Biosensors-Basel
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2026
·Vol. 16
·期 7
·388
·
IF 6.2
Yaning Liang,Shiyi Fang,Zhuoer Chen,Yuzhuo Chen,Qingqing Yang,Xuelan Shu,Tao Le
Gold nanoparticles (AuNPs) are widely used in aptasensors because of their high extinction coefficient and aggregation-dependent color differences. However, recent studies have indicated that nonspecific interactions between target molecules and AuNPs may dominate the detection signal rather than aptamer–target specific binding. This study systematically investigated the interactions between 13 aminoglycoside antibiotics and AuNPs. We found that all aminoglycoside antibiotics interacted strongly with AuNPs, considerably reducing their salt stability. Furthermore, methoxy polyethylene glycol thiol reversed AuNP aggregation induced by aminoglycoside antibiotics, indicating that it occurs at the secondary minimum. Using density functional theory, we analyzed the molecular structures and charge distribution characteristics of the aminoglycoside antibiotics, elucidating that they replace citrate ions on AuNP surfaces via a ligand exchange mechanism, thereby inducing aggregation. Additionally, both aptamer targets and complementary DNA struggled to desorb the aptamer (KAN6-1) from the AuNP surfaces. Our study demonstrates that the label-free colorimetric assay based on aggregation of unmodified citrate–AuNPs is neither suitable for characterizing the binding affinity of aminoglycoside aptamers nor viable for constructing corresponding colorimetric sensors to detect this class of antibiotics. Thus, researchers should incorporate mechanistic verification and rigorous controls when employing this system to ensure reliable results.
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ANALYTICAL CHEMISTRY
·
2026
·
IF 7.3
Liang Zhu,Lejun Liao,Yan Huang,Zhou Nie,Chunyang Lei
The highly sensitive analysis of small-molecule targets holds profound significance across diverse fields, ranging from clinical diagnosis and environmental monitoring to food safety. Herein, we developed a label-free electrochemical CRISPR platform gated by allosteric transcription factors (aTFs) for the ultrasensitive detection of various small molecules. In this system, the specific binding of target analytes to their cognate aTFs induces the release of programmable DNA adaptors, which subsequently trigger Cas12a to trans-cleave DNA probes anchored to the electrode surface. Consequently, the truncated DNA probes serve as initiators to form electroactive G-quadruplex/hemin complexes in situ via terminal deoxynucleotidyl transferase (TdT)-mediated elongation, generating a robust electrochemical response signal. Using TetR as a model aTF, this integrated electrochemical CRISPR biosensor achieved tetracycline detection with picomolar sensitivity. Furthermore, the versatility of this platform was demonstrated by extending its application to p-hydroxybenzoic acid and copper ions through the simple substitution of the aTF modules. The practical utility of the assay was further demonstrated by the robust detection of tetracycline in complex matrices such as milk. Ultimately, this study not only provides a novel strategy for constructing universal, label-free electrochemical CRISPR platforms but also paves the way for the sensitive detection of low-abundance non-nucleic acid targets.
