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Pratheek Pandesha

@hadse.bsky.social
166 followers 88 following 1 posts

PhD Candidate @Slotkin_Lab @WUSTLdbbs @DanforthCenter🌱 | @GenScientists | #Epigenetics #Plantbiology

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Reposted by Pratheek Pandesha
Post-transcriptional Gene Regulation in Plants - PGRP2026 @pgrp2026.bsky.social · 04/06/2026
⚠️ Last call for #PGRP2026! Tomorrow (5 June) is the final day to: 🎤 Submit an abstract for consideration for an oral presentation 🎟️ Register at the early bird rate If you've been meaning to register or submit your work, now is the time! 🌱 See you at #PGRP2026
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Reposted by Pratheek Pandesha
Sunil Kenchanmane Raju @kenchanmane.bsky.social · 01/02/2026
We’re #hiring a #postdoc @ucriverside.bsky.social 🌿 Work on cis-regulatory evolution, gene family diversification, and cell-type-specific climate responses using single-cell and comparative genomics - kenchanmanelab.com/research/ Deadline: Feb 5, 2026 Apply: aprecruit.ucr.edu/apply/JPF02058
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bioRxivpreprint @biorxivpreprint.bsky.social · 01/02/2026
Genome Position Does Not Impact Transgene Expression Efficiency in the Ancient Red Alga Cyanidioschyzon merolae www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 17/12/2025
RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing www.biorxiv.org/content/10.64898/20…
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Julius Brennecke @juliusbrennecke.bsky.social · 22/12/2025
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.
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Claudia Köhler @claudiakohler11.bsky.social · 14/04/2025
Excited about the future of plant epigenetics? Join us at the Keystone Symposium Plant Epigenetics & Epigenome Engineering in Fort Collins, October 13-16, 2025! keystonesymposia-19559593.hs-sites.com/%F0%9F%8C%BF... Registration is open! #PlantScience #Epigenetics #KeystoneSymposia
keystonesymposia-19559593.hs-sites.com
🌿 Join Us for Plant Epigenetics in Fort Collins! 🌿
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Reposted by Pratheek Pandesha
jlawlab.bsky.social @jlawlab.bsky.social · 11/12/2025
Have you ever wondered how new DNA methylation patterns are established? Paradigm shift ahead! We discovered a new mode of DNA methylation targeting in plants that relies on transcription factors and sequence motifs rather than chromatin modifications to regulate the methylome. rdcu.be/eQ6L5 1/8
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jlawlab.bsky.social @jlawlab.bsky.social · 11/12/2025
And this great Nature Plants News & Views by Pandesha and Slotkin covering this breakthrough discovery www.nature.com/articles/s41... @hadse.bsky.social @KeithSlotkin @natplants.nature.com 8/8
nature.com
Transcription factor-mediated recruitment of small interfering RNA production - Nature Plants
Decades of research in plants has established that the protein complexes that transcribe small interfering RNAs (siRNAs) are not targeted to DNA in a sequence-specific manner. Two independent studies ...
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Reposted by Pratheek Pandesha
Hannes Stark @hannes-stark.bsky.social · 26/10/2025
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
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Elise Kerdoncuff @ekerdoncuff.bsky.social · 26/06/2025
Our paper out today: 50,000 years of evolutionary history of India: Impact on health and disease variation: Cell www.cell.com/cell/fulltex...
cell.com
50,000 years of evolutionary history of India: Impact on health and disease variation
A genomic study of 2,762 individuals from India offers important insights into the genomic diversity and evolutionary history of the subcontinent and highlights the extensive genetic variation, gene f...
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Reposted by Pratheek Pandesha
Donald Danforth Plant Science Center @danforthcenter.bsky.social · 17/07/2025
It’s back! Our annual night of fun and fundraising, Party with the Plants, is September 26. 🌺 Theme is “Plants in Paradise.” 🍍 Discounted tickets on sale now: bit.ly/4kXoRSn #STLEvents #PartyWithThePlants
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Donald Danforth Plant Science Center @danforthcenter.bsky.social · 14/07/2025
Spearhead Bio, a Danforth Technology Company startup, has received a grant from NSF that will allow them to fast-track their breakthrough genome engineering technology to develop corn varieties equipped for ag’s biggest challenges. Read more: loom.ly/zHfitlo
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Rodrigo Reis @rodrigoreislab.com · 13/07/2025
Very useful tool to map TDNA insertion site using RNAseq data genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com
T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data - Genome Biology
Agrobacterium-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into th...
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Chenxin Li, PhD @chenxinli2.bsky.social · 11/07/2025
Has anyone tried RUBY in a fungus?
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Gitta Coaker @gittacoaker.bsky.social · 08/07/2025
Nice preprint! Structure of AVRcap1b from Phytophthora reveals a novel fold, and structural effector family. AVRcap1b targets the helper NLR NbNRC2. #plantimmunity www.biorxiv.org/content/10.1...
biorxiv.org
An effector from the potato late blight pathogen bridges ENTH-domain protein TOL9a to an activated helper NLR to suppress immunity
Pathogens counteract central nodes of NLR immune receptor networks to suppress immunity. However, the mechanisms by which pathogens hijack helper NLR pathways are poorly understood. Here, we show that an effector from the potato late blight pathogen Phytophthora infestans bridges the host protein NbTOL9a, a putative member of the host ESCRT pathway, to a helper NLR to suppress immunity. In this work, we solved the crystal structure of the RXLR-LWY effector AVRcap1b in complex with the ENTH domain of NbTOL9a. The structure revealed that unlike other RXLR-LWY effectors, AVRcap1b has a novel L-shaped fold and defines a new structural family of effectors in the Phytophthora genus. Moreover, we defined the AVRcap1b/NbTOL9a binding interface and designed effector mutants that don't bind NbTOL9a, impairing immune suppression. This indicates that ENTH binding is required for full virulence activity of this effector. Lastly, we show that AVRcap1b associates specifically with activated NbNRC2 independently of NbTOL9a binding. This suggests that the effector functions as a bridge that interconnects NbNRC2 with the NbTOL9a pathway. These results illustrate an unprecedented pathogen mechanism to hijack helper NLR pathways and suppress immunity. ### Competing Interest Statement T.O.B. and S.K. receive funding from industry on NLR biology and cofounded a start-up company (Resurrect Bio Ltd.) on resurrecting disease resistance. M.P.C., L.D., and S.K. have filed patents on NLR biology. M.P.C. and L.D. have received fees from Resurrect Bio Ltd. The other authors declare that they have no competing interests. European Research Council, https://ror.org/0472cxd90, 743165 British Society for Plant Pathology, https://ror.org/04zj17j36 Biotechnology and Biological Sciences Research Council, BB/P012574, BBS/E/J/000PR9795, BBS/E/J/000PR9796, BBS/E/J/000PR9797, BBS/E/J/000PR9798, BB/V002937/1
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Greg Tucker-Kellogg @gtuckerkellogg.bsky.social · 08/07/2025
As an undergraduate who loved physical chemistry and was just starting biology, I thought the Meselson-Stahl experiment was the coolest thing ever. It was so simple in its application of physical theory and experiment to prove a biological truth that it was perfect. www.nytimes.com/2025/07/07/s...
nytimes.com
Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment
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The Plant Cell @theplantcell.bsky.social · 07/07/2025
The histone acetyltransferase GCN5 regulates floral meristem activity and flower development in Arabidopsis (Amangul Hawar , Wei Chen , Tao Zhu , Xin Wang , Jiaxin Liu , Shiqi Xiong , Toshiro Ito , Dijun Chen , Bo Sun) doi.org/10.1093/plce... #PlantScience
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Chenxin Li, PhD @chenxinli2.bsky.social · 07/07/2025
Cytokinin-ESR module promoting pluripotent stem cell identity in moss. From: www.cell.com/developmenta...
cell.com
snRNA-seq analysis of the moss Physcomitrium patens identifies a conserved cytokinin-ESR module promoting pluripotent stem cell identity
Pluripotent stem cells in the apical meristem have been a key innovation that allows plants to flourish. Hata et al. identified transcriptomic characters of a pluripotent stem cell in Physcomitrium pa...
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Reposted by Pratheek Pandesha
Silvia Manrique @tank-silvia.bsky.social · 04/07/2025
🧪🧵 Check out this preprint dealing with one of my favorite gene families: ✨✨the Reproductive Meristem (REM) transcription factor family!✨✨ REMs are B3 TFs just like ARFs or RAVs but they are much less studied than their other B3 “cousins”. 1/4
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Chenxin Li, PhD @chenxinli2.bsky.social · 04/07/2025
Amazing. First cell cycle, then DNA methylation (paper/preprints posted somewhat recently), now sex determination. A class of TF that definitely needs more love.
