Commit 64c95478 authored by Matthieu Gobin's avatar Matthieu Gobin
Browse files

Merge branch 'master' into 'matthieu.gobin-master-patch-55947'

# Conflicts:
#   frozen/c80y-2k58.md
parents 70895f14 d8331ddc
*.webm filter=lfs diff=lfs merge=lfs -text
*.mp4 filter=lfs diff=lfs merge=lfs -text
......@@ -42,4 +42,4 @@ gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
# Performance-booster for watching directories on Windows
gem "wdm", "~> 0.1.1" if Gem.win_platform?
gem 'jekyll-spaceship', "0.6.0"
gem 'jekyll-spaceship', "0.10.0"
......@@ -43,8 +43,8 @@ plugins:
- jekyll-feed
- jekyll-paginate-v2
- jekyll-theme-lcsb-frozen-components
- jekyll-redirect-from
- jekyll-spaceship
# Produces a cleaner folder structure when using categories
permalink: /:year/:month/:title.html
......@@ -62,6 +62,10 @@ pagination:
before: 2
after: 2
jekyll-spaceship:
processors:
- media-processor
# Exclude from processing.
# The following items will not be processed, by default. Create a custom list
# to override the default setting.
......
......@@ -43,3 +43,7 @@ This website is under version control on the [LCSB Gitlab](https://gitlab.lcsb.u
* **[Functional meta-omics provide critical insights into long and short read assemblies]({{ "frozen/sgzt-ad12" | relative_url }})**
* **[Protein Relative Abundance Quantification Algorithm for 3d fluorescent images from tissue]({{ "frozen/PRAQA" | relative_url }})**
* **[Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene]({{ "frozen/1yzp-qv41" | relative_url }})**
* **[ A "two-hit" pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain]({{ "frozen/77zg-bc41" | relative_url }})**
---
layout: default
order: -1
title: "Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene"
permalink: /frozen/1yzp-qv41
---
{% rtitle Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene %}
Jennifer Modamio, Cláudia Saraiva, Gemma Gomez-Giro, Sarah Nickels, Javier Jarazo, Paul Antony, Silvia Bolognin, Peter Barbuti, Rashi Halder, Christian Jäger, Rejko Krueger, Enrico Glaab, Jens Schwamborn
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Manuscript %}
A preprint of the manuscript is available <a href="">here</a>.
{% endrblock %}
{% rblock Data %}
The data is available <a href="https://webdav-r3lab.uni.lu/public/data/1yzp-qv41/">here</a>.
{% endrblock %}
{% rblock source code %}
The source code is available <a href="https://github.com/LCSB-DVB/Modamio_2021">here</a>.
{% endrblock %}
{% endrgridblock %}
---
layout: default
order: -1
title: A two-hit pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain
permalink: /frozen/77zg-bc41
---
{% rtitle A "two-hit" pharmacological seizure model in zebrafish for studying microglia dynamics in the developing epileptic brain %}
Teresa G. Martins, Remon Soliman, Cristina Donato, Maria Lorena Cordero-Maldonado, Corrado Ameli, Laurent Mombaerts, Alexander Skupin, Francesca Peri, Alexander D. Crawford
Epilepsy is a chronic brain disorder characterized by unprovoked and recurrent seizures, of which 60% are of unknown etiology. Recent studies implicate microglia in the pathophysiology of epilepsy. However, their role in this process, e.g. following early-life seizures, remains poorly understood in part due to the lack of suitable experimental models allowing the in vivo imaging of microglial activity using minimally-invasive techniques. Given the advantage of zebrafish larvae for such imaging approaches, we sought to develop a "two-hit" pharmacological seizure model in zebrafish suitable for studying microglia response after acute seizures. Towards this end, different concentrations of kainate were microinjected intravenously into 3 days post-fertilization transgenic zebrafish larvae with mCherry-labeled microglia followed by acute incubation with pentylenetetrazole at 5 days post-fertilization. Kainate-treated larvae exhibited increased numbers of microglia in the brain, and were more susceptible to subsequent pentylenetetrazole-induced seizures, as shown by higher locomotor and encephalographic activity as compared to vehicle-injected larvae. These results are comparable to experimental kainate-induced rodent seizure models and suggest the suitability of our model for future studies. Such studies could contribute to elucidate microglial dynamic changes after seizure induction in the developing brain, and to understand how these modulate seizure susceptibility later in life.
{% endrtitle %}
{% rblock Videos %}
**Videos demonstrating the phenotypes after KA injection.**
![](assets/77zg-bc41/S1File_Video_PBS-injected.mp4?preload=auto)
3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with PBS. The video shows that all the larvae display normal behavior and respond to touch (escape response) upon a soft tail touch with a fine pointer.
