Advances in Parasitology includes medical studies on parasites of major influence, such as Plasmodium falciparum and Trypanosomes. The series also contains reviews of more traditional areas, such as zoology, taxonomy, and life history, which shape current thinking and applications.
Eclectic volumes are supplemented by thematic volumes on various topics including Remote Sensing and Geographical Information Systems in Epidemiology and The Evolution of Parasitism - a phylogenetic persepective.
First published in 1963, Advances in Parasitology contains comprehensive and up-to-date reviews in all areas of interest in contemporary parasitology. Advances in Parasitology includes medical studies on parasites of major influence, such as Plasmodium falciparum and Trypanosomes. The series also contains reviews of more traditional areas, such as zoology, taxonomy, and life history, which shape current thinking and applications. Eclectic volumes are supplemented by thematic volumes on various topics including Remote Sensing and Geographical Information Systems in Epidemiology and The Evolution of Parasitism - a phylogenetic persepective.
Front Cover 1
Advances in Parasitology 4
Copyright Page 5
Contents 6
Contributors 8
Preface 12
Chapter 1: ABO Blood Group Phenotypes and Plasmodium falciparum Malaria: Unlocking a Pivotal Mechanism 14
1. Introduction 15
2. Methods 16
2.1. Inclusion Criteria 17
2.2. Data analysis 17
3. The Nature of ABO Histo-Blood Antigens 18
4. ABO Phenotypes and Malaria Risk 22
4.1. Population genetics 22
4.2. Infection risk 24
4.3. Severe malaria 32
4.4. Placental malaria 39
5. Biological Basis for ABO Phenotype-Related Susceptibility to Malaria 40
5.1. Affinity for Anopheles gambiae 40
5.2. Shared antigens 40
5.3. Inflammatory response 41
5.4. Invasion of RBCs 42
5.5. Rosetting 48
5.6. Cytoadherence 49
6. Conclusions and Research Implications 52
Acknowledgements 54
References 54
Chapter 2: Structure and Content of the Entamoeba histolytica Genome 64
1. Introduction 66
2. Genome Structure 68
2.1. The E. histolytica genome sequencing, assembly and annotation process 68
2.2. Karyotype and chromosome structure 69
2.3. Ribosomal RNA genes 71
2.4. tRNA genes 71
2.5. LINEs 72
2.6. SINEs 74
2.7. Other repeats 75
2.8. Gene number 76
2.9. Gene structure 77
2.10. Gene size 77
2.11. Protein domain content 79
2.12. Translation-related proteins 82
2.13. Analysis of cell cycle genes 83
2.14. Transcription 85
3. Virulence Factors 88
3.1. Gal/GalNAc lectin 88
3.2. Cysteine endopeptidases 90
3.3. Amoeba pores and related proteins 97
3.4. Antioxidants 101
4. Metabolism 105
4.1. Energy metabolism 105
4.2. Amino acid catabolism 112
4.3. Polyamine metabolism 117
4.4. Biosynthesis of amino acids 118
4.5. Lipid metabolism 120
4.6. Coenzyme A biosynthesis and pantothenate metabolism 125
4.7. Nucleic acid metabolism 126
4.8. Missing pieces 126
4.9. Transporters 126
5. The Cytoskeleton 127
5.1. Actin and microfilaments 127
5.2. Tubulins and microtubules 129
5.3. Molecular motors 130
6. Vesicular Traffic 132
6.1. Complexity of vesicle trafficking 132
6.2. Proteins involved in vesicle formation 133
6.3. Proteins involved in vesicle fusion 137
6.4. Comparisons and implications 141
6.5. Glycosylation and protein folding 142
7. Proteins Involved in Signalling 147
7.1. Phosphatases 147
7.2. Kinases 151
7.3. Calcium binding proteins 154
8. The Mitosome 155
9. Encystation 156
9.1. Chitin synthases 156
9.2. Chitin deacetylases 156
9.3. Chitinases 158
9.4. Jacob lectins 158
9.5. Gal/GalNAc lectins 158
9.6. Summary and comparisons 159
10. Evidence of Lateral Gene Transfer in the E. histolyticaGenome 160
10.1. How do the 96 LGT cases stand up? 160
10.2. Where do the genes come from? 170
10.3. What kinds of gene are being transferred? 171
11. Microarray Analysis 171
12. Future Prospects for the E. histolyticaGenome 176
Acknowledgements 177
References 177
Chapter 3: Epidemiological Modelling for Monitoring and Evaluation of Lymphatic Filariasis Control 204
1. Introduction 206
2. Why Monitor and Evaluate Filariasis Control Programmes 208
3. Mathematical Models and the Design of Monitoring and Evaluation Plans 209
3.1. Three roles of mathematical models in parasite monitoring programmes 210
4. Models and Quantifying Intervention Endpoint Targets 211
4.1. Parasite elimination endpoints: Vector biting thresholds and worm break points 211
4.2. Vector infection thresholds 215
4.3. Disease control targets 216
5. Monitoring Changes in Infection Levels Due to Interventions for Aiding Management Decision Making 221
