Nematodes as Model Organisms

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Nematodes as Model Organisms
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Contents
1 The Genus Pristionchus: a Model for Phenotypic Plasticity, Predatory Behavior, Self-Recognition and Other Complex Traits
	Introduction
	Evo-devo Beginnings and Developmental Systems Drift
	Rapid Genome Evolution and Taxonomically Restricted Genes
	The Phylogeny of the Genus Pristionchus
	The Life History and Ecology of P. pacificus
	Developmental Plasticity and Predatory Feeding
		Mouth-form plasticity in P. pacificus
		Genetic basis and environmental influence
		eud-1 and the gene regulatory network
		Mouth-form plasticity and evolutionary novelty
		Convergent evolution of predation in nematodes and organismal consequences
	From Behavior to Neuroscience
		Predatory behaviors
		Environmental sensing and its associated behaviors
	Self-recognition and Cannibalism
	Complex Small Molecule Chemistry
	Conclusions and Outlook
	References
2 Aging
	Introduction
	Advantages of Worms for Aging Studies
	Aging and Lifespan
	Healthspan
	History of C. elegans for Aging Research
	The Insulin/IGF-1 Signaling Pathway
	Dauer Formation and Longevity
	Why IIS?
	Tissues Changing with Age
	Caloric Restriction (CR)
	Additional Inputs to the IIS
		C. elegans SIRT1/sir-2.1
		Adenosine 5’monophosphate-activated protein kinase (AMPK)
	Target of Rapamycin (TOR)
	Cellular Processes That Modulate Longevity
		Autophagy
		Protein translation
		Mitophagy
	Reproductive System
	Summary/Future Studies
	Acknowledgements
	References
3 Entomopathogenic Nematodes as a Model for Probing the Insect Immune System
	Introduction
	Entomopathogenic Nematode Life Cycle
		Mutualism regulators
	Insect Innate Immune Signaling and Function
		Insect humoral immunity
			Imd and Toll pathways
			Other immune pathways
			Insect cellular immunity
			Coagulation
	Nematode Immunomodulatory Strategies
		Nematode immunomodulation in insects
	Insect Immune Response toEntomopathogenic Nematodes
	Conclusions and Perspectives
	References
4 The Use of the Root-knot Nematodes, Meloidogyne spp., for Studying Biotrophic Parasitic Interactions
	Introduction: Root-knot Nematode, Meloidogyne spp., a Global Pest
	Giant Cells, the Unique Feeding Structures of the Root-knot Nematodes
	The Emergence of Plant Parasitism in Nematodes
	Suppression, Manipulation and Induction of Host Defenses
		Nematode NAMPS induce PTI in host plants
		RKN effectors involvement in suppressing plant immunity system
	Peptides Mimicking Plant Hormones – a Special Class of Effector
		CLE-like peptide
		C-terminally encoded peptides
		IDA-like peptides
	The Trend Toward Genome Reduction in Plant Parasites
	Horizontal Acquisition of Parasitism Genes
	The Repertoire of Plant Cell Wall-degrading Enzymes in Root-knot Nematode Genomes
	References
5 Nematodes as Models for Symbiosis
	Introduction to Symbiosis
	Diverse Nematode Models of Symbiosis
	Entomopathogenic Nematodes: a Versatile Platform for Symbiosis Research
		Discovery of entomopathogenic nematodes
		Advancement of EPNs as a model for host–microbe interaction
		EPNs as a model for host–microbe interaction
			Bacterial surface proteins mediating host interactions
			Nutrition and secondary metabolism
		EPN–symbiont pairs as models of symbiont specificity and host switching
		Role of non-obligate symbionts in EPN life cycles
		Advantages of EPNs as a model system for symbiosis research
		Nematode–microbiome models of insect and gastropod pathogenesis
	C. elegans as a Model for Symbiosis
		History of microbial community research in C. elegans
		C. elegans as a model for host–microbe interaction
			Characterization of native microbiome of Caenorhabditis
			Tools for microbiome research
		Responding to bacteria: C. elegans innate immunity
		Advantages of C. elegans as a model system for symbiosis research
	Nematode Models of Intracellular Endosymbiosis
		The intracellular endosymbionts of an insect-parasitic nematode
