7,231 results match your criteria chapter describes


Structures and functions of multi-tRNA synthetase complexes.

Enzymes 2020 8;48:149-173. Epub 2020 Sep 8.

Medicinal Bioconvergence Research Center, College of Pharmacy & School of Medicine, Yonsei University, Incheon, South Korea. Electronic address:

Human body is a finely-tuned machine that requires homeostatic balance based on systemically controlled biological processes involving DNA replication, transcription, translation, and energy metabolism. Ubiquitously expressed aminoacyl-tRNA synthetases have been investigated for many decades, and they act as cross-over mediators of important biological processes. In particular, a cytoplasmic multi-tRNA synthetase complex (MSC) appears to be a central machinery controlling the complexity of biological systems. Read More

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September 2020

Web-Based Radiology Learning Module Design: The Author Perspective.

Acad Radiol 2021 Apr 6. Epub 2021 Apr 6.

Department of Radiology, University of North Carolina School of Medicine, North Carolina.

Rationale And Objectives: Over recent years, e-learning has become an integral component of radiology education. While demands for innovative, interactive e-learning resources have increased, the availability of viable solutions have not kept pace. As a result, many educators are authoring their own e-learning content. Read More

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Computational Analysis of Single-Cell RNA-Seq Data.

Methods Mol Biol 2021 ;2284:289-301

Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy.

Single-cell RNAseq data can be generated using various technologies, spanning from isolation of cells by FACS sorting or droplet sequencing, to the use of frozen tissue sections retaining spatial information of cells in their morphological context. The analysis of single cell RNAseq data is mainly focused on the identification of cell subpopulations characterized by specific gene markers that can be used to purify the population of interest for further biological studies. This chapter describes the steps required for dataset clustering and markers detection using a droplet dataset and a spatial transcriptomics dataset. Read More

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January 2021

Computational Analysis of circRNA Expression Data.

Methods Mol Biol 2021 ;2284:181-192

Department of Computer Science, University of Turin, Turin, Italy.

Analysis of circular RNA (circRNA) expression from RNA-Seq data can be performed with different algorithms and analysis pipelines, tools allowing the extraction of heterogeneous information on the expression of this novel class of RNAs. Computational pipelines were developed to facilitate the analysis of circRNA expression by leveraging different public tools in easy-to-use pipelines. This chapter describes the complete workflow for a computationally reproducible analysis of circRNA expression starting for a public RNA-Seq experiment. Read More

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January 2021

Advanced Design of Structural RNAs Using RNARedPrint.

Methods Mol Biol 2021 ;2284:1-15

LIX, CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France.

RNA design addresses the need to build novel RNAs, e.g., for biotechnological applications in synthetic biology, equipped with desired functional properties. Read More

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January 2021

Pharmacogenetic/Pharmacogenomic Tests for Treatment Prediction in Depression.

Adv Exp Med Biol 2021 ;1305:231-255

Pharmacogenetics Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada.

Genetic factors play a significant but complex role in antidepressant (AD) response and tolerability. During recent years, there is growing enthusiasm in the promise of pharmacogenetic/pharmacogenomic (PGx) tools for optimizing and personalizing treatment outcomes for patients with major depressive disorder (MDD). The influence of pharmacokinetic and pharmacodynamic genes on response and tolerability has been investigated, including those encoding the cytochrome P450 superfamily, P-glycoprotein, monoaminergic transporters and receptors, intracellular signal transduction pathways, and the stress hormone system. Read More

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January 2021

Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application.

Prog Mol Biol Transl Sci 2020 30;176:141-178. Epub 2020 Sep 30.

Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, United States; The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC, United States. Electronic address:

The scientific community currently defines the human microbiome as all the bacteria, viruses, fungi, archaea, and eukaryotes that occupy the human body. When considering the variable locations, composition, diversity, and abundance of our microbial symbionts, the sheer volume of microorganisms reaches hundreds of trillions. With the onset of next generation sequencing (NGS), also known as high-throughput sequencing (HTS) technologies, the barriers to studying the human microbiome lowered significantly, making in-depth microbiome research accessible. Read More

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September 2020

Microarray Analysis of Whole-Transcriptome RNAs Including Non-Coding RNAs.

