Strategies to Enrich Electrochemical Sensing Data with Analytical Relevance for Machine Learning Applications: A Focused Review.

In this review, recent advances regarding the integration of machine learning into electrochemical analysis are overviewed, focusing on the strategies to increase the analytical context of electrochemical data for enhanced machine learning applications. While information-rich electrochemical data offer great potential for machine learning applications, limitations arise when sensors struggle to identify or quantitatively detect target substances in a complex matrix of non-target substances. Advanced machine learning techniques are crucial, but equally important is the development of methods to ensure that electrochemical systems can generate data with reasonable variations across different targets or the different concentrations of a single target. We discuss five strategies developed for building such electrochemical systems, employed in the steps of preparing sensing electrodes, recording signals, and analyzing data. In addition, we explore approaches for acquiring and augmenting the datasets used to train and validate machine learning models. Through these insights, we aim to inspire researchers to fully leverage the potential of machine learning in electroanalytical science.

Graphene for Nanobiosensors and Nanobiochips.

Graphene family nanomaterials have interesting electronic structures which determine their electrical, optical, and mechanical properties. Especially, their unique chemical properties enable interactions with biological substances and chemical reagents, and the interactions have further an influence on the observable properties of the graphene family nanomaterials. Such aspects render graphene family nanomaterials versatile for various types of biosensing as a target recognition unit and a recognition-to-signal transduction unit. In this chapter, we look over the recent progress on the graphene-based biosensors, which is categorized in terms of (1) the role of graphene family nanomaterials (target recognition, signal transduction), (2) the sensing mechanisms and modes (electrochemical, electrical, fluorescent, Raman scattering), and (3) the formats of sensing devices (paper, lab-on-a-chip, wearable devices).

Wearable Sensing Systems for Monitoring Mental Health.

Wearable systems for monitoring biological signals have opened the door to personalized healthcare and have advanced a great deal over the past decade with the development of flexible electronics, efficient energy storage, wireless data transmission, and information processing technologies. As there are cumulative understanding of mechanisms underlying the mental processes and increasing desire for lifetime mental wellbeing, various wearable sensors have been devised to monitor the mental status from physiological activities, physical movements, and biochemical profiles in body fluids. This review summarizes the recent progress in wearable healthcare monitoring systems that can be utilized in mental healthcare, especially focusing on the biochemical sensors (i.e., biomarkers associated with mental status, sensing modalities, and device materials) and discussing their promises and challenges.

Me-too validation study for in vitro skin irritation test with a reconstructed human epidermis model, KeraSkin™ for OECD test guideline 439.

We conducted a me-too validation study to confirm the reproducibility, reliability, and predictive capacity of KeraSkin™ skin irritation test (SIT) as a me-too method of OECD TG 439. With 20 reference chemicals, within-laboratory reproducibility (WLR) of KeraSkin™ SIT in the decision of irritant or non-irritant was 100%, 100%, and 95% while between-laboratory reproducibility (BLR) was 100%, which met the criteria of performance standard (PS, WLR≥90%, BLR≥80%). WLR and BLR were further confirmed with intra-class correlation (ICC, coefficients >0.950). WLR and BLR in raw data (viability) were also shown with a scatter plot and Bland-Altman plot. Comparison with existing VRMs with Bland-Altman plot, ICC and kappa statistics confirmed the compatibility of KeraSkin™ SIT with OECD TG 439. The predictive capacity of KeraSkin™ SIT was estimated with 20 reference chemicals (the sensitivity of 98.9%, the specificity of 70%, and the accuracy of 84.4%) and additional 46 chemicals (for 66 chemicals [20 + 46 chemicals, the sensitivity, specificity and accuracy: 95.2%, 82.2% and 86.4%]). The receiver operating characteristic (ROC) analysis suggested a potential improvement of the predictive capacity, especially sensitivity, when changing cut-off (50% → 60-75%). Collectively, the me-too validation study demonstrated that KeraSkin™ SIT can be a new me-too method for OECD TG 439.

