iiinova — where your digital self keeps evolving

Pat Heslop-Harrison @pathh.bsky.social · 06/05/2025

Many opportunities to exploit rhizosphere microbiome for crops. No longer only consider plant genome/GWAS for traits: look at fungi/bacteria. New multisite field trial complexity we can analyse @TrendsPlantSci Rodomiro Ortiz, Sangam Dwivedi, @plgepts EtAl www.sciencedirect.co...

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Pat Heslop-Harrison @pathh.bsky.social · 03/05/2025

Are others getting 'verify' boxes when wanting to access published papers (even open access)? Is this major publishers trying to stop Deep Learning / Generative AI / ChatGPT accessing refereed work? I want my papers used by AI models easily, not push them to Reddit or Facebook

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Pat Heslop-Harrison @pathh.bsky.social · 10/01/2025

It's early 2025, but I think I've found product-of-the-year: a USB Tester / Power Meter. Shows what is charging, measures voltage, battery mAh or Wh, tests batteries, adaptors, whether "PD" on a USB C means "power delivery" or "display port", graphs transfers etc. for c 10£$€

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Pat Heslop-Harrison @pathh.bsky.social · 09/01/2025

Immediate action point/question for me is: 'How do I get my material used for AI training/answers?' I'm impressed by Google "Search Labs AI Overview" accurately summarizing, in context, our paper from Sept 2024, when I use "flavonoids musaceae chromosomal location" as search keywords.

Google search with AI generated summary as an answer to my query

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Pat Heslop-Harrison @pathh.bsky.social · 02/12/2024

Genome-Wide Identification of Lectin Receptor-like Kinase Gene Family in Avena sativa and Role in Salt Stress Tolerance with Xiong Gui & Qing Liu: genomics, localization and expression shows the value of these genes www.mdpi.com/3062188 #mdpiijms @IJMS_MDPI @MDPIOpenAccess

RLK genes in oats - genes, synteny, sub cellular localization and expression in salt stress

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Pat Heslop-Harrison @pathh.bsky.social · 21/10/2024

Second issue of "Biological Diversity" journal now online onlinelibrary.wiley.... @BD_SCBG Diversity of content nicely reflects the title: birds, farmland and rewilding, plant reproduction, fungal pathogens, new species and population biology. #PlantSci #Science #Biology

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Pat Heslop-Harrison @pathh.bsky.social · 06/09/2024

UK Dairy Day Banner for genetic research - sometimes graphic does not show in main post

Banner showing genetics of animals, feed/food and microbes all contribute to reducing methane production from cows

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Pat Heslop-Harrison @pathh.bsky.social · 06/09/2024

Our Food from grass: Genetics and Digital Twins to optimize sustainability, including methane greenhouse gas reduction approaches, ready for science area @UKDairyDay #DairyDay Looking forward to seeing the best stock and best farming anywhere next week

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Pat Heslop-Harrison @pathh.bsky.social · 27/07/2024

After Muthama Muasya 's talk, I'm even more looking forward to @IBCCapeTown2029 #IBC2029 #IBCXXI in Greater Cape Floristic Region #biodiversity hotspot with <<1% of area but 20% of African diversity. #IBC2024 and wonderful science in Capetown, Stellenbosch, Kirstenbosch and beyond

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Pat Heslop-Harrison @pathh.bsky.social · 27/07/2024

Muthama Muasya Cape Town goes through special & unique African habitats and traits with unique evolutionary opportunities: C4, spines, epiphytes, underground structures, fire, trees/shrubs in @annbot @AoBPlants @InSilicoPlants talk (report @TrudeSch as I'm isolated) #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 27/07/2024

John Pannell Lausanne gives a comprehensive talk on dioecy, monoecy, and resource allocation with floristics, ecology, genetics & genomics. I've had enough of online talks, but needed for me today. Super integration of diverse publications. #IBC2024 scholar.google.se/ci...

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Pat Heslop-Harrison @pathh.bsky.social · 27/07/2024

Aaahhh. Choice made between Muthama Muasya and Toby Kellogg at 8.30 in N104 & N103. Neither. Sorry. I'm Feeling fine, as expected from 8am starts and 1am finishes: Thought I'd use the last test I've got. Stay well all. #IBC2024 #COVID19 #Covid_19

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Doug Soltis & Mark Chase moves to APG5 APGV. Shows phylogenetics corrected w DNA taxonomy: Nymphaea not close to Nelumbo etc! Base pattern settled but more needed, integrating incongruent nuclear/chloroplast trees. #IBC2024 I love Cronquist's bubbles & Dahlgren's Dahlgrenograms!

