scholarly journals Regional Localization of Mouse Brain Slices Based on Unified Modal Transformation

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 929
Author(s):  
Songwei Wang ◽  
Yuhang Wang ◽  
Ke Niu ◽  
Qian Li ◽  
Xiaoping Rao ◽  
...  
Keyword(s):  
Image Registration ◽  
Brain Slice ◽  
Brain Slices ◽  
Science Research ◽  
Brain Regions ◽  
Regional Localization ◽  
Registration Method ◽  
Accurate Localization ◽  
Novel Method ◽  
The Brain

Brain science research often requires accurate localization and quantitative analysis of neuronal activity in different brain regions. The premise of related analysis is to determine the brain region of each site on the brain slice by referring to the Allen Reference Atlas (ARA), namely the regional localization of the brain slice. The image registration methodology can be used to solve the problem of regional localization. However, the conventional multi-modal image registration method is not satisfactory because of the complexity of modality between the brain slice and the ARA. Inspired by the idea that people can automatically ignore noise and establish correspondence based on key regions, we proposed a novel method known as the Joint Enhancement of Multimodal Information (JEMI) network, which is based on a symmetric encoder–decoder. In this way, the brain slice and the ARA are converted into a segmentation map with unified modality, which greatly reduces the difficulty of registration. Furthermore, combined with the diffeomorphic registration algorithm, the existing topological structure was preserved. The results indicate that, compared with the existing methods, the method proposed in this study can effectively overcome the influence of non-unified modal images and achieve accurate and rapid localization of the brain slice.

TMOD-31. AN ORGANOTYPIC TISSUE PLATFORM TO BRIDGE IN VITRO AND IN VIVO ASSAYS FOR BRAIN CANCER TREATMENT

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi222-vi222
Author(s):  
Breanna Mann ◽  
Noah Bell ◽  
Denise Dunn ◽  
Scott Floyd ◽  
Shawn Hingtgen ◽  
...  
Keyword(s):  
Cell Lines ◽  
Brain Cancer ◽  
Brain Slice ◽  
Brain Slices ◽  
In Vitro Assays ◽  
Preclinical Model ◽  
Short Period ◽  
The Brain

Abstract Brain cancers remain one of the greatest medical challenges. The lack of experimentally tractable models that recapitulate brain structure/function represents a major impediment. Platforms that enable functional testing in high-fidelity models are urgently needed to accelerate the identification and translation of therapies to improve outcomes for patients suffering from brain cancer. In vitro assays are often too simple and artificial while in vivo studies can be time-intensive and complicated. Our live, organotypic brain slice platform can be used to seed and grow brain cancer cell lines, allowing us to bridge the existing gap in models. These tumors can rapidly establish within the brain slice microenvironment, and morphologic features of the tumor can be seen within a short period of time. The growth, migration, and treatment dynamics of tumors seen on the slices recapitulate what is observed in vivo yet is missed by in vitro models. Additionally, the brain slice platform allows for the dual seeding of different cell lines to simulate characteristics of heterogeneous tumors. Furthermore, live brain slices with embedded tumor can be generated from tumor-bearing mice. This method allows us to quantify tumor burden more effectively and allows for treatment and retreatment of the slices to understand treatment response and resistance that may occur in vivo. This brain slice platform lays the groundwork for a new clinically relevant preclinical model which provides physiologically relevant answers in a short amount of time leading to an acceleration of therapeutic translation.

scholarly journals Functionnectome: a framework to analyse the contribution of brain circuits to fMRI

2021 ◽  
Author(s):  
Victor Nozais ◽  
Stephanie Forkel ◽  
Chris Foulon ◽  
Laurent Petit ◽  
Michel Thiebaut de Schotten
Keyword(s):  
White Matter ◽  
Functional Neuroimaging ◽  
Brain Regions ◽  
Functional Networks ◽  
Language Functions ◽  
Brain Circuits ◽  
Novel Method ◽  
Joint Contribution ◽  
The Relationship ◽  
The Brain

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.

scholarly journals Rhes protein transits from neuron to neuron and facilitates mutant huntingtin spreading in the brain.

