DIA-based quantitative proteomics analysis of plasma exosomes in rat model of allergic rhinitis
The objective of this study was to quantify the proteomics of plasma exosomes using data independent acquisition (DIA) in combination with liquid chromatography-mass spectrometry (LC-MS/MS) to identify the key proteins involved in the development and progression of AR. In the AR rat model, a total of 41 proteins demonstrated significant up-regulation, while 51 proteins were found to be significantly down-regulated. Gene ontology (GO) analysis results indicated that the altered proteins were highly enriched in cellular regulatory processes and enzymatic activity in AR rats. Kyoto Encyclopedia of Genes and Genomes (KEGG) enr...
Source: Analytical Biochemistry - January 20, 2024 Category: Biochemistry Authors: Ran Ding Zhen Liu Jin Wang Tong Xia Lei Li Source Type: research

Solvent effect on the detection of peptides and proteins by nanoelectrospray ionization mass spectrometry: Anomalous behavior of aqueous 2-propanol
Anal Biochem. 2024 Jan 18;688:115461. doi: 10.1016/j.ab.2024.115461. Online ahead of print.ABSTRACTTo investigate the solvent effect on the detection of peptides and proteins, nanoelectrospray mass spectra were measured for mixtures of 1 % acetic acid and 5 × 10-6 M gramicidin S (G), ubiquitin (U), and cytochrome c (C) in water (W), methanol (MeOH), 1-propanol (1-PrOH), acetonitrile (AcN), and 2-propanol (2-PrOH). Although doubly protonated G (G2+) and multiply protonated U (Un+) and C (Cn+) were readily detected with a wide range of mixing ratios of W solutions for MeOH, 1-PrOH, and AcN, Cn+ was totally suppressed for th...
Source: Analytical Biochemistry - January 20, 2024 Category: Biochemistry Authors: Satoshi Ninomiya Stephanie Rankin-Turner Satoko Akashi Kenzo Hiraoka Source Type: research

Disposable biosensor based on nanodiamond particles, ionic liquid and poly-l-lysine for determination of phenolic compounds
This study describes the development of a highly sensitive amperometric biosensor for the analysis of phenolic compounds such as catechol. The biosensor architecture is based on the immobilization of tyrosinase (Tyr) on a screen-printed carbon electrode (SPE) modified with nanodiamond particles (ND), 1-butyl-3-methylimidazolium hexafluorophosphate (IL) and poly-l-lysine (PLL). Surface morphologies of the electrodes during the modification process were evaluated by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were ...
Source: Analytical Biochemistry - January 20, 2024 Category: Biochemistry Authors: Damla Şener P ınar Esra Erden Ceren Ka çar Selvi Source Type: research

iSUMO-RsFPN: A predictor for identifying lysine SUMOylation sites based on multi-features and feature pyramid networks
In this study, we constructed a novel deep neural network Residual Pyramid Network (RsFPN), and developed an ensemble deep learning predictor called iSUMO-RsFPN. Initially, three feature extraction methods were employed to extract features from samples. Following this, weak classifiers were trained based on RsFPN for each feature type. Ultimately, the weak classifiers were integrated to construct the final classifier. Moreover, the predictor underwent systematically testing on an independent test dataset, where the results demonstrated a significant improvement over the existing state-of-the-art predictors. The code of iSU...
Source: Analytical Biochemistry - January 8, 2024 Category: Biochemistry Authors: Zhe Lv Xin Wei Siqin Hu Gang Lin Wangren Qiu Source Type: research

iSUMO-RsFPN: A predictor for identifying lysine SUMO-ylation sites based on multi-features and feature pyramid networks
In this study, we constructed a novel deep neural network Residual Pyramid Network (RsFPN), and developed an ensemble deep learning predictor called iSUMO-RsFPN. Initially, three feature extraction methods were employed to extract features from samples. Following this, weak classifiers were trained based on RsFPN for each feature type. Ultimately, the weak classifiers were integrated to construct the final classifier. Moreover, the predictor underwent systematically testing on an independent test dataset, where the results demonstrated a significant improvement over the existing state-of-the-art predictors. The code of iSU...
Source: Analytical Biochemistry - January 8, 2024 Category: Biochemistry Authors: Zhe Lv Xin Wei Siqin Hu Gang Lin Wangren Qiu Source Type: research

Microfluidic bead-based biosensor: Ultrasensitive ctDNA detection based on duplex-functional split-DNAzyme and dendritic enzyme-free signal amplification
Anal Biochem. 2024 Jan 4:115457. doi: 10.1016/j.ab.2024.115457. Online ahead of print.ABSTRACTCirculating tumor DNA (ctDNA) is a crucial cancer biomarker for early or noninvasive monitoring, which is essential for developing ultrasensitive and selective assays in cancer diagnosis and treatment. Herein, a cascade signal amplification of duplex-functional split-DNAzyme and dendritic probes was proposed for ultrasensitive and specific detection of nasopharyngeal carcinoma-associated Epstein-Barr virus (EBV) DNA on microfluidic microbead array chips. With the assistance of Pb2+, the duplex-functional split-DNAzyme recognizes E...
Source: Analytical Biochemistry - January 6, 2024 Category: Biochemistry Authors: Xin Fu Mei Yang He Zhang Qing Wang Yu Fu Qiong Liu Source Type: research

Microfluidic bead-based biosensor: Ultrasensitive ctDNA detection based on duplex-functional split-DNAzyme and dendritic enzyme-free signal amplification
Anal Biochem. 2024 Jan 4:115457. doi: 10.1016/j.ab.2024.115457. Online ahead of print.ABSTRACTCirculating tumor DNA (ctDNA) is a crucial cancer biomarker for early or noninvasive monitoring, which is essential for developing ultrasensitive and selective assays in cancer diagnosis and treatment. Herein, a cascade signal amplification of duplex-functional split-DNAzyme and dendritic probes was proposed for ultrasensitive and specific detection of nasopharyngeal carcinoma-associated Epstein-Barr virus (EBV) DNA on microfluidic microbead array chips. With the assistance of Pb2+, the duplex-functional split-DNAzyme recognizes E...
Source: Analytical Biochemistry - January 6, 2024 Category: Biochemistry Authors: Xin Fu Mei Yang He Zhang Qing Wang Yu Fu Qiong Liu Source Type: research

Signal-off nanozyme-based colorimetric aptasensor for sensitive detection of ampicillin using MnO < sub > 2 < /sub > nanoflowers and gold nanoparticles
Anal Biochem. 2024 Jan 3:115459. doi: 10.1016/j.ab.2024.115459. Online ahead of print.ABSTRACTThe combination of nanomaterials possessing distinct characteristics and the precision of aptamers facilitates the creation of biosensors that exhibit exceptional selectivity and sensitivity. In this manuscript, we present a highly sensitive aptasensor that utilizes the distinctive characteristics of MnO2 nanoflowers and gold nanoparticles to selectively detect ampicillin (AMP). In this aptasensor, the mechanism of signal change is attributed to the difference in the oxidase-mimicking activity of MnO2 nanoflowers in the presence o...
Source: Analytical Biochemistry - January 5, 2024 Category: Biochemistry Authors: Masoomeh Esmaelpourfarkhani Mohammad Ramezani Mona Alibolandi Khalil Abnous Seyed Mohammad Taghdisi Source Type: research

Analysis and characterization of sulfane sulfur
Anal Biochem. 2024 Jan 3:115458. doi: 10.1016/j.ab.2024.115458. Online ahead of print.ABSTRACTIn the late 1970s, sulfane sulfur was defined as sulfur atoms covalently bound only to sulfur atoms. However, this definition was not generally accepted, as it was slightly vague and difficult to comprehend. Thus, in the early 1990s, it was defined as "bound sulfur," which easily converts to hydrogen sulfide upon reduction with a thiol-reducing agent. H2S-related bound sulfur species include persulfides (R-SSH), polysulfides (H2Sn, n ≥ 2 or R-S(S)nS-R), and protein-bound elemental sulfur (S0). Many of the biological effects curr...
Source: Analytical Biochemistry - January 5, 2024 Category: Biochemistry Authors: Shin Koike Yuki Ogasawara Source Type: research

Signal-off nanozyme-based colorimetric aptasensor for sensitive detection of ampicillin using MnO < sub > 2 < /sub > nanoflowers and gold nanoparticles
Anal Biochem. 2024 Jan 3:115459. doi: 10.1016/j.ab.2024.115459. Online ahead of print.ABSTRACTThe combination of nanomaterials possessing distinct characteristics and the precision of aptamers facilitates the creation of biosensors that exhibit exceptional selectivity and sensitivity. In this manuscript, we present a highly sensitive aptasensor that utilizes the distinctive characteristics of MnO2 nanoflowers and gold nanoparticles to selectively detect ampicillin (AMP). In this aptasensor, the mechanism of signal change is attributed to the difference in the oxidase-mimicking activity of MnO2 nanoflowers in the presence o...
Source: Analytical Biochemistry - January 5, 2024 Category: Biochemistry Authors: Masoomeh Esmaelpourfarkhani Mohammad Ramezani Mona Alibolandi Khalil Abnous Seyed Mohammad Taghdisi Source Type: research

