Ulrich Elling
@ulielling.bsky.social
Molecular Biology, SARS-CoV-2, science communication, sanity, evidence based decision making. Living in Austria.
Die Zeichen stehen auf Covid-Sommerwelle (was auch immer das heisst).
Die relevanten Varianten sind XFG und NB.1.8.1. Leider macht das Abwassermonitoring-Dashboard seit eineinhalb Jahren nur noch auf blau.
abwassermonitoring.at/dashboard/
Die relevanten Varianten sind XFG und NB.1.8.1. Leider macht das Abwassermonitoring-Dashboard seit eineinhalb Jahren nur noch auf blau.
abwassermonitoring.at/dashboard/
May 26, 2025 at 6:41 AM
Die Zeichen stehen auf Covid-Sommerwelle (was auch immer das heisst).
Die relevanten Varianten sind XFG und NB.1.8.1. Leider macht das Abwassermonitoring-Dashboard seit eineinhalb Jahren nur noch auf blau.
abwassermonitoring.at/dashboard/
Die relevanten Varianten sind XFG und NB.1.8.1. Leider macht das Abwassermonitoring-Dashboard seit eineinhalb Jahren nur noch auf blau.
abwassermonitoring.at/dashboard/
So endet derzeit der Radweg am Rennweg aus dem 10. Bezirk kommend an der Grenze zum 3. Bezirk kurz vor mehreren Universitäten und Forschungsinstituten, wo viele Menschen mit dem Rad kommen.
April 12, 2025 at 6:37 AM
So endet derzeit der Radweg am Rennweg aus dem 10. Bezirk kommend an der Grenze zum 3. Bezirk kurz vor mehreren Universitäten und Forschungsinstituten, wo viele Menschen mit dem Rad kommen.
This image I recently took sort of reflects all too many comments on X.
And yes, it stinks of rotten fish…
Glad you are all here now!
And yes, it stinks of rotten fish…
Glad you are all here now!
December 29, 2024 at 2:21 PM
This image I recently took sort of reflects all too many comments on X.
And yes, it stinks of rotten fish…
Glad you are all here now!
And yes, it stinks of rotten fish…
Glad you are all here now!
This allowed us to map the in vivo essentialome of therapy resistant melanoma next to the cell culture model and uncovered many genetic dependencies, that only hold true in vivo. Oxidative phosphorylation e.g. is a strong genetic dependency only in vivo.
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December 16, 2024 at 12:28 PM
This allowed us to map the in vivo essentialome of therapy resistant melanoma next to the cell culture model and uncovered many genetic dependencies, that only hold true in vivo. Oxidative phosphorylation e.g. is a strong genetic dependency only in vivo.
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With this we dared a genome wide screen in a cell line with particularly poor engraftment ability. And sure enough conventional screening failed completely at a complexity of <2cells/sgRNA, but CRRISPR-StAR delivered and nicely separated positive and negative controls.
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December 16, 2024 at 12:26 PM
With this we dared a genome wide screen in a cell line with particularly poor engraftment ability. And sure enough conventional screening failed completely at a complexity of <2cells/sgRNA, but CRRISPR-StAR delivered and nicely separated positive and negative controls.
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POC experiments in vitro showed the power of this approach. At 1000 cells per sgRNA conventional screening paradigms work very well. Of course! But as you go down e.g. to 4 cells/sgRNA it’s a mess.
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December 16, 2024 at 12:25 PM
POC experiments in vitro showed the power of this approach. At 1000 cells per sgRNA conventional screening paradigms work very well. Of course! But as you go down e.g. to 4 cells/sgRNA it’s a mess.
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This controls for intrinsic and extrinsic heterogeneity. It further samples only the desired cell type and time as editing is controlled by CreERT induction. That’s all possible by intercalated loxP sites and Stochastic Activation by Recombination: CRISPR-StAR
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December 16, 2024 at 12:14 PM
This controls for intrinsic and extrinsic heterogeneity. It further samples only the desired cell type and time as editing is controlled by CreERT induction. That’s all possible by intercalated loxP sites and Stochastic Activation by Recombination: CRISPR-StAR
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For example upon engraftment in an experimental xenograft setting, half of the cells of a clonal population will activate the sgRNA while the other half will remain inactive. As phenotypes manifest, the salt-and-pepper control population will experience all the same complex biology.
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December 16, 2024 at 12:14 PM
For example upon engraftment in an experimental xenograft setting, half of the cells of a clonal population will activate the sgRNA while the other half will remain inactive. As phenotypes manifest, the salt-and-pepper control population will experience all the same complex biology.
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Now all ingredients were ready to build an entirely new paradigm of CRISPR screening. Instead of comparing sgRNA abundance to the historical control of before phenotypes manifest, we run an internal control population.
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December 16, 2024 at 12:13 PM
Now all ingredients were ready to build an entirely new paradigm of CRISPR screening. Instead of comparing sgRNA abundance to the historical control of before phenotypes manifest, we run an internal control population.
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Last piece in the puzzle: We needed a much better sgRNA prediction algorithm to empower CRISPR screening in vivo. We also developed that by implementing target protein features to sgRNA design.
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www.nature.com/articles/s41...
9/
www.nature.com/articles/s41...
