scholarly journals A Transcriptome Community-and-Module Approach of the Human Mesoconnectome

Entropy ◽  
2021 ◽  
Vol 23 (8) ◽  
pp. 1031
Author(s):  
Omar Paredes ◽  
Jhonatan B. López ◽  
César Covantes-Osuna ◽  
Vladimir Ocegueda-Hernández ◽  
Rebeca Romo-Vázquez ◽  
...  

Graph analysis allows exploring transcriptome compartments such as communities and modules for brain mesostructures. In this work, we proposed a bottom-up model of a gene regulatory network to brain-wise connectome workflow. We estimated the gene communities across all brain regions from the Allen Brain Atlas transcriptome database. We selected the communities method to yield the highest number of functional mesostructures in the network hierarchy organization, which allowed us to identify specific brain cell functions (e.g., neuroplasticity, axonogenesis and dendritogenesis communities). With these communities, we built brain-wise region modules that represent the connectome. Our findings match with previously described anatomical and functional brain circuits, such the default mode network and the default visual network, supporting the notion that the brain dynamics that carry out low- and higher-order functions originate from the modular composition of a GRN complex network

2020 ◽  
Vol 4 (Supplement_1) ◽  
Author(s):  
Bianca S Bono ◽  
Persephone A Miller ◽  
Nikita K Koziel Ly ◽  
Melissa J Chee

Abstract Fibroblast growth factor 21 (FGF21) has emerged as a critical endocrine factor for understanding the neurobiology of obesity, such as by the regulation thermogenesis, food preference, and metabolism, as well as for neuroprotection in Alzheimer’s disease and traumatic brain injury. FGF21 is synthesized primarily by the liver and pancreas then crosses the blood brain barrier to exert its effects in the brain. However, the sites of FGF21 action in the brain is not well-defined. FGF21 action requires the activation of FGF receptor 1c as well as its obligate co-receptor beta klotho (KLB). In order to determine the sites of FGF21 action, we mapped the distribution of Klb mRNA by in situ hybridization using RNAscope technology. We labeled Klb distribution throughout the rostrocaudal axis of male wildtype mice by amplifying Klb hybridization using tyramine signal amplification and visualizing Klb hybridization using Cyanine 3 fluorescence. The resulting Klb signal appears as punctate red “dots,” and each Klb neuron may express low (1–4 dots), medium (5–9 dots), or high levels (10+ dots) of Klb hybridization. We then mapped individual Klb expressing neuron to the atlas plates provided by the Allen Brain Atlas in order to determine Klb distribution within the substructures of each brain region, which are defined by Nissl-based parcellations of cytoarchitectural boundaries. The distribution of Klb mRNA is widespread throughout the brain, and the brain regions analyzed thus far point to notable expression in the hypothalamus, amygdala, hippocampus, and the cerebral cortex. The highest expression of Klb was localized to the suprachiasmatic nucleus in the hypothalamus, which contained low and medium Klb-expressing neurons in the lateral hypothalamic area and ventromedial hypothalamic nucleus while low expressing Klb neurons were seen in the paraventricular and dorsmedial hypothalamic nucleus. Hippocampal Klb expression was limited to the dorsal region and largely restricted to the pyramidal cell layer of the dentate gyrus, CA3, CA2, and CA1 but at low levels only. In the amygdala, low and medium Klb expressing cells were seen in lateral amygdala nucleus while low levels were observed in the basolateral amygdala nucleus. Cortical Klb expression analyzed thus far included low Klb-expressing neurons in the olfactory areas, including layers 2 and 3 of piriform cortex and nucleus of the lateral olfactory tract. These findings are consistent with the known roles of FGF21 in the central regulation of energy balance, but also implicates potentially wide-ranging effects of FGF21 such as in executive functions.


2019 ◽  
Author(s):  
Mélissa Cizeron ◽  
Zhen Qiu ◽  
Babis Koniaris ◽  
Ragini Gokhale ◽  
Noboru H. Komiyama ◽  
...  

AbstractHow synapses change molecularly during the lifespan and across all brain circuits is unknown. We analyzed the protein composition of billions of individual synapses from birth to old age on a brain-wide scale in the mouse, revealing a program of changes in the lifespan synaptome architecture spanning individual dendrites to the systems level. Three major phases were uncovered, corresponding to human childhood, adulthood and old age. An arching trajectory of synaptome architecture drives the differentiation and specialization of brain regions to a peak in young adults before dedifferentiation returns the brain to a juvenile state. This trajectory underscores changing network organization and hippocampal physiology that may account for lifespan transitions in intellectual ability and memory, and the onset of behavioral disorders.One sentence summaryThe synaptome architecture of the mouse brain undergoes continuous changes that organize brain circuitry across the lifespan.


2021 ◽  
Author(s):  
Victor Nozais ◽  
Stephanie Forkel ◽  
Chris Foulon ◽  
Laurent Petit ◽  
Michel Thiebaut de Schotten

Abstract In recent years, the field of functional neuroimaging has moved from a pure localisationist approach of isolated functional brain regions to a more integrated view of those regions within functional networks. The methods used to investigate such networks, however, rely on local signals in grey matter and are limited in identifying anatomical circuitries supporting the interaction between brain regions. Mapping the brain circuits mediating the functional signal between brain regions would propel forward our understanding of the brain’s functional signatures and dysfunctions. We developed a novel method to unravel the relationship between brain circuits and functions: The Functionnectome. The Functionectome combines the functional signal from fMRI with the anatomy of white matter brain circuits to unlock and chart the first maps of functional white matter. To showcase the versatility of this new method, we provide the first functional white matter maps revealing the joint contribution of connected areas to motor, working memory, and language functions. The Functionnectome comes with an open source companion software and opens new avenues into studying functional networks by applying the method to already existing dataset and beyond task fMRI.


2019 ◽  
Author(s):  
Dominic Kaul ◽  
Sibylle Schwab ◽  
Naguib Mechawar ◽  
Natalie Matosin

Exposure to stressful or traumatic experiences is one of the most robust risk factors for severe psychiatric disorders and has been shown to reshape entire brain regions, especially those involved in processing the stress response. This is likely underpinned by alterations to brain cell shapes, numbers and their connections, thus changing brain circuitry to enable coping with the current and future stress. In this review, we present a model for how stress re-shapes the brain, consolidating evidence of morphometric changes and the cellular and molecular mechanisms that underlie them. We illustrate how the temporal effects of stress can cause persistent remodelling of brain cells, highlighting that an individual's stress history is important for understanding psychiatric disorder risk and development. Understanding how stress re-shapes the brain is a critical step for understanding stress as a risk factor for brain pathology, and to develop appropriate biomarkers, treatments and intervention strategies.


2011 ◽  
Vol 366 (1564) ◽  
pp. 468-475 ◽  
Author(s):  
David Melcher

Our vision remains stable even though the movements of our eyes, head and bodies create a motion pattern on the retina. One of the most important, yet basic, feats of the visual system is to correctly determine whether this retinal motion is owing to real movement in the world or rather our own self-movement. This problem has occupied many great thinkers, such as Descartes and Helmholtz, at least since the time of Alhazen. This theme issue brings together leading researchers from animal neurophysiology, clinical neurology, psychophysics and cognitive neuroscience to summarize the state of the art in the study of visual stability. Recently, there has been significant progress in understanding the limits of visual stability in humans and in identifying many of the brain circuits involved in maintaining a stable percept of the world. Clinical studies and new experimental methods, such as transcranial magnetic stimulation, now make it possible to test the causal role of different brain regions in creating visual stability and also allow us to measure the consequences when the mechanisms of visual stability break down.


e-Neuroforum ◽  
2012 ◽  
Vol 18 (1) ◽  
Author(s):  
M. Wilke ◽  
P. Dechent ◽  
C. Schmidt-Samoa

AbstractSpatial neglect is a debilitating neuropsy­chological disorder that is characterized by an impaired or lost ability to explore the space contralateral to the lesion and to re­act to stimuli presented on this side. Lesion sites that have been implicated in spatial ne­glect form a widely distributed network con­sisting of a number of cortical (i.e., frontopa­rietal) and subcortical (i.e., thalamic) areas that are activated during attention and vi­suomotor tasks in healthy individuals. While detailed understanding of the brain circuits and mechanisms involved in spatial neglect is a prerequisite for the development of ef­fective therapies, this has proven to be dif­ficult in human patients because of the size and variability of lesion sites. Therefore, ex­perimental models where predefined brain regions can be systematically inactivated are of great advantage. Neglect models have been developed in nonhuman primates in whom it is possible to pharmacologically in­activate small brain regions and in humans by means of noninvasive stimulation/inacti­vation methods such as transcranial magnet­ic stimulation. In this article, we discuss theo­ries about the mechanisms of spatial neglect such as the hemispheric imbalance model and the supporting experimental evidence, with an emphasis on imaging experiments that have explored the effects of lesions on dynamic brain activity.


2018 ◽  
Author(s):  
Philip Shamash ◽  
Matteo Carandini ◽  
Kenneth D Harris ◽  
Nicholas A Steinmetz

It is now possible to record from hundreds of neurons across multiple brain regions in a single electrophysiology experiment. An essential step in the ensuing data analysis is to assign recorded neurons to the correct brain regions. Brain regions are typically identified after the recordings by comparing images of brain slices to a reference atlas by eye. This introduces error, in particular when slices are not cut at a perfectly coronal angle or when electrode tracks span multiple slices. Here we introduce SHARP-Track, a tool to localize regions of interest and plot the brain regions they pass through. SHARP-Track offers a MATLAB user interface to explore the Allen Mouse Brain Atlas, register asymmetric slice images to the atlas using manual input, and interactively analyze electrode tracks. We find that it reduces error compared to localizing electrodes in a reference atlas by eye. See github.com/cortex-lab/allenCCF for the software and wiki.


2021 ◽  
Author(s):  
Cuihua Xia ◽  
Rujia Dai ◽  
Jing Yu ◽  
Chunling Zhang ◽  
Ma-li Wong ◽  
...  

Abstract Alternative splicing (AS) contributes to the increased cellular and functional tissue complexity that is substantial in the brain. AS is tightly regulated because it is critical to many biological processes. Defective splicing is observed in several neurological and psychiatric disorders. While exonic mutations usually affect the splicing of an individual RNA, mutations in the splicing factors (components of spliceosome) frequently produce widespread disruption in the processing of many precursor-mRNAs. Thus, we tested the hypotheses that expression changes of spliceosome genes may be a common process and shared splicing pathways may be involved in complex polygenic brain disorders. We searched for expression changes of spliceosome-related genes (SGs) using a transcriptome database of several brain regions in 6 neurological and psychiatric disorders, namely Alzheimer’s disease, and autism spectrum, bipolar and major depressive disorder, Parkinson’s disease, and schizophrenia. Out of 255 SGs detected in brain, 138 showed excessive, significant changes in one or more of these disorders. Dysregulation of 10 SGs was shared in 4 disorders, and they were mostly downregulated. Six associated pathways were over-represented in all 6 disorders, including the major and the minor mRNA splicing pathways and RNA metabolism. Therefore, we found that aberrations in the mRNA splicing process may be a common trajectory to many complex brain disorders involving the spliceosome complex.


Science ◽  
2020 ◽  
Vol 367 (6482) ◽  
pp. eaay5947 ◽  
Author(s):  
Evelina Sjöstedt ◽  
Wen Zhong ◽  
Linn Fagerberg ◽  
Max Karlsson ◽  
Nicholas Mitsios ◽  
...  

The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.


2021 ◽  
Vol 55 (2) ◽  
pp. 120-130
Author(s):  
Alexander Kiss ◽  
Jana Osacka

Abstract It is apparent that the c-Fos and FosB/ΔFosB immunohistochemistry has generally become a useful tool for determining the different antipsychotic (AP) drugs activities in the brain. It is also noteworthy that there are no spatial limits, while to the extent of their identification over the whole brain axis. In addition, they can be in a parallel manner utilized in the unmasking of the brain cell phenotype character activated by APs and by this way also to identify the possible brain circuits underwent to the APs action. However, up to date, the number of APs involved in the extra-striatal studies is still limited, what prevents the possibility to fully understand their extra-striatal effects as a complex as well as differentiate their extra-striatal impact in qualitative and quantitative dimensions. Actually, it is very believable that more and more anatomical/functional knowledge might bring new insights into the APs extra-striatal actions by identifying new region-specific activities of APs as well as novel cellular targets affected by APs, which might reveal more details of their possible side effects of the extra-striatal origin.


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