Analysis and characterization of sulfane sulfur
Anal Biochem. 2024 Jan 3:115458. doi: 10.1016/j.ab.2024.115458. Online ahead of print.ABSTRACTIn the late 1970s, sulfane sulfur was defined as sulfur atoms covalently bound only to sulfur atoms. However, this definition was not generally accepted, as it was slightly vague and difficult to comprehend. Thus, in the early 1990s, it was defined as "bound sulfur," which easily converts to hydrogen sulfide upon reduction with a thiol-reducing agent. H2S-related bound sulfur species include persulfides (R-SSH), polysulfides (H2Sn, n ≥ 2 or R-S(S)nS-R), and protein-bound elemental sulfur (S0). Many of the biological effects curr...
Source: Analytical Biochemistry - January 5, 2024 Category: Biochemistry Authors: Shin Koike Yuki Ogasawara Source Type: research

Evaluation of lipid extraction methods for fatty acid quantification and compound-specific δ < sup > 13 < /sup > C and δ < sup > 2 < /sup > H < sub > n < /sub > analyses
In this study, we examined the efficacy of seven well-established sample preparation methods, specifically focusing on their effectiveness in total lipid and fatty acid extraction and their impact on compound-specific stable hydrogen (δ2H) and carbon (δ13C) isotope values. We also considered the repercussions of FA removal efficacy on residual bulk tissue δ2Hn analysis, because lipids typically have low δ2H values. Our findings showed that in most cases chloroform-based extraction methods outperformed those without chloroform. While discrepancies were not as evident for smaller organisms, such as plankton, marked varia...
Source: Analytical Biochemistry - January 1, 2024 Category: Biochemistry Authors: Matthias Pilecky Martin J Kainz Leonard I Wassenaar Source Type: research

Evaluation of lipid extraction methods for fatty acid quantification and compound-specific δ < sup > 13 < /sup > C and δ < sup > 2 < /sup > H < sub > n < /sub > analyses
In this study, we examined the efficacy of seven well-established sample preparation methods, specifically focusing on their effectiveness in total lipid and fatty acid extraction and their impact on compound-specific stable hydrogen (δ2H) and carbon (δ13C) isotope values. We also considered the repercussions of FA removal efficacy on residual bulk tissue δ2Hn analysis, because lipids typically have low δ2H values. Our findings showed that in most cases chloroform-based extraction methods outperformed those without chloroform. While discrepancies were not as evident for smaller organisms, such as plankton, marked varia...
Source: Analytical Biochemistry - January 1, 2024 Category: Biochemistry Authors: Matthias Pilecky Martin J Kainz Leonard I Wassenaar Source Type: research

Evaluation of lipid extraction methods for fatty acid quantification and compound-specific δ < sup > 13 < /sup > C and δ < sup > 2 < /sup > H < sub > n < /sub > analyses
In this study, we examined the efficacy of seven well-established sample preparation methods, specifically focusing on their effectiveness in total lipid and fatty acid extraction and their impact on compound-specific stable hydrogen (δ2H) and carbon (δ13C) isotope values. We also considered the repercussions of FA removal efficacy on residual bulk tissue δ2Hn analysis, because lipids typically have low δ2H values. Our findings showed that in most cases chloroform-based extraction methods outperformed those without chloroform. While discrepancies were not as evident for smaller organisms, such as plankton, marked varia...
Source: Analytical Biochemistry - January 1, 2024 Category: Biochemistry Authors: Matthias Pilecky Martin J Kainz Leonard I Wassenaar Source Type: research

Evaluation of lipid extraction methods for fatty acid quantification and compound-specific δ < sup > 13 < /sup > C and δ < sup > 2 < /sup > H < sub > n < /sub > analyses
In this study, we examined the efficacy of seven well-established sample preparation methods, specifically focusing on their effectiveness in total lipid and fatty acid extraction and their impact on compound-specific stable hydrogen (δ2H) and carbon (δ13C) isotope values. We also considered the repercussions of FA removal efficacy on residual bulk tissue δ2Hn analysis, because lipids typically have low δ2H values. Our findings showed that in most cases chloroform-based extraction methods outperformed those without chloroform. While discrepancies were not as evident for smaller organisms, such as plankton, marked varia...
Source: Analytical Biochemistry - January 1, 2024 Category: Biochemistry Authors: Matthias Pilecky Martin J Kainz Leonard I Wassenaar Source Type: research