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Oats Avena: Qing Liu puts mitochondrial genome assembly into wider context of evolution of her Avena genome assemblies and polyploid chromosomal rearrangements, with organelle-nuclear sequence transfer #IBC2024 link.springer.com/ar... genome expansion: link.springer.com/ar...

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

I love talks at #IBC2024 sorting out really complex taxa - underpin all biodiversity studies with implications for CBD, climate, SDGs and more. Ambika I, Calicut, Kerala, Does a brilliant job telling us about features & boundaries of grass tribe Jansenelleae Voronts (Poaceae)

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Cassiano Welker gives impressive coverage of Brazil grass diversity, including sister to other grasses in Anomochoolideae #IBC2024 Now what about genome assemblies from these (& I want other Brazilian spp in Joinvillea & other Ecdeiocoleaceae) ?

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Extremeophile grasses from @AelysHumphreys Stockholm 70°C /69° soil temperature is not a problem! Finds new clade / geothermal lineage. & my ?: can you see selected be sweeps at genomic level (&metagenomics soil too) - which needs her discovery of origin of populations #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Oh dear, 100,000 disposable cups later, #IBC2024 is contributing unjustifiably to unnecessary pollution. Next time, @Annbot @BotanyOne @WileyGlobal @OUPAcademic sponsor a reusable mug for us all and have coffee urns. Get another location if centre don't agree!

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Angela Moles @AngelaMoles1 points out fecundity can matter a lot to adaptation, thinks that extreme climate events may be overemphasized. She also asks why we see plants moving range so much already when there is such a diversity of microhabitats #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Angela Moles Rapid evolution is happening, but spp and communities are changing, adapting & going extinct in different ways. Some biomes have gone on ancient past, predicted to go now. Must look forward maximum biodiversity #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Soon is Qing Liu, South China Botanical Garden SCBG adding to the complex grass mitochondrial genomes - & showing why, contrasting to chloroplasts & animals, they are +/- useless for phylogeny #IBC2024 in @VorontsovaMS Poaceae Grass Roots A10.08 c. 12.20 bmcplantbiol.biomedc...

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Plant responses to climate change beautifully discussed @AngelaMoles1 Species are shifting range, but 37% of species move (anthropocentrically) the wrong way! It's complex. Now asking if movement of some spp will threaten another set of spp - is this the Trolley problem? #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Mike Baker shows palaeologs are so important in crops with super Brassica data! The story of plant evolution is the story of polyploidy! #IBC2024 & to my question, yes, polyploids will do even better!

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Mike Baker asks why does number of WGD events average 3.5 and not 1or2 or 8 more. And polyploids diversify more slowly than diploids. Nice models and now simulations (missed his pp event slide so mine from Alix HH 2017) #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 26/07/2024

Mike Baker discusses ubiquity of palaeopolyploidy or WGD in all plant groups and recent polyploidy, now revealed with genome assembly (as well as cytogenetics!) #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 25/07/2024

Sara Lopez-Gomollon @GomollonSara Role of small sRNA / RNA silencing pathways in tomato 🍅 hybrids. Differently expressed sRNA correlated with EPRV expression, the sRNA mapping to EPRV with dicer2. The sRNAome! NM,Complements @TrudeSchw in Petunia next talk. #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 25/07/2024

Diversity of Transposable Elements TE in beet Beta species by @NicolaSchmidt15 showing huge differences in TEs with parallels in different taxonomic groups onlinelibrary.wiley.... #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 25/07/2024

Christian Parisod shows TE-driven based genome fractionation in Brassicaeae, along with recent activities, methylation and centromeric abundance driving reorganization. www.biorxiv.org/cont... #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 25/07/2024

Ped Casacuberta Barcelona opens transposon TE transposable element session @Ibc2024 #IBC2024 Great use of long read assemblies of 2x and 4x cotton showing different behaviours of Athila, York & Tekay elements with different dynamics on the genomes

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Pat Heslop-Harrison @pathh.bsky.social · 24/07/2024

Grass Taxonomy Expert Network TEN meeting with Bat @VorontsovaMS leads on from key concepts of being open, representative, inclusive and collaborative to asking key questions about naming of grasses and the world flora online WFO #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 24/07/2024

