Computational Analysis of T-Cell Receptor Repertoire Workflow: From T-Cell Isolation to Bioinformatics Analysis.

The T-cell receptor (TCR) is the key molecule involved in the adaptive immune response. It is generated by the V(D)J recombination, responsible of the enormous diversity of the TCR repertoire, a crucial feature determining the individual capability to response to antigens and to build immunological memory. A pivotal role in the recognition of antigen is played by the hypervariable complementarity-determining region 3 (CDR3) of the V-beta chain of TCR. Investigating the CDR3 supports the understanding of the adaptive immune system dynamics in physiological processes, such as immune aging, and in disease, especially autoimmune disorders in which T cells are main actors. High-throughput sequencing (HTS) paved the way for a great progress in the investigation of TCR repertoire, enhancing the read depth in the process of library generation of sequencing and the number of samples that can be analyzed simultaneously. Therefore, the leverage of big datasets stressed the need to develop computational approach, by bioinformatics, to unravel the characteristics of the TCR repertoire.

Formation of self-assembled fibril aggregates of trypsin-controllably hydrolyzed soy protein and its regulation on stability of high internal phase Pickering emulsions.

The mechanisms of trypsin hydrolysis time on the structure of soy protein hydrolysate fibril aggregates (SPHFAs) and the stability of SPHFAs-high internal phase Pickering emulsions (HIPPEs) were investigated. SPHFAs were prepared using soy protein hydrolysate (SPH) with different trypsin hydrolysis time (0 min-120 min) to stabilize SPHFAs-HIPPEs. The results showed that moderate trypsin hydrolysis (30 min, hydrolysis degree of 2.31 %) induced SPH unfolding and increased the surface hydrophobicity of SPH, thereby promoting the formation of flexible SPHFAs with maximal thioflavin T intensity and ζ-potential. Moreover, moderate trypsin hydrolysis improved the viscoelasticity of SPHFAs-HIPPEs, and SPHFAs-HIPPEs remained stable after storage at 25 °C for 80 d and heating at 100 °C for 1 h. Excessive trypsin hydrolysis (> 30 min) decreased the stability of SPHFAs-HIPPEs. In conclusion, moderate trypsin hydrolysis promoted the formation of flexible SPHFAs with high surface charge by inducing SPH unfolding, thereby promoting the stability of SPHFAs-HIPPEs.

Computational Toxicology Methods in Chemical Library Design and High-Throughput Screening Hit Validation.

The discovery of molecular toxicity in a clinical drug candidate can have a significant impact on both the cost and timeline of the drug discovery process. Early identification of potentially toxic compounds during screening library preparation or, alternatively, during the hit validation process is critical to ensure that valuable time and resources are not spent pursuing compounds that may possess a high propensity for human toxicity. This report focuses on the application of computational molecular filters, applied either pre- or post-screening, to identify and remove known reactive and/or potentially toxic compounds from consideration in drug discovery campaigns.

In Vitro Cell-Based MTT and Crystal Violet Assays for Drug Toxicity Screening.

The development of novel drug candidates is a current challenge in pharmacology where therapeutic benefits must exceed side effects. Toxicology testing is therefore a fundamental step in drug discovery research. Herein, we describe the first line of toxicology testing program, consisting in cell-based high-throughput screening assays, which have the advantage of being easy, rapid, cheap, and reproducible while providing quantitative information. We illustrate MTT and Crystal Violet assays, two common colorimetric tests able to assess both cytostatic and cytotoxic effects, respectively, of a drug candidate. MTT assay allows evaluation of cellular metabolic activity, by which cell viability can be inferred; Crystal Violet staining is directly correlated with attached viable cells, thus allowing direct assessment of cell survival and death. Therefore, combination of the two methodologies represents a useful tool for predicting drug sensitivity and efficacy, the first milestones in pre-clinical toxicology workflow.

Binding and distribution regularity of water molecules in high-moisture textured Antarctic krill (Euphausia superba) meat.

High-moisture extrusion technique with the advantage of high efficiency and low energy consumption is a promising strategy for processing Antarctic krill meat. Consequently, this study aimed to prepare high-moisture textured Antarctic krill meat (HMTAKM) with a rich fiber structure at different water contents (53 %, 57 %, and 61 %) and to reveal the binding and distribution regularity of water molecules, which is closely related to the fiber structure of HMTAKM and has been less studied. The hydrogen-bond network results indicated the presence of at least two or more types of water molecules with different hydrogen bonds. Increasing the water content of HMTAKM promoted the formation of hydrogen bonds between the water molecules and protein molecules, leading to the transition of the ß-sheet to the α-helix. These findings offer a novel viable processing technique for Antarctic krill and a new understanding of the fiber formation of high-moisture textured proteins.

