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  • Springer  (1,657,556)
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  • 1
    Keywords: Biochemistry ; Protein Science ; Springer eBooks
    Description / Table of Contents: Making the Case for Functional Proteomics -- Methods to Monitor the Functional Subproteomes of SERPIN Protease Inhibitors -- Two-dimensional 16-BAC/SDS polyacrylamide gel electrophoresis of mitochondrial membrane proteins -- Systematic Glycolytic Enzyme Activity Analysis from Human Serum with PEP Technology -- A protein decomplexation strategy in snake venom proteomics -- Fractionation Techniques to Increase Plant Proteome Coverage: Combining Separation in Parallel at the Protein and the Peptide Level -- A systematic analysis workflow for high-density customized protein microarrays in biomarker screening -- Metaproteomics study of the gut microbiome -- Double-One Dimensional Electrophoresis (D1-DE) Adapted for Immunoproteomics -- BioID: A proximity dependent labeling approach in proteomics study -- Functional application of snake venom proteomics in in vivo antivenom assessment -- Proteomic detection of carbohydrate-active enzymes (CAZymes) in microbial secretomes -- An Overview of Mass Spectrometry-based Methods for Functional Proteomics -- Functional proteomic analysis to characterize signaling crosstalks -- Identification of unexpected protein modifications by mass spectrometry based proteomics -- Label-free LC-MS/MS Strategy for Comprehensive Proteomic Profiling of Human Islets Collected using Laser Capture Microdissection from Frozen Pancreata -- Mass Spectrometry based targeted proteomics for cell and tissue analysis -- Metabolomic investigation of Staphylococcus aureus antibiotic susceptibility by liquid chromatography coupled to high resolution mass spectrometry -- Nuts and bolts of protein quantification by on-line trypsin digestion coupled LC-MS/MS analysis -- Proteases: Pivot Points in Functional Proteomics -- The Use of Combinatorial Hexapeptide Ligand Library (CPLL) in Allergomics -- Efficient Extraction and Digestion of Gluten Proteins -- Glycosylation profiling of tumor marker in plasma using bead-based immunoassay -- Protein-specific analysis of invertebrate glycoproteins -- The use of proteomics studies in identifying moonlighting proteins -- Two-dimensional biochemical purification for global proteomic analysis of macromolecular protein complexes -- A data analysis protocol for quantitative data-independent acquisition proteomics
    Abstract: This book seeks to fill in the current technology gap with a specific collection of technologies developed for the study of protein function at a proteome scale. Chapters explore topics from protein functions to other aspects of protein analysis, especially in post-translational modification, as most proteomes use this mechanism in some capacity to carry out their unique role in cellular regulation. By comparing functional proteomes, this presents a bridge to other levels of system biology research including genomics and metabolomics in order to provide readers with a relatively complete picture for how one might study the biological system of their interest. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Functional Proteomics: Methods and Protocols collects these novel technologies in the hope that new frontiers in biological research will be created, important drug targets can be identified, and clinically validated biomarkers and diagnostic tests can be further developed
    Pages: XII, 477 p. 89 illus., 63 illus. in color. : online resource.
    ISBN: 9781493988143
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  • 2
    Keywords: Biochemistry ; Protein Science ; Springer eBooks
    Description / Table of Contents: Biophysical and Spectroscopic Methods for Monitoring Protein Misfolding and Amyloid Aggregation -- Ultrasensitive RT-QuIC Seed Amplification Assays for Disease-Associated Tau, α-Synuclein, and Prion Aggregates -- Vesicle-Based Assays to Study Membrane Interactions of Amyloid Peptides -- Differential Scanning Fluorimetry and Hydrogen Deuterium Exchange Mass Spectrometry to Monitor the Conformational Dynamics of NBD1 in Cystic Fibrosis -- A Multipronged Method for Unveiling Subtle Structural-Functional Defects of Mutant Chaperone Molecules Causing Human Chaperonopathies -- High-Throughput Microplate-Based Fluorescence Assays for Studying Stochastic Aggregation of Superoxide Dismutase-1 -- Methods for Structural Analysis of Amyloid Fibrils in Misfolding Diseases -- Assays for Light Chain Amyloidosis Formation and Cytotoxicity -- Monitoring Aggregate Clearance and Formation in Cell-Based Assays -- Monitoring Proteome Stress in Live Cells Using HaloTag-Based Fluorogenic Sensor -- Quantification of Protein Aggregates Using Bimolecular Fluorescence Complementation -- Screening Protein Aggregation in Cells Using Fluorescent Labels Coupled to Flow Cytometry -- Induction of Cu/Zn Superoxide Dismutase (SOD1) Aggregation in Living Cells -- A Cell Model for HSP60 Deficiencies: Modeling Different Levels of Chaperonopathies Leading to Oxidative Stress and Mitochondrial Dysfunction -- Super-Resolution Fluorescence Imaging of Mutant Huntingtin Aggregation in Cells -- Thermal Shift and Stability Assays of Disease-Related Misfolded Proteins Using Differential Scanning Fluorimetry -- Methods to Screen Compounds against Mutant p53 Misfolding and Aggregation for Cancer Therapeutics -- Early Stage Discovery and Validation of Pharmacological Chaperones for the Correction of Protein Misfolding Diseases -- Constructing Kinetically Controlled Denaturation Isotherms of Folded Proteins Using Denaturant-Pulse Chaperonin Binding -- In Vitro Prion Amplification Methodology for Inhibitor Screening -- SolubiS: Optimizing Protein Solubility by Minimal Point Mutations
    Abstract: This detailed book gathers a broad collection of experimental approaches to assist researchers in setting up different methods to investigate protein conformational disorders. Beginning with a section on assays focusing on biophysical approaches to study protein (mis)folding, the volume continues with sections on cellular and proteostasis assays as well as assays for protein folding correction and recovery, combining methods such as thermal shift assays, in silico improvement of protein solubility, and compound screening, an important area of research as it may open avenues for therapeutic strategies. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips for troubleshooting and avoiding known pitfalls. Authoritative and practical, Protein Misfolding Diseases: Methods and Protocols serves as an ideal guide for researchers seeking to advance our knowledge of protein conformational disorders
    Pages: XIII, 338 p. 77 illus., 58 illus. in color. : online resource.
    ISBN: 9781493988204
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  • 3
    Keywords: Botany ; Plant Sciences ; Springer eBooks
    Description / Table of Contents: Phytoplasmas: An Introduction -- Micro-tom Tomato Grafting for Stolbur-phytoplasma Transmission: Different Grafting Techniques -- Phytoplasma Transmission: Insect Rearing and Infection Protocols -- Sampling Methods for Leafhopper, Planthopper, and Psyllid Vectors -- Symptoms of Phytoplasma Diseases -- Comparison of Different Procedures for DNA Extraction for Routine Diagnosis of Phytoplasmas -- Standard Detection Protocol: PCR and RFLP Analyses Based on 16S rRNA Gene -- PCR-based Sequence Analysis on Multiple Genes other than 16S rRNA Gene for Differentiation of Phytoplasmas -- Real-time PCR Protocol for Phytoplasma Detection and Quantification -- Duplex TaqMan Real-Time PCR for Rapid Quantitative Analysis of a Phytoplasma in its Host Plant without External Standard Curves -- A Multiplex-PCR Method for Diagnosis of AY-Group Phytoplasmas -- One-step Multiplex Quantitative RT-PCR for the Simultaneous Detection of Viroids and Phytoplasmas -- A Rapid Protocol of Crude RNA/DNA Extraction for RT-qPCR Detection and Quantification -- Quantitative Analysis with Droplet Digital PCR -- Rapid Sample Preparation and LAMP for Phytoplasma Detection -- Assembly of Phytoplasma Genome Drafts from Illumina Reads using Phytoassembly -- Protocol for the Definition of a Multi-Spectral Sensor for Specific Foliar Disease Detection: Case of ‘Flavescence Dorée’ -- Transcriptomic Analyses of Phytoplasmas -- Transcriptomic Analyses of Phytoplasmas -- Laser Microdissection of Phytoplasma-infected Grapevine Leaf Phloem Tissue for Gene Expression Study -- Collection of Phloem Sap in Phytoplasma-infected Plants -- DAPI and Confocal Laser-Scanning Microscopy for in vivo Imaging of Phytoplasmas -- Immunofluorescence Assay to Study Early Events of Vector Salivary Gland Colonization by Phytoplasmas -- Characterization of Phytoplasmal Effector Protein Interaction with Proteinaceous Plant Host Targets using Bimolecular Fluorescence Complementation (BiFC) -- Collection, Identification, and Statistical Analysis of Volatile Organic Compound Patterns Emitted by Phytoplasma Infected Plants -- Quantification of Phytohormones by HPLC-MS/MS Including Phytoplasma-infected Plants
    Abstract: This book presents a set of modern protocols forming a solid background for who want to start or improve research programme on phytoplasmas. Chapters guide readers through detailed techniques for maintaining phytoplasma collections, border inspection, detection of different phytoplasma strains, new pipelines to produce phytoplasma genome draft, protocols for phytoplasma gene expression analyses, and methods for the investigation of the phloem tissue. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Phytoplasmas: Methods and Protocols aims to ensure successful results in the further study of this vital field
    Pages: XI, 362 p. 75 illus., 64 illus. in color. : online resource.
    ISBN: 9781493988372
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  • 4
    Keywords: Oncology ; Neurosciences ; Cancer Research ; Neurosciences ; Springer eBooks
    Description / Table of Contents: Introduction to Brain Tumor Stem Cells -- Isolation and Culture of Glioblastoma Brain Tumor Stem Cells -- Establishment and Culture of Patient-Derived Primary Medulloblastoma Cell Lines -- Bioinformatic Strategies for the Genomic and Epigenomic Characterization of Brain Tumors -- Detecting Stem Cell Marker Expression Using the NanoString nCounter System -- Flow Cytometric Analysis of Brain Tumor Stem Cells -- In Vitro Self-Renewal Assays for Brain Tumor Stem Cells -- Differentiation of Brain Tumor Initiating Cells -- The Study of Brain Tumor Stem Cell Migration -- The Study of Brain Tumor Stem Cell Invasion -- Cell Cycle Dynamics in Glioma Cancer Stem Cells -- Embryonic Stem Cell Models of Human Brain Tumors -- Chromatin Immunoprecipitation (ChIP) Protocols for the Cancer and Developmental Biology Laboratory -- EPH Profiling of BTIC Populations in Glioblastoma Multiforme Using CyTOF -- Pooled Lentiviral CRISPR-Cas9 Screens for Functional Genomics in Mammalian Cells -- In Vitro Assays for Screening Small Molecules -- Drug Delivery in an Orthotopic Tumor Stem Cell-Based Model of Human Glioblastoma -- Engineering Inducible Knock-In Mice to Model Oncogenic Brain Tumor Mutations from Endogenous Loci -- In Vivo Murine Models of Brain Metastasis -- Cellular Magnetic Resonance Imaging for Tracking Metastatic Cancer Cells in the Brain
    Abstract: This detailed volume compiles the best methodologies and experimental techniques to profile and extract maximal data from brain tumor stem cells (BTSCs), the experimental paradigm for brain cancer research that offers insights into cancer stem cell populations that may drive not only tumor initiation but tumor recurrence and patient relapse. The BTSC model recapitulates scientific observations made in brain cancer patients, and these chapters provide the reader with a comprehensive understanding of the skills and techniques that will unlock data from this most informative subset of cells. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Brain Tumor Stem Cells: Methods and Protocols serves as an ideal guide for researchers seeking to better understand the complexities of brain cancer
    Pages: XII, 254 p. 40 illus., 34 illus. in color. : online resource.
    ISBN: 9781493988051
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  • 5
    Keywords: Cytology ; Cell Biology ; Springer eBooks
    Description / Table of Contents: Detecting Cellular Senescence in Reprogramming -- DNA Damage In situ Ligation followed by Proximity Ligation Assay (DI-PLA) -- Reactive Oxygen Species Detection in Senescent Cells -- Cellular Identification and Quantification of Senescence-associated β-Galactosidase Activity in vivo -- Relative Human Telomere Length Quantification by Real-time PCR -- Assessing Functional Roles of the Senescence-associated Secretory Phenotype (SASP) -- Measuring the Inflammasome in Oncogene-induced Senescence -- Alarmin Detection in Senescent Cells -- IMR90 ER:RAS: A Cell Model of Oncogene-induced Senescence -- Genotoxic Stress-induced Senescence -- A Multi-parametric Assay to Evaluate Senescent Cells -- A Novel Quantitative Method for the Detection of Lipofuscin, the Main Byproduct of Cellular Senescence, in Fluids -- Measurement of Metabolite Changes in Senescent Cells by Mass Spectrometry -- Quantification of Autophagy during Senescence -- Quantification of Aneuploidy in Mammalian Systems -- Identification of Genomic Alterations Through Multi-Level DNA Structural Analysis -- Mouse Models of Accelerated Cellular Senescence -- Methods to Quantify the NF-kB Pathway during Senescence
    Abstract: This book describes current methods for the identification and characterization of the major hallmarks of senescent cells. Chapters focus on the high heterogeneity of the senescence phenotypes, and techniques to induce and identify specific senescence programs. Additional chapters describe cellular and mouse models in which is possible to study the complex cell and non-cell autonomous functions of senescent cells. Written in the highly successful Methods in Molecular Biologyseries format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Cellular Senescence: Methods and Protocols aims to ensure successful results in the further study of this vital field
    Pages: XII, 253 p. 45 illus., 38 illus. in color. : online resource.
