Strategy evolution on higher-order networks.

Cooperation is key to prosperity in human societies. Population structure is well understood as a catalyst for cooperation, where research has focused on pairwise interactions. But cooperative behaviors are not simply dyadic, and they often involve coordinated behavior in larger groups. Here we develop a framework to study the evolution of behavioral strategies in higher-order population structures, which include pairwise and multi-way interactions. We provide an analytical treatment of when cooperation will be favored by higher-order interactions, accounting for arbitrary spatial heterogeneity and nonlinear rewards for cooperation in larger groups. Our results indicate that higher-order interactions can act to promote the evolution of cooperation across a broad range of networks, in public goods games. Higher-order interactions consistently provide an advantage for cooperation when interaction hyper-networks feature multiple conjoined communities. Our analysis provides a systematic account of how higher-order interactions modulate the evolution of prosocial traits.

Constructing temporal networks with bursty activity patterns.

Human social interactions tend to vary in intensity over time, whether they are in person or online. Variable rates of interaction in structured populations can be described by networks with the time-varying activity of links and nodes. One of the key statistics to summarize temporal patterns is the inter-event time, namely the duration between successive pairwise interactions. Empirical studies have found inter-event time distributions that are heavy-tailed, for both physical and digital interactions. But it is difficult to construct theoretical models of time-varying activity on a network that reproduce the burstiness seen in empirical data. Here we develop a spanning-tree method to construct temporal networks and activity patterns with bursty behavior. Our method ensures any desired target inter-event time distributions for individual nodes and links, provided the distributions fulfill a consistency condition, regardless of whether the underlying topology is static or time-varying. We show that this model can reproduce burstiness found in empirical datasets, and so it may serve as a basis for studying dynamic processes in real-world bursty interactions.

Evolutionary dynamics on sequential temporal networks.

Population structure is a well-known catalyst for the evolution of cooperation and has traditionally been considered to be static in the course of evolution. Conversely, real-world populations, such as microbiome communities and online social networks, frequently show a progression from tiny, active groups to huge, stable communities, which is insufficient to be captured by constant structures. Here, we propose sequential temporal networks to characterize growing networked populations, and we extend the theory of evolutionary games to these temporal networks with arbitrary structures and growth rules. We derive analytical rules under which a sequential temporal network has a higher fixation probability for cooperation than its static counterpart. Under neutral drift, the rule is simply a function of the increment of nodes and edges in each time step. But if the selection is weak, the rule is related to coalescence times on networks. In this case, we propose a mean-field approximation to calculate fixation probabilities and critical benefit-to-cost ratios with lower calculation complexity. Numerical simulations in empirical datasets also prove the cooperation-promoting effect of population growth. Our research stresses the significance of population growth in the real world and provides a high-accuracy approximation approach for analyzing the evolution in real-life systems.

Hydrazone chemistry-mediated CRISPR/Cas12a system for bacterial analysis.

In this study, a hydrazone chemistry-mediated clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system has been proposed for the fist time and constructed. In our system, hydrazone chemistry is designed and employed to accelerate the formation of a whole activation strand by taking advantage of the proximity effect induced by complementary base pairing, thus activating the CRISPR/Cas12a system quickly and efficiently. Moreover, the introduction of hydrazone chemistry can improve the specificity of the CRISPR/Cas12a system, allowing it to effectively distinguish single-base mismatches. The established system has been further applied to analyze Pseudomonas aeruginosa by specific recognition of the probe strand with a characteristic fragment in 16S rDNA to release the hydrazine group-modified activation strand. The method shows a wide linear range from 3.8 × 102 colony-forming units (CFU)/ml to 3.8 × 106 CFU/ml, with the lowest detection limit of 24 CFU/ml. Therefore, the introduction of hydrazone chemistry may also broaden the application of the CRISPR/Cas12a system.

Boronic Ester-Mediated Dual Recognition Coupled with a CRISPR/Cas12a System for Lipopolysaccharide Analysis.

In this work, boronic ester-mediated dual recognition has been coupled with a CRISPR/Cas12a system; thus, a new method for highly specific and sensitive detection of lipopolysaccharide (LPS) is proposed via the simultaneous recognition of boronic acid and an LPS aptamer (LPSA) as well as signal amplification by CRISPR/Cas12a. Specifically, boronic acid-modified magnetic beads (MB@APBA) and aptamers are employed for the simultaneous dual recognition of LPS, while polymerase isotherm amplification is further utilized to induce LPS cycling and form a double strand, which can activate the CRISPR/Cas12a system so as to amplify the signal. Consequently, a linear detection range can be obtained from 0.05 to 5000 ng/mL, with the lowest detection limit of 44.86 pg/mL. The capturing of MB@APBA on 1, 2- and 1, 3-cis dihydroxyl-containing substances can not only eliminate the interference of other molecules but also enhance the highly specific recognition of LPSA on LPS. Moreover, MB@APBA can be reused by adjusting the pH value of the reaction system. The method can be developed as a universal platform for the analytical detection of other carbohydrates.