5.1. Assessing intervention progress and specification of the frequency of monitoring 222
5.2. Role of spatial distribution of infection for monitoring and evaluation 224
6. Mathematical Models and the Selection of Monitoring Indicators 228
6.1. Models and the impact of diagnostic accuracy of indicators for monitoring filariasis control 228
6.2. Selecting appropriate monitoring indicators 231
6.3. Models and sampling for parasite monitoring 233
6.4. Applying a decision-theoretical approach to selecting cost-effective monitoring tools for assessing filariasis control 237
7. Using Monitoring Data for Programme Management 239
8. Uncertainty, Monitoring and Adaptive Management 240
9. Conclusions 242
Acknowledgements 245
References 245
Chapter 4: The Role of Helminth Infections in Carcinogenesis 252
1. Introduction 253
2. Trematoda 254
2.1. S. haematobium 254
2.2. S. mansoni 264
2.3. S. japonicum 268
2.4. O. viverrini 273
2.5. C. sinensis 280
2.6. F. hepatica 286
3. Cestoidea and Nematoda 290
4. Mechanisms of Carcinogenesis 290
5. Concluding Remarks 297
References 298
Chapter 5: A Review of the Biology of the Parasitic Copepod Lernaeocera branchialis (L., 1767) (Copepoda: Pennellidae) 310
1. Introduction 311
2. Taxonomy 312
3. Adult Morphology of the Female 313
4. Life Cycle 314
4.1. Nauplius I-II 314
4.2. Copepodid 316
4.3. Chalimus I-IV 317
4.4. Adult 320
5. Reproduction 327
5.1. Mating strategies 327
5.2. Copulation 328
5.3. Male competition 329
5.4. Fecundity 329
5.5. Female fitness 330
5.6. Egg strings and egg-string attachment 330
5.7. The male reproductive system and spermatozoon ultrastructure 331
6. Physiology 331
6.1. Feeding and maintenance of the internal environment 331
6.2. Respiration 333
7. Distribution 334
7.1. Geographic distribution 334
7.2. Prevalence and intensity of host infection 336
7.3. Seasonality 341
8. Pathogenicity 345
9. Concluding Remarks 348
References 349
Index 356
Contents of Volumes in This Series 366
Colour Plate Section 372
Structure and Content of the Entamoeba Histolytica Genome
C.G. Clark*; U.C.M. Alsmark†; M. Tazreiter‡; Y. Saito‐Nakano§; V. Ali¶; S. Marion||,1; C. Weber||; C. Mukherjee#; I. Bruchhaus**; E. Tannich**; M. Leippe††; T. Sicheritz‐Ponten‡‡; P.G. Foster§§; J. Samuelson¶¶; C.J. Noël†; R.P. Hirt†; T.M. Embley†; C.A. Gilchrist||||; B.J. Mann||||; U. Singh##; J.P. Ackers*; S. Bhattacharyaa; A. Bhattacharyab; A. Lohia#; N. Guillén||; M. Duchêne‡; T. Nozaki¶; N. Hallc,2 * Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
† Division of Biology, Newcastle University, Newcastle NE1 7RU, UK
‡ Department of Specific Prophylaxis and Tropical Medicine, Center for Physiology and Pathophysiology, Medical University of Vienna, A‐1090 Vienna, Austria
§ Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
¶ Department of Parasitology, Gunma University Graduate School of Medicine, Maebashi, Japan
|| Institut Pasteur, Unité Biologie Cellulaire du Parasitisme and INSERM U786, F‐75015 Paris, France
# Department of Biochemistry, Bose Institute, Kolkata 700054, India
** Bernhard Nocht Institute for Tropical Medicine, D‐20359 Hamburg, Germany
†† Zoologisches Institut der Universität Kiel, D‐24098 Kiel, Germany
‡‡ Center for Biological Sequence Analysis, BioCentrum‐DTU, Technical University of Denmark, DK‐2800 Lyngby, Denmark
§§ Department of Zoology, Natural History Museum, London, SW7 5BD, UK
¶¶ Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts 02118
|||| Department of Medicine, Division of Infectious Diseases, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908
## Departments of Internal Medicine, Microbiology, and Immunology, Stanford University School of Medicine, Stanford, California 94305
a School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
b School of Life Sciences and Information Technology, Jawaharlal Nehru University, New Delhi 110067, India
c The Institute for Genomic Research, Rockville, Maryland 20850
1 Present address: Cell Biology and Biophysics Program, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
2 Present address: School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
1 Introduction
Entamoeba histolytica is one of the most widespread and clinically important parasites, causing both serious intestinal (amoebic colitis) and extraintestinal (amoebic liver abscess) diseases throughout the world. A recent World Health Organization estimate (WHO, 1998) places E. histolytica second after Plasmodium falciparum as causing the most deaths annually (70,000) among protistan parasites.
