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John Hodge

@jghodge

Post-doc at UIUC studying stomatal patterning. Botanist by training with interests broadly in evo-devo, mechanistic modeling, and genetics, particularly in relation to grasses and cereals. Opinions my own.

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15.11.2024
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Latest posts by John Hodge @jghodge

Congrats all!! Been fun watching this work come together from afar!

09.03.2026 22:00 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Mutant alleles that affect pollen fitness can generate spatial inheritance patterns on maize ears – see the article by Ruggiero et al. Top Left: Maize pollen grains germinated on a silk, with pollen tubes (stained with aniline blue) growing into the silk interior. Image Credit: Caity Smyth. Bottom Left: Unpollinated maize ear with silks arranged to show that silks derived from ovules at the base of the ear are longer than silks from ovules at the ear apex. Image Credit: Elyse Vischulis. Right: Ear projection from a mature ear pollinated with the pollen from a plant heterozygous for the  bag1*::Ds-GFP insertion, oriented apex-to-base top-to-bottom (as in bottom left ear/silk image). The GFP-marked bag1* allele is associated with a spatial pattern of fewer fluorescent kernels towards the base of the ear – i.e., kernels generated following pollen tube growth down the longest silks.

Mutant alleles that affect pollen fitness can generate spatial inheritance patterns on maize ears – see the article by Ruggiero et al. Top Left: Maize pollen grains germinated on a silk, with pollen tubes (stained with aniline blue) growing into the silk interior. Image Credit: Caity Smyth. Bottom Left: Unpollinated maize ear with silks arranged to show that silks derived from ovules at the base of the ear are longer than silks from ovules at the ear apex. Image Credit: Elyse Vischulis. Right: Ear projection from a mature ear pollinated with the pollen from a plant heterozygous for the bag1*::Ds-GFP insertion, oriented apex-to-base top-to-bottom (as in bottom left ear/silk image). The GFP-marked bag1* allele is associated with a spatial pattern of fewer fluorescent kernels towards the base of the ear – i.e., kernels generated following pollen tube growth down the longest silks.

Very pleased to see this work from the group out in The Plant Journal - led by PhD student Diana Ruggiero from the Leiboff group, a truly collaborative project, addressing the question: how often does pollen genotype influence spatial patterns of inheritance? onlinelibrary.wiley.com/doi/10.1111/...

09.03.2026 20:25 πŸ‘ 20 πŸ” 7 πŸ’¬ 2 πŸ“Œ 0
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How to choose a sweet cherry tree. All of these are self fertile, hardy, and decent on disease/cracking resistance.

Lapin - Highest yield and more 'rich' flavor
Black Gold - Easy to grow, less yield than lapin, clean flavor
Sweetheart - Late season. Rich flavor
Stella - Early Season. Clean Flavor

09.03.2026 01:19 πŸ‘ 39 πŸ” 3 πŸ’¬ 4 πŸ“Œ 0
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Prof Marie Maynard Daly, Biochemist Marie Maynard Daly was a biochemist who co-discovered the link between high cholesterol, high blood pressure, and the clogged arteries that can cause heart disease and strokes.

Marie Maynard Daly co-discovered the link between high cholesterol, high blood pressure, and the clogged arteries that can cause heart disease and strokes. She also studied the damage that cigarettes have on the heart & lungs. adalovelaceday.subst...

08.03.2026 20:18 πŸ‘ 496 πŸ” 154 πŸ’¬ 3 πŸ“Œ 1
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Common Plant Proteins Found to Calm the Immune System - Harvard University - Department of Molecular & Cellular Biology A new study co-led by MCB’s Kazuki Nagashima and published in Science Immunology (PDF) identifies plant-derived molecules that help quiet the immune system, preventing inflammatory reactions to the […...

Common Plant Proteins Found to Calm the Immune System πŸ§ͺ 🧬 #AcademicSky #higherEd
www.mcb.harvard.edu/department/n... @microbiometcell.bsky.social @rachellegaudet.bsky.social @dulaclab.bsky.social @rivaselenarivas.bsky.social @science.org @harvard.edu

08.03.2026 17:47 πŸ‘ 29 πŸ” 15 πŸ’¬ 1 πŸ“Œ 1

I am also shocked by the lack of coverage of this fire. It’s so far only affecting the Union Street buildings, but one of those has partially collapsed, from what I can tell backwards into the station. And it’s not yet contained. This is major and more than halfway down BBC’s homepage.

08.03.2026 21:43 πŸ‘ 848 πŸ” 317 πŸ’¬ 37 πŸ“Œ 13

🌿 Postdoc opportunity in plant evolutionary ecology/genetics!

My lab in the Dept. of Ecology & Evolutionary Biology at the University of Michigan is recruiting a postdoctoral researcher to start Fall 2026.

We study plant adaptation, using weeds as model systems.

#Postdoc #EcoEvo

Pls RT!

08.03.2026 21:27 πŸ‘ 111 πŸ” 151 πŸ’¬ 2 πŸ“Œ 0

As someone who is a chronic pacer as part of my writing process, leg injuries are THE WORST…

08.03.2026 17:38 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
A detailed digital composite image based on the 1947 historical photograph of geneticist Barbara McClintock. McClintock, with her characteristic short hair and round glasses, is seated at a microscope, using tweezers in a Petri dish. While based on the original photo distributed for her AAUW award, this image presents a significantly expanded and fictionalized laboratory environment. The simple wooden workbench is now densely populated with a vast, colorized collection of complex glassware, numerous amber-colored reagent bottles, intricate distillation columns, and botanical specimens relevant to maize cytogenetics, creating a rich, illustrative narrative of her "jumping gene" research context that was not present in the original photo. The expanded background shows complex vintage laboratory cabinetry. This image explicitly states it is a composite: a digital recreation where Seriously Scientific has taken the historical figure and placed them into an augmented, complex fictionalized environment. Based on original source from Smithsonian Institution Archives. Digital composite by Seriously Scientific.

A detailed digital composite image based on the 1947 historical photograph of geneticist Barbara McClintock. McClintock, with her characteristic short hair and round glasses, is seated at a microscope, using tweezers in a Petri dish. While based on the original photo distributed for her AAUW award, this image presents a significantly expanded and fictionalized laboratory environment. The simple wooden workbench is now densely populated with a vast, colorized collection of complex glassware, numerous amber-colored reagent bottles, intricate distillation columns, and botanical specimens relevant to maize cytogenetics, creating a rich, illustrative narrative of her "jumping gene" research context that was not present in the original photo. The expanded background shows complex vintage laboratory cabinetry. This image explicitly states it is a composite: a digital recreation where Seriously Scientific has taken the historical figure and placed them into an augmented, complex fictionalized environment. Based on original source from Smithsonian Institution Archives. Digital composite by Seriously Scientific.

Remembering Barbara McClintock on International Women's Day!
She discovered that genes aren't static, they can actually "jump" around on a chromosome.

Her discovery of transposons ("jumping genes") fundamentally changed how we understand evolution and the complexity of DNA! 🧬🌽

#WomenInScience

08.03.2026 12:24 πŸ‘ 563 πŸ” 162 πŸ’¬ 6 πŸ“Œ 3
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#SpatialTranscriptomics

Optimizing Xenium In Situ data utility by quality assessment & best-practice analysis workflows

Must-read for Xenium userπŸ”₯

πŸ‘‰Segmentation
πŸ‘‰Spatially variable feature selection
πŸ‘‰Imputation
πŸ‘‰Spatial domain identification

#NatMethods 2025
www.nature.com/articles/s41...

07.03.2026 13:40 πŸ‘ 9 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0
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πŸ”ŠA long time ago in a microscopic galaxy far, far away....

🎬Episode IV - A NEW MICROSCOPE πŸ”¬
"It is period of cellular rebellion. Arabidopsis root cells have won first victory against the dark forces of DNA damage"

Thanks to @dvonwangenheim.bsky.social and new i3 spinning disk @the.3i.social

07.03.2026 16:11 πŸ‘ 26 πŸ” 7 πŸ’¬ 0 πŸ“Œ 0
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Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

06.03.2026 19:32 πŸ‘ 181 πŸ” 86 πŸ’¬ 6 πŸ“Œ 8

HCR is gonna be such a fantastic technique for the field of developmental biology in the years going forward

07.03.2026 12:57 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Please check out our new preprint! Using single cell analysis paired with HCR to visualize transcript localization we have identified cell and tissue-specific expression of various genes encoding tubulins, kifs, and dyneins during neural crest development!

07.03.2026 03:43 πŸ‘ 92 πŸ” 28 πŸ’¬ 5 πŸ“Œ 2
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Ummm... Excuse me, can I help you find something?

06.03.2026 22:10 πŸ‘ 845 πŸ” 184 πŸ’¬ 25 πŸ“Œ 18

If you're doomscrolling, guess what? So far there are 51 kākāpō chicks hatched and thriving this season, the same number of birds as we had in TOTAL in the 90s! Only one chick has died and there are still fertile eggs waiting to hatch!

06.03.2026 04:31 πŸ‘ 6393 πŸ” 1743 πŸ’¬ 67 πŸ“Œ 65
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An unconventional Rubisco small subunit underpins the CO2-concentrating organelle in land plants In many algae, photosynthesis is boosted by biophysical CO2-concentrating mechanisms, which pack the CO2-fixing enzyme Rubisco into liquid-like organelles called pyrenoids. Engineering C3 crops with a...

Our work on #hornwort #pyrenoids is finally out in @science.org! πŸŽ‰ We uncovered how hornworts pack their Rubisco into pyrenoids and successfully recreated them in Arabidopsis. A key step toward engineering more efficient photosynthesis in crops @btiscience.bsky.social www.science.org/doi/10.1126/...

05.03.2026 20:03 πŸ‘ 124 πŸ” 63 πŸ’¬ 6 πŸ“Œ 7
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This odd little plant could help turbocharge crop yields - Boyce Thompson Institute

An odd little plantβ€”the hornwortβ€”just gave scientists a blueprint for how to make crops more efficient.
New paper out today in Science from BTI, Cornell & the University of Edinburgh. Here's why it matters: btiscience.org/explore-bti/...

05.03.2026 19:12 πŸ‘ 4 πŸ” 2 πŸ’¬ 1 πŸ“Œ 0
This Brazilian frog might be the first pollinating amphibian known to science
Nectar-loving tree frog likely moves pollen from flower to flower

This Brazilian frog might be the first pollinating amphibian known to science Nectar-loving tree frog likely moves pollen from flower to flower

It’s the first time a frogβ€”or any amphibianβ€”has been observed pollinating a plant, researchers reported in 2023.

Learn more on #WorldWildlifeDay: https://scim.ag/4riUU1G

04.03.2026 00:11 πŸ‘ 374 πŸ” 134 πŸ’¬ 3 πŸ“Œ 17

Researchers in the US might be having feelings about writing grants atm-I know I am!

We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal.

His advice is gold, and helpful regardless of funder. Pls RT!

02.03.2026 15:32 πŸ‘ 58 πŸ” 42 πŸ’¬ 2 πŸ“Œ 0

<reads in Adam Sandler voice>

02.03.2026 10:39 πŸ‘ 1 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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BLM Announces Plan to Fell Oregon's Last Great Forests One billion board feet per year... 30 days to make your voice heard.

EMERGENCY, #oregon forest friends!

Three more weeks to comment. No public hearings scheduled.

01.03.2026 22:20 πŸ‘ 390 πŸ” 345 πŸ’¬ 20 πŸ“Œ 31
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(1/5)

I am very excited to share my simultaneous triple staining method for monocot roots. This method is not only faster but also utilizes a smaller volume of stain than traditional methods and minimizes mechanical tissue damage.

www.biorxiv.org/content/10.6...

18.02.2026 00:30 πŸ‘ 69 πŸ” 22 πŸ’¬ 2 πŸ“Œ 2
Alternative periodic system of chemical elements (source: Wikimedia)

Alternative periodic system of chemical elements (source: Wikimedia)

This periodic table shows the origins(!) of chemical elements: The carbon in your bones was created under extreme conditions within dying stars. The iron in your blood comes from exploding stars & the gold in your teeth from neutron stars. We are literally made of star stuff. #science #sagan #stars

01.03.2026 08:57 πŸ‘ 30 πŸ” 14 πŸ’¬ 5 πŸ“Œ 1
Grey cat sitting on a table, gazing pensively onto the middle distance.
He has amber eyes and pronounced cheeks. A luxuriant mane, and a walrus moustache.

Grey cat sitting on a table, gazing pensively onto the middle distance. He has amber eyes and pronounced cheeks. A luxuriant mane, and a walrus moustache.

Nobly gracing the table

28.02.2026 15:49 πŸ‘ 885 πŸ” 85 πŸ’¬ 30 πŸ“Œ 4
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Aridity mediates the scale-dependent relationship between plant diversity and soil multifunctionality Dryland ecosystems are now exposed to intensifying aridity and plant diversity loss, posing significant threats to the maintenance of ecosystem multif…

Our new study highlights the importance of #biodiversity #conservation across scales in #drylands and provides insights for designing aridity-specific biodiversity conservation policies.
www.sciencedirect.com/science/arti...

28.02.2026 08:09 πŸ‘ 8 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
Schematic diagram summarizing the key results from this study for heart rot stems, no heart rot stems, heart rot stems with bark fractures of sugar maple (Acer saccharum Marshall), and soil.

Schematic diagram summarizing the key results from this study for heart rot stems, no heart rot stems, heart rot stems with bark fractures of sugar maple (Acer saccharum Marshall), and soil.

Source or sink? #Trees with heart rot disease emit more #methane, upending forest carbon models

news.nd.edu/news/source-...

Read the research by Chathuranga K. Senevirathne πŸ‘‡
nph.onlinelibrary.wiley.com/doi/10.1111/...

#PlantScience #PressRelease

27.02.2026 18:00 πŸ‘ 14 πŸ” 5 πŸ’¬ 0 πŸ“Œ 0
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So, any other news yesterday?
Anything important?

27.02.2026 10:54 πŸ‘ 700 πŸ” 421 πŸ’¬ 17 πŸ“Œ 41

In principle the main extent of explorable morphospace should saturate in reasonably short order if there isn’t a strong penalty for such random walks, at which point more incremental tweaking would take over, so is this approaching a textbook case of neutral evolution?

27.02.2026 00:51 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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Propagation of Amorphophallus by leaf petiole cuttings - Juniper Level Botanic Garden Species Source Date stuck Year Hormone # stuck # rooted % rooted Tuber size A. aberransΒ  AGA-1066 8/25 2004 H #1 20 4 20.0 0.32 A. aberrans AGA-1066 9/7 2005 H #3 27 25 92.6 .32-2.54 A. abyssinicus HA...

Apparently Amorphophallus can in fact spontaneously regen from leaf cuttings sensu web searches…? TIL: www.juniperlevelbotanicgarden.org/propagation-...

27.02.2026 00:15 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0