Kooperativer Bibliotheksverbund

UID:

Format: VIII, 221 S. , Ill.

ISBN: 3437204025

Series Statement: Uni-Taschenbücher 1478

Uniform Title: A dictionary of genetic engineering

Language: German

Subjects: Biology

Keywords: Englisch ; Wörterbuch ; Gentechnologie ; Enzyklopädie ; Wörterbuch

UID:

Format: 1 online resource (XIV, 535p. 85 illus., 2 illus. in color.)

Edition: 1st ed. 2011.

ISBN: 1-61779-173-3

Series Statement: Methods in Molecular Biology, 759

Content: Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems.  Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques  for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine.  These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases.  Written for the highly successful Methods in Molecular Biology™ series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results.   Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all ‘omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.

Note: Bibliographic Level Mode of Issuance: Monograph , Yeast Systems Biology: The Challenge of Eukaryotic Complexity -- Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State-of-the-Art Through Comparative Genomics -- Genome-Wide Measurement of Histone H3 Replacement Dynamics in Yeast -- Genome-Wide Approaches to Studying Yeast Chromatin Modifications -- Absolute and Relative Quantification of mRNA Expression (Transcript Analysis) -- Enrichment of Unstable Non-Coding RNAs and Their Genome-Wide Identification -- Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays -- RNA Sequencing -- Polyadenylation State Microarray (PASTA) Analysis -- Enabling Technologies for Yeast Proteome Analysis -- Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC -- Protein-Protein Interactions and Networks: Forward and Reverse Edgetics -- Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases -- Fit for Purpose Quenching and Extraction Protocols for Metabolic Profiling of Yeast Using Chromatography-Mass Spectrometry Platforms -- The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening -- Competition Experiments Coupled with High-Throughput Analyses for Functional Genomics Studies in Yeast -- Fluorescence Fluctuation Spectroscopy and Imaging Methods for Examination of Dynamic Protein Interactions in Yeast -- Nutritional Control of Cell Growth Via TOR Signaling in Budding Yeast -- Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade -- Standards, Tools, and Databases for the Analysis of Yeast 'Omics Data -- A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements -- High Throughput Analyses and Curation of Protein Interactions in Yeast -- Noise in Biological Systems: Pros, Cons, and Mechanisms of Control -- Genome-Scale Integrative Data Analysis and Modeling of Dynamic Processes in Yeast -- Genome-Scale Metabolic Models of Saccharomyces cerevisiae -- Representation, Simulation, and Hypothesis Generation in Graph and Logical Models of Biological Networks -- Use of Genome-Scale Metabolic Models in Evolutionary Systems Biology -- Saccharomyces cerevisiae Contributions Towards Understanding Mammalian Gene Function and Therapy. , English

Additional Edition: ISBN 1-61779-172-5

Language: English

DOI: 10.1007/978-1-61779-173-4

UID:

Format: VIII, 221 S.

ISBN: 3-334-00268-3

Uniform Title: A dictionary of genetic engineering

Note: A dictionary of genetic engineering 〈dt.〉

Language: German

Keywords: Englisch ; Wörterbuch ; Gentechnologie ; Wörterbuch ; Enzyklopädie ; Wörterbuch

UID:

Format: V, 153 S.

Edition: 1. publ.

ISBN: 0-521-26080-9

Content: Over 500 terms defined; intended as technical terminology and slang or jargon also used in the field. Will interest workers and students in cell biology, developmental biology, genetics, chemical engineering, as well as those in commerce and politics with a concern for the new technology. Contains illustrations. Miscellaneous appendixes.

Language: English

Subjects: Biology

Keywords: Englisch ; Wörterbuch ; Gentechnologie ; Englisch ; Gentechnologie ; Wörterbuch ; Enzyklopädie

UID:

Format: VIII, 221 S. , Ill., graph. Darst. , 19 cm

Edition: 1. Aufl.

ISBN: 3334002683

Uniform Title: A dictionary of genetic engineering 〈dt.〉

Language: German

Subjects: Biology

Keywords: Gentechnologie ; Wörterbuch

URL: Inhaltsverzeichnis

UID:

Format: 221 S. , Abb., Tab.

ISBN: 3334002683

Language: Undetermined

Keywords: Fachlexikon

UID:

Format: VIII, 221 S. : Ill.

