Note: Intro -- Preface -- Contents -- Chapter 1: Introduction -- Part I: Genetics and Genomics -- Chapter 2: The Continuously Expanding Universe of Entamoeba -- 2.1 Background -- 2.1.1 History of Entamoeba Taxonomy from 1875 to 1919: Lösch to Dobell -- 2.1.2 Taxonomy of Entamoeba in the Pre-molecular Era: Entamoeba dispar, Entamoeba moshkovskii, Entamoeba hartmanni, etc. -- 2.1.3 The Early Use of Molecular but Non-sequence Data in Taxonomic Analysis: Isoenzymes, DNA Hybridization, and Antibody -- 2.2 The Impact of Ribosomal DNA on Entamoeba Taxonomy: Riboprinting, Sequences from Cultures, and Sequences from Stool DNA -- 2.3 The Current Situation: Phylogeny, Diversity, Nomenclature, Host Specificity, and Impact of the Lack of Morphology -- 2.3.1 Recent Surge in Reports of Novel Ribosomal Lineages -- 2.3.2 Phylogeny and Host Specificity -- 2.3.3 Intraspecies Diversity of Entamoeba -- 2.3.4 Impact of the Lack of Morphology -- 2.4 The Future -- References -- Chapter 3: The Genomics of Entamoebae: Insights and Challenges -- 3.1 Introduction -- 3.2 Phylogeny of the Entamoebae -- 3.3 Genome Sequencing and Annotation of Entamoeba histolytica -- 3.4 Why Is Entamoeba Genome Assembly So Challenging? -- 3.5 The Genomes of Other Entamoeba Species -- 3.6 Interspecific Variation Among Entamoeba Genomes -- 3.7 Intraspecific Variation Among Entamoeba Genomes -- 3.8 Conclusions and Future Prospects -- References -- Chapter 4: Multilocus Sequence Typing System (MLST): Genetic Diversity and Genetic Components to Virulence -- 4.1 Introduction -- 4.2 Multilocus Sequence Typing (MLST): A Balance Between Variability and Stability -- 4.2.1 E. histolytica Multilocus Sequence Typing Schema -- 4.3 Evaluation of the Entamoeba histolytica MLST System -- 4.4 Massive Parallel Sequencing -- 4.5 Illumina Library Complexity -- 4.6 MLST Analysis. , 4.7 Identification of SNP Markers That Are Informative Regarding the Virulence Potential of These Parasites -- 4.8 Future Directions -- References -- Chapter 5: The tRNA Gene-Linked STRs and Other Genetic Typing Methods -- 5.1 Introduction -- 5.2 Genotyping Methods for Entamoeba histolytica -- 5.2.1 The tRNA Gene-Linked STRs in E. histolytica -- 5.2.1.1 Initial Studies of Polymorphism in Repeat Loci Containing tRNA Genes -- 5.3 Development of the tRNA Gene-Linked Six-Loci Genotyping System -- 5.3.1 A Nonrandom Distribution of Parasite Genotype with Respect to Infection Outcome Was Detected -- 5.3.1.1 Limitations of the Foregoing Study -- 5.3.1.2 Other Limitations of tRNA Gene-Linked STR Markers -- 5.3.2 Application of the tRNA Gene-Linked STRs -- 5.3.2.1 Detection of a New Infection or Genotype in Follow-Up Samples -- 5.3.2.2 Detection of Genetic Selection or Organ Tropism in the Same ALA Patients -- 5.3.2.3 Identification of a Unique Avirulent E. histolytica Strain -- 5.3.2.4 Tracking the Disease Transmission Within Family Members (in South Africa) -- 5.3.3 E. histolytica Diversity Based on Sequence Types in tRNA Gene-Linked Loci -- 5.3.4 Future Work: Genome-Wide SNPs in E. histolytica -- References -- Chapter 6: Genetic Manipulation