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IMMUNOLOGY
·
2026
·
IF 5.4
Sisi Zhang,Zhou Jingxiang,Caixia Tan,Yuanyuan Xiao,Ju Zou,Biyue Tian,Anhua Wu,Chunhui Li
Clostridioides difficile infection (CDI) remains a major cause of antibiotic-associated colitis and is characterized by excessive intestinal inflammation, epithelial barrier disruption and impaired mucosal repair. Although sodium butyrate (NaB), a microbiota-derived short-chain fatty acid, has demonstrated anti-inflammatory and barrier-protective properties, the immunological mechanisms underlying its protective effects during CDI remain incompletely understood. In this study, we investigated the role of NaB in regulating macrophage polarization and epithelial repair using murine CDI models, primary bone marrow-derived macrophages, THP-1-derived macrophages, Caco-2 epithelial cells and macrophage–epithelial co-culture systems. NaB treatment significantly alleviated CDI-associated weight loss, colonic shortening, histopathological injury and inflammatory cytokine production while restoring epithelial barrier integrity and tight junction protein expression. Mechanistically, NaB promoted macrophage polarization towards an anti-inflammatory M2 phenotype, characterized by increased CD206 and IL-10 expression and reduced CD86 and IL-1β expression. These immunomodulatory effects were accompanied by suppression of PI3K/Akt/mTOR signalling in both colonic tissues and macrophages. Pharmacological inhibition and activation studies further supported the involvement of this pathway in NaB-mediated macrophage reprogramming. Importantly, conditioned medium from NaB-treated macrophages enhanced epithelial viability, migration and barrier-associated protein expression, whereas IL-10 neutralization partially abolished these protective effects, highlighting a critical role for macrophage–epithelial crosstalk. Collectively, our findings demonstrate that low-dose NaB protects against CDI-induced intestinal injury through coordinated regulation of macrophage polarization and epithelial barrier repair, at least in part via modulation of PI3K/Akt/mTOR signalling. These results identify NaB as a promising host-directed therapeutic strategy for CDI and provide new insights into microbiota-derived metabolite–immune interactions during intestinal inflammation.
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Cell Chemical Biology
·
2026
·
IF 9
Hanzhong Feng,Hang Xu,Zhuangzhuang Chu,Xuelin Li,Jun Hou,Jiarong Wang,Hang Xu,Haonan Cao,Wei Ming,Hao Yang,Xinxiang Lei,Yong-Xing He
RiPP structural complexity is significantly expanded by multinuclear non-heme iron-dependent oxidative enzymes (MNIOs). Here, we characterize pseudoprobactin 1 and 2, two MNIO-modified proteins from Pseudomonas protegens Pf-5. Using MS, NMR, and X-ray crystallography, we show that the PbnBC converts precursor cysteines into 5-thiooxazoles. While the precursors feature an N-terminal signal peptide and an intramolecular disulfide, both are dispensable for catalysis. Instead, residues downstream of the target cysteines are the primary determinants of substrate recognition. Furthermore, PbnB2C2 modifies multiple sites in a strictly ordered, stepwise manner. Functionally, pseudoprobactins coordinate Cu 2+ , enhancing bacterial fitness under chlorite-induced oxidative stress. This work establishes 5-thiooxazole as a widespread MNIO-mediated modification, defines its biosynthetic logic, and reveals a role for MNIO-modified proteins in bacterial oxidative stress defense.
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APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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2026
·
IF 4.2
Haiqin Meng,Shun Pan,Zening Chai,Lixiang Zhou,Tianyu Zheng,Hanyu Zhang,He Fu,Lei Zou,Dongqi Liu,Jingcheng Dai,Dazhong Yan,Hong-Jun Chao
The catabolism of the priority environmental pollutant 2,4-xylenol requires bacteria to oxidize its ortho-methyl group. Its exact biochemical mechanism is uncharacterized until now. In this study, we resolve key metabolic bottlenecks in Pseudomonas putida NCIMB 9866. We demonstrate that functionally redundant Rieske oxygenase systems ensure the robust ortho-methyl oxidation of 2,4-xylenol. On the para-methyl oxidation branch, PchA2 acts as the main aldehyde dehydrogenase. It shows significantly higher catalytic efficiency than the previously reported PchA. Additionally, we characterized PmmA1B1, a newly identified three-component Rieske oxygenase system responsible for ortho-methyl oxidation, which is supported by two redundant isoenzymes (PmmA2B2 and PmmA3B3), by recruiting the shared endogenous ferredoxin Orf05169. The PmmA1B1-Orf05169 system catalyzes the successive oxidation of the ortho-methyl group of 4-hydroxy-3-methylbenzoate to a carboxyl group, yielding the high-value pharmaceutical precursor 4-hydroxyisophthalate. Structural and kinetic data revealed that the active site architecture of PmmA1 enables efficient successive oxidation, distinguishing it from isoenzymes PmmA2B2 and PmmA3B3 that, when coupled with Orf05169, catalyze only incomplete oxidation. Overall, these results complete the 2,4-xylenol catabolic pathway by defining the enzymes required for both para- and ortho-methyl oxidation. They also reveal functional redundancy as an adaptive feature of microbial aromatic degradation and establish Rieske oxygenases as biocatalysts for converting methylated aromatic pollutants into value-added chemicals.