    ISBN: 9781493989317
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  • 6
    Keywords: Medicine ; Molecular Medicine ; Springer eBooks
    Description / Table of Contents: Traditional Prenatal Diagnosis: Past to Present -- Overview of Preimplantation Genetic Diagnosis (PGD): Historical Perspective and Future Direction -- Non-Invasive Approaches to Prenatal Diagnosis: Historical Perspective and Future Directions -- Molecular Testing for Preimplantation Genetic Diagnosis of Single Gene Disorders -- Detection of Aneuploidy and Unbalanced Rearrangements using Comparative Genomic Hybridization Microarrays -- Aneuploidy Screening using Next Generation Sequencing -- DNA Extraction from Various Types of Prenatal Specimens -- Assessment of Maternal Cell Contamination in Prenatal Samples by Quantitative Fluorescent PCR (QF-PCR) -- Rapid Prenatal Aneuploidy Screening by Fluorescence In Situ Hybridization (FISH) -- Prenatal Detection of Chromosome Aneuploidy by Quantitative Fluorescence PCR -- Multiplex Ligation-Dependent Probe Amplification (MLPA) for Prenatal Diagnosis of Common Aneuploidies -- Chromosomal Microarray Analysis using Array Comparative Genomic Hybridization on DNA from Amniotic Fluid and Chorionic Villus Sampling -- Prenatal Diagnosis using Chromosomal SNP Microarrays -- Rapid Detection of Fetal Mendelian Disorders: Thalassemia and Sickle Cell Syndromes -- Prenatal Diagnosis of Cystic Fibrosis -- Prenatal Diagnosis of Tay-Sachs Disease -- Next-Generation Sequencing of Prenatal Structural Chormosomal Rearrangements using Large-Insert Libraries -- Prenatal Diagnosis by Whole Exome Sequencing in Fetuses with Ultrasound Abnormalities -- Quad Screen Test, A Multiplexed Biomarker Assay for Prenatal Screening to Assess Birth Defects: The Columbia University Experience using the Beckman Access2 Immunoassay Analyzer and Benetech PRA -- Isolation of Cell-Free DNA from Maternal Plasma -- Noninvasive Detection of Fetal Aneuploidy using Next-Generation Sequencing -- Noninvasive Antenatal Screening for Fetal RHD in RhD Negative Women to Guide Targeted Anti-D Prophylaxis
    Abstract: This second edition volume expands on the first edition with more detailed methodologies on prenatal testing and diagnosis, and also covers next-generation sequencing techniques. The chapters in this book are divided into three sections: preimplantation genetic testing, traditional prenatal testing, and non-invasive prenatal testing. This book covers topics such as molecular testing for preimplantation genetic diagnosis of single gene disorders; DNA extraction from various types of prenatal specimens; prenatal diagnosis of cystic fibrosis and Tay-Sachs disease; chromosomal SNP microarrays; and isolation of cell-free DNA from maternal plasma. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Prenatal Diagnosis, Second Edition is a valuable resource for any researcher interested in reproducing these techniques in their clinical laboratories
    Pages: XI, 363 p. 35 illus., 28 illus. in color. : online resource.
    Edition: 2nd ed. 2019.
    ISBN: 9781493988891
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  • 7
    Keywords: Plant Ecology ; Anthropology ; Plant anatomy ; Plant physiology ; Plant Systematics/Taxonomy/Biogeography ; Plant Ecology ; Anthropology ; Plant Anatomy/Development ; Plant physiology ; Springer eBooks
    Description / Table of Contents: Preface -- Overview -- Preparation of qualitative research -- Execution of the qualitative research -- Participant observation and Field Journal -- Audio and video recording techniques for ethnobiological research -- Discourse of the collective subject as a method for analysis of data in ethnobiological research -- Qualitative data analysis -- The meta-analytical and macroecological approach of Ethnobiology -- Collection and analysis of risks associated with environmental changes -- Sensitivity to harvesting and local risk indexes in ethnobotanical research -- The use of multivariate tools in the study of traditional resource management systems -- Multidimensional analysis for testing conservation, ecological and ethnobiological hypotheses -- Ethnoecology in pluricultural contexts -- Ethnobotany and ethnoecology applied to historical ecology -- Biocultural collections -- Accessing the traditional knowledge on the use of cryptogams -- Ethical considerations and protocols in ethnoecological and ethnobiological research -- Challenges in ethnozoological research -- Methodology applied to geographical indication -- Recent advances in research methods and techniques -- Chemical profile and antioxidant activity of natural products.-Collection and extraction of fatty acids from animals and their possible applications in ethnopharmacological research -- Advanced methods in the chemical analysis of medicinal plants -- Population ecology of plant species submitted to extractivism -- Methods for measuring hunting pressure -- Rapid sampling techniques for vertebrate fauna -- Techniques for analyzing the sustainability of hunting -- Description of technological processes for optimization and enhancement of local uses -- Index
    Abstract: Ethnobiology and ethnoecology have become very popular in recent years. Particularly in the last 20 years, many manuals of methods have published the most classical approaches to the subject. There have been, however, many advances in research as a result of interaction with different disciplines, but also due to more recent results, new original and interesting questions. This handbook provides the current state of the art methods and techniques in ethnobiology and ethnoecology, and related fields. This new volume, besides bringing new and original aspects of what is found in the literature, fills some of the gaps in volume one by including the most systematic and extensive treatment of methods and techniques in qualitative research. Along with the various methods covered in the individual chapters, the handbook also includes an extensive bibliography that details the current literature in the field
    Pages: XVI, 342 p. 42 illus., 24 illus. in color. : online resource.
    Edition: 2nd ed. 2019.
    ISBN: 9781493989195
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  • 8
    Keywords: Biochemistry ; Protein Science ; Springer eBooks
    Description / Table of Contents: How It All Began: A Personal History of Gel-Electrophoresis -- Introduction to Protein Electrophoresis -- Concentrating Proteins by Salt, Polyethylene Glycol, Solvent, SDS Precipitation, Three Phase Partitioning, Dialysis, Centrifugation, Ultrafiltration, Lyophilisation, Affinity Chromatography, Immunoprecipitation or Increased Temperature for Protein Isolation, Drug Interaction, and Proteomic and Peptidomic Evaluation -- Lysis Buffer Choices are Key Considerations to Ensure Effective Sample Solubilization for Protein Electrophoresis -- The Cydex Blue Assay: A One Step Protein Assay for Samples Prior to SDS Electrophoresis -- Cellulose-Acetate Electrophoresis of Hemoglobin -- Native Polyacrylamide Gels -- Isoelectric Focusing on Non-Denaturing Gels -- Determination of protein Molecular weights on SDS-PAGE -- Two-Dimensional Gel Electrophoresis by Glass Tube-Based IEF and SDS-PAGE -- Cationic Electrophoresis -- Two-Dimensional Gel Electrophoresis with Immobilized pH Gradients -- SARCOSYL-PAGE: Optimized Protocols for the Separation and Immunological Detection of PEGylated Proteins -- Tricine-SDS-PAGE -- Analysis of Protein Glycation using Phenylboronate Acrylamide Gel Electrophoresis -- Immunofixation Electrophoresis for Identification of Proteins and Specific Antibodies -- Electrophoretic Separation of Very Large Molecular Weight Proteins in SDS-Agarose -- Increase in Local Protein Concentration by Field-Inversion Gel Electrophoresis -- Two-Dimensional Difference Gel Electrophoresis -- Immunoelectrophoresis: A Method with Many Faces -- Tris-Acetate Polyacrylamide Gradient Gels for the Simultaneous Electrophoretic Analysis of Proteins if Very High and Low Molecular Mass -- Diagnoal Electrophoresis for Detection of Proteins Involved in Disulfide Bonds -- Identification of Proteins on Archived 2D Gels -- Two-Dimensional Gel Electrophoresis: Vertical Isoelectric Focusing -- A Foodomics Approach: CE-MS for Comparative Metabolomics of Colon Cancer Cells Treated with Dietary Polyphenols -- Characterization of New Cyclic D, L – α – Alternate Amino Acid Peptides by Capillary Electrophoresis Coupled to Electrospray Ionization Mass Spectrometry -- “Microchip Electrophoresis”, with Respect to “Profiling of Aß Peptides in the Cerebrospinal Fluid of Patients with Alzheier’s Disease” -- Measuring Low-Picomolar Apparent Binding Affinities by Minigel Electrophoretic Mobility Shift -- Identification of Proteins Interacting with Single Nucleotide Polymorphisms (SNPs) by DNA Pull-Down Assay -- Horizontal Agarose Gel Mobility Shift Assay for Protein-RNA Complexes -- Applications of Immobilized Metal affinity Electrophoresis -- Isoelectric Focusing in Agarose Gel for Detection of Oligoclonal Bands in Cerebrospinal and Other Biological Fluids -- A Combined Free Flow Electrophoresis and DIGE Approach to Compare Proteins in Complex Biological Samples -- SDS PAGE for 35S Immunoprecipitation and Immunoprecipitation Western Blotting -- A Multichannel Gel Electrophoresis and Continuous Fraction Collection Apparatus for High-Throughput Protein Separation and Characterization -- Cell Surface Protein Biotinylation for SDS-PAGE Analysis -- Isolation of Proteins from Polyacrylamide Gels -- Continuous Elution SDS-PAGE with a Modified Standard Gel Apparatus to Separate and Isolate an Array of Proteins from Complex Mixtures -- Protein Extraction from Gels: A Brief Review -- Gel Absorption-Based Sample Preparation Method for Shotgun Analysis of Membrane Proteome -- Ultra-Rapid Sodium Dodecyl Sulfate Polyacrylamide Mini-Gel Electrophoresis -- A Brief Review of Other Notable Electrophoretic Methods -- Single-Cell High Resolution Detection and Quantification of Protein Isoforms Differing by a Single Charge Unit -- Artifacts and Common Errors in Protein Gel Electrophoresis
    Abstract: This volume expands upon Protein Electrophoresis (2012) and provides readers with easy-to-follow and reproducible methods to study electrophoresis. The chapters in this book cover topics such as the Cydex Blue assay; cellulose-acetate electrophoresis of hemoglobin; cationic electrophoresis; tricine-SDS-Page; identification of proteins on archived 2-D gels; cell surface protein biotinylation of SDS-PAGE analysis; and artifacts and common errors in protein gel electrophoresis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Electrophoretic Separation of Proteins: Methods and Protocols is a valuable resource for researchers who are interested in learning and experimenting with this field
    Pages: XV, 523 p. 112 illus., 61 illus. in color. : online resource.
    ISBN: 9781493987931
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  • 9
    Keywords: Human Genetics ; Human Genetics ; Springer eBooks
    Description / Table of Contents: Arthropod Genome Sequencing and Assembly Strategies -- Genome Size Estimation and Quantitative Cytogenetics in Insects -- Isolation of HMW DNA from Insects Chapter -- Long range sequencing and assembly QC -- Integrated modeling of structural genes using MCuNovo -- Using BUSCO to Assess Insect Genomic Resources -- The GFF3toolkit—QC and Merge Pipeline for Genome Annotation -- Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to identify functional regulatory DNA in insect genomes -- Using RAMPAGE to identify and annotate promoters in insect genomes -- CRM Beyond Model Insects -- Whole-genome bisulfite sequencing for the methylation analysis of insect genomes -- Bioinformatic analysis of methylation patterns using bisulfite sequencing data -- Physical Genome Mapping Using Fluorescence in Situ Hybridization with Mosquito Chromosomes -- Target enriched RAD sequencing (TEEseq): A new high-throughput sequencing approach applied to the comprehensive characterization of endosymbionts
    Abstract: This volume focuses on the latest methods used to sequence, assemble, and analyze insect genomes. The collection of protocols in this book provides an introduction to the workflows and bioinformatics tools available for researchers. The chapters cover a range of useful topics such as determining genome size by flow cytometry; High Molecular Weight DNA extraction; improvements to a genome assembly provided by long-range sequencing approaches; assessments of orthology and single-copy genes at different phylogenetic levels; detecting regulatory regions with FAIRE, RAMPAGE, and computational analysis of cis-regulatory modules in insects; bioinformatics analysis of epigenetic modifications, high-throughput scanning of insect genomes (TEEseq) for the presence of endosymbionts, and leveraging genome sequence information to design RNAi strategies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Insect Genomics: Methods and Protocols is a valuable resource for graduate students, postdocs, and novice research scientists who are interested in learning more about this developing field
    Pages: XI, 237 p. 34 illus., 23 illus. in color. : online resource.
    ISBN: 9781493987757
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  • 10
    Keywords: Medicine ; Molecular Medicine ; Springer eBooks
    Description / Table of Contents: Common Cell Lines Used to Study Bone Morphogenetic Proteins (BMPs) -- In Vitro and In Vivo Osteogenic Differentiation of Human Adipose-Derived Stromal Cells -- Cell-based Gene Therapy System for Delivering BMPs -- Generation of Endogenous BMP Transcriptional Reporter Cells through CRISPR/Cas9 Genome Editing -- High-Throughput, Biosensor-based Approach to Examine Bone Morphogenetic Protein (BMP) – Receptor Interactions -- Mutagenesis and Imaging studies of BMP Signaling Mechanisms in C. elegans -- Gene Regulation of BMP Ligands in Drosophila -- Using Amphioxus as a Basal Chordate Model to Study BMP Signaling Pathway -- Proteolytic Activation of Bmps: Analysis of Cleavage in Xenopus Oocytes and Embryos -- Imaging and quantification of P-Smad1/5 in zebrafish blastula and gastrula embryos -- An Adult Zebrafish Model of Fibrodysplasia Ossificans Progressiva -- Generation and Identification of Genetically Modified Mice for BMP Receptors -- Phenotypic Analyses of Genetically Modified Mice for BMP Receptors -- Immunofluorescent Visualization of BMP Signaling Activation on Paraffin-embedded Tissue Sections -- Spatial and Quantitative Detection of BMP Activity in Mouse Embryonic Limb Buds -- Pharmacologic Strategies for Assaying BMP Signaling Function -- Bone Morphogenetic Proteins (BMPs) and Bone Regeneration -- Heterotopic Ossification in Mouse Models of Fibrodysplasia Ossificans Progressiva -- Double-Humanized Mouse Model to Study Bone Morphogenetic Protein (BMP) Signaling in Tumor Xenografts
    Abstract: This volume provides methods to study bone morphogenetic proteins (BMPs) and BMP modulators in cell culture, in both invertebrate and vertebrate animal models, and for therapeutic applications. Chapters guide the reader in the use of primary and immortalized cell lines, methodologies that exploit transcription and receptor mechanisms, newly developed animal models using nematodes, flies, amphioxus, frogs, zebrafish, and genetically engineered mice, and pre-clinical approaches to understanding BMP function in bone regeneration, heterotopic ossification, and cancers. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bone Morphogenetic Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field
    Pages: XII, 265 p. 37 illus., 27 illus. in color. : online resource.