Redox Is a Global Biodevice Information Processing Modality.

Biology is well-known for its ability to communicate through (i) molecularly-specific signaling modalities and (ii) a globally-acting electrical modality associated with ion flow across biological membranes. Emerging research suggests that biology uses a third type of communication modality associated with a flow of electrons through reduction/oxidation (redox) reactions. This redox signaling modality appears to act globally and has features of both molecular and electrical modalities: since free electrons do not exist in aqueous solution, the electrons must flow through molecular intermediates that can be switched between two states - with electrons (reduced) or without electrons (oxidized). Importantly, this global redox modality is easily accessible through its electrical features using convenient electrochemical instrumentation. In this review, we explain this redox modality, describe our electrochemical measurements, and provide four examples demonstrating that redox enables communication between biology and electronics. The first two examples illustrate how redox probing can acquire biologically relevant information. The last two examples illustrate how redox inputs can transduce biologically-relevant transitions for patterning and the induction of a synbio transceiver for two-hop molecular communication. In summary, we believe redox provides a unique ability to bridge bio-device communication because simple electrochemical methods enable global access to biologically meaningful information. Further, we envision that redox may facilitate the application of information theory to the biological sciences.

Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human.

Telomerase is an RNA-protein complex that includes a unique reverse transcriptase that catalyzes the addition of single-stranded telomere DNA repeats onto the 3' ends of linear chromosomes using an integral telomerase RNA (TR) template. Vertebrate TR contains the template/pseudoknot (t/PK) and CR4/5 domains required for telomerase activity in vitro. All vertebrate pseudoknots include two subdomains: P2ab (helices P2a and P2b with a 5/6-nt internal loop) and the minimal pseudoknot (P2b-P3 and associated loops). A helical extension of P2a, P2a.1, is specific to mammalian TR. Using NMR, we investigated the structures of the full-length TR pseudoknot and isolated subdomains in Oryzias latipes (Japanese medaka fish), which has the smallest vertebrate TR identified to date. We determined the solution NMR structure and studied the dynamics of medaka P2ab, and identified all base pairs and tertiary interactions in the minimal pseudoknot. Despite differences in length and sequence, the structure of medaka P2ab is more similar to human P2ab than predicted, and the medaka minimal pseudoknot has the same tertiary interactions as the human pseudoknot. Significantly, although P2a.1 is not predicted to form in teleost fish, we find that it forms in the full-length pseudoknot via an unexpected hairpin. Model structures of the subdomains are combined to generate a model of t/PK. These results provide evidence that the architecture for the vertebrate t/PK is conserved from teleost fish to human. The organization of the t/PK on telomerase reverse transcriptase for medaka and human is modeled based on the cryoEM structure of Tetrahymena telomerase, providing insight into function.

Prediction of the skin sensitization potential of didecyldimethylammonium chloride and 3,7-dimethyl-2,6-octadienal and mixtures of these compounds with the excipient ethylene glycol through the human Cell Line Activation Test and the Direct Peptide Reactivity Assay.

In commercial products such as household deodorants or biocides, didecyldimethylammonium chloride (DDAC) often serves as an antimicrobial agent, citral serves as a fragrance agent, and the excipient ethylene glycol (EG) is used to dissolve the active ingredients. The skin sensitization (SS) potentials of each of these substances are still being debated. Moreover, mixtures of DDAC or citral with EG have not been evaluated for SS potency. The in vitro alternative assay called human Cell Line Activation Test (h-CLAT) and Direct Peptide Reactivity Assay (DPRA) served to address these issues. On three independent runs of h-CLAT, DDAC and citral were predicted to be sensitizers while EG was predicted to be a non-sensitizer and also by the DPRA. Mixtures of DDAC or citral with EG at ratios of 7:3 and 1:4 w/v were all positive by the h-CLAT in terms of SS potential but SS potency was mitigated as the proportion of EG increased. Citral and its EG mixtures were all positive but DDAC and its EG mixtures were all negative by the DPRA, indicating that the DPRA method is not suitable for chemicals with pro-hapten characteristics. Since humans can be occupationally or environmentally exposed to mixtures of excipients with active ingredients, the present study may give insights into further investigations of the SS potentials of various chemical mixtures.

