scholarly journals Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics

2013 ◽  
Author(s):  
Adam H Marblestone ◽  
Evan R Daugharthy ◽  
Reza Kalhor ◽  
Ian D Peikon ◽  
Justus M Kebschull ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Mouse Brain ◽  
Large Scale ◽  
Fluorescent Microscopy ◽  
Electron Microscopic ◽  
Fixed Tissue ◽  
Isotropic Resolution ◽  
Brain Connectome ◽  
Electron Microscopic Image ◽  
Axon Tracing

We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered: electron microscopic axon tracing, optical imaging of combinatorial molecular markers at synapses, and bulk DNA sequencing of trans-synaptically exchanged nucleic acid barcode pairs. Due to advances in parallel-beam instrumentation, whole mouse brain electron microscopic image acquisition could cost less than $100 million, with total costs presently limited by image analysis to trace axons through large image stacks. Optical microscopy at 50 to 100 nm isotropic resolution could potentially read combinatorially multiplexed molecular information from individual synapses, which could indicate the identifies of the pre-synaptic and post-synaptic cells without relying on axon tracing. An optical approach to whole mouse brain connectomics may be achievable for less than $10 million and could be enabled by emerging technologies to sequence nucleic acids in-situ in fixed tissue via fluorescent microscopy. Novel strategies relying on bulk DNA sequencing, which would extract the connectome without direct imaging of the tissue, could produce a whole mouse brain connectome for $100k to $1 million or a mouse cortical connectome for $10k to $100k. Anticipated further reductions in the cost of DNA sequencing could lead to a $1000 mouse cortical connectome.

scholarly journals Optimization of large-scale mouse brain connectome via joint evaluation of DTI and neuron tracing data

NeuroImage ◽  
2015 ◽  
Vol 115 ◽  
pp. 202-213 ◽  
Author(s):  
Hanbo Chen ◽  
Tao Liu ◽  
Yu Zhao ◽  
Tuo Zhang ◽  
Yujie Li ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Large Scale ◽  
Neuron Tracing ◽  
Brain Connectome ◽  
Joint Evaluation

A New Human Breast Tumor Cell Line

1975 ◽  
Vol 33 ◽  
pp. 388-389
Author(s):  
R.E. Nordquist ◽  
R.M. Wasik ◽  
P.J. Riggs ◽  
P.L. Munson ◽  
F.B. Schafer
Keyword(s):  
Electron Microscopy ◽  
Cell Line ◽  
Calf Serum ◽  
Tumor Cell Line ◽  
Electron Microscopic Examination ◽  
Epithelial Cell Line ◽  
Electron Microscopic ◽  
Fixed Tissue ◽  
Excised Tissue ◽  
Caucasian Female

An infiltrating ductal cell carcinoma was removed from the breast of a postmenopausal Caucasian female. The excised tissue was divided into three parts; one part for electron microscopy, one part for tissue culture and the remainder frozen for immunological studies.The tissue for culture was minced finely with sterile razor blades and cultured in Falcon flasks containing Eagel's MEM supplemented with 10% heat denatured fetal calf serum. The tissue for electron microscopy was fixed in 6.25% glutaraldehyde in 0.1 M PO4 buffer plus 5% sucrose and postfixed in 1% OsO4 in the same buffer. The fixed tissue was dehydrated in graded ethanol and embedded in Spurr.The tissue which was cultured began to grow out after approximately six weeks and became a continuous epithelial cell line which was designated BOT-2 (Breast Original Tumor). Electron microscopic examination revealed that these cells had epithelial characteristics, i.e. the presence of tonofilaments and well formed desmosomes.

scholarly journals Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

2021 ◽  
Author(s):  
Nestor Timonidis ◽  
Alberto Llera ◽  
Paul H. E. Tiesinga
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
Structural Connectivity ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Synaptic Function ◽  
Reticular Nucleus ◽  
Sources Of Information ◽  
Independent Components ◽  
Brain Connectome

AbstractFinding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.

