Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains

Brain development and function are governed by precisely regulated protein expressions in different regions. To date, multiregional brain proteomes have been systematically analyzed only for adult human and mouse brains. To understand the underpinnings of brain development and function, we generated proteomes from six regions of the postnatal brain at three developmental stages of domestic dogs (Canis familiaris), which are special among animals in terms of their remarkable human-like social cognitive abilities. Quantitative analysis of the spatiotemporal proteomes identified region-enriched synapse types at different developmental stages and differential myelination progression in different brain regions. Through integrative analysis of inter-regional expression patterns of orthologous proteins and genome-wide cis-regulatory element frequencies, we found that proteins related with myelination and hippocampus were highly correlated between dog and human but not between mouse and human, although mouse is phylogenetically closer to human. Moreover, the global expression patterns of neurodegenerative disease and autism spectrum disorder–associated proteins in dog brain more resemble human brain than in mouse brain. The high similarity of myelination and hippocampus-related pathways in dog and human at both proteomic and genetic levels may contribute to their shared social cognitive abilities. The inter-regional expression patterns of disease-associated proteins in the brain of different species provide important information to guide mechanistic and translational study using appropriate animal models.     

A cell type annotation Jamboree—Revival of а communal science forum

Cell Atlases are currently being constructed for human tissues as well as several model organisms. New technologies make creation of vast datasets in many species possible, but the value of such data crucially depends on the quality of annotation. The tools of annotating single cell data and creating knowledge representations comparable across organisms have been lagging. We argue that successfully creating Cell Atlases will require a revival of a boot‐camp style forum for communal annotation combined with an intensive learning workshop, dubbed a “Jamboree”. We report on our experience of successfully developing a structure and curriculum and running such a Jamboree for Xenopus Embryonic Cell Types at the Janelia Farms campus of the Howard Hughes Medical Institute.     

Integrative strategies to identify candidate genes in rodent models of human alcoholism.

The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait loci to uncover candidate genes for the ethanol-preference phenotype. In our study, 2 genes, retinaldehyde binding protein 1 (Rlbp1) and syntaxin 12 (Stx12), were found to be strong candidates for ethanol preference. Such experimental approaches have the power and the potential to greatly speed up the laborious process of identifying candidate genes for the animal models of human alcoholism.     

Dipole Source Localization of Mouse Electroencephalogram Using the Fieldtrip Toolbox

The mouse model is an important research tool in neurosciences to examine brain function and diseases with genetic perturbation in different brain regions. However, the limited techniques to map activated brain regions under specific experimental manipulations has been a drawback of the mouse model compared to human functional brain mapping. Here, we present a functional brain mapping method for fast and robust in vivo brain mapping of the mouse brain. The method is based on the acquisition of high density electroencephalography (EEG) with a microarray and EEG source estimation to localize the electrophysiological origins. We adapted the Fieldtrip toolbox for the source estimation, taking advantage of its software openness and flexibility in modeling the EEG volume conduction. Three source estimation techniques were compared: Distribution source modeling with minimum-norm estimation (MNE), scanning with multiple signal classification (MUSIC), and single-dipole fitting. Known sources to evaluate the performance of the localization methods were provided using optogenetic tools. The accuracy was quantified based on the receiver operating characteristic (ROC) analysis. The mean detection accuracy was high, with a false positive rate less than 1.3% and 7% at the sensitivity of 90% plotted with the MNE and MUSIC algorithms, respectively. The mean center-to-center distance was less than 1.2 mm in single dipole fitting algorithm. Mouse microarray EEG source localization using microarray allows a reliable method for functional brain mapping in awake mouse opening an access to cross-species study with human brain.     

Human brain evolution: harnessing the genomics (r)evolution to link genes, cognition, and behavior

The evolution of the human brain has resulted in numerous specialized features including higher cognitive processes such as language. Knowledge of whole-genome sequence and structural variation via high-throughput sequencing technology provides an unprecedented opportunity to view human evolution at high resolution. However, phenotype discovery is a critical component of these endeavors and the use of nontraditional model organisms will also be critical for piecing together a complete picture. Ultimately, the union of developmental studies of the brain with studies of unique phenotypes in a myriad of species will result in a more thorough model of the groundwork the human brain was built upon. Furthermore, these integrative approaches should provide important insights into human diseases.     

