iiinova — where your digital self keeps evolving

Freya Harrison @friendlymicrobe.bsky.social · 03/09/2026

Perhaps the most surprising result was that we attempted to select for resistance to the reconstructed eyesalve using different experimental evolution protocols, but utterly failed - it seems relatively difficult for resistance to happen. Graph below is from a ramp experiment. #MicroSky [3/n]

S. aureus Newman, A. baumannii ATCC 19606, and P. aeruginosa PA14 were selected for resistance to Bald’s eyesalve or antibiotic using an evolutionary ramp approach for 14 days. The y axes show the higher of two tested concentrations in which cultures grew at each time point, expressed as a multiple of the ancestral MIC. Each line shows one of three independent populations.

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Freya Harrison @friendlymicrobe.bsky.social · 03/09/2026

It's taken 12 years and a lot of work from many fantastic people, but we have published an analysis of how our reconstruction of Bald's eyesalve kills bacteria. This was driven by @tosinorababa.bsky.social & Jess Furner-Pardoe through their PhD work #MicroSky journals.asm.org/doi/10.1128/... [1/n]

Jess in the lab, holding an onion and a garlic bulb and talking; Tosin in the lab holding a petri dish and inspecting it; two glass bottles labelled "eyesalve 33/6/14"

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Freya Harrison @friendlymicrobe.bsky.social · 02/09/2026

@rachelmwheatley.bsky.social and I really enjoyed putting together a special issue of Essays in Biochemistry on the social lives of bacteria. All the papers are now out, and here's our editorial :D @biochemsoc.bsky.social #MicroSky portlandpress.com/essaysbioche...

The journal cover, showing a CLASI-FISH image of a structured bacterial community.

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Freya Harrison @friendlymicrobe.bsky.social · 01/09/2026

The use of Galleria mellonella to study microbial interactions, immune responses, & substrate interactions - super, comprehensive review from Evgenia Maslova, Ciaram Staber & @ronanmccarthy.bsky.social portlandpress.com/essaysbioche... #MicroSky

Schematic representation of G. mellonella applications for investigating interbacterial interactions
The upper half (A) of the figure depicts experimental methods in which bacteria are introduