Fig. 3.Gynoecial and ovule development. (A–F) The wild type (WT), (G–L) ant-1, (M–R) gif1 gif2 gif3, and (S–Y) ant-1 gif1 gif2 gif3. The numbers on top indicate floral stages (Smyth et al., 1990). The first three columns, SEM analysis; the next two, histological analysis; the last, light microscopy with DIC optics. Asterisks indicate CMMs. iv, immature carpel valve; o, ovule; r, replum; s, septum; sg, stigma; st, style; tt, transmitting tract; v, mature carpel valve. Scale bars=100 µm, except for (F), (L), and (R) (10 µm).

🌼 RESEARCH 🌼

The GRF–GIF transcriptional complex and the ANT transcription factor act cooperatively to endow leaf and floral organs with cell proliferation/differentiation activity, leading to optimal growth and successful reproduction - Jung et al.

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪

Is there a reason they do this? Do they exchange anything?

You also have ChIP-ChIP pull downs as well as double DAP-seq. But neither are great for exhaustive protein X protein interactions

Screenshot showing a pink petunia flowers

Efficient creation of decorative double-flowered petunia through CRISPR/Cas9.

From: onlinelibrary.wiley.com/doi/full/10....

Where do I get cheap plant tissue culture stuff? E.g., MS, agar, and plant hormones?

Also, CTAB?

Beyond supergenes: the diverse roles of inversions in trait evolution Chromosomal inversions are ubiquitous across the Tree of Life, with genome-wide studies revealing a bias toward smaller inversions, yet research has disproportionately focused on large, supergene-like...

Beyond supergenes: the diverse roles of inversions in trait evolution www.cell.com/trends/ecolo...

(no title) droso4public is a central resource store supporting science communication and advocacy for Drosophila

Dear GenZ members of the #Drosophila community! You are needed to make cool fly research viral in your social media world! As a boomer I do not understand that sphere, but I can consult and contribute our enormous fund of outreach resources: droso4public.wordpress.com. Please, get in contact!

Hey Drosophilists: Might you maintain Fuyama's original gynogenetic "gyn-F9" (BDSC #5353) stock in your library?

The current stock from Bloomington is not producing progeny with ms(k81) males.

Thank you!!!

Fields in science often lionize early researchers. Whether it’s McClintock in maize or Thomas Hunt in Drosophila land.

I think the plant single cell community should really work to highlight the work of Esau highlight her work as the basis of much of our understanding of

Gene Trap Tagging of PROLIFERA, an Essential MCM2-3-5-Like Gene in Arabidopsis Gene trap transposon mutagenesis can identify essential genes whose functions in later development are obscured by an early lethal phenotype. In higher plants, many genes are required for haploid game...

The fact that a paper from 1995 is still behind paywall is...what's the word I'm looking for...egregious. That was 30 years ago.

www.science.org/doi/abs/10.1...

#PlantBio2025
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!

Up next at the Presidential Plenary Seminar: Bob Schmitz takes the stage to discuss “Leveraging Plant Epigenomics to Decode the Complexity of Non-Coding Regulation.” 🌱🧬 #PlantBio2025

Can anyone point me to full resolution versions of these classic images from NHGRI that show the growth of GWAS from ~2006--2015? I'm looking for the timelapse versions.
(I know many of you are waiting for the GWAS chapters of my free online textbook on human genetics--they are coming, but slowly!)

Fuckin cooooool

Very excited that our work on directional symplastic transport in differentiated root is now published!A developmental switch controls cell-to-cell transport in roots via pectin-linked plasmodesmata changes: Molecular Plant www.cell.com/molecular-pl...

Recruitment, rewiring and deep conservation in flowering plant gene regulation - Nature Plants A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the re...

"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."

From: www.nature.com/articles/s41...

This is wild - I had no clue that there were empty mitochondria at all in plants cells. Is there any understanding how this happens? Like is this an accidental process innate to mitochondrial replication or is there a specific purpose?

Cool story! Congratulations to everyone involved.
#plantscience

Li's lab logo. It has a pink Catharanthus flower with green leaves on the left, and green kalanchoe leaf with a plantlet on the right. The structure of vindoline at the center top, and symbol about gene regulation at the center bottom, text "cxLi Lab" near the bottom, and a grey circle as background.

I'll be joining the Department of Plant Biology at Michigan State University in Mid August as an Assistant Professor.

cxli233.github.io/cxLi_lab/

A meme-style comic panel with three parts. Left: A stylized enhancer with a mutation, surrounded by colored blocks representing functional motifs, a neural network diagram, chromatin accessibility signal traces, and a sequence motif. Two cartoon mouse embryos below show different LacZ reporter activity patterns. Top right: A hand hovers anxiously between two red buttons labeled “Experiments” and “AI,” with the caption “HOW DO ENHANCERS REALLY WORK?” Bottom right: A sweating superhero wipes his forehead, looking stressed about the difficult choice.

Textbooks: “Enhancers are just a bunch of TFBSs”

But how do they REALLY work?

New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social

A 🧵 (1/n)

Free access link: rdcu.be/erD22

Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) - Genome Biology Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproduct...

Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

Standard methods are equivalent to a flashlight, looking at each gene independently. We combine signals from multiple genes, turning a floodlight onto the genome.

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/aertslab/CRE...

Design principles of cell-state-specific enhancers in hematopoiesis Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...

How do enhancers drive cell specificity? 🤔 Fascinating study used 64k+ synthetic sequences in blood cell differentiation & found activating TF sites often show negative synergy, converting TF gradients into sharp gene patterns! #Bioinformatics
www.cell.com/cell/fulltex...

Dissecting regulatory syntax in human development with scalable multiomics and deep learning Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!

key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity

many are "negative regulators" & misexpressed in cancer

www.sciencedirect.com/science/arti...

PhD Timeline xkcd.com/3081

Zero-shot evaluation reveals limitations of single-cell foundation models - Genome Biology Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of mode...

genomebiology.biomedcentral.com/articles/10....

Quite an indictment of some of the current single cell "virtual cell" foundation models. Even for the relatively mundane applications, cell labeling, batch correction etc, they are poor compared to much simpler & cheaper methods.

Camptotheca and Catharanthus, both produced alkaloids that are used in cancer chemotherapy, last shared a common ancestor ~115 mya. They shared an iridoid biosynthetic pathway. We found new, rare biosynthetic genes in Camptotheca that are different from those in Catharanthus.

New preprint! We used single cell sequencing & metabolomics to look at cell type specificity of specialized metabolism in Camptotheca, the source of chemotherapeutic agent camptothecin, as well as comparative analyses w/ Catharanthus, which we previously worked on. 🧵

www.biorxiv.org/content/10.1...