دانلود کتاب Gene Environment Interactions: Nature and Nurture in the Twenty-first Century

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Cover Gene Environment Interactions : Nature and Nurture in theTwenty-first Century Copyright Acknowledgments Epigraph 1 Interacting with the environment receiving and interpreting signals Sensory receptors General factors Touch sensation Nociceptors Sodium ion channels Therapeutic agents to treat pain specific that act on ion channels. Neuropathic pain Transient receptor potential (TRP) channels Potassium channels Hearing Gap junctions Fluid filled cavities of the inner ear Hair cells Sound waves and the inner ear The vestibular system Vestibular disorders Congenital hearing loss Potassium ion channel KCNQ1 Hearing impairment and deafness Epidemiology Genetic etiology of deafness Deafness due to environmental factors in the perinatal period Newborn screening for deafness Electrophysiological exploration of hearing Auditory brain response test (ABR) Benefits of newborn screening and early detection of hearing loss Treatment options for hearing impairment Public health and pediatric hearing impairment Hearing loss in adults Cochlear implants, vestibular implants Advances in the treatment of hearing defects Auditory neuropathy Spectrum disorder Usher syndrome Vision and the retina Regions of the retina Retinal pigment epithelium Melanin in the retinal pigment epithelium The visual cycle, retinal pigmentary epithelium and photoreceptor interactions Retinal dystrophies Retinitis pigmentosa Clinical manifestations Leber’s congenital amaurosis Mitochondrial functional defects leading to visual impairment Age related macular dystrophy (AMD) Newborn eye screening and retinopathy of prematurity Blindness in children Retinopathy of prematurity References 2 Environment as provider Introduction Nutrients Nutrient production food security and environmental sustainability Ecosystems and food security Pollinator services Agroecology Nutrition and ecology Food production trends Nutritional deficiencies Vitamin A Nutrition and growth Undergrowth Genetic factors and height Overall increase in population height Requirement for specific minerals Zinc and zinc deficiency Iron Uptake of iron into cells Iron homeostasis Hemochromatosis Gene discoveries and identification of key functional proteins in iron metabolism Dietary iron overload Iron deficiency Calcium and vitamin D Insights gained into bone formation through studies in osteogenesis imperfecta Hypophosphatasia and alkaline phosphatase Rickets/osteomalacia due to genetic defects Autosomal dominant hypophosphatemic rickets (ADHR) and X-linked hypophosphatemic rickets Iodine and thyroid function Congenital hypothyroidism Iodine deficiency goiter, hypothyroidism Requirement of other minerals present in soil Water Water pollution Pesticides Air and oxygen Central nervous system and air pollution References 3 Evolution Connections between paleoclimate and evolution Modern humans and their relationship to archaic humans Archaic genomes Genomic sequencing Introgression from of archaic sequences into genomes of modern humans Population migrations The ice-age and its impact on populations Minoans and Myceneans Africa Brain evolution: Primate and human divergence The DUF1220/NBPF domain also known as the Olduvai domain Documenting gene, metabolite differences and brain differences between primates and humans Foxp2 Trajectory of brain evolution Products expressed primarily in excitatory neurons Products expressed primarily in inhibitory neurons Genomes, gene expression, evolution, intellect NOTCH2 gene expansion and impact on cortical neurogenesis Brain development, genes and environment The advantages and disadvantages of extra-copies of genomic segments Structural variants and adaptation Segmental duplications Whole genome sequencing and segmental duplications Comprehensive population studies of segmental duplications Phenotypic plasticity and evolution Mitochondrial DNA variations and population divergence Nutritional factors and genomic adaptations Polygenic adaptations to changing environments Studies on expression quantitative trait loci (eQTLs) References 4 Gene and environment interactions and phenotypes Introduction Skin pigmentation Oculocutaneous albinism Syndromic albinism Melanocytes and melanin Melanin and melanosome transcription factors Hyper pigmentation disorders Congenital hypopigmentation disorders Population studies