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Allen human brain atlas

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https://www.readbyqxmd.com/read/28720872/associating-transcription-factors-and-conserved-rna-structures-with-gene-regulation-in-the-human-brain
#1
Nikolai Hecker, Stefan E Seemann, Asli Silahtaroglu, Walter L Ruzzo, Jan Gorodkin
Anatomical subdivisions of the human brain can be associated with different neuronal functions. This functional diversification is reflected by differences in gene expression. By analyzing post-mortem gene expression data from the Allen Brain Atlas, we investigated the impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expression in the human brain. First, we modeled the expression of a gene as a linear combination of the expression of TFs. We devised an approach to select robust TF-gene interactions and to determine localized contributions to gene expression of TFs...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716961/the-structural-basis-of-large-scale-functional-connectivity-in-the-mouse
#2
Joanes Grandjean, Valerio Zerbi, Joshua Balsters, Nicole Wenderoth, Markus Rudina
Translational neuroimaging requires approaches and techniques that can bridge between multiple different species and disease states. One candidate method, which offers insights into the brain's functional connectivity (FC), is resting state fMRI (rs-fMRI). In both humans and non-human primates, patterns of functional connectivity (often referred to as the functional connectome) have been related to the underlying structural connectivity (structural connectome). Given the recent rise in pre-clinical neuroimaging of mouse models it is an important question whether the mouse functional connectome conforms to the underlying structural connectivity...
July 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28630769/comparing-the-expression-of-genes-related-to-serotonin-5-ht-in-c57bl-6j-mice-and-humans-based-on-data-available-at-the-allen-mouse-brain-atlas-and-allen-human-brain-atlas
#3
C A Acevedo-Triana, L A León, F P Cardenas
Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression) in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004) for mice (C57BL/6J) and Allen Human Brain Atlas (2010) for humans (6 donors) to compare the expression of serotonin-related genes...
2017: Neurology Research International
https://www.readbyqxmd.com/read/28612935/early-adversity-and-brain-response-to-faces-in-young-adulthood
#4
Johannes Lieslehto, Vesa Kiviniemi, Pirjo Mäki, Jenni Koivukangas, Tanja Nordström, Jouko Miettunen, Jennifer H Barnett, Peter B Jones, Graham K Murray, Irma Moilanen, Tomáš Paus, Juha Veijola
Early stressors play a key role in shaping interindividual differences in vulnerability to various psychopathologies, which according to the diathesis-stress model might relate to the elevated glucocorticoid secretion and impaired responsiveness to stress. Furthermore, previous studies have shown that individuals exposed to early adversity have deficits in emotion processing from faces. This study aims to explore whether early adversities associate with brain response to faces and whether this association might associate with the regional variations in mRNA expression of the glucocorticoid receptor gene (NR3C1)...
June 14, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28558017/a-dual-strategy-expression-screen-for-candidate-connectivity-labels-in-the-developing-thalamus
#5
Olivia Bibollet-Bahena, Tatsuya Okafuji, Karsten Hokamp, Guy Tear, Kevin J Mitchell
The thalamus or "inner chamber" of the brain is divided into ~30 discrete nuclei, with highly specific patterns of afferent and efferent connectivity. To identify genes that may direct these patterns of connectivity, we used two strategies. First, we used a bioinformatics pipeline to survey the predicted proteomes of nematode, fruitfly, mouse and human for extracellular proteins containing any of a list of motifs found in known guidance or connectivity molecules. Second, we performed clustering analyses on the Allen Developing Mouse Brain Atlas data to identify genes encoding surface proteins expressed with temporal profiles similar to known guidance or connectivity molecules...
2017: PloS One
https://www.readbyqxmd.com/read/28515688/insulin-resistance-as-a-link-between-amyloid-beta-and-tau-pathologies-in-alzheimer-s-disease
#6
Roger J Mullins, Thomas C Diehl, Chee W Chia, Dimitrios Kapogiannis
Current hypotheses and theories regarding the pathogenesis of Alzheimer's disease (AD) heavily implicate brain insulin resistance (IR) as a key factor. Despite the many well-validated metrics for systemic IR, the absence of biomarkers for brain-specific IR represents a translational gap that has hindered its study in living humans. In our lab, we have been working to develop biomarkers that reflect the common mechanisms of brain IR and AD that may be used to follow their engagement by experimental treatments...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28461466/oxytocin-under-opioid-antagonism-leads-to-supralinear-enhancement-of-social-attention
#7
Olga Dal Monte, Matthew Piva, Kevin M Anderson, Marios Tringides, Avram J Holmes, Steve W C Chang
To provide new preclinical evidence toward improving the efficacy of oxytocin (OT) in treating social dysfunction, we tested the benefit of administering OT under simultaneously induced opioid antagonism during dyadic gaze interactions in monkeys. OT coadministered with a μ-opioid receptor antagonist, naloxone, invoked a supralinear enhancement of prolonged and selective social attention, producing a stronger effect than the summed effects of each administered separately. These effects were consistently observed when averaging over entire sessions, as well as specifically following events of particular social importance, including mutual eye contact and mutual reward receipt...
May 16, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28420888/global-gene-expression-profiling-of-healthy-human-brain-and-its-application-in-studying-neurological-disorders
#8
Simarjeet K Negi, Chittibabu Guda
Brain function is governed by precise regulation of gene expression across its anatomically distinct structures; however, the expression patterns of genes across hundreds of brain structures are not clearly understood. Here, we describe a gene expression model, which is representative of the healthy human brain transcriptome by using data from the Allen Brain Atlas. Our in-depth gene expression profiling revealed that 84% of genes are expressed in at least one of the 190 brain structures studied. Hierarchical clustering based on gene expression profiles delineated brain regions into structurally tiered spatial groups and we observed striking enrichment for region-specific processes...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334178/inter-regional-variations-in-gene-expression-and-age-related-cortical-thinning-in-the-adolescent-brain
#9
Angelita Pui-Yee Wong, Leon French, Gabriel Leonard, Michel Perron, G Bruce Pike, Louis Richer, Suzanne Veillette, Zdenka Pausova, Tomáš Paus
Age-related decreases in cortical thickness observed during adolescence may be related to fluctuations in sex and stress hormones. We examine this possibility by relating inter-regional variations in age-related cortical thinning (data from the Saguenay Youth Study) to inter-regional variations in expression levels of relevant genes (data from the Allen Human Brain Atlas); we focus on genes coding for glucocorticoid receptor (NR3C1), androgen receptor (AR), progesterone receptor (PGR), and estrogen receptors (ESR1 and ESR2)...
February 25, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28321948/gene-networks-show-associations-with-seed-region-connectivity
#10
Marie Forest, Yasser Iturria-Medina, Jennifer S Goldman, Claudia L Kleinman, Amanda Lovato, Kathleen Oros Klein, Alan Evans, Antonio Ciampi, Aurélie Labbe, Celia M T Greenwood
Primary patterns in adult brain connectivity are established during development by coordinated networks of transiently expressed genes; however, neural networks remain malleable throughout life. The present study hypothesizes that structural connectivity from key seed regions may induce effects on their connected targets, which are reflected in gene expression at those targeted regions. To test this hypothesis, analyses were performed on data from two brains from the Allen Human Brain Atlas, for which both gene expression and DW-MRI were available...
June 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28320311/a-receptor-based-analysis-of-local-ecosystems-in-the-human-brain
#11
Skirmantas Janušonis
BACKGROUND: As a complex system, the brain is a self-organizing entity that depends on local interactions among cells. Its regions (anatomically defined nuclei and areas) can be conceptualized as cellular ecosystems, but the similarity of their functional profiles is poorly understood. The study used the Allen Human Brain Atlas to classify 169 brain regions into hierarchically-organized environments based on their expression of 100 G protein-coupled neurotransmitter receptors, with no a priori reference to the regions' positions in the brain's anatomy or function...
March 20, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28221363/premature-primary-tooth-eruption-in-cognitive-motor-delayed-adnp-mutated-children
#12
I Gozes, A Van Dijck, G Hacohen-Kleiman, I Grigg, G Karmon, E Giladi, M Eger, Y Gabet, M Pasmanik-Chor, E Cappuyns, O Elpeleg, R F Kooy, S Bedrosian-Sermone
A major flaw in autism spectrum disorder (ASD) management is late diagnosis. Activity-dependent neuroprotective protein (ADNP) is a most frequent de novo mutated ASD-related gene. Functionally, ADNP protects nerve cells against electrical blockade. In mice, complete Adnp deficiency results in dysregulation of over 400 genes and failure to form a brain. Adnp haploinsufficiency results in cognitive and social deficiencies coupled to sex- and age-dependent deficits in the key microtubule and ion channel pathways...
February 21, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28132031/brainscope-interactive-visual-exploration-of-the-spatial-and-temporal-human-brain-transcriptome
#13
Sjoerd M H Huisman, Baldur van Lew, Ahmed Mahfouz, Nicola Pezzotti, Thomas Höllt, Lieke Michielsen, Anna Vilanova, Marcel J T Reinders, Boudewijn P F Lelieveldt
Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: a web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome. Through a novel methodology to explore high-dimensional data (dual t-SNE), BrainScope enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28105773/exosomal-biomarkers-of-brain-insulin-resistance-associated-with-regional-atrophy-in-alzheimer-s-disease
#14
Roger J Mullins, Maja Mustapic, Edward J Goetzl, Dimitrios Kapogiannis
Brain insulin resistance (IR), which depends on insulin-receptor-substrate-1 (IRS-1) phosphorylation, is characteristic of Alzheimer's disease (AD). Previously, we demonstrated higher pSer312-IRS-1 (ineffective insulin signaling) and lower p-panTyr-IRS-1 (effective insulin signaling) in neural origin-enriched plasma exosomes of AD patients vs. CONTROLS: Here, we hypothesized that these exosomal biomarkers associate with brain atrophy in AD. We studied 24 subjects with biomarker-supported probable AD (low CSF Aβ42 )...
April 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28053035/a-high-resolution-in-vivo-atlas-of-the-human-brain-s-serotonin-system
#15
Vincent Beliveau, Melanie Ganz, Ling Feng, Brice Ozenne, Liselotte Højgaard, Patrick M Fisher, Claus Svarer, Douglas N Greve, Gitte M Knudsen
The serotonin (5-hydroxytryptamine, 5-HT) system modulates many important brain functions and is critically involved in many neuropsychiatric disorders. Here, we present a high-resolution, multidimensional, in vivo atlas of four of the human brain's 5-HT receptors (5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4) and the 5-HT transporter (5-HTT). The atlas is created from molecular and structural high-resolution neuroimaging data consisting of positron emission tomography (PET) and magnetic resonance imaging (MRI) scans acquired in a total of 210 healthy individuals...
January 4, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28034760/insulin-resistance-in-alzheimer-s-disease
#16
REVIEW
Thomas Diehl, Roger Mullins, Dimitrios Kapogiannis
The links between systemic insulin resistance (IR), brain-specific IR, and Alzheimer's disease (AD) have been an extremely productive area of current research. This review will cover the fundamentals and pathways leading to IR, its connection to AD via cellular mechanisms, the most prominent methods and models used to examine it, an introduction to the role of extracellular vesicles (EVs) as a source of biomarkers for IR and AD, and an overview of modern clinical studies on the subject. To provide additional context, we also present a novel analysis of the spatial correlation of gene expression in the brain with the aid of Allen Human Brain Atlas data...
May 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28018170/mrna-transcriptomics-of-galectins-unveils-heterogeneous-organization-in-mouse-and-human-brain
#17
Sebastian John, Rashmi Mishra
Background: Galectins, a family of non-classically secreted, β-galactoside binding proteins is involved in several brain disorders; however, no systematic knowledge on the normal neuroanatomical distribution and functions of galectins exits. Hence, the major purpose of this study was to understand spatial distribution and predict functions of galectins in brain and also compare the degree of conservation vs. divergence between mouse and human species. The latter objective was required to determine the relevance and appropriateness of studying galectins in mouse brain which may ultimately enable us to extrapolate the findings to human brain physiology and pathologies...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27913432/von-economo-neurons-and-fork-cells-a-neurochemical-signature-linked-to-monoaminergic-function
#18
Anke A Dijkstra, Li-Chun Lin, Alissa L Nana, Stephanie E Gaus, William W Seeley
The human anterior cingulate and frontoinsular cortices are distinguished by 2 unique Layer 5 neuronal morphotypes, the von Economo neurons (VENs) and fork cells, whose biological identity remains mysterious. Insights could impact research on diverse neuropsychiatric diseases to which these cells have been linked. Here, we leveraged the Allen Brain Atlas to evaluate mRNA expression of 176 neurotransmitter-related genes and identified vesicular monoamine transporter 2 (VMAT2), gamma-aminobutyric acid (GABA) receptor subunit θ (GABRQ), and adrenoreceptor α-1A (ADRA1A) expression in human VENs, fork cells, and a minority of neighboring Layer 5 neurons...
December 1, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27909009/association-of-protein-distribution-and-gene-expression-revealed-by-pet-and-post-mortem-quantification-in-the-serotonergic-system-of-the-human-brain
#19
A Komorowski, G M James, C Philippe, G Gryglewski, A Bauer, M Hienert, M Spies, A Kautzky, T Vanicek, A Hahn, T Traub-Weidinger, D Winkler, W Wadsak, M Mitterhauser, M Hacker, S Kasper, R Lanzenberger
Regional differences in posttranscriptional mechanisms may influence in vivo protein densities. The association of positron emission tomography (PET) imaging data from 112 healthy controls and gene expression values from the Allen Human Brain Atlas, based on post-mortem brains, was investigated for key serotonergic proteins. PET binding values and gene expression intensities were correlated for the main inhibitory (5-HT1A) and excitatory (5-HT2A) serotonin receptor, the serotonin transporter (SERT) as well as monoamine oxidase-A (MAO-A), using Spearman's correlation coefficients (rs) in a voxel-wise and region-wise analysis...
January 1, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/27896963/exploring-brain-transcriptomic-patterns-a-topological-analysis-using-spatial-expression-networks
#20
Zhana Kuncheva, Michelle L Krishnan, Giovanni Montana
Characterizing the transcriptome architecture of the human brain is fundamental in gaining an understanding of brain function and disease. A number of recent studies have investigated patterns of brain gene expression obtained from an extensive anatomical coverage across the entire human brain using experimental data generated by the Allen Human Brain Atlas (AHBA) project. In this paper, we propose a new representation of a gene's transcription activity that explicitly captures the pattern of spatial co-expression across different anatomical brain regions...
2016: Pacific Symposium on Biocomputing
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