Analytical Biochemistry

The quantification of antibiotics, using mass spectrometry, for monitoring therapeutic drugs is a key benefit in infection management for many hospitals. After an easy work-up of plasma samples, analysis were performed using both We aimed to evaluate the differences and agreements between the two widely used acquisition modes: MRM for the triple quadrupole spectrometer and fullMS/ddMS2 for the HRMS to quantify twelve antibiotics. Comparison between the two acquisition modes were performed. Validation parameters and sample values were used as comparison criteria...

DNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensitive frequency-domain electrochemical analysis strategy to effectively separate the weak signals from background current...

Biologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the eight given proteins examined...

The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0...

Bioactive peptides can hinder oxidative processes and microbial spoilage in foodstuffs and play important roles in treating diverse diseases and disorders. While most of the methods focus on single-functional bioactive peptides and have obtained promising prediction performance, it is still a significant challenge to accurately detect complex and diverse functions simultaneously with the quick increase of multi-functional bioactive peptides. In contrast to previous research on multi-functional bioactive peptide prediction based solely on sequence, we propose a novel multimodal dual-branch (MMDB) lightweight deep learning model that designs two different branches to effectively capture the complementary information of peptide sequence and structural properties...

Cardiovascular diseases (CVD) are a range of diseases, pointing the functional hindrances in the heart and blood vessels of the human system that contributes to 48.6 % of the world's adult death rate. The diagnosis of CVD relies upon the Electro Cardio Gram (ECG) and detection of muscle markers such as troponins. Among the cardiac trio, Cardiac Troponin I (cTnI) weighing 23 KiloDalton (kDa) is a sorted biomarker for CVD. cTnI remains high in the blood after 1-2 weeks of myocardial damage. Testing of cTnI in CVD patients aids in diagnosis and risk stratification of the disease...

Prolidase (EC.3.4.13.9) is a dipeptidase known nowadays to play a pivotal role in several physiological and pathological processes. More in particular, this enzyme is involved in the cleavage of proline- and hydroxyproline-containing dipeptides (imidodipeptides), thus finely regulating the homeostasis of free proline and hydroxyproline. Abnormally high or low levels of prolidase have been found in numerous acute and chronic syndromes affecting humans (chronic liver fibrosis, viral and acute hepatitis, cancer, neurological disorders, inflammation, skin diseases, intellectual disability, respiratory infection, and others) for which the content of proline is well recognized as a clinical marker...

DNA 4 mC plays a crucial role in the genetic expression process of organisms. However, existing deep learning algorithms have shortcomings in the ability to represent DNA sequence features. In this paper, we propose a 4 mC site identification algorithm, DNABert-4mC, based on a fusion of the pruned pre-training DNABert-Pruning model and artificial feature encoding to identify 4 mC sites. The algorithm prunes and compresses the DNABert model, resulting in the pruned pre-training model DNABert-Pruning...

SARS-CoV-2 emerged in late 2019 and quickly spread globally, resulting in significant morbidity, mortality, and socio-economic disruptions. As of now, collaborative global efforts in vaccination and the advent of novel diagnostic tools have considerably curbed the spread and impact of the virus in many regions. Despite this progress, the demand remains for low-cost, accurate, rapid and scalable diagnostic tools to reduce the influence of SARS-CoV-2. Herein, the angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoV-2, was immobilized on two types of electrodes, a screen-printed gold electrode (SPGE) and a screen-printed carbon electrode (SPCE), to develop electrochemical biosensors for detecting SARS-CoV-2 with high sensitivity and selectivity...

Terpenes play a vital role in plant defense; tomato plants produce a diverse range of terpenes within specialized glandular trichomes, influencing interactions with herbivores, predators, and pollinators. This study employed two distinct methods, namely leaf dip and maceration, to extract trichomes from tomato leaves. Terpene quantification was carried out using Gas Chromatography-Mass Spectrometry (GC-MS). The leaf dip method proved effective in selectively targeting trichome content, revealing unique extraction patterns compared to maceration...

Vonoprazan and amoxicillin are pharmacological combinations that demonstrate synergistic effects in treating Helicobacter pylori (H. pylori), a global public health concern associated with peptic ulcer disease and gastric cancer. Four spectrophotometric methods were developed, including two univariate techniques (Fourier self-deconvolution and ratio difference) and two multivariate chemometric approaches (partial least squares and principal component regression). These methods provide innovative solutions for effectively resolving and accurately quantifying the overlapping spectra of Vonoprazan and amoxicillin...

Myoglobin (Myo), creatine kinase-MB (CKMB), and cardiac troponin I (cTnI) are crucial biomarkers for diagnosing acute myocardial infarction (AMI) The accurate and rapid detection of these three targets can greatly improve the prognosis of AMI patients. Herein, this study developed a microfluidic immunofluorescence method that can detect all three targets in 10-15 minutes. Ultrasonic atomization and spray technology are used to modify the surface of the injection-molded microfluidic chip (MFC), which effectively solves the problem of biological cross-linking and antibody immobilization on the MFC surface...

RNA modification, N4-acetylcytidine (ac4C), is enzymatically catalyzed by N-acetyltransferase 10 (NAT10) and plays an essential role across tRNA, rRNA, and mRNA. It influences various cellular functions, including mRNA stability and rRNA biosynthesis. Wet-lab detection of ac4C modification sites is highly resource-intensive and costly. Therefore, various machine learning and deep learning techniques have been employed for computational detection of ac4C modification sites. The known ac4C modification sites are limited for training an accurate and stable prediction model...

MicroRNAs (miRNAs) are crucial biomarkers for the early detection and monitoring of disease progression of chronic obstructive pulmonary disease (COPD). Herein, we have devised a method for detecting miRNA using a combination of colorimetric and graphene oxide-based fluorescent techniques. The target miRNA in our design could precisely activate the trans-cleavage activity of the CRISPR-Cas13a system. The activated Cas13a enzyme cuts the "rUrU" section in the P1 probe, generating a nicking site to induce entropy-driven amplification (EDA)...

Disturbances in the diurnal pattern are associated with several clinical and psychological conditions, including depression and fatigue. Salivary sampling for melatonin, cortisol and cortisone provides a non-invasive method for frequent sampling and obtaining biochemical insight into the diurnal pattern of individuals. Therefore, a new liquid chromatography-tandem mass spectrometry-based method for the measurement of salivary melatonin, cortisol and cortisone was developed and validated. The method required 250 μl saliva, used isotope dilution methodology and was based on a liquid-liquid extraction for sample preparation, reversed-phase chromatography and multiple reaction monitoring on a mass spectrometer for quantitation...

Early detection of the coronavirus is acknowledged as a crucial measure to mitigate the spread of the pandemic, facilitating timely isolation of infected individuals, and disrupting the transmission chain. In this study, we leveraged the properties of synthesized Ag-MOF, including high porosity and increased flow intensity. Electrochemical techniques such as cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were employed to develop an economical and portable sensor with exceptional selectivity for COVID-19 detection...

We studied the spectral properties of 4'-6-diamidino-2-phenylindole (DAPI) in poly (vinyl alcohol) (PVA) films. Absorption and fluorescence spectra, emission and excitation spectra, quantum yield, and fluorescence lifetime have been characterized. An efficient room temperature phosphorescence (RTP) of DAPI has been observed with UV and blue light excitations. A few hundred millisecond phosphorescence lifetime enables a gated detection with sufficient background reduction. We found the phosphorescent Quantum Yield of DAPI in PVA Film to be 0...

Aflatoxin B1 (AF-B1 ) are toxins secreted by secondary metabolites of molds that have adverse effects on humans and animals resulting in huge economic losses. Here we report on field useable, cost effective and direct electrochemical sensor based on conducting polymer composite electrode, Poly (3,4-ethylenedioxythiophene): polystyrene sulphonic acid (PEDOT-PSS) for label-free detection of AF-B1 . Structural and morphological characterization of composite electrodes were carried out using XRD and SEM. We compared two different electroanalytical techniques namely, transient capacitance and differential pulse voltammetry, to select the most prominent technique for analyzing the mycotoxin easily...

Invasive Aspergillosis is a high-risk illness with a high death rate in immunocompromised people due to a lack of early detection and timely treatment. Based on immunology study, we achieved an efficient production of anti-galactomannan antibody by Chinese hamster ovary (CHO) cells and applied it to time-resolved fluoroimmunoassay for Aspergillus galactomannan detection. We first introduced dual promoter expression vector into CHO host cells, and then applied a two-step screening strategy to screen the stable cell line by methionine sulfoximine pressurization...

Cheap chicken meat is often used as an undeclared substitute in meat products. In this study, two formats of the immunochromatographic assay (ICA) of immunoglobulins of class Y (IgY) as a biomarker for chicken authentication were developed. In both competitive ICA (cICA) and sandwich ICA (sICA), gold nanoparticles (GNP) were conjugated with anti-species antibodies. A simple procedure of sample preparation, which took only 30 min, was proposed. Test systems demonstrated high sensitivity and rapidity: visual limits of detection of IgY and assay durations were 12/14 ng/mL and 10/15 min for cICA and sICA, respectively...