Bøger udgivet af Springer-Verlag New York Inc.

This detailed volume presents status and management protocols with the objective of identifying proper guidelines and materials for research related to the most common malignant neoplasm in the thyroid gland, papillary thyroid carcinoma.

Part I: Strategies to Induce ROS Production 1. Modification of Chloroplast Antioxidant Capacity by Plastid Transformation            Shengchun Li, Pan Shen, Bipeng Wang, Xiujie Mu, Mimi Tian, Tao Chen, and Yi Han 2. Analysis of Ascorbate Metabolism in Arabidopsis under High-Light-Stress            Takanori Maruta and Takahiro Ishikawa 3. Genetic Manipulation of Reactive Oxygen Species (ROS) Homeostasis Utilizing CRISPR/Cas9-Based Gene Editing in Rice            Sheng Xu, Tao Chen, Mimi Tian, Marie-Sylviane Rahantaniaina, Linlin Zhang, Ren Wang, Wei Xuan, and Yi Han 4. Studying Plant Stress Reactions In Vivo by PAM Chlorophyll Fluorescence Imaging            Alexey Shapiguzov and Jaakko Kangasj├ñrvi Part II: Methods to Visualize ROS and to Detect Changes in Redox Homeostasis 5. Live Monitoring of ROS-Induced Cytosolic Redox Changes with roGFP2-Based Sensors in Plants            Jos├⌐ Manuel Ugalde, Lara Fecker, Markus Schwarzl├ñnder, Stefanie J. M├╝ller-Sch├╝ssele, and Andreas J. Meyer 6. Quantitative Measurement of Ascorbate and Glutathione by Spectrophotometry            Graham Noctor and Amna Mhamdi 7. Measurement of NAD(P)H and NADPH-Generating Enzymes            Amna Mhamdi, Frank Van Breusegem, and Graham Noctor 8. Quantitative Analysis for ROS-Producing Activity and Regulation of Plant NADPH Oxidases in HEK293T Cells            Sachie Kimura, Hidetaka Kaya, Kenji Hashimoto, Michael Wrzaczek, and Kazuyuki Kuchitsu Part III: Small-Scale Targeted Analysis of ROS Accumulation during Stress and Effects on Plant Physiology 9. Estimation of the Level of Abasic Sites in Plant mRNA Using Aldehyde Reactive Probe            Jagna Chmielowska-B─àk, Karolina Izbia┼äska-Jankowska, and Joanna Deckert 10. A Simplified Method to Assay Protein Carbonylation by Spectrophotometry            Corentin Moreau and Emmanuelle Issakidis-Bourguet 11. In Vitro Biochemical Analysis of Recombinant Plant Proteins under Oxidation            Zeya Chen and Jingjing Huang 12. Methods to Analyze the Redox Reactivity of Plant Proteins            Thualfeqar Al-Mohanna, George V. Popescu, and Sorina C. Popescu 13. Determination of ROS-Induced Lipid Peroxidation by HPLC-Based Quantification of Hydroxy Polyunsaturated Fatty Acids            Brigitte Ksas and Michel Havaux 14. Detection of Lipid Peroxidation-Derived Free Azelaic Acid, a Biotic Stress Marker and Other Dicarboxylic Acids in Tobacco by Reversed Phase HPLC-MS under Non-Derivatized Conditions            Attila L. ├üd├ím, Gy├╢rgy K├ítay, Andr├ís K├╝nstler, and L├│r├ínt Kir├íly

1. RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR            Trevor. R Simmons, Andrew D. Ellington, and Lydia M. Contreras 2. Computational Design of RNA Toehold-Mediated Translation Activators            Kaiyue Wu, Zhaoqing Yan, and Alexander A. Green 3. Design of RNA-Based Translational Repressors            Seongho Hong, Dongwon Park, Soma Chaudhary, Griffin McCutcheon, Alexander A. Green, and Jongmin Kim 4. Design of Ribocomputing Devices for Complex Cellular Logic            Griffin McCutcheon, Soma Chaudhary, Seongho Hong, Dongwon Park, Jongmin Kim, and Alexander A. Green 5. Computational Design of Small Transcription Activating RNAs (STARs)            Baiyang Liu and James Chappell 6. Design and Assembly of Multi-Level Transcriptional and Translational Regulators for Stringent Control of Gene Expression            F. Veronica Greco, Thea Irvine, Claire S. Grierson, and Thomas E. Gorochowski 7. Model-Based Design of Synthetic Antisense RNA for Predictable Gene Repression            Tae Seok Moon 8. Design of a Toolbox of RNA Thermometers            Shaunak Sen, Abhilash Patel, and Krishan Kumar Gola 9. Development of Synthetic Riboswitches to Guide the Evolution of Metabolite Production in Microorganisms            Minsun Kim, Sungho Jang, and Gyoo Yeol Jung 10. Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening            Janice Kramat and Beatrix Suess 11. RNA Design Principles for Riboswitches that Regulate RNase P-Mediated tRNA Processing            Anna Ender, Peter Stadler, Mario M├╢rl, and Sven Findei├ƒ 12. Design, Characterization, and Application of Targeted Gene Activation in Bacteria Using a Modular CRISPRa System            Maria Claudia Villegas Kcam and James Chappell 13. Reprogramming TracrRNAs for In Vitro RNA Detection and In Vivo Transcriptional Recording            Chunlei Jiao and Chase L. Beisel 14. Harnessing CRISPR-Cas9 for Epigenetic Engineering            Rosa S. Guerra-Resendez and Isaac B. Hilton 15. RNA Structure Prediction, Analysis, and Design: An Introduction to Web-Based Tools            Raphael Angelo I. Zambrano, Carmen Hernandez-Perez, and Melissa K. Takahashi 16. Single-Molecule FRET Studies of RNA Structural Rearrangements and RNA-RNA Interactions            Ewelina M. Ma┼éecka, Boyang Hua, and Sarah A. Woodson 17. Cotranscriptional RNA Chemical Probing     

Part I: Animal Experimentation1. Experimental Diets (Normocaloric and Hypercaloric Diets) La├¡s Marinho Aguiar, Juliana Kelly da Silva Maia, Cinthia Ba├║ Betim Cazarin 2. Measures of Food Intake, Body Weight Gain, and Energy Efficiency in Mice - C├¡ntia Reis Ballard and Cinthia Ba├║ Betim Cazarin 3. The assessment of glucose homeostasis in rodents: Glucose, Insulin and Pyruvate Tolerance Tests  Nathalia R. V. Dragano and Edward Milbank 4. Histopathological Evaluation of Steatohepatitis in Animal ExperimentsYoshihisa Takahashi, Erdenetsogt Dungubat, Toshio Fukusato 5. Quantification of short-chain fatty acids in fecesMirella Romanelli Vicente Bertolo, and  Stanislau Bogusz Junior 6. Quantification of non-esterified fatty acids in serum and plasmaMirella Romanelli Vicente Bertolo, and Stanislau Bogusz Junior 7. Lipid Peroxidation (TBARS) in biological samples Lilian R. B. Mariutti 8. Extraction of Bile Acids from Biological Samples and Quantification Using Ultra-High-Performance Liquid Chromatography-Orbitrap Mass Spectrometry Shota Hori, Hongxia Liu, Riho Yamada, Shun Ichitsubo, Ayana Sakaguchi, Fumika Yokoyama, and Satoshi Ishizuka 9. Glycogen measurementCavaglieri, C.R.; Silva, C.A.; and  Bernardes, C.F. 10. Evaluation of the minerals and trace elements in the biological samplesDuygu Aydemir and Nuriye Nuray Ulusu 11. Microbiome Evaluation Alba Rodr├¡guez-Nogales, Antonio Jes├║s Ruiz-Malag├│n, Jose Alberto Molina-Tijeras, Maria Elena Rodr├¡guez-Cabezas, Julio G├ílvez 12. The GSH colorimetric method as measurement of antioxidant status in serum and rodent tissues Milena Morandi Vuolo, Juliana Kelly Silva Maia, ├éngela Giovana Batista 13. Guidance for designing a preclinical bioavailability study of bioactive compoundsHelena Dias de Freitas Queiroz Barros, Cinthia Ba├║ Betim Cazarin, Mario Roberto Mar├│stica Junior  Part II: Clinical Trials14. Protocols related to Nutritional Anamnesis in Head and Neck Cancer PatientsJudith B├╝ntzel and Jens B├╝ntzel 15. Food Diary, Food Frequency Questionnaire, and 24-hour dietary recall Luisa Saravia, Paula Moliterno, Estela Skapino, and  Luis A. Moreno 16. The Use of Questionnaires to Measure Appetite James H Hollis 17. Protocols for the Use of Indirect Calorimetry in Clinical Research Katherine L Ford, Camila LP Oliveira, Stephanie Ramage, and Carla M Prado 18. Anthropometric Assessment Methods for Adults and Older PeopleThalita Cremonesi Pereira and Cinthia Ba├║ Betim Cazarin 19. MRI-based Body Composition AnalysisMagnus Borga, Andr├⌐ Ahlgren, and Sarah Weston 20. Functional tests for assessing human beta-cell function and insulin sensitivityMarcelo Miranda de Oliveira Lima and Bruno Geloneze 21. Maximum oxygen consumption - VO2max laboratory assessment Mara Patr├¡cia Traina Chacon-Mikahil, Alex Castro, Danilo dos Santos Caruso, and Arthur Fernandes G├íspari 2. 2Muscle and Fat Biopsy and Metabolomics Cl├íudia Regina Cavaglieri, Mara Patr├¡cia Traina Chacon-Mikahil., Renata Garbellini Duft, Ivan Luiz Padilha Bonfante, Arthur Fernandes G├íspari, and  Alex Castro          

