Helmut Heinsen, Lea Tenenholz Grinberg, Simone Bohnert
{"title":"Structural and functional anatomy of the brainstem.","authors":"Helmut Heinsen, Lea Tenenholz Grinberg, Simone Bohnert","doi":"10.1016/B978-0-443-15736-3.00015-9","DOIUrl":"10.1016/B978-0-443-15736-3.00015-9","url":null,"abstract":"<p><p>The brainstem connects the forebrain to the spinal cord. It consists of three layers, the ventral basis, the intermediate tegmentum, and the dorsal tectum. Caudo-rostrally, the brainstem is divided into the medulla oblongata or myelencephalon, the metencephalon, and the mesencephalon. The tegmentum is the most conserved part of the brainstem and contains the motor and sensory nuclei of cranial nerves (CN) III-XII. They are arranged in a mediolateral direction, and, unlike the spinal cord, their afferent and efferent fibers are not macroscopically separated. The tegmental reticular formation, the brainstem core, has a lattice structure with manifold longitudinal and transverse fibers and stacked neurons. Its architecture provides maximum convergence and divergence of intrinsic and ascending/descending information from the spinal cord and forebrain. It coordinates brainstem-based vital functions, and its integrity is essential for arousal, consciousness, and goal-directed behavior. Its small aminergic and cholinergic telencephalic projection nuclei have a profound impact on mood, motivation, and cognition. Human telencephalic evolution manifests in volume increases of the cerebral crura, pons, cerebellar hemispheres, olives, pyramidal tract, and medial lemniscus. However, the spatial constraints of the posterior fossa limited the proportional expansion of the brainstem during human telencephalic evolution, rendering this evolutionarily conserved structure increasingly vulnerable to malfunction and disease.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"216 ","pages":"17-57"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147528431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The human fovea.","authors":"Joseph Carroll, Aliya Siddiqui, Joseph Kreis","doi":"10.1016/B978-0-443-22193-4.00001-9","DOIUrl":"10.1016/B978-0-443-22193-4.00001-9","url":null,"abstract":"<p><p>While the fovea occupies only about 0.1% of the total retinal surface area, it is arguably the most important region of the human retina. The human fovea is characterized by unique anatomic specializations relative to the rest of the retina, which include an absence of inner retinal layers and the accompanying vasculature, an increased density of cone photoreceptors, a near-absence of rod photoreceptors, and a unique \"private-line\" midget ganglion cell circuitry. These anatomic specializations are responsible for our high-acuity vision. Unfortunately, as a result, even minor disruptions to foveal structure can have dire consequences for visual function. There is a growing number of noninvasive imaging modalities that enable direct visualization of foveal structure in humans, some with the ability to resolve individual cone photoreceptor cells. Through the lens of these in vivo imaging advances, we provide a general overview of the basic anatomic specializations of the human fovea, define the normal variation in foveal anatomy, and describe the foveal manifestations of some well-studied developmental and degenerative retinal disorders (e.g., albinism, premature birth, and achromatopsia).</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"217 ","pages":"83-97"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147863969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic mechanisms in brain aging and their role in cognitive decline and mental health disorders.","authors":"Carlene Chinn, Marcelo Wood","doi":"10.1016/B978-0-443-19043-8.00023-2","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00023-2","url":null,"abstract":"<p><p>The aging brain accumulates increased variability of gene expression over time, in part due to environmental and lifestyle factors that influence an individual's biologic processes underlying healthy and diseased age-related pathology. Targeted by such external factors is the epigenome, a collection of chemical marks on DNA and histone proteins that can change dynamically in response to stimuli and can alter transcriptional machinery to regulate gene expression and protein synthesis. Recent work has revealed epigenetic mechanisms - such as DNA methylation, histone posttranslational modifications, and chromatin remodeling complexes - as key drivers of variation across the genomic landscape in aging. Epigenetic mechanisms integral to cognitive performance and behavior are both permissive and repressive, allowing for either the facilitation or negative regulation of gene expression that enables memory encoding and recall. The epigenome is modified by a large number of molecular processes utilized during the lifespan, which lends itself to exploration of aberrant genetic events accumulated in aging that may contribute to disease. This chapter synthesizes current knowledge in neuroepigenetics as specifically related to age-dependent cognitive processes and discusses new avenues as potential therapeutic or predictive markers for age-related diseases.