Sturkie's Avian Physiology (7th edition)

Sturkie’s Avian Physiology Copyright Dedication Contributors 1. The importance of avian physiology 1.1 Specific examples of the importance of avian physiology 1.1.1 Physiology and poultry production 1.1.2 Physiological ecology and birds, marine, freshwater, and terrestrial 1.2 Conclusions References 2. Avian genomics 2.1 Introduction 2.2 Genome 2.2.1 Size 2.2.2 Karyotype 2.3 Genome assemblies 2.3.1 Chicken legacy genomes 2.3.2 Future chicken genome assembly 2.3.3 Genes 2.3.4 Transposons and endogenous viral elements 2.3.5 Genome browsers 2.4 Connecting genome sequence to phenotype 2.4.1 Connecting genotype to phenotype 2.4.2 Genome wide association study 2.4.3 Resequencing 2.4.4 Annotation 2.4.5 CRISPR 2.5 Conclusions References 3. Transcriptomic analysis of physiological systems 3.1 Introduction 3.2 Early efforts 3.3 Nervous system 3.4 Endocrine system 3.5 Reproductive system 3.6 Immune system 3.7 Muscle, liver, adipose, and gastrointestinal tissues 3.8 Cardiovascular system 3.9 Hurdles and future developments References 4. Avian proteomics 4.1 Introduction 4.2 Protein identification and analysis 4.2.1 Historical to current techniques 4.3 Quantitative proteomics 4.4 Structural proteomics 4.5 Application of proteomics in avian research 4.5.1 Proteomics of egg physiology, embryonic development, and reproduction 4.5.2 Proteomics of behavior and plumage 4.5.3 Proteomics of performance and physiology 4.5.4 Proteomics of disease, myopathy, and infection 4.5.4.1 Disease proteomics 4.5.4.2 Proteomics of muscle myopathy 4.5.4.3 Proteomics of infections 4.5.5 Proteomics of avian welfare 4.6 Conclusions References Further reading 5. Avian metabolomics 5.1 Introduction to metabolomics 5.2 Methods of metabolomics 5.2.1 Instrumentation 5.2.1.1 Nuclear magnetic resonance spectroscopy 5.2.1.2 Mass spectrometry 5.2.1.2.1 Separation 5.2.1.2.2 Identification—targeted versus untargeted mass spectrometric analysis 5.2.1.2.3 Data processing 5.2.2 Data analysis and interpretation 5.3 Applications of metabolomics to avian physiology 5.3.1 Growth and efficiency 5.3.2 Consequences of selection 5.3.2.1 Accretion of excess body fat 5.3.2.2 Muscle myopathies 5.3.2.3 Ascites syndrome 5.3.2.4 Heat stress/stress 5.3.3 Mechanisms of antibiotic growth promoters 5.3.4 Toxicology 5.4 Conclusions References 6. Mitochondrial physiology—Sturkie's book chapter 6.1 Overview of mitochondria 6.1.1 Introduction 6.1.2 Physical description 6.1.3 Mitochondrial and nuclear DNA interaction for assembly and function 6.1.4 The respiratory chain and adenosine triphosphate synthesis 6.1.4.1 Ubiquinone (coenzyme Q) 6.1.4.2 Cardiolipin 6.1.5 Assessing mitochondrial function 6.1.5.1 Polarographic method 6.1.5.2 Flux analysis 6.1.6 Mitochondrial role in apoptosis 6.2 Mitochondrial inefficiencies, oxidative stress, and antioxidants 6.2.1 Electron transport defects and oxidative stress 6.2.1.1 Reactive oxygen species 6.2.1.2 Identification of site-specific defects in electron transport 6.2.1.3 Nitric oxide and reactive nitrogen species 6.2.1.4 DNA damage and respiratory chain complex activities 6.2.1.5 Specific protein targets of mitochondrial reactive oxygen species 6.2.1.6 Mitochondrial reactive oxygen species generation in avian species 6.2.2 Mitochondrial uncoupling and attenuation of oxidative stress 6.2.3 Antioxidants 6.3 Signal transduction and reverse electron transport 6.3.1 Low mitochondrial reactive oxygen species levels 6.3.2 Cellular nutrient utilization 6.3.3 Macrophage function 6.3.4 Ischemia-reperfusion injury 6.3.5 Muscle differentiation 6.3.6 Aging and longevity 6.4 Matching energy production to energy need 6.4.1 Mitochondrial dynamics 6.4.2 Mitochondrial biogenesis 6.4.3 Adenosine