Global incorporation of synthetic adenosine analogs reveals poly(A)-dependent translation differences in mRNA.

Dragon fruit, also known as pitahaya, has become increasingly popular in Europe and the United States owing to its nutritional value and potential health‐promoting properties. This study describes a patient with anaphylaxis after the ingestion of dragon fruit. We present the case of a patient who experienced a systemic reaction requiring hospitalization 1 h after consuming dragon fruit. His medical history includes allergic rhinitis to Salsola kali pollen. The diagnostic worked‐up included prick‐by‐prick testing with fruits, skin prick testing with aeroallergens, and measurement of specific IgE using ImmunoCAP and ISAC. These tests confirmed sensitization to dragon fruit, several pollens including S. kali, and peach allergens. A protein extract was prepared from dragon fruit pulp. In the protein profile, the most intense bands were observed at 9, 26, and 54 kDa. The patient’s IgE recognized multiple bands ranging from 16 to >100 kDa. Immunoblot inhibition demonstrated cross‐reactivity: S. kali extract almost completely inhibited IgE recognition of dragon fruit proteins, leaving only faint recognition of a 54‐kDa band (identified as catalase), while peach peel extract completely inhibited IgE binding to the dragon fruit extract. In conclusion, sensitization to dragon fruit in this patient was probably due to cross‐reactivity with S. kali and peach allergens. This case highlights the potential risks associated with the introduction of novel foods into the diet, particularly in patients previously sensitized to pollen or other plant‐derived foods.

Protein biomarker detection has considerable potential applications in facilitating rapid, low-cost, point-of-care diagnostics. This can be achieved electrochemically via a redox active surface incorporating a recognition site. Polymelamine (pMel) films exhibit a reversible redox couple at a mild potential. Herein we report the fabrication of a pMel film and subsequent functionalization of the interface by the electrografting of a reactive diazonium-derived layer. This allowed for immobilization of protein recognition sites on the interface enabling the selective electrochemical detection of proteins by observing the attenuation of the pMel redox system. Bovine serum albumin and anti-asparaginase were detected in a linear range of 1–10,000 pM, with limits of detection of 0.42 and 0.32 pM, respectively. The latter is a biomarker of clinical importance in the monitoring of chemotherapy treatment—with its detection demonstrated within the clinically relevant concentration range. The sensor response time was 25 minutes, with the results reproducible over three independent electrodes for each target. Sensor construction was verified using voltammetry, electrochemical impedance spectroscopy, x-ray photoelectron spectroscopy, and scanning electron microscopy. Signal transduction of the sensing interface was observed voltametrically, through attenuation of the pMel redox couple. The versatile, novel, and simple strategy outlined herein can be applied to produce pMel interfaces functionalized with a wide range of functionalities to tailor the interfaces for specific sensing applications.

Electrochemically activated DNA circuit for the amplified and accurate biosensing of cancer cells.

Chimeric antigen receptor (CAR) T cells have robust antitumor activity against hematologic malignancies and have the potential to benefit patients with solid tumors. Immune recognition of murine proteins expressed in adoptively transferred T cells and the lack of homeostatic cytokines in the tumor microenvironment can limit the expansion and persistence of CAR T cells. CARs generated only from human sequences could reduce the risk of immune-mediated rejection, and interleukin 15 (IL15), which promotes T-cell survival and fitness, may improve the expansion and persistence of CAR T cells. In this study, we report a CAR construct (ABBz) assembled from human sequences including a single-chain variable fragment (scFv) specific to alkaline phosphatase, placental-like 2 (ALPPL2). This binder was selected through an unbiased, high-throughput screen of a human antibody-derived, phage-displayed scFv library based on binding specificity, stringency, and low dissociation constant. We demonstrated specificity to the antigen, effective cytolytic function, and cytokine production in ABBz T cells. We showed NK-like effector differentiation with sustained proliferative capacity specific to secreted IL15 coexpression in ABBz T cells. Lastly, we demonstrated that ABBz CAR T cells had robust antitumor activity, which was further enhanced through IL15 coexpression, resulting in NK-like effector differentiation with increased cytotoxicity and superior expansion capacity due to reduced apoptosis of CAR T cells. These results demonstrate that IL15 coexpression can promote effector differentiation while maintaining the proliferative capacity of huALPPL2-CAR T cells and provide a foundation for further clinical development of IL15-coexpressing huALPPL2-CAR T cells in patients.

