Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026Any labels or quantitative data (e.g. transcriptomic datasets) also integrate easily to the BAT pipeline. There is built-in FASTA header parsing ensures gene labels always match the dataset you are visualizing. For plant folks: we ship a subset of the Klepikova expression atlas. 141 4
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026Molecular biologists are especially interested in domains and motifs with known functions. BAT can highlight user-provided HMM profiles and amino acid motifs (via the ggtree R package) to visualize these features on a gene tree. Domain gain/loss is placed in evolutionary context. 131 3
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026As an example, immune receptor homologs often have complex evolutionary relationships collapsed by genome-wide orthogroup analyses. We show a BAT example for the NAIP family of mammalian NLRs, where mouse lineage-specific paralogs are known to have distinct recognition functions. 111 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026BLAST-Align-Tree (BAT) does what it says on the tin: 1) finds homologs 2) aligns gene sequences 3) constructs a gene tree This is how you start any gene family analysis, but is still difficult to do from scratch or in genome portals. It's prohibitively hard in non-model species 112 2
Adam Steinbrenner @adsteinbrenner.bsky.social · 13/05/2026We are excited to release the BAT!🦇🚨 We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint. I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵 26831 68
Adam Steinbrenner @adsteinbrenner.bsky.social · 26/03/2026Four amazing summer interns got the work done, and did a great job applying modern genomic technologies! A fun way to connect to the heritage of our favorite trees 🌸🌸 Read more here: facilities.uw.edu/blog/posts/2... 041 4
Adam Steinbrenner @adsteinbrenner.bsky.social · 26/03/2026Our tree was most closely related to a lineage of trees sampled in Tokyo (Ueno park), Okayama, and Shimane University. We hope as additional trees are sequenced we will find even closer relatives. 120 2
Adam Steinbrenner @adsteinbrenner.bsky.social · 26/03/2026Students used simple phylogenetic inference to determine relatedness based on the very small number of SNP difference among trees of the Somei-Yoshino variety. A recently published resequencing study made the comparisons possible academic.oup.com/dnaresearch/... 110 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 26/03/2026Our trees were moved to the UW quad in the 1960s from their original (1930s) arboretum location. But planting records haven't been found, so their origin is unknown. To investigate, we collected leaves of the northernmost tree outside Raitt hall and performed PacBio sequencing. 110 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 26/03/2026This cherry blossom season is extra fun for us.🌸 Students sequenced the genome of one of the iconic Yoshino cherry trees on the University of Washington quad, and found nearly identical clonal relatives in Japan! A great project with Alex Harkess and the American Campus Tree Genomes (ACTG) project 2398 39
Adam Steinbrenner @adsteinbrenner.bsky.social · 05/09/2025What about the caterpillars? We generated low expression (inr-2 allele) near-isogenic lines, but interestingly, In11 pretreatment still protected these plants from attack. We conclude that insensitivity with common lab assays for PTI does not necessary correspond with resistance. 120 2
Adam Steinbrenner @adsteinbrenner.bsky.social · 05/09/2025Promoter alleles from different In11-reponsive or non-responsive varieties corresponded with strength driving luciferase expression in transient expression assays. Thus, low INR expression seems to mediate insensitivity to In11 in lab conditions. 110 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 05/09/2025We found just a few insensitive accessions among hundreds of tested USDA-GRIN varieties. One variety was associated with lower expression of the INR gene. The low expression INR haplotype turned out to be locally prevalent in varieties from Jujuy province in Argentina. 110 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 05/09/2025More fruits of studying natural variation in common bean (Phaseolus vulgaris): an interesting genetic basis for insensitivity to caterpillars' In11 elicitor 🐛 Our new bioRxiv preprint from star technicians Brian Behnken and Wesley George below 🧵 www.biorxiv.org/content/10.1... 2166 16
Adam Steinbrenner @adsteinbrenner.bsky.social · 02/08/2025How do predatory wasps find their caterpillar prey? In our new preprint on Biorxiv we show that the host plant's immune system detects herbivory to sound the alarm. 🌱🐛 See thread from @nataliagupa.bsky.social -- a surprising role for a plant PRR in indirect defense against herbivores. 0134 13
Adam Steinbrenner @adsteinbrenner.bsky.social · 17/07/2025Second, work from Eunyoung Chae on autoimmunity mediated by the NLR DM2 and DM3 "Dangerous mix". CryoEM structures show a shift in enzyme hexamer stability to be the allele-specific trigger for DM2. We highlight that Alphafold can't predict this structural shift. www.cell.com/molecular-ce... 141 4
Adam Steinbrenner @adsteinbrenner.bsky.social · 17/07/2025First, work from Chang-Bao Li and Chuanyou Li (Shandong Ag U) on regulation of SYR1 receptor. The paralog SYR2 is an induced negative regulator w/ lower binding affinity. @nataliagupa.bsky.social highlighted that the module is only found in Solanoideae www.sciencedirect.com/science/arti... 111 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/07/2025See our latest work on an LRR-RLP receptor and plant-caterpillar interactions this Wed at #2025ISMPMI The legume receptor INR attracts predatory wasps in the field!🍀🐛 💀 @nataliagupa.bsky.social presents in CS: Microbe-mediated impacts on plant-parasite interaction (we sneak in among the microbes) 2205 20
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/05/2025Love this Darwin quote on display at the Linnaean Society in London: "Trust nothing to the memory, for the memory becomes a fickle guardian when one interesting object is succeeded by another still more interesting" darwin-online.org.uk/content/fram... 061 6
Adam Steinbrenner @adsteinbrenner.bsky.social · 04/12/2024We had a lab discussion of time management using concepts from the book "Make Time" -- how do we avoid "Busy Bandwagons" / "Infinity Pools" , and how do we pick and carry out a high-priority task each day? We listed some examples and strategies. Any other ideas? 140 4
Adam Steinbrenner @adsteinbrenner.bsky.social · 18/11/2024Reintroducing myself on Bluesky @adsteinbrenner.bsky.social -- I'm a plant biologist at UW Seattle (just recently made Associate Professor!) We study the plant immune system with a special interest in recognition of chewing herbivores and host-pest molecular evolution. 75916 59
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/04/2024I had exciting conversations and enjoyed the excellent talks. A very high quality conference overall -- thanks to the organizers Sarah O'Connor, Barbara Halkier, and Detlef Weigel. Prost! 100 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/04/2024On biotic interactions: - dissecting plasmodesmatal closure from PTI responses @pd_christine - apparency as critical trait for Scaptomyza leaf miner choice @NKWhiteman - applications of GWAS in local populations Andy Gloss, hiring soon @ UGA @ADGloss 000 0
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/04/2024We heard from the forefront of tool development: - single cell multi-omics from Robin Buell (UGA) - chromosome engineering from Michelle Rönspies (Karlsruhe) - field-bulked EMS mutants for many species from Agnieszka Nielsen of Traitomic (supported by Carlsberg foundation🍻!) 100 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 15/04/2024I really enjoyed this EMBL "Plant Genomes" symposium last week, a small conference with some of the very best talks I have heard on novel functions emerging at multiple phylogenetic scales 🌲🌿🌸🌾 Some highlights below 🧵 165 6
Adam Steinbrenner @adsteinbrenner.bsky.social · 16/02/2024Importantly, host targets monitored by CHS3-CSA1 ( plant kinases BAK1/BIR1/BIR3) promote the inactive dimer state, although it would be great to see more details presented about the potential NLR-kinase interfaces 000 0
Adam Steinbrenner @adsteinbrenner.bsky.social · 16/02/2024For the second, it was hard to imagine paired NLRs as homomeric resistosomes given the implications of shared promoter and observed RPS4-RRS1 heterodimer (Williams 2014 24744375). The current work helps understand the transition to a large mw complex, a putative mixed tetramer 100 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 16/02/2024For the first, PvPGIP2 was the first plant leucine-rich repeat protein with a crystal structure (template for many PRR/NLR homology models!) Amazing to see a surprising mechanism -- beyond inhibition of PG enzymes, PvPGIP2 promotes formation of long-oligogalacturonide elicitors 100 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 02/02/2024Fantastic new work on volatile-induced responses in Arabidopsis. - Initial green leafy volatile (GLV) perception occurs in guard cells (rapid pGC1::GCaMP3 response) - Ca2+ increase is specific to C6 aldehydes but not other GLVs/terpenes/MeJA) www.nature.com/articles/s41... 110 1
Adam Steinbrenner @adsteinbrenner.bsky.social · 11/12/2023Just heard of another @NSF GRFP rejection of a basic plant biology research proposal It is crazy to disqualify students based on highly subjective categories of "ineligible research" www.nsf.gov/pubs/2023/ns... 121 2
Adam Steinbrenner @adsteinbrenner.bsky.social · 05/12/2023A USDA Economic Information Bulletin from June 2023: "Concentration and Competition in U.S. Agribusiness" Market share for top 5 firms is 84% for corn and 79% for soybean. Massive changes in two decades since major mergers began www.ers.usda.gov/webdocs/publ... 000 0
Adam Steinbrenner @adsteinbrenner.bsky.social · 02/09/2023Attempt #3. (A threadreader style webpage that was compatible with bluesky preview images would be ideal!) threadreaderapp.com/thread/16960... 000 0