December 16, 2024 at 12:11 PM
Last piece in the puzzle: We needed a much better sgRNA prediction algorithm to empower CRISPR screening in vivo. We also developed that by implementing target protein features to sgRNA design.
9/
www.nature.com/articles/s41...
9/
www.nature.com/articles/s41...
We then developed inducible sgRNAs to allow for controlling of gene editing activity. This system allowed for inducing as well as inactivating of sgRNAs to enable e.g. time-controlled sequential editing.
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www.nature.com/articles/s41...
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www.nature.com/articles/s41...
December 16, 2024 at 12:10 PM
We then developed inducible sgRNAs to allow for controlling of gene editing activity. This system allowed for inducing as well as inactivating of sgRNAs to enable e.g. time-controlled sequential editing.
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www.nature.com/articles/s41...
8/
www.nature.com/articles/s41...
Yet if we want to truly understand biology, we need to embrace its complexity by studying it in it’s native environment. You will not understand the function of the parts of a sailboat unless you study it in it’s native environment.
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December 16, 2024 at 12:06 PM
Yet if we want to truly understand biology, we need to embrace its complexity by studying it in it’s native environment. You will not understand the function of the parts of a sailboat unless you study it in it’s native environment.
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The challenge with pooled genetic CRISPR screening is that every guide RNA must be assayed hundreds to thousands of times in parallel to obtain reproducible results. But in vivo very few cells will transduce/engraft resulting in a bottleneck of 1000-10000 cells.
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December 16, 2024 at 12:04 PM
The challenge with pooled genetic CRISPR screening is that every guide RNA must be assayed hundreds to thousands of times in parallel to obtain reproducible results. But in vivo very few cells will transduce/engraft resulting in a bottleneck of 1000-10000 cells.
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Pooled CRISPR screening has revolutionized functional genomics as we accumulate causative genotype-phenotype linkeage. Yet, that data stems almost exclusively from 2D cell culture, a condition creating reproducibility by reducing the complexity of biology.
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December 16, 2024 at 12:04 PM
Pooled CRISPR screening has revolutionized functional genomics as we accumulate causative genotype-phenotype linkeage. Yet, that data stems almost exclusively from 2D cell culture, a condition creating reproducibility by reducing the complexity of biology.
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Interested in the lineages driving this? Well, it’s 50 shades of black…
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December 10, 2024 at 7:44 PM
Interested in the lineages driving this? Well, it’s 50 shades of black…
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Here we go again, national sewage monitoring detects a rise of SARS-CoV-2. Not at all dramatic yet, but starting.
abwassermonitoring.at/dashboard/
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abwassermonitoring.at/dashboard/
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December 10, 2024 at 7:42 PM
Here we go again, national sewage monitoring detects a rise of SARS-CoV-2. Not at all dramatic yet, but starting.
abwassermonitoring.at/dashboard/
1/2
abwassermonitoring.at/dashboard/
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Schwarz-Rot-Pink bleibt auch für AI ungreifbar wie mir scheint. Aber die Hoffnung stirbt zuletzt, vielleicht sehen wir ja doch noch den Mut zu überfälligen Entscheidungen: Pensionen, Klima, Föderalismus, Bürokratieabbau, Neutralität, ... Themen gibt es genug! Danach gerne Party wie im Moulin Rouge!
November 18, 2024 at 8:11 AM
Schwarz-Rot-Pink bleibt auch für AI ungreifbar wie mir scheint. Aber die Hoffnung stirbt zuletzt, vielleicht sehen wir ja doch noch den Mut zu überfälligen Entscheidungen: Pensionen, Klima, Föderalismus, Bürokratieabbau, Neutralität, ... Themen gibt es genug! Danach gerne Party wie im Moulin Rouge!
Upload of SARS-CoV-2 sequences from France today. Based on current data, growth of the Pirola sublineage JN.1 is remarkable. This is relative growth, fraction still small, soon dominant.
Add that to the absolute growth of SARS-CoV-2 right now and you know what's brewing. #winteriscoming
Add that to the absolute growth of SARS-CoV-2 right now and you know what's brewing. #winteriscoming
October 24, 2023 at 8:21 PM
Upload of SARS-CoV-2 sequences from France today. Based on current data, growth of the Pirola sublineage JN.1 is remarkable. This is relative growth, fraction still small, soon dominant.
Add that to the absolute growth of SARS-CoV-2 right now and you know what's brewing. #winteriscoming
Add that to the absolute growth of SARS-CoV-2 right now and you know what's brewing. #winteriscoming
France is a good place to compare relative fitness of Pirola clan members with each other as they are all around and sequencing is still decent. For now JN.1 still appears as the fastest, no surprise. It combines one of the FLip mutations as in HK.3 and others with the Pirola backbone.
October 16, 2023 at 1:44 PM
France is a good place to compare relative fitness of Pirola clan members with each other as they are all around and sequencing is still decent. For now JN.1 still appears as the fastest, no surprise. It combines one of the FLip mutations as in HK.3 and others with the Pirola backbone.
Let's get started in the new universe by a reminder of the most pressing problem.
October 8, 2023 at 10:36 AM
Let's get started in the new universe by a reminder of the most pressing problem.