Biology subjects

Shamir, I.

Publications and source records attributed to Shamir, I..

5 recordsLinked to original sources

bioRxiv2024

Laminar RNNs: using biologically-inspired network topology on the cortical laminar level in memory tasks

Advancements in neuroscience and artificial intelligence have been fueling one another for decades. In this study, we integrate a neuroimaging model of laminar-level connectomics into a biologically-inspired deep learning model of recurrent neural networks (RNNs) for working memory tasks. The resulting model offers a way to incorporate a more comprehensive representation of brain topology into artificial intelligence without diminishing the performance of the network compared to previous models.

neuroscience↗

bioRxiv2022

Clustering multilayered cytoarchitectonic surface-based data in the brain

The laminar microstructure of the cerebral cortex is considered a unique anatomical mark of the development, function, connectivity, and even various pathologies of the brain. In recent years, multiple neuroimaging studies have utilized magnetic resonance imaging (MRI) relaxometry to visualize and explore this intricate microstructure. By successfully delineating the cortical laminar components, the applicability of T1 relaxometry has been expanded beyond solely a direct measure of myeline content. However, validating its applicability as a measure of cortical cytoarchitecture demands analyzing the complex resulting laminar datasets. In this study, we adapt and implement an algorithm for clustering cell omics profiles to cluster these complex microstructural cortical datasets. The resulting clusters correspond with an established atlas of cytoarchitectonic features, providing robust validation of T1 imaging as a tool for exploring cortical laminar composition. Lastly, we demonstrate the applicability of this framework in the exploration of the cytoarchitectonic features behind various unique skillsets.

neuroscience↗

bioRxiv2020

Modelling cortical laminar connectivity in the macaque brain

In 1991, Felleman and Van Essen published their seminal study regarding hierarchical processing in the primate cerebral cortex. Their work encompassed a widescale analysis of connections reported through tracing between 35 regions in the macaque visual cortex, extending from cortical regions to the laminar level. In this work, we revisit laminar-level connectivity in the macaque brain using a whole-brain MRI-based approach. We use multi-modal ex-vivo MRI imaging of the macaque brain in both white and grey matter, which are then integrated via a simple model of laminar connectivity. This model uses a granularity-based approach to define a set of rules that expands cortical connections to the laminar level. Different fiber tracking routines are then examined in order to explore the ability of our model to infer laminar connectivity. The network of macaque cortical laminar connectivity resulting from the chosen routine is then validated in the visual cortex by comparison to findings from Felleman and Van Essen with an 83% accuracy level. By using a more comprehensive definition of the cortex that addresses its heterogenous laminar composition, we can explore a new avenue of structural connectivity on the laminar level.

neuroscience↗

bioRxiv2018

A Framework for Cortical Layer Composition Analysis using Low Resolution T1 MRI Images

The layer composition of the cerebral cortex represents a unique anatomical fingerprint of brain development, function, connectivity and pathology. Historically the cortical layers were investigated solely ex-vivo using histological means, but recent magnetic resonance imaging (MRI) studies suggest that T1 relaxation images can be utilized to separate the layers. Despite technological advancements in the field of high resolution MRI, accurate estimation of whole brain layer composition has remained limited due to partial volume effects, leaving some layers far beyond the image resolution. In this study we offer a simple and accurate method for layer composition analysis, resolving partial volume effects and cortical curvature heterogeneity. We use a low resolution echo planar imaging inversion recovery (EPI IR) MRI scan protocol that provides fast acquisition (~12 minutes) and enables extraction of multiple T1 relaxation time components per voxel, which are assigned to types of brain tissue and utilized to extract the subvoxel composition of each T1 layer. While previous investigation of the layers required the estimation of cortical normals or smoothing of layer widths (similar to VBM), here we developed a sphere-based approach to explore the inner mesoscale architecture of the cortex. Our novel algorithm conducts spatial analysis using volumetric sampling of a system of virtual spheres dispersed throughout the entire cortical space. The methodology offers a robust and powerful framework for quantification and visualization of the layers on the cortical surface, providing a basis for quantitative investigation of their role in cognition, physiology and pathology.

neuroscience↗

bioRxiv2017

Study of the mitotic chromatin shows involvement of histone modifications in bookmarking and reveals nucleosome deposition patterns

Mitosis encompasses key molecular changes including chromatin condensation, nuclear envelope breakdown, and reduced transcription levels. Immediately after mitosis, the interphase chromatin structure is reestablished and transcription resumes. The reestablishment of the interphase chromatin is probably achieved by bookmarking, i.e., the retention of at least partial information during mitosis. Yet, while recent studies demonstrate that chromatin accessibility is generally preserved during mitosis and is only locally modulated, the exact details of the bookmarking process and its components are still unclear. To gain a deeper understanding of the mitotic bookmarking process, we merged proteomics, immunofluorescence, and ChIP-seq approaches to study the mitotic and interphase genomic organization of human cells. We focused on key histone modifications and employed HeLa-S3 cells as a model system. Generally, we observed a global concordance between the genomic organization of histone modifications in interphase and mitosis, yet the abundance of the two types of modifications we investigated was different. Whereas histone methylation patterns remain highly similar, histone acetylation patterns show a general reduction while maintaining their genomic organization. These results demonstrate that the epigenomic landscape can serve as a major component of the mitotic bookmarking process. Next, to further investigate mitosis-associated chromatin changes, we followed up on previous studies that showed that nucleosome depleted regions (NDRs) become occupied by a nucleosome during mitosis. Surprisingly, we observed that the nucleosome introduced into the NDR during mitosis encompasses a distinctive set of histone modifications, differentiating it from the surrounding nucleosomes. We show that the nucleosomes near the NDR appear to both shift into the NDR during mitosis and adopt a unique modification pattern. HDAC inhibition by the small molecule TSA reverts this pattern. These results provide evidence for a mitotic deposition and change in the modifications of the nucleosomes surrounding the NDR. Altogether, by merging multiple approaches, our study provides evidence to support a model where mitotic bookmarking is achieved by histone modifications and uncovers new insights into the deposition of nucleosomes during mitosis.

genomics↗