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"429-447"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic architecture of the developing brain.","authors":"Moshe Szyf","doi":"10.1016/B978-0-443-19043-8.00022-0","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00022-0","url":null,"abstract":"<p><p>This chapter reviews the evolution of DNA methylation programs during brain development, focusing on how DNA methylation patterns define cell identity and regulate gene expression. It traces early hypotheses about tissue-specific DNA methylation and highlights limitations of bulk tissue analysis. Advances in genome-wide mapping, cell sorting, and single-cell sequencing have clarified the roles of CG and non-CG methylation in neuronal and glial differentiation. The chapter details how enhancer and gene body methylation correlate with transcriptional activity and how transcription factors, like Early Growth Response 1, recruit demethylation machinery during development. It also discusses the emergence of non-CG methylation in neurons, its association with gene repression, and its potential role in neurodevelopmental disorders. Differentially methylated regions and methylation-sensitive genetic variants are increasingly linked to neurodevelopmental disease risk, such as autism and schizophrenia, highlighting the relevance of epigenetic mapping for understanding brain pathology. Finally, integrated methylome and chromatin accessibility data are used to classify neuronal subtypes and link methylation states to 3D genome architecture.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"75-82"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Animal models with construct validity for studying epigenetic processes in neurobehavior.","authors":"Elad Lax, Meklit Berhe, Gal Yadid","doi":"10.1016/B978-0-443-19043-8.00028-1","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00028-1","url":null,"abstract":"<p><p>Many ethical and technical challenges hinder exploration of molecular mechanisms, including epigenetic processes underlying neuropsychiatric disorders in humans. Therefore, there is a need for animal models for such disorders that will allow a better understanding of disease mechanisms. Here, we explore the use of animal models with construct validity for such disorders. The chapter emphasizes the importance of construct validity of the models and highlights key considerations, including the temporal dynamics of disorders, relevant tissues and brain regions, and the need for genetic and environmental components of the model to align with the human pathophysiology. We review several of the most established models for major neuropsychiatric disorders such as anxiety, depression, posttraumatic stress disorder, and substance use disorder. We describe why models such as the Chronic Social Defeat Stress model, which closely replicates the types of social stressors that are known to contribute to depression; the drug self-administration model, which captures the motivational processes underlying substance use disorder; or the Predator Scent Stress model, which uses ecologically relevant stimuli that mimic the types of psychologic threat and traumatic experiences implicated in human posttraumatic stress disorder, are important. We discuss models that have construct validity and provide examples and use cases for these models in studies that explored the epigenetic mechanisms of neuropsychiatric disorders. Overall, this chapter underscores the importance of choosing a valid animal model for research to allow for a better understanding of the underlying epigenetic mechanisms of neuropsychiatric disorders.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"527-536"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic mechnisms involved in posttraumatic stress disorder.","authors":"David Cheishvili, Yaakov Hoffman, Amit Shrira","doi":"10.1016/B978-0-443-19043-8.00027-X","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00027-X","url":null,"abstract":"<p><p>Posttraumatic stress disorder (PTSD) is a complex mental health condition influenced by various factors, including the environment, biology, and genetic variations. This chapter delves into how these factors interact, focusing on trauma exposure, brain mechanisms, and genetic expression changes that contribute to the development of PTSD. The chapter provides an overview of PTSD prevalence, diagnostic criteria, key patterns in its occurrence, interindividual symptoms variations, and factors that increase the risk of developing PTSD, such as inherited trauma effects passed down from one generation to the next. It then explores the biologic underpinnings of the disorder, including disruptions in the brain's fear and stress response systems, irregularities in the hypothalamic-pituitary-adrenal axis, and genetic influences that either increase or decrease PTSD risk. Treatment efficacy is also addressed. A significant emphasis is placed on discussing epigenetic mechanisms that may be involved in the molecular pathology of PTSD, mainly focusing on DNA methylation and histone modifications. Research findings from genome-wide studies and research targeting specific stress-related genes, such as the glucocorticoid receptor, its cochaperon FK506 binding protein 5 (FKBP5), or its modulator kinetochore associated complex subunit 2 (SKA2), demonstrate how their epigenetic modulation impacts an individual's stress tolerance. The chapter also covers how trauma-related changes in the body, such as chronic inflammation and immune system irregularities, may be biologically inherited by future generations. Finally, the discussion highlights the potential of epigenetic interventions - targeting the biologic effects of trauma on genes - to pave the way for personalized treatments. Insights from research involving both humans and animals suggest new therapeutic approaches that align with psychologic and biologic perspectives.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"247-268"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149193022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kenneth Blum, Chynna B Levin, Alireza Sharafshah, Kai-Uwe Lewandowski
{"title":"Epigenetic processes in substance abuse, and behavioral addictions: Involvement of dopaminergic pathways.","authors":"Kenneth Blum, Chynna B Levin, Alireza Sharafshah, Kai-Uwe Lewandowski","doi":"10.1016/B978-0-443-19043-8.00031-1","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00031-1","url":null,"abstract":"<p><p>Substance abuse and behavioral addictions, characterized by compulsive engagement in rewarding stimuli despite adverse consequences, represent significant public health concerns. These disorders are underpinned by complex neurobiologic mechanisms, particularly involving the brain's reward circuitry, which is primarily mediated by the dopaminergic system. The accumulated findings underscore the significant environmental effects on the epigenetic state of reward system- related genes, which may predispose individuals to addiction. This review synthesizes current literature on the epigenetic landscape associated with substance and behavioral addictions, emphasizing dopamine dysregulation in the brain as a critical factor. We explore how alterations in DNA methylation and histone modifications within dopaminergic pathways contribute to the addiction phenotype. Our research underscores the necessity of understanding the interplay between genetic predisposition and epigenetic influences in shaping addiction vulnerability.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"307-319"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149193027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The role of epigenetic DNA modifications in the brain: Focus on cell specification, neuropathology, and environmental influences.","authors":"André Oliveira, Ana Grangeia, C Joana Marques","doi":"10.1016/B978-0-443-19043-8.00013-X","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00013-X","url":null,"abstract":"<p><p>Epigenetics plays a fundamental role in the regulation of transcriptional landscapes that define cellular identity and the ability of cells and tissues, and ultimately organisms, to adapt to a changing environment. DNA methylation is a stable and heritable epigenetic mark that is involved in cellular differentiation and homeostasis; nevertheless, methylation marks can be reversed by oxidation of 5-methylcytosine into 5-hydroxymethylcytosine and other derivatives, through the action of TET (ten-eleven translocation) dioxygenase enzymes. This provides a mechanism for the active DNA demethylation observed in key developmental stages, where epigenetic reprogramming events take place, and in postmitotic mature neurons, contributing to brain plasticity. Several lines of evidence, both from animal models and human diseases, enhance our understanding of the essential roles of epigenetic modifiers in brain functions and further strengthen the importance of considering these molecular pathways as therapeutic targets in neuropsychiatric disorders.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"19-34"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149193028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic processes in Parkinson disease.","authors":"Andrea Stoccoro, Martina Lari, Fabio Coppedè","doi":"10.1016/B978-0-443-19043-8.00009-8","DOIUrl":"https://doi.org/10.1016/B978-0-443-19043-8.00009-8","url":null,"abstract":"<p><p>Numerous investigations performed over the last 20 years revealed various epigenetic modifications in both postmortem brain samples and in peripheral tissues of individuals with Parkinson disease (PD), as well as in neuronal and animal models of the disease. These include changes in DNA methylation and hydroxymethylation, histone-tail modifications, and a dysregulated expression of both short- and long-noncoding RNA molecules. Overall, there is no doubt that epigenetic modifications occur within the neurodegenerative process linked to PD, resulting in altered expression of PD-linked genes. However, it is not yet completely clear which of these epigenetic changes are a consequence of the neurodegenerative process and which are instead early events capable of contributing to it. Indeed, studies in peripheral tissues of patients at different disease stages are attempting to provide early epigenetic biomarkers of clinical utility. Similarly, the epigenetic properties of ascertained PD risk factors, including metals, herbicides, and pesticides, are being tested in animal and cell culture models to detect environmentally induced epigenetic changes potentially contributing to the disease. The potential of epigenetic treatments and epigenome editing for PD is another area of active research.</p>","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"219 ","pages":"321-344"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149193035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Foreword.","authors":"Aminoff Michael J, Boller François, Swaab Dick F","doi":"10.1016/B978-0-443-22193-4.00023-8","DOIUrl":"https://doi.org/10.1016/B978-0-443-22193-4.00023-8","url":null,"abstract":"","PeriodicalId":12907,"journal":{"name":"Handbook of clinical neurology","volume":"217 ","pages":"ix"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147863668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}