Partition coefficient screening - An effective approach for finding the best conditions for byproduct removal as demonstrated by a bispecific antibody purification case.

In recombinant protein purification, differences in isoelectric point (pI)/surface charge and hydrophobicity between the product and byproducts generally form the basis for separation. For bispecific antibodies (bsAbs), in many cases the physicochemical difference between product and byproducts is subtle, making byproduct removal considerably challenging. In a previous report, with a bsAb case study, we showed that partition coefficient (Kp) screening for the product and byproducts under various conditions facilitated finding conditions under which effective separation of two difficult-to-remove byproducts was achieved by anion exchange (AEX) chromatography. In the current work, as a follow-up study, we demonstrated that the same approach enabled identification of conditions allowing equally good byproduct removal by mixed-mode chromatography with remarkably improved yield. Results from the current and previous studies proved that separation factor determination based on Kp screening for product and byproduct is an effective approach for finding conditions enabling efficient and maximum byproduct removal, especially in challenging cases.

Characterization of Foodborne Pathogens in Biofilms: A Four-Dimensional Structural Dynamics Approach Using HCS-CLSM.

The functional properties of biofilms are intimately related to their spatial architecture. Structural data are therefore of prime importance to dissect the complex social and survival strategies of biofilms and ultimately to improve their control. Confocal laser scanning microscopy (CLSM) is the most widespread microscopic tool to decipher biofilm structure, enabling noninvasive three-dimensional investigation of their dynamics down to the single-cell scale. The emergence of fully automated high content screening (HCS) systems, associated with large-scale image analysis, has radically amplified the flow of available biofilm structural data. In this contribution, we present a HCS-CLSM protocol used to analyze biofilm four-dimensional structural dynamics at high throughput. Meta-analysis of the quantitative variables extracted from HCS-CLSM will contribute to a better biological understanding of biofilm traits.

Modular, Scalable, and Customizable LC-HRMS for Exposomics.

In this chapter, we describe a multi-purpose, reversed-phase liquid chromatography-high-resolution mass spectrometry (LC-HRMS) workflow for acquiring high-quality, non-targeted exposomics data utilizing data-dependent acquisition (DDA) combined with the use of toxicant inclusion lists for semi-targeted analysis. In addition, we describe expected retention times for >160 highly diverse xenobiotics in human plasma and serum samples. The method described is intended to serve as a generic LC-HRMS exposomics workflow for research and educational purposes. Moreover, it may be employed as a primer, allowing for further adaptations according to specialized research needs, e.g., by including reference and/or internal standards, by expanding to data-independent acquisition (DIA), or by modifying the list of compounds prioritized in fragmentation experiments (MS2).

Stable Isotope Tracing Experiments Using LC-MS.

Metabolomics has emerged as a pivotal field in understanding cellular function, particularly in the context of disease. In numerous diseases, including cancer, alterations in metabolism play an essential role in disease progression and drug response. Hence, unraveling the metabolic rewiring is of importance to find novel diagnostic and therapeutic strategies. Isotope tracing is a powerful technique for delving deeper into the metabolic wiring of cells. By tracking an isotopically labeled substrate through biochemical reactions in the cell, this technique provides a dynamic understanding of cellular metabolism. This chapter outlines a robust isotope tracing protocol utilizing high-resolution mass spectrometry coupled to liquid chromatography in cell culture-based models. We cover essential aspects of experimental design and analyses, providing a valuable resource for researchers aiming to employ isotopic tracing.

Quantification of Total Ketone Bodies in Biological Matrices Using Stable Isotope-Labeled Internal Standards and RP-UHPLC-MS/MS.