monophosphate–activated protein kinase 6.4.4 Sirtuins Acknowledgments References 7. Evolution of birds 7.1 Introduction 7.2 The dinosaur–bird transition 7.2.1 Theropod dinosaurs 7.2.2 Feathers first 7.2.3 Taking wing 7.2.4 Archaeopteryx, the first bird? 7.2.5 Flight in Archaeopteryx 7.3 The Mesozoic avifauna 7.3.1 Basal birds 7.3.2 Enantiornithes: the opposite birds 7.3.3 Cretaceous Ornithuromorpha: forerunners of modern birds 7.4 Assembling the modern bird 7.4.1 Freeing the tail for flight 7.4.2 Perfecting the wing 7.4.3 Neuroanatomy 7.4.4 Respiration and vocalization 7.4.5 Teeth and beaks 7.4.6 Digestive system 7.5 Reproduction and development 7.5.1 Sexual dimorphism 7.5.2 Eggs 7.5.3 Nesting 7.5.4 Development and growth 7.6 The rise of modern birds 7.6.1 The shallow Cretaceous roots of crown birds 7.6.2 Survival and extinction 7.6.3 An explosive Paleogene radiation 7.7 The shape of modern bird diversity 7.7.1 Palaeognathae 7.7.2 Galloanserae 7.7.3 Neoaves 7.8 The impact of humans on birds Acknowledgments References 8. Domestication of poultry 8.1 Introduction 8.2 Domestication 8.2.1 Chickens 8.2.2 Turkeys 8.2.3 Ducks 8.2.4 Geese 8.2.5 Other domesticated birds 8.3 Conclusions References 9. The avian somatosensory system: a comparative view 9.1 Introduction 9.2 Body somatosensory primary afferent projections in different species 9.2.1 Spinal cord 9.2.2 Brainstem 9.3 Ascending projections of the dorsal column nuclei 9.4 Telencephalic projections of thalamic nuclei receiving somatosensory input 9.5 Somatosensory primary afferent projections from the beak, tongue, and syrinx to the trigeminal column 9.5.1 The principal sensory trigeminal nucleus 9.5.2 Nucleus of the descending trigeminal tract 9.6 Nucleus basorostralis 9.7 The meeting of the spinal and trigeminal systems 9.8 The somatosensorimotor system in birds 9.9 Somatosensory projections to the cerebellum 9.10 Magnetoreception and the trigeminal system 9.11 Summary and conclusions References 10. Avian vision 10.1 Introduction 10.2 What vision does? 10.3 Variations in avian vision 10.4 Variations in eyes 10.5 Bird eyes: function, structure, and variations 10.5.1 The optical system 10.5.1.1 Variation in the optical systems of bird eyes 10.5.2 Vision under water 10.5.3 The image analysis system 10.5.3.1 Photoreceptors and visual pigments 10.5.3.2 Variation in the image analysis systems of bird eyes 10.5.3.3 Variation in the distribution of receptor types 10.5.3.4 Variation in the densities of receptor types 10.6 The visual fields of birds 10.7 Spatial resolution in birds 10.8 Contrast sensitivity 10.9 Closing remarks References 11. Avian hearing 11.1 Introduction: what do birds hear? 11.2 Outer and middle ear 11.2.1 No specialized outer ear structures except in owls 11.2.2 The single-ossicle middle ear 11.2.3 Internally coupled middle ears 11.3 Basilar papilla (cochlea) 11.3.1 General morphology and physiology 11.3.2 Hair cell types: a remarkable example of evolutionary convergence in birds and mammals 11.3.3 Hair cell regeneration: birds never lose their hearing 11.3.4 Cochlear specializations: auditory foveae, infrasound hearing 11.3.5 Auditory nerve: what the ear conveys to the brain 11.4 The auditory brain 11.4.1 Basic organization of auditory pathways 11.4.2 The generation of an auditory space map in the barn owl 11.4.3 Developmental plasticity: auditory space is calibrated by vision 11.4.4 The special processing of birdsong 11.4.5 Echolocating birds 11.5 Summary References 12. Chemesthesis and olfaction 12.1 Chemical senses 12.2 Chemesthesis 12.3 Neural organization 12.3.1 Peptides involved in pain perception 12.3.2 Responses to chemicals 12.3.3 Structure-activity relationships 12.3.4 Transient receptor potential channels 12.4 Olfaction 12.4.1 Olfactory morphology, neural architecture, and transduction of chemical signals 12.4.2 Olfactory bulb size, olfactory acuity, and genomics of olfactory receptors 12.4.3 Laboratory detection thresholds, discrimination, and seasonal change 12.4.4 Odor detection during development 12.4.5 How do birds use olfactory cues? 12.5 Summary References 13. Taste in birds 13.1 Introduction 13.1.1 What is taste? 