Alexandre Marand

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

Very proud to share our latest preprint: postdoc/LRSF fellow Yue Rui studies the mechanisms regulating attachment of the cell wall to the plasma membrane. The Cellulose Synthase Complex and REMORINs determine the extent of attachment and root osmotic stress tolerance. www.biorxiv.org/content/10.1...

Pantropical tree rings show small effects of drought on stem growth Increasing drought pressure under anthropogenic climate change may jeopardize the potential of tropical forests to capture carbon in woody biomass and act as a long-term carbon dioxide sink. To evalua...

#drought in #tress researchers find that Gymnosperms experienced larger growth deficits, especially during dry season, whereas wet-season droughts were more detrimental for angiosperms. Increasing drought frequency and severity may lead to stronger growth deficits.

www.science.org/doi/10.1126/...

The histone core domain evolves at single-residue resolution to directly orchestrate transcription Nucleosomes are thought to be structural barriers to transcription, establishing a restrictive ground state that must be destabilized for gene express…

Happy to share our new paper out today in @cp-cellreports.bsky.social in collaboration with @tobiaswarnecke.bsky.social @akihisaosakabe.bsky.social about how evolution can do big things with small changes. www.sciencedirect.com/science/arti...

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

Image credit: @gloglita.bsky.social‬ @lifescienceeditors.bsky.social‬ captured DynaTag in action: a pA-Tn5 probe (multicoloured) binds an antibody (white), which binds p53 DNA-binding domain (green) on DNA (blue) within 2 nucleosomes

🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)

This is one of the most exciting emerging fields in plant biology today and a great, welcoming, and collaborative community. Deadline for application and registration is next Monday! Apply here: lnkd.in/gvkMxuKR

Extensive modulation of a conserved cis-regulatory code across 589 grass species The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation through comparative genomics. While cis-regulatory regions ...

New preprint from my PhD! How cis-regulatory evolution shaped grass diversification worldwide
www.biorxiv.org/content/10.1...

We looked across 589 (!) grass species to ask:
— What regulatory changes enabled grasses to adapt?
— How can this inform crop breeding for resilience?

Here’s what we found:

There are over 200 posters from 40+ institutes and 300 registrants already. This is promising to be an exciting meeting and networking of plant scientists, especially those in the midwest. Register and join the community!

Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling By designing synthetic toolkits for contact-based signaling (MARS) and cell-cell adhesion (SATURN), we program yeast to form multicellular structures and perform complex tasks, like building logic cir...

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

Senate panel rejects Trump’s proposed cuts to agricultural research House spending committee has taken similar position on 2026 request

A key Senate spending committee has joined its House of Representatives counterpart in rejecting deep cuts that President Donald Trump’s administration proposed for research at the USDA for the 2026 fiscal year that begins on 1 October. scim.ag/3InyWcQ

Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...

Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5

Our latest! K63-polyUb of the ERECTA receptor kinase by PUB30/31 is required for the ligand induced receptor endocytosis for stomatal patterning. Our results show that ERECTA signals at the PM. Congrats, Liangliang, Minh & the team🌱!
www.biorxiv.org/content/10.1...

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits Gene circuits that control transcriptional regulation of nitrate-responses have similarities and differences, despite the equivalent effects of nitrogen on

At long last, our paper on conservation and divergence of a nitrogen circuit upstream of NLP6/7 &NIR1 in Arabidopsis and tomato is published! It's an exciting combo of whole plant, in vitro, protoplast and systems bio approaches: tinyurl.com/nitrogencirc... @gozdedemirel.bsky.social

This opinion piece, just published in my hometown newspaper in GA, seeks to make a strong case for continued federal support for scientific research in the USA. It's one of many across the nation, part of the #McClintockLetters Initiative www.theclaytontribune.com/opinion-edit...

Promotional image for the "Single-Cell Approaches in Plant Biology GRC Conference" focusing on meeting the speakers. This promo includes an image of Dr. Tatsuya Nobori from The Sainsbury Laboratory, UK with a short bio on Dr. Nobori.

Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference!

@tatsuyanobori.bsky.social

To Apply to the GRC: lnkd.in/gvkMxuKR

To Learn More About Dr. Nobori's Research: www.tatsuyanobori.com

Promotional image for the "Single-Cell Approaches in Plant Biology GRC Conference" focusing on meeting the speakers. This promo includes an image of Dr. Rachel Shahan from UCLA with a short bio on Dr. Shahan.

Meet The Speakers of the Single-Cell Approaches in Plant Biology GRC Conference!

To Apply to the GRC: lnkd.in/gvkMxuKR

To Learn More About Dr. Shahan's Research: sites.lifesci.ucla.edu/mcdb-shahan/

@rachelmshahan.bsky.social

Over the last couple of years I have been writing individual chapters of what I call

𝗔 𝗦𝗵𝗼𝗿𝘁 𝗛𝗶𝘀𝘁𝗼𝗿𝘆 𝗼𝗳 𝗣𝗹𝗮𝗻𝘁 𝗦𝗰𝗶𝗲𝗻𝗰𝗲

Each chapter covers a specific, basic, but for some reason special and interesting aspect of #PlantScience research.

