq data. In contrast to current Boolean models, scGATE eliminates the need for individual formulations and likelihood calculations for each Boolean rule (e.g. AND, OR, XOR). By employing a Bayesian framework, scGATE infers the Boolean rule after fitting the model to the data, resulting in significant reductions in time-complexities for logic-based studies. We have applied assay for transposase-accessible chromatin with sequencing (scATAC-seq) data and TF DNA binding motifs to filter out non-relevant TFs in gene regulations. By integrating single-cell clustering with these external cues, scGATE is able to infer context specific networks. The performance of scGATE is evaluated using synthetic and real single-cell multi-omics data from mouse tissues and human blood, demonstrating its superiority over existing tools for reconstructing TF-gene networks. Additionally, scGATE provides a flexible framework for understanding the complex combinatorial and cooperative relationships among TFs regulating target genes by inferring Boolean logic gates among them.

Reconfigurable Neuromorphic Computing with 2D Material Heterostructures for Versatile Neural Information Processing.

Reconfigurable neuromorphic computing holds promise for advancing energy-efficient neural network implementation and functional versatility. Previous work has focused on emulating specific neural functions rather than an integrated approach. We propose an all two-dimensional (2D) material-based heterostructure capable of performing multiple neuromorphic operations by reconfiguring output terminals in response to stimuli. Specifically, our device can synergistically emulate the key neural elements of the synapse, neuron, and dendrite, which play important and interrelated roles in information processing. Dendrites, the branches that receive and transmit presynaptic action potentials, possess the ability to nonlinearly integrate and filter incoming signals. The proposed heterostructure allows reconfiguration between different operation modes, demonstrating its potential for diverse computing tasks. As a proof of concept, we show that the device can perform basic Boolean logic functions. This highlights its applicability to complex neural-network-based information processing problems. Our integrated neuromorphic approach may advance the development of versatile, low-power neuromorphic hardware.

Reconfigurable aJ-Level Ferroelectric Transistor-Based Boolean Logic for Logic-in-Memory.

Logic-in-memory (LIM) architecture holds great potential to break the von Neumann bottleneck. Despite the extensive research on novel devices, challenges persist in developing suitable engineering building blocks for such designs. Herein, we propose a reconfigurable strategy for efficient implementation of Boolean logics based on a hafnium oxide-based ferroelectric field effect transistor (HfO2-based FeFET). The logic results are stored within the device itself (in situ) during the computation process, featuring the key characteristics of LIM. The fast switching speed and low power consumption of a HfO2-based FeFET enable the execution of Boolean logics with an ultralow energy of lower than 8 attojoule (aJ). This represents a significant milestone in achieving aJ-level computing energy consumption. Furthermore, the system demonstrates exceptional reliability with computing endurance exceeding 108 cycles and retention properties exceeding 1000 s. These results highlight the remarkable potential of a FeFET for the realization of high performance beyond the von Neumann LIM computing architectures.

Genetically encoded Boolean logic operators to sense and integrate phenylpropanoid metabolite levels in plants.

Synthetic biology has the potential to revolutionize biotechnology, public health, and agriculture. Recent studies have shown the enormous potential of plants as chassis for synthetic biology applications. However, tools to precisely manipulate metabolic pathways for bioproduction in plants are still needed. We used bacterial allosteric transcription factors (aTFs) that control gene expression in a ligand-specific manner and tested their ability to repress semi-synthetic promoters in plants. We also tested the modulation of their repression activity in response to specific plant metabolites, especially phenylpropanoid-related molecules. Using these aTFs, we also designed synthetic genetic circuits capable of computing Boolean logic operations. Three aTFs, CouR, FapR, and TtgR, achieved c. 95% repression of their respective target promoters. For TtgR, a sixfold de-repression could be triggered by inducing its ligand accumulation, showing its use as biosensor. Moreover, we designed synthetic genetic circuits that use AND, NAND, IMPLY, and NIMPLY Boolean logic operations and integrate metabolite levels as input to the circuit. We showed that biosensors can be implemented in plants to detect phenylpropanoid-related metabolites and activate a genetic circuit that follows a predefined logic, demonstrating their potential as tools for exerting control over plant metabolic pathways and facilitating the bioproduction of natural products.

Energy Efficient All-Electric-Field-Controlled Multiferroic Magnetic Domain-Wall Logic.