2021 ◽  
Author(s):  
Uri Nimrod Ramirez Jarquin ◽  
Manish Sharma ◽  
Neelam Shahani ◽  
Yunqing Li ◽  
Siddaraju Boregowda ◽  
...  
Keyword(s):  
Protein Transport ◽  
Brain Slices ◽  
Brain Regions ◽  
Medium Spiny Neurons ◽  
Striatal Neurons ◽  
Spiny Neurons ◽  
Tunneling Nanotube ◽  
Intact Brain ◽  
Cortical Regions ◽  
The Brain

Rhes (RASD2) is a thyroid hormone-induced gene that regulates striatal motor activity and promotes neurodegeneration in Huntington disease (HD) and tauopathy. Previously, we showed that Rhes moves between cultured striatal neurons and transports the HD protein, polyglutamine-expanded huntingtin (mHTT) via tunneling nanotube (TNT)-like membranous protrusions. However, similar intercellular Rhes transport has not yet been demonstrated in the intact brain. Here, we report that Rhes induces TNT-like protrusions in the striatal medium spiny neurons (MSNs) and transported between dopamine-1 receptor (D1R)-MSNs and D2R-MSNs of intact striatum and organotypic brain slices. Notably, mHTT is robustly transported within the striatum and from the striatum to the cortical areas in the brain, and Rhes deletion diminishes such transport. Moreover, we also found transport of Rhes to the cortical regions following restricted expression in the MSNs of the striatum. Thus, Rhes is a first striatum-enriched protein demonstrated to move and transport mHTT between neurons and brain regions, providing new insights on interneuronal protein transport in the brain.

scholarly journals Image-based stroke rat brain atrophy volume and infarct volume computation

2020 ◽  
Vol 76 (12) ◽  
pp. 10090-10121
Author(s):  
Yung-Kuan Chan ◽  
Chun-Fu Hong ◽  
Meng-Hsiun Tsai ◽  
Ya-Lan Chang ◽  
Ping-Hsuan Sun
Keyword(s):  
Ischemic Stroke ◽  
Rat Brain ◽  
Brain Slice ◽  
Infarct Volume ◽  
Brain Slices ◽  
Artery Occlusion ◽  
Tetrazolium Chloride ◽  
Rat Brain Slice ◽  
Cerebral Artery Occlusion ◽  
The Brain

Abstract Stroke is one of the leading causes of death as well as results in a massive economic burden for society. Stroke is a cerebrovascular disease mainly divided into two types: ischemic stroke and hemorrhagic stroke, which, respectively, refer to the partial blockage and bleeding inside brain blood vessels. Both stroke types lead to nutrient and oxygen deprivation in the brain, which ultimately cause brain damage or death. This study focuses on ischemic stroke in rats with middle cerebral artery occlusion (MCAO) as experimental subjects, and the volumes of infarct and atrophy are calculated based on the brain slice images of rat brains stained with 2,3,5-triphenyl tetrazolium chloride. In this study, a stroke rat brain infarct and atrophy volumes computation system (SRBIAVC system) is developed to segment the infarcts and atrophies from the rat brain slice images. Based on the segmentation results, the infarct and atrophy volumes of a rat brain can be computed. In this study, 168 images of brain slices cut from 28 rat brains with MCAO are used as the test samples. The experimental results show that the segmentation results obtained by the SRBIAVC system are close to those obtained by experts.