    ISBN: 9781493989041
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  • 11
    Keywords: Cytology ; Cell Biology ; Springer eBooks
    Description / Table of Contents: A Protocol to Compare Methods for Untargeted Metabolomics -- High Throughput Measure of Bioactive Lipids Using Non-targeted Mass Spectrometry -- Measuring the Nutrient Metabolism of Adherent Cells in Culture -- 13C Tracer Analysis and Metabolomics in 3D Cultured Cancer Cells -- Measuring In Vivo Tissue Metabolism using 13C Glucose Infusions in Mice -- Measuring Human Lipid Metabolism using Deuterium Labeling: In vivo and in vitro -- Measuring Rates of ATP Synthesis -- Direct Estimation of Metabolic Flux by Heavy Isotope Labeling Simultaneous with Pathway Inhibition: Metabolic Flux Inhibition Assay -- Measuring Glycolytic and Mitochondrial Fluxes in Endothelial Cells using Radioactive Tracers -- Determining Compartment Specific Metabolic Fluxes -- Determining the Impact of Metabolic Nutrients on Autophagy -- Measuring the Activation of Cell Death Pathways upon Inhibition of Metabolism -- Determining Macrophage Polarization upon Metabolic Perturbation -- Assessing the Impact of the Nutrient Microenvironment on The Metabolism of Effector CD8+ T Cells -- Development of Patient-derived Tumor Xenograft Models -- Imaging Glioma Progression by Intravital Microscopy -- Lipectomizing Mice for Applications in Metabolism -- Quantitative Multiplex Immunoassay for Profiling Bone Turnover Biomarkers in Human Bone Tissue Culture Supernatants -- Determining the Intracellular Organization of Organelles -- The Fundamentals of Constructing and Interpreting Heat Maps
    Abstract: This book provides protocols to quantify metabolism, to identify metabolic crosstalk, and to setup and develop tools and models to gain insight into metabolic signaling using experimental and computational approaches. Chapters detail protocols to quantify metabolism, identify metabolic crosstalk, and develop tools and models to gain a systems-level insight into metabolic signaling. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metabolic Signaling: Methods and Protocols aims to provide researchers with methods to study, perturb, and functionally interpret metabolism and metabolic signaling from the sub-cellular to the whole-body level
    Pages: XII, 294 p. 67 illus., 53 illus. in color. : online resource.
    ISBN: 9781493987696
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  • 12
    Keywords: Biochemistry ; Biochemistry, general ; Springer eBooks
    Description / Table of Contents: Molecular Dynamics Simulations of the SNARE Complex -- Mesoscale Computational Modelling of Protein-membrane Interactions based on Continuum Mean-field Theory -- EPR Lineshape Analysis to IOnvestigate the SNARE Folding Intermediates -- Dynamic Light Scattering Analysis to Dissect Intermediates of SNARE-Mediated Membrane Fusion -- Kinetic and Thermodynamic Quantification of Protein Complex Assembly: The Example of SNAREpins -- Single-molecule Optical Tweezers Study of Regulated SNARE Assembly -- Studying Munc18:Syntaxin Interactions using Small-angle Scattering -- Using Force Spectroscopy to Probe Coiled-Coil Assembly and Membrane Fusion -- SNAP25 S-Guanylation and SNARE Complex Formation -- Analysis of the Role of Sec3 in SNARE Assembly and Membrane Fusion -- Use of Microscale Thermophoresis (MST) to Measure Binding Affinities of Components of the Fusion Machinery -- Use of Surface Plasmon Resonance (SPR) to Determine Binding Affinities and Kinetic Parameters Between Components Important in Fusion Machinery -- Determination of Sec18-Lipid Interactions by Liposome Binding Assay -- Using Nanodiscs to Probe Ca2+-dependent Membrane Interaction of Synaptotagmin-1 -- Functional reconstitution of Intracellular Vesicle Fusion using Purified SNAREs and Sec1/Munc18 (SM) Proteins -- Assay of Lipid Mixing and Fusion Pore Formation in the Fusion of Yeast Vacuoles -- A nanodisc-cell Fusion Assay with Single Pore Sensitivity and Sub-millisecond Time Resolution -- An In Vitro Assay of trans-SNARE Complex Formation during Yeast Vacuole Fusion using Epitope Tag-free SNAREs -- A Cell-Free Content Mixing Assay for SNARE-Mediated Multivesicular Body-Vacuole Membrane Fusion -- Reconstituted Proteoliposome Fusion Mediated by yeast SNARE-family Proteins -- Real-Time Fluorescence Detection of Calcium Efflux during Vacuolar Membrane Fusion -- Single Molecule Fluorescence Measurement of SNARE-mediated Vesicle Fusion -- Quantifying Intramolecular Protein Conformational Dynamics under Lipid Interaction using smFRET and FCCS -- Visualization of SNARE-Mediated Organelle Membrane Hemifusion By Electron Microscopy -- Studies of the Secretory Machinery Dynamics by Total Internal Reflection Fluorescence Microscopy in Bovine Adrenal Chromaffin Cells -- Imaging SNAP-29 in Drosophila
    Abstract: This book details multiple ways that soluble N-ethylmaleimide-sensitive factor attachment protein receptors( SNAREs) and their function are examined in the laboratory. The methods described in each chapter are described in detail so that novice as well as experienced researchers can explore the mechanisms of SNARE-mediated membrane fusion. Chapters guide readers through an overview of the basic properties of SNAREs, distribution and interaction with regulators of membrane fusion, activation of SNAREs in the priming stage by NSF/Sec18 and a-SNAP/Sec17, examining the structures and interactions of SNAREs, measuring the interactions of SNAREs, interactions of SNAREs, and post-translational modifications of SNAREs and how they affect function.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, SNAREs: Methods and Protocols aims to be a valuable tool for all investigators interested in the field
    Pages: XIV, 407 p. 74 illus., 66 illus. in color. : online resource.
    ISBN: 9781493987603
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  • 13
    Keywords: Oncology ; Cancer Research ; Springer eBooks
    Description / Table of Contents: Usage of Droplet Digital PCR (ddPCR) Assays for T Cell Quantification in Cancer -- An Economical, Quantitative, and Robust Protocol for High Throughput T Cell Receptor Sequencing from Tumor or Blood -- Generation of Tumor Antigen-Specific Cytotoxic T Lymphocytes from Pluripotent Stem Cells -- Expansion and Adoptive Transfer of Human Vδ2+ T Cells to Assess Anti-Tumor Effects In Vivo -- Usage of Single-Cell RNA-Sequencing to Unveil Immune Lymphoid Cell Precursors -- Isolation, Expansion, and Characterization of Natural Killer Cells and Their Precursors as a Tool to Study Cancer Immunosurveillance -- CD107a Degranulation Assay to Evaluate Immune Cell Anti-Tumor Activity -- A Flow Cytometric NK Cell-Mediated Cytotoxicity Assay to Evaluate Anti-Cancer Immune Responses In Vitro -- Mouse Models to Study Natural Killer Cell-Mediated Immunosurveillance and Metastatic Latency -- Tumor-Associated Macrophage Isolation and In Vivo Analysis of their Tumor Promoting Activity -- Conditional Genetic Ablation Mouse Models as a Tool to Study Cancer Immunosurveillance In Vivo -- Determination and Isolation of Immune Populations from Brain Tumor Microenvironments -- Mouse Model of Colitis Associated Colorectal Cancer (CAC): Isolation and Characterization of Mucosal-Associated Lymphoid Cells -- Cancer Exome-Based Identification of Tumor Neo-Antigens Using Mass Spectrometry -- Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways -- Purification of Leukemia-Derived Exosomes to Study Microenvironment Modulation -- Molecular Characterization of Circulating Tumor Cells to Study Cancer Immunoevasion -- Quantitative Identification of Senescent Cells in Cancer -- Generation and Harnessing of Heterotypic Tumor-Stroma Spheroids to Study Cancer Immunosurveillance -- Establishment of Slice Cultures as a Tool to Study the Cancer Immune Microenvironment -- Gold Standard Assessment of Immunogenic Cell Death in Oncological Mouse Models -- A Novel Dendritic Cell-Based Vaccination Protocol to Stimulate Immunosurveillance of Aggressive Cancers -- Development of Bi-Specific Antibody Derivatives for Cancer Immunotherapy -- Generation of CAR-T Cells for Cancer Immunotherapy
    Abstract: This volume explores the latest techniques used to study tumor immunology. The chapters in this book detail methodologies for functional analysis and expansion of T lymphocytes for cancer research. The chapters also cover topics such as how single-cell RNA-sequencing can be exploited to dissect immune cell heterogeneity and precursors; isolating and expanding natural killer (NK) cells; evaluating NK cell-mediated anti-tumor killing activity in vitro; immunosurveillance orchestrated by specific immune subsets; use of HLA peptidomics for cancer-exome based identification of tumor neo-antigens; gold standard assessment of immunogenic cell death in oncological mouse models and methods to look at the therapeutic relevance of immune modulation in cancer. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Cancer Immunosurveillance: Methods and Protocols is a valuable resource to aid researchers in better understanding and experimenting in this exciting and developing field
    Pages: XIII, 363 p. 76 illus., 63 illus. in color. : online resource.
    ISBN: 9781493988853
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  • 14
    Keywords: Plant breeding ; Agriculture ; Plant Breeding/Biotechnology ; Agriculture ; Springer eBooks
    Description / Table of Contents: An Introduction to Barley: The Crop and the Model -- Mutation Breeding in Barley: Historical Overview -- A Practical Guide to Barley Crossing -- Barley Anther Culture -- Isolated Microspore Culture in Barley -- TILLING in Barley -- Virus-Induced Gene Silencing (VIGS) for Functional Characterization of Disease Resistance Genes in Barley Seedlings -- Agrobacterium-Mediated Transformation of Barley Immature Embryos -- Methods for the Simple and Reliable Assessment of Barley Sensitivity to Abiotic Stresses during Early Development -- Preparation of Barley Roots for Histological, Structural, and Immunolocalization Studies Using Light and Electron Microscopy -- Preparation of Barley Pollen Mother Cells for Confocal and Super Resolution Microscopy -- Microarrays for High-Throughput Gene Expression Analysis of Barley -- Genome Engineering Using TALENs -- Creating Targeted Gene Knock-Outs in Barley Using CRISPR/Cas9 -- Genotyping-by-Sequencing on the Ion Torrent Platform in Barley -- DNA Methylation Analysis in Barley and Other Species with Large Genomes -- High Resolution RT-PCR Analysis of Alternative Barley Transcripts -- Exome Capture for Variant Discovery and Analysis in Barley
    Abstract: This detailed volume explores barley as both a crop and a model, with practical techniques such as crossing barley, a range of tissue culture methods, the preparation of barley tissues for different forms of microscopy, and the assessment of sensitivity to abiotic stresses. Efficient protocols are provided for transformation, TILLING, virus-induced gene silencing and genome editing. There is also particular emphasis on a range of protocols for genotyping and for the analysis of gene expression. Written for the highly successful Methods in Molecular Biology series, chapters include introductions on their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and easy-to-use, Barley: Methods and Protocols serves as a valuable reference volume for cereal researchers and breeders by providing detailed protocols covering important traditional skills such as crossing and tissue culture through to the latest technologies for genotyping, expression analysis, and genome editing
    Pages: XI, 313 p. 113 illus., 95 illus. in color. : online resource.
    ISBN: 9781493989447
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  • 15
    Keywords: Toxicology ; Pharmacology/Toxicology ; Springer eBooks
    Description / Table of Contents: An Introduction to Drug Testing – The Expanding Role of Mass Spectrometry -- Quantification of Eight Cannabinoids Including Cannabidiol in Human Urine Via Liquid Chromatography Tandem Mass Spectrometry -- Analysis of Benzodiazepines for Drug Facilitated Assaults and Abuse Settings (Urine) -- Targeted Opioid Screening Assay for Pain Management Using High Resolution Mass Spectrometry -- Measurement of Buprenorphine and Norbuprenorphine in Urine -- Quantitation of Tapentadol by Liquid Chromatography – Tandem Mass Spectrometry -- Therapeutic Drug Monitoring of Lacosamide by LC-MS/MS -- LC-MS/MS method for the quantification of the Leflunomide metabolite, Teriflunomide, in Human Serum/Plasma -- Analysis of Tryptic Peptides from Therapeutic Monoclonal Antibodies using LC-MS/MS -- Quantification of Methotrexate in Human Serum and Plasma by Liquid Chromatography Tandem Mass Spectrometry -- Simultaneous Determination of Tacrolimus and Cyclosporine A in Whole Blood by Ultra-Fast LC-MS/MS -- Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS) Method to Quantify Gabapentin and Pregabalin in Urine -- The Evolving Landscape of Designer Drugs -- Analysis of Synthetic Cannabinoid Metabolites by Liquid Chromatography-Tandem Mass Spectrometry -- Quantification of Designer Opioids by Liquid Chromatography Tandem Mass Spectrometry -- Screening Analysis for Designer Stimulants by LC-MS/MS -- Drug Screening Using Liquid Chromatography Quadrupole Time of Flight (LC-QqTOF) Mass Spectrometry -- Alternate Matrices – Meconium, Cord Tissue, Hair, and Oral Fluid -- Salt-assisted Liquid-Liquid Extraction of Meconium for Analysis of Cocaine and Amphetamines by Liquid Chromatography-tandem Mass Spectrometry -- Detection of In Utero Cannabis Exposure in Umbilical Cord Tissue by A Sensitive Liquid Chromatography–Tandem Mass Spectrometry Method -- Quantitation of Ethyl β-D-glucuronide in Human Umbilical Cord Tissue by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) -- Analysis of Drugs in Oral Fluid using LC-MS/MS -- Determination of Cocaine and Metabolites in Dried Blood Spots by LC-MS/MS
    Abstract: This second edition provides detailed LC-MS(/MS) procedures for the analysis of compounds of clinical and toxicological significance. Chapters detail new and updated methods for analyzing drugs focusing on advances in technology, alternate matrices, and rapidly-changing classes of drugs of abuse, compounds pertinent to toxicology, and therapeutic agents. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, LC-MS in Drug Analysis: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field
    Pages: X, 274 p. 36 illus., 24 illus. in color. : online resource.
    Edition: 2nd ed. 2019.
    ISBN: 9781493988235
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  • 16
    Keywords: Medicine ; Molecular Medicine ; Springer eBooks
    Description / Table of Contents: Identification and Analysis of Genes Associated with Inherited Retinal Diseases -- eQTL Analysis in Retinal Research -- Testing for known Retinal Degeneration Mutants in Mouse Strains -- CRISPR/Cas9 Gene Editing In Vitro and in Retinal Cells In Vivo -- Monitoring Surface Reactions by Combined Western Blot-ELISA Analysis -- Generation of Functional Retinal Pigment Epithelium from Human Induced Pluripotent Stem Cells -- Advanced Analysis of Photoreceptor Outer Segment Phagocytosis by RPE Cells in Culture -- Porcine RPE/Choroidal Explant Cultures -- The Mouse Retinal Organoid Trisection Recipe: Efficient Generation of 3D Retinal Tissue from Mouse Embryonic Stem Cells -- Cell Death Analysis in Retinal Cultures -- Fate Mapping In Vivo to Distinguish Bona Fide Microglia Versus Recruited Monocyte-derived Macrophages in Retinal Disease -- Light Damage Models of Retinal Degeneration -- Induction and Readout of Oxygen-Iinduced Retinopathy -- Generation and Analysis of Xenopus laevis Models of Retinal Degeneration using CRISPR/Cas9 -- Gene Knockdown in Zebrafish (Danio rerio) as a Tool to Model Photoreceptor Diseases -- Drosophila melanogaster - A Valuable Genetic Model Organism to Elucidate the Biology of Retinitis Pigmentosa -- Retinal Fundus Imaging in Mouse Models of Retinal Diseases -- Phenotyping of Mouse Models with OCT -- Cell-specific Markers for the Identification of Retinal Cells and Subcellular Organelles by Immunofluorescence Microscopy -- Immuno-TEM/STEM in Retinal Research -- Noninvasive Two-photon Microscopy Imaging of Mouse Retina and Retinal Pigment Epithelium -- Cell-based Therapy for Retinal Disease: The New Frontier -- In Vitro Evaluation of AAV Vectors for Retinal Gene Therapy -- Nanoparticles Targeting Retinal and Choroidal Capillaries In Vivo -- Optimized Subretinal Injection Technique for Gene Therapy Approaches
    Abstract: This volume provides key updates on several of the first edition chapters and also includes new novel techniques, addressing the most recent technological developments and their applications in retinal research. Chapters guide readers through gene identification approaches, detailed protocols to generate functional retinal pigment epithelium cells, mouse retina and other animal models, fundus imaging and angiography, and cell-based treatment approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Retinal Degeneration: Methods and Protocols, Second Edition aims to ensure successful scientific work in the further study of this vital field
    Pages: XIV, 417 p. 108 illus., 56 illus. in color. : online resource.