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BIOELECTROCHEMISTRY
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2026
·
IF 4.9
Hua Ma,Xia Gu,Hao Yang,Qiuyan Lan,Dandan Wang,Yu Huang,Yanru Fan
Misuse of kanamycin in animal husbandry has led to serious food safety issues. In this study, a label-free electrochemical aptasensor based on the base mismatch and strand displacement was developed for detection of kanamycin residue in agricultural products. A novel ferrocene-naphthalimide derivative was employed as the electroactive indicator. The effects of complementary DNA (cDNA) probe length, position and number of mismatched bases in aptamer-cDNA duplex on the performance of displacement-based aptasensor were systematically investigated. The experimental results were in well accordance with the molecular simulation results. Under optimal conditions, the aptasensor exhibited good reproducibility, stability, selectivity, and a wide linear range of 1.0 × 10 −10 –1.0 × 10 −4 g/mL, with a LOD of 1.1 × 10 −11 g/mL (S/N = 3). The proposed aptasensor was used to detect kanamycin residues in milk and chicken liver. Satisfactory recoveries and relative standard deviations indicated that the aptasensor was competent for detection of kanamycin residues in agricultural products.
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ANALYTICAL CHEMISTRY
·
2026
·
IF 6.7
Xiao Lian,Fang Chen,Yuchen Li,Ruilong Zhang,Helin Niu,Zhongping Zhang
Residual kanamycin from veterinary use poses a persistent threat to environmental safety and public health, as its accumulation in water systems and animal-derived foods can foster antibiotic resistance and induce toxic effects. To address the urgent need for on-site monitoring, we developed mechanically robust, self-healing, dual-network hydrogels (Gel-1 and Gel-2) coordinated with lanthanide ions (Eu3+ and Tb3+). The hydrogels exhibit tunable porosity, mechanical robustness, and autonomous damage recovery, making them ideal for field use. Upon interaction with kanamycin, the tailored ligands trigger distinct fluorescence responses via ligand-to-lanthanide energy transfer, as confirmed by experimental and theoretical studies. We designed a hierarchical detection strategy integrating four complementary modes: (1) single-emission turn-on fluorescence for coarse screening; (2) self-calibrated ratiometric sensing for improved accuracy; (3) machine learning-assisted full-spectrum analysis for high-precision quantification; and (4) smartphone-based colorimetric detection for equipment-free on-site use. This multimodal sensor achieves a remarkable detection limit of 0.950 ppm and a broad dynamic range of 1–5000 μM. The synergy between material design and data science underscores the potential of intelligent hydrogel sensors for monitoring antibiotic residues in food and environmental safety.