on skin pigmentation Complexities in determination of pigmentation Milk as nutrient and lactase persistence Recognizing non-self: The immune system Innate immunity NOD-like receptors and Inflammasome Adaptive immunity Components and functions of the adaptive immune system B cells and antibody production Cytidine deaminases and their roles in the immune system APOBEC proteins ADAR enzymes adenosine deaminase RNA specific Genome diversity and protection against malaria infection Thalassemias Malaria parasite erythrocyte interactions Glucose-6-phosphate dehydrogenase (G6PD) variants and malaria resistance Malaria infestation and immune response Trypanosome infection and adaptations Selective forces of pathogens on human populations Immune response, pathogens and adaptations in different environments Natural selection and infectious diseases Polygenic adaptations to pathogens Adaptation of organisms to different environments Polygenic adaptation Evolutionary adaptations of microorganisms and their hosts Human adaptations to high altitude References 5 Signals, epigenetics, regulation of gene expression Conveying signals into cells to modify gene expression Signaling pathways Ion channels and transmission of signals to alter gene expression MTORC1 and MRNA translation MTORC1 and MRNA translation Transcription factors NFkappaB transcription factor complex Pathologies associated with defective functions of these proteins Nuclear receptors The nuclear pore complex Transport of mRNA from the nucleus to the cytoplasm Epigenetics Epigenetic mechanisms Epigenetics and aging Accelerated aging in down syndrome role of methylation Epigenetics, nutritional resources and metabolism DNA methylation and environmental exposures Epigenetic status and behavior following early childhood deprivation Epigenetics and cell type specificity Epigenetic differences in monozygotic twins Environmental agents and epigenetic changes Metabolism derived substrates and cofactors involved in epigenetic modifications Epigenetic states and gene expression Transcription factor binding to DNA and impact of epigenetic processes Transcription regulation and the mediator complex Activity dependent transcription Calcium dependent gene transcription Studies on epigenetic modifications, gene expression and memory Regulation of gene expression Alternative splicing of mRNA Chromatin architecture folding and modeling Genetic variations in regulators of gene expression RNA modifications The epitranscriptome References 6 Maintaining homeostasis and mitigating effects of harmful factors in the intrinsic or extrinsic environment Concepts of homeostasis Metabolism and homeostasis The MTOR system as sensor and as molecular integrator of cellular environmental conditions Energy stress MTOR as a major link between nutrient availability, and anabolic and catabolic processes Importance of TSC complex in inhibiting MTORC1 activity during endoplasmic reticulum stress MTOR signaling and mitochondrial function Sensors of specific metabolites Metabolism and co-factors Nicotinamide adenine dinucleotide (NAD) Molecular machinery and cholesterol homeostasis Sterol element binding proteins (SREBPs) Free fatty acid receptors and sensing Mitochondria and metabolism, new insights Reactive oxygen species and superoxide dismutases Nutrient sensing that impacts mitochondrial function Mitochondria and endoplasmic reticulum metabolism and nutrient sensing Metabolic flexibility and metabolic inflexibility Adipose tissue Metalloregulators factors Harmful damaging factors, endogenous or exogenous Oxidative stress and mitochondria Oxidative damage to molecules Systems to repair or remove damaged components Oxidative DNA damage Environmental agents and oxidative stress Bisphenol A Damaging metabolites DNA damage detection, consequences, and repair Gene products involved in excision repair Mismatch repair Mismatch DNA repair genes in humans Signaling DNA damage Double stranded DNA damage Interstrand cross-linking of DNA and the Fanconi pathway Exogenous and endogenous agents leading to DNA damage Tobacco DNA damage response and the cell cycle Heavy metal exposure Removal of damaged cellular material Cellular stress and the unfolded protein response Telomere shortening Tissue homeostasis and cell death Molecular mechanisms to counteract and detoxify xenobiotics Pharmacologic agents as xenobiotics and pharmacogenetics Arylhydrocarbon receptor (AHR) References 7 Microorganisms and microbiome