Methods Mol Biol 2021 ;2300:143-164

Université de Lorraine, CNRS, IMoPA, Nancy, France.

Non-coding RNAs participate in most cellular processes and play a causative role in several diseases. In addition to their relevance as targets or tools for therapy, ncRNAs have been extensively detected in body fluids supporting their role as easily accessible and minimally invasive biomarkers. However, the precise measurement of circulating ncRNAs remains challenging due to their low abundance and the heterogeneity of the ncRNA population (size, polyadenylation status, circular forms). Read More

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January 2021

Gene Reporter Assays to Study miRNA Function.

Methods Mol Biol 2021 ;2300:119-131

Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.

This chapter describes one of the most reliable quantitative assays to test the silencing of a possible target gene by a specific miRNA using a luciferase reporter gene. The experimental procedure first consists in cloning both the wild-type and mutated forms of the 3'UTR of the miRNA-predicted mRNA target downstream of a firefly luciferase reporter. Next, each construct is co-transfected together with the miRNA into HeLa cells, and the reporter expression is monitored. Read More

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January 2021

Fluorescence In Situ Hybridization of Small Non-Coding RNAs.

Methods Mol Biol 2021 ;2300:73-85

Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.

The determination of the cellular localization of a noncoding RNA (ncRNA) is highly helpful to decipher its function. RNA-FISH is a powerful method to detect specific RNAs in fixed cells. It allows both localization and quantification of RNA molecules within individual cells and tissues. Read More

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January 2021

RNA Precipitation.

Methods Mol Biol 2021 ;2300:11-16

Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France.

Precipitation is a critical step to recover RNA of high purity. This chapter describes the principles of alcoholic precipitation as well as a standard, basic protocol with key advices to observe, but numerous variations on the theme are discussed. Indeed, several important parameters, such as the choice of salt, alcohol, or carrier, have to be considered to improve the efficiency of precipitation and the yield of RNA recovery. Read More

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January 2021

NMR-Based Metabolomics.

Adv Exp Med Biol 2021 ;1280:19-37

Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.

Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Read More

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Chemical Isotope Labeling LC-MS for Metabolomics.

Adv Exp Med Biol 2021 ;1280:1-18

Department of Chemistry, University of Alberta, Edmonton, AB, Canada.

Due to the great diversity of chemical and physical properties of metabolites as well as a wide range of concentrations of metabolites present in metabolomic samples, performing comprehensive and quantitative metabolome analysis is a major analytical challenge. Conventional approach of combining various techniques and methods with each detecting a fraction of the metabolome can lead to the increase in overall metabolomic coverage. However, this approach requires extensive investment in equipment and analytical expertise with still relatively low coverage and low sample throughput. Read More

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History, evolution and classification of CRISPR-Cas associated systems.

Prog Mol Biol Transl Sci 2021 9;179:11-76. Epub 2021 Feb 9.

Daulat Ram College, University of Delhi, New Delhi, Delhi, India. Electronic address:

This chapter provides a detailed description of the history of CRISPR-Cas and its evolution into one of the most efficient genome-editing strategies. The chapter begins by providing information on early findings that were critical in deciphering the role of CRISPR-Cas associated systems in prokaryotes. It then describes how CRISPR-Cas had been evolved into an efficient genome-editing strategy. Read More

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February 2021

Prevention of NAFLD/NASH by Astaxanthin and β-Cryptoxanthin.

Authors:
Tsuguhito Ota

Adv Exp Med Biol 2021 ;1261:231-238

Department of Cell Metabolism and Nutrition, Brain/Liver Interface Medicine Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan.

Metabolic disorders, such as lipid accumulation, insulin resistance, and inflammation, have been implicated in the pathogenesis of NAFLD/NASH. Both innate and recruited immune cells mediate the development of insulin resistance and NASH. Oxidative stress is also pivotal for the progression of NASH. Read More

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Fecal Microflora from Dragonflies and Its Microorganisms Producing Carotenoids.

Adv Exp Med Biol 2021 ;1261:209-216

Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan.