Acetoacetate (AcAc) and D-beta-hydroxybutyrate (D-ßOHB), the two major ketone bodies found in circulation, are linked to multiple physiological and pathophysiological states. Therefore, analytical methodologies surrounding the quantification of total ketone body (TKB) concentrations in biological matrices are paramount. Traditional methods to quantify TKBs relied on indirect spectrophotometric assays with narrow dynamic ranges, which have been significantly improved upon by modern mass spectrometry (MS)-based approaches. However, the lack of stable isotope-labeled internal standards (ISs) for AcAc and the need to distinguish D-ßOHB from its closely related structural and enantiomeric isomers pose significant obstacles. Here, we provide a protocol to synthesize and quantify a [13C] stable isotope-labeled IS for AcAc, which, in conjunction with a commercially available [2H] stable isotope-labeled IS for ßOHB, allows TKBs to be measured across multiple biological matrices. This rapid (7 min) analysis employs reverse phase ultra-high performance liquid chromatography (RP-UHPLC) coupled to tandem MS (MS/MS) to distinguish ßOHB from three structural isomers using parallel reaction monitoring (PRM), providing excellent specificity and selectivity. Finally, a method is provided that distinguishes D-ßOHB from L-ßOHB using a simple one-step derivatization to produce the corresponding diastereomers, which can be chromatographically resolved using the same rapid RP-UHPLC separation with new PRM transitions. In summary, this method provides a rigorous analytical pipeline for the analysis of TKBs in biological matrices via leveraging two authentic stable isotope-labeled ISs and RP-UHPLC-MS/MS.

Reversed-Phase Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry Method for High-Throughput Lipidomic Quantitation.

Reversed-phase ultrahigh-performance liquid chromatography-mass spectrometry (RP-UHPLC/MS) method is optimized for the quantitation of a large number of lipid species in biological samples, primarily in human plasma and serum. The method uses a C18 bridged ethylene hybrid (BEH) column (150 × 2.1 mm; 1.7 µm) for the separation of lipids from 23 subclasses with a total run time of 25 min. Lipid species separation allows the resolution of isobaric and isomeric lipid forms. A triple quadrupole mass spectrometer is used for targeted lipidomic analysis using multiple reaction monitoring (MRM) in the positive ion mode. Data are evaluated by Skyline software, and the concentrations of analytes are determined using internal standards per each individual lipid class.

Rapid Lipid Mediator Profiling by Convergence Chromatography-MS/MS.

Bioactive lipid mediators derived from arachidonic acid constitute an attractive pool of metabolites that reflect cellular function and signaling, as well as potential biomarkers that may respond quantitatively to disease progression or pharmacological treatment. Their quantitative measurement in biological samples is complicated by the number of isomers that share common structural features, which are not easily distinguished by immunoassays or reverse phase chromatography-tandem mass spectrometry. Here, we present a method that enables the rapid analysis of a panel of over 25 biologically important eicosanoids in a 96-well format for cell culture supernatants, plasma, and organ tissues using convergence chromatography-tandem mass spectrometry to resolve these analytes of interest.

Recommendations for Accurate Lipid Annotation and Semi-absolute Quantification from LC-MS/MS Datasets.

Recent developments in LC-MS instrumentation and analytical technologies together with bioinformatics tools supporting high-throughput processing of large omics datasets significantly enhanced our capabilities and efficiency of identification and quantification of lipids in diverse biological materials. However, each biological matrix is characterized by its unique lipid composition, thus requiring optimization of analytical and bioinformatics workflows for each studied lipidome. Here, we describe an integrated workflow for deep lipidome profiling, accurate annotation, and semi-absolute quantification of complex lipidomes based on reversed phase chromatography and high resolution mass spectrometry. This chapter provides details on selection of the optimal extraction protocol, acquisition of LC-MS/MS data for accurate annotation of lipid molecular species, and design of lipidome-specific mixtures of internal standards to assist quantitative analysis of complex, native lipidomes.

Ultrahigh-Performance Supercritical Fluid Chromatography-Mass Spectrometry in the Clinical Lipidomic Analysis.

Ultrahigh-performance supercritical fluid chromatography-mass spectrometry (UHPSFC/MS) method is optimized for the high-throughput quantitation of lipids in human serum and plasma with an emphasis on robustness and accurate quantitation. Bridged ethylene hybrid (BEH) silica column (100 × 3 mm; 1.7 µm) is used for the separation of 17 nonpolar and polar lipid classes in 4.4 min using the positive ion electrospray ionization mode. The lipid class separation approach in UHPSFC/MS results in the coelution of all lipid species within one lipid class in one chromatographic peak, including two exogenous internal standards (IS) per lipid class, which provides the optimal conditions for robust quantitation. The method was validated according to European Medicines Agency and Food and Drug Administration recommendations. UHPSFC/MS combined with LipidQuant software allows a semiautomated process to determine lipid concentrations with a total run time of only 8 min including column equilibration, which enables the analysis of 160 samples per day.