Microorganisms in soil Horizontal gene transfer between microorganisms Efforts to restore degraded soils Plant root exudates Climate change and microorganisms Agroecosystems Antibiotic resistance Mechanisms by which microorganisms develop antibiotic resistance Antibiotic resistance in Gram negative organisms Antibiotic tolerant persisters and microfilms Antibiotic use in animal food production Antibiotic stewardship programs Mycobacterium tuberculosis (M. Tb) and antibiotic resistance Point of care diagnostics M. Tb drug susceptibility testing Diagnostic tests for tuberculosis New techniques for identifying anti-microbial agents Diffusion chambers and I-chip techniques Nucleotide analyses and identification of anti-bacterial products The search for anti-microbial medicines in plants Phage therapy Implication of bacteriophage therapies for clinical laboratories Microbiome Comprehensive microbiome analyses The microbiome in early post-natal life Breast feeding Microbiome, intestinal function and health Short chain fatty acids Low density lipoproteins Amino acids Bile components secreted into the intestine Microbiota and the immune system development Gut microbiota, diet and health Microbiome related disorders and antibiotic usage The microbiome in malnutrition Kwashiorkor Interaction of the human genome and the gut microbiome Gut microbiome and colorectal cancer Gut/brain axis and the intestinal microbiome The lung microbiome Respiratory diseases Skin microbiome Allergic responses and gene environment interactions The skin disease psoriasis Microorganisms environmental influences. Host factors and auto-immune diseases Auto-immunity and molecular mimicry References 8 Genomic changes and environmental factors in causation of birth defects and neurodevelopmental disorders Birth defects Introduction Mosaicism Holoprosencephaly Ethanol as holoprosencephaly inducing teratogen Holoprosencephaly in cases where definitively classified pathogenic mutations SHH pathways genes were not identified Cleft lip and palate: Gene variants and environmental pathways Studies in multi-generational families each with multiple cases of cleft lip and palate Neurodevelopmental disorders: Genetic and environmental factors Introduction Genomic and genetic factors in neurodevelopment Concepts relevant to neurodevelopmental disorders Infant and child development, environment, genes and their interactions Developmental trajectories of neuronal circuits and networks Key factors in child development Autism Syndromic autism Autism epidemiology Possible causative environmental factors in autism Epigenetics and autism Non-syndrome autism and common risk variants Genome-wide analyses of de novo variants in autism Functional magnetic neuroimaging in autism Epilepsy Epilepsy due to rare genomic changes of major effect Common epilepsy (idiopathic generalized epilepsy) Genomic and genetic mosaicism in epilepsy References 9A Personalized precision medicine—Part A: Concepts and relevance in Mendelian disorders Concepts Precision medicine goals Important definitions related to precision medicine studies The UK Biobank: An example of connecting genomic and phenotypic data and health Studies that have utilized data from UK Biobank UK Biobank data and calcific aortic stenosis Factors to take into account in connecting genotype and phenotype: Variable penetrance Allelic exclusion Segmental genomic copy number variants and disease manifestations Modifier genes and networks Modes of effects of modifier genes Modifiers of complex traits Disorders that can result from environmental factors, single rare gene defects or common gene variants Nephrotic syndrome The continuum of rare and common diseases Personalized precision medicine in individuals with Mendelian disorders Definitive diagnoses of Mendelian disorders and inborn errors of metabolism Discovery of genes that harbored variants that cause rare diseases Problems in exome sequencing Databases with information on human genes, mutations and disease relevance The ClinGen endeavor Functional validation of genetic variants in cases with inborn errors of metabolism (IEM) Mosaicism RNA analyses to improve diagnosis Multidisciplinary precision medicine Enzyme assays in inborn errors of metabolism Next-generation sequencing for diagnosis of genetic diseases Additional factors to be taken into account following molecular diagnosis of Mendelian disease Modifier genes International collaborations on rare