13.1.2 Taste perception 13.1.2.1 Role of taste 13.1.2.2 The five taste modalities 13.1.3 Anatomy of taste buds 13.1.3.1 Taste buds 13.1.3.2 Morphology 13.1.3.3 Types of taste buds 13.1.3.4 Taste buds markers in chickens 13.1.3.5 Taste bud number and distribution 13.1.3.5.1 Distribution in different vertebrates 13.1.3.5.2 Distribution in birds 13.1.3.6 Afferent nerves from the taste buds 13.1.3.7 Changes in taste buds during growth and development 13.1.4 Taste receptors 13.1.4.1 Overview 13.1.4.2 Caveat on taste receptors 13.1.4.3 Taste receptor type 1 receptors (tas1r family) 13.1.5 Sweet taste 13.1.5.1 Overview 13.1.5.2 Sweet preferences in birds 13.1.5.3 The sweet dilemma 13.1.5.4 Evolutionary considerations of Tas1r2 13.1.6 Umami taste 13.1.6.1 Overview 13.1.6.2 Umami preference test in birds 13.1.7 Taste receptor type 2 receptors 13.1.8 GPCRs' taste signal transduction 13.1.8.1 Overview 13.1.8.2 Sequencing of taste receptor type 2 receptors (TAS2R) in birds 13.1.8.2.1 TAS2R1 and TAS2R2 13.1.8.2.2 Other TAS2R genes 13.1.8.2.3 Evolutionary aspects of taste receptor type 2 receptors 13.1.9 Bitter taste 13.1.9.1 Overview 13.1.9.2 Agonists of bitter receptors (TAS2R) 13.1.9.3 Ecological influence on bitter taste 13.1.10 Salt and sour taste 13.1.10.1 Salt taste receptor in birds 13.1.10.2 Salty preferences tests 13.1.10.3 Sour taste receptor in birds 13.1.10.4 Sour preferences tests 13.1.11 Fatty acid taste 13.1.12 Extra gustatory taste in birds 13.1.12.1 Overview 13.1.12.2 Gene expression of taste receptors and signaling molecules in extra-gustatory tissues in chicken 13.1.12.3 Effect of tastants on gene expression 13.1.13 Measuring taste perception in birds: aversion or preference testing 13.1.13.1 Methods for taste perception tests 13.1.13.2 Preference tests in birds 13.1.13.3 In vivo versus in vitro thresholds 13.1.14 Conclusions References 14. Avian nociception and pain 14.1 Introduction 14.1.1 What is pain and what is it for? 14.1.2 Why does pain matter? 14.2 What evidence is required to demonstrate the capacity for pain? 14.2.1 What is needed for nociception? 14.2.1.1 Transduction, transmission, and modulation of nociceptive information 14.2.1.2 Nocifensive responses 14.2.2 What is needed for pain? 14.2.2.1 Higher brain processing of nociceptive inputs 14.2.2.2 Complex behavioral responses 14.3 Conclusions References 15. Magnetoreception in birds and its use for long-distance migration 15.1 Introduction 15.2 Magnetic fields 15.3 The Earth's magnetic field 15.4 Changing magnetic fields for experimental purposes 15.5 Birds use information from the Earth's magnetic field for various behaviors 15.5.1 Orientation and navigation 15.6 The magnetic compass of birds 15.7 Do birds possess a magnetic map? 15.8 Interactions with other cues 15.9 How do birds sense the Earth's magnetic field? 