Techniques -- 6.1 Introduction -- 6.2 Transfections and Episomal Expression of Exogenous Genes -- 6.3 Downregulation of Gene Expression -- 6.4 Modulation of Gene Expression by a Dominant- Negative Effect -- 6.5 Gene Silencing in Entamoeba histolytica -- 6.5.1 RNAi-Based Methods for Silencing of Gene Expression -- 6.5.2 Epigenetic Gene Silencing in E. histolytica -- 6.5.3 Silencing of Additional Genes in the Plasmid-Less G3 Trophozoites -- 6.5.4 Molecular Mechanism of Gene Silencing in Entamoeba histolytica -- 6.6 Concluding Remarks -- References -- Part II: Regulation of Gene Expression. , Chapter 7: Surveying Entamoeba histolytica Transcriptome Using Massively Parallel cDNA Sequencing -- 7.1 From a Few Transcripts to an Atlas of Transcriptome: 25 Years in Retrospect -- 7.1.1 Full-Length cDNA Sequencing: Started Out Small -- 7.1.2 Large-Scale EST Sequencing: Kick It Up a Notch -- 7.1.3 Genome Sequence Unleashed: Budding Blossoms of Spring -- 7.1.4 Microarrays Took Off: Ripening Fruits of Summer -- 7.1.5 RNA-Seq Takes Over: The Future Is Here -- 7.2 RNA-Seq: Mapping the Transcriptome at Its Highest Resolution -- 7.3 Think Before You Start Sequencing! Caveats and Tips of RNA-Seq for Entamoeba -- 7.3.1 RNA Fractionation and Depletion of Ribosomal RNA -- 7.3.2 Strand Specificity and Overestimation of Coding mRNA Abundance -- 7.3.3 Depth of Sequencing and Multiplexing -- 7.3.4 Quality of Predicted Gene Models for Downstream Analyses -- 7.4 How Much of the Genome Is Transcribed? Hunting for Hidden Transcripts -- 7.4.1 Overall Composition of the E. histolytica Transcriptome -- 7.4.2 Genomic Regions Being Transcribed as Poly(A)+ Transcripts -- 7.4.3 Hunting for Unannotated Transcripts -- 7.5 How Good (or Bad) Are the Predicted Gene Models? Defining Bona Fide Gene Models -- 7.5.1 Genome Quality and Gene Model Accuracy -- 7.5.2 How Many of the Splicing Junctions Can be Confirmed? -- 7.5.3 Defining a Set of Bona Fide Gene Models -- 7.6 How Many of the Alternative mRNA Isoforms Are Functionally Relevant? Quantifying the Stochastic Noise of RNA Processing -- 7.6.1 Alternatively Splicing and Polyadenylation Events Are Pervasive -- 7.6.2 Quantifying the Stochastic Noise to Identify the Nonstochastic Events -- 7.7 Conclusions and Perspectives -- 7.7.1 Mapping the Start and End of Transcripts -- 7.7.2 Simultaneous Profiling of Long and Small RNAs -- 7.7.3 CLIP-Seq: Characterization of RNA-Binding Protein -- References. , Chapter 8: Ribosomal RNA Genes and Their Regulation in Entamoeba histolytica -- 8.1 Introduction -- 8.2 The Transcriptional Apparatus of Entamoeba histolytica: An Overview -- 8.3 The rRNA Genes in Entamoeba Are Extrachromosomal -- 8.4 The Nucleolus in Entamoeba Is at the Nuclear Periphery -- 8.5 Organization of the rRNA Gene Promoter in E. histolytica -- 8.6 The rRNA Genes in E. histolytica Are Transcribed from Two Promoters -- 8.7 Unprocessed Pre-rRNA Accumulates During Growth Stress -- 8.8 The 5′-ETS RNA Accumulates as Circular Molecules Under Stress -- 8.9 Circular Noncoding RNAs May Regulate Pre-rRNA Levels -- 8.10 Summary and