Diep Ganguly

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

NIH wants to hear from you. No really.

Request for Information on Maximizing Research Funds by Limiting Allowable Publishing Costs
grants.nih.gov/grants/guide...

How do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...

When my friends were reading and watching ‘Lessons in Chemistry’, I tried to convey that the misogyny of the sixties is still very much alive and well for many #WomenInStem.
This article tells a sad, real tale that needs to be heard.

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...

"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪

Increasing the number of anthropogenic stressors reduces the effects of plant diversity.

Increasing the number of anthropogenic stressors reduces the effects of plant diversity.

A study by Yanjie Zhu, et al. represents a first attempt to address the effect of plant diversity under multiple stressors.

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

@mrillig.bsky.social #LatestIssue

Cytosolic water potential as a mechanistic driver of leaf airspace unsaturation and non-stomatal control of transpiration Mesophyll cells exhibit a previously underappreciated capacity to regulate water loss via low plasma membrane conductance ( L p), offering a non-stomatal mechanism for transpiration control. However, ...

Cytosolic water potential as a mechanistic driver of leaf airspace unsaturation and non-stomatal control of transpiration

From @florianabusch.bsky.social and team

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

#ASPBPlantCellTuesday #ICYMI

Recipients of a U.S. Climate Science Fellowship Are Put on Unpaid Leave

I'm sadly leaving Hawaii and the USA today. This NYT article, with comment from me, @solilyquy.bsky.social and @leafwax.bsky.social, explains one (of several) reasons why. www.nytimes.com/2025/07/09/c...

Endogenous Arabidopsis messenger RNAs transported to distant tissues - Nature Plants There's a lack of knowledge on the extent to which mRNAs are transported across tissues in plants. Now a study combining RNA-seq with grafting experiments identifies 2,006 genes in Arabidopsis thalian...

Based on #community feedback, we've updated locus & gene summaries and annotations to remove “the mRNA is cell to cell mobile” labeling based on www.nature.com/articles/npl.... h/t @pdchristine.bsky.social @plantophagy.bsky.social & others who alerted us by Bluesky, email, & in person at ICAR2025.

If you put googly eyes on the Pillars of Creation you get muppets 😄😄

Transgenesis and transposition combined in transposon-mediated ultra-clean selectable transformation (TRUST).

TRUSTing transposable elements to create ultra-clean transgene insertions

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

👆 A #Commentary by Ryan Swanson, Brooke Diehl & Keith Slotkin on this article by Ma et al. 👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue

Defining and benchmarking open problems in single-cell analysis - Nature Biotechnology Nature Biotechnology - Defining and benchmarking open problems in single-cell analysis

Defining and benchmarking open problems in single-cell analysis - @krishnaswamylab.bsky.social @fabiantheis.bsky.social bit.ly/4l8dsiF

Here’s some dog content to temporarily distract you from the mess happening in the world

Image text: Welcome to the Editorial Board. Hervé Vaucheret. Institut Jean-Pierre Bourgin for Plant Sciences. Expertise: Epigenetics, gene silencing, siRNA, miRNA, RNA biology, genetics. Featuring Hervé Vaucheret's photo and ASPB and The Plant Cell logos

📣 The Plant Cell is proud to announce the appointment of Hervé Vaucheret!🌱 academic.oup.com/plcell/

#plantscience #WeAreASPB

A host organelle integrates stolen chloroplasts for animal photosynthesis Sea slugs steal foreign chloroplasts and store them in specialized organelles that facilitate photosynthesis and eventual digestion to mediate starvation resistance.

Remarkable paper explaining how sea slugs maintain chloroplasts obtained by kleptoplasty active for many month & eventually digest them for resources www.cell.com/cell/fulltex...

Must read for all who use Nicotiana benthamiana as a platform: “Causes and consequences of experimental variation in Nicotiana benthamiana
transient expression”
#plantscience

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

Boromir Meme: One does not simply select the longest ORF

I am super excited to announce the first (brief) pre-print purely from my group:

Start right to end right: authentic open reading frame selection matters

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

This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!

At the risk of sounding like a big nerd, I love when assumed/perceived trends are found to be the result of the Simpson's paradox! Here, the gender-equality paradox is getting fried! 🧪 #science 📊 #stats #equality

#PlantScience colleagues, please think twice before working with the new Springer Nature Discover branded journals. And then don't.

Black text on grey background. Screenshot of a Bluesky chat message from a researcher waiting in the delayed Linkage Project announcements.

ARC’s Linkage Projects delay is already having huge knock-on effects. This researcher’s work with their industry partner (remote community groups) will be delayed by a year!👇

RNA-seq analysis of early embryos display only minor splicing effects in Arabidopsis hapless1 (hap1-1) mutant.

Mago nashi controls auxin-mediated #embryo patterning in #Arabidopsis by regulating transcript abundance

A #Letter by Liu et al. 👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue

Just a thought! Instead of buying fireworks buy 2 cans of pet food for a shelter animal. Don't make a noise, make a difference.

Or consider making a donation to a veterans organization that helps with PTSD.

Please consider doing this. It doesn't have to be an either or thing, one could do both fireworks and donate.
.

Sequence and parent-of-origin dependent m6A contribute to allele-specific gene expression
Guan-Zheng Luo and colleagues
www.embopress.org/doi/full/10....

Emerging leaves of a lime (Tilia) tree. The leaves are a fresh and vibrant green and the reddish-brown buds are also visible.

📜 75 years on since our very first issue, JXB continues to publish cutting-edge photosynthesis research ☀️🌱

☀️🌱 Start exploring the new Photosynthesis Virtual Issue on now ⬇️

🔗 academic.oup.com/jxb...

#JXB75 #PlantScience 🧪

@sebiology.bsky.social @oxfordacademic.bsky.social

🧵2/2

Image Text: The Plant Cell. Call for Assistant Features Editors. Deadline for applications: September 15, 2025. Featuring The Plant Cell logo.

📣The Plant Cell is recruiting Assistant Features Editors. The application period opens now and runs through September 15, 2025!🌱

👉Application information can be found at this link: blog.aspb.org/the-plant-ce...

#plantscience

Protecting against downside risk doesn’t have to come at the expense of continued increases in the yield potential.
No evidence of a tradeoff between yield stability and maximum yield in an analysis of hybrid performance across 34 environments. New pub led by @jensinadavis.bsky.social

CO₂ at Mauna Loa just reached a monthly average of >430 ppm for the first time.

That's possibly higher than in over 3.3 million years.

The global RATE of increase is off the chart.

It's hard to exaggerate how unprecedented this is!

Molecular_Bio - YouTube

Re-upping this: I curated a YouTube playlist on molecular biology. I use it to train undergrads and new grad students. I usually have them watch the playlist first before showing them how to do in the lab.

www.youtube.com/playlist?lis...