ISBN: 3-437-20402-5

Series Statement: Uni-Taschenbücher 1478

Uniform Title: A dictionary of genetic engineering

Language: German

Subjects: Biology

Keywords: Englisch ; Wörterbuch ; Gentechnologie ; Enzyklopädie ; Wörterbuch ; Enzyklopädie ; Wörterbuch

UID:

Format: VIII, 221 S. : , 49 Abb. u. 5 Tab.

ISBN: 3-437-20402-5

Series Statement: UTB für Wissenschaft : Uni-Taschenbücher 1478

Uniform Title: A dictionary of genetic engineering 〈dt.〉

Note: 12603

Language: German

UID:

Format: 153 S. , graph. Darst.

Edition: Reprint

Language: English

Keywords: Enzyklopädie

UID:

Format: 1 online resource (445 pages)

Edition: 2nd ed.

ISBN: 1-4939-9736-X

Series Statement: Methods in Molecular Biology ; v.2049

Note: Intro -- Dedication -- Author Biography -- Preface -- Contents -- Contributors -- Part I: Yeast Systems Biology -- Chapter 1: Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity -- 1 Introduction -- 2 Advances in `Omic Technologies -- 3 Multiple Levels of Control -- 4 The Rise of Mathematical Modeling and the Integration of Data from the Different `Omic Domains and Timescales -- 5 The Relationship Between Systems and Synthetic Biology and New Biological Workbenches -- 6 Yeast as a Model for Both Infectious and Systemic Human Diseases -- 7 Conclusions and Prospects -- References -- Part II: Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies -- Chapter 2: Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq -- 1 Introduction -- 2 Materials -- 2.1 Yeast Genomic DNA Extraction -- 2.2 Annealing of Ribose-Seq Adaptor Oligonucleotides -- 2.3 Ribose-Seq -- 2.3.1 Fragmentation of DNA -- 2.3.2 dA-Tailing and Adaptor Ligation -- 2.3.3 Alkali Treatment -- 2.3.4 AtRNL Ligation -- 2.3.5 T5 Exonuclease Degradation -- 2.3.6 Tpt1 Reaction -- 2.3.7 PCR Amplification of DNA Libraries -- 2.3.8 PAGE Visualization -- 2.4 Equipment -- 3 Methods -- 3.1 Yeast Genomic DNA Extraction -- 3.2 Preparation of Ribose-Seq Adaptor -- 3.3 Ribose-Seq -- 3.3.1 Fragmentation of Genomic DNA -- 3.3.2 dA-Tailing and Adaptor Ligation -- 3.3.3 Alkali Treatment -- 3.3.4 Self-Ligation (Circularization) of 2'-Phosphate Terminal of rNMP to 5'-Phosphate of the DNA by AtRNL -- 3.3.5 Removal of Linear ssDNA -- 3.3.6 Removal of 2'-Phosphate -- 3.4 PCR -- 3.4.1 PCR 1 -- 3.4.2 PCR 2 -- 3.5 PAGE -- 3.6 Size Selection and Gel Purification -- 4 Notes -- References -- Chapter 3: Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9 -- 1 Introduction -- 2 Materials -- 2.1 Cas9 Yeast Strain. , 2.2 DNA Constructs and Templates -- 2.3 Primers -- 2.4 Lithium Acetate Transformation -- 2.5 Yeast Media -- 3 Methods -- 3.1 Preparation of Cas9-Expressing Base Strain -- 3.2 Colony PCR Confirmation of the Cas9 Base Strain -- 3.3 CRISPR Target Site Selection for Deletion of an Open Reading Frame or Region -- 3.4 CRISPR Target Site Selection for Integration of a Point Mutation -- 3.5 Cloning-Free Generation of Guide RNA Constructs -- 3.6 Generation of Linear Entry Vector -- 3.7 Donor DNA Design -- 3.8 Generation of Short Donor DNAs (Including the JEN1 Control Donor) by Primer Extension -- 3.9 Markerless, Multiplex Engineering in the Cas9 Base Strain -- 4 Notes -- Appendix: Primers and Sequences -- Genbank Sequence: pAH1 gRNA Expression Plasmid -- Genbank Sequence: pAH2 Cas9 Expression Construct 1 of 2 (PmeI