Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples
Anal Biochem. 2023 Dec 23:115449. doi: 10.1016/j.ab.2023.115449. Online ahead of print.ABSTRACTDetermining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to b...
Source: Analytical Biochemistry - December 25, 2023 Category: Biochemistry Authors: Gabriela Merker Breyer Silvia De Carli Maria Eduarda Rocha Jacques Da Silva Maria Eduarda Dias Ana Paula Muterle Varela Michele Bertoni Mann Jeverson Frazzon Fabiana Quoos Mayer Arist óteles Góes Neto Franciele Maboni Siqueira Source Type: research

A novel dual-mode aptasensor based colorimetry and electrochemical detection of norovirus in fecal sample
Anal Biochem. 2023 Dec 21:115444. doi: 10.1016/j.ab.2023.115444. Online ahead of print.ABSTRACTNorovirus is a leading cause of acute gastroenteritis in humans. This paper presents the development of a novel dual-mode aptasensor for detecting norovirus using colorimetry and electrochemical methods. The initial colorimetric method utilizes gold nanoparticles (AuNPs) and sodium chloride to establish a positive correlation between the concentration of norovirus in a solution and the absorbance ratio A650/A520. The naked eye can detect concentrations as low as 0.1 μg/mL, corresponding to a Ct value of 33 (2.2 copies/μL, CT = ...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Xinyue Li Yongqiang Zhao Wenchao Gu Yong Qian Qi Huang Xiaojun Hu Haibo Xing Source Type: research

MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites
In this study, we proposed a Multi-View Neural Network for identification of Human Non-Histone Crotonylation sites, named MVNN-HNHC. MVNN-HNHC integrated multi-view encoding features and adaptive encoding features through multi-channel neural network to deeply learn about attribute differences between crotonylation sites and non-crotonylation sites from various aspects. In MVNN-HNHC, convolutional neural networks can obtain local information from these features, and bidirectional long short term memory networks were utilized to extract sequence information. Then, we employ the attention mechanism to fuse the outputs of var...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Jun Gao Yaomiao Zhao Chen Chen Qiao Ning Source Type: research

Differences in nonoxidative sulfur metabolism between normal human breast MCF-12A and adenocarcinoma MCF-7  cell lines
Anal Biochem. 2023 Dec 21:115434. doi: 10.1016/j.ab.2023.115434. Online ahead of print.ABSTRACTRecent studies have revealed the role of endogenous hydrogen sulfide (H2S) in the development of breast cancer. The capacity of cells to generate H2S and the activity and expression of the main enzymes (cystathionine beta synthase; CBS, cystathionase γ-lyase; CGL, 3-mercaptopyruvate sulfurtransferase; MPST and thiosulfate sulfurtransferase; TST) involved in H2S metabolism were analyzed using an in vitro model of a non-tumourigenic breast cell line (MCF-12A) and a human breast adenocarcinoma cell line (MCF-7). In both cell lines,...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Patrycja Bronowicka-Adamska Marta Kaczor-Kami ńska Maria Wr óbel Anna Bentke-Imiolek Source Type: research

Gold nanoparticle-powered screening of membrane protein-specific lipids from complex lipid mixtures
Anal Biochem. 2023 Dec 21:115447. doi: 10.1016/j.ab.2023.115447. Online ahead of print.ABSTRACTMembrane proteins (MPs) are affected by binding of specific lipids. We previously developed a methodology for systematically analyzing MP-lipid interactions leveraging surface plasmon resonance (SPR). In this method, the gold sensor chip surface was modified with a self-assembled monolayer (SAM), which allowed for a larger amount of MP-immobilization. However, the laborious lipid purification step remained a bottleneck. To address this issue, a new strategy has been developed utilizing gold nanoparticles (AuNPs) instead of the go...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Supakorn Wangamnuayporn Masanao Kinoshita Takayuki Kawai Nobuaki Matsumori Source Type: research

A novel dual-mode aptasensor based colorimetry and electrochemical detection of norovirus in fecal sample
Anal Biochem. 2023 Dec 21:115444. doi: 10.1016/j.ab.2023.115444. Online ahead of print.ABSTRACTNorovirus is a leading cause of acute gastroenteritis in humans. This paper presents the development of a novel dual-mode aptasensor for detecting norovirus using colorimetry and electrochemical methods. The initial colorimetric method utilizes gold nanoparticles (AuNPs) and sodium chloride to establish a positive correlation between the concentration of norovirus in a solution and the absorbance ratio A650/A520. The naked eye can detect concentrations as low as 0.1 μg/mL, corresponding to a Ct value of 33 (2.2 copies/μL, CT = ...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Xinyue Li Yongqiang Zhao Wenchao Gu Yong Qian Qi Huang Xiaojun Hu Haibo Xing Source Type: research

MVNN-HNHC:A multi-view neural network for identification of human non-histone crotonylation sites
In this study, we proposed a Multi-View Neural Network for identification of Human Non-Histone Crotonylation sites, named MVNN-HNHC. MVNN-HNHC integrated multi-view encoding features and adaptive encoding features through multi-channel neural network to deeply learn about attribute differences between crotonylation sites and non-crotonylation sites from various aspects. In MVNN-HNHC, convolutional neural networks can obtain local information from these features, and bidirectional long short term memory networks were utilized to extract sequence information. Then, we employ the attention mechanism to fuse the outputs of var...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Jun Gao Yaomiao Zhao Chen Chen Qiao Ning Source Type: research

Differences in nonoxidative sulfur metabolism between normal human breast MCF-12A and adenocarcinoma MCF-7  cell lines
Anal Biochem. 2023 Dec 21:115434. doi: 10.1016/j.ab.2023.115434. Online ahead of print.ABSTRACTRecent studies have revealed the role of endogenous hydrogen sulfide (H2S) in the development of breast cancer. The capacity of cells to generate H2S and the activity and expression of the main enzymes (cystathionine beta synthase; CBS, cystathionase γ-lyase; CGL, 3-mercaptopyruvate sulfurtransferase; MPST and thiosulfate sulfurtransferase; TST) involved in H2S metabolism were analyzed using an in vitro model of a non-tumourigenic breast cell line (MCF-12A) and a human breast adenocarcinoma cell line (MCF-7). In both cell lines,...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Patrycja Bronowicka-Adamska Marta Kaczor-Kami ńska Maria Wr óbel Anna Bentke-Imiolek Source Type: research

Gold nanoparticle-powered screening of membrane protein-specific lipids from complex lipid mixtures
Anal Biochem. 2023 Dec 21:115447. doi: 10.1016/j.ab.2023.115447. Online ahead of print.ABSTRACTMembrane proteins (MPs) are affected by binding of specific lipids. We previously developed a methodology for systematically analyzing MP-lipid interactions leveraging surface plasmon resonance (SPR). In this method, the gold sensor chip surface was modified with a self-assembled monolayer (SAM), which allowed for a larger amount of MP-immobilization. However, the laborious lipid purification step remained a bottleneck. To address this issue, a new strategy has been developed utilizing gold nanoparticles (AuNPs) instead of the go...
Source: Analytical Biochemistry - December 23, 2023 Category: Biochemistry Authors: Supakorn Wangamnuayporn Masanao Kinoshita Takayuki Kawai Nobuaki Matsumori Source Type: research

REAP+: A single preparation for rapid isolation of nuclei, cytoplasm, and mitochondria
Anal Biochem. 2023 Dec 20:115445. doi: 10.1016/j.ab.2023.115445. Online ahead of print.ABSTRACTREAP+ is an enhanced version of the rapid, efficient, and practical (REAP) method designed for the isolation of nuclear fractions. This improved version, REAP+, enables fast and effective extraction of mitochondria, cytoplasm, and nuclei. The mechanical cell disruption process has been optimized to cerebral tissues, snap-frozen liver, and HT22 cells with remarkable fraction enrichment. REAP+ is well-suited for samples containing minimal protein quantities, such as mouse hippocampal slices. The method was validated by Western blot...
Source: Analytical Biochemistry - December 22, 2023 Category: Biochemistry Authors: Barbara Dos Santos Monique Coelho Bion Marie Goujon-Svrzic Pamela Maher Alcir Luiz Dafre Source Type: research

REAP+: A single preparation for rapid isolation of nuclei, cytoplasm, and mitochondria
Anal Biochem. 2023 Dec 20:115445. doi: 10.1016/j.ab.2023.115445. Online ahead of print.ABSTRACTREAP+ is an enhanced version of the rapid, efficient, and practical (REAP) method designed for the isolation of nuclear fractions. This improved version, REAP+, enables fast and effective extraction of mitochondria, cytoplasm, and nuclei. The mechanical cell disruption process has been optimized to cerebral tissues, snap-frozen liver, and HT22 cells with remarkable fraction enrichment. REAP+ is well-suited for samples containing minimal protein quantities, such as mouse hippocampal slices. The method was validated by Western blot...
Source: Analytical Biochemistry - December 22, 2023 Category: Biochemistry Authors: Barbara Dos Santos Monique Coelho Bion Marie Goujon-Svrzic Pamela Maher Alcir Luiz Dafre Source Type: research

Evaluation of AgNCs@PEI and their integrated hydrogel for colorimetric and fluorometric detection of ascorbic acid
Anal Biochem. 2023 Dec 19:115433. doi: 10.1016/j.ab.2023.115433. Online ahead of print.ABSTRACTA dual-mode colorimetric and fluorometric sensor based on water soluble silver nanoclusters(AgNCs@PEI) is developed for quantitative and visual detection of ascorbic acid (Asc A). The detection method relies on the Asc A induced aggregation of AgNCs@PEI, which resulted in fluorecsence quenching of the sensor. The clusters exhibited a unique combination of static and collisional quenching with a wide range of dynamic detection (1-10 [(Atacan et al., 2022) 55 μM). Linear relationship was observed in the concentration range 102-10 ...
Source: Analytical Biochemistry - December 21, 2023 Category: Biochemistry Authors: Rocky Raj None Mradula Pradipta Samanta Ravinderjit Singh Abhay Sachdev Sunita Mishra Source Type: research

Evaluation of AgNCs@PEI and their integrated hydrogel for colorimetric and fluorometric detection of ascorbic acid
Anal Biochem. 2023 Dec 19:115433. doi: 10.1016/j.ab.2023.115433. Online ahead of print.ABSTRACTA dual-mode colorimetric and fluorometric sensor based on water soluble silver nanoclusters(AgNCs@PEI) is developed for quantitative and visual detection of ascorbic acid (Asc A). The detection method relies on the Asc A induced aggregation of AgNCs@PEI, which resulted in fluorecsence quenching of the sensor. The clusters exhibited a unique combination of static and collisional quenching with a wide range of dynamic detection (1-10 [(Atacan et al., 2022) 55 μM). Linear relationship was observed in the concentration range 102-10 ...
Source: Analytical Biochemistry - December 21, 2023 Category: Biochemistry Authors: Rocky Raj None Mradula Pradipta Samanta Ravinderjit Singh Abhay Sachdev Sunita Mishra Source Type: research

Application and integration of deep learning in FAIMS for identifying acetone concentration
Anal Biochem. 2023 Dec 18:115427. doi: 10.1016/j.ab.2023.115427. Online ahead of print.ABSTRACTIn practical applications, analytical instruments are used for both qualitative and quantitative analysis. However, for high-field asymmetric-waveform ion mobility spectrometry (FAIMS), most studies to date have been focused on the qualitative analysis of substances, with limited research on quantitative analysis. Explored here is the feasibility of using deep learning in FAIMS for quantitative analysis, aided by redesigning the FAIMS upper computer. Integrating spectrum creation and deep learning analysis into the FAIMS upper co...
Source: Analytical Biochemistry - December 20, 2023 Category: Biochemistry Authors: Lei Zhao Ruilong Zhang Hao Zeng Yefan Shao Xiaoxia Du Hua Li Source Type: research

A vector projection similarity-based method for miRNA-disease association prediction
Anal Biochem. 2023 Dec 18:115431. doi: 10.1016/j.ab.2023.115431. Online ahead of print.ABSTRACT[S U M M A R Y] Many miRNA-disease association prediction models incorporate Gaussian interaction profile kernel similarity(GIPS). However, the GIPS fails to consider the specificity of the miRNA-disease association matrix, where matrix elements with a value of 0 represent miRNA and disease relationships that have not been discovered yet. To address this issue and better account for the impact of known and unknown miRNA-disease associations on similarity, we propose a method called vector projection similarity-based method for mi...
Source: Analytical Biochemistry - December 20, 2023 Category: Biochemistry Authors: Guobo Xie Weijie Xie Guosheng Gu Zhiyi Lin Ruibin Chen Shigang Liu Junrui Yu Source Type: research