Self-assembled high-entropy Prussian blue analogue nanosheets enabling efficient sodium storage.

High entropy material (HEM) has emerged as an appealing material platform for various applications, and specifically, the electrochemical performances of HEM could be further improved through self-assembled structure design. However, it remains a big challenge to construct such high-entropy self-assemblies primarily due to the compositional complexity. Herein, we propose a bottom-up directional freezing route to self-assemble high-entropy hydrosols into porous nanosheets. Taking Prussian blue analogue (PBA) as an example, the simultaneous coordination-substitution reactions yield stable high-entropy PBA hydrosols. During subsequent directional freezing process, the anisotropic growth of ice crystals could guide the two-dimensional confined assembly of colloidal nanoparticles, resulting in high-entropy PBA nanosheets (HE-PBA NSs). Thanks to the high-entropy and self-assembled structure design, the HE-PBA NSs manifests markedly enhanced sodium storage kinetics and performances in comparison with medium/low entropy nanosheets and high entropy nanoparticles.

Strain engineering of PtMn alloy enclosed by high-indexed facets boost ethanol electrooxidation.

Surface strain engineering has proven to be an efficient strategy to enhance catalytic properties of platinum (Pt)-based catalysts for electrooxidation reactions. Herein, the S-doped PtMn concave cubes (CNCs) enclosed with high index facets (HIFs) and regulatable surface strain are successfully fabricated by two steps hydrothermal method. The S element with electrophilic property can modify the near-surface of PtMn nanocrystals, altering the electronic structure of Pt to effectively regulate the adsorption/desorption of intermediates in the ethanol electrooxidation reaction (EOR). The PtMnS1.1 catalyst with optimal surface strain delivered extraordinary catalytic performance on EOR in acidic media, with a specific activity of 2.88 mA/cm2 and mass activity of 1.10 mA/µgPt, which is 4.1 and 2.2 times larger than that of state-of-the-art Pt/C catalyst, respectively. Additionally, the PtMnS1.1 catalyst also achieve excellent catalytic properties in alkaline electrolyte for EOR. The results of kinetic studies indicated that the surface strain and modified electronic structure can degrade the activation energy barrier during the process of EOR, which is beneficial for enhance the reaction rate. This work provides a promising approach to construct highly efficient electrocatalysts with tunable surface strain effects for clean energy electro-chemical reactions.

Regulating the zinc ion transport kinetics of Mn3O4 through copper doping towards high-capacity aqueous Zn-ion battery.

High working voltage, large theoretical capacity and cheapness render Mn3O4 promising cathode candidate for aqueous zinc ion batteries (AZIBs). Unfortunately, poor electrochemical activity and bad structural stability lead to low capacity and unsatisfactory cycling performance. Herein, Mn3O4 material was fabricated through a facile precipitation reaction and divalent copper ions were introduced into the crystal framework, and ultra-small Cu-doped Mn3O4 nanocrystalline cathode materials with mixed valence states of Mn2+, Mn3+ and Mn4+ were obtained via post-calcination. The presence of Cu acts as structural stabilizer by partial substitution of Mn, as well as enhance the conductivity and reactivity of Mn3O4. Significantly, based on electrochemical investigations and ex-situ XPS characterization, a synergistic effect between copper and manganese was revealed in the Cu-doped Mn3O4, in which divalent Cu2+ can catalyze the transformation of Mn3+ and Mn4+ to divalent Mn2+, accompanied by the translation of Cu2+ to Cu0 and Cu+. Benefitting from the above advantages, the Mn3O4 cathode doped with moderate copper (abbreviated as CMO-2) delivers large discharge capacity of 352.9 mAh g-1 at 100 mA g-1, which is significantly better than Mn3O4 (only 247.8 mAh g-1). In addition, CMO-2 holds 203.3 mAh g-1 discharge capacity after 1000 cycles at 1 A g-1 with 98.6 % retention, and after 1000 cycles at 5 A g-1, it still performs decent discharge capacity of 104.2 mAh g-1. This work provides new ideas and approaches for constructing manganese-based AZIBs with long lifespan and high capacity.