Fragment) -- Genbank Sequence: pAH3 Cas9 Expression Construct 2 of 2 (PmeI Fragment) -- Genbank Sequence: pAH2 Recombined with pAH3 at Integration Site -- References -- Chapter 4: Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate -- 1 Introduction -- 2 Materials -- 2.1 Strains and Plasmids for Generation of Query Strains -- 2.2 Drug Concentrations -- 2.3 Transformation Media and Solutions -- 2.4 Transformation Media for DAmP Essential Strains -- 2.5 Synthetic Genetic Array (SGA) Screen -- 2.5.1 Strains -- 2.5.2 Media -- 3 Methods -- 3.1 Designing Transformation Products -- 3.2 Making Yeast Query Competent Cells -- 3.3 Cell Transformation for Essential and Nonessential Genes -- 3.4 Validate Strains (Colony PCR) -- 3.5 Yeast DAmP Protocol for Making Essential Strains -- 3.6 Synthetic Genetic Array (SGA) -- 3.6.1 Preparing Query Lawn -- 3.6.2 Preparing Library (See Note 12) -- 3.6.3 Mating -- 3.6.4 Diploid Selection -- 3.6.5 Sporulation -- 3.6.6 Haploid Selection 1 -- 3.6.7 Haploid Selection 2 -- 3.6.8 Single Mutant Selection. , 3.6.9 Double Mutant Selection -- 3.7 Digital Imaging -- 3.8 Data Analysis -- 3.8.1 Image Processing and Spot Size Detection -- 3.8.2 Compute S-Scores -- 4 Notes -- References -- Chapter 5: Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode-ChIP-Seq -- 1 Introduction -- 2 Materials -- 2.1 Yeast Strains and Plasmids -- 2.2 Yeast Media and Drugs -- 2.3 Yeast Plates and Accessories -- 2.4 Buffers -- 2.5 Equipment -- 3 Methods -- 3.1 Cell Culture and Preparation of Cell Pellets -- 3.2 Coupling Beads and Antibody -- 3.3 Chromatin Preparation -- 3.3.1 Preparing 15 ml Bioruptor Pico Tubes for Sonication -- 3.3.2 Preparing Chromatin -- 3.3.3 Check the Chromatin Size -- 3.4 Chromatin Immunoprecipitation -- 3.5 Library Preparation -- 3.5.1 Test PCR Analysis for ChIP Efficiency -- 3.5.2 Library Preparation -- 3.6 Sequencing and Data Analysis -- 4 Notes -- References -- Chapter 6: Transcript Profiling Analysis Through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Reveals Transcri... -- 1 Introduction -- 2 Materials -- 2.1 Strain, Growth Conditions -- 2.2 M280 Beads Buffer -- 3 Methods -- 3.1 RNA Extraction and mRNA Isolation -- 3.2 PET Library Preparation -- 3.2.1 10 μg mRNA Is Reversely Transcribed (RT) into cDNA with GsuI-Oligo dT Primer (Table 1) as Below -- 3.2.2 Full-Length cDNA Selection -- 3.2.3 Rolling Circle Amplification (RCA) of Circular Full-Length DNA Molecules -- 3.2.4 PET Fragment Generation -- 3.3 Data Processing -- 3.4 Uncharacterized Transcript Validation -- 3.5 Rapid Amplification of cDNA Ends (RACE) Validation -- 3.6 Gene Ontology Analysis -- 4 Notes -- References -- Chapter 7: RNA Sequencing Best Practices: Experimental Protocol and Data Analysis -- 1 Introduction -- 2 Materials -- 2.1 Experimental Design -- 2.2 RNA Isolation and Quality Control (See Note 1). , 2.3 RNA-Seq Read Processing (See Note 3) -- 2.4 Downstream Analysis of RNA-Seq Count Data (See Note 6) -- 3 Methods -- 3.1 Experimental Design -- 3.2 RNA Isolation and Quality Control (See Note 8) -- 3.3 RNA-Sequencing -- 3.4 RNA-Seq Read Processing -- 3.5 Downstream Analysis of RNA-Seq Count Data -- 3.6 Database Submission -- 4 Notes -- References -- Chapter 8: Advanced Methods for the Analysis of Altered Pre-mRNA Splicing in Yeast and Disease -- 1 Introduction -- 2 Materials -- 2.1 Yeast Culture -- 2.2 RNA Extraction -- 2.3 Bioinformatic Analysis (Software and Reference Files) -- 2.4 cDNA Synthesis -- 2.5 PCR Amplification -- 2.6 Agarose Gel Electrophoresis -- 3 Methods -- 3.1 Yeast Culture -- 3.2 RNA Isolation and Preparation -- 3.3 Bioinformatic Analyses -- 3.4 Data Validation by RT-PCR -- 4 Notes -- References -- Chapter 9: PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distr... -- 1 Introduction -- 2 Materials -- 2.1 End Extension of Adenylated RNA to Generate the 3'-Tag -- 2.2 Limited Fragmentation of RNA with RNaseT1 -- 2.3 Enrichment of 3' Fragments and Their 5' Phosphorylation -- 2.4 Ligation of 5'-Splint-Linker to the 5'-Ends of 3' Fragments -- 2.5 Reverse Transcription -- 2.6 Size Selection of PAT-Seq Library -- 2.7 Barcoded PAT-Seq Library Amplification -- 2.8 Facility for Illumina-Based NGS -- 3 Methods -- 3.1 End-Extension of Adenylated RNA to Generate the 3'-Tag -- 3.2 Limited Fragmentation of RNA with RNaseT1 -- 3.3 Enrichment of 3' Fragments and Their 5' Phosphorylation -- 3.4 Phosphorylation of 5'-Ends of RNA Fragments -- 3.5 Ligation of 5'-Splint-Adapter to the 5'-Ends of 3'Fragments -- 3.6 Reverse Transcription -- 3.7 Urea-PAGE Size Selection of PAT-Seq Library -- 3.8 PCR Amplification and Indexing of the PAT-Seq Library -- 3.9 Sequencing of PAT-Seq Libraries. , 3.10 Concluding Remarks -- 4 Notes -- References -- Chapter 10: Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT -- 1 Introduction -- 2 Materials and Equipment -- 2.1 Cell Culture and Harvest -- 2.2 Cell Pretreatment and Lysis -- 2.3 Ultracentrifugation -- 2.4 Protein Fraction Processing and Concentration Estimation -- 2.5 Digestion, TMT Labeling, Peptide Desalting, and Prefractionation -- 3 Methods -- 3.1 Cell Culture -- 3.2 Cell Harvest and Preprocessing -- 3.3 Nuclear Preparation (Optional) -- 3.4 Spheroplast Lysis for Density Gradient Fractionation -- 3.5 Subcellular Fractionation -- 3.6 Fraction Processing -- 3.7 Tryptic Digestion -- 3.8 TMT Labeling -- 3.9 Sample Cleanup by Solid-Phase Extraction on Sep Pak Reversed Phase Cartridges -- 3.10 Off-Line High pH Reversed Phase Fractionation -- 3.11 Mass Spectrometry Data Processing -- 3.12 Analysis of Spatial Proteomics Data, Protein Classification and Assignment -- 4 Notes -- References -- Chapter 11: Data-Independent Acquisition for Yeast Glycoproteomics -- 1 Introduction -- 1.1 Mass Spectrometry Proteomics -- 1.2 N-Glycoproteins and Their Relevance in Physiology -- 1.3 Diversity in N-Glycosylation -- 1.4 Glycoproteomics as a Tool to Study Protein Glycosylation -- 2 Materials -- 2.1 Cell Growth and Harvest -- 2.2 Cell Lysis and Preparation for MS Analysis -- 2.3 Solutions for Cell Lysis and Preparation for MS Analysis (See Note 1) -- 2.4 Zip-Tipping with C18 ZipTips -- 2.5 Solutions for Zip-Tipping with a C18 ZipTip -- 3 Methods -- 3.1 Yeast Growth and Harvest -- 3.2 Cell Wall Preparation -- 3.3 Deglycosylation of Cell Wall Protein Extracts (See Note 16) -- 3.4 ZipTipping Protocol for C18 Ziptips (See Notes 18 and 19) -- 3.5 Mass Spectrometry -- 3.5.1 Analyze Peptides and Glycopeptides with Data Dependent Acquisition Mass Spectrometry. , 3.5.2 Analyze Peptides and Glycopeptides with Data-Independent Acquisition (SWATH) Mass Spectrometry.

Additional Edition: ISBN 1-4939-9735-1

Language: English