Application of Chemoselective Ligation in Biosensing.

With the advantages of mild reaction condition as well as high stereoselectivity and efficiency, chemoselective ligations including oxime chemistry, hydrazone chemistry, cycloaddition reaction, C-C multiple bond addition reaction, nucleophilic rings opening reaction, and alkynes-based reaction, have been applied in the field of biosensing. In this review, the roles of these chemoselective ligations for the construction of biosensors have been summarized. The ligations can serve for reactant preparation, interface modification, signal probe synthesis, molecular recognition, signal amplification, and output. Meanwhile, their recent applications for detection of various targets including small molecules, metal ions, protein, and nucleic acid so on, have been reviewed. Moreover, the development trend of these ligations in biosensing has also been prospected in this review.

DNAzyme-based colorimetric assay and its application for lipopolysaccharide analysis assisted by oxime chemistry.

Herein, for the first time, we propose that the cleavage activity of DNAzyme is accompanied by the release of hydroxyl ions, which can be used for colorimetric assay. Subsequently, we further construct a colorimetric strategy for lipopolysaccharide (LPS) analysis by using this property. Detailly, DNAzyme is split into two fragments separately modified with aldehyde group and hydroxylamine group, which can be linked together through oxime chemistry and the presence of LPS can prevent the formation of oxime bond. The formed whole DNAzyme can mediate the release of hydroxyl ions serving for colorimetric signal output. Taking LPS as model targets, DNAzyme-based colorimetric assay has been successfully constructed. This work not only provides a colorimetric strategy to analyze DNAzyme activity, but also gives a new insight to enrich the versatility of DNAzymes and to enhance their multifunctionality.

MXene Coupled with CRISPR-Cas12a for Analysis of Endotoxin and Bacteria.

With hydrophilic surface and high density of functional groups, MXene can efficiently adsorb single-stranded DNA to enhance target-induced strand release and quench the fluorescence. Herein, MXene is coupled with CRISPR-Cas12a to sensitively detect LPS and bacteria. Specifically, the aptamer is well designed to initiate the trans-cleavage activity of CRISPR-Cas12a to indiscriminately cleave single-stranded DNA, resulting it to be far away from MXene and the recovery of fluorescence. The target can effectually induce the release of the aptamer strand from the hybrid duplex with the assistance of MXene. The formed aptamer/target complex will inhibit the activation of CRISPR-Cas12a and its trans-cleavage on single-stranded DNA. The established method can selectively and sensitively quantify LPS and Gram-negative bacteria in different samples with detection limits of 11 pg/mL and 23 CFU/mL, respectively. Our study provides a new insight for exploration of universal analytical methods based on MXene coupled with CRISPR-Cas12a.

Hydrazone chemistry mediated toehold strand displacement cascade and its application for 5-hydroxymethylfurfural analysis.

Hydrazone chemistry has been firstly explored as capturing mode for interface supported toehold strand displacement cascade (TSDC). The method has been further established for analysis of 5-hydroxymethylfurfural (HMF) based on hydrazone chemistry-mediated TSDC. HMF containing aldehyde group can be covalently captured by hydrazine group around magnetic bead through the formation of hydrazone bond, so as to inhibit the immobilization of hybrid duplex and the occurrence of TSDC. Thereby, HMF will cause the change of the fluorescence of modified magnetic bead. With simplicity, specificity, and sensitivity, the method has been successfully applied to analyze HMF in food samples. This paper gives a new insight to explore capturing mode for interface supported TSDC and the established method can be extended for analysis of saccharic derivatives.

Fabrication of pH-Adjusted Boronic Acid-Aptamer Conjugate for Electrochemical Analysis of Conjugated N-Glycolylneuraminic Acid.

In this work, the boronic acid-aptamer conjugate (BAAC) is elaborately designed and explored as a recognition unit. The admirable properties of the pH-dependent boronic acid ester are integrated with the specific capturing capability of the modified aptamer; thus, BAAC can efficiently and selectively bind with the target by adjusting the pH values. An electrochemical biosensor based on pH-adjusted BAAC has been further developed for the analysis of CNeu5Gc, an important biomarker of different kinds of cancer. The boronic acid moiety in BAAC can react with CNeu5Gc to form a BAAC-CNeu5Gc complex under acidic conditions, followed by the release of CNeu5Gc from the complex and subsequent capture by the aptamer moiety with the adjustment of the pH value to alkalinity. With simplicity, high specificity, and efficiency, the biosensor exhibits a wide linear range from 2.816 to 3603.960 ng/mL with a low detection limit of 1.224 ng/mL and can be applied to analyze CNeu5Gc in animal food samples. Besides, this work can also provide a kind of modified aptamer, i.e., the chemical capturing group-modified aptamer, to give a new viewpoint for the exploration of other functionalized aptamers.