Recently a draft of the complete genome of E. histolytica was published (Loftus et al., 2005) making it one of the first protist genomes to be sequenced. The E. histolytica genome project was initiated in 2000 with funding from the Wellcome Trust and the National Institute of Allergy and Infectious Diseases to the Wellcome Trust Sanger Institute and The Institute for Genomic Research (TIGR) in the UK and the USA, respectively. The publication describing the draft sequence concentrated on the expanded gene families, metabolism and the role of horizontal gene transfer in the evolution of E. histolytica. In this chapter we summarise the structure and content of the E. histolytica genome in comparison to other sequenced parasitic eukaryotes, provide a description of the current assembly and annotation, place the inferred gene content in the context of what is known about the biology of the organism and discuss plans for completing the E. histolytica genome project and extending genome sequencing to other species of Entamoeba.
The fact that the genome sequence is still a draft has several important consequences. The first is that a few genes may be missing from the sequence data we have at present, although the number is likely to be small. For example, at least one gene (amoebapore B) is not present in the genome data despite it having been cloned, sequenced and the protein extensively characterised well before the start of the genome project. The second consequence is that the assembly contains a number of large duplicated regions that may be assembly artefacts, meaning that the number of gene copies is overestimated in several cases. These problems cannot as yet be resolved but should be eventually as more data becomes available. Nevertheless, it is important to remember these issues when reading the rest of this chapter.
As the number of genes in E. histolytica runs into several thousands, it is not possible to discuss all of them. However, we have generated a number of tables that identify many genes and link them to their entries in GenBank using the relevant protein identifier. Only a few tables are included in the text of this chapter, but the others are available online as supplementary material, http://pathema.tigr.org/pathema/entamoeba_resources.shtml. The E. histolytica genome project data are being ‘curated’ at the J. Craig Venter Institute (JCVI, formerly TIGR), and it is on that site that the most current version of the assembled genome will be found. The ‘Pathema’ database will hold the data and the annotation (http://pathema.tigr.org/). The gene tables are also linked to the appropriate entry in the Pathema database, and the links will be maintained as the genome structure is refined over time.
Reference is made throughout the text to other species of Entamoeba where data are available. Entamoeba dispar is the sister species to E. histolytica and infects humans without causing symptoms. Entamoeba invadens is a reptilian parasite that causes invasive disease, primarily in snakes and lizards, and is widely used as a model for E. histolytica in the study of encystation, although the two species are not very closely related (Clark et al., 2006b). Genome projects for both these species are under way at TIGR, and it is anticipated that high‐quality draft sequences will be produced for both in the near future. It is hoped that the E. dispar sequence will prove useful in identifying genomic differences linked to disease causation while that of E. invadens will be used to study patterns of gene expression during encystation. Small‐scale genome surveys have been performed for two other species: Entamoeba moshkovskii, which is primarily a free‐living species although it occasionally infects humans, and Entamoeba terrapinae, a reptilian commensal species, http://www.sanger.ac.uk/Projects/Comp_Entamoeba/
2 Genome Structure
2.1 The E. histolytica genome sequencing, assembly and annotation process
The first choice to be made in the genome project was perhaps the easiest—the identity of the strain to be used for sequencing. A significant majority of the existing sequence data prior to the genome project was derived from one strain: HM‐1:IMSS. This culture was established in 1967 from a rectal biopsy of a Mexican man with amoebic dysentery and axenised shortly thereafter. It has been used widely for virulence, immunology, cell biology and biochemistry in addition to genetic studies. In an attempt to minimise the effects of long‐term culture cryopreserved cells that had been frozen in the early 1970s were revived and this uncloned culture used to generate the DNA for sequencing.
Before undertaking a genome scale analysis, it is important to understand the quality and provenance of the underlying data. The E. histolytica genome was sequenced by whole genome shotgun approach with each centre generating roughly half of the reads. Several different DNA libraries containing inserts of different sizes were produced using DNA that had been randomly sheared and sequences were obtained from both ends of each cloned fragment. The Phusion assembler (Mullikin and Ning, 2003) was used to assemble the 450,000 short...
Erscheint lt. Verlag | 5.12.2007 |
---|---|
Mitarbeit |
Herausgeber (Serie): S.I. Hay, Ralph Muller, David Rollinson |
Sprache | englisch |
Themenwelt | Sachbuch/Ratgeber ► Gesundheit / Leben / Psychologie |
Medizin / Pharmazie ► Allgemeines / Lexika | |
Medizin / Pharmazie ► Gesundheitsfachberufe | |
Medizin / Pharmazie ► Medizinische Fachgebiete ► Mikrobiologie / Infektologie / Reisemedizin | |
Studium ► Querschnittsbereiche ► Epidemiologie / Med. Biometrie | |
Studium ► Querschnittsbereiche ► Infektiologie / Immunologie | |
Studium ► Querschnittsbereiche ► Prävention / Gesundheitsförderung | |
Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie | |
Technik | |
ISBN-10 | 0-08-055682-5 / 0080556825 |
ISBN-13 | 978-0-08-055682-6 / 9780080556826 |
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