Radical Scavenging Activities of Biomimetic Catechol-Chitosan Films.

Recent studies showed that melanin-mimetic catechol-chitosan films are redox-active and their ability to exchange electrons confers pro-oxidant activities for the sustained, in situ generation of reactive oxygen species for antimicrobial bandages. Here we electrofabricated catechol-chitosan films, demonstrate these films are redox-active, and show their ability to exchange electrons confers sustained radical scavenging activities that could be useful for protective coatings. Electrofabrication was performed in two steps: cathodic electrodeposition of a chitosan film followed by anodic grafting of catechol to chitosan. Spectroelectrochemical reverse engineering methods were used to characterize the catechol-chitosan films and demonstrate the films are redox-active and can donate electrons to quench oxidative free radicals and can accept electrons to quench reductive free radicals. Electrofabricated catechol-chitosan films that were peeled from the electrode were also shown to be capable of donating electrons to quench an oxidative free radical, but this radical scavenging activity decayed upon depletion of electrons from the film (i.e., as the film became oxidized). However, the radical scavenging activity could be recovered by a regeneration step in which the films were contacted with the biological reducing agent ascorbic acid. These results demonstrate that catecholic materials offer important redox-based and context-dependent properties for possible applications as protective coatings.

Redox Probing for Chemical Information of Oxidative Stress.

Oxidative stress is implicated in many diseases yet no simple, rapid, and robust measurement is available at the point-of-care to assist clinicians in detecting oxidative stress. Here, we report results from a discovery-based research approach in which a redox mediator is used to probe serum samples for chemical information relevant to oxidative stress. Specifically, we use an iridium salt (K2IrCl6) to probe serum for reducing activities that can transfer electrons to iridium and thus generate detectable optical and electrochemical signals. We show that this Ir-reducing assay can detect various biological reductants and is especially sensitive to glutathione (GSH) compared to alternative assays. We performed an initial clinical evaluation using serum from 10 people diagnosed with schizophrenia, a mental health disorder that is increasingly linked to oxidative stress. The measured Ir-reducing capacity was able to discriminate people with schizophrenia from healthy controls (p < 0.005), and correlations were observed between Ir-reducing capacity and independent measures of symptom severity.

Spectroelectrochemical Reverse Engineering DemonstratesThat Melanin's Redox and Radical Scavenging Activities Are Linked.

Melanins are ubiquitous in nature but their biological activities and functions have been difficult to discern. Conventional approaches to determine material function start by resolving structure and then characterize relevant properties. These approaches have been less successful for melanins because of their complex structure and insolubility, and because their relevant properties are not readily characterized by conventional methods. Here, we report a novel spectroelectrochemical reverse engineering approach that focuses on redox and radical scavenging activities. In this method, the melanin is immobilized in a permeable hydrogel film adjacent to an electrode and this immobilized melanin is probed using diffusible mediators and complex electrical inputs. Response characteristics are measured using two modalities, electrochemical currents associated with the reaction of diffusible mediators, and optical absorbance associated with the presence of diffusible free radicals. Using this method, we observed that both Sepia and fungal melanins are redox active and can repeatedly exchange electrons to be switched between oxidized and reduced states. Further, we observed that these melanins can quench radicals either by donating or accepting electrons. Finally, we demonstrate that the melanins' radical scavenging activities are dependent on their redox state such that a melanin must be reduced to have donatable electrons to quench oxidative free radicals, or must be oxidized to accept electrons from reductive free radicals. While the observation that melanin is redox-active is consistent with their well-accepted beneficial (radical-scavenging) and detrimental (pro-oxidant) activities, these observations may also support less well-accepted proposed functions for melanin in energy harvesting and redox communication.

Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA.