		Filarial parasitic nematodes
			Transmission mechanisms of Wolbachia in Brugia malayi
			Brugia malayi and wBm Wolbachia genomes
			Wolbachia endosymbionts as a therapeutic target
		Advantages of filarial nematodes as a model system for symbiosis research
	Plant-parasitic Nematodes (PPNs)
		Cardinium and Wolbachia endosymbionts of PPNs
		Xiphinematobacter endosymbionts
		Advantages of PPNs as a model system for symbiosis research
	Chemosynthetic Intracellular Endosymbionts and Ectosymbionts of Marine Nematodes
		Marine nematodes with intracellular endosymbionts
		Stilbonematine nematodes with ectosymbionts
		The molecular and cellular basis of ectosymbiosis
		Advantages and future directions of marine nematode–thiosymbiont interactions as a model system for symbiosis research
	Conclusions
	Acknowledgements
	References
6 Nematode Pharmacology: Neurotransmitters, Receptors, and Experimental Approaches
	Introduction
	Main Pharmacological Models: Advantages and Limitations
	Overview of Neurotransmitter
		Acetylcholine (ACh)
		5-Hydroxytryptamine (5-HT, serotonin)
		Dopamine (DA)
		Tyramine (TYR)
		Octopamine (OA)
		Glutamate
		GABA
		Nitric oxide (NO)
		Neuropeptides
	C. elegans and Drug Discovery
	Outlook
	References
7 Nematodes as Ecological and Environmental Indicators
	Introduction
	Toxicity Testing
		Single-species toxicity testing
			Chemical and material testing
			Standardization
			Testing of environmental samples
			Eco(toxico)logical modeling
			Toxicokinetic modeling
		Multi-species toxicity testing (model ecosystems)
		In situ bioindication
			The NemaSPEAR[%]-index for freshwater systems
			Trait-based indices for soil systems
	Nematodes in Ecological
		Model of metacommunity structure
		Models of biodiversity
	Conclusions
	References
8 Use in Soil Agro-Ecology
	Introduction: Soil as Live Resource
	Nematodes as Soil Organisms
	Evaluation of the Nematodes in the Soil for Ecological Studies
		Isolation of nematodes
		Method for identification and quantification: from visual to molecular approaches
		Functional diversity and the employment of indexes for ecological approaches
	Examples of Use of Nematodes as Model System in Soil Ecology Approaches
		Use of nematodes as model system in plant protection
		Use of nematodes as model system in community changes due to disturbance
	Conclusions and Future Directions
	Acknowledgements
	References
9 Stress and Survival Mechanisms
	Introduction
	Nematode Life Cycle in Relation to Survival
	The Nematode Species Used for Survival Studies
	How Nematodes Encounter Extreme Conditions
		Desiccation tolerance
		Osmotic stress
		Extreme temperatures
			Cold tolerance
			Heat tolerance
		Oxidative stress
	Conclusions and Future Directions
	References
10 Molecular Toxicology in Caenorhabditis elegans
	Introduction
	Oxidative Stress-related Molecular Signals
		Roles of mitochondrial complex signals
			Complex I (NADH ubiquinone oxidoreductase)
			Complex II (succinate ubiquinone oxidoreductase)
			Complex III
			Complex IV
			Coenzyme Q (ubiquinone, CoQ) synthesis
		Roles of superoxide dismutases (SODs)
		Roles of catalase (CTL-1-3) proteins
		Roles of glutathione-requiring prostaglandin D synthases (GSTs)
	MAPK Signaling Pathways
		p38 MAPK signaling pathway
			Duox1/BLI-3
			TIR-1 and VHP-1
			MEK-1
			Mitochondrial complex I
		JNK signaling pathway
		ERK signaling pathway
			SOD-3
			Antimicrobial proteins
			MTL-1 and MTL-2
			NATC-1
			HSF-1
			GPD-2
			SMK-1
			AAK-2
			HCF-1
			SIR-2.1/SIRT1
			PRDX-2
	Insulin and the Related Signaling Pathways
	Development-related Signaling Pathways
		Wnt signaling pathway
			POP-1
			DAF-16
			UNC-62
			EGL-5
			PRX-5
		TGF-β signaling pathway
			DBL-1-mediated TGF-β signaling pathway
			DAF-7-mediated TGF-β signaling pathway
		Notch signaling pathway
		Developmental timing control-related signals
			HBL-1 and LIN-41
			SDZ-24
	Cell Death and DNA Damage-related Signaling Pathways
		Apoptosis signaling pathway
		DNA damage signaling pathway
			mir-360
			ABL-1
			NOL-6