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Reposted by Pratheek Pandesha
Penelope Lindsay @penlindsay.bsky.social · 04/07/2025
maize shoot apical meristems are the cutest! 😍 plasma membrane labeled with PIP2A-CFP
a maize shoot apical meristem labeled with a plasma membrane marker fused to cyan fluorescent protein
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Reposted by Pratheek Pandesha
Journal of Experimental Botany @jxbotany.bsky.social · 04/07/2025
🌾🧬 SPECIAL ISSUE RESEARCH 🌾🧬 📝 Varying gene dosage through mutating DNA methyltransferase 1-1 (MET1-1 ) in polyploid wheat generates quantitative changes to CG methylation without the lethal consequences observed in other crops - Burrows et al. 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪
Fig. 1. (short legend see paper for full description): Null met1-1 mutants cannot be produced by crossing TILLING lines with disruptions in the three MET1-1 homoeologues. (A) Evolutionary relationships between MET1 homologues in Arabidopsis (AtMET1), rice (OsMET1a and OsMET1b), and wheat (homoeologue groups TaMET1-1, TaMET1-2, and TaMET1-3). (B) Crossing schematic showing the generation of the hexaploid MET1-1 populations: the C0465×C0884 population (top) and the C0451×C2028×C1292 population (bottom). (C) Structure of the three MET1-1 homoeologues. Filled rectangles represent exons, open rectangles represent untranslated regions, and lines represent introns. Triangles indicate the positions of the premature termination codon mutations in the TILLING lines used to produce the two hexaploid F2 populations (C0465×C0884, orange; C0451×C2028×C1292, purple). The green box signifies the Bromo adjacent homology domain (BAH) and the blue box signifies the C-5 cytosine methyltransferase domain.
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Pratheek Pandesha @hadse.bsky.social · 02/07/2025
Here it is! www.biorxiv.org/content/10.1...
biorxiv.org
Transcription factors instruct DNA methylation patterns in plant reproductive tissues
DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail ...
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Reposted by Pratheek Pandesha
Chenxin Li, PhD @chenxinli2.bsky.social · 02/07/2025
Transcription factors targeting RNA-directed DNA methylation machinery in Arabidopsis reproductive tissues. From: www.nature.com/articles/s41... I think I saw another preprint on this by another lab too.
nature.com
REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes - Nature Cell Biology
Wu et al. demonstrate that REM transcription factors and GDE1 guide RNA polymerase IV to specific genomic loci, establishing a DNA sequence-dependent mechanism for siRNA biogenesis and DNA methylation...
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Reposted by Pratheek Pandesha
North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · 16/06/2025
Joanna Friesner- NAASC- honored for her support of the Arabidopsis community #ICAR2025
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Reposted by Pratheek Pandesha
Abby Dernburg @adernburg.bsky.social · 08/09/2023
Our department mcb.berkeley.edu is soliciting applications for an Assistant Professor position studying fundamental aspects of genetics, genomics, evolution, and/or developmental biology. Bring it on! aprecruit.berkeley.edu/JPF04110
aprecruit.berkeley.edu
Assistant Professor - Genetics, Genomics, Evolution and Development - Department of Molecular and Ce...
University of California, Berkeley is hiring. Apply now!
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Liz Haswell @ehaswell.bsky.social · 31/08/2023
I've 4 invite codes and would love to recruit some #plantscience folks. Pass it on!
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 01/09/2023
Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler www.biorxiv.org/content/10.1101/202…
biorxiv.org
Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler https://www.biorxiv.org/content/10.1101/2023.08.31.555833v1
Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable element
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Mary Williams @PlantTeaching @plantteaching.bsky.social · 02/09/2023
I'm writing up the @root-shoot.bsky.social Inclusive Conferences Working Group efforts to date & next steps. Q for #PlantScience community. What in your opinion / experiences are biggest barriers to inclusion + belonging at meetings, & how to remedy? We've got funds to put towards this objective!
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Travis Lee @tralee-sci.bsky.social · 03/09/2023
In addition to the updated manuscript, we have expanded our online browser to enable the viewing of all transcripts detected in each of our single-nucleus RNA-seq datasets! arabidopsisdevatlas.salk.edu
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Reposted by Pratheek Pandesha
Mark Rubin @markrubin.bsky.social · 23/08/2023
Scientist? New to BlueSky? Trying to figure out what the hell a "feed" is and why hashtags aren't working the same as on Twitter? Check out this quick start guide by @steveharoz.com and me 👇
docs.google.com
BlueSky for Scientists
BlueSky for Scientists Authors: Steve Haroz and Mark Rubin URL: http://blueskyscience.steveharoz.com Features you may miss from Twitter or Mastodon As BlueSky is in beta, some features are not impleme...
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Nina Bravo @bmnina.bsky.social · 02/09/2023
Plant biologists! Please, please, please pass it on to undergrads! I'd love to have known undergrads can apply unlimited times. forms.gle/WRPwv92TVQDX...
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Mark Rubin @markrubin.bsky.social · 03/09/2023
Scientist? ✔️ New to BlueSky? ✔️ Wanna get your posts seen by people in your field? ✔️ Check out this list of 42 science-related feeds 👇 You can add specific feeds to your timeline to see their posts, and you can include your own posts in a feed by including a feed-specific tag. #AcademicSky 🧪
docs.google.com
BlueSky Science-Related Feeds
Sheet1 Likes,Name (Click to visit feed),Tags,Contact to ask to be added to contributor list 2452,<a href="https://bsky.app/profile/did:plc:jfhpnnst6flqway4eaeqzj2a/feed/for-science">What's Science</a...
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