15.10 The induction hypothesis 15.11 The magnetic-particle–based hypothesis 15.12 The light-dependent hypothesis 15.13 Irreproducible results and the urgent need for independent replication 15.14 Where do we go from here? References 16. The avian subpallium and autonomic nervous system 16.1 Introduction 16.2 Components of the subpallium 16.2.1 Dorsal somatomotor basal ganglia 16.2.1.1 Structures 16.2.1.2 Functions 16.2.2 Ventral viscerolimbic basal ganglia 16.2.2.1 Structures 16.2.2.2 Functions 16.2.3 Extended amygdaloid complex: central extended amygdala and medial extended amygdala 16.2.3.1 Central extended amygdala 16.2.3.1.1 Structures 16.2.3.1.2 Functions 16.2.3.2 Medial extended amygdala 16.2.3.2.1 Structures 16.2.3.2.2 Functions 16.2.4 Basal telencephalic cholinergic and noncholinergic corticopetal system 16.2.4.1 Structures 16.2.4.2 Functions 16.2.5 Septum and septal neuroendocrine systems 16.2.5.1 Divisions and structures 16.2.5.1.1 Lateral septal division 16.2.5.1.2 Medial septal division 16.2.5.1.3 Septohippocampal septal division 16.2.5.1.4 Caudocentral septal division 16.2.5.2 Functions 16.2.5.2.1 Septal-hypothalamic-pituitary-gonadal neuroendocrine system 16.2.5.2.2 Septal-hypothalamic-pituitary-adrenal neuroendocrine system 16.2.5.2.3 Other functions related to structures within the septum 16.2.6 Preoptic area 16.2.6.1 Structures 16.2.6.2 Functions 16.3 Components of the autonomic nervous system 16.3.1 Sympathetic nervous system 16.3.2 Parasympathetic nervous system 16.4 Integration of the subpallium and ANS in complex neural circuits in birds: two examples involving vasoactive intestinal pol ... 16.4.1 The social behavior network 16.4.2 Poikilostasis or shifts in homeostasis: an hypothesis involving the visceral forebrain system 16.4.2.1 Regulation of annual cycles of avian species 16.4.2.2 Some current metabolic and behavioral issues with breeding stock of broilers and turkeys 16.5 Summary and conclusions Acknowledgments References Further reading 17. Blood 17.1 Introduction 17.2 Plasma 17.2.1 Circulating electrolytes 17.2.2 Circulating nutrients and other small organic molecules 17.2.2.1 Plasma concentrations of glucose 17.2.2.2 Plasma concentrations of fatty acids 17.2.2.3 Plasma concentrations of lactate 17.2.2.4 Uric acid and urea 17.2.2.5 Circulating antioxidants 17.2.2.6 Carotenoids 17.2.3 Plasma proteins 17.2.3.1 Extracellular fluid 17.2.3.2 Albumin 17.2.3.3 Globulins 17.2.3.4 Specific proteins including vitamin and cation binding proteins 17.2.3.4.1 Ceruloplasmin 17.2.3.4.2 Retinol-binding protein 17.2.3.4.3 Transferrin 17.2.3.4.4 Proteins protecting against tissue damage from hemoglobin 17.2.3.4.5 Hormone binding proteins 17.2.3.4.6 Sex hormone–binding protein 17.2.3.4.7 Thyroid hormones/transthyretin 17.2.3.4.8 Transcortin (corticosteroid bonding globulin) 17.2.3.5 Gamma globulins 17.2.3.6 Enzymes 17.2.3.7 Yolk precursors 17.3 Erythrocytes 17.3.1 Structure of the erythrocyte 17.3.1.1 Nucleus 17.3.1.2 Plasma and nuclear membranes 17.3.1.2.1 Lipid composition 17.3.1.2.2 Carbohydrates in the erythrocyte plasma membrane 17.3.1.2.3 Proteins in the erythrocyte plasma membrane 17.3.1.3 Microtubules 17.3.1.4 Mitochondria 17.3.2 Erythrocyte chromatin and transcription 17.3.2.1 Transcription and translation 17.3.2.2 Stress and erythrocyte DNA 17.3.2.3 Telomeres 17.3.3 Metabolism of erythrocytes 17.3.3.1 Mitochondrial functioning in avian erythrocytes 17.3.3.2 Enzymes in erythrocytes 17.3.4 Number of avian erythrocytes and packed cell volume 17.3.5 Production 17.3.6 Erythropoietin 17.3.7 Lifespan 17.3.8 Hemoglobin 17.3.8.1 Hemoglobin genes 17.3.8.2 Adaptations of hemoglobin to flight at high altitudes 17.3.8.3 Glycation of hemoglobin 17.3.8.4 Hemoglobin and nutrition 17.3.9 Carbonic anhydrase 17.3.9.1 Intracellular pH 17.3.10 Transporters in erythrocyte plasma membrane 17.3.10.1 Anion transporter 17.3.10.2 Sodium and potassium transport 17.3.11 Glucose 17.3.11.1 Amino acids and urea 17.3.12 Hormonal effect on erythrocytes 17.3.13 Effect of stressors of erythrocytes 17.3.14 Avian erythrocytes and the innate immune system 17.4 Blood gases 17.5 Leukocytes 17.5.1 Number of leukocytes 17.5.2 Heterophils 17.5.2.1 Structure 17.5.2.2 Function 17.5.2.2.1 Heterophils and phagocytosis 