CRISPR-enhanced ELISA based on ssDNA-triggered Cas13a-Csm6 cascade for sensitive profiling of inflammatory biomarkers in sports-related osteoarthritis among martial arts athletes.

Structural basis of Wnt signalosome extracellular complex assembly.

The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity is thought to be mediated by the recognition of the ubiquitnated protein itself. In addition to their catalytic domain, USPs have one or more auxiliary domains (ADs) with key functions in regulating DUB activity and localization. We hypothesize that some ADs bind short linear motifs (SLiMs) typically found in intrinsically disordered regions of proteins to achieve targeting to substrates and multiprotein complexes. To test this, we systematically assess the potential of 29 USP-ADs and two full-length USPs for SLiM binding using a combination of proteomic-peptide phage display, peptide SPOT arrays and affinity measurements. We discover SLiM-based interactions for 14 ADs from 9 USP-DUBs, including CYLD, USP11, USP19, USP20, USP22 and USP33, and define the consensus motif and properties of the SLiM-AD binding. Interestingly, we establish that the zf-UBP and DUSP2 domains of USP20 and USP33 are SLiM binding ADs with similar binding profiles, explaining the functional redundancy between the two DUBs. Our work reveals unique motifs recognized by the auxiliary domains CAP-Gly, UBL, zf-UBP and DUSP, with potential functional implications for substrate recognition and complex assemblies.

The antioxidant properties of Nickel(II) 5,10,15,20-tetraphenylporphyrin (NiTPP) and Zinc(II) 5,10,15,20-tetrakis(4-methylphenyl)porphyrin (ZnTMPP) were examined using complementary experimental and computational approaches. Radical-scavenging activity was evaluated in the DPPH system by cyclic voltammetry and UV–visible spectroscopy, using α-tocopherol as a benchmark. Electrochemical measurements showed EC50 values of 139.1 ± 1.3 µM for NiTPP and 269.9 ± 4.5 µM for ZnTMPP, while α-tocopherol exhibited an EC50 of 90.99 ± 0.61 µM. In contrast, spectrophotometric analysis yielded EC50 values of 164.1 ± 2.3 µM for NiTPP and 142.1 ± 0.8 µM for ZnTMPP, indicating more efficient radical quenching by ZnTMPP in solution. Both metalloporphyrins displayed stronger binding affinities toward DPPH than α-tocopherol, with NiTPP showing the highest association constant (Kb = 7.49 × 104 L·mol−1; ΔG = −27.95 kJ·mol−1), followed by ZnTMPP (Kb = 3.14 × 104 L·mol−1; ΔG = −25.08 kJ·mol−1). Protein-level interactions relevant to antioxidant regulation were explored through molecular docking and 300 ns molecular dynamics simulations targeting the Keap1 Kelch domain. Both porphyrins occupied the canonical binding site, with NiTPP exhibiting the most favorable docking score (−9.4 kcal·mol−1). Molecular dynamics and MM-GBSA analyses confirmed greater structural stability and stronger binding for the NiTPP–Keap1 complex. These findings highlight a complementary antioxidant behavior, where ZnTMPP favors direct radical scavenging, while NiTPP shows enhanced protein recognition and stabilization.