Conclusions -- References -- Chapter 9: Small RNAs and Regulation of Gene Expression in Entamoeba histolytica -- 9.1 RNA Interference and Small RNAs -- 9.2 Primary and Secondary Small RNAs -- 9.3 RNAi Pathway-Related Protein Homologues in E. histolytica -- 9.4 Endogenous Small RNA Populations in Entamoeba -- 9.5 Characteristics of Argonaut-Associated Small RNAs in E. histolytica Trophozoites -- 9.6 Small RNAs Map to Amebic Genes in Varying Patterns -- 9.7 Gene Knockdown Technique Based on the Endogenous RNAi Pathway -- 9.8 Functional Analysis of Small RNAs That Associate with Argonaut Proteins -- 9.9 Final Remarks -- References -- Chapter 10: The Biology of Retrotransposition in Entamoeba histolytica -- 10.1 Transposable Elements: An Overview -- 10.1.1 TEs in Protozoan Parasites -- 10.1.2 TEs in Entamoeba -- 10.2 The LINEs and SINEs of Entamoeba histolytica -- 10.2.1 Sequence Comparison of the Three LINE/SINE Families -- 10.2.2 Genomic Location of LINEs/SINEs in E. histolytica and E. dispar -- 10.3 Sequence Organization of the Major E. histolytica Retrotransposon: EhLINE1 -- 10.3.1 Properties of ORF1p and RT Domain of ORF2p -- 10.3.2 Properties of the EhLINE1 Endonuclease. , 10.4 Induction of De Novo Retrotransposition in Cultured Cells -- 10.4.1 Use of the Cell Culture System to Understand Biology of Retrotransposition -- 10.4.2 Construction of a Retrotransposition-Competent Cell Line of E. histolytica -- 10.4.3 Evidence of Recombination Between SINEs During Retrotransposition in E. histolytica -- 10.5 Summary and Conclusions -- References -- Chapter 11: Entamoeba histolytica: Bridging the Gap Between Environmental Stress and Epigenetic Regulation -- 11.1 Entamoeba histolytica: Life Cycle and Environmental Challenges -- 11.2 Epigenetics as a Tool for Adaptation -- 11.3 Evidence for 5-Methylcytosine in the Genome of E. histolytica -- 11.4 E. histolytica Dnmt2 (Ehmeth) is a DNA Methyltransferase -- 11.5 Ehmeth is a tRNA MT -- 11.6 Regulation of Ehmeth Activity and the Role of the Environment -- 11.7 Ehmeth Protects E. histolytica from Oxidative and Nitrosative Stresses -- 11.8 Recognition of Methylated Cytosine by EhMLBP -- 11.9 Concluding Remarks -- References -- Part III: Cell Biology and Signaling -- Chapter 12: Phagocytosis in Entamoeba histolytica -- 12.1 Introduction -- 12.2 Mechanism of Phagocytosis in Other Organisms -- 12.2.1 Definition and Variation of Phagocytosis -- 12.2.2 The Molecular Mechanism of Phagocytosis and Cytoskeletal Rearrangements -- 12.3 Phagocytosis in Entamoeba histolytica -- 12.3.1 Surface Molecules Involved in Target Recognition -- 12.3.2 Initiation of Signaling Event and Cytoskeleton Reorganization -- 12.3.3 Role of Ca2+ in Phagocytosis -- 12.3.4 Actin Cytoskeleton Remodeling in E. histolytica -- 12.3.5 Phagosome Maturation -- 12.4 Conclusion -- References -- Chapter 13: Signaling Pathways in Entamoeba histolytica -- 13.1 Introduction -- 13.2 Ca2+ Signaling in Eukaryotes -- 13.2.1 Calcium Homeostasis -- 13.2.1.1 Regulation of the Intracellular Ca2+ Concentration. , 13.2.2 Intracellular Calcium-Binding Proteins.