Magnetic domain wall (DW)-based logic devices offer numerous opportunities for emerging electronics applications allowing superior performance characteristics such as fast motion, high density, and nonvolatility to process information. However, these devices rely on an external magnetic field, which limits their implementation; this is particularly problematic in large-scale applications. Multiferroic systems consisting of a piezoelectric substrate coupled with ferromagnets provide a potential solution that provides the possibility of controlling magnetization through an electric field via magnetoelastic coupling. Strain-induced magnetization anisotropy tilting can influence the DW motion in a controllable way. We demonstrate a method to perform all-electrical logic operations using such a system. Ferromagnetic coupling between neighboring magnetic domains induced by the electric-field-controlled strain has been exploited to promote noncollinear spin alignment, which is used for realizing essential building blocks, including DW generation, propagation, and pinning, in all implementations of Boolean logic, which will pave the way for scalable memory-in-logic applications.

ExBoX - a simple Boolean exclusion strategy to drive expression in neurons.

The advent of modern single-cell biology has revealed the striking molecular diversity of cell populations once thought to be more homogeneous. This newly appreciated complexity has made intersectional genetic approaches essential to understanding and probing cellular heterogeneity at the functional level. Here, we build on previous knowledge to develop a simple adeno-associated virus (AAV)-based approach to define specific subpopulations of cells by Boolean exclusion logic (AND NOT). This expression by Boolean exclusion (ExBoX) system encodes for a gene of interest that is turned on by a particular recombinase (Cre or FlpO) and turned off by another. ExBoX allows for the specific transcription of a gene of interest in cells expressing only the activating recombinase, but not in cells expressing both. We show the ability of the ExBoX system to tightly regulate expression of fluorescent reporters in vitro and in vivo, and further demonstrate the adaptability of the system by achieving expression of a variety of virally delivered coding sequences in the mouse brain. This simple strategy will expand the molecular toolkit available for cell- and time-specific gene expression in a variety of systems.

A logical way to reprogram plants.

Living cells constantly monitor their external and internal environments for changing conditions, stresses or developmental cues. Networks of genetically encoded components sense and process these signals following pre-defined rules in such a way that specific combinations of the presence or absence of certain signals activate suitable responses. Many biological signal integration mechanisms approximate Boolean logic operations, whereby presence or absence of signals are computed as variables with values described as either true or false, respectively. Boolean logic gates are commonly used in algebra and in computer sciences, and have long been recognized as useful information processing devices in electronic circuits. In these circuits, logic gates integrate multiple input values and produce an output signal according to pre-defined Boolean logic operations. Recent implementation of these logic operations using genetic components to process information in living cells has allowed genetic circuits to enable novel traits with decision-making capabilities. Although several literature reports describe the design and use of these logic gates to introduce new functions in bacterial, yeast and mammalian cells, similar approaches in plants remain scarce, likely due to challenges posed by the complexity of plants and the lack of some technological advances, e.g., species-independent genetic transformation. In this mini review, we have surveyed recent reports describing synthetic genetic Boolean logic operators in plants and the different gate architectures used. We also briefly discuss the potential of deploying these genetic devices in plants to bring to fruition a new generation of resilient crops and improved biomanufacturing platforms.

Advances in plant synthetic biology approaches to control expression of gene circuits.

The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.

A Universal Multichannel Platform for Assembling Enzyme-Based Boolean Logic Gates.

Concatenated enzyme-based Boolean logic gates activated with 5 chemical input signals were analyzed with a smartphone photo camera. Simultaneous detection of 32 input combinations was conveniently performed using enzyme-modified fiberglass sensing spots generating fluorescence with different intensities for the 0 and 1 binary outputs. The developed technology offers an easy readout method for multi-channel logic systems.

Boolean Logic Networks Mimicked with Chimeric Enzymes Activated/Inhibited by Several Input Signals.

Reactions catalyzed by artificial allosteric enzymes, chimeric proteins with fused biorecognition and catalytic units, were used to mimic multi-input Boolean logic systems. The catalytic parts of the systems were represented by pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH). Two biorecognition units, calmodulin or artificial peptide-clamp, were integrated into PQQ-GDH and locked it in the OFF or ON state respectively. The ligand-peptide binding cooperatively with Ca2+ cations to a calmodulin bioreceptor resulted in the enzyme activation, while another ligand-peptide bound to a clamp-receptor inhibited the enzyme. The enzyme activation and inhibition originated from peptide-induced allosteric transitions in the receptor units that propagated to the catalytic domain. While most of enzymes used to mimic Boolean logic gates operate with two inputs (substrate and co-substrate), the used chimeric enzymes were controlled by four inputs (glucose - substrate, dichlorophenolindophenol - electron acceptor/co-substrate, Ca2+ cations and a peptide - activating/inhibiting signals). The biocatalytic reactions controlled by four input signals were considered as logic networks composed of several concatenated logic gates. The developed approach allows potentially programming complex logic networks operating with various biomolecular inputs representing potential utility for different biomedical applications.

Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions.

The enzyme system mimicking Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates has been designed. The same enzyme system was used to operate as the IMPLY or INHIB gate simply by reformulating the input signals. The optical analysis of the logic operation confirmed the output generation as expected for the studied logic gates. The conceptual approach to the IMPLY and INHIB logic gates allows their construction with many other enzymes operating in a similar way.

Methylated Eu(III) metal-organic framework as a fluorescent probe for constructing molecular logic gates and monitoring of F-, I-, and S2.

A novel fluorescent and electron-deficient hybrid, N-methylated [Eu (pddb)phen(ox)0.5]n (Eu-MOF-Me) has been prepared via post-synthetic modification. Considering its special luminescent properties and cationic framework, Eu-MOF-Me is developed as a visualized fluorescent probe. Notably, water-stable Eu-MOF-Me exhibits advantages like good structural and fluorescent stability in a wide range of pH value (3.39-10.86), excellent identification ability for F-, I-, and S2- (it can easily distinguish F- and I- from other halogen ions and can realize naked eye identification of F-, I-, and S2-), relatively low detection limits (6.61 µM for S2-, 7.57 µM for F-), and reusability. More importantly, it has been utilized for the construction of a Boolean logic gate system. In this system, Eu-MOF-Me serves as the gate, by taking F-, I-, and S2- as the inputs and fluorescence emission bands (UV380, B437, and R612) as the outputs; some primary logic gates (NOR, IMP, YES, NOT) and the combination of them have been realized. Moreover, we achieved a cascaded logic gate (NOR+OR). For further application, a molecular computing keypad-lock security system has been obtained. Graphical abstract A novel fluorescent and electron-deficient hybrid named Eu-MOF-Me has been prepared via post-synthetic methylation. Considering its special luminescent properties and cationic framework, Eu-MOF-Me was developed as a fluorescent probe for the visual monitoring of important anions. In addition, it was used for the construction of Boolean logic library and a keypad-lock system was achieved.

Boolean Logic Gates Realized with Enzyme-catalyzed Reactions - Unusual Look at Usual Chemical Reactions.

Research in the area of molecular computing systems, in the general framework of unconventional computing, has received high attention and resulted in rapid progress in formulating signal-controlled switchable molecules capable to perform Boolean logic operations and basic arithmetic functions. Extension of this research to biomolecular systems allowed sophisticated computational functions much easier than using synthetic molecular and supramolecular species. The advantage of biomolecular systems comparing with synthetic molecular systems is in their complementarity and compatibility allowing easy assembling multi-component systems from various biomolecules, thus increasing their functional complexity. While DNA-based computing systems are promising faster computing than Si-based electronics, at least for solving some combinatorial problems, due to massive parallel operation, enzyme-based logic systems are less promising for computational applications in their narrow definition. However, they offer novel biosensing and bioactuation features operating in binary Yes/No format. The present review article overviews different kinds of enzyme logic gates exemplified with specific enzymatic reactions/cascades. Motivation for this research and its possible applications are discussed. The review will be helpful to researchers working in this specific area to see the comprehensive collection of logic operations performed by the enzyme reactions. The newcomers to the reviewed area will benefit from the example systems representing various logic functions systematically.

Integrated Molecular Logic Using a Multistate Electrochromic Platform.

Herein, we present an approach that integrates molecular logic functions using surface-confined metallo-organic assemblies. These assemblies are electrochromic and mimic the behaviour of logic elements. The logic elements are addressed individually by electrochemical methods, and their outputs are simultaneously read-out optically by UV/Vis absorption spectroscopy. The versatility of our setup is demonstrated by the integration of two multi-component assemblies; each acting as ternary logic elements. We used also a laminated cell configuration to demonstrate color-to-color and color-to-transparent transitions. This concept offers a route for the future development of devices with multiple logic states.

Modelling GTPase dynamics to understand RhoA-driven cancer cell invasion.

Metastasis, initially driven by cells migrating and invading through the local environment, leads to most cancer-associated deaths. Cells can use a variety of modes to move in vitro, all of which depend on Rho GTPases at some level. While traditionally it was thought that Rac1 activity drives protrusive lamellipodia at the leading edge of a polarised cell while RhoA drives rear retraction, more recent work in 3D microenvironments has revealed a much more complicated picture of GTPase dynamics. In particular, RhoA activity can dominate the leading edge polymerisation of actin to form filopodial actin-spike protrusions that drive more invasive cell migration. We recently described a potential mechanism to abrogate this pro-invasive localised leading edge Rac1 to RhoA switch via manipulation of a negative feedback loop that was revealed by adopting a logical modelling approach. Both challenging dogma and taking a formal, mathematical approach to understanding signalling involved in motility may be vital to harnessing harmful cell migration and preventing metastasis in future research.