DNA is not merely a linear code of bases, but a mechanically constrained polymer whose backbone continuity restricts the conformations accessible during protein recognition. Yet, although base-sequence preferences have been extensively mapped across human transcription factor (TF) families, we lack comparable maps of how TFs read backbone continuity and DNA mechanics, leaving these layers of recognition poorly understood. Here we introduce PIC-NIC, a high-throughput platform that uses site-specific backbone nicks to perturb DNA mechanics while preserving base identity and minimizing accompanying chemical changes. Across 15 TFs spanning eight structural families, PIC-NIC reveals a highly position-dependent response to backbone disruption: most positions are permissive, whereas nicking at mechanically sensitive sites can substantially reshape binding. Mechanistic analyses integrating PIC-NIC maps with newly determined TF–DNA structures, structural comparisons, binding kinetics, and molecular simulations show that sensitive positions often coincide with strain-adapted DNA geometries, including Hoogsteen conformations, whose relaxation can enhance binding or rewire sequence specificity. Genomic single-strand breaks and repair maps further suggest that TF retention at nicked DNA may influence local repair-factor accessibility. Together, these findings systematically map DNA backbone mechanics as a position-resolved layer of TF recognition across diverse protein families, showing how this layer can reshape binding specificity and may influence repair-factor accessibility.

A point-of-care test (POCT) based on low-cost and highly sensitive disposable chips was designed for the sensitive and selective detection of proteins. In particular, a pollen-based plasmonic nanostructured probe coupled, for the first time, with biomimetic receptors custom-designed as molecularly imprinted nanoparticles (MIP-NPs) for protein recognition, was developed and interrogated by an extrinsic optical fiber (OF)-based scheme. To this purpose, bovine serum albumin (BSA) was chosen in a proof-of-concept frame as an example of a protein.

Zinc finger proteins are essential for the proper functioning of eukaryotic organisms, while their artificial variants can be used in cancer therapy or gene editing via their specific DNA recognition. Zn(II) binding is indispensable for the structural integrity of zinc fingers. While metal ion binding of zinc fingers has been extensively investigated in vitro, intracellular studies are rather scarce. Herein, we utilized the novel I-Block assay, based on the regulation of β-galactosidase expression via the transcription inhibition ability of zinc finger proteins inside the modified ER1821ΔLacI Escherichia coli cells. The results indicated that the performance of the assay largely depends on the position of the DNA sequence targeted by the zinc finger protein, but once optimized, specific DNA binding of even the rather small three-membered 1MEY# artificial zinc finger protein can be detected without large fusion tags. By fusion of 1MEY# with the nuclease domain of FokI restriction endonuclease leading to an artificial zinc finger nuclease, we demonstrated that the I-Block system can distinguish between DNA binding and DNA cleavage inside the cells allowing for zinc finger nuclease screening. The investigation of metal ion/metalloid-zinc finger protein interactions within cellular conditions provided direct proof for the inhibitory effect of Cd(II), Hg(II), and As(III) on the DNA binding of a zinc finger protein at a molecular level.

Simple, modular platforms for detecting biologically relevant proteins are critical for applications in clinical diagnostics, healthcare, and research. Here, we have combined aptamer-based protein recognition with our conformationally-responsive DNA nanoswitches to enable simple, sensitive and specific protein detection. We demonstrate dual detection of two clinically relevant blood proteins, thrombin and VEGF as initial proof of concept.

Excessive sugar intake remains a major health challenge, motivating the development of safe and effective alternatives. Thaumatin, a natural high-intensity sweet protein, elicits sweetness through activation of the sweet taste receptor (T1R2/T1R3), yet its molecular recognition mechanism remains understudied. An integrated computational strategy combining comparative modeling, protein–protein docking, and 500 ns molecular dynamics simulations (triplicates) was employed to elucidate the thaumatin–receptor binding. Structural modeling identified the closed conformation of the Venus flytrap domain (VFT) as optimal for ligand engagement. Modeling revealed a stable binding interface characterized by electrostatic complementarity and van der Waals interactions, characterized by interfacial contacts of receptors and hydrogen bonding networks. Residue-level energy decomposition highlighted key residues (W418 and E422 of T1R2; S59 of T1R3) and thaumatin residues (K67, R82, and K137) that contribute substantially to complex stabilization, consistent with experimentally reported sweetness determinants. These findings provide molecular-level insight into sweet protein recognition and establish a structural framework for rational engineering of protein-based sweeteners with enhanced potency and selectivity.

Rapid and sensitive detection of H3 AIV HA1 protein using a quantum dot-labeled immunochromatographic strip.