17.5.2.2.2 Heterophils and cytokines 17.5.2.2.3 Heterophils and antimicrobial peptides 17.5.2.2.4 Toll-like receptors and heterophils 17.5.2.2.5 Stressors and heterophil functioning 17.5.2.3 Number 17.5.2.4 Production 17.5.3 Lymphocytes 17.5.3.1 Structure 17.5.3.2 Function 17.5.3.3 Numbers 17.5.4 Eosinophils 17.5.4.1 Structure 17.5.4.2 Function 17.5.4.3 Number 17.5.5 Monocytes 17.5.5.1 Structure 17.5.5.2 Function 17.5.5.3 Number 17.5.5.4 Production 17.5.6 Basophils 17.5.6.1 Structure 17.5.6.2 Function 17.5.6.3 Number 17.5.7 Heterophil: lymphocyte ratios 17.6 Thrombocytes 17.6.1 Structure 17.6.2 Function 17.6.3 Number 17.6.4 Production 17.6.5 Thrombopoietin 17.7 Other cells types in avian plasma 17.7.1 Reticulocytes 17.7.2 Mott cells 17.7.3 Natural killer cells 17.8 Parasites and blood cells 17.9 Clotting References Further reading 18. The cardiovascular system 18.1 Introduction 18.2 Heart 18.2.1 Gross structure and function 18.2.1.1 Functional anatomy 18.2.1.2 Heart size 18.2.1.3 Cardiac chambers 18.2.1.4 Valves 18.2.1.5 Coronary circulation 18.2.2 Cardiac variables 18.2.3 Fine structure and cardiac electrophysiology 18.2.3.1 Fine structure 18.2.3.2 Excitation–contraction coupling 18.2.3.3 Conduction system 18.2.3.4 Electrophysiology 18.3 General circulatory hemodynamics 18.4 The vascular tree 18.4.1 Arterial system 18.4.1.1 Gross anatomy 18.4.1.2 Functional morphology of the arterial wall 18.4.1.3 Relationship between arterial pressure and flow 18.4.2 Capillary beds 18.4.2.1 Gas exchange 18.4.2.2 Microvascular fluid exchange 18.4.2.3 Distribution of blood flow at rest 18.4.3 Venous system 18.4.3.1 Functional development of venous system 18.4.3.2 Capacitance function 18.4.3.3 Physiological role of veins in exercise and submersion 18.4.3.4 Renal portal system 18.4.4 Embryonic shunts 18.5 Control of the cardiovascular system 18.5.1 Control systems 18.5.2 Control of peripheral blood flow 18.5.2.1 Mechanism of vascular reactivity 18.5.2.2 Autoregulation 18.5.2.3 Humoral factors 18.5.2.3.1 Chemical factors 18.5.2.3.2 Locally released vasoactive agents 18.5.2.3.3 Circulating agents 18.5.2.4 Neural control 18.5.2.4.1 Systemic arterial innervation 18.5.2.4.2 Systemic venous innervation 18.5.2.4.3 Pulmonary vessel innervation 18.5.2.4.4 Autonomic pathways 18.5.3 Control of the heart 18.5.3.1 Catecholamine effects on the heart 18.5.3.2 Neural control 18.5.3.2.1 Sympathetic innervation 18.5.3.2.1.1 Anatomy 18.5.3.2.1.2 Sympathetic control 18.5.3.2.2 Parasympathetic innervation 18.5.3.2.2.1 Anatomy 18.5.3.2.2.2 Parasympathetic control 18.5.3.2.2.2.1 Dromotropic effects 18.5.3.2.2.2.2 Chronotropic effects 18.5.3.2.2.2.3 Inotropic effects 18.5.3.2.2.2.4 Tonic parasympathetic activity 18.5.3.2.3 Control of CO 18.5.3.2.3.1 Role of heart rate in control of CO 18.5.3.2.3.2 Role of stroke volume in control of CO 18.5.4 Reflexes controlling the circulation 18.5.4.1 Chemoreflexes 18.5.4.2 Baroreflexes 18.5.4.3 Reflexes from cardiac receptors 18.5.4.4 Reflex cardiovascular effects from skeletal muscle afferents 18.5.5 Integrative neural control 18.5.6 Development of cardiovascular control 18.5.6.1 Ontogeny of autonomic nervous system control of the heart 18.5.6.1.1 Cardiac autonomic innervation 18.5.6.1.2 Cardiac cholinergic and adrenergic receptors 18.5.6.2 Ontogeny of vascular contractility 18.5.6.2.1 Vascular reactivity regulation 18.5.6.2.2 Vascular adrenergic receptors 18.5.6.2.3 Vascular cholinergic receptors and endothelial control 18.5.6.3 Developmental integration of autonomic cardiovascular regulation 18.5.6.3.1 Afferent pathways 18.5.6.3.2 Tonic heart regulation 18.5.6.3.3 Tonic vasculature regulation 18.5.6.3.4 Baroreflex regulation 18.5.6.3.5 Cardiovascular response to hypoxia 18.5.6.4 