    Edition: 2nd ed. 2019.
    ISBN: 9781493986699
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  • 17
    Keywords: Biotechnology ; Human Genetics ; Biotechnology ; Human Genetics ; Springer eBooks
    Description / Table of Contents: Microinjection and Micromanipulation: A Historical Perspective -- Production of Transgenic Mice by Pronuclear Microinjection -- Transgene Recombineering in Bacterial Artificial Chromosomes -- Using TARGATTTM Technology to Generate Site-Specific Transgenic Mice -- Generating Genetically Engineered Mice Using a Spermatogonial Stem Cell-Mediated Method -- Chimeric Mouse Generation by ES Cell Blastocyst Microinjection and Uterine Transfer -- Creating Knock-In Alleles in Mouse Embryonic Stem Cells by CRISPR/Cas9-Mediated Homologous Recombination without Drug Selection -- Using CRISPR/Cas9 for Gene Knockout in Immunodeficient NSG Mice -- Generation of CRISPR-Edited Rodents Using a Piezo-Driven Zygote Injection Technique -- Delivery of CRISPR-Cas9 into Mouse Zygotes by Electroporation -- Generation of Conditional Knockout Mice by Sequential Insertion of Two loxP Sites In Cis Using CRISPR/Cas9 and Single-Stranded DNA Oligonucleotides -- Improvement of Mouse Cloning from Any Type of Cell by Nuclear Injection -- The CARD Method for Simple Vitrification of Mouse Oocytes: Advantages and Applications -- The CARD Method for Mouse Sperm Cryopreservation and In Vitro Fertilization Using Frozen-Thawed Sperm -- Isolation and Analysis of a Genome-Edited Single-Hepatocyte from a Cas9 Transgenic Mouse Line -- Microinjection and Oviduct Transfer Procedures for Rat Model Generation with CRISPR-Cas9 Technology -- Molecular Aspects of Zinc Finger Nucleases (ZFNs)-Mediated Gene Editing in Rat Embryos -- Organ Generation from Knocked-Out Rat Blastocysts Complemented with Pluripotent Stem Cells -- Generation of Rabbit Models by Gene Editing Nucleases -- Production of Genetically Engineered Porcine Embryos by Handmade Cloning -- Electrofusion of 2-Cell Embryos for Porcine Tetraploid Embryo Production -- Gene Knockouts in Goats Using CRISPR/Cas9 System and Somatic Cell Nuclear Transfer -- Generating Goat Mammary Gland Bioreactors for Producing Recombinant Proteins by Gene Targeting -- Production of Transgenic Chickens Using Cultured Primordial Germ Cells and Gonocytes -- Using Microinjection to Generate Genetically Modified Caenorhabditis elegans by CRISPR/Cas9 Editing -- Microinjection in Zebrafish for Genome Editing and Functional Studies -- Microinjection of Marine Fish Eggs -- Generating Gene Knockout Oryzias Latipes and Rice Field Eel Using TALENs Method -- Functional Studies of Transcriptional Cofactors via Microinjection-Mediated Gene Editing in Xenopus -- Microinjection of Live Mammalian Cells: A Delivery Method that Provides Added Versatility to the Study of Cellular Function
    Abstract: This detailed book explores how microinjection will be used in the foreseeable future, not only for generating animal models for biomedical research but also for changing economically or ecologically important species that can broadly impact our society in general. The opening half of the book focuses on methods for generating mouse models, as they are still the most popular in genome engineering research, while the second half examines gene-editing in a variety of other species, opened up by the developments in ZFN, TALEN, and CRISPR techniques. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microinjection: Methods and Protocols serves as an ideal guide for researchers looking to take advantage of the breakthrough technologies in gene-editing and embryo micromanipulations
    Pages: XIV, 540 p. 134 illus., 96 illus. in color. : online resource.
    ISBN: 9781493988310
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  • 18
    Keywords: Cytology ; Cell Biology ; Springer eBooks
    Description / Table of Contents: Purification of Myogenic Progenitors from Human Muscle Using Fluorescence-Activated Cell Sorting (FACS) -- Electrical Pulse Stimulation of Primary Human Skeletal Muscle Cells -- Transdifferentiation of Muscle Satellite Cells to Adipose Cells Using CRISPR/Cas9-Mediated Targeting of MyoD -- Chromatin Immunoprecipitation in Skeletal Myoblasts -- Exercising Bioengineered Skeletal Muscle In Vitro: Biopsy to Bioreactor -- Isolation and Purification of Satellite Cells from Young Rats by Percoll Density Gradient Centrifugation -- Lentivirus-Mediated RNAi in Skeletal Myogenesis -- Adipogenesis from Bovine Precursors -- Transcriptomic Profiling during Myogenesis -- Co-Culture Method to Obtain Endothelial Networks within Human Tissue-Engineered Skeletal Muscle -- Interaction between Skeletal Muscle Cells and Extracellular Matrix Proteins Using a Serum Free Culture System -- LC-MS Analyses of Lipid Species in Skeletal Muscle Cells and Tissue -- siRNA Gene Silencing during C2C12 Myogenesis -- Fluorescence-Activated Cell Sorting of Larval Zebrafish Muscle Stem/Progenitor Cells Following Skeletal Muscle Injury -- Preparation of Proliferated Bovine Primary Skeletal Muscle Cells for Bottom-Up Proteomics by LC-MSMS Analysis -- Myogenesis in Drosophila melanogaster: Dissection of Distinct Muscle Types for Molecular Analysis -- Measuring Both Glucose Uptake and Myosin Heavy Chain Isoform Expression in Single Rat Skeletal Muscle Fibers -- Myoblast Phosphoproteomics as a Tool to Investigate Global Signalling Events during Myogenesis -- Preparation and Culturing of Atlantic Salmon Muscle Cells for In Vitro Studies -- RNA Interference Screening for Genes Regulating Drosophila Muscle Morphogenesis
    Abstract: This detailed volume collects many of the common experimental approaches used to study myogenesis. It covers subjects ranging from isolation and purification protocols, manipulation of muscle cells, transcriptomics and proteomics, metabolism and exercise, and tissue engineering. Presented methods involve different species, including human, bovine, Atlantic salmon, rats, mice, larval zebrafish, and Drosophila melanogaster. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Myogenesis: Methods and Protocols aims to serve as an essential part of many laboratory libraries and to assist researchers throughout the world in revealing the unknowns of myogenesis
    Pages: XII, 351 p. 84 illus., 64 illus. in color. : online resource.
    ISBN: 9781493988976
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  • 19
    Keywords: Microbiology ; Microbiology ; Springer eBooks
    Description / Table of Contents: 1. Isolation and identification of lactic acid bacteria from environmental samples -- 2. Isolation and identification of lactic acid bacteria from environmental samples -- 3. Isolation and identification of lactic acid bacteria from environmental samples -- 4. Isolation and identification of lactic acid bacteria from environmental samples -- 5. Isolation and identification of lactic acid bacteria from environmental samples -- 6. Isolation and identification of lactic acid bacteria from environmental samples -- 7. Isolation and identification of lactic acid bacteria from environmental samples -- 8. Isolation and identification of lactic acid bacteria from environmental samples -- 9. Isolation and identification of lactic acid bacteria from environmental samples -- 10. Isolation and identification of lactic acid bacteria from environmental samples -- 11. Isolation and identification of lactic acid bacteria from environmental samples -- 12. Isolation and identification of lactic acid bacteria from environmental samples -- 13. Isolation and identification of lactic acid bacteria from environmental samples -- 14. Isolation and identification of lactic acid bacteria from environmental samples -- 15. Isolation and identification of lactic acid bacteria from environmental samples -- 16. Isolation and identification of lactic acid bacteria from environmental samples
    Abstract: This detailed book provides a collection of protocols for numerous experimental approaches perfected by the authors for lactic acid bacteria (LAB) research. Split in to three parts, the volume delves into the identification and metabolism of LABs, the applications of the bacteria for the food industry, as well as healthy functions of LAB. Written for the highly successful Methods in Molecular Biology series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Lactic Acid Bacteria: Methods and Protocols serves as an ideal inspiration for many research efforts in the domains of food science and health science
    Pages: X, 194 p. 58 illus., 10 illus. in color. : online resource.
    ISBN: 9781493989072
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  • 20
    Keywords: Electrophoresis ; Biotechnology ; Electrophoresis ; Biotechnology ; Springer eBooks
    Description / Table of Contents: Fabrication of Glass Microfluidic Devices -- Soft Lithography, Molding, and Micromachining Techniques for Polymer Micro Devices -- Sample Injection Techniques -- Sample Preconcentration Protocols in Microfluidic Electrophoresis -- Microchip Electrophoresis Containing Electrodes for Integrated Electrochemical Detection -- Micellar Electrokinetic Chromatography -- Microchip Isotachophoresis: Analysis of Pharmaceuticals -- Microfluidic Free-Flow Isoelectric Focusing with Real-Time pI Determination -- Nanochannel Gradient Separations -- Paper-Based Electrophoresis Microchip as a Powerful Tool for Bioanalytical Applications -- Band Broadening Theories in Capillary Electrophoresis -- Estimating Stream Broadening in Free-Flow Electrophoretic Systems Based on the Method-of-Moments Formulation -- Microchip Electrophoresis Tools for the Analysis of Small Molecules -- Integrated Microfluidic System for Rapid DNA Fingerprint Analysis: A Miniaturized Integrated DNA Analysis System (MiDAS): Swab Sample-In to DNA Profile-Out -- Achieving Stable Electrospray Ionization Mass Spectrometry (ESI-MS) Detection from Microfluidic Chips -- Microchip-Based Electrophoretic Separations with a Pressure-Driven Backflow
    Abstract: This detailed book provides a set of protocols necessary for the development of a variety of microchip-based electrophoretic assays. It compiles a range of such electrophoretic methods by leading researchers in the field, covering subjects such as microfluidic device fabrication, on-chip sample preparation, theoretical/simulation protocols for assessing these separation methods, as well as common practices followed when applying them to important real world applications. The contents of the book range from protocols for classical assays to those involving pioneering separation techniques recently developed by the scientific community for advancing our analytical capabilities. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Microfluidic Electrophoresis: Methods and Protocols serves as an convenient text for academic researchers as well as practicing engineers, biochemists, and analytical laboratory professionals
    Pages: X, 255 p. 93 illus., 47 illus. in color. : online resource.
    ISBN: 9781493989645
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  • 21
    Keywords: Orthopedics ; Sports Medicine ; Orthopedics ; Sports Medicine ; Springer eBooks
    Description / Table of Contents: General Considerations and Preoperative Work-up -- Periprosthetic Fractures about the Acetabulum with a Stable Cup -- Periprosthetic Fractures about the Acetabulum with a Loose Cup -- Periprosthetic Fractures of the Greater Trochanter and Proximal Femur with a Stable Prosthesis -- Periprosthetic Fractures of the Proximal Femur with a Loose Prosthesis -- Interprosthetic and Interimplant Fractures -- Periprosthetic Fractures of the Distal Femur with a Stable Prosthesis -- Periprosthetic Fractures of the Distal Femur with a Loose Prosthesis -- Periprosthetic Fractures of the Tibia with a Stable Prosthesis -- Periprosthetic Fractures of the Tibia with a Loose Prosthesis
    Abstract: This up-to-date, comprehensive yet concise guide for orthopedic surgeons covers the salient points of anatomy and operative approaches for the management of periprosthetic fractures of the hip and knee: breaks in bone that occur around the components or implants of a total joint replacement. The opening chapter focuses on the general considerations and work-up of these injuries, including epidemiology, classification, anatomy, and knowledge of the biomechanics and biology behind the treatments. The subsequent sections then discuss the hip and knee, respectively, and are case-based. These describe management strategies for the particular periprosthetic fracture with either a stable or a loose prosthesis as well as associated complications, including fractures of the acetabulum, the greater trochanter and proximal femur, distal femur, tibia, and interprosthetic and interimplant fractures. Written by experts in the field and replete with plentiful, practical tips and tricks, Periprosthetic Fractures of the Hip and Knee is a valuable resource for orthopedic and trauma surgeons, residents and fellows
    Pages: X, 161 p. 60 illus., 25 illus. in color. : online resource.
    ISBN: 9783319430089
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  • 22
    Keywords: Microbiology ; Microbiology ; Springer eBooks
    Description / Table of Contents: Microbial Metabolomics: A General Overview -- Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications -- Metabolomics: A Microbial Physiology and Metabolism Perspective -- Untargeted Soil Metabolomics Using Liquid Chromatography-Mass Spectrometry and Gas Chromatography-Mass Spectrometry -- Fatty Acid Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis -- Total Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis -- High-Throughput Solid Phase Microextraction-Liquid Chromatography-Mass Spectrometry for Microbial Untargeted Metabolomics -- Targeted Metabolomics of Xylose Fermenting Yeasts Based on Mass Spectrometry -- Exploiting High-Resolution Mass Spectrometry for Targeted Metabolite Quantification and 13C-labeling Metabolism Analysis -- Quantitative Profiling of Endogenous Metabolites Using Hydrophilic Inter-Action Liquid Chromatography-Tandem Mass Spectrometry (HILIC-MS/MS) -- Liquid Chromatography and Mass Spectrometry Analysis of Isoprenoid Intermediates in Escherichia coli -- Determining the Mode of Action of Antimalarial Drugs Using Time-Resolved LC-MS-Based Metabolite Profiling -- Use of Liquid Chromatography-Mass Spectrometry-Based Metabolomics to Identify Biomarkers of Tuberculosis -- Metabolomics Analysis of Leishmania by Capillary Electrophoresis and Mass Spectrometry -- A High-Throughput Targeted Metabolomics Workflow for the Detection of 200 Polar Metabolites in Central Carbon Metabolism -- Cluster Analysis of Untargeted Metabolomic Experiments -- Machine Learning in Untargeted Metabolomics Experiments -- Dynamic 13C Labeling of Fast Turnover Metabolites for Analysis of Metabolic Fluxes and Metabolite Channeling -- Genome-Scale 13C Fluxomics Modeling for Metabolic Engineering of Saccharomyces cerevisiae
    Abstract: This detailed volume includes protocols that represent the breadth of microbial metabolomics approaches to both large-scale and small-scale experiments with intention of highlighting techniques that can be used for applications ranging from environmental microbiology to human disease. Utilizing mass spectrometry as their primary measurement tool, the chapters explore microbial metabolomics, metabolism and microbial physiology, metabolite sample preparation, current analytical techniques used to profile primary and secondary metabolites and lipids, as well as establishing data analysis workflows for targeted metabolomics, untargeted metabolomics, analysis of metabolic fluxes, and genome-scale models. Written for the highly successful Methods in Molecular Biology series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Metabolomics: Methods and Protocols serves as an ideal reference for both novice and advanced users and can be adapted to similar analytical platforms or customized to suit the needs of the researcher
    Pages: X, 351 p. 83 illus., 50 illus. in color. : online resource.