Preface...Table of Contents...Contributing Authors...1. Proteoforms and Proteoform Families: Past, Present, and Future Lloyd M. Smith2. Membrane Ultrafiltration-Based Sample Preparation Method and Sheath-Flow CZE-MS/MS for Top-Down ProteomicsZhichang Yang and Liangliang Sun3. Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform CharacterizationTimothy N. Tiambeng, Zhijie Wu, Jake A. Melby, and Ying Ge4. RPLC-RPLC-MS/MS for Proteoform IdentificationKellye A. Cupp-Sutton, Zhe Wang, Dahang Yu, and Si Wu5. Monolithic Materials-Based RPLC-MS for Proteoform Separation and IdentificationYu Liang, Lihua Zhang, and Yukui Zhang6. Capillary Isoelectric Focusing: Mass Spectrometry Method for the Separation and Online Characterization of Monoclonal Antibody Charge Variants at Intact and Subunit LevelJun Dai, Qiangwei Xia, and Chengjie Ji7. Proteoform Analysis and Construction of Proteoform Families in Proteoform SuiteLeah V. Schaffer, Michael R. Shortreed, and Lloyd M. Smith8. Top-Down Mass Spectrometry Data Analysis Using TopPIC SuiteIn Kwon Choi and Xiaowen Liu9. Accurate Proteoform Identification and Quantitation Using pTop 2.0Rui-Xiang Sun, Rui-Min Wang, Lan Luo, Chao Liu, Hao Chi, Wen-Feng Zeng, and Si-Min He10. Proteoform Identification and Quantification using Intact Protein Database Search Engine ProteinGoggleSuideng Qin and Zhixin Tian11. Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconvKyowon Jeong, Jihyung Kim, and Oliver Kohlbacher12. Deconvolving Native and Intact Protein Mass Spectra with UniDecMarius M. Kostelic and Michael T. Marty13. Discovery of Unknown Post-Translational Modifications by Top-Down Mass SpectrometryJesse W. Wilson and Mowei Zhou14. Determining Copper and Zinc Content in Superoxide Dismutase using Electron Capture Dissociation under Native Spray ConditionsRachel Franklin, Michael Hare, and Joseph S. Beckman15. Surface-Induced Dissociation for Protein Complex CharacterizationSophie R. Harvey, Gili Ben-Nissan, Michal Sharon, and Vicki H. WysockiSubject Index List...

This volume looks at the framework in which different scientific disciplines are integrated into the latest studies in behavioral neurogenetics, and covers new approaches toward understanding the system that controls behavior across the animal kingdom. automated behavior analysis using a YOLO-based object detection system;

Recent developments in lesion-symptom mapping (LSM) have spurred rapid growth. The chapters cover the definition and types of brain lesions, how to prepare them for analysis, standard LSM methods, network-based LSM methods, and approaches of transient lesions induced by brain stimulation.

The collected research methods and protocols include the dissection of Notch functional sites, Notch regulators, Notch activity reporters and analysis, roles of Notch in development and diseases, wet and dry lab tools and studies, and bioinformatics analysis.

This book brings together a unique collection of protocols that cover novel and specialized techniques as well as updated and improved adaptations of more standard procedures involving the cell cycle and its regulation by oscillatory networks, exploring recent progress in the field from both holistic and reductionist perspectives.

This detailed book provides an accessible compendium of up-to-date methods in the fields of environmental toxicology, molecular toxicology, and toxicogenomics.

This second edition volume expands on the previous edition with discussions of recently developed techniques that use RNA scaffolds as molecular tools.

