@LabTakagi

Synthetic and structural biology- newly minted cryoEM expert- Indiana University School of Medicine “That’s not exactly my 2D projection but close”

Joined March 2019
  • Tweets102
  • Following232
  • Followers185
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1/2: Publication Announcement! In a new manuscript published in Nature Communications, Dr. Yuichiro Takagi @LabTakagi and collaborators used Cryo-EM to reveal the catalytic mechanism of Human Asparagine Synthetase (ASNS): nature.com/articles/s41467-0…

3D variability analysis reveals a hidden conformational change controlling ammonia transport in...

Nature Communications - Working on human asparagine synthetase, Coricello et al show that combining 3D variability analysis (3DVA) of cryo-EM data with MD simulations is a valid approach to study...

nature.com
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Working on ASNS, authors from @LabTakagi @WenZhu_Lab and colaborators combine cryo-EM 3D variability analysis with MD simulations to study conformation of amino acid side chains. nature.com/articles/s41467-0…
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Matthijn Vos is evaluating student grids at the ⁦@cshlcourses⁩ cryo-em course. He is a tough judge - a lot of 0/10 grids! ⁦@LanderLab⁩ ⁦@Jen_Cash_11⁩
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can't wait to join in on the 🔥🔥🔥 #cryoEM program led by @yifan_ucsf and superstars @mcianfro @mimi1inh @fitzpatricklab @davidwtaylor @YuanHe_NWU @Mel_Ohi_Lab @AlexisRohou @BrentNannenga Anchi and more at #ACA2023.. 'American Cryo-EM Association'!! 😂
Chi-Min Ho@mimi1inh7 Jul 2023
Packed house for the Advanced Topics in #CryoEM & #CryoET Workshop today #ACA2023!!! Awesome #CryoEM line-up this morning, with exciting talks from @davidwtaylorjr @therickybaker & @FitzpatrickLab!! ❄️🔬 Stay tuned for the stellar #teamtomo line-up on deck after lunch!! ♥️❄️🔬
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We are delighted to share our work, now available in @Nature: nature.com/articles/s41586-0… Our scoring system can be accessed here: kinase-library.phosphosite.o… Coming soon --> the tyrosine kinome and an improved system with many new functionalities & features! #TheKinaseLibrary #KL

An atlas of substrate specificities for the human serine/threonine kinome

Nature - Analysis of the kinase activity of 300 protein Ser/Thr kinases reveals that the substrate specificity of the kinome is substantially more diverse than expected and is driven extensively by...

nature.com
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Takagi_Lab retweeted
Lander Lab@LanderLab7 Nov 2022
Finally able to kick off the @CSHL cryoEM course originally scheduled for March 2020! It’s great to be back
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🔥hot off the press from the @kellogg_liz lab 🔥 We report the first cryo-EM structure of a CAST catalytic component, commonly called the transposase. In the V-K CAST system this component is named TnsB, published this week in PNAS! (1/9) pnas.org/doi/full/10.1073/pn…
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Takagi_Lab retweeted
biohub
@biohub26 Jul 2022
We’re excited to announce that David Agard, Bridget Carragher + Clint Potter have joined our new @ChanZuckerberg Imaging Institute to bring together scientists and engineers to develop new cryoelectron microscopy imaging hardware and software 🧵czi.co/ImagingInstitute

Biohub

Our mission is to cure or prevent all disease.

biohub.org
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New Pikaard lab paper, showing how alternative dicing patterns are programmed for maximal siRNA-directed DNA methylation, just published in eLife. Kudos to former PhD students Loffer and Singh and postdocs Fukudome, Mishra and Wang doi.org/10.7554/eLife.73260

A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed...

Double-stranded precursors of siRNAs involved in RNA-directed DNA methylation have initiating sequences and overhangs imparted by the RNA polymerases that synthesize them, programming alternative...

elifesciences.org
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Here's more on Pol IV-RDR2 coupling, highlighted by the spectacular new Science paper from the Zhang lab and new PNAS paper by Fukudome et al. in my lab. Here is our version of the model for how Pol IV arrest and backtracking enables RDR2 synthesis of the 2nd RNA strand.
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'Making #cryoEM grids' - add your sample and hope for the best😅😬
Farbod Saraf@farbodsaraf18 Jun 2020
The surface tension of water and flower petals xitter.cf/ThespaceAcad/status/12…
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Takagi_Lab retweeted
Lander Lab@LanderLab22 May 2020
We'd put an exclamation mark in the title as well! Really impressive work from the Stark group - single particle #cryoEM closing in on 1 Å resolution! (and so happy we can finally tweet about it @HaselbachLab 😉) biorxiv.org/content/10.1101/…
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I couldn't be prouder and happier to be part of the #Conawaylab family and join this amazing #zoomsurprisebirthdayparty today to celebrate Joan's #birthday and scientific life achievements! #scientificlegacy #NatlAcadofSciences #StowersInstitute #WomenInScience
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Since everyone is talking about #nCoV19 #nCoV2019 #COVID2019 #SARSCoV2, I though I would look at some of the cryo-EM structures (since that's what I do :). I made an animation comparing the recent maps from @veeslerlab, also aligning an X-ray map of the receptor
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Takagi_Lab retweeted
Lander Lab@LanderLab16 Mar 2020
If anyone is collecting the data at 200 keV email me. 😜
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Takagi_Lab retweeted
Alice Ting
@aliceyting9 Dec 2019
Directed evolution of “ultraTEV”, a faster variant of the biotechnological workhorse TEV protease, is out in Nature Methods. Tour de force by super-talented postdoc Mateo I Sanchez. Plasmids will be up on Addgene soon! nature.com/articles/s41592-0…

Directed evolution improves the catalytic efficiency of TEV protease

Nature Methods - An optogenetic strategy enables selection of proteases with improved catalytic rates. The developed TEV protease variants are well suited for biotechnology applications, including...

nature.com
Nature Methods@naturemethods9 Dec 2019
Interested in developing or using better proteases? @aliceyting Alice Ting's lab has developed a platform for evolving proteases and used it to improve the catalytic efficiency of TEV protease. nature.com/articles/s41592-0…
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Takagi_Lab retweeted
Lander Lab@LanderLab4 Dec 2019
Accepting applications for the 2020 Cryo-EM course at Cold Spring Harbor Lab @CSHL! 2 weeks of hands-on training in sample prep, microscope alignment, data collection, and processing - with @Mel_Ohi_lab, @kollmanlab, @MatthijnVos, and invited instructors. meetings.cshl.edu/courses.as…

Cryoelectron Microscopy (canceled)

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu
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Takagi_Lab retweeted
KaelinLab@kaelin_lab7 Oct 2019
There he is!!!!! What a day!
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Sad to hear of the passing of Kiyoshi Nagai, a leader in the structural biology of splicing for more than 30 years. He taught us all so much. www2.mrc-lmb.cam.ac.uk/group…
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Our new pre-print about Fanconi Anemia-independent ICL repair is live on bioRxiv. This is a collabo between us, the Takagi lab at IUSM, and Sua Myong's group at Johns Hopkins. disq.us/t/3icna1o
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