Empowering lithium-ion storage: unveiling the superior performance of niobium-based oxide/perovskite heterojunction with built-in electric field.

The increasing demand for high-performance electrode materials in lithium-ion batteries has driven significant attention towards Nb2O5 due to its high working voltage, large theoretical capacity, environmental friendliness, and cost-effectiveness. However, inherent drawbacks such as poor electrical conductivity and sluggish electrochemical reaction kinetics have hindered its lithium storage performance. In this study, we introduced KCa2Nb3O10 into Nb2O5 to form a heterojunction, creating a built-in electric field to enhance the migration and diffusion of Li+, effectively promoting electrochemical reaction kinetics. Under the regulation of the built-in electric field, the charge transfer resistance of the KCa2Nb3O10/Nb2O5 anode decreased by 3.4 times compared to pure Nb2O5, and the Li+ diffusion coefficient improved by two orders of magnitude. Specifically, the KCa2Nb3O10/Nb2O5 anode exhibited a high capacity of 276 mAh g-1 under 1 C, retaining a capacity of 128 mAh g-1 even at 100 C. After 3000 cycles at 25 C, the capacity degradation was only 0.012% per cycle. Through combined theoretical calculations and experimental validation, it was found that the built-in electric field induced by the heterojunction interface contributed to an asymmetric charge distribution, thereby improving the rates of charge and ion migration within the electrode, ultimately enhancing the electrochemical performance of the electrode material. This study provides an effective approach for the rational design of high-performance electrode materials.

Interfacial study and modulation of high-voltage layered cathode based all-solid-state batteries.

Employing layered materials as the cathodes for solid-state batteries (SSBs) is vital in enhancing the batteries' energy density, whereas numerous issues are present regarding the compatibilities between cathode electrode and modified solid electrolyte (ME) in this battery configuration. By investigating the electrochemical performance and interfacial properties of SSBs using various cathodes, the fundamental reason for the poor compatibility between layered cathodes, especially LiCoO2 with ME is revealed. Because of the Li(solvent)+ intercalation environments formed in the ME, the resultant weak-interacted TFSI- could be adsorbed and destabilized by Co ions on the surface. Besides, the high energy level offsets between LiCoO2 and ME lead to Li-ion transferring from the bulk electrode to the electrolyte, resulting in a pre-formed interface on the cathode particles before the electric current is applied, affects the formation of effective cathode-electrolyte interface (CEI) film during electrochemical process and deteriorated overall battery performance. From this view, an interlayer is pre-added on the LiCoO2 surface through an electrostatic adsorption method, to adjust the energy level offsets between the cathode and ME, as well as isolate the direct contact of surface Co ions to TFSI-. The cycling properties of the SSB using modified LiCoO2 are greatly enhanced, and a capacity retention of 68.72 % after 100 cycles could be achieved, against 8.28 % previously, certifying the rationality of the understanding and the effectiveness of the proposed modification method. We believe this research could provide basic knowledge of the compatibility between layered cathodes and MEs, shedding light on designing more effective strategies for achieving SSBs with high energy density.

Reinforcing Cd-S bonds through morphology engineering for enhanced intrinsic photocatalytic stability of CdS.

Effectively mitigating photocorrosion is paramount for achieving high-efficiency and sustainable hydrogen production through photocatalytic water splitting over CdS. In this work, we develop a morphology engineering strategy with adjustable Cd-S bond energy through a simple chemical bath deposition method to synthesize novel hollow hemispherical CdS (H-CdS). The morphologic structure CdS can be precisely controlled by adjusting the reaction temperature, time and pH. Compared with common morphologies of CdS, H-CdS, with its reinforced Cd-S bonding, exhibits not only improved photocatalytic hydrogen evolution activity (20.04 mmol/g/h) but also exceptional resistance to photocorrosion, resulting in outstanding cyclic stability even without the aid of cocatalysts or the introduction of other semiconductors. Comprehensive characterizations reveal that the photocorrosion resistance of H-CdS stems from the high Cd-S bond strength. Moreover, in-situ infrared spectroscopy confirms alterations in the properties and activities of the various CdS morphologies after photocatalytic reaction due to photocorrosion. We thoroughly describe the relationship among morphology, surface energy, bond energy and photocorrosion resistance. Our findings present a novel strategy for mitigating the photocorrosion of CdS and offer valuable insights for future research on CdS photocatalysts aimed at stable water splitting.