Development of humoral and local effectors of cardiovascular function 18.6 Environmental cardiovascular physiology 18.6.1 Flight 18.6.1.1 Altitude 18.6.1.2 Migration 18.6.2 Swimming and diving References 19. Renal and extrarenal regulation of body fluid composition 19.1 Introduction 19.2 Intake of water and solutes 19.2.1 Drinking 19.2.2 Solute intake 19.3 The kidneys 19.3.1 Anatomy 19.3.1.1 Gross anatomy 19.3.1.2 Nephron types and numbers 19.3.1.3 Blood flow 19.3.1.3.1 Arterial supply 19.3.1.3.2 Renal portal system 19.3.1.3.3 Venous drainage 19.3.2 Physiology 19.3.2.1 Overview 19.3.2.2 Renal blood flow 19.3.2.3 Glomerular filtration 19.3.2.4 Regulation of water excretion 19.3.2.4.1 Arginine vasotocin 19.3.2.4.2 Regulation of glomerular filtration rate 19.3.2.4.3 Tubular water reabsorption and the urinary concentrating mechanism 19.3.2.4.3.1 Descending thin limb 19.3.2.4.3.2 Thick ascending limb 19.3.2.4.3.3 Collecting duct 19.3.2.4.3.4 Urinary concentrating mechanism 19.3.2.4.3.5 Net effect: avian urinary concentrating ability 19.3.2.5 Regulation of sodium excretion 19.3.2.5.1 Patterns of response 19.3.2.5.2 Mechanisms of regulation 19.3.2.5.2.1 Arginine vasotocin 19.3.2.5.2.2 Renin/angiotensin 19.3.2.5.2.3 Aldosterone 19.3.2.5.2.4 Atrial natriuretic peptide 19.3.2.6 Regulation of calcium and phosphate excretion 19.3.2.6.1 Calcium 19.3.2.6.2 Phosphate 19.3.2.7 Nitrogen excretion 19.3.2.8 Renal contribution to acid/base regulation 19.3.2.9 Molecular regulation: the next frontier 19.3.2.10 The final urine-composition and flow 19.3.2.11 Function of the ureters 19.4 Extrarenal organs of osmoregulation: introduction 19.5 The lower intestine 19.5.1 Introduction 19.5.2 Transport properties of coprodeum, colon, and cecum 19.5.2.1 Basic transport mechanisms in coprodeum and colon 19.5.2.1.1 Transport of NaCl and water 19.5.2.1.2 Transport of other ions 19.5.2.1.3 Quantitative role of coprodeum versus colon 19.5.2.2 Dietary and hormonal regulation of coprodeal and colonic transport 19.5.2.3 Ultrastructural adaptation and molecular induction 19.5.2.4 Salt and water transport in the caeca 19.5.3 Postrenal modification of ureteral urine 19.5.3.1 Basic patterns: Hydration/NaCl loading 19.5.3.2 Basic patterns: Dehydration/NaCl depletion 19.5.3.3 Special case: birds with salt glands 19.5.3.4 Special case: the ratites 19.5.3.5 Quantitative role of the caeca in osmoregulation 19.5.3.6 Overall: integration of kidneys and lower intestine 19.6 Salt glands 19.6.1 Anatomy 19.6.2 Function 19.6.2.1 Stimulus for secretion 19.6.2.2 Secretion mechanism and fluid composition 19.6.2.3 Regulatory mediators 19.6.3 Contribution of the salt glands to osmoregulation 19.7 Evaporative water loss Acknowledgments References 20. Respiration 20.1 Overview 20.1.1 Oxygen cascade 20.1.2 Symbols and units 20.2 Anatomy of the avian respiratory system 20.2.1 Upper airways 20.2.2 Lungs 20.2.2.1 Conducting airways 20.2.2.2 Parabronchi 20.2.2.3 Frontiers: evolution of the blood-gas barrier 20.2.3 Air sacs 20.2.4 Respiratory system volumes 20.3 Ventilation and respiratory mechanics 20.3.1 Respiratory muscles 20.3.2 Mechanical properties 20.3.2.1 Compliance 20.3.2.2 Resistance 20.3.2.3 Air capillary surface forces 20.3.3 Ventilatory flow patterns 20.3.3.1 Air sac ventilation 20.3.3.2 Pulmonary ventilation 20.3.3.3 Air sac PO2 and PCO2 20.3.3.4 Effective parabronchial ventilation 20.3.3.5 Artificial ventilation 20.3.3.6 Frontiers: lung structure-function in dinosaurs 20.4 Pulmonary circulation 20.4.1 Anatomy of the pulmonary circulation 20.4.2 Pulmonary capillary volume 20.4.3 Pulmonary vascular pressures, resistance, and flow 20.4.3.1 Pulmonary vascular resistance and pressures 20.4.3.2 Distribution of blood flow 20.4.3.3 Frontiers: pulmonary