![](assets/77zg-bc41/S1File_Video_0.25mM-KA-injected.mp4?preload=auto)
3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 0.25 mM KA. The video shows that for some larvae only there is occasional mild whole-body trembling and no escape response upon a soft tail touch with a fine pointer.
![](assets/77zg-bc41/S1File_Video_0.5mM-KA-injected.mp4?preload=auto)
3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 0.5 mM KA. The video shows that all larvae display occasional whole-body trembling and movement. Additionally they do not respond to touch (escape response) upon a soft tail touch with a fine pointer.
![](assets/77zg-bc41/S1File_Video_1mM-KA-injected.mp4?preload=auto)
3 days post-fertilization larvae from the line *Tg(csf1r:Gal4)i186; Tg(UAS.nfsB.mCherry)i149* outcrossed to *nac<sup>w2</sup>* after systemic injection with 1 mM KA. The video shows that all larvae have occasional whole-body trembling and do not respond to a soft tail touch with a fine pointer.
{% endrblock %}
---
layout: default
order: -1
title: "Single cell transcriptomics of human iPSC differentiation dynamics reveal a core network of Parkinson’s disease"
permalink: /frozen/cca2-s098
---
{% rtitle Single cell transcriptomics of human iPSC differentiation dynamics reveal a core network of Parkinson’s disease %}
Gabriela Novak, Dimitrios Kyriakis, Kamil Grzyb, Michela Bernini, Sophie Rodius, Gunnar Dittmar, Steven Finkbeiner, and Alexander Skupin
permalink: [doi:10.17881/cca2-s098](https://doi.org/10.17881/cca2-s098)
{% endrtitle %}
{% rgridblock a-unique-id %}
{% rblock Proteomics data %}
The Proteomics data is available <a href="https://www.ebi.ac.uk/pride/">here</a>.
{% endrblock %}
{% rblock scRNAseq data %}
The data is available <a href="https://www.ncbi.nlm.nih.gov/geo/">here</a>
{% endrblock %}
{% rblock source code %}
The source code is available <a href="https://gitlab.lcsb.uni.lu/dimitrios.kyriakis/ipscs_pink1/">here</a>.
{% endrblock %}
{% endrgridblock %}
---
layout: default
order: -1
title: "PRAQA: Protein Relative Abundance Quantification Algorithm for 3D Fluorescent Images from Tissue"
title: "PaFSe: a Parameter Free Segmentation Approach for 3D Fluorescent Images"
permalink: /frozen/PRAQA/
---
......@@ -10,19 +10,8 @@ permalink: /frozen/PRAQA/
{% rtitle Protein Relative Abundance Quantification Algorithm for 3D Fluorescent Images from Tissue %}
Corrado Ameli, Sonja Fixemer, David Bouvier, Alexander Skupin.
In confocal fluorescent microscopy, the quality of the acquisition strongly depends on diverse factors including
the microscope parameterization, the light exposure time, the type and concentration of the antibodies used,
the thickness of the sample and the degradation of the biological tissue itself. All these factors critically
influence the final result and render tissue protein quantification challenging due to intra- and inter-sample
variability. Therefore, image processing techniques need to address the acquisitions variability to minimize the
risk of bias coming from changes in signal intensity, noise and parameterization. Here, we introduce Protein
Relative Abundance Quantification Algorithm (PRAQA), a 1-parameter based, fast and adaptive approach for
quantifying protein abundance in 3D fluorescent-immunohistochemistry stained tissues that requires no image
preprocessing. Our method is based on the assessment of the global pixel intensity neighborhood dispersion
that allows to statistically infer whether each small region of an image can be considered as positive signal
or background noise. We benchmark our method with alternative approaches from literature and validate its
applicability and efficiency based on synthetic scenarios and a real-world application to post-mortem human
brain samples of Alzheimer’s Disease and Lewy Body Dementia patients.
In confocal fluorescent microscopy, the quality of the acquisition depends on several factors including the microscope parameterization, the light exposure time, the type and concentration of the antibodies used, the thickness of the sample and the tissue degradation. Due to these factors, intra-sample and inter-sample variability inevitably arises. Protein segmentation and quantification can thus become a challenging process. Therefore, image processing techniques need to address the acquisitions variability to minimize the risk of bias coming from changes in signal intensity, background noise and parameterization.
permalink: [doi:10.17881/j20h-pa27](https://doi.org/10.17881/j20h-pa27)
{% endrtitle %}
......@@ -33,7 +22,7 @@ permalink: [doi:10.17881/j20h-pa27](https://doi.org/10.17881/j20h-pa27)
{% rblock source code %}
The source code for the program is available on [Github](https://github.com/CorradoAmeliLU/PRAQA).
The source code for the program is available on [Github](https://github.com/CorradoAmeliLU/PaFSe).
{% endrblock %}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment