Journal of Integrated -OMICS
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215 research outputs found
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Advancing Diversity, Equity & Inclusion in Scientific Research, Public Health and Biomedical Innovation
Full text linkDifferential Urinary Proteomics and Absolute Protein Quantification Reveal Biomarkers of Muscle-Invasive and Non-Muscle-Invasive Bladder Cancer
Full text linkA comparative urinary proteomic analysis using the Total Protein Approach (TPA) revealed distinct protein abundance profiles between patients with muscle-invasive (MIBC) and non-muscle-invasive bladder cancer (NMIBC), suggesting potential diagnostic utility. Notably, several proteins, including periostin (POSTN), immunoglobulin variable regions (IGLV3-21, IGHV3-49, IGHV5-51), and complement regulator (C4BPB), were found at significantly higher concentrations in the urine of MIBC patients. These findings support their value as non-invasive indicators of tumour aggressiveness. The TPA-based urinary protein signature holds promise for improving early risk stratification, detecting biological features associated with invasive disease, and may inform treatment strategies
Transformational Goal for Science Education: The 1Student - 1Apparatus (1S1A) Model
Full text linkLimited access to hands-on laboratory equipment remains a significant barrier to effective science education. To address this challenge, we evaluated the analytical performance of the Doctor Vida® Education platform - an ultra-compact, low-cost, multifunctional analytical device designed under the ‘One Student–One Apparatus’ (1S1A) model. Using the Bradford method, we quantified total protein in urine and serum samples and compared results against those obtained from a commercial CLARIOstar® microplate reader. Calibration curves constructed from eight independent replicates revealed comparable slopes and intercepts between the two systems, with Doctor Vida® Education device demonstrating high linearity and repeatability. Despite the CLARIOstar® achieving lower limits of detection and quantification, the Doctor Vida® Education device showed superior reproducibility, with consistently lower relative standard deviations across operators and experimental conditions. Statistical analysis of urine and serum measurements confirmed strong agreement between methods, with no significant differences in most samples and improved precision observed with Doctor Vida® Education device in serum analysis. With a unit cost below 1000 €, the Doctor Vida® Education device platform proves to be a reliable, robust, and accessible solution for individualized, competence-based learning in analytical sciences
A study of SARS-CoV-2 genomic profiles, evolutionary changes, and transmission dynamics in Southeastern India during three pandemic waves
Full text linkSARS-CoV-2 bio-surveillance at all levels is crucial for understanding its genetic evolution and vaccine effectiveness.This study investigated the emergence and evolution of new SARS-CoV-2 variants in the city of Puducherry, India throughout the three peaks of infection. A total of 128 samples were subjected to Illumina deep RNA sequencing. The results indicate that the first wave was dominated by uncommon variants, the second by Delta, and the third by Omicron. Lineages B.1.560 and B.1.617.2 were most prevalent. Analysis of 3133 common and 11 new mutations revealed Spike_D614G as the most common mutation and a novel set of mutations was observed in NS16, a key immune evasion factor. These NS16 mutations raise concerns about increased virulence, reduced vaccine efficacy, and potential antiviral resistance, warranting further investigation. Our findings contribute to SARS-CoV-2 evolutionary and genetic epidemiology research and highlight the need for ongoing surveillance to anticipate future variant threats
DTT protein equalization and Tryptophan protein quantification as a powerful tool in analytical proteomics.
Full text linkAssessing total protein levels in biological samples is a common procedure in biochemistry and molecular biology. In this study, we compare tryptophan fluorescence (WF) with Bradford and BCA assays to determine total protein in serum samples. Our results indicate that tryptophan fluorescence spectrometry is an efficient, sensitive, and straightforward technique for quantifying proteins in serum. We observed minimal variation between the three methods: BCA de one with the lowers LOD and LOQ. The tryptophan method offers the possibility of reusing the intact sample that does not need colourimetric reagents for quantification. Consequently, free tryptophan serves as a reliable universal standard. This assay can be performed using a conventional fluorescence spectrometer with cuvettes or in a 96-well plate format with a plate reader. The method was successfully used as proof of concept, using serum from patients diagnosed with myeloma and serum from healthy donors
Ultrasound-Assisted Extraction- and Liquid Chromatography-Based Method Development and Validation for Obtaining and Qualitative Determination of Apple Pomace Three Triterpene Acids using Analytical Quality by Design
Full text linkBackground: Apple pomace has garnered significant attention within the life sciences domain due to its underutilized status as a waste material from apple processing. It represents a cost-effective and abundant source of triterpene acids due to its multifunctional clinical, nutritional, and pharmaceutical benefits.
Purpose: The present study aimed to develop and validate a new, selective, effective, robust and reproducible laboratory methodology based on extraction, purification and analytical procedures to obtain and determining three major triterpene acids – Ursolic acid (UA), Oleanolic acid (OA) and Betulinic acid (BA) into the dry extracted product from apple pomace.
Method: A new, cost-efficient, rapid, selective and high-yield two-stage ultrasound-assisted extraction procedure was developed and the effect of critical parameters: ultrasonic power, extraction time, solvent volume, temperature, and the amount of raw material on the extraction process were investigated. The dry column vacuum chromatography technique was used for purification to remove unwanted non-polar and polar impurities from the target bioactive compounds; A new, effective, specific, sensitive, and rapid HPLC analytical procedure was developed using analytical quality by design (AQbD) approach and validated according to ICH guidelines.
Conclusion: The method has a good accuracy (the mean recovery >95 %) and linearity (R2>0.999). The limit of quantitation (LOQ) is 0.0001 mg/mL for UA, 0.00005 mg/mL for OA and 0.000025 mg/mL for BA. The validation results confirm that the method is specific, precise and robust. The purity of the extracted and purified target product from apple pomace is not less than 93 %. The developed laboratory methodology is capable of being considered for industrial purposes and through the appropriate technology transfer process can be successfully transferred to the industrial scale
Computational Screening of Natural Compounds as Antiviral Candidates Targeting the SARS-CoV-2 Main Protease
Full text linkThe onset of the global pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Wuhan in December 2019 has led to an urgent need for effective preventive and therapeutic solutions. Among the various approaches explored, natural products have shown potential in the fight against COVID-19. This study employed computational techniques to screen and evaluate six natural antiviral compounds for their effectiveness against the SARS-CoV-2 Main Protease (Mpro). By using molecular docking simulations, the interactions between these natural compounds and the target proteins were predicted and analyzed, focusing on factors such as binding affinity, interaction patterns, and structural compatibility within the active sites. The analysis indicated that Cladosin C and Rhodatin formed the most stable interactions with Mpro, engaging with several critical residues. Cannabidiol, Capsaicin, and Kappa-Carrageenan also demonstrated promising interactions, though with some variability. On the other hand, Astaxanthin exhibited the least stable binding, suggesting limited antiviral potential. This research provides insights into the possible roles of these natural compounds as antagonists of the SARS-CoV-2 Mpro enzyme. Further in vitro and in vivo studies are necessary to confirm the antiviral properties of these compounds, and future research should investigate their broader antiviral applications