vascular pressures during exercise in birds 20.4.4 Fluid balance 20.5 Gas transport by blood 20.5.1 Oxygen 20.5.1.1 Hemoglobin 20.5.1.2 O2-blood equilibrium curves 20.5.1.3 Physiological control of O2-hemoglobin affinity 20.5.1.4 Frontiers: hemoglobin adaptations to high altitude 20.5.1.5 Factors affecting O2 capacity 20.5.2 Carbon dioxide 20.5.2.1 Forms of CO2 in blood 20.5.2.2 Factors affecting blood-CO2 equilibrium curves 20.5.3 Acid-base 20.5.3.1 Henderson-Hasselbalch equation 20.5.4 Blood gas measurements 20.6 Pulmonary gas exchange 20.6.1 Basic principles of oxygen transport 20.6.1.1 Convection 20.6.1.2 Diffusion 20.6.2 Cross-current gas exchange 20.6.2.1 Cross-current O2 exchange 20.6.2.2 Cross-current CO2 exchange 20.6.3 Lung diffusing capacity 20.6.3.1 Gas transport in air capillaries 20.6.3.2 Blood-gas barrier diffusion 20.6.3.3 O2-hemoglobin reaction rates 20.6.3.4 Physiological estimates of DLO2 20.6.4 Heterogeneity in the lung 20.6.4.1 Physiological dead space 20.6.4.2 Shunt 20.6.4.3 V./Q. mismatching 20.6.4.4 Temporal heterogeneity 20.6.5 Frontiers: pulmonary gas exchange during high altitude flight 20.7 Tissue gas exchange 20.7.1 Microcirculation 20.7.1.1 Skeletal muscle 20.7.1.2 Cerebral circulation 20.7.2 Myoglobin 20.7.3 Effects of hypoxia and exercise 20.8 Control of breathing 20.8.1 Respiratory rhythm generation 20.8.2 Sensory inputs 20.8.2.1 Central chemoreceptors 20.8.2.2 Arterial chemoreceptors 20.8.2.2.1 Intrapulmonary chemoreceptors 20.8.2.3 Other receptors affecting breathing 20.8.3 Ventilatory reflexes 20.8.3.1 CO2 response 20.8.3.2 Hypoxic ventilatory response 20.8.3.3 Ventilatory response to exercise 20.8.3.4 Frontiers: extreme hyperventilation at high altitude 20.9 Defense systems in avian lungs References 21. Gastrointestinal anatomy and physiology 21.1 Anatomy of the digestive tract 21.1.1 Beak, mouth, and pharynx 21.1.2 Esophagus and crop 21.1.3 Stomach 21.1.4 Small intestine 21.1.5 Ceca 21.1.6 Colon (rectum) and cloaca 21.2 Anatomy of the accessory organs 21.2.1 Pancreas 21.2.2 Liver 21.3 Motility 21.3.1 Esophagus 21.3.2 Gastrointestinal cycle 21.3.3 Small intestine 21.3.4 Ceca 21.3.5 Colon 21.3.6 Other influences on motility 21.4 Neural and hormonal control of motility 21.4.1 Rate of passage 21.5 Secretion and digestion 21.5.1 Mouth 21.5.2 Esophagus and crop 21.5.3 Stomach 21.5.4 Intestines 21.5.5 Colon 21.5.6 Pancreas 21.5.7 Bile 21.6 Absorption 21.6.1 Carbohydrates 21.6.2 Amino acid and peptides 21.6.3 Fatty acids and bile acids 21.6.4 Volatile fatty acids 21.6.5 Calcium and phosphorus 21.6.6 Potassium and magnesium 21.6.7 Water, sodium, and chloride 21.6.8 Vitamins 21.7 Age-related effects on gastrointestinal function 21.8 Gastrointestinal microbiota 21.9 Intestinal barrier References 22. Avian bone physiology and poultry bone disorders 22.1 Introduction 22.2 Embryonic skeletal differentiation 22.3 Cartilage 22.3.1 Cartilage of endochondral bone 22.3.2 Articular cartilage 22.4 Bone 22.4.1 Cellular components 22.4.2 Bone tissue 22.5 Poultry bone disorders 22.5.1 Cage layer fatigue/osteoporosis 22.5.2 Keel bone deformity and fracture 22.5.3 Cervical scoliosis 22.5.4 Chondrodystrophy, slipped tendon/perosis, and rickets 22.5.5 Valgus-varus deformity 22.5.6 Tibial dyschondroplasia 22.5.7 Femoral head separation 22.5.8 Femoral head necrosis, osteomyelitis, bacterial chondronecrosis 22.5.9 Amyloid arthropathy 22.6 Conclusion References 23. Skeletal muscle 23.1 Introduction 23.2 Diversity of avian skeletal muscle 23.3 Muscle structure and contraction 23.4 Skeletal muscle fiber types 23.5 Embryonic development of skeletal muscle 23.6 Postnatal or posthatch skeletal muscle development 23.7 Muscle development: function of myogenic regulatory factors 23.8 