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Blog.

AT people, technology, science, ideas, images

Volume EM of Myelin

17/1/2024

1 Comment

 
Mark:
   This volume EM study of myelin could only have been done by array tomography!   We searched low resolution volume EM images of mouse spinal cord to find the initial segment of motor neurons. We then re-imaged the sections to obtain high resolution data of the unpaired myelin para-node at the distal edge of the axon initial segment.  In newborn mice, the organization resembles the paranodes of nodes of Ranvier. However, in 3 month old mice, approximately half of the paranodes at the initial segment were modified.  Some examples were found in the process of re-modeling. They showed a glial cell breaking the contacts between the paranodal loops and axolemma, and that the inner tongue subsequently extended a process underneath the original loops and formed new loops.
   Furusho, M., and Terasaki, M.  2024.  Evidence for glia-mediated, age-dependent remodeling of myelin at the axon initial segment.  J. Comparative Neurology (in press). ​
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1 Comment

Antibodies!

22/12/2023

0 Comments

 
Kristina:
   It took more than 10 years, but our study on validating antibodies for AT (and for postembedding immunolabeling in general) is finally out! Including a long list of antibodies that we tested for AT - both the ones that worked and the ones that didn't.
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses
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AT & ET

11/10/2023

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Martina:
   We developed a hybrid approach that combines the strengths of AT and ET (electron tomography). Thanks so much to our collaborators for making this possible! Check out our preprint to find out which role a marker pen (“edding”) plays in this approach that we call ‘ATUM-Tomo’:
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vem gordon research conference - part 2

28/7/2023

4 Comments

 
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Kristina:
   Emails, zoom calls, twitter, slack, gather town… - most of us had already met each other one way or another. But meeting in person was so much better! There were the obvious inconsequential things we had missed in our online interactions (“I didn’t realize you were so tall!”), but way more important was the full human presence, as online media can still convey only small fragments of it. The conference was superbly organized, I learned a lot, and thoroughly enjoyed it throughout!
   Some observations: the most popular organelle highlighted in quite a few talks was the cilium (I can’t resist taking pictures of it either), followed closely by mitochondria! And, I have to admit, I didn’t know that mitochondria can also be found in some dendritic spines of neurons, even though I’ve been working with spines for ages now.
   As for array tomography, we had a good showing! About a quarter of the talks had AT in one form or another. It was interesting that molecular information, when available, was often obtained before embedding and sectioning (pre-embedding). As far as I remember, only one talk (mine) had the classical post-embedding AT immunolabeling. Which makes me think that a combination of pre-embedding for some antibodies and post-embedding for others, may turn out to be the most flexible and convenient approach. There are a few proteins where all the antibodies that I’ve tested refuse to work on resin sections – it is about time to try pre-embedding for these targets.
   There were many new cool things that we heard and saw. But I was surprised at how many already published works I had missed. Here are several on sample preparation and sectioning:
Help with finding and trimming the region of interest:
Meechan_schwab 2022
Automated large volume sample preparation:
Stempinski_López 2023
Working with human brain tissue: brain pH is a very good indicator of autopsy tissue quality:
Glausier_Lewis 2019
Human biopsy tissue sample preparation:
Karlupia_lichtman 2023
X-ray and AT?
Dr. Alexandra Pacureanu presented impressive studies using the European Synchrotron. It could be very useful to combine with AT and image much larger volumes with lower resolution, and also do elemental analysis.
​Examples:

Myelin looks great! (with 3D synchrotron X-ray nano-holotomography):
Dahlin_Bech 2020
Andersson_Dyrby 2020
4 Comments

vem gordon research conference

22/7/2023

0 Comments

 
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Mark:
   I enjoyed meeting many people for the first time. Although zoom is great, it is nothing compared to in person! So it was very good to meet Naomi and Jemima from our AT group.  I met several people that I knew only from the literature, and met several promising young people and some useful commercial vendors.  Half or more of the people at the meeting were from Europe - there is a lot happening there!
  It was useful for me to get exposed to widely used software like webknossos, napari, microscopy image browser, empanada, etc. Although I have my own (imperfect) solutions to handling big data, it's great to know that there are alternatives are constantly being developed. 
   I saw lots of impressive computer simulations but I came away with the general impression that there are lots of things to be discovered in biology by volume EM!  Fib-SEM is moving forward fast, and it is the method of choice for certain kinds of subjects / problems.  But I also came away with the conviction that array tomography / ATUM tape collector has its place.  The capabilities for re-imaging and localization of molecules are big advantages. 
   As for work that we can mention, I had a nice talk with Xiaomeng Han from the Lichtman lab about preserving extracellular space in the brain, and pre-embedding labeling of brain with single chain antibodies: 
Lu_lichtman 2023
han_Lichtman 2023
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July 11th, 2023

11/7/2023

0 Comments

 
Martina:
   Our study on the correlation of Spatial Transcriptomics and AT is online: rdcu.be/dgAIU
Grateful for a great collaborative effort!
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elmi 2023 Noordwijkerhout

14/6/2023

0 Comments

 
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Martina:
   Announcing our CZI AT initiative at ELMI 2023 in Noordwijkerhout. Hope to infect the light microscopy and CLEM community with AT!
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neurons on tape

6/2/2023

0 Comments

 
Martina:
   Glad to be part of the latest Methods in Cell Biology edition on volume EM. Check out our chapter on ATUM, where we review this approach, provide a step-by-step protocol and show its application for imaging amyloid plaques in an Alzheimer's mouse model.
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CZI Grant

25/1/2023

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Get your diamond knives ready! The Array Tomography Training and Network received funding from the Chan Zuckerberg Initiative for Advancing Imaging Through Collaborative Projects. Thank you! We will be working to develop workshops and an online hub for array tomography - both light and electron microscopy. 
Check this space to access the resources that we put together and to learn about new technological developments and new science enabled by array tomography.

czi announcement
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