scholarly journals Uncovering the transcriptional signatures of hub connectivity in neural networks

2018 ◽  
Author(s):  
Aurina Arnatkeviciute ◽  
Ben Fulcher ◽  
Alex Fornito
Keyword(s):  
Gene Expression ◽  
Neural Networks ◽  
Large Scale ◽  
Expression Patterns ◽  
Genetic Influences ◽  
Gene Expression Patterns ◽  
Small Subset ◽  
Present Evidence ◽  
Large Scale Network ◽  
Scale Network

Connections in nervous systems are disproportionately concentrated on a small subset of neural elements that act as network hubs. Hubs have been found across different of species and scales ranging from C.elegans to mouse, rat, cat, macaque and human, suggesting a role for genetic influences. The recent availability of brain-wide gene expression atlases provides new opportunities for mapping the transcriptional correlates of large-scale network-level phenotypes. Here we review studies that use these atlases to investigate gene expression patterns associated with hub connectivity in neural networks and present evidence that some of these patterns are conserved across species and scales.

scholarly journals Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Ettore Tiraboschi ◽  
Ramon Guirado ◽  
Dario Greco ◽  
Petri Auvinen ◽  
Jose Fernando Maya-Vetencourt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Visual Cortex ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Monocular Deprivation ◽  
Adult Brain ◽  
Gene Expression Patterns ◽  
Postnatal Life ◽  
Critical Periods

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

scholarly journals A Large Scale Genetic Analysis of c-Myc-regulated Gene Expression Patterns

2003 ◽  
Vol 278 (14) ◽  
pp. 12563-12573 ◽  
Author(s):  
Brenda C. O'Connell ◽  
Ann F. Cheung ◽  
Carl P. Simkevich ◽  
Wanny Tam ◽  
Xiaojia Ren ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Analysis ◽  
Large Scale ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Regulated Gene Expression

Classification of the images of gene expression patterns using neural networks based on multivalued neurons with the minimal number of inputs

2002 ◽  
Author(s):  
Igor N. Aizenberg ◽  
Constantine Butakoff ◽  
Ekaterina Myasnikova ◽  
Maria Samsonova ◽  
John Reinitz
Keyword(s):  
Gene Expression ◽  
Neural Networks ◽  
Expression Patterns ◽  
Gene Expression Patterns

scholarly journals Local vulnerability and global connectivity jointly shape neurodegenerative disease propagation

2018 ◽  
Author(s):  
Ying-Qiu Zheng ◽  
Yu Zhang ◽  
Yvonne Yau ◽  
Yahar Zeighami ◽  
Kevin Larcher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Structural Connectivity ◽  
Brain Network ◽  
Subcortical Structures ◽  
Neurodegenerative Process ◽  
Axonal Projections ◽  
Large Scale Network ◽  
Regional Vulnerability ◽  
Scale Network

AbstractIt is becoming increasingly clear that brain network organization shapes the course and expression of neurodegenerative diseases. Parkinson’s disease (PD) is marked by progressive spread of atrophy from the midbrain to subcortical structures and eventually, to the cerebral cortex. Recent discoveries suggest that the neurodegenerative process involves the misfolding and prion-like propagation of endogenous α-synuclein via axonal projections. However, the mechanisms that translate local “synucleinopathy” to large-scale network dysfunction and atrophy remain unknown. Here we use an agent-based epidemic spreading model to integrate structural connectivity, functional connectivity and gene expression, and to predict sequential volume loss due to neurodegeneration. The dynamic model replicates the spatial and temporal patterning of empirical atrophy in PD and implicates the substantia nigra as the disease epicenter. We reveal a significant role for both connectome topology and geometry in shaping the distribution of atrophy. The model also demonstrates that SNCA and GBA transcription influence α-synuclein concentration and local regional vulnerability. Functional co-activation further amplifies the course set by connectome architecture and gene expression. Altogether, these results support the theory that the progression of PD is a multifactorial process that depends on both cell-to-cell spreading of misfolded proteins and regional vulnerability.

scholarly journals LogicSNN: A Unified Spiking Neural Networks Logical Operation Paradigm

Electronics ◽  
2021 ◽  
Vol 10 (17) ◽  
pp. 2123 ◽  
Author(s):  
Lingfei Mo ◽  
Minghao Wang
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Network Structure ◽  
Large Scale ◽  
Spike Timing ◽  
Spiking Neural Networks ◽  
Logical Operation ◽  
Large Scale Network ◽  
Learning Capabilities ◽  
Scale Network

LogicSNN, a unified spiking neural networks (SNN) logical operation paradigm is proposed in this paper. First, we define the logical variables under the semantics of SNN. Then, we design the network structure of this paradigm and use spike-timing-dependent plasticity for training. According to this paradigm, six kinds of basic SNN binary logical operation modules and three kinds of combined logical networks based on these basic modules are implemented. Through these experiments, the rationality, cascading characteristics and the potential of building large-scale network of this paradigm are verified. This study fills in the blanks of the logical operation of SNN and provides a possible way to realize more complex machine learning capabilities.

scholarly journals Evolution of gene expression across species and specialized zooids in Siphonophora

2021 ◽  
Author(s):  
Catriona Munro ◽  
Felipe Zapata ◽  
Mark Howison ◽  
Stefan Siebert ◽  
Casey W Dunn
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Trees ◽  
Species Trees ◽  
Examine Gene Expression ◽  
Specialized Tissue ◽  
Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

Sign in / Sign up

Export Citation Format

Share Document