Chemical targeting of voltage sensitive dyes to specific cells and molecules in the brain

2020 ◽  
Author(s):  
Tomas Fiala ◽  
Jihang Wang ◽  
Matthew Dunn ◽  
Peter Šebej ◽  
Se Joon Choi ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Brain Tissue ◽  
Fluorescent Dyes ◽  
Brain Slices ◽  
Brain Regions ◽  
Expression Levels ◽  
Specific Targeting ◽  
The Impact ◽  
Voltage Sensitive Dyes ◽  
The Brain

Voltage sensitive fluorescent dyes (VSDs) are important tools for probing signal transduction in neurons and other excitable cells. These sensors, rendered highly lipophilic to anchor the conjugated pi-wire molecular framework in the membrane, offer several favorable functional parameters including fast response kinetics and high sensitivity to membrane potential changes. The impact of VSDs has, however, been limited due to the lack of cell-specific targeting methods in brain tissue or living animals. We address this key challenge by introducing a non-genetic molecular platform for cell- and molecule-specific targeting of synthetic voltage sensitive dyes in the brain. We employ a dextran polymer particle to overcome the inherent lipophilicity of voltage sensitive dyes by dynamic encapsulation, and high-affinity ligands to target the construct to specific neuronal cells utilizing only native components of the neurotransmission machinery at physiological expression levels. Dichloropane, a monoamine transporter ligand, enables targeting of dense dopaminergic axons in the mouse striatum and sparse noradrenergic axons in the mouse cortex in acute brain slices. PFQX in conjunction with ligand-directed acyl imidazole chemistry enables covalent labeling of AMPA-type glutamate receptors in the same brain regions. Probe variants bearing either a classical electrochromic ANEP dye or state-of-the-art VoltageFluor-type dye respond to membrane potential changes in a similar manner to the parent dyes, as shown by whole-cell patch recording. We demonstrate the feasibility of optical voltage recording with our probes in brain tissue with one-photon and two-photon fluorescence microscopy and define the signal limits of optical voltage imaging with synthetic sensors under a low photon budget determined by the native expression levels of the target proteins. We envision that modularity of our platform will enable its application to a variety of molecular targets and sensors, as well as lipophilic drugs and signaling modulators. This work demonstrates the feasibility of a chemical targeting approach and expands the possibilities of cell-specific imaging and pharmacology.

Author Correction: Neural and sociocultural mediators of ethnic differences in pain (Nature Human Behaviour, (2020), 10.1038/s41562-020-0819-8)

2020 ◽  
Author(s):  
EAR Losin ◽  
CW Woo ◽  
NA Medina ◽  
JR Andrews-Hanna ◽  
Hedwig Eisenbarth ◽  
...  
Keyword(s):  
Ethnic Differences ◽  
Brain Slice ◽  
Brain Slices ◽  
Human Behaviour ◽  
The Brain

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. In the version of this article initially published, in Figs. 3a and 5a the labels on the brain slices labelled NAc should read ‘y = 5’ instead of ‘y = –12’, and in Fig. 3a the label ‘x = 45’ on the top brain slice labeled mFG was missing. The errors have been corrected in the HTML and PDF versions of the article.

Author Correction: Neural and sociocultural mediators of ethnic differences in pain (Nature Human Behaviour, (2020), 10.1038/s41562-020-0819-8)

2020 ◽  
Author(s):  
EAR Losin ◽  
CW Woo ◽  
NA Medina ◽  
JR Andrews-Hanna ◽  
Hedwig Eisenbarth ◽  
...  
Keyword(s):  
Ethnic Differences ◽  
Brain Slice ◽  
Brain Slices ◽  
Human Behaviour ◽  
The Brain

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. In the version of this article initially published, in Figs. 3a and 5a the labels on the brain slices labelled NAc should read ‘y = 5’ instead of ‘y = –12’, and in Fig. 3a the label ‘x = 45’ on the top brain slice labeled mFG was missing. The errors have been corrected in the HTML and PDF versions of the article.