    ISBN: 9781493987573
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  • 23
    Keywords: Biochemistry ; Protein Science ; Springer eBooks
    Description / Table of Contents: Introduction to FOXO Biology -- Characterization of microRNAs Regulating FOXO Expression -- Identification of Transcription Factor Binding Sites in the Mouse FoxO1 Promoter -- Investigating Mechanisms that control Ubiquitin-mediated DAF-16/FOXO Protein Turnover -- Phosphorylation of FOXO Proteins as a Key Mechanism to Regulate their Activity -- Methodological Approach for the Evaluation of FOXO as a Positive Regulator of Antioxidant Genes -- Characterization of FOXO Acetylation -- Transcriptional Activity of FoxO Transcription Factors Measured by Luciferase Assays -- Monitoring the Transcriptional Activity of FOXO Transcription Factors by Analyzing their Target Genes -- Using ChIP-based Approaches to Characterize FOXO Recruitment to its Target Promoters -- RNAi Mediated Silencing of FoxO Factors -- Immunofluorescence Analysis by Confocal Microscopy for Detecting Endogenous FOXO -- High Throughput Image-based Screening to Identify Chemical Compounds Capable of Activating FOXO -- Image-based Identification of Chemical Compounds Capable of Trapping FOXO in the Cell Nucleus -- Quantifying Tissue-specific Overexpression of FOXO in Drosophila via mRNA Fluorescence in situ Hybridization using Branched DNA Probe Technology -- Genome-wide Analysis for Identifying FOXO Protein Binding Sites -- Mathematical Modeling of Nuclear Trafficking of FOXO Transcription Factors -- Following Transcriptome to Uncover FOXO Biological Functions -- Hydra as Model to Determine the Role of FoxO in Longevity -- Genetic Ablation of FOXO in Mice to Investigate its Physiological Role -- Analysis of FOXO3 Gene Polymorphisms Associated with Human Longevity -- Analysis of FOXO3a Gene Polymorphism Associated with Asthma
    Abstract: This volume provides an overview of experimental procedures and state-of art methods to investigate FOXOs. Chapters guide readers through biochemical and molecular methods, imaging approaches to monitor the subcellular localization of FOXO factors, omics and bioinformatics approaches, different animal models used in FOXO research, and human studies to investigate the role of FOXO factors in human disease and longevity. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge FOXO Transcription Factors: Methods and Protocols aims to ensure successful results in the further study of this vital field
    Pages: XII, 270 p. 54 illus., 33 illus. in color. : online resource.
    ISBN: 9781493989003
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  • 24
    Keywords: Biochemistry ; Protein Science ; Springer eBooks
    Description / Table of Contents: Nitrogenases -- Bacteriochlorophyll and Coenzyme F430 -- Carbon Monoxide Dehydrogenases -- Molybdenum-Containing Enzymes -- Hydrogenases -- Genomic Manipulations of the Diazotroph Azotobacter vinelandii -- Purification of Nitrogenase Proteins -- Expression, Purification and Activity Analysis of Chlorophyllide Oxidoreductase and Ni2+-Sirohydrochlorin a,c-Diamide Reductase -- Reconstitution of Molybdoenzymes with Bis-Molybdopterin Guanine Dinucleotide Cofactor -- Crystallization of Nitrogenase Proteins -- X-Ray Crystallography of Carbon Monoxide Dehydrogenases -- X-Ray Absorption Spectroscopy of Metalloproteins -- Electron Paramagnetic Resonance Spectroscopy of Metalloproteins -- Magnetic Circular Dichroism Spectroscopy of Metalloproteins -- Chemical Synthesis of an Asymmetric Mimic of the Nitrogenase Active Site -- Computational Methods for Modeling Metalloproteins
    Abstract: This volume provides an up-to-date, in-depth overview of the methods that have been applied to studying the complex metalloproteins at a molecular level. Chapters cover a wide range of approaches focusing on genetic, biochemical, spectroscopic, chemical methods, and theoretical calculations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Metalloproteins: Methods and Protocols aims to be useful for anyone who is interested in metalloprotein research and wants to address the unanswered mechanistic and biosynthetic questions of these fascinating enzyme systems
    Pages: X, 275 p. 62 illus., 40 illus. in color. : online resource.
    ISBN: 9781493988648
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  • 25
    Keywords: Botany ; Plant Sciences ; Springer eBooks
    Description / Table of Contents: Repurposing macromolecule delivery tools for plant genetic modification in the era of precision genome engineering -- The use of an automated platform to assemble multigenic constructs for plant transformation -- Ensifer-mediated transformation (emt) of rice (monocot) and oilseed rape (dicot) -- Setaria viridis as a model plant for functional genomic studies in C4 crops -- Transient transformation using particle bombardment for gene expression analysis -- Maize transformation using the morphogenic genes babyboom and wuschel2 -- Efficient and fast production of transgenic rice plants by agrobacterium-mediated transformation -- Protocol for Agrobacterium-mediated transformation and transgenic plant production of switchgrass -- Biolistic transformation of wheat -- Mesophyll protoplasts and PEG-mediated transfections: Transient assays and generation of stable transgenic canola plants -- A Unified Agrobacterium-mediated transformation protocol for alfalfa (Medicago sativa l.) and medicago truncatula -- Poplar transformation -- The genetic transformation of sweet orange (Citrus sinensis L. Osbeck) for enhanced resistance to citrus canker -- Genetic modification of grapevine embryogenic culture -- Agrobacterium-mediated transformation of Solanum tuberosum L., potato -- Agrobacterium tumefaciens-mediated transformation of tomato -- DNA break repair in plants and its application for genome engineering -- Gene stacking in plants through the application of site-specific recombination and nuclease activity -- CRISPR/Cas9 for mutagenesis in rice -- Plant biotechnology applications of zinc fingers technology -- Overview of biotechnology-derived herbicide tolerance and insect resistance traits in plant agriculture -- Developing transgenic agronomic traits for crops: targets, methods and challenges -- Transgenic and genome editing approaches for modifying plant oils -- Summary of molecular analysis methods for characterizing transgenic events -- Detection of transgenic proteins by immunoassays -- Systematic evaluation of field crop performance using modern phenotyping tools and techniques
    Abstract: This book provides thorough coverage of transgenic plants with methods on plant transformation, biotechnological application of transgenic plants, and future developments. Chapters are grouped into sections focusing on transformation model and crop plants, genome engineering, and transgenic event characterization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Transgenic Plants: Methods and Protocols aims to broaden the utility for readers, provide additional references for further understanding, and present the technology’s potential for solving some of our most urgent global challenges in food security
    Pages: XIV, 444 p. 77 illus., 73 illus. in color. : online resource.
    ISBN: 9781493987788
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  • 26
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  • 27
    Publication Date: 2018-03-05
    Description: Recent genome-wide association studies of glioma have led to the discovery of single nucleotide polymorphisms (SNPs) at 25 loci influencing risk. Gliomas are heterogeneous, hence to investigate the relationship between risk SNPs and glioma subtype we analysed 1659 tumours profiled for IDH mutation, TERT promoter mutation and 1p/19q co-deletion. These data allowed definition of five molecular subgroups of glioma: triple-positive (IDH mutated, 1p/19q co-deletion, TERT promoter mutated); TERT -IDH (IDH mutated, TERT promoter mutated, 1p/19q-wild-type); IDH-only (IDH mutated, 1p/19q wild-type, TERT promoter wild-type); triple-negative (IDH wild-type, 1p/19q wild-type, TERT promoter wild-type) and TERT -only ( TERT promoter mutated, IDH wild-type, 1p/19q wild-type). Most glioma risk loci showed subtype specificity: (1) the 8q24.21 SNP for triple-positive glioma; (2) 5p15.33, 9p21.3, 17p13.1 and 20q13.33 SNPs for TERT -only glioma; (3) 1q44, 2q33.3, 3p14.1, 11q21, 11q23.3, 14q12, and 15q24.2 SNPs for IDH mutated glioma. To link risk SNPs to target candidate genes we analysed Hi-C and gene expression data, highlighting the potential role of IDH1 at 2q33.3, MYC at 8q24.21 and STMN3 at 20q13.33. Our observations provide further insight into the nature of susceptibility to glioma.
    Print ISSN: 0001-6322
    Electronic ISSN: 1432-0533
    Topics: Medicine
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  • 28
    Publication Date: 2018-03-05
    Description: Although concussion is now recognized as a major health issue, its non-lethal nature has limited characterization of the underlying pathophysiology. In particular, potential neuropathological changes have typically been inferred from non-invasive techniques or post-mortem examinations of severe traumatic brain injury (TBI). Here, we used a swine model of head rotational acceleration based on human concussion to examine blood–brain barrier (BBB) integrity after injury in association with diffuse axonal injury and glial responses. We then determined the potential clinical relevance of the swine concussion findings through comparisons with pathological changes in human severe TBI, where post-mortem examinations are possible. At 6–72 h post-injury in swine, we observed multifocal disruption of the BBB, demonstrated by extravasation of serum proteins, fibrinogen and immunoglobulin-G, in the absence of hemorrhage or other focal pathology. BBB disruption was observed in a stereotyped distribution consistent with biomechanical insult. Specifically, extravasated serum proteins were frequently observed at interfaces between regions of tissue with differing material properties, including the gray–white boundary, periventricular and subpial regions. In addition, there was substantial overlap of BBB disruption with regions of axonal pathology in the white matter. Acute perivascular cellular uptake of blood-borne proteins was observed to be prominent in astrocytes (GFAP-positive) and neurons (MAP-2-positive), but not microglia (IBA1-positive). Parallel examination of human severe TBI revealed similar patterns of serum extravasation and glial uptake of serum proteins, but to a much greater extent than in the swine model, attributed to the higher injury severity. These data suggest that BBB disruption represents a new and important pathological feature of concussion.
    Print ISSN: 0001-6322
    Electronic ISSN: 1432-0533
    Topics: Medicine
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  • 29
    Publication Date: 2018-03-05
    Description: Amyloid-β (Aβ) is a peptide deposited in the brain parenchyma in Alzheimer’s disease and in cerebral blood vessels, causing cerebral amyloid angiopathy (CAA). Aβ pathology is transmissible experimentally in animals and through medical procedures in humans, such as contaminated growth hormone or dura mater transplantation in the context of iatrogenic prion disease. Here, we present four patients who underwent neurosurgical procedures during childhood or teenage years and presented with intracerebral haemorrhage approximately three decades later, caused by severe CAA. None of these patients carried pathogenic mutations associated with early Aβ pathology development. In addition, we identified in the literature four patients with a history of neurosurgical intervention and subsequent development of CAA. These findings raise the possibility that Aβ pathology may be transmissible, as prion disease is, through neurosurgical procedures.
    Print ISSN: 0001-6322
    Electronic ISSN: 1432-0533
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  • 30
    Publication Date: 2018-03-05
    Description: Multiple sclerosis (MS) is a highly heterogeneous disease with large inter-individual differences in disease course. MS lesion pathology shows considerable heterogeneity in localization, cellular content and degree of demyelination between patients. In this study, we investigated pathological correlates of disease course in MS using the autopsy cohort of the Netherlands Brain Bank (NBB), containing 182 MS brain donors. Using a standardized autopsy procedure including systematic dissection from standard locations, 3188 tissue blocks containing 7562 MS lesions were dissected. Unbiased measurements of lesion load were made using the tissue from standard locations. Lesion demyelinating and innate inflammatory activity were visualized by immunohistochemistry for proteolipid protein and human leukocyte antigen. Lesions were classified into active, mixed active/inactive (also known as chronic active), inactive or remyelinated, while microglia/macrophage morphology was classified as ramified, amoeboid or foamy. The severity score was calculated from the time from first symptoms to EDSS-6. Lesion type prevalence and microglia/macrophage morphology were analyzed in relation to clinical course, disease severity, lesion load and sex, and in relation to each other. This analysis shows for the first time that (1) in progressive MS, with a mean disease duration of 28.6 ± 13.3 years (mean ± SD), there is substantial inflammatory lesion activity at time to death. 57% of all lesions were either active or mixed active/inactive and 78% of all patients had a mixed active/inactive lesion present; (2) patients that had a more severe disease course show a higher proportion of mixed active/inactive lesions ( p  = 6e−06) and a higher lesion load ( p  = 2e−04) at the time of death, (3) patients with a progressive disease course show a higher lesion load ( p  = 0.001), and a lower proportion of remyelinated lesions ( p  = 0.03) compared to patients with a relapsing disease course, (4) males have a higher incidence of cortical grey matter lesions ( p  = 0.027) and a higher proportion of mixed active/inactive lesions compared to females across the whole cohort ( p  = 0.007). We confirm that there is a higher proportion of mixed active/inactive lesions ( p  = 0.006) in progressive MS compared to relapsing disease. Identification of mixed active/inactive lesions on MRI is necessary to determine whether they can be used as a prognostic tool in living MS patients.
    Print ISSN: 0001-6322
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  • 31
    Publication Date: 2018-03-05
    Description: In the published article, the author B. Babbitt was cited as affiliation 9, but should have been cited as affiliation 2. In addition, there are 2 errors in the affiliations. The correct affiliations are shown in this erratum.
