DEPARTMENT OF BIOCHEMISTRY

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

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Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

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Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

อ่านเพิ่มเติม

Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways

Abstract Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple [...]

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Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion’s Polarizability and Molecular Mass with Limited Data

Abstract The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated [...]

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GLIMMERS: glioma molecular markers exploration using long-read sequencing

Abstract Summary The revised WHO guidelines for classifying and grading brain tumors include several copy number variation (CNV) markers. The turnaround time for detecting CNVs and alterations throughout the entire genome is drastically reduced with the customized read incremental approach on the nanopore platform. However, this approach is challenging for non-bioinformaticians due to the need to use multiple software tools, [...]

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Is Exon Skipping a Viable Therapeutic Approach for Vascular Ehlers–Danlos Syndrome with Mutations in COL3A1 Exon 10 or 15?

Abstract Vascular Ehlers–Danlos syndrome or Ehlers–Danlos syndrome type IV (vEDS) is a connective tissue disorder characterised by skin hyperextensibility, joint hypermobility and fatal vascular rupture caused by COL3A1 mutations that affect collagen III expression, homo-trimer assembly and secretion. Along with collagens I, II, V and XI, collagen III plays an important role in the extracellular matrix, particularly in the inner organs. To [...]

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CAIM: coverage-based analysis for identification of microbiome

Abstract Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification [...]

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Identification of RNF213 as a Potential Suppressor of Local Invasion in Intrahepatic Cholangiocarcinoma

Abstract Intrahepatic cholangiocarcinoma (ICC) is a lethal cancer with poor survival especially when it spreads. The histopathology of its rare intraductal papillary neoplasm of the bile duct type (IPNB) characteristically shows cancer cells originating within the confined bile duct space. These cells eventually invade and infiltrate the nearby liver tissues, making it a good model to study the mechanism of [...]

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Discovery of procyanidin condensed tannins of (-)-epicatechin from Kratom, Mitragyna speciosa, as virucidal agents against SARS-CoV-2.

Abstract Kratom, Mitragyna speciosa, is one of the most popular herbs in the West and Southeast Asia. A number of previous works have focused on bioactive alkaloids in this plant; however, non-alkaloids have never been investigated for their biological activities. Antiviral and virucidal assays of a methanol leaf extract of Kratom, M. speciosa, revealed that a crude extract displayed virucidal [...]

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Identification of Candidate Genes for Salt Tolerance at Seedling Stage in Rice Using QTL-Seq and Chromosome Segment Substitution Line-Derived Population

Abstract Rice is a staple food for more than half of the world’s population. However, the pervasive problem of salinity is severely undermining rice production, especially in coastal and low-lying areas where soil salinization is widespread. This stress, exacerbated by climate change, necessitates the development of salt-tolerant rice varieties to ensure food security. In this study, an F2:3 population (n [...]

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Single-cell RNA sequencing reveals the expansion of circulating tissue-homing B cell subsets in secondary acute dengue viral infection

Abstract The roles of antibodies secreted by subsets of B cells in dengue virus (DENV) infection have been extensively studied, yet, the contribution of tissue-homing B cells to antiviral immunity remains unclear. In this study, we performed a comprehensive analysis of B cell subpopulations in peripheral blood samples from DENV-infected patients using single-cell RNA-sequencing (scRNA-seq) datasets and flow cytometry. We [...]

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Quantifying fecal and plasma short-chain fatty acids in healthy Thai individuals

Abstract Short-chain fatty acids (SCFAs) are involved in important physiological processes such as gut health and immune response, and changes in SCFA levels can be indicative of disease. Despite the importance of SCFAs in human health and disease, reference values for fecal and plasma SCFA concentrations in healthy individuals are scarce. To address this gap in current knowledge, we developed [...]

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Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

Abstract The collision cross-sections (CCS) measurement using ion mobility spectrometry (IMS) in combination with mass spectrometry (MS) offers a great opportunity to increase confidence in metabolite identification. However, owing to the lack of sensitivity and resolution, IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites (VLMs ≤ 250 Da). Here, we describe an analytical method [...]

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Data processing solutions to render metabolomics more quantitative: case studies in food and clinical metabolomics using Metabox 2.0

Abstract The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated [...]

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A Precision Therapy Approach for Retinitis Pigmentosa 11 Using Splice-Switching Antisense Oligonucleotides to Restore the Open Reading Frame of PRPF31

Abstract Retinitis pigmentosa 11 is an untreatable, dominantly inherited retinal disease caused by heterozygous mutations in pre-mRNA processing factor 31 PRPF31. The expression level of PRPF31 is linked to incomplete penetrance in affected families; mutation carriers with higher PRPF31 expression can remain asymptomatic. The current study explores an antisense oligonucleotide exon skipping strategy to treat RP11 caused by truncating mutations [...]

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Angiotensin II promotes erythroid proliferation in a three-stage erythroid culture system

Abstract At present, the numbers of cultured erythroid cells obtained from culture systems are not on a scale that can be used for therapeutics since the cultured erythroid cells have limited proliferation capacity. Stromal cells are believed to play important roles during erythropoiesis. Our previous study shows that factors secreted by stromal cells enhance the proliferation capacity of adult erythroid [...]

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Transcriptomic screening of novel targets of sericin in human hepatocellular carcinoma cells

Abstract Sericin, a natural protein derived from Bombyx mori, is known to ameliorate liver tissue damage; however, its molecular mechanism remains unclear. Herein, we aimed to identify the possible novel targets of sericin in hepatocytes and related cellular pathways. RNA sequencing analysis indicated that a low dose of sericin resulted in 18 differentially expressed genes (DEGs) being upregulated and 68 [...]

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Epigallocatechin Gallate Potentiates the Anticancer Effect of AFP-siRNA-Loaded Polymeric Nanoparticles on Hepatocellular Carcinoma Cells

Abstract Sericin, a natural protein derived from Bombyx mori, is known to ameliorate liver tissue damage; however, its molecular mechanism remains unclear. Herein, we aimed to identify the possible novel targets of sericin in hepatocytes and related cellular pathways. RNA sequencing analysis indicated that a low dose of sericin resulted in 18 differentially expressed genes (DEGs) being upregulated and 68 [...]

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