Biochemistry

1936 ◽  
Vol 82 (339) ◽  
pp. 431-433
Author(s):  
J. H. Quastel
Keyword(s):  
Nervous System ◽  
Brain Tissue ◽  
Brain Slice ◽  
Brain Slices ◽  
Ringer Solution ◽  
Living Animal ◽  
Dominant Form ◽  
Straight Line ◽  
The Brain

I want to speak of the work we have been doing in Cardiff on the metabolism of the nervous system. The work was carried out there because of the importance of the narcosis treatment. It seemed to us there a pity that a treatment such as that should be given up because of the considerable toxicity possible in relation to it. The research was undertaken to see if we could diminish the toxicity, at the same time seeking an idea as to how narcotics work. I ask that you will realize that the main substance burned by the brain is glucose. The dominant form of metabolism in the nervous system is connected with the breakdown of glucose and lactic acid, and this can be proved by experiment in the living animal and with brain-tissue in vitro. In doing experiments we are not able to carry out work with human brain, because we cannot get human tissue fresh enough, so we have to carry out experiments with animals. They are carried out in this way. We cut slices of the cortex of the brain as soon as the animal is dead, that is to say, within ten minutes of death the brain is out and slices have been cut. They are placed in a physiological medium in the presence of glucose, and we follow the metabolism of that tissue, which allows us to estimate the amount of oxygen being taken up by the brain. If luminal, chloretone, hyoscine or somnifaine be placed with the brain-tissue, then the respiration, instead of being at the usual level, starts lower down, and maintains a straight line. We wanted to see whether this action is reversible or irreversible. If the latter, then on removing the brain-slices from the narcotic it should no longer behave like a normal piece of tissue. Actually, when the brain-slice is removed and placed in Ringer solution, with no narcotic, the respiration goes up and becomes equal to that shown by the slice which had no narcotic. That is to say, the process is reversible.

scholarly journals A tool for analyzing electrode tracks from slice histology

2018 ◽  
Author(s):  
Philip Shamash ◽  
Matteo Carandini ◽  
Kenneth D Harris ◽  
Nicholas A Steinmetz
Keyword(s):  
Data Analysis ◽  
Brain Slices ◽  
Brain Regions ◽  
Regions Of Interest ◽  
Brain Atlas ◽  
Essential Step ◽  
Pass Through ◽  
Manual Input ◽  
The Brain ◽  
Allen Mouse Brain Atlas

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.

scholarly journals Validation of the Image Registration Technique from Functional Near Infrared Spectroscopy (fNIRS) Signal and Positron Emission Tomography (PET) Image

2020 ◽  
Vol 4 (9) ◽  
pp. 63-69
Keyword(s):  
Positron Emission Tomography ◽  
Infrared Spectroscopy ◽  
Image Registration ◽  
Near Infrared Spectroscopy ◽  
Near Infrared ◽  
Emission Tomography ◽  
Functional Near Infrared Spectroscopy ◽  
Registration Method ◽  
Positron Emission ◽  
The Brain

: Functional near infrared spectroscopy (fNIRS) is an imaging system that can measure hemodynamic changes of the brain. However, the system incapability to measure beyond the brain cortex region make it usage less appealing for in-depth brain studies. To overcome this, many researchers combine fNIRS with other imaging modalities to gain better understanding of the brain activities. In this paper, we described the theory of the registering fNIRS signals and positron emission tomography (PET) image method and performed experiments to validate it. The registration method was validated using specially designed phantom for fNIRS and PET. Polaris system was used to track the position of the phantom which is based on the Polaris markers during fNIRS and PET procedures. The Polaris markers share the same coordinate, thus the fNIRS and PET were calibrated to each other through these markers. To register the fNIRS signal on the PET image, the phantom position in fNIRS coordinate is translated to PET coordinate which allow the probe and the markers being coordinated in PET. Polaris markers were used as the references marker to determine the transformation matrices. The result shows that the fNIRS channel can be viewed on the PET image of the phantom. The transformation error from Polaris to PET is less than 1.00 mm and the precision test is less than 0.1mm while the accuracy is less than 2.8 mm. This result suggests that our theory on the registration method could be used for multimodal image registration between fNIRS and other modalities.

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