The intestines of insects are assumed to be the niche of various microbial groups, and a unique microflora could be formed under environmental conditions different from mammalian intestinal tracts. This chapter describes the bacterial flora formed in the intestines of two dragonfly species, "akatombo" (the red dragonfly; Sympetrum frequens) and "usubaki-tombo" (Pantala flavescens), which fly over a long distance, and carotenoid-producing microorganisms isolated from this flora. C carotenoids, which were produced by a bacterium Kurthia gibsonii isolated from S. Read More

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Xanthophyllomyces dendrorhous, a Versatile Platform for the Production of Carotenoids and Other Acetyl-CoA-Derived Compounds.

Adv Exp Med Biol 2021 ;1261:137-151

Biosynthesis Group, Molecular Biosciences, Goethe University, Frankfurt, Germany.

Xanthophyllomyces dendrorhous (with Phaffia rhodozyma as its anamorphic state) is a basidiomycetous, moderately psychrophilic, red yeast belonging to the Cystofilobasidiales. Its red pigmentation is caused by the accumulation of astaxanthin, which is a unique feature among fungi. The present chapter reviews astaxanthin biosynthesis and acetyl-CoA metabolism in X. Read More

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Introduction of Nanobiotechnology.

Adv Exp Med Biol 2021 ;1309:1-22

Department of Bioscience and Biotechnology, Konkuk University, Seoul, South Korea.

Nano is a fine metric unit which means "one billionth." Nanotechnology is attracting attention as a technological basis to lead the fourth industry. By utilizing synergistic properties obtained from controlling the structure or arrangement of materials at the nanoscale, nanotechnology has evolved rapidly over the past half century and is active in a variety of fields such as materials, pharmaceuticals, and biology. Read More

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Exomeres: A New Member of Extracellular Vesicles Family.

Subcell Biochem 2021 ;97:89-97

Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.

Extracellular vesicles (EVs) are described as membranous vesicles that are secreted by various cell types. EVs can be categorised as exosomes, ectosomes, apoptotic bodies, large oncosomes and migrasomes. EVs are heterogeneous in nature according to their origin, mode of release, size, and biochemical contents. Read More

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January 2021

Purification of Total RNA from Stomach Tissue Biopsies.

Methods Mol Biol 2021 ;2283:51-59

Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland.

In order to further our understanding of the physiological consequences of Helicobacter pylori infection , analysis of clinical tissue specimens is required. To this end, RNA is frequently isolated from stomach biopsies of H. pylori-infected patients and compared to samples from uninfected controls to monitor gene expression using molecular methods such as reverse-transcription real-time PCR, microarrays, and next-generation sequencing. Read More

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January 2021

Molecular Detection of Antibiotic-Resistant Helicobacter pylori.

Methods Mol Biol 2021 ;2283:29-36

Department of Clinical Medicine, Trinity College Dublin, School of Medicine, Dublin 2, Ireland.

Antimicrobial susceptibility testing (AST) for H. pylori is essential to accurately assess the prevalence of antibiotic resistance in each population. Antibiotic resistance rates form the basis of local guidelines for H. Read More

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January 2021

Using D- and L-Amino Acid Oxidases to Generate the Imino Acid Substrate to Measure the Activity of the Novel Rid (Enamine/Imine Deaminase) Class of Enzymes.

Methods Mol Biol 2021 ;2280:199-218

Department of Biosciences, University of Milan, Milan, Italy.

This chapter describes a method to assay the activity of reactive intermediate deaminases (Rid), a large family of conserved soluble enzymes, which have been proposed to prevent damages from metabolic intermediates such as the highly reactive and unstable compounds enamines/imines. In this method, the flavin adenine dinucleotide-dependent L- or D-amino acid oxidases generate an imino acid starting from a L- or D- amino acid, respectively. This reaction is coupled to the hydrolysis of the imino acid to the corresponding α-keto acid and ammonium ion catalyzed by a Rid enzyme. Read More

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January 2021

A Bioinformatic Pipeline to Identify Biomarkers for Metastasis Formation from RNA Sequencing Data.

Methods Mol Biol 2021 ;2294:221-238

Translational Oncology of Solid Tumors Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.

Deep molecular characterization of tumors is a prerequisite for precision oncology and personalized anticancer treatment. Analyzing the tumor transcriptome by RNA sequencing (RNAseq) allows the quantification of individual isoforms and also the detection of sequence alteration in the expressed genes. This chapter describes an analysis pipeline that focuses both on accurate quantification of transcripts and on the occurrence of cancer-associated mutations. Read More

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January 2021

Lipid Metabolism and Tumor Antigen Presentation.

Authors:
Hong Qin Yaxi Chen

Adv Exp Med Biol 2021 ;1316:169-189

Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Institute for Viral Hepatitis, Centre for Lipid Research, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.

Tumors always evade immune surveillance and block T cell activation in a poorly immunogenic and immunosuppressive environment. Cancer cells and immune cells exhibit metabolic reprogramming in the tumor microenvironment (TME), which intimately links immune cell function and edits tumor immunology. In addition to glucose metabolism, amino acid and lipid metabolism also provide the materials for biological processes crucial in cancer biology and pathology. Read More

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A Belief Degree-Associated Fuzzy Multifactor Dimensionality Reduction Framework for Epistasis Detection.

Methods Mol Biol 2021 ;2212:307-323

Department of Computer Science, College of Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong.

Epistasis is a challenge in prediction, classification, and suspicion of human genetic diseases. Many technologies, methods, and tools have been developed for epistasis detection. Multifactor dimensionality reduction (MDR) is the method commonly used in epistasis detection. Read More

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Epistasis-Based Feature Selection Algorithm.

Methods Mol Biol 2021 ;2212:37-44

Federal Institute of Bahia, Santo Antonio de Jesus, BA, Brazil.

Variable selection is an important procedure to select relevant features from large datasets in optimization problems. The use of epistasis concepts becomes an alternative to assess the gene (variable) interdependence and select the most significative variables. This chapter describes the Epistasis-based Feature Selection Algorithm (EbFSA). Read More

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SNPInt-GPU: Tool for Epistasis Testing with Multiple Methods and GPU Acceleration.

Methods Mol Biol 2021 ;2212:17-35

Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.

We present SNPInt-GPU, a software providing several methods for statistical epistasis testing. SNPInt-GPU supports GPU acceleration using the Nvidia CUDA framework, but can also be used without GPU hardware. The software implements logistic regression (as in PLINK epistasis testing), BOOST, log-linear regression, mutual information (MI), and information gain (IG) for pairwise testing as well as mutual information and information gain for third-order tests. Read More

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Aiming student pharmacist organizations toward professional success: Mapping student activities to a professional development program.

Curr Pharm Teach Learn 2021 Apr 13;13(4):346-352. Epub 2020 Dec 13.

University of Louisiana Monroe College of Pharmacy, Monroe, Louisiana, United States. Electronic address:

Introduction: This project describes the mapping of the Accreditation Council for Pharmacy Education (ACPE) Accreditation Standards to activities of a student pharmacist organization and to assess student perceptions of the process' utility in completing a professional growth and development program (PGDP).

Methods: A list of activities from the student pharmacist organization for academic year 2018-2019 was compiled at the start of each semester. ACPE Standards 3 and 4 were mapped to each chapter activity using a spreadsheet. Read More

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Isolation and Characterization of Shiga Toxin-Associated Microvesicles.

Methods Mol Biol 2021 ;2291:207-228

Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden.

Microvesicles are shed from cell surfaces during infectious or inflammatory conditions and may contribute to the pathogenesis of disease. During Shiga toxin-producing Escherichia coli (STEC) infection, microvesicles are released from blood cells. These microvesicles play a part in inflammation, thrombosis, hemolysis, and the transfer of the main virulence factor of STEC strains, Shiga toxin, to target organ cells. Read More

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Lambda Red-Mediated Recombination in Shiga Toxin-Producing Escherichia coli.

Methods Mol Biol 2021 ;2291:145-162

Department of Molecular & Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.

The bacteriophage Lambda (λ) "Red" recombination system has enabled the development of efficient methods for engineering bacterial chromosomes. This system has been particularly important to the field of bacterial pathogenesis, where it has advanced the study of virulence factors from Shiga toxin-producing and enteropathogenic Escherichia coli (STEC and EPEC). Transient plasmid-driven expression of Lambda Red allows homologous recombination between PCR-derived linear DNA substrates and target loci in the STEC/EPEC chromosomes. Read More

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