Have a look here 👇🧵

Happy to see this out! @reginafairbanks.bsky.social analysis of perhaps the most famous maize domestication locus, teosinte glume architecture 1, which controls much of the change from the enclosed fruitcase (top) in teosinte to the "naked" grains of maize (bottom) www.pnas.org/doi/10.1073/... 1/2

The genetic architecture of cell type–specific cis regulation in maize Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, ...

New data from the Bob Schmitz lab (Marand 2025) on cell type-specific cis-regulation in maize! This study, in @science.org, reveals how DNA changes impact expression and maize traits. Explore the 176 new tracks on the browser under Epigenetics and DNA binding.

➡️ www.science.org/doi/10.1126/...

Make your own maize mutants! Raj Khangura, Norman Best and I contributed maize pollen and seed EMS mutagenesis protocols for the new maize handbook! Updated practices 1/n cshprotocols.cshlp.org/content/earl...
cshprotocols.cshlp.org/content/earl...
cshprotocols.cshlp.org/content/earl...

A graphic promoting GLPSC 2025 with a background image of blurred leaves and an outline of the Great Lakes. The graphic features a QR code for the conference website and the logos of the organizing institutions. The text says, "1st Great Lakes Plant Science Conference, September 12-14, 2025, the Lansing Center, Lansing, MI, research.msu.edu/glpsc2025, Register and submit a poster abstract! Poster abstracts due: June 30, 2025, General registration closes: August 31, 2025, Organized by 10 universities around the Great Lakes to push the boundaries of plant science, promote collaborations, and empower the next-generation plant science leaders. Hosted by Michigan State University and the Plant Resilience Institute."

🚨 Abstracts to present a poster at the 1st Great Lakes Plant Science Conference are due June 30, 2025 at 11:59 p.m. ET! Don’t miss this chance to showcase your research and connect with prominent Great Lakes region plant scientists!

Visit the #GLPSC2025 website to submit: research.msu.edu/glpsc2025

Why do so many disease risk variants show no regulatory effects in GTEx and/or other standard eQTL studies?

What do we mean when we say a regulatory effect is "context-specific" and how do we define the context?

We explored these questions using brain organoids and oxygen stress.

New paper from Sasha Bishop’s PhD in the lab - we combine quan gen with resurrection ecology to examine plant evolution in light of global change.

The take-home is that constraints among floral traits have ⬆️ in strength leading to a decline in the rate of adaptation by 96% over a 9-yr time span.

Super excited to release a huge evolution project on the works for many years:

Evolution experiments synchronized across climates to understand rapid adaptation

Preprint: doi.org/10.1101/2025...
All data available: www.grene-net.org/data

#MOILAB
@ucberkeleyofficial.bsky.social
@hhmi.org

🧵👇

Remember folks, the budget cuts for NSF and NIH *can still be stopped*. That is a luxury not granted to our agency science colleagues who have or could still lose their jobs from the top down. So - Fight! Speak up! Pay attention!

Tuning the interaction of a ParA-type ATPase with its partner separates bacterial organelle positioning from partitioning The maintenance of carboxysome distribution (Mcd) system comprises the proteins McdA and McdB, which spatially organize carboxysomes to promote efficient carbon fixation and ensure their equal inherit...

New @biorxiv-microbiol.bsky.social PrePrint from the Vecchiarelli Lab! 🧵
In collaboration with Jian Liu's lab at Johns Hopkins

doi.org/10.1101/2025...

Congratulations to first author Jordan Byrne!
@sickbyrne.bsky.social

P.S. She is looking for jobs!

Pls ReSkeet

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics - Nature Methods This work presents SUM-seq, an ultra-high-throughput method for co-profiling chromatin accessibility and gene expression in single nuclei across multiplexed samples, advancing the study of gene regula...

SUM-seq out @natmethods.nature.com !


🚀 Ultra-high-throughput Multiplexed snATAC+RNA

Used to:
⏳ link temporal macrophage GRNs to immune disease genetics
🩸 map T cell regulatory landscapes
🧬✂️ dissect TF function in hiPSC differentiation via CRISPRi/a screens
doi.org/10.1038/s41592-025-02700-8
🧵

Grass Rhizome Proteomics Reveals Convergent Freezing-Tolerance Strategies Early maize planting requires cold tolerance in temperate regions, which elite maize lacks. Extending the growing season could boost productivity along with more efficient nutrient use. Wild PACMAD gr...

New comparative proteomics study from our lab, led by Elad Oren! Contrasting summer and winter protein expression in five perennial grass species, we identified three proteins consistently linked to freezing tolerance across independent adaptations.
www.biorxiv.org/content/10.1...

Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...

Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. 🧵 www.biorxiv.org/content/10.1...