    Electronic ISSN: 1550-7416
    Topics: Chemistry and Pharmacology
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  • 32
    Publication Date: 2018-03-05
    Description: The healing professions have only about four main therapeutic tools at their disposal—surgery, drugs, physical therapy, and psychotherapy. For the general profession of internal medicine, drug therapy is its primary tool. Providing an understanding of the state-of-the-art in therapeutic methods, grounded in solid scientific and mathematical rigor, is therefore of the utmost clinical importance for both physicians and clinical pharmacists. This is particularly true where rapidly evolving scientific changes require an up-to-date education upon which students can rely. Unfortunately, relatively little attention has been paid to training clinical pharmacokineticists and physicians to manage drug therapy optimally for patients under their care in their everyday practice. In this paper, we discuss one of these basic deficiencies from the perspective of the longstanding controversy in pharmacokinetic modeling: whether the volume and clearance approach or the volume and rate constant approach is somehow “better”. We examine this controversy using the mathematical principle of invariance, which to our knowledge has not been done before. The conclusion of this analysis is that both approaches are rigorously proven mathematically to be equally valid. We also discuss some implications of these equally valid approaches from the framework of mechanistic and non-compartmental models. Ultimately, the conclusion is that the choice of one parameterization over the other is based on preference or usefulness for research or clinical practice, but no longer, because of this analysis, on science.
    Electronic ISSN: 1550-7416
    Topics: Chemistry and Pharmacology
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  • 33
    Publication Date: 2018-03-06
    Description: Engineering of the yeast Saccharomyces cerevisiae towards efficient d-xylose assimilation has been a major focus over the last decades since d-xylose is the second most abundant sugar in nature, and its conversio...
    Electronic ISSN: 2191-0855
    Topics: Biology
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  • 34
    Publication Date: 2018-03-06
    Description: Bacterial strains were isolated from the sediments of the Baltic Sea using ferulic acid, guaiacol or a lignin-rich softwood waste stream as substrate. In total nine isolates were obtained, five on ferulic acid...
    Electronic ISSN: 2191-0855
    Topics: Biology
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  • 35
    Publication Date: 2018-03-06
    Description: A novel sample preparation technique named capsule phase microextraction (CPME) is presented here. The technique utilizes a miniaturized microextraction capsule (MEC) as the extraction medium. The MEC consists of two conjoined porous tubular polypropylene membranes, one of which encapsulates the sorbent through sol-gel technology, while the other encapsulates a magnetic metal rod. As such, MEC integrates both the extraction and stirring mechanisms into a single device. The aim of this article is to demonstrate the application potential of CPME as sample preparation technique for the extraction of a group of personal care products (PCPs) from water matrices. Among the different sol-gel sorbent materials (UCON ® , poly(caprolactone-dimethylsiloxane-caprolactone) (PCAP-DMS-CAP) and Carbowax 20M (CW-20M)) evaluated, CW-20M MEC demonstrated the best extraction performance for the selected PCPs. The extraction conditions for sol-gel CW-20M MEC were optimized, including sample pH, stirring speed, addition of salt, extraction time, sample volume, liquid desorption solvent, and time. Under the optimal conditions, sol-gel CW-20M MEC provided recoveries, ranging between 47 and 90% for all analytes, except for ethylparaben, which showed a recovery of 26%. The method based on CPME with sol-gel CW-20M followed by liquid chromatography-tandem mass spectrometry was developed and validated for the extraction of PCPs from river water and effluent wastewater samples. When analyzing different environmental samples, some analytes such as 2,4-dihydroxybenzophenone, 2,2-dihydroxy-4-4 methoxybenzophenone and 3-benzophenone were found at low ng L −1 .
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 36
    Publication Date: 2018-03-06
    Description: The enzymatic system in saliva, consisting of salivary peroxidase (SPO), hydrogen peroxide (H 2 O 2 ), and thiocyanate (SCN − ), produces hypothiocyanite (OSCN − ) as a high effective antibacterial compound. OSCN − is of great importance for the natural non-specific antibacterial resistance in the oral cavity. However, no analytical method currently exists to selectively quantify OSCN − in saliva samples. A robust and specific analytical method for the determination of OSCN − was developed based on ion chromatography with combined UV and electrochemical detection. Calibration was achieved by calculating a derived calibration factor based on the known ratio of molar extinction coefficients of SCN − and OSCN − . Thus, the specific quantification of OSCN − in saliva samples is possible, as demonstrated here. The median value of 200 saliva samples was determined to be 0.56 mg L −1 (median), with a maximum of 3.9 mg L −1 ; the minimum value was below the detection limit (〈 0.09 mg L −1 ). The recovery rate in individual saliva samples was 95 ± 8%.
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 37
    Publication Date: 2018-03-06
    Description: The authors would like to call the reader’s attention to the fact that unfortunately during a recent cross-check of the experimental record, they found that the positions of intercept and slope were reversed in Table 1 in the original manuscript. The authors apologize for the mistake.
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 38
    Publication Date: 2018-03-06
    Description: Mycotoxins produced by different species of fungi may coexist in cereals and feedstuffs, and could be highly toxic for humans and animals. For quantification of multiple mycotoxins in cereals, we developed a paper-based mycotoxin immune-affinity array. First, paper-based microzone arrays were fabricated by photolithography. Then, monoclonal mycotoxin antibodies were added in a copolymerization reaction with a cross-linker to form an immune-affinity monolith on the paper-based microzone array. With use of a competitive immune-response format, paper-based mycotoxin immune-affinity arrays were successfully applied to detect mycotoxins in samples. The detection limits for deoxynivalenol, zearalenone, T-2 toxin, and HT-2 toxin were 62.7, 10.8, 0.36, and 0.23 μg·kg -1 , respectively, which meet relevant requirements for these compounds in food. The recovery rates were 81–86% for deoxynivalenol, 89–117% for zearalenone, 79–86% for T-2 toxin, and 78–83% for HT-2 toxin, and showed the paper-based immune-affinity arrays had good reproducibility. In summary, the paper-based mycotoxin immune-affinity array provides a sensitive, rapid, accurate, stable, and convenient platform for detection of multiple mycotoxins in agro-foods. Graphical abstract Paper-based immune-affinity monolithic array. DON deoxynivalenol, HT-2 HT-2 toxin, T-2 T-2 toxin, PEGDA polyethylene glycol diacrylate, ZEN zearalenone
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 39
    Publication Date: 2018-03-06
    Description: The development of simple methods with high sensitivity and selectivity to differentiate toxic aromatic thiols (thiophenols) from aliphatic thiols (cysteine, homocysteine, and glutathione) and hydrogen sulfide (H 2 S) is of great significance. Herein, we report on the fabrication of a novel near-infrared (NIR) fluorescent sensor for rapid and highly selective detection of thiophenols through the photoinduced electron transfer (PET) mechanism. In the presence of the thiophenols, an obvious enhancement of NIR fluorescence at 658 nm could be visualized with the aid of nucleophilic aromatic substitution (S N Ar) reaction. The sensor displays large Stokes shift (~ 227 nm), fast response time (〈 30 s), high sensitivity (~ 8.3 nM), and good biocompatibility. Moreover, the as-prepared sensor possesses an excellent anti-interference feature even when other possible interferents exist (aliphatic thiols and H 2 S) and has been successfully utilized for thiophenol detection in both water samples and living cells. Graphical abstract Illustration of the sensor for thiophenol imaging in living cells
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 40
    Publication Date: 2018-03-06
    Description: Based on the foaming property of the honey, a rapid, simple, and effective method solvent floatation (SF) was developed and firstly applied to the extraction and separation of triazine herbicides in honey. The analytes were determined by high-performance liquid chromatography. Some parameters affecting the extraction efficiencies, such as the type and volume of extraction solvent, type of salt, amount of (NH 4 ) 2 SO 4 , pH value of sample solution, gas flow rate, and floatation time, were investigated and optimized. The limits of detection for analytes are in the range of 0.16–0.56 μg kg −1 . The recoveries and relative standard deviations for determining triazines in five real honey samples are in the range of 78.2–112.9 and 0.2–9.2%, respectively.
    Print ISSN: 1618-2642
    Topics: Chemistry and Pharmacology
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  • 41
    Publication Date: 2018-03-06
    Description: Cancer cells are able to induce immune system tolerance through different mechanisms. Recent achievements in the understanding of tumor microenvironment, invasion, and metastasizing have contributed to accelerated drug developments and approvals. Hodgkin lymphoma (HL) cells are the minority in a lymphocyte-rich microenvironment of HL tissue. The program death-1 (PD-1)/PD-ligand-1 checkpoint is one of the known effective pathways in classical HL to escape the immune system cells. The approval of PD-1 inhibitors in different cancer types with exciting response rates is truly revolutionizing our treatment armamentarium against cancer in general and classical HL in specific. Although the disease is one of the most curable tumors, we still need better outcome with more gentle treatment, especially for relapsed and refractory (r/r) patients. In this article, we review the current literature on immune checkpoint inhibitors and currently ongoing studies with nivolumab and pembrolizumab in r/r classical HL.
    Print ISSN: 0939-5555
    Electronic ISSN: 1432-0584
    Topics: Medicine
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  • 42
    Publication Date: 2018-03-06
    Print ISSN: 0939-5555
    Electronic ISSN: 1432-0584
    Topics: Medicine
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  • 43
    Publication Date: 2018-03-06
    Print ISSN: 0939-5555
    Electronic ISSN: 1432-0584
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  • 44
    Publication Date: 2018-03-06
    Description: Diffuse large B cell lymphoma (DLBCL) is recognized as the most common non-Hodgkin lymphoma subtype. Advanced high-resolution digital scans of pathology slides have enabled the development of computer-based image analysis algorithms that may assist pathologists in quantifying immunohistochemical stains. In this retrospective study, we reviewed data from 29 patients affected by DLBCL. In order to evaluate the number of tumor cells and microenvironment T cells, we performed an analysis of CD20, Ki67, and CD3 counts, assessed with the Positive Pixel Count algorithm embedded in the Aperio ImageScope software. A lower tumor cell count was observed in patients with a non-germinal center immunophenotype, high LDH, splenomegaly and an IPI ≥ 3. A lower number of CD3 was observed in patients with bulky disease, an IPI ≥ 3 and disease stage 3–4. Overall, these data confirm that quantitative analysis of the tumor cells and of the tumor microenvironment by means of computer-driven quantitative image analysis may add new information in DLBCL diagnosis.
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  • 45
    Publication Date: 2018-03-06
    Print ISSN: 0939-5555
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  • 46
    Publication Date: 2018-03-06
    Description: We identified a novel heterozygous ITGB3 p.T720del mutation in a pedigree with macrothrombocytopenia exhibiting aggregation dysfunction. Platelet aggregation induced by ADP and collagen was significantly reduced, while ristocetin aggregation was normal. Integrin αIIbβ3 was partially activated in a resting status, but platelet expression of αIIbβ3 was downregulated. Functional analysis using a cell line showed spontaneous phosphorylation of FAK in αIIb/β3 (p.T720del)-transfected 293T cells in suspension conditions. Abnormal cytoplasmic protrusions, membrane ruffling, and cytoplasmic localization of αIIbβ3 were observed in αIIb/β3 (p.T720del)-transfected CHO cells. Such morphological changes were reversed by treatment with an FAK inhibitor. These findings imply spontaneous, but partial, activation of αIIbβ3 followed by phosphorylation of FAK as the initial mechanism of abnormal thrombopoiesis. Internalization and decreased surface expression of αIIbβ3 would contribute to aggregation dysfunction. We reviewed the literature of congenital macrothrombocytopenia associated with heterozygous ITGA2B or ITGB3 mutations. Reported mutations were highly clustered at the membrane proximal region of αIIbβ3, which affected the critical interaction between αIIb R995 and β3 D723, resulting in a constitutionally active form of the αIIbβ3 complex. Macrothrombocytopenia caused by a heterozygous activating mutation of ITGA2B or ITGB3 at the membrane proximal region forms a distinct entity of rare congenital thrombocytopenia.
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  • 47
    Publication Date: 2018-03-06
    Description: Background Malignant pleural mesothelioma (MPM), a devastating neoplasm, is traditionally considered to be resistant to antitumor therapy. Identification of clinical prognostic indicators is therefore needed. Although the C-reactive protein/albumin ratio (CAR) has been used to predict the prognosis of many types of malignancy, its utility in patients with MPM is unknown. Methods The data of 100 patients diagnosed as having MPM from 1995 to 2015 at the National Kyushu Cancer Center and Kyushu University were analyzed. The CAR was calculated as serum C-reactive protein concentration divided by albumin concentration. A cutoff for CAR was set at 0.58 according to a receiver operating characteristics curve for 1-year survival. Results Thirty-five of the 100 (35.0%) patients were classified as having a high CAR. A high CAR was significantly associated with advanced clinical stage ( p  〈 0.001) and chemotherapy alone ( p  = 0.002). Patients with a high CAR had significantly shorter overall survival (OS) ( p  〈 0.001) and disease- or progression-free survival (DFS/PFS) ( p  〈 0.001). These associations between CAR and prognosis remained significant after propensity score-matching. In multivariate analysis, a high CAR was an independent predictor of shorter OS and DFS/PFS ( p  = 0.003 and p  = 0.008, respectively). Multivariate analyses of the subgroups of patients who had received chemotherapy and of patients who had undergone surgery also showed that a high CAR was an independent predictor of shorter OS and DFS/PFS. Conclusions CAR is an independent predictor of prognosis in MPM patients. This prognostic index contributes to clinicians’ ability to predict benefit from treatment. Further larger, prospective studies are necessary to validate these findings.
    Print ISSN: 1068-9265
    Electronic ISSN: 1534-4681
    Topics: Medicine
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  • 48
    Publication Date: 2018-03-06
    Description: Purpose Adrenocortical carcinoma (ACC) is a rare, aggressive cancer; complete surgical resection offers the best chance for long-term survival. The impact of surgical margin status on survival is poorly understood. Our objective was to determine the association of margin status with survival. Methods Patients with ACC were identified from the National Cancer Data Base, 1998–2012, and stratified based on surgical margin status (negative vs. microscopically positive [+] vs. macroscopically [+]). Univariate/multivariate regression/survival analyses were utilized to determine factors associated with margin status and overall survival (OS). Results A total of 1553 patients underwent surgery at 589 institutions: 86% had negative, 12% microscopically (+), and 2% macroscopically (+) margins. Those with microscopically (+) and macroscopically (+) margins more often received adjuvant chemotherapy (39.4% macroscopically (+) vs. 38.5% microscopically (+) vs. 25.2% negative margins, p  〈 0.001). For unadjusted analysis, there was a significant difference in OS between the groups (log-rank p  〈 0.001), with median survival times of 58 months (95% confidence interval [CI] 49–66) for those with negative margins, 22 months (95% CI 18–34) microscopically (+), and 14 months (95% CI 6–27) macroscopically (+) margins. After adjustment, both microscopically (+) (HR 1.76, p  〈 0.001) and macroscopically (+) (HR 2.10, p  = 0.0019) margin status were associated with compromised survival. Conclusions Having micro- or macroscopically (+) margin status after ACC resection is associated with dose-dependent compromised survival. These results underscore the importance of achieving negative surgical margins for optimizing long-term patient outcomes.
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  • 49
    Publication Date: 2018-03-06
    Description: Introduction The aim of this study was to analyze global variations in the level of cancer-related research activity and correlate this with cancer-specific mortality. Methods The SCOPUS database was explored to obtain data relating to the number of cancer-related publications per country. Cancer-specific mortality rates were obtained from the World Health Organization. Global variations in the level of scholarly activity were analyzed and correlated with variations in cancer-specific mortality. Results Data for 142 countries were obtained and significant variations in the level of research activity was noted. The level of research activity increased with rising socio-economic status. The United States was the most prolific country with 222,300 publications followed by Japan and Germany. Several countries in different regions of the world had a low level of research activity. An inverse relationship between the level of research activity and cancer-specific mortality was noted. This relationship persisted even in countries with a low level of research activity. The socioeconomic status of a nation and geographic location (continent) had a mixed influence with an overall apparent correlation with cancer-related research activity. Conclusion This study demonstrates significant global variation in the level of cancer-related research activity and a correlation with cancer-specific mortality. The presence of a minimum set of standards for research literacy, as proposed by the European Society of Surgical Oncology and the Society of Surgical Oncology may contribute to enhanced research activity and improve outcomes for cancer patients worldwide.
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  • 50
    Publication Date: 2018-03-06
    Description: Background Detection of peritoneal metastasis remains challenging due to the limited sensitivity of current examination methods. This study aimed to establish a prediction model for estimating the individual risk of postoperative peritoneal metastasis from colon cancer to facilitate early interventions for high-risk patients. Methods This study investigated 1720 patients with stages 1–3 colon cancer who underwent curative resection at the University of Tokyo Hospital between 1997 and 2015. The data for the patients were retrospectively retrieved from their medical records. The risk score was developed using the elastic net techniques in a derivation cohort (973 patients treated in 1997–2009) and validated in a validation cohort (747 patients treated in 2010–2015). Results The factors selected using the elastic net approaches included the T stage, N stage, number of examined lymph nodes, preoperative carcinoembryonic antigen level, large bowel obstruction, and anastomotic leakage. The model had good discrimination (c-index, 0.85) and was well-calibrated after application of the bootstrap resampling method. Discrimination and calibration were favorable in external validation (c-index, 0.83). The model presented a clear stratification of patients’ risk for postoperative peritoneal recurrence, and decision curve analysis showed its net benefit across a wide range of threshold probabilities. Conclusions This study established and validated a prediction model that can aid clinicians in optimizing postoperative surveillance and therapeutic strategies according to the individual patient risk of peritoneal recurrence.
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  • 51
    Publication Date: 2018-03-06
    Description: Background Cytoreductive surgery and hyperthermic intraperitoneal chemotherapy (CRS/HIPEC) is a treatment option in patients with carcinomatosis from high-grade appendiceal (HGA) primaries. It is unknown if there is a Peritoneal Carcinomatosis Index (PCI) upper limit above which a complete CRS/HIPEC does not assure long-term survival. Methods Retrospective analysis from three centers was performed. The PCI was used to grade volume of of disease. Survival in relation to PCI was studied on patients with complete cytoreduction. Results Overall, 521 HGA patients underwent CRS/HIPEC from 1993 to 2015, with complete CRS being achieved in 50% (260/622). Mean PCI was 14.8 (standard deviation 8.7, range 0–36). Median survival for the complete CRS cohort was 6.1 years, while 5- and 10-year survival was 51.7% (standard error [SE] 4.6) and 36.1% (SE 6.3), respectively. Arbitrary cut-off PCI limits with 5-point splits ( p  = 0.63) were not predictive of a detrimental effect on survival as long as a complete CRS was achieved. A linear effect of the PCI on survival ( p  = 0.62) was not observed, and single-point PCI cohort splits within a PCI range of 〈 5 to 〉 10 were not predictive of survival for complete CRS patients. The PCI correlated with the ability to achieve a complete CRS, with a mean PCI of 14.7 (8.7) for completeness of cytoreduction (CC)0, 22.3 (7.8) for CC1 and 26.1 (9.5) for CC2/3 resections ( p  = 0.0001, hazard ratio 1.12, 95% confidence interval 1.09), with an HR of 1.15 for each 1-unit increase in the PCI score. Only 21% of the cohort achieved a complete CRS with a PCI ≥ 21. Conclusions The PCI correlates with the ability to achieve a complete CRS in carcinomatosis from HGA. PCI is not associated with survival as long as a complete CRS can be achieved.
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  • 52
    Publication Date: 2018-03-06
    Description: Background Lung squamous cell carcinoma (LSCC) is a major histological subtype of lung cancer. In this study, we investigated genomic alterations in LSCC and evaluated the clinical implications of mutation burden (MB) in LSCC. Methods Genomic alterations were determined in Japanese patients with LSCC ( N  = 67) using next-generation sequencing of 415 known cancer genes. MB was defined as the number of non-synonymous mutations per 1 Mbp. Programmed death-ligand 1 (PD-L1) protein expression in cancer cells was evaluated by immunohistochemical analysis. Results TP53 gene mutations were the most common alteration ( n  = 51/67, 76.1%), followed by gene alterations in cyclin-dependent kinase inhibitor 2B ( CDKN2B ; 35.8%), CDKN2A (31.3%), phosphatase and tensin homolog (30.0%), and sex-determining region Y-box 2 ( SOX2 , 28.3%). Histological differentiation was significantly poorer in tumors with high MB (greater than or equal to the median MB) compared with that in tumors with low MB (less than the median MB; p = 0.0446). The high MB group had more tumors located in the upper or middle lobe than tumors located in the lower lobe ( p = 0.0019). Moreover, cancers in the upper or middle lobes had significantly higher MB than cancers in the lower lobes ( p = 0.0005), and tended to show higher PD-L1 protein expression ( p  = 0.0573). SOX2 and tyrosine kinase non-receptor 2 amplifications were associated with high MB ( p  = 0.0065 and p  = 0.0010, respectively). Conclusions The MB level differed according to the tumor location in LSCC, suggesting that the location of cancer development may influence the genomic background of the tumor.
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  • 53
    Publication Date: 2018-03-06
    Description: Unprecedented advances in the treatment of cancer have occurred through the use of immunotherapy, with several agents currently approved by the Food and Drug Administration (FDA) for the treatment of widespread metastatic disease across cancer types. Immune checkpoint blockade represents a particularly promising class of agents that block inhibitory molecules on the surface of T cells, resulting in their activation and propagation of an immune response. Treatment with these agents may re-invigorate anti-tumor immunity, resulting in therapeutic responses, and use of these agents currently is being studied in the adjuvant setting. Additionally, a strong rationale exists for their use in the neoadjuvant setting for high-risk resectable disease (e.g., regional nodal disease in the case of melanoma). This rationale is based on the relatively high risk of relapse for these patients, as well as on scientific evidence suggesting that long-term immunologic memory and tumor control may be superior in the setting of treatment for an intact tumor (i.e., neoadjuvant therapy) as opposed to treatment in the setting of micrometastatic disease (e.g., adjuvant treatment). The potential advantages of this approach and the current landscape for neoadjuvant immune checkpoint blockade is discussed in this report, as well as caveats that should be considered by clinicians contemplating this strategy.
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  • 54
    Publication Date: 2018-03-06
    Description: Background The accuracy of sentinel lymph node biopsy (SLNB) after neoadjuvant therapy (NAT) has been improved with the placement of a clip in the positive node prior to treatment. Several methods have been described for clipped node excision during SLNB after NAT. We assessed the feasibility of intraoperative ultrasound (IOUS)-guided excision of the clipped node during SLNB and investigated whether the accuracy of SLNB is improved. Methods After approval by the Institutional Ethics Committee, all breast cancer patients undergoing NAT had an US-visible clip placed in the positive node. The ILINA trial consisted of IOUS-guided excision of the clipped node along with SLNB and axillary lymph node dissection (ALND). Results Forty-six patients had a clip placed in the positive node. In two (4.3%) cases, the clip could not be seen prior to surgery and the patient underwent ALND; however, the clipped node was successfully removed by IOUS-guided excision in 44 patients. Thirty-five patients (79.5%) underwent SLNB along with IOUS-guided excision of the clipped node and ALND, and were subsequently included in the ILINA trial. Nine patients were not included (five patients with SLNB only and four patients with ALND without SLNB). SLNB matched the clipped node in 27 (77%) patients. The false negative rate for the ILINA protocol was 4.1% (95% confidence interval 0.1–21.1%). Conclusions IOUS-guided excision of the axillary clipped node after NAT was feasible, safe, and successful in 100% of cases. The ILINA trial is accurate in predicting axillary nodal status after NAT.
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  • 55
    Publication Date: 2018-03-06
    Description: Fe promoted Rh–Mn/Al 2 O 3 catalysts with different Fe impregnation sequences were used for ethanol formation from syngas. The effect of Fe impregnation sequence on the structure and performance of the catalysts was investigated by means of N 2 adsorption, CO adsorption, H 2 -TPR, H 2 -TPD, CO-TPD, XPS and DRIFTS. The results showed that the RhMnFe/Al 2 O 3 catalyst prepared by co-impregnation method showed higher ethanol selectivity than those prepared by sequential impregnation methods. Characterization results indicated that the RhMnFe/Al 2 O 3 catalyst exhibited moderate CO hydrogenation and dissociation ability, stronger CO insertion ability and synergistic effect, which was responsible for its higher ethanol selectivity.
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    Topics: Chemistry and Pharmacology
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  • 56
    Publication Date: 2018-03-06
    Description: Public policy, dollar rate, market prices, contracts values and equipment efficiency influence the costs of the energy sources at an ethylene plant. The aim of this research is to identify energy efficiency opportunities at the energy management resources in a petrochemical industry. It was proved that using MILP makes it possible to achieve energy efficiency gains. MILP proved to be effective, accurate and robust. It confirmed the importance of modeling and simulation with quick response and its implementation in a higher possible rate, since the potential gains running the model once per day were 81% higher than performing it once a month. The optimal resources choice had an average annual potential saving of US$ 556.000/year.
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  • 57
    Publication Date: 2018-03-06
    Description: Substantial quantities of energy are required in conventional distillation columns applied in high-purity separation of close-boiling mixtures. To achieve energy saving of distillation, a novel different pressure thermally coupled distillation (DPTCD) was proposed for separating the close-boiling mixture of n -butanol and iso-butanol. Both this intensified energy integration technique and two other processes, namely conventional distillation (CD) and vapor recompression column (VRC), were simulated in process simulator Aspen Plus. The optimization was carried out to determine the optimal values of design and operating variables on the basis of minimizing energy consumption. Subsequently, the energy saving and economic efficiency of the DPTCD scheme were evaluated through the comparison with the other two processes. The results showed that, compared to the CD and VRC processes, the energy consumption of DPTCD process was decreased by 65.21 and 15.79%, respectively, and the total annual cost (TAC) of DPTCD process can be reduced by 33.75 and 10.46%. It demonstrated that DPTCD scheme was the most promising alternative to reduce the total energy consumption and TAC with high purity (99.1 wt%) n -butanol and iso-butanol products among these separation processes.
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  • 58
    Publication Date: 2018-03-06
    Description: An ultrasound condition associated with phase-transfer catalyst (PTC) has great diverse applications in synthesis of various organic and polymeric materials because of its fast reaction and high yield in short period of time. Phase transfer catalyst (cetyltrimethylammonium bromide as PTC) extracts the reactive radical anion from aqueous phase and transfer to organic phase whilst ultrasound condition enhances the radical formation; consequently, acrylonitrile was polymerized in ethyl acetate/water two-phase system at 60 ± 1 °C under ultrasound (25 kHz/300 W) and silent condition. The rate of polymerization ( R p ) was doubled under ultrasound compare to silent condition. The various experimental parameters such as monomer, initiator, catalyst and temperature, solvent polarity on the rate of polymerization was studied in both conditions. The activation energy ( E a ) and other thermodynamic parameters were calculated. The E a value of ultrasound condition supports the enhancement of rate of polymerization. On the basis of observed results, a suitable kinetic model, mechanism and effect of ultrasound in the rate of polymerization were discussed. The obtained polymer was analyzed by TG/DTA and FT-IR. The viscosity average molecular weight of the polymer was found to be 6.8526 × 10 4  g mol −1 .
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  • 59
    Publication Date: 2018-03-06
    Description: Disulfide oil (DSO) mostly burned or stored is known as a low-grade byproduct in gas refining industries. This material is highly perilous to environment. A common way to reduce the environmental impact of DSO is blending in a specific ratio with gas condensate stream in gas refinery. This would improve DSO quality and consequently strengthen its unique application. In this work, density, viscosity and surface tension of DSO and gas condensate mixtures were measured and modeled. Viscosity and density of DSO, gas condensate, and their mixtures were measured in temperature range of 283.15–318.15 K. In addition, surface tension was measured at 298.15 K at different volumetric fractions of DSO–gas condensate mixture. Excess molar volume ( V E ), viscosity deviation (∆ μ ), deviation of excess Gibbs free energy (∆ G E ), and excess surface tension ( σ E ) were determined based on measured properties. Results showed a positive and negative trend for excess molar volume and excess surface tension, respectively. While fluctuation was observed in viscosity deviation and deviation of excess Gibbs free energy and results showed positive and negative values in different mole fraction. In addition, Redlich–Kister equation is proposed to predict excess properties of DSO and gas condensate mixtures.
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  • 60
    Publication Date: 2018-03-06
    Description: Methyl and ethyl methacrylate was polymerized in heterogeneous system with the help of newly synthesized multi-site phase-transfer catalyst and using water-soluble initiator at 60 ± 1 °C under unstirred inert atmospheric condition. Polymer yield was increased with increasing molar concentrations of monomer, initiator, catalyst and temperature. Polymerization follows first-order kinetics with respect to monomer and half-order with respect to catalyst and initiator, respectively. PTC has myriads of applications in the synthesis of various organic and polymeric materials because of its fast reaction and high yield in short period of time. Without addition of PTC, polymerization did not occur; this indicates that catalyst plays the pivotal role on initiation of polymerization. It extracts the reactive radical anion from aqueous phase and transfers to the organic phase where acrylates were polymerized. Polymerization reactivity of methyl and ethyl methacrylate under PTC conditions was studied by various parameters. The activation energy (Ea) and other thermodynamic parameters were calculated. The Ea value supports the reactivity of acrylates. The results obtained from this investigation were used for inferring the radical mechanism of phase-transfer-catalyzed polymerization. The obtained polymers were analyzed by spectral and thermal analyses.
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  • 61
    Publication Date: 2018-03-06
    Description: Serotonin (5-hydroxytryptamine or 5-HT) is a neurotransmitter in itch and impaired serotonin signaling has been linked to a variety of itch conditions. Intradermal injection of 5-HT induces scratching behavior in mice through stimulation of 5-HT receptors. Previous studies have demonstrated that selective 5-HT1B/1D receptors agonists, including sumatriptan, inhibits neurotransmission. We have also reported that sumatriptan suppresses chloroquine-induced itch. Therefore, we investigated if sumatriptan has inhibitory effects on serotonin-induced itch in mice. Here, we show that intradermal and intraperitoneal administration of sumatriptan significantly reduce 5-HT-induced scratching behavior in mice. While intradermal injection of GR-127935, a selective 5-HT1B/1D receptors antagonist, reverses the anti-pruritic effects of sumatriptan. In addition, we show that intradermal and intraperitoneal naltrexone (NTX), a non-specific opioid receptor antagonist, and methylnaltrexone (MNTX), a peripherally acting opioid receptor antagonist, significantly decrease the 5-HT-induced scratching behavior. Additionally, combined treatment with sub-effective doses of sumatriptan and an opioid receptor antagonist, naltrexone, decreases 5-HT-evoked scratching responses. We conclude that sumatriptan inhibits 5-HT-induced itch by activating the peripheral 5-HT1B/1D receptors. Moreover, peripheral opioid receptors have a role in serotonin-induced itch, and anti-pruritic effects of sumatriptan seem to involve the opioid system. These data suggest that 5-HT1B/1D receptors agonists maybe useful to treat a variety of pathologic itch conditions with impaired serotonergic system.
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  • 62
    Publication Date: 2018-03-06
    Description: Lupus erythematosus is a chronic autoimmune disease characterized by remissions and exacerbations. Accumulated evidence indicated that matrix metalloproteinases (MMPs) are upregulated in inflammatory cells of cutaneous lupus erythematosus (CLE); however, the activity levels of these proteases have remained uncharacterized. To elucidate the significance of MMP-2, MMP-9, and TIMP-1 in CLE pathogenesis, gelatin zymography was used to investigate pro and active levels of MMP-2 and MMP-9 in lesional and perilesional skin biopsies obtained from twenty-two CLE patients. TIMP-1 protein levels were detected by ELISA in the biopsy specimens. The correlation between biochemical parameters and clinical characteristics of the disease was also evaluated. Significantly higher levels of active MMP-2, active MMP-9, proMMP-9, active/proMMP-2, and TIMP-1 were detected in lesional skin samples. Besides, the active/proMMP-9 was elevated in female and smoking patients. Active MMP-9 levels and active/proMMP-9 were also increased in elderly patients. Active MMP-9 levels were lower in patients who had smaller total damage score. Consistently, active/proMMP-9 and active/proMMP-2 were positively correlated with CLASI. Interestingly, in hydroxychloroquine or topical corticosteroid-treated patients, MMP-2/-9 activity levels were found to be higher compared to untreated patients. These findings suggest that increased MMP-2 and MMP-9 activities may contribute to the pathogenesis of CLE and cutaneous disease severity.
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  • 63
    Publication Date: 2018-03-06
    Description: Keratin-17 (K17) is a cytoskeletal protein produced by keratinocytes (KCs), which is overexpressed in psoriasis and may play a pivotal role in its pathogenesis. Narrow-band ultraviolet B (NB-UVB) irradiation is used as a general treatment for psoriasis, although its impact on K17 expression has yet to be determined. In this study, we aimed to investigate the effect of NB-UVB irradiation on K17 expression and its signaling pathways. After exposure to NB-UVB irradiation, immortalized human keratinocytes (HaCaT cells) were analyzed by flow cytometry, CCK-8 assays and transmission electron microscopy to examine proliferation. Meanwhile, K17 expression in primary human epithelial keratinocytes was detected by quantitative real-time polymerase chain reaction (qRT-PCR), western blot analysis and immunofluorescence. HaCaT cells pre-incubated with PD-98059 and piceatannol were subjected to western blot analysis to examine ERK1/2 and STAT3 phosphorylation. The ears of mice treated with imiquimod (IMQ) and irradiated by NB-UVB were taken to examine K17 expression by qRT-PCR, western blot analysis, and immunofluorescence. Our results showed that 400 mJ/cm 2 of NB-UVB irradiation was the maximum tolerable dose for HaCaT cells and could cause inhibited HaCaT cell proliferation and moderate increase of the early apoptosis. Furthermore, NB-UVB irradiation could downregulate K17 expression by inhibiting the ERK1/2 and STAT3 signaling pathways. In experiments conducted in vivo, NB-UVB irradiation with doses of MED or higher could eliminate the IMQ-induced psoriasis-like dermatitis and inhibit K17 expression. These results indicated that NB-UVB irradiation may eliminate chronic psoriatic plaques by suppressing K17 expression via the ERK1/2 and STAT3 signaling pathways.
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  • 64
    Publication Date: 2018-03-06
    Description: The role of leptin in cutaneous wound healing process has been suggested in genetically obese mouse studies. However, the molecular and cellular effects of leptin on human epidermal keratinocytes are still unclear. In this study, the whole-genome-scale microarray analysis was performed to elucidate the effect of leptin on epidermal keratinocyte functions. In the leptin-treated normal human keratinocytes (NHKs), we identified the 151 upregulated and 53 downregulated differentially expressed genes (DEGs). The gene ontology (GO) enrichment analysis with the leptin-induced DEGs suggests that leptin regulates NHKs to promote pro-inflammatory responses, extracellular matrix organization, and angiogenesis. Among the DEGs, the protein expression of IL-8, MMP-1, fibronectin, and S100A7, which play roles in which is important in the regulation of cutaneous inflammation, was confirmed in the leptin-treated NHKs. The upregulation of the leptin-induced proteins is mainly regulated by the STAT3 signaling pathway in NHKs. Among the downregulated DEGs, the protein expression of nucleosome assembly-associated centromere protein A (CENPA) and CENPM was confirmed in the leptin-treated NHKs. However, the expression of CENPA and CENPM was not coupled with those of other chromosome passenger complex like Aurora A kinase, INCENP, and survivin. In cell growth kinetics analysis, leptin had no significant effect on the cell growth curves of NHKs in the normal growth factor-enriched condition. Therefore, leptin-dependent downregulation of CENPA and CENPM in NHKs may not be directly associated with mitotic regulation during inflammation.
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  • 65
    Publication Date: 2018-03-06
    Description: Skin fibrosis has been reported in Borrelia burgdorferi infection in Europe, but has been questioned by several authors. The objective of the present study was to examine the interaction of skin fibroblasts with B. burgdorferi sensu stricto B31 (BB) and B. afzelii (BA) in vitro by electron microscopy. We also determined the expression of collagen type I, TGF-β, FGF-1, calreticulin (CALR), decorin (DCN), and PDGF-α at the mRNA level in Borrelia /fibroblast co-cultures. Intact Borrelia attach to and transmigrate fibroblasts, and undergo cystic transformation outside the fibroblasts. Fibroblasts preserve their vitality and express a prominent granular endoplasmic reticulum, suggesting activated protein synthesis. On two different semi-quantitative real-time PCR assays, BB- and BA/fibroblast co-cultures showed a significant induction of type I collagen mRNA after 2 days compared to fibroblasts (fourfold for BA and 1.8-fold for BB; p  〈 0.02). In addition, there was a significant upregulation of mRNA expression of TGF-β, CALR, PDGF-α, and DCN in BA and BB co-cultures compared to control fibroblasts in monolayer cultures after 2 days ( p  〈 0.01). The BA/fibroblast co-culture induced a considerably greater upregulation of collagen and growth factor mRNA compared to BB/fibroblast co-culture. In contrast, a significant down-regulation of FGF-1 (20-fold for BA and 4.5-fold for BB) mRNA expression was detected in co-cultures compared to controls ( p  〈 0.01). The results of the study support the hypothesis that BB sensu lato, and BA in particular, enhances collagen mRNA expression and can stimulate growth factors responsible for increased collagen production.
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  • 66
    Publication Date: 2018-03-06
    Description: Fibroblasts secrete several growth factors which are important for the regulation of skin pigmentation. Dickkopf1 (DKK1) is also secreted by fibroblasts which inhibit the growth and function of melanocytes. Therefore, the study was designed to check the role of DKK1 in vitiligo pathogenesis. This study confirmed the higher expression of DKK1 in lesional skin of vitiligo patients. In vitro effect of DKK1 on cultured melanocytes revealed decrease in the melanocytes proliferation and pigmentation. In vitro effect of DKK1 was then checked on the melanocytes senescence and found that DKK1 induced senescence in the treated melanocytes. Expression of senescence markers was significantly higher in DKK1 treated melanocytes. This study suggests that higher expression of DKK1 in the dermis induced senescence in melanocytes that may lead to hypopigmentation and play role in vitiligo pathogenesis.
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  • 67
    Publication Date: 2018-03-06
    Description: The histopathologic differentiation between Spitz nevus and melanoma is of particular interest in routine diagnostic procedures of melanocytic tumors. Atypical Spitz nevi are sometimes difficult to distinguish from melanoma. There is still no single criterion that ensures a distinction of melanoma and atypical Spitz nevus. The aim of this study was to reevaluate established and new criteria to differentiate Spitz nevus from melanoma more reliably. We analyzed 25 melanomas with a Breslow index ≥ 1 mm and 18 classical compound Spitz nevi concerning their histopathologic, immunohistochemical and molecular genetic characteristics. Moreover, clinical follow-up data for 5 years were collected. We found statistically significant differences between Spitz nevus and melanoma for the following features: pagetoid spread, atypia, maturation, elastosis, Kamino bodies, p16 expression, and the staining pattern of HMB45. BRAF was positive in 7/21 melanomas and in 1/14 Spitz nevi. Fluorescence in situ hybridization confirmed the histopathologic diagnosis in 36/37 cases. The established clinical, histopathologic, and immunohistochemical criteria to differentiate Spitz nevus and melanoma could be reproduced in our collective. Especially, the expression of p16, BRAF analysis and fluorescence in situ hybridization proved to be helpful tools to improve the differentiation of Spitz nevus and melanoma in our study. Nevertheless, there is—until now—no reliable histopathologic and immunohistochemical parameter which can discriminate Spitz nevus and melanoma with absolute certainty.
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  • 68
    Publication Date: 2018-03-06
    Description: The emergence of drug-resistant tuberculosis has generated great concern in the control of tuberculosis and HIV/TB patients have established severe complications that are difficult to treat. Although, the gold standard of drug-susceptibility testing is highly accurate and efficient, it is time-consuming. Diagnostic biomarkers are, therefore, necessary in discriminating between infection from drug-resistant and drug-susceptible strains. One strategy that aids to effectively control tuberculosis is understanding the function of secreting proteins that mycobacteria use to manipulate the host cellular defenses. In this study, culture filtrate proteins from Mycobacterium tuberculosis H37Rv, isoniazid-resistant, rifampicin-resistant and multidrug-resistant strains were gathered and profiled by shotgun-proteomics technique. Mass spectrometric analysis of the secreted proteome identified several proteins, of which 837, 892, 838 and 850 were found in M. tuberculosis H37Rv, isoniazid-resistant, rifampicin-resistant and multidrug-resistant strains, respectively. These proteins have been implicated in various cellular processes, including biological adhesion, biological regulation, developmental process, immune system process localization, cellular process, cellular component organization or biogenesis, metabolic process, and response to stimulus. Analysis based on STITCH database predicted the interaction of DNA topoisomerase I, 3-oxoacyl-(acyl-carrier protein) reductase, ESAT-6-like protein, putative prophage phiRv2 integrase, and 3-phosphoshikimate 1-carboxyvinyltransferase with isoniazid, rifampicin, pyrazinamide, ethambutol and streptomycin, suggesting putative roles in controlling the anti-tuberculosis ability. However, several proteins with no interaction with all first-line anti-tuberculosis drugs might be used as markers for mycobacterial identification.
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  • 69
    Publication Date: 2018-03-06
    Description: A novel bacterial strain MAH-8 T was isolated from a soil sample of a Korean pine garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, pinkish yellow colored, motile and vibrio-shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28–30 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-8 T belongs to the genus Caenispirillum and is most closely related to Caenispirillum bisanense KCTC 12839 T (98.14%), Caenispirillum deserti KCTC 42064 T (96.35%), and Caenispirillum salinarum JCM 17360 T (95.76%). In DNA–DNA hybridization tests, the DNA relatedness between strain MAH-8 T and its closest phylogenetic neighbor was below 45.0%. The DNA G + C content was 70.5 mol% and the predominant respiratory quinone was ubiquinone-10. Flexirubin-type pigments were present and the major cellular fatty acids were C 18:1 ω 7 c /C 18:1 ω 6 c , C 16:1 ω 7 c /C 16:1 ω 6 c and C 16:0 . The results of DNA–DNA hybridization and genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-8 T represented a novel species within the genus Caenispirillum , for which the name Caenispirillum humi , is proposed. The type strain is MAH-8 T (= KACC 19294 T  = CGMCC 1.16224 T ). The NCBI GenBank Accession Number for the 16S rRNA gene sequence of strain MAH-8 T is KY964275.
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  • 70
    Publication Date: 2018-03-06
    Description: The study was conducted to evaluate the microbiological and chemical profiles of elephant grass inoculated with and without different wild strains of lactic acid bacteria. Silage was prepared of four treatments and one control with three replicates as control (EKC, adding 2 ml/kg sterilizing water), Lactobacillus plantarum (USA commercial bacteria) (EKP), Lactobacillus plantarum (EKA), Pediococcus acidilactici (EKB), and Pediococcus acidilactici (SKD) isolated from King grass. Silage were prepared using polyethylene terephthalate bottles, and incubated at room temperature for different ensiling days. The pH and acetic acid (AA) were significantly ( P  〈 0.05) reduced and lactic acid (LA), butyric acid (BA), and ethanol were significantly increased ( P  〈 0.05) at 3, 5, 7, and 14 days in treatment groups as compared to control. Water-soluble carbohydrate (WSC) and NH 3 –N concentration was not affected at days 3, 5, and 7, but significantly ( P  〈 0.05) reduced at 14 days in treatment groups as compared to control. The LA, BA, and ethanol were significantly ( P  〈 0.05) increased and AA, WSC NH 3 –N, and yeast were significantly ( P  〈 0.05) decreased at 30 days of ensiling in treatment groups as compared to control. It is recommended that the inoculation of LAB could improve the fermentation quality of elephant grass silage and further effort is needed to evaluate these effects on silage produced on farm scale and on animal production performance.
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