Singleton {NOT} and Doubleton {YES; NOT} Gates Act as Functionally Complete Sets in DNA-Integrated Computational Circuits.

A functionally complete Boolean operator is sufficient for computational circuits of arbitrary complexity. We connected YES (buffer) with NOT (inverter) and two NOT four-way junction (4J) DNA gates to obtain IMPLY and NAND Boolean functions, respectively, each of which represents a functionally complete gate. The results show a technological path towards creating a DNA computational circuit of arbitrary complexity based on singleton NOT or a combination of NOT and YES gates, which is not possible in electronic computers. We, therefore, concluded that DNA-based circuits and molecular computation may offer opportunities unforeseen in electronics.

Challenges and innovations in CAR-T cell therapy: a comprehensive analysis.

Recent years have seen a marked increase in research on chimeric antigen receptor T (CAR-T) cells, with specific relevance to the treatment of hematological malignancies. Here, the structural principles, iterative processes, and target selection of CAR-T cells for therapeutic applications are described in detail, as well as the challenges faced in the treatment of solid tumors and hematological malignancies. These challenges include insufficient infiltration of cells, off-target effects, cytokine release syndrome, and tumor lysis syndrome. In addition, directions in the iterative development of CAR-T cell therapy are discussed, including modifications of CAR-T cell structures, improvements in specificity using multi-targets and novel targets, the use of Boolean logic gates to minimize off-target effects and control toxicity, and the adoption of additional protection mechanisms to improve the durability of CAR-T cell treatment. This review provides ideas and strategies for the development of CAR-T cell therapy through an in-depth exploration of the underlying mechanisms of action of CAR-T cells and their potential for innovative modification.

Bi-Directional and Operand-Controllable In-Memory Computing for Boolean Logic and Search Operations with Row and Column Directional SRAM (RC-SRAM).

The von Neumann architecture is no longer sufficient for handling large-scale data. In-memory computing has emerged as the potent method for breaking through the memory bottleneck. A new 10T SRAM bitcell with row and column control lines called RC-SRAM is proposed in this article. The architecture based on RC-SRAM can achieve bi-directional and operand-controllable logic-in-memory and search operations through different signal configurations, which can comprehensively respond to various occasions and needs. Moreover, we propose threshold-controlled logic gates for sensing, which effectively reduces the circuit area and improves accuracy. We validate the RC-SRAM with a 28 nm CMOS technology, and the results show that the circuits are not only full featured and flexible for customization but also have a significant increase in the working frequency. At VDD = 0.9 V and T = 25 °C, the bi-directional search frequency is up to 775 MHz and 567 MHz, and the speeds for row and column Boolean logic reach 759 MHz and 683 MHz.

Multicolor Fluorescent Inks Based on Lanthanide Hybrid Organogels for Anticounterfeiting and Logic Circuit Design.

With the rapid development of information technology, the encrypted storage of information is becoming increasingly important for human life. The luminescent materials with a color-changed response under physical or chemical stimuli are crucial for information coding and anticounterfeiting. However, traditional fluorescent materials usually face problems such as a lack of tunable fluorescence, insufficient surface-adaptive adhesion, and strict synthesis conditions, hindering their practical applications. Herein, a series of luminescent lanthanide hybrid organogels (Ln-MOGs) were rapidly synthesized using a simple method at room temperature through the coordination between lanthanide ions and 2,6-pyridinedicarboxylic acid and 5-aminoisophthalic acid. And the multicolor fluorescent inks were also prepared based on the Ln-MOG and hyaluronic acid, with the advantages of being easy to write, color-adjustable, and water-responsive discoloration, which has been applied to paper-based anticounterfeiting technology. Inspired by the responsiveness of the fluorescent inks to water, we designed a logic system that can realize single-input logic operations (NOT and PASS1) and double-input logic operations (NAND, AND, OR, NOR, XOR). The encryption of a binary code can be actualized utilizing different luminescent response modes based on the logic circuit system. By adjusting the energy sensitization and luminescence mechanism of lanthanide ions in the gel structure, the information reading and writing ability of the fluorescent inks were verified, which has great potential in the field of multicolor pattern anticounterfeiting and information encryption.