disease research Genetic disorders in which causation cannot be easily resolved by genomic studies Gene environment interactions in causation of congenital malformation Importance of genome studies in providing insight into underlying gene mechanisms Rare diseases and development of therapies Predicting phenotype from genotype Hemochromatosis, rare and common gene variants and gene-environment interactions Gene defects with low penetrance except under specific environmental conditions Porphyrias Acute intermittent porphyria (AIP) Coproporphyria References 9B Personalized medicine. Precision medicine: PART B multifactorial diseases, genes, environments, interactions Cardiac conditions Long QT syndrome Founder mutations and the study genetic and environmental modifiers Dilated cardiomyopathy Lamin mutations Testing of family members of patients with cardiomyopathy inducing variants Cardio-vascular diseases and precision medicine Rare genetic variants in familial hypercholesterolemia Studies of genetic variants associated with common disease and polygenic risk scores Age related macular degeneration: Gene variants and environmental interactions Environmental factors in macular degeneration Specific AMD risk variants Age related neurodegenerative disorders Alzheimer’s disease Different forms of Alzheimer’s disease Late onset Alzheimer’s disease (LOAD) and APOE4 Analyses of gene variants in Alzheimer’s disease Amyotrophic lateral sclerosis also known as Lou Gehrig disease, motor neuron disease Evidence for RNA dysregulation in amyotrophic lateral sclerosis Gene-time-environment models Parkinson’s disease ( PD) Exome sequencing in Parkinson’s disease Environmental factors and Parkinson’s disease Traumatic brain injury and consequences Psychiatric disorders Personalized medicine and Cancer prevention Germline mutations in cancer risk genes Cancer gene panels Classification of cancer risk genes Pathogenic BRCA mutations and incomplete penetrance Cancer risk genes and genetic testing Lynch syndrome Molecular pathogenesis of Lynch syndrome DNA mismatch repair and its role in cancer Mismatch DNA repair gene defects in tumors and immunotherapy Identifying cancer risk mutations Microbiome and colorectal cancer Multiple endocrine neoplasia syndromes Melanoma References 10 Integrating Genetic, Epigenetic And Environmental Information To Improve Health And Well-Being Integrating information on genetic variants and environmental factors in analyses of disease risk factors Expression quantitative trait loci Aspects of hypertension Systolic hypertension Carotid artery intima and media thickness and carotid plaque Monogenic factors in hypertension Monogenic forms of endocrine related hypertension: Adrenocortical hormones Cushing syndrome arising from excess adrenocortical function Blood pressure abnormalities due to mutations in ion channels Sympathetic and central nervous systems in hypertension Renal factors involved in blood pressure control Kidney disease and hypertension Epigenetics and hypertension High blood pressure predisposition, polygenic and environmental effects Stroke Polygenic factors life-style factors and stroke Single gene defects, small vessel disease and stroke Cadasil Cerebral amyloid angiopathy Coagulation and atherothrombosis Environmental factors and stroke Coronary heart disease (CAD) Heritability of coronary artery disease Treatment of broadly relevant causes and specific drivers of coronary heart disease Polygenic risk scores Core genes and peripheral genes in complex common diseases Modifiable risk factors in coronary heart disease Hypercholesterolemia Polygenic risk studies and complex common diseases Gene interactions Regulation of gene expression Regulatory element variations Transcription analyses Transcriptome wide association studies Genome wide studies in common metabolic diseases Interactions between allelic variants and the environment Rare genetic defects that increase the impact of specific environmental factors Infectious agents Parvovirus B19 Cystic fibrosis Adjusting the environment particularly nutrition to compensate for inborn errors of metabolism Metabolic studies Sequence analysis Transcriptome studies Protein complex profiling Inborn errors of metabolism due to defects in mitochondrial function Emergence of the phenotype in a specific metabolic disease Compensatory mechanisms that can reduce the impact of specific gene mutations Mitochondrial related disorders and compensatory