Growth factors affecting skeletal muscle myogenesis 23.9 Satellite cells and myoblast heterogeneity 23.10 Novel genes involved in avian myogenesis 23.11 Recent emerging breast muscle necrotic and fibrotic myopathies 23.12 The effect of fibrillar collagen on the phnotype of necrotic breast muscle myopathies resulting in fibrosis 23.13 Relationship of fibrillar collagen organization to the phnotype of breast muscle necrotic/fibrotic myopathies 23.14 Regulation of muscle growth properties by cell-membrane associated extracellular matrix macromolecules 23.15 Strategies to reduce myopathies 23.16 Summary Acknowledgments References Further reading 24. Immunophysiology of the avian immune system 24.1 Introduction 24.2 Innate immune system recognition, sensing, and function 24.2.1 Innate cell receptors: pattern recognition receptors 24.2.1.1 Toll-like receptors 24.2.1.2 Nod-like receptors 24.2.1.3 RIG-like receptors 24.2.1.4 C-type lectin receptors 24.2.2 Host defense peptides 24.2.3 Innate immune memory: trained immunity 24.3 Acquired immune recognition and function 24.3.1 The major histocompatibility complex 24.3.2 Th1/Th2 paradigm and T helper cell subsets 24.4 Gastrointestinal tract and immune system of poultry 24.4.1 Mucosal lymphoid tissues and cells 24.4.2 Intestinal barrier system 24.4.3 Intestinal microbiota 24.4.4 Intestinal immune functionality 24.4.4.1 Gut microbiota-immunity communication 24.4.4.1.1 Components of the microbiota 24.4.4.1.2 Microbial metabolites 24.4.4.1.3 Microbial epigenetic modifications 24.4.5 Gut microbiota: immune homeostasis 24.4.5.1 Gut microbiota: immune dysfunction—dysbiosis 24.4.5.2 Gut microbiota: immune dysfunction—inflammation 24.4.5.2.1 Inflammatory phenotypes 24.4.5.3 Induction of inflammatory phenotypes 24.4.5.3.1 Physiological inflammation 24.4.5.3.2 Pathological inflammation 24.4.5.3.3 Sterile inflammation 24.4.5.3.4 Metabolic inflammation 24.5 Tissue immunometabolism: tissue homeostasis and tissue resident immune cells References 25. Carbohydrate metabolism 25.1 Overview of carbohydrate metabolism in birds 25.1.1 Introduction 25.2 Carbohydrate chains in glycoproteins 25.2.1 Glucose 25.2.1.1 Circulating concentrations of glucose across avian species 25.2.1.1.1 Introduction: circulating concentrations of glucose across avian species 25.2.1.1.2 Domestication and circulating concentrations of glucose 25.2.1.1.3 Fasting and circulating concentrations of glucose 25.2.1.1.4 Influence of feeding 25.2.1.1.5 Shifts in circulating concentration with age, reproductive state, and migration 25.2.1.1.6 Shifts in circulating concentrations of glucose due to disease, toxicants, and husbandry practices 25.2.1.1.7 Temperature and circulating concentrations of glucose 25.2.1.1.8 Issues with the circulating concentrations of glucose 25.2.1.2 Glucose concentrations in the cerebrospinal fluid 25.2.1.3 Glucose concentrations in muscle 25.3 Lactate and pyruvate 25.3.1 Introduction 25.3.2 Circulating concentrations of lactate and pyruvate 25.3.3 Muscle concentrations of lactate 25.4 Glycerol 25.4.1 Introduction 25.4.2 Circulating concentrations of glycerol 25.5 Glycogen 25.5.1 Introduction 25.5.2 Synthesis and breakdown 25.5.2.1 Glycogenesis (synthesis) 25.5.2.1.1 Phosphoglucomutase 25.5.2.1.2 Uridine triphosphate-glucose pyrophosphorylase 25.5.2.1.3 Glycogen synthase 25.5.3 Glycogenolysis (breakdown) 25.5.3.1 Glycogen phosphorylase 25.5.3.2 Glycogenesis (breakdown) 25.5.4 What is the concentration of glycogen in avian hepatocytes? 25.5.5 Hepatic concentrations of glycogen 25.5.5.1 Overview 25.5.5.2 Effects of nutrition 25.5.5.3 Developmental changes 25.5.5.4 Effects of perihatch nutrition 25.5.5.5 Developmental changes in glycogenesis 25.5.5.6 Other effects on hepatic glyc