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Processes
·
2026
·Vol. 14
·期 7
·1051
·
IF 3.4
Sipeng Yang,Zhikai Liu,Junbing Tao,Fengxu Xiao,Guiyang Shi,Youran Li
This study employed near-infrared (NIR) spectroscopy for real-time spectral acquisition of fermentation broth in lab-scale bioreactors, comparing the performance of transflectance and transmission sensors through glucose modeling and prediction while optimizing modeling approaches. The results demonstrated superior adaptability of transflectance sensors in fermentation environments: in conventional fermentation, glucose models exhibited lower errors (RMSEC = 4.087 g/L, RMSEV = 9.829 g/L) compared to transmission sensors (RMSEC = 5.972 g/L, RMSEV = 10.904 g/L), with significantly higher predictive performance (RPD = 3.735 vs. 2.369), indicating enhanced fitting accuracy and stability. In complex natural media containing peptone and yeast extract, transmission sensor performance deteriorated dramatically due to turbidity interference (R2cal= 0.134), whereas transflectance sensors maintained robust performance (R2cal= 0.993), confirming their adaptability to complex matrices. Regarding modeling strategies, the 1550–1700 nm spectral region demonstrated optimal feature extraction capability (RMSEC = 3.269 g/L, R2cal= 0.987). Basic preprocessing methods such as the moving average smoothing method have become the preferred preprocessing methods, as they strike a balance between calibration and prediction performance. Outlier removal analysis revealed that moderate elimination of 12 high-error samples (accounting for 30% of the total 39 samples) reduced RMSEC to 1.441 g/L and improved R2cvto 0.996, optimizing model performance; however, excessive removal of outlier samples degraded model capability, necessitating judicious sample selection. For fixed total sample sizes, calibration sets comprising 70–80% of samples yielded more reliable predictions. In conclusion, transflectance sensors demonstrate superior compatibility with multicomponent fermentation systems. Combined with wavelength selection, moving average preprocessing, and rational sample removal and partitioning strategies, this approach provides an effective solution for NIR-based online glucose monitoring.
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ANALYTICA CHIMICA ACTA
·
2026
·
IF 6.1
Jiawei Bian,Shixin Cai,Xin Chen,Xiaoli Wang,Yuting Zhang,Nandi Zhou
Background The widespread antibiotic residues pose significant risks for public health, food and environmental safety, necessitating rapid on-site monitoring tools, while conventional methods for antibiotics detection often rely on complex instrumentation, limiting their field applicability. This study presented a versatile portable aptasensor utilizing pseudoisocyanine (PIC) fluorescent dye for different antibiotics detection. The sensing mechanism was based on target-induced displacement of the dye from the aptamer-dye complex, resulting in fluorescence quenching. The interactions among PIC, aptamer and antibiotics were investigated and discussed. Results The biosensing system using a microplate reader was optimized for detection of vancomycin (VAN), oxytetracycline (OTC) and kanamycin (KAN) using their corresponding aptamers, achieving the detection limits of 88.3 nM, 187.0 nM and 316.3 nM, respectively. Subsequently, the assay was integrated with a customized 3D-printed device with smartphone-based readout, enabling on-site quantitative detection with acceptable performance for field applications compared to the microplate reader-based detection. The biosensor demonstrated highly specific and accurate detection of the three antibiotics in spiked lake water and milk samples, with the recoveries ranging from 93.24% to 106.54%. Meanwhile, the reasons for the significant difference in the performance of fluorescent biosensors employing different targets/aptamers were preliminarily discussed. Significance This label-free assay together with the rationally designed portable device provide a cost-effective, instrument-free, and user-friendly platform for rapid monitoring of antibiotic residues in resource-limited settings, while the mechanism discussion may instruct the design of fluorescent aptasensors.
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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
·
2026
·
IF 6.7
Bingbing Liu,Lin Jiang,Lvyang Lin,Wulong Yang,Mian Li,Jianping Lin,Yiqi Jiang,Zehua Bao,Mianbin Wu
Xylitol is industrially synthesized by d-xylose, which is more expensive than glucose. However, de novo xylitol biosynthesis from glucose remains challenging in Escherichia coli. To address these challenges, this study first developed a biosynthetic pathway from glucose via an arabitol intermediate with arabitol phosphate dehydrogenase (APDH). Chassis optimization through knocking out key genes (rpiA/B, pgi, tktA, tktB, xylB) enhanced flux and increased arabitol yield to 1.61 g/L. Subsequently, the arabitol-to-xylitol route was established using arabitol dehydrogenase (ArDH2) and xylitol dehydrogenase (XDH1) enzymes, showing a 52.1% conversion rate in vitro. The heterologous AXA module (APDH, ArDH2, XDH1) was multicopy integrated into the optimized chassis W3P-5ΔB. The strain W3P4A produced 5.04 g/L arabitol and 1.89 g/L xylitol in shake-flasks. Fed-batch fermentation with a plasmid-carrying strain achieved 5.11 g/L xylitol and 18.5% (g/g) yield from glucose. This work establishes a new platform for xylitol bioproduction from glucose and provides a foundational framework for industrial-scale implementation.
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ANALYTICA CHIMICA ACTA
·
2026
·
IF 6.1
Jiacheng Dong,Yu Zhang,Yanhua Rao,Jiabao Yang,Duoshuang Xu,Yongteng Long,Ying Liu,Nannan Liu
The ultrasensitive detection of kanamycin is important for acidic-condition analytical sensing. However, pH variations in acidic samples often trigger significant background interference, leading to false positive or negative results. In this study, a machine learning-assisted dual-probe nanoconfined sensor (KBA&C4/SiNWs/GMP) was developed for the precise identification of kanamycin under acidic fluctuations. By co-functionalizing a glass micropipette (GMP) filled with silica nanowires (SiNWs) with a kanamycin-binding aptamer (KBA) and a proton-responsive DNA strand (C4 DNA), the sensing interface integrates target recognition with pH-responsive interfacial regulation. To enhance recognition reliability, machine learning algorithms, including Support Vector Machine (SVM), K-Nearest Neighbors (KNN), and Linear Discriminant Analysis (LDA), were employed to classify the ionic current responses. The machine learning models accurately classified concentration-dependent ionic current responses despite signal variations caused by acidity fluctuations, enabling the sensor to maintain a low limit of detection (7.31 fM) and a high classification accuracy (94.17%) in acidic matrices. This work provides a promising strategy for reliable kanamycin detection in acidic and complex sample environments.
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Analysis & Sensing
·
2026
·Vol. 6
·期 5
·e70116
·
IF 3.3
Keren Chen,Lingyun Wang,Qingfang Zheng,Longjiao Zhu,Liangjuan Zhao,Wenjie Zheng,Wentao Xu
Kanamycin residues pose potential risks to food safety and public health, highlighting the need for rapid, low-cost, and sensitive detection methods. However, developing label-free aptasensors that integrate target recognition and signal output remains challenging. Herein, a label-free fluorescent aptasensor was developed using a SMART-derived fluorescent aptamer and a competitive-equilibrium biosensing mechanism. The fluorescent aptamer MC-DA-LG was employed as an integrated signal-output and kanamycin-responsive aptamer module. MC-DA-LG generated a fluorescence signal upon binding to the fluorescent molecule, whereas the addition of kanamycin resulted in a concentration-dependent fluorescence decrease, suggesting a shift in the aptamer–dye binding equilibrium. Circular dichroism spectroscopy indicated conformational changes in MC-DA-LG upon the addition of kanamycin or malachite green, while molecular docking suggested partially overlapping binding regions for the two small molecules, collectively supporting the proposed mechanism. Under optimized conditions, the biosensor showed a linear response from 0.1 to 10 μM, with an ultralow detection limit of 400 pM. Moreover, the biosensor exhibited favorable selectivity over other antibiotics and satisfactory recoveries of 94.1%–97.3% in milk and fetal bovine serum samples. This simple, low-cost, rapid, and ultrasensitive assay enables direct fluorescence detection without labeling, immobilization, or complex procedures, demonstrating the potential of SMART-tailored fluorescent aptamers for integrated label-free biosensing of kanamycin. Graphical A SMART-derived fluorescent aptamer was designed as an integrated recognition and signal-output module for label-free kanamycin detection. The aptamer first binds malachite green to generate fluorescence, while kanamycin disrupts the aptamer–dye equilibrium through competitive interaction, producing a measurable signal change. This rapid and low-cost biosensor enables sensitive kanamycin detection in milk and FBS samples.
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