The modified nucleotide queuosine (Q) is almost universally found in the anticodon wobble position of specific tRNAs. In many bacteria, biosynthesis of Q is modulated by a class of regulatory mRNA elements called riboswitches. The preQ(1) riboswitch, found in the 5'UTR of bacterial genes involved in synthesis of the Q precursors preQ(0) and preQ(1), contains the smallest known aptamer domain. We report the solution structure of the preQ(1) riboswitch aptamer domain from Bacillus subtilis bound to preQ(1), which is a unique compact pseudoknot with three loops and two stems that encapsulates preQ(1) at the junction between the two stems. The pseudoknot only forms in the presence of preQ(1), and the 3' A-rich tail of the aptamer domain is an integral part of the pseudoknot. In the absence of preQ(1), the A-rich tail forms part of the antiterminator. These structural studies provide insight into riboswitch transcriptional control of preQ(1) biosynthesis.

Structural determinants for ligand capture by a class II preQ1 riboswitch.

Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the 5' UTR of genes involved in the biosynthesis and transport of preQ1, a precursor of the modified base queuosine universally found in four tRNAs. The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translational level. We present the solution NMR structure and conformational dynamics of the 59 nucleotide Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1. Unlike in the preQ1 class I (preQ1-I) riboswitch, divalent cations are required for high-affinity binding. The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, which forms a three-way junction with the other two stems. (13)C relaxation and residual dipolar coupling experiments revealed interhelical flexibility of P4. We found that the P4 helix and flanking adenine residues play crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shine-Dalgarno sequence. Aided by divalent cations, P4 is poised to act as a "screw cap" on preQ1 recognition to block ligand exit and stabilize the binding pocket. Comparison of preQ1-I and preQ1-II riboswitch structures reveals that whereas both form H-type pseudoknots and recognize preQ1 using one A, C, or U nucleotide from each of three loops, these nucleotides interact with preQ1 differently, with preQ1 inserting into different grooves. Our studies show that the preQ1-II riboswitch uses an unusual mechanism to harness exquisite control over queuosine metabolism.

Structure and function of preQ1 riboswitches.

PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.

Composition-selective fabrication of ordered intermetallic Au-Cu nanowires and their application to nano-size electrochemical glucose detection.

Bimetallic nanostructures can provide distinct and improved physicochemical properties by the coupling effect of the two metal components, making them promising materials for a variety of applications. Herein, we report composition-selective fabrication of ordered intermetallic Au-Cu nanowires (NWs) by two-step chemical vapor transport method and their application to nano-electrocatalytic glucose detection. Ordered intermetallic Au3Cu and AuCu3 NWs are topotaxially fabricated by supplying Cu-containing chemicals to pre-synthesized single-crystalline Au NW arrays. The composition of fabricated Au-Cu NWs can be selected by changing the concentration of Cu-containing species. Interestingly, Au3Cu NW electrodes show unique electrocatalytic activity for glucose oxidation, allowing us to detect glucose without interference from ascorbic acid. Such interference-free detection of glucose is attributed to the synergistic effect, induced by incorporation of Cu in Au. We anticipate that Au3Cu NWs could show possibility as efficient nano-size electrochemical glucose sensors and the present fabrication method can be employed to fabricate valuable ordered intermetallic nanostructures.

Electrotriggered, spatioselective, quantitative gene delivery into a single cell nucleus by Au nanowire nanoinjector.

Delivery of bioactive materials into a cell is highly important in the study of cell biology and medical treatments. Ideal nanoinjectors should be able to deliver biomaterials with high spatial resolution while causing minimum cell damage. We developed a Au nanowire (NW) nanoinjector that has the thinnest diameter (100­150 nm) among the DNA delivering devices as well as optimum mechanical properties, minimizing cell damage. Well-defined (111) single-crystalline Au surface and high electric conductivity of a Au NW nanoinjector allow precisely timed and efficient electrochemical release of DNA molecules attached on a Au NW surface. Both linear DNA and plasmid DNA were delivered separately and showed successful expression. The Au NW nanoinjector would find important biomedical applications in the fields such as gene therapy, DNA vaccination, targeted drug delivery, and probe/control of cell signaling events.