	Metabolism-related Signaling Pathways
		Functions of fat metabolic sensors
			SBP-1
			NHR-49
			MDT-15
			NHR-80
		AMPK signaling pathway
		ACC and FAS
		FAT-6 and FAT-7
		ELO proteins
		Fatty acid transport protein ACS-22
	Protective Response-related Signaling Pathways
		Antimicrobial proteins
		Mitochondrial unfolded protein response (mt UPR)
		Endoplasmic reticulum (ER) UPR
			HSP-4
			ABU (activated in blocked UPR) proteins
			p38 MAPK signaling cascade (PMK-1-SKN-1/ATF-7)
			MDT-15 and SBP-1
			CDC-48-RUVB-2 signaling cascade
			CED-1
		Autophagy
		Mitophagy
	G-Protein Coupled Receptors and Ion Channels and Downstream Cytoplasmic Signals
		GPCRs
			Epidermal DCAR-1
			Intestinal FSHR-1
			Neuropeptide receptors
			Neuronal SRH-220
		Ion channels
			Cyclic nucleotide-gated ion channels
			Voltage-gated calcium ion channel UNC-2
			Potassium ion channel KVS-1
			Chloride intracellular channel EXL-1
		ARR-1/arrestin
		G proteins
			Gqα signaling
			Goα signaling
		PLC-DAG-PKD signaling
			PLC-PKD-TFEB signaling cascade
			DKF-2
		Ca2+ signaling
			UNC-31
			CRT-1
	Epigenetic Regulation of Toxicity of Environmental Toxicants or Stresses
		Methylation regulation
			Methylation of histone H3K4
			Methylation of histone H3K9
			Methylation of HIS-24K14
			Methylated glycans
		Histone acetylation regulation
			MYST family histone acetyltransferase complex
			N-terminal acetyltransferase C (NAT) complex
			CBP-1
		MicroRNAs (miRNAs) regulation
		LncRNAs regulation
		Circular RNAs (circRNAs)
	Perspectives
	References
11 Nematode Use for Testing Theoretical Models of Behavioral Ecology
	Introduction: Models of Behavioral Ecology
	Resource Acquisition
		Foraging
		Recognition
		Exploitation
		Optimal strategies above and beyond resource acquisition: bet hedging and the preference–performance hypothesis
	Competition
	Communication and Dispersal
	Aging and Behavior
		Aging of free-living nematodes
		Impact of aging on mobility and locomotion
		Aging of parasitic nematodes
		Impact of aging on infectivity in parasitic nematodes
		Strategies to delay the effects of aging
	Learning
	Conclusions
	References
12 Entomopathogenic Nematodes as Models for Inundative Biological Control
	Introduction
		Basic biology and life cycle
		Foraging behavior
		Biocontrol production and application technology
		Justification of EPNs as a model system for inundative biocontrol
	Factors Affecting Efficacy
		Abiotic factors
		Biotic factors
	Approaches to Improve Efficacy
		Improving production technology
		Improving formulation and application technology
	Biocontrol in Practice: Successes and Failures
	Conclusion
	References
13 Parasitic Nematodes: Model Systems for Studying Parasitism and Pathogenesis
	Introduction: Origin of Parasitism in Nematoda
		Fossil records and phylogenetic hypotheses
		Evolutionary trajectories of nematode parasites and bacteria symbioses
			Animal and human parasites: filarial nematodes
			Insect parasites: entomopathogenic nematodes
			Plant parasites
	Parasitic Nematode Models
		Animal and human parasites: filarial nematodes
			Life cycle
			Microfilariae–vector host interactions
			Regulation of host’s immune response
			Experimental models
		Insect parasites: entomopathogenic nematodes
			Life cycle
			Role of the infective juvenile stage
			Experimental models
		Plant parasites
			Life cycle
			Experimental models
	Role of Symbionts in Disease Control
		Filarial symbionts
		Entomopathogenic nematode symbionts
		Plant parasite symbionts
	Emerging Tools for the Study of Parasitism and Pathogenesis of Nematode–Bacteria Partnerships
	References
14 Genetic Improvement of Beneficial Organisms
	Introduction
	Approaches to Genetic Improvement
		Discovery
		Selection
		Hybridization
		Mutagenesis and genetic engineering approaches
	Case Studies: Improvement of Nematode Efficacy
	Case Study: Improvement of Survival and Persistence
	Trait Stability
	Future Prospects of Genetic Improvement in EPNs
	References
Index
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