Parasite Genomics: Methods and Protocols

ISBN-13: 9781071616802 / Angielski / Twarda / 2021 / 336 str.

Luis M. de Pablos; Javier Sotillo

Spis treści

Part I: Novel Sequencing and Bioinformatic Pipelines for the Study of Parasite Genomes

 

1. Nanopore Long Read DNA Sequencing of Protozoan Parasites: Hybrid Genome Assembly of Trypanosoma cruzi

            Florencia Díaz-Viraqué, Gonzalo Greif, Luisa Berná, and Carlos Robello

 

2. Chromosomes Conformation Capture Coupled with Next Generation Sequencing (Hi-C) in Plasmodium falciparum

            Mohit Gupta, Todd Lenz, and Karine G. Le Roch

 

3. Sequencing and Reconstructing Helminth Mitochondrial Fenomes Directly from Genomic Next-Generation Sequencing Data

            Nikola Palevich and Paul Haydon Maclean

 

4. Automated Phylogenetic Analysis Using Best Reciprocal BLAST

            Erin R. Butterfield, James C. Abbott, and Mark C. Field

 

Part II: Diagnostic Approaches Using Genomic Tools

 

5. An Illumina MiSeq-Based Amplicon Sequencing Method for the Detection of Mixed Parasite Infections Using the Blastocystis SSU rRNA Gene as an Example

            Jenny G. Maloney, Nadja S. George, Aleksey Molokin, and Monica Santin

 

6. Giardia duodenalis: Detection by Quantitative Real-Time PCR and Molecular Diversity

            Alejandro Dashti, Pamela C. Köster, and David Carmena

 

Part III: Host-Parasite Interactions: Deciphering Gene Function and Molecular Processes in Parasites

 

7. Conditional Gene Deletion in Mammalian and Mosquito Stages of Plasmodium berghei Using Dimerizable Cre Recombinase

            Priyanka Fernandes, Manon Loubens, Olivier Silvie, and Sylvie Briquet

 

8. Coupling Auxin-Inducible Degron System with Ultrastructure Expansion Microscopy to Accelerate the Discovery of Gene Function in Toxoplasma gondii

            Nicolas Dos Santos Pacheco and Dominique Soldati-Favre

 

9. Genome-Wide Analysis of RNA-Protein Interactions in Plasmodium falciparum Using eCLIP-Seq

            Thomas Hollin, Steven Abel, and Karine G. Le Roch

 

10. Transcriptional Analysis of Tightly Synchronized Plasmodium falciparum Intraerythrocytic Stages by RT-qPCR

            Núria Casas-Vila, Anastasia K. Pickford, Harvie P. Portugaliza, Elisabet Tintó-Font, and Alfred Cortés

 

11. Analysis of the Interaction between Plasmodium falciparum-Infected Erythrocytes and Human Endothelial Cells Using a Laminar Flow System, Bioinformatic Tracking and Transcriptome Analysis

            Yifan Wu, Philip Bouws, Stephan Lorenzen, Iris Bruchhaus, and Nahla Galal Metwally

 

12. Integration of Genomic and Transcriptomic Data to Elucidate Molecular Processes in Babesia divergens

            Luis Miguel González, Elena Sevilla, Miguel Fernández-García, Alejandro Sánchez-Flores, and Estrella Montero

 

13. Integration of Functional Genomic, Transcriptomic, and Metabolomic Data to Identify Key Features in Genomic Expression, Metabolites, and Metabolic Pathways of Babesia divergens

            Miguel Fernández-García, Alejandro Sanchez-Flores, Luis Miguel González, Coral Barbas, Mª Fernanda Rey-Stolle, Elena Sevilla, Antonia García, and Estrella Montero

 

14. Genome Analysis of Programmed DNA Elimination in Parasitic Nematodes

            Jianbin Wang

 

15. Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining

            Fabio Formenti, Gabriel Rinaldi, Cinzia Cantacessi, and Alba Cortés

 

Part IV: Genomics of Parasite-Derived Extracellular Vesicles

 

16. Methods for the Isolation and Study of Exovesicle DNA from Trypanosomatid Parasites

            Lina María Orrego, Romina Romero, Antonio Osuna, and Luis M. de Pablos

 

17. Isolation and Analysis of MicroRNAs from Extracellular Vesicles of the Parasitic Model Nematodes Nippostrongylus brasiliensis and Trichuris muris

            Ramon M. Eichenberger

Blurb

This detailed book provides a comprehensive series of innovative research techniques and methodologies applied to the parasite genomics research area, all applying different approaches to analyzing parasite genomes and furthering the study of genetic complexity and the mechanisms of regulation. Beginning with chapters on novel sequencing and the bioinformatics pipeline, the volume continues by exploring diagnostic approaches using genomic tools, host-parasite interactions, as well as the genomics of parasite-derived extracellular vesicles. 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, Parasite Genomics: Methods and Protocols creates a detailed picture of genomic approaches for researchers seeking a better understanding of characterizing parasite nucleic acid content.