mechanisms Treatment of inborn errors of metabolism Newborn screening and inborn errors of metabolism Analyzing utility of nutritional interventions Interactions Integrating gene expression and environmental nutrient conditions Gene product modifications Mitochondrial functions and adaptations Homeostasis cofactors and their relationship to vitamins Sunlight Genetic disorders where individuals have increased sensitivity to sunlight and UVB Porphyrias Genes, networks, society and patients Systems perspectives Genes networks, society and patients Health disease and society References 11 Environments, resources, and health Green-house gas production and climate change problems and potential solutions Ozone Countries with highest energy use and percentage of energy generated from renewable resources Renewable energy resources Rockefeller Foundation Lancet Commission on planetary health report 2015 (RFLC) Documenting the scope and depth of problems Effects of climate change on waterways and marine ecosystems Loss of protection in coastal regions Loss of Behring sea ice and Arctic temperatures Retreat of the Antarctic ice sheet Invasive insects Downgrading of biodiversity protection areas Climate change, questions relating to sustainability and human health Climate change and human well-being Questions of environmental state, sustainability human interactions and human health Spread of disease across borders Population aging Gerontology Extending life and growing numbers of older individuals Networks and determinants of aging Nutrient sensing pathways Mitochondria Oxidative stress and DNA damage Telomeres Epigenetics and aging Sirtuins, NAD and aging NAD sources and availability DNA methylation changes in aging Proteins and aging Translation of information The Millennium ecosystem assessment Ecosystem changes Climate change World population growth Refugees and migrants Achievements in world-health HIV incidence Malaria Tuberculosis Hepatitis Trachoma that leads to blindness Vaccines Emerging diseases and vaccines Vaccine availability GAVI the global alliance for vaccines and immunization Vaccine shortages Non-Communicable cases of death Obesity Malnutrition Family planning Ecosystem services The one health concept Additional approaches to health: The one health concept Ecosystem dynamics Ecotoxicology Child development and nurture Environmental agent exposures and child development Child development, physical environment and green space Social ecology and health Health and employment Sustainable development goals The WHO comprehensive Mental Health Action plan 2013–2020 64 Mental health and sustainable development Reframing mental health Limitations in diagnosing mental disorders Genomic studies of value in certain neurodevelopmental disorders in childhood Importance for human health of contact with nature The Biophilia hypothesis Partnerships and interconnections in dealing with challenges Efforts to counteract climate change and associated devastations Striving toward solutions Dietary changes to benefit health and mitigate climate change Proposed transformative changes in energy generation Physiological adaptations The heat shock response and heat-shock proteins Documenting problems and sometimes proposing solutions Loss of large carnivores and consequences Rewilding Perspectives on limitations Efforts to counteract climate change and associated devastations Drawdown Celebrations of nature in human endeavors References 12 Summary chapter epilogue Chapter 1 Interacting with the environment receiving and interpreting signals Chapter 2 Environment as provider Chapter 3 Evolution Chapter 4 Gene and environment interactions and phenotypes Chapter 5 Signals, epigenetics, regulation of gene expression Chapter 6 Maintaining homeostasis and mitigating effects of harmful factors in the intrinsic or extrinsic environment Chapter 7 Microorganisms and microbiome Chapter 9 Precision medicine and personalized medicine Personalized medicine in Mendelian disorders Personalized precision medicine in multifactorial diseases Chapter 10 Integrating genetic, epigenetic and environmental information to improve health and well-being Rare genetic defects and approaches to management Adjusting environments to compensate for inborn errors of metabolism Networks and gene interactions Chapter 11 Environments, resources, and health Greenhouse gas production climate change and potential solutions The one health concept Index Back Cover