The book integrates mitochondria with other cellular components, discussing the dynamic properties of mitochondria with an emphasis on how these processes respond to signaling events and how they affect cellular metabolism.

Part I: Bioinformatic Tools to Study RNA Modifications 1. RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework            Ilaria Manfredonia and Danny Incarnato 2. An Informatics Pipeline for Profiling and Annotating RNA Modifications            Qi Liu, Xiaoqiang Lang, and Richard I. Gregory Part II: Detecting RNA Modifications Using Nanopore Direct RNA Sequencing 3. EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing            Huanle Liu, Oguzhan Begik, and Eva Maria Novoa 4. Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides            Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin Abu-Shumays Part III: Next-Generation Sequencing Approaches to Detect and Capture Modified RNAs 5. AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-Guanosine (m7G) and 3-Methyl-Cytidine (m3C) in RNAs by High-Throughput Sequencing            Virginie Marchand, Lilia Ayadi, Val├⌐rie Bourguignon-Igel, Mark Helm, and Yuri Motorin 6. Transcriptome-Wide Detection of Internal N7-Methylguanosine            Li-Sheng Zhang, Chang Liu, and Chuan He 7. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA Methylating Enzyme Using Mechanistic Crosslinking and Mismatch Profiling            Vanja Stojkovi─ç, David E. Weinberg, and Danica Galoni─ç Fujimori 8. Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing            Bryan R. Cullen and Kevin Tsai 9. Quantitative and Single Nucleotide Resolution Profiling of RNA 5-Methylcytosine            Jun Li, Xingyu Wu, Trung Do, Vy Nguyen, Jing Zhao, Pei Qin Ng, Alice Burgess, Rakesh David, and Iain Searle 10. A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2''-O-Methyl RNAs            Erwin L. van Dijk and Claude Thermes Part IV: Assessing RNA Modifications Using qPCR- and Molecular Biology-Based Methods 11. Assessing 2''-O-Methylation of mRNA Using Quantitative PCR            Brittany A. Elliott and Christopher L. Holley 12. Relative Quantification of Residue Specific m6A RNA Methylation Using m6A-RT-QPCR            Ane Olazagoitia-Garmendia and Ainara Castellanos-Rubio 13. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease            Jenna M. Lentini and Dragony Fu 14. Analysis of Queuosine tRNA Modifications Using APB Northern Blot Assays            Cansu Cirzi an

This volume discusses the latest experimental and clinical approaches to study seizures and epilepsy. Chapters in this book cover detailed protocols for ex vivo and in vitro experimental models and widely-used in vivo (acute and chronic seizure) models in epilepsy research.

Part I: Small Molecules 1. Measurement of Transcellular Transport Rates and Intracellular Drug Sequestration in the Presence of an Extracellular Concentration Gradient            Kyoung Ah Min and Gus R. Rosania 2. Kinetic Design for Establishing Long Term Stationary Cytosol Concentrations during Drug Transport across P-gp Expressing Confluent Cell Monolayers to Facilitate Measuring Cytosol Concentration, Fitting Drug Molar Partition Coefficients into the Cytosolic Monolayer of the Plasma Membrane and Kinetically Identifying Drug Uptake Transporters            Joe Bentz 3. In Vitro Methodologies to Assess Potential for Transporter-Mediated Drug-Drug Interactions            Jibin Li, Qing Wang, and Ismael J. Hidalgo 4. Determination of Fraction Unbound and Unbound Partition Coefficient to Estimate Intracellular Free Drug Concentration            Sangwoo Ryu, Keith Riccardi, Samantha Jordan, Nathaniel Johnson, and Li Di 5. Quantitative Analysis of Intracellular Drug Concentrations in Hepatocytes            Chitra Saran, James J. Beaudoin, Nathan D. Pfeifer, and Kim L.R. Brouwer 6. Quantification of Intracellular Drug Aggregates and Precipitates            Phillip Rzeczycki and Gus R. Rosania 7. Quantitative Phenotypic Analysis of Drug Sequestering Macrophage Subpopulations            Mikhail D. Murashov 8. Using an Integrated QSAR Model to Check Whether Small-Molecule Xenobiotics Will Accumulate in Biomembranes, with Particular Reference to Fluorescent Imaging Probes            Richard W. Horobin and Juan C. Stockert 9. Diversity-Oriented Fluorescence Library Approach (DOFLA) for Discovery of Cell-Permeable Probes for Applications in Live Cell Imaging            Dongdong Su and Young-Tae Chang Part II: Macromolecules, Biologics, and Nanoparticles 10. Overcoming Cellular and Systemic Barriers to Design the Next Wave of Peptide Therapeutics            Jerome Hochman, Tomi Sawyer, and Ruchia Duggal 11. Intracellular Targeting of Cyclotides for Therapeutic Applications            Nicole Lawrence and David J. Craik 12. Cellular Trafficking of Monoclonal and Bispecific Antibodies            John J. Rhoden and Christopher M. Wiethoff 13. Quantitative Drug Target Imaging Using Paired-Agent Principles            Kenneth M. Tichauer, Negar Sadeghipour, Yu "Winston" Wang, Summer L. Gibbs, Jonathan T.C. Liu, and Kimberley S. Samkoe 14. Quantitative Determination of Intracellular Bond Cleavage            Joshua A. Walker, Michelle R. Sorkin, and Christopher A. Alabi 15. Development and Application of a Single Cell-Level PK-PD Model for ADCs 

1. Isolation of Lipid Rafts by the Detergent and Non-Detergent Based Methods for Localization of GPCRs with Immunoblotting and Laser Scanning Confocal Microscopy            Peter Abdelmaseeh, Andrew C. Tiu, Selim Rozyyev, Laureano D. Asico, Pedro A. Jose, Van Anthony M. Villar 2. Detection of GPCR mRNA Expression in Primary Cells via qPCR, Microarrays, and RNA-Sequencing            Krishna Sriram, Cristina Salmer├│n, Anna Di Nardo, and Paul A. Insel 3. Construction of Recombinant Cell Lines for GPCR Expression            Philip J. Reeves 4. Recombinant Expression and Purification of Cannabinoid Receptor CB2, a G Protein-Coupled Receptor            Alexei A. Yeliseev 5. Screening for Serotonin Receptor 4 Agonists Using GPCR-Based Sensor in Yeast            Emily A. Yasi and Pamela Peralta-Yahya 6. Immobilization of Olfactory Receptors Carried by Nanosomes onto a Gold Sensor Surface            Jasmina Vidic and Yanxia Hou 7. Screening Methods for Cell-Free Synthesized GPCR/Nanoparticle Samples            Zoe K├╢ck, Volker D├╢tsch, and Frank Bernhard 8. Fluorescence Anisotropy-Based Assay for Characterization of Ligand Binding Dynamics to GPCRs: The Case of Cy3B-Labelled Ligands Binding to MC4 Receptors in Budded Baculoviruses            Santa Veiksina, Maris-Johanna Tahk, T├╡nis Laasfeld, Reet Link, Sergei Kopanchuk, and Ago Rinken 9. Bioluminescence in G Protein-Coupled Receptors Drug Screening Using Nanoluciferase and Halo-Tag Technology            Hannes Schihada, Katarina Nemec, Martin J. Lohse, and Isabella Maiellaro 10. Nanoluciferase-Based Complementation Assay to Detect GPCR-G Protein Interaction            C├⌐line Laschet and Julien Hanson 11. Imaging of Genetically-Encoded FRET-Based Biosensors to Detect GPCR Activity            Luca Bordes, Sergei Chavez-Abiega, and Joachim Goedhart 12. cAMP Biosensor Assay Using BacMam Expression System: Studying the Downstream Signaling of LH/hCG Receptor Activation            Darja Lavogina, T├╡nis Laasfeld, Maris-Johanna Tahk, Olga Kukk, Anni Allikalt, Sergei Kopanchuk, and Ago Rinken 13. FLIPR Calcium Mobilization Assays in GPCR Drug Discovery            Grzegorz Woszczek, Elisabeth Fuerst, and Thomas J.A. Maguire 14. Live Cell Imaging and Optogenetics-Based Assays for GPCR Activity            Xenia Meshik and N. Gautam 15. Split-Tobacco Etch Virus (Split-TEV) Method in G Protein-Coupled Receptor Interacting Proteins            Marta Alonso-Gard├│n and Ra├║l Est├⌐vez 16. NanoLuc-Based Methods to Measure ╬▓-Arrestin2 Recruitment to G Protein-Coupled

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms.

The aim of this book is to describe the underlying principles of algebraic geometry, some of its important developments in the twentieth century, and some of the problems that occupy its practitioners today. It is intended for the working or the aspiring mathematician who is unfamiliar with algebraic geometry but wishes to gain an appreciation of its foundations and its goals with a minimum of prerequisites. Few algebraic prerequisites are presumed beyond a basic course in linear algebra.