Unveiling functions of the visual cortex using task-specific deep neural networks

The human visual cortex enables visual perception through a cascade of hierarchical computations in cortical regions with distinct functionalities. Here, we introduce an AI-driven approach to discover the functional mapping of the visual cortex. We related human brain responses to scene images measured with functional MRI (fMRI) systematically to a diverse set of deep neural networks (DNNs) optimized to perform different scene perception tasks. We found a structured mapping between DNN tasks and brain regions along the ventral and dorsal visual streams. Low-level visual tasks mapped onto early brain regions, 3-dimensional scene perception tasks mapped onto the dorsal stream, and semantic tasks mapped onto the ventral stream. This mapping was of high fidelity, with more than 60% of the explainable variance in nine key regions being explained. Together, our results provide a novel functional mapping of the human visual cortex and demonstrate the power of the computational approach.     

An integrative approach for the identification of quantitative trait loci

The genetic dissection of complex traits is one of the most difficult and most important challenges facing science today. We discuss here an integrative approach to quantitative trait loci (QTL) mapping in mice. This approach makes use of the wealth of genetic tools available in mice, as well as the recent advances in genome sequence data already available for a number of inbred mouse strains. We have developed mapping strategies that allow a stepwise narrowing of a QTL mapping interval, prioritizing candidate genes for further analysis with the potential of identifying the most probable candidate gene for the given trait. This approach integrates traditional mapping tools, fine mapping tools, sequence-based analysis, bioinformatics and gene expression.     

History of the mainstream scientific research at the Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences

The classical reflex theory of the higher nervous activity has been developed in the works of E.A. Asratyan, the first director of the Institute, and his scientific school. The novel aspects of the theory have been developed: the principle of system organization; the concept of the nervous center as a set of structures located in different areas of the central nervous system; conditioned switchover, the mechanism of conditioned connection closure; the origin and localization of conditioned inhibition; the two-way, forward and backward conditioned connections. The elaboration of physiological mechanisms of the active goal-directed motivated behavior was begun. V.S. Rusinov and his collaborates have developed the concept of the dominanta and role of the stationary excitation foci in the integrative brain activity. M.N. Livanov has created the concept of the spatio-temporal organization of bioelectric potential and systemic organization of brain activity. P.V. Simonov, beginning from 1964, has developed the need-informational theory of the human and animal higher nervous activity (behavior). As distinct from the theories that originate from a single viewpoint and reject all the others, Simonov's theory is integrative and follows the logic of development of brain science.     

Computer-aided mapping of specific neuronal populations in the human brain

Antibody-staining methods and computer-aided microscopic systems have been used to generate high-resolution panoramic maps of specific neuronal populations in the human brain (4,6,11). This report focuses on the problems inherent in attempting high-resolution mapping of large brain sections, and describes how they are solved by computer-aided mapping. Further applications of computers to the study of brain structure are considered.     

Mapping brains without coordinates

Brain mapping has evolved considerably over the last century. While most emphasis has been placed on coordinate-based spatial atlases, coordinate-independent parcellation-based mapping is an important technique for accessing the multitude of structural and functional data that have been reported from invasive experiments, and provides for flexible and efficient representations of information. Here. we provide an introduction to motivations, concepts, techniques and implications of coordinate-independent mapping of microstructurally or functionally defined brain structures. In particular, we explain the problems of constructing mapping paths and finding adequate heuristics for their evaluation. We then introduce the three auxiliary concepts of acronym-based mapping (AM), of a generalized hierarchy (GM ontology), and of a topographically oriented regional map (RM) with adequate granularity for mapping between individual brains with different cortical folding and between humans and non-human primates. Examples from the CoCoMac database of primate brain connectivity demonstrate how these concepts enhance coordinate-independent mapping based on published relational statements. Finally, we discuss the strengths and weaknesses of spatial coordinate-based versus coordinate-independent microstructural brain mapping and show perspectives for a wider application of parcellation-based approaches in the integration of multi-model structural, functional, and clinical data.     

Learning and memory: neurophysiological mechanisms

The analytical review of study of neurophysiological basis in different kinds of learning and memory in animal and human is given. The main attention is paid to the consideration of systemic and neuronal levels of habituation and conditioned reflexes. A conception on the brain functional state as the main mechanisms of learning and distributed multicomponent engram corresponding to the integrative process peculiarities is developed.     

Lateralized ultradian rhythms of the right and left brain: temporal variations of tactile discrimination tested in German subjects.

Endogenous ultradian rhythms with a periodicity of 2-3 hours operate separately in the right and left hemispheres of the human brain and modulate physiological functions, perception and cognition. Since sensory pathways from either hand terminate in the contralateral hemisphere, ultradian rhythms of the right and left brain can be monitored by variations in the tactile discrimination of the left and right hand, respectively. Thirteen right-handed German males were tested every 15 minutes for 8 hours. Time series of the tactile error rate determined for the right and left hands oscillate with significantly different ultradian periodicities. Whereas cycles in tactile discrimination of the right hand (left hemisphere) have a periodicity of about 2 hours, tactile discrimination of the left hand (right hemisphere) is modulated by longer periods of about 3 hours. This is interpreted in terms of the overall functional asymmetry of the human brain. Since the left brain is the specialized locus for verbal processing and the right brain for visual-spatial processing, lateralized ultradian rhythms operating in the hemispheres may provide a distinct frame for long-term timing of neuronal processes underlying semantic and spatial mapping of the environment. This is particularly important for interpreting biosocial behavioural rhythms seen in humans living under natural conditions.     

认知地图的神经环路基础

空间记忆是人类认识世界和改造世界的基本认知能力,与我们的生活息息相关.无论是寻找常用的生活物件,如钥匙和手机,还是外出上班、购物和约会,都依赖我们对周围环境的记忆.截止到目前已有大量研究从不同水平探讨大脑如何表征其周围环境,但仍然有很多未解的问题.本文系统综述了基于脑成像和神经电生理技术开展的空间记忆研究进展.通过梳理以往研究中有关生物体在构建认知地图的神经结构和神经活动规律,提出了海马结构和新皮层对空间记忆的编码环路和表征机制,并在此基础上对未来研究进行了展望.     

Conditional visuo-motor learning in primates: a key role for the basal ganglia

Sensory guidance of behavior often involves standard visuo-motor mapping of body movements onto objects and spatial locations. For example, looking at and reaching to grasp a glass of wine requires the mapping of the eyes and hand to the location of the glass in space, as well as the formation of a hand configuration appropriate to the shape of the glass. But our brain is far more than just a standard sensorimotor mapping machine. Through evolution, the brain of advanced mammals, in particular human and non-human primates, has acquired a formidable capacity to construct non-standard, arbitrary mapping using associations between external events and behavioral responses that bear no direct relationship. For example, we have all learned to stop at a red traffic light and to go at a green one, or to wait for a specific tone before dialing a phone number and to hang up when hearing a busy signal. These arbitrary associations are acquired through experience, thereby providing primates with a rich and flexible sensorimotor repertoire. Understanding how they are learned, and how they are recalled and used when the context requires them, has been one of the challenging issues for cognitive neuroscience. Valuable insights have been gained over the last two decades through the convergence of multiple complementary approaches. Human neuropsychology and experimental lesions in monkeys have identified a network of brain structures important for conditional sensorimotor associations, whereas imaging studies in healthy human subjects and electrophysiological recordings in awake monkeys have sought to identify the different functional processes underlying the overall function. The present review focuses on the contribution of a network linking the prefrontal cortex, basal ganglia, and dorsal premotor cortex, with special emphasis on results from recording experiments in monkeys. We will first review data pointing to a specific contribution of each component of the network to the performance of well-learned arbitrary visuo-motor associations, as well as data suggesting how novel associations are formed. Then we will propose a model positing that each component of the fronto-striatal network makes a specific contribution to the formation and/or execution of sensorimotor associations. In this model, the basal ganglia are thought to play a key role in linking the sensory, motor, and reward information necessary for arbitrary mapping.     

Noninvasive brain stimulation with transcranial magnetic or direct current stimulation (TMS/tDCS)—From insights into human memory to therapy of its dysfunction

Noninvasive stimulation of the brain by means of transcranial magnetic stimulation (TMS) or transcranial direct current stimulation (tDCS) has driven important discoveries in the field of human memory functions. Stand-alone or in combination with other brain mapping techniques noninvasive brain stimulation can assess issues such as location and timing of brain activity, connectivity and plasticity of neural circuits and functional relevance of a circumscribed brain area to a given cognitive task. In this emerging field, major advances in technology have been made in a relatively short period. New stimulation protocols and, especially, the progress in the application of tDCS have made it possible to obtain longer and much clearer inhibitory or facilitatory effects even after the stimulation has ceased. In this introductory review, we outline the basic principles, discuss technical limitations and describe how noninvasive brain stimulation can be used to study human memory functions in vivo. Though improvement of cognitive functions through noninvasive brain stimulation is promising, it still remains an exciting challenge to extend the use of TMS and tDCS from research tools in neuroscience to the treatment of neurological and psychiatric patients.     

Noninvasive brain stimulation with transcranial magnetic or direct current stimulation (TMS/tDCS)-From insights into human memory to therapy of its dysfunction

Noninvasive stimulation of the brain by means of transcranial magnetic stimulation (TMS) or transcranial direct current stimulation (tDCS) has driven important discoveries in the field of human memory functions. Stand-alone or in combination with other brain mapping techniques noninvasive brain stimulation can assess issues such as location and timing of brain activity, connectivity and plasticity of neural circuits and functional relevance of a circumscribed brain area to a given cognitive task. In this emerging field, major advances in technology have been made in a relatively short period. New stimulation protocols and, especially, the progress in the application of tDCS have made it possible to obtain longer and much clearer inhibitory or facilitatory effects even after the stimulation has ceased. In this introductory review, we outline the basic principles, discuss technical limitations and describe how noninvasive brain stimulation can be used to study human memory functions in vivo. Though improvement of cognitive functions through noninvasive brain stimulation is promising, it still remains an exciting challenge to extend the use of TMS and tDCS from research tools in neuroscience to the treatment of neurological and psychiatric patients.     

Human brain GABA transaminase is immunologically distinct from those of other mammalian brains

Monoclonal antibodies (mAbs) to bovine brain γ-aminobutyric acid (GABA) transaminase were characterized by epitope mapping analysis, and used as probes to compare the epitopes of the enzymes from several mammalian brains including man. From the epitope mapping analysis, three subgroups of mAbs recognizing different peptide fragments were identified. In the immunoblots probed with the mAbs, only one out of the three subgroups of mAbs reacted with a protein band of 50 kDa from human brain; the two other mAbs failed to detect any signal on the blots. In contrast, all of the mAbs did recognize a GABA-T protein band on immunoblots of all other mammalian brains tested. The results suggest that human brain GABA transaminase is immunologically distinct from those of other mammalian brains.     

综述: 人脑视觉意识的神经机制

意识的存在决定了人类生命的意义.意识问题被认为是21世纪科学要回答的一个最重要问题.意识科学正在成为认知和心理科学的皇冠,成为基础科学的顶峰.近20年来,随着认知科学、心理科学、神经科学和脑成像技术的发展,人们开始通过实验科学地研究意识问题,特别是与视觉意识相关的研究工作取得了很多重要进展.在这篇综述中,我们对以往的视觉意识研究工作进行了总结,并对未来的研究方向进行了展望.     

The role of vestibular afferent input in systemic interactions of cortical areas in the human brain

To investigate the role of vestibular afferent input in systemic interactions between cortical areas of the human brain, the dynamics of interregional cortical interactions has been studied in patients with cervical dystonia during their therapy by the removal of the transtympanic chemical vestibular receptor. It has been found that even unilateral vestibular dereception leads to a profound reorganization of systemic interactions between remote cortical areas, particularly, the anterior and posterior associative areas in both hemispheres. Relationships indicating the role of vestibular input in the organization of integrative brain activity have been found, which confirms its systemic role.