DNA Nanomachine with Multitentacles for Integral Processing of Nanoparticles and Its Application in Biosensing.

DNA nanomachines developed by DNA nanotechnology, an attractive branch of nanoengineering, have been widely applied in drug delivery, biomarker detection, etc. However, the existing DNA nanomachines are mainly conducted in solution systems and the application of surface-confined DNA nanomachines is limited due to the less variety and lower efficiency than those in a solution. The efficiency is greatly limited due to the fact that the surface-confined substances cannot freely perform the Brownian movement, which is not conducive to performance improvement. In this work, we proposed a DNA nanomachine with multitentacles based on the multivalent effect and confirmed that the processing efficiency of multitentacles is much higher than that of a single tentacle by kinetic experiments. Interestingly, a multitentacle DNA nanomachine enables stable capture and integral processing of nanoparticles through only one collision between the surface and the nanoparticle, avoiding the loss of efficiency caused by repeated collisions. In addition, a multitentacle DNA nanomachine-based immunoassay exhibits comparable sensitivity to traditional enzyme-linked immunosorbent assay (ELISA) methods in practical applications. Therefore, it is believed that the construction and application of a multitentacle DNA nanomachine expand the application of DNA nanomachines in interfacial biosensing systems, e.g., ELISA and electrochemical biosensors, and provide ideas for the design of other nanomachines working on the interface.

Hydrazone chemistry assisted DNAzyme for the analysis of double targets.

In this work, a hydrazone chemistry assisted DNAzyme has been designed and constructed. The introduction of hydrazone chemistry increases the versatility of DNAzymes. With superior catalytic capability, the hydrazone chemistry assisted DNAzyme has been successfully applied for the analysis of double targets. Taking 5-hydroxymethylfurfural (HMF) and lipopolysaccharide (LPS) as samples, the hydrazone chemistry assisted DNAzyme can be used for the detection of different combinations of targets. Moreover, because hydrazone chemistry is popular in nature, this work may also provide a new insight for the development of DNAzymes and their multifunctionality.

A novel method to engineer proteases for selective enzyme inhibition.

In this work, we have proposed a new strategy to expand the function of a protein. By taking a protease as an example, it can be engineered to make up the shortcoming of natural proteases, and thus it can efficiently and selectively hydrolyze a desired protein even in a complex biological fluid.

Dual-Responsive DNA Nanodevice for the Available Imaging of an Apoptotic Signaling Pathway in Situ.

Fluorescence imaging tools enable the in situ visualization of those molecules involved in various cell signaling pathways, but directly describing these pathways instead of the separate mediators in situ is much more meaningful and still full of challenges. In this work, a dual-responsive DNA nanodevice that allows the available imaging of an apoptotic signaling pathway in living cells has been developed. The nanodevice is constructed through assembling an elaborately designed Y-shaped DNA (Y-DNA) layer on gold nanoparticles (AuNPs). Only if an apoptotic signaling pathway involving the manganese superoxide dismutase (MnSOD) mRNA and downstream cytochrome c (Cyt c) is presented to serve as the input, the nanodevice can perform an "AND" logic gate operation, disassembling the Y-DNA from the AuNP surface and thereafter outputting a fluorescence signal. In comparison with the fluorescence imaging methods that target individual specific molecules, our strategy allows direct profiling of a specific signaling pathway by connected characterization of two correlative targets. The programmable feature of this strategy also shows the potential for the profiling of other signaling pathways. The concept of studying the line connecting two points will contribute to the systematic interrogation on the signaling networks in situ as the networks are composed of lines instead of individual points.

A new colorimetric assay method for the detection of anti-hepatitis C virus antibody with high sensitivity.

The early detection of low abundance anti-hepatitis C virus antibody (anti-HCV Ab) is critical for efficient diagnosis and treatment of HCV infection. In this work, a new colorimetric assay method has been proposed for the sensitive detection of anti-HCV Ab. In this method, the antibody-induced DNA strand displacement and the resulting rolling circle amplification (RCA) are integrated to generate a large amount of tandemly repeated G-quadruplex DNAzymes on the arm of the "Y"-shaped antibody. Consequently, oxidation of 3,3',5,5'-tetramethylbenzidine can be extensively catalyzed by the peroxidase-mimicking DNAzymes. Therefore, the readout signal can be greatly amplified. Further studies reveal that 0.998 pM anti-HCV Ab can be detected by this newly developed assay method. Moreover, the strategy proposed in this method can be adapted for the detection of other antibodies or bivalent targets.