Recent Advances in Photoacoustic Agents for Theranostic Applications.

Photoacoustic agents are widely used in various theranostic applications. By evaluating the biodistribution obtained from photoacoustic images, the effectiveness of theranostic agents in terms of their delivery efficiency and treatment responses can be analyzed. Through this study, we evaluate and summarize the recent advances in photoacoustic-guided phototherapy, particularly in photothermal and photodynamic therapy. This overview can guide the future directions for theranostic development. Because of the recent applications of photoacoustic imaging in clinical trials, theranostic agents with photoacoustic monitoring have the potential to be translated into the clinical world.

Revealing Redox Behavior of Molybdenum Disulfide and Its Application as Rechargeable Antioxidant Reservoir.

Molybdenum disulfide (MoS2) is a representative two-dimensional transition metal dichalcogenide and has a unique electronic structure and associated physicochemical properties. The redox property of MoS2 has recently attracted significant attention from various fields, such as biomedical applications. Intriguingly, MoS2 functions as an antioxidant in certain applications and as a pro-oxidant in others. We use the mediated electrochemical probing method to understand the redox behavior of MoS2. This method reveals that MoS2 (i) has a reversible and fast redox activity at a mild potential (between -0.20 and +0.25 V vs Ag/AgCl), (ii) functions as an antioxidant for molecules that have different redox mechanisms (electron or hydrogen atom transfer), and (iii) is electrochemically or molecularly rechargeable. Finally, we show that MoS2 reduces oxidized molecules more efficiently than the potent natural antioxidant, curcumin. This study enhances our understanding of MoS2 and shows its potential as an advanced antioxidant reservoir.

Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection.

We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.

Ultrafast dynamics of Förster resonance energy transfer and photo-induced charge transfer in cationic polyfluorene/dye-labeled DNA complex.

The ultrafast dynamics of Förster resonance energy transfer (FRET) and photo-induced charge transfer (PCT) has been investigated in an electrostatic complex of a fluorescein-labeled single-stranded DNA (as a FRET acceptor) and a cationic polyfluorene copolymer (as a FRET donor). The donor-acceptor intermolecular distance and total energy transfer efficiency are determined for a polymer/DNA complex with two different counter-ions and compared with those obtained using a theoretical model by considering the competition between FRET and PCT processes. The maximum total energy transfer efficiency (0.47) was estimated at the optimum donor-acceptor intermolecular distance of 39.6 A.

Enzyme Nanosheet-Based Electrochemical Aspartate Biosensor for Fish Point-of-Care Applications.

Bacterial infections in marine fishes are linked to mass mortality issues; hence, rapid detection of an infection can contribute to achieving a faster diagnosis using point-of-care testing. There has been substantial interest in identifying diagnostic biomarkers that can be detected in major organs to predict bacterial infections. Aspartate was identified as an important biomarker for bacterial infection diagnosis in olive flounder (Paralichthys olivaceus) fish. To determine aspartate levels, an amperometric biosensor was designed based on bi-enzymes, namely, glutamate oxidase (GluOx) and aspartate transaminase (AST), which were physisorbed on copolymer reduced graphene oxide (P-rGO), referred to as enzyme nanosheets (GluOx-ASTENs). The GluOx-ASTENs were drop casted onto a Prussian blue electrodeposited screen-printed carbon electrode (PB/SPCE). The proposed biosensor was optimized by operating variables including the enzyme loading amount, coreactant (α-ketoglutarate) concentration, and pH. Under optimal conditions, the biosensor displayed the maximum current responses within 10 s at the low applied potential of -0.10 V vs. the internal Ag/AgCl reference. The biosensor exhibited a linear response from 1.0 to 2.0 mM of aspartate concentrations with a sensitivity of 0.8 µA mM-1 cm-2 and a lower detection limit of approximately 500 µM. Moreover, the biosensor possessed high reproducibility, good selectivity, and efficient storage stability.