Targeting tau-mitochondrial crosstalk in Alzheimer's disease with an Integrative multi-omics and artificial intelligence driven tools for the development of disease-modifying therapeutics.

The recognition of RAS proteins by LZTR1 shares a conserved mechanism among the GTPase superfamily.

Epitope-imprinted polymers (EIPs) represent an advanced evolution of molecular imprinting technology for selective bacterial recognition. By using short, surface-exposed peptide fragments derived from bacterial proteins rather than whole cells or full-length proteins, EIPs enable the formation of structurally defined and chemically robust recognition cavities with improved accessibility, stability, and reproducibility. To the best of our knowledge, this review provides the first dedicated and focused overview of EIPs in bacterial detection. The fundamental principles of epitope imprinting are discussed, including rational epitope selection, computational modeling, monomer optimization, imprinting strategies (bulk, surface, nanoMIP, and electropolymerization), and template removal approaches. Representative applications targeting clinically significant pathogens such as Mycobacterium leprae, Salmonella Typhi, and Neisseria meningitidis are critically examined, highlighting analytical performance parameters including detection limits, imprinting factors, selectivity in complex biological matrices, and integration with electrochemical and piezoelectric transducers. In addition to summarizing current achievements, this review evaluates practical limitations related to epitope accessibility, matrix interference, fabrication reproducibility, scalability, and hospital-based implementation. Emerging strategies, including AI-assisted epitope design, multiepitope imprinting, nanomaterial-enhanced architectures, and portable point-of-care systems, are discussed as potential solutions to improve robustness and translational applicability. By consolidating current progress and identifying key scientific and technological gaps, this work clarifies the position of EIPs as promising synthetic recognition elements for next-generation bacterial diagnostics in clinical, food safety, and environmental monitoring.

Cyanine dyes have found great applications in bioimaging due to their NIR-emitting capabilities. In this work, six heptamethine cyanine dyes (TEA1-6) were designed, synthesized, and photophysically studied. While they had strong absorption, their fluorescence was quenched in aqueous solutions. The dyes incorporated amide linkages and amino acid moieties, intended to mimic the peptide bonds to potentially improve biological interactions. This hypothesis was tested by examining the potential interactions between the dyes and two common biological proteins, bovine serum albumin (BSA) and human parvalbumin (HPA). Interestingly, the dyes' nonfluorescent behavior in aqueous solutions was reversed upon the addition of the proteins BSA or HPA. This was hypothesized to be due to the binding interactions with these proteins and the disruption of the aggregates formed in aqueous solutions. These findings showed that peptide-like substituents could help promote protein recognition and open the horizon for more implementation in biomedical applications.

Digital immunoassays enable highly sensitive detection of biomolecules, offering absolute quantification rather than relying on bulk signal intensity. We adapt a digital immunoassay scheme for a nanopore sensor, a versatile platform for single-molecule counting. Current nanopore sensors have demonstrated great progress when counting nucleic acids but struggle with proteins due to variability in translocation behavior and limited recognition strategies. While recent advancements have highlighted the promise of nanopore platforms for protein studies, precise quantification remains a challenge. Here, building on previous work, we present a nanopore-based digital immunoassay that employs gold nanoparticle-mediated molecular amplification with a single-molecule readout. This approach translates protein recognition into quantifiable DNA, enabling a precise digital assay. This assay employs a DNA NanoLock probe combined with a paramagnetic bead-based immunocapture, where the target proteins trigger a structural transformation of the NanoLock, converting their presence into a binary DNA-based signal. By incorporating AuNPs carrying hundreds of DNA proxy reporters, we effectively amplify the detectable signal by 2 orders of magnitude, significantly improving sensitivity. We validate the performance of this system by detecting the glial fibrillary acidic protein, a biomarker for traumatic brain injury and neurodegenerative diseases, in plasma samples and demonstrate high femtomolar-level sensitivity (∼40 pg/mL). Using the NanoLock probe, we further mitigate previous challenges, with reduced assay times (hours) and extended dynamic range (3-log). The self-calibrating nature of this digital approach offers robust, reproducible measurements across different nanopores, eliminating interdevice variability.