Colorimetric Sensor Array for Human Semen Identification Designed by Coupling Zirconium Metal-Organic Frameworks with DNA-Modified Gold Nanoparticles.

Rapid and accurate identification of semen is critical for male infertility diagnosis and the arrangement of personalized treatment. However, the complexity and diversity of samples impose lots of restrictions in detection. To solve this problem, we propose a colorimetric sensor array in this work by coupling zirconium metal-organic frameworks (Zr-MOFs) with single-stranded-DNA-decorated gold nanoparticles (ssDNA-AuNPs) for human semen identification. Because of the coordination interactions between the Zr6 clusters and the DNA phosphate backbone, as well as π-π stacking and H-bonding, Zr-MOFs can absorb and precipitate AuNPs with the aid of single-stranded DNA. What's more, addition of semen samples in the test solution, proteins, or other contents in the samples will affect the co-precipitation of Zr-MOFs and ssDNA-AuNPs. Subsequently, the color of the supernatant will change and a method to identify human semen can be developed. Further studies reveal that the method can completely detect different semen cases based on the differences in inclusions, demonstrating the characteristics of simplicity, feasibility, and sensitivity in the application of male infertility diagnosis.

Rhodopsin-Like Ionic Gate Fabricated with Graphene Oxide and Isomeric DNA Switch for Efficient Photocontrol of Ion Transport.

Rhodopsin, composed of opsin and isomeric retinal, acts as the primary photoreceptor by converting light into electric signals. Inspired by rhodopsin, we have fabricated a light-regulated ionic gate on the basis of the design of a graphene oxide (GO)-biomimetic DNA-nanochannel architecture. In this design, photoswitchable azobenzene (Azo)-DNA is introduced to the surface of porous anodic alumina (PAA) membrane. With modulation of the interaction between the GO blocker and Azo-DNA via flexibly regulating trans and cis states of Azo under the irradiation of visible and ultraviolet light, alternatively, the ionic gate is switched between ON and OFF states. This newly constructed ionic gate can possess high efficiency for the control of ion transport because of the high blocking property of GO and the rather tiny path within the barrier layer which are both first employed to fabricate ionic gate. We anticipate that this rhodopsin-like ionic gate may provide a new model and method for the investigation of ion channel, ion function, and ion quantity. In addition, because of the advantages of simple fabrication, good biocompatibility, and universality, this bioinspired system may have potential applications as optical sensors, in photoelectric transformation, and in controllable drug delivery.

New method for detection of T4 polynucleotide kinase phosphatase activity through isothermal EXPonential amplification reaction.

As a bifunctional enzyme, T4 polynucleotide kinase phosphatase (T4 PNKP) catalyzes the phosphorylation of 5'-hydroxyl, and also removes the terminal 3'-phosphate group. This is closely related to the restructuring, replication, and damage repair of nucleic acid. In this paper, we describe a new method for the sensitive detection of T4 PNKP activity based on the isothermal EXPonential amplification reaction (EXPAR). T4 PNKP can be linearly assayed in the range from 0.001 to 0.01 U mL-1 with a detection limit of 7.9 × 10-4 U mL-1. Moreover, the method exhibits high specificity and sensitivity and can be applied in the enzyme analysis of complex serum samples. In view of its simplicity and moderate experimental conditions, the method may suitable for use in a commercial kit for the analysis of T4 PNKP activity.

Modularization of three-dimensional gold nanoparticles/ferrocene/liposome cluster for electrochemical biosensor.

For electrochemical biosensors, just like a computer, the modularization and coordinated operation of different components will facilitate the development of versatile biosensors and effectively reduce costs. However, the efficient synergy between different modules is always difficult. It would be a beneficial way to construct the multi-functional module. In this work, a three-dimensional gold nanoparticles/ferrocene/liposome cluster (GFLC) is fabricated and explored as a building block for the fabrication of an electrochemical biosensor, in which gold nanoparticles, ferrocene and liposome cluster work as a signal amplification component, a signal output component and a molecular recognition component, respectively. With the synergy of multi-functions, GFLC has been successfully applied for electrochemical analysis of lipopolysaccharide (LPS) in food samples. LPS can be linearly assayed in the range from 2 × 10-9 µg/mL to 8 µg/mL with a detection limit of 0.51 × 10-10 µg/mL. In view of the favorable modularization effect, GFLC shows a great potential in the development of electrochemical biosensor with considerable versatility and cost-efficiency.

A method to directly assay circRNA in real samples.

A method to directly assay circular RNA (circRNA) is proposed in this work by utilizing the 'microRNA (miRNA) sponge' nature of circRNA and by taking the advantage of duplex-specific nuclease. Moreover, miRNA absorption site-mediated hairpin DNA unfolding and nuclease-assisted target recycling have also been designed in this method to amplify the signal readout, thus sensitive assay of circRNA can be achieved in real samples.