Role of interfacial interactions to control the extent of wrapping of polymer chains on multi-walled carbon nanotubes

RSC Advances ◽  
2016 ◽  
Vol 6 (48) ◽  
pp. 42334-42346 ◽  
Author(s):  
Suchitra Parija ◽  
Arup R. Bhattacharyya
Keyword(s):  
Polymer Chains ◽  
Electron Microscopic ◽  
Α Phase ◽  
Transmission Electron ◽  
Transmission Electron Microscopic ◽  
Electron Microscopic Image ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
Transmission Electron Microscopic Image

Transmission electron microscopic image of separated MWCNTs (N51L15G5) showing the wrapped polymer chains on the MWCNTs surface, which corresponds to the α-phase of the PP.

scholarly journals Cholinergic and serotonergic modulations differentially affect large-scale functional networks in the mouse brain

2015 ◽  
Vol 221 (6) ◽  
pp. 3067-3079 ◽  
Author(s):  
Disha Shah ◽  
Ines Blockx ◽  
Georgios A. Keliris ◽  
Firat Kara ◽  
Elisabeth Jonckers ◽  
...  
Keyword(s):  
Mouse Brain ◽  
Large Scale ◽  
Functional Networks

scholarly journals Deciphering the role of trehalose in hindering antithrombin polymerization

2019 ◽  
Vol 39 (4) ◽  
Author(s):  
Asma Naseem ◽  
Mohammad Sazzad Khan ◽  
Hashim Ali ◽  
Irshad Ahmad ◽  
Mohamad Aman Jairajpuri
Keyword(s):  
Conformational Change ◽  
Large Scale ◽  
Guanidine Hydrochloride ◽  
Microscopic Analysis ◽  
Normal Activity ◽  
Significant Loss ◽  
Coagulation Cascade ◽  
Disulfonic Acid ◽  
Electron Microscopic ◽  
Polymer Formation

Abstract Serine protease inhibitors (serpins) family have a complex mechanism of inhibition that requires a large scale conformational change. Antithrombin (AT), a member of serpin superfamily serves as a key regulator of the blood coagulation cascade, deficiency of which leads to thrombosis. In recent years, a handful of studies have identified small compounds that retard serpin polymerization but abrogated the normal activity. Here, we screened small molecules to find potential leads that can reduce AT polymer formation. We identified simple sugar molecules that successfully blocked polymer formation without a significant loss of normal activity of AT under specific buffer and temperature conditions. Of these, trehalose proved to be most promising as it showed a marked decrease in the bead like polymeric structures of AT shown by electron microscopic analysis. A circular dichroism (CD) analysis indicated alteration in the secondary structure profile and an increased thermal stability of AT in the presence of trehalose. Guanidine hydrochloride (GdnHCl)-based unfolding studies of AT show the formation of a different intermediate in the presence of trehalose. A time-dependent fluorescence study using 1,1′-bi(4-anilino)naphthalene-5,5′-disulfonic acid (Bis-ANS) shows that trehalose affects the initial conformational change step in transition from native to polymer state through its binding to exposed hydrophobic residues on AT thus making AT less polymerogenic. In conclusion, trehalose holds promise by acting as an initial scaffold that can be modified to design similar compounds with polymer retarding propensity.

scholarly journals Investigating structure function relationships in the NOTCH family through large-scale somatic DNA sequencing studies

2020 ◽  
Author(s):  
Michael W J Hall ◽  
David Shorthouse ◽  
Philip H Jones ◽  
Benjamin A Hall
Keyword(s):  
Dna Sequencing ◽  
Structure Function ◽  
Calcium Binding ◽  
Large Scale ◽  
Driver Mutations ◽  
Missense Mutations ◽  
Mutant Selection ◽  
Ligand Interaction ◽  
Binding Interface

AbstractThe recent development of highly sensitive DNA sequencing techniques has detected large numbers of missense mutations of genes, including NOTCH1 and 2, in ageing normal tissues. Driver mutations persist and propagate in the tissue through a selective advantage over both wild-type cells and alternative mutations. This process of selection can be considered as a large scale, in vivo screen for mutations that increase clone fitness. It follows that the specific missense mutations that are observed in individual genes may offer us insights into the structure-function relationships. Here we show that the positively selected missense mutations in NOTCH1 and NOTCH2 in human oesophageal epithelium cause inactivation predominantly through protein misfolding. Once these mutations are excluded, we further find statistically significant evidence for selection at the ligand binding interface and calcium binding sites. In this, we observe stronger evidence of selection at the ligand interface on EGF12 over EGF11, suggesting that in this tissue EGF12 may play a more important role in ligand interaction. Finally, we show how a mutation hotspot in the NOTCH1 transmembrane helix arises through the intersection of both a high mutation rate and residue conservation. Together these insights offer a route to understanding the mechanism of protein function through in vivo mutant selection.

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