Is anybody up to make a database geolocating where specimens come from or ecosystems are, in every Botanical publication with locality data? Would be great to have map to click & enlarge. I wanted to do @annbot @botany.one but no time. cf Pam Soltis herbarium records #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 24/07/2024

Pam Soltis celebrates the world's 3600 herbaria. Evolving uses of herbarium specimens, DNA and super digitised images metadata records www.idigbio.org/portal #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 24/07/2024

Are ecotypes on the way to becoming species? asks Steven Johnson. A few are, most go extremely nct. Small divergence events and extinction lead to speciation and macro-evolution correlates with micro. Many examples given support fig below - & work of Darin & Wallace #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 24/07/2024

Amazing ecotypes correlating with pollination niches from Steven Johnson Natal, South Africa. So many examples with moths, bees, mammals, reptiles, scent or not, colours, corrola length. Great videos of pollinators in action. Great anecdotes too! #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Hearing about commitment of Darwin Tree of Life project to early open publication from Ilia Leitch. Such a change from a decade ago when Institutes / Universities had the worst sharing policies. Critical now that deep learning & machine learning will need all the data #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Xu Xun from BGI breaks another technical barrier with single cell transcriptomics : what an advance on mRNA in situ hybridisation #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Pam Soltis talks about genome assembly consortia and important outputs. Eg the title Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation given take-home message #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Eliska Zaveska Prague introduces complexity of Zingiberales, with great data showing adaptive role of genome size with light intensity and seasonality ... And exciting thoughts too on transposable elements and polyploidy #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Sophie Maiwald Dresden with @toheitka evolving retrotransposons and 5S rDNA together. Lots of coevolution, but no full 5S rRNA gene with retrotransposon LTR#IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Great to hear more about 5S rDNA expression and variants in hybrids in Cardamine from Ales Kovarik Wonderful FISH chromosomes to support with @TeriMandakova pubmed.ncbi.nlm.nih.... #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Roman Volkot, Ukraine, 5S rDNA organization in 6 diverse angiosperms, showing transcription initiation elements, with very different TIRegion motifs in monocots. Termination (of polIII) some evolutionary differences too. Amazing conserved elements discussed #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

Natalia Borowska-Zuchowska uses modern methods and EM ultrastructure to track nuclear and nucleolus organization of rDNA and where it is expressed and fibrillar centres www.cell.com/trends/... is background #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 23/07/2024

rDNA session opens with Nikolai Borisuk showing polymorphisms in transcription initiation sites in duckweed Lemna species and then assembling 5S arrays with Nanopore long reads. #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 22/07/2024

Maria Decena Rodríguez shows repetitive DNA elements with contrasting evolutionary responses to polyploidization events in Brachypodium grass. Repeats from 25% to 60% of genome and Repeatome is half difference in genome sizes #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 22/07/2024

Tony Heitkam shows incredible results from the large 3.5Gb Saffron Crocus genome: shows it is basically autotriploid but with variation between the ancestral genomes @toheitka #IBC2024

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Pat Heslop-Harrison @pathh.bsky.social · 21/07/2024

Looking forward to hearing all about repetitive DNA and discussions at this (Sunday) afternoons Repeatome session 15.00-17.30 N115 at #IBC2024 one of the first events after the nomenclature section. Repetitive DNA sessions later in meeting

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Pat Heslop-Harrison @pathh.bsky.social · 12/04/2024

I did my own chatGPT review of our same manuscript bmcplantbiol.biomedcentral.com/articles/10.... Some parts are more specific than the actual review as on the BMC Plant Biology website.

ChatGPT asked to review our published manuscript with some generic and some specific points

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Pat Heslop-Harrison @pathh.bsky.social · 12/04/2024

Nature news article on chatbots and peer review www.nature.com/articles/d41... What do people think about the referee report on our paper in #BMCPlantBiol? Public peer review link, screenshot below, is halfway down on bmcplantbiol.biomedcentral.com/articles/10.... Paper is doi.org/10.1186/s128...

Referee report on our paper, published along with final manuscript.

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Pat Heslop-Harrison @pathh.bsky.social · 15/03/2024

and the patent has some additional information about this remarkable inhibitor of post-germination ethylene production response patents.google.com/patent/WO202...

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Pat Heslop-Harrison @pathh.bsky.social · 15/03/2024

Delighted to announce launch of "Biological Diversity", new not-for-profit journal published by @WileyGlobal onlinelibrary.wiley.com/journal/2994... Covering all kingdoms (+viruses!), from molecular to ecosystem, and genomic, taxonomic, ecological to sociological.

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