Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra
This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.PMID:38360171 | DOI:10.1016/j.ab.2024.115483 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - February 15, 2024 Category: Biochemistry Authors: Christopher Jones Source Type: research
Evaluation of semi-quantitative colorimetric assays based on loop-mediated isothermal amplification indicators by using image analysis
Anal Biochem. 2024 Feb 13:115481. doi: 10.1016/j.ab.2024.115481. Online ahead of print.ABSTRACTColorimetric assays are some of the most convenient detection methods, creating discoloration in solutions that is visible to the naked eye. However, colorimetric reactions have some limitations regarding the variability in the color perception of individuals caused by factors such as color blindness, experience, and gender. Semi-quantitative chromatic analysis has been used as an alternative method to differentiate between two colors and accurately interpret the results from a numerical value, with high confidence. Therefore, we...
Source: Analytical Biochemistry - February 15, 2024 Category: Biochemistry Authors: Wasin Panich Sirapat Nak-On Metawee Sabaijai Awika Raksaman Chokchai Puttharugsa Thanawan Tejangkura Thapana Chontananarth Source Type: research
Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra
This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.PMID:38360171 | DOI:10.1016/j.ab.2024.115483 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - February 15, 2024 Category: Biochemistry Authors: Christopher Jones Source Type: research
Rapid high-resolution size distribution protocol for adeno-associated virus using high speed SV-AUC
Anal Biochem. 2024 Feb 9:115482. doi: 10.1016/j.ab.2024.115482. Online ahead of print.ABSTRACTSimulated SV-AUC data for an adeno-associated virus (AAV) sample consisting of four components having closely spaced sedimentation coefficients were used to develop a high-speed protocol that optimized the size distribution analysis resolution. The resulting high speed (45K rpm) SV-AUC (hs-SV-AUC) protocol poses several experimental challenges: 1) the need for rapid data acquisition, 2) increased potential for optical artifacts from steep boundaries and 3) the increased potential for convection. To overcome these challenges the pr...
Source: Analytical Biochemistry - February 11, 2024 Category: Biochemistry Authors: Steven A Berkowitz Nicholas Larson George Bou-Assaf Thomas Laue Source Type: research
Antimicrobial, antioxidant, cell imaging and sensing applications of fluorescein derivatives: A review
Anal Biochem. 2024 Feb 9;688:115479. doi: 10.1016/j.ab.2024.115479. Online ahead of print.ABSTRACTFluorescein itself is a synthetic organic compound and a prominent member of the xanthene dye family. It exhibits strong fluorescence under ultraviolet (UV) or blue light excitation, making it widely used in various applications, including fluorescence microscopy, flow cytometry, immunoassays, and molecular biology techniques. One of the reasons fluorescein derivatives are highly valuable is their tunable fluorescence properties. Through chemical modifications of the fluorescein structure, different functional groups or substi...
Source: Analytical Biochemistry - February 11, 2024 Category: Biochemistry Authors: Amani H Alharbi Sikandar Khan Source Type: research
Qualification of a LC-HRMS platform method for biosimilar development using NISTmab as a model
Anal Biochem. 2024 Feb 8;688:115475. doi: 10.1016/j.ab.2024.115475. Online ahead of print.ABSTRACTBiosimilars are a cost-effective alternative to biopharmaceuticals, necessitating rigorous analytical methods for consistency and compliance. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is a versatile tool for assessing key attributes, encompassing molecular mass, primary structure, and post-translational modifications (PTMs). Adhering to ICH Q2R1, we validated an LC-HRMS based peptide mapping method using NISTmab as a reference. The method validation parameters, covering system suitability, ...
Source: Analytical Biochemistry - February 9, 2024 Category: Biochemistry Authors: Paresh Tank Shruti Vora Sarita Tripathi Fatima D'Souza Source Type: research
Single-tube four-target lateral flow assay detects human papillomavirus types associated with majority of cervical cancers
In this study, we developed a multiplexed loop-mediated isothermal amplification (LAMP) reaction to detect the three most common hrHPV types that cause cervical cancer (HPV16, HPV18, and HPV45) and a cellular control for sample adequacy. First, we characterized the assay limit of detection (LOD) in a real-time reaction with fluorescence readout; after 30 min of amplification the LOD was 100, 10, and 10 copies/reaction of HPV16, HPV18, and HPV45, respectively, and 0.1 ng/reaction of human genomic DNA (gDNA). Next, we implemented the assay on lateral flow strips, and the LOD was maintained for HPV16 and HPV18, but increased ...
Source: Analytical Biochemistry - February 8, 2024 Category: Biochemistry Authors: Maria Barra Megan Chang Mila P Salcedo Kathleen Schmeler Michael Scheurer Mauricio Maza Leticia Lopez Karla Alfaro Rebecca Richards-Kortum Source Type: research
A simple polyarginine membrane electrochemical sensor for the determination of MDMA and MDA
In this study, a simple electrochemical sensor based on l-arginine membrane (P-L-arg/GCE) was developed for rapid and sensitive detection of MDMA and MDA. A polyarginine membrane was obtained through one-step direct electropolymerization, which provides more reaction sites for the analyte and improves the sensitivity of the sensor. Following the optimized selection parameters, the MDMA detection range was established at 1.0 × 10-7∼3.5 × 10-5 mol L-1, with a detection limit of 3.3 × 10-8 mol L-1. Similarly, the detection range for MDA was established at 1.0 × 10-7∼5.3 × 10-5 mol L-1 with a detection limit of 3.3 ×...
Source: Analytical Biochemistry - February 3, 2024 Category: Biochemistry Authors: Shimeng Duan Haiou Chen Anyun Xu Ying He Meng Li Ru Zhang Ruilin Zhang Huiping Bai Source Type: research
A simple molecularly imprinted electrochemical sensor for determination of propyl gallate in food samples
Anal Biochem. 2024 Jan 29:115477. doi: 10.1016/j.ab.2024.115477. Online ahead of print.ABSTRACTPropyl gallate (PG), a prevalent synthetic phenolic antioxidant found in food products, has generated considerable apprehension owing to its potential adverse impacts on human health. Therefore, as a result of the current inquiry, an innovative electrochemical sensor with improved sensitivity and selectivity for PG detection has been created. Under optimal conditions, the manufactured sensor exhibits the capability to identify PG within a broad range from 0.01 μM to 5 μM and from 5 μM to 1000 μM with a limit of detection (LOD...
Source: Analytical Biochemistry - January 31, 2024 Category: Biochemistry Authors: Safaa Hash ım Mohammed Albayatı Pervin Deveci Source Type: research
Determination of acetochlor by UPLC-MS < sup > 3 < /sup > in cells and its application to a cellular pharmacokinetic study
Anal Biochem. 2024 Jan 28;688:115476. doi: 10.1016/j.ab.2024.115476. Online ahead of print.ABSTRACTThe aim of this work was to develop a fast, simple, and reliable UPLC-MS3 method for the sensitive detection of acetochlor in biological samples. In MS3 mode, the ion transition m/z 270.1 → 224.1→148.1 was chosen for quantification with butachlor as the internal standard. In the UPLC system, separation was performed on a UPLC column (2.1 × 50 mm ID, 1.7 μm) with 0.1 % FA in water and acetonitrile as mobile phases. After simple protein precipitation via acetonitrile, the method was well validated with good linearity (0.5...
Source: Analytical Biochemistry - January 29, 2024 Category: Biochemistry Authors: Di Lu Xinyue Zheng Hongyu Xue Jiansong You Lei Yin Meiyun Shi Source Type: research
CFHR1 involvement in bile duct carcinoma: Insights from a data mining study
Anal Biochem. 2024 Jan 28;688:115474. doi: 10.1016/j.ab.2024.115474. Online ahead of print.ABSTRACTThe aim of this study is to investigate the role of CFHR1 in bile duct carcinoma (BDC) and its mechanism of action, and we hope that our analysis and research will contribute to a better understanding of cholangiocarcinoma (BDC) disease genesis, progression and the development of new therapeutic strategies. The prognostic receiver operating characteristic curve of CFHR1 was generated using survival ROC. The ROC curve for CFHR1 showed that there is a correlation between CFHR1 expression and clinicopathological parameters and h...
Source: Analytical Biochemistry - January 29, 2024 Category: Biochemistry Authors: Yan Liu Tianhao Shen Jianming Liu Xue Yu Qiuying Li Tingsong Chen Tinghui Jiang Source Type: research
Caspase-like activity is associated with bacterial infection of the urine in urinary tract diseases
In this study, we used a panel of chromogenic substrates for the qualitative determination of specific enzyme activity in the urine of patients with confirmed bacterial infection and/or urinary tract disease. Healthy patients were used as a control group. It turned out that in the case of Escherichia coli infection, we observed the activity of the caspase subunit of the human 20S proteasome. We did not observe similar correlations for infections with other types of bacteria.PMID:38280678 | DOI:10.1016/j.ab.2024.115473 (Source: Analytical Biochemistry)
Source: Analytical Biochemistry - January 27, 2024 Category: Biochemistry Authors: Natalia Gruba Honorata Sikora Justyna Ciesielska Wiktoria Rejmak Adam Lesner Source Type: research
Measurement of microRNA-106b as a gastric cancer biomarker based on Zn-BTC MOF label-free genosensor
Anal Biochem. 2024 Jan 23;688:115472. doi: 10.1016/j.ab.2024.115472. Online ahead of print.ABSTRACTDue to the late detection of stomach cancer, this cancer usually causes high mortality. The development of an electrochemical genosensor to measure microRNA 106b (miR-106b), as a gastric cancer biomarker, is the aim of this effort. In this regard, first, 1,3,5-benzenetricarboxylate (BTC) metal-organic frameworks (Zn-BTC MOF) were self-assembled on the glassy carbon electrode and then the probe (ssDNA) was immobilized on it. The morphology Zn-BTC MOF was characterized by SEM, FT-IR, Raman and X-Ray techniques. Zn-BTC MOF as a ...
Source: Analytical Biochemistry - January 24, 2024 Category: Biochemistry Authors: Mohammad Kuche-Meshki Hamid R Zare Azam Akbarnia S Mohammad Moshtaghioun Source Type: research
A FRET based ultrasensitive fluorescent aptasensor for 6'-sialyllactose detection
Anal Biochem. 2024 Jan 19;688:115462. doi: 10.1016/j.ab.2024.115462. Online ahead of print.ABSTRACTAs a kind of human milk oligosaccharide, 6'-sialyllactose (6'-SL) plays an important role in promoting infant brain development and improving infant immunity. The content of 6'-SL in infant formula milk powder is thus one of the important nutritional indexes. Since the lacking of efficient and rapid detection methods for 6'-SL, it is of great significance to develop specific recognition elements and establish fast and sensitive detection methods for 6'-SL. Herein, using 6'-SL specific aptamer as the recognition element, catal...
Source: Analytical Biochemistry - January 21, 2024 Category: Biochemistry Authors: Jinri Chen Yuting Zhang Xiaoli Wang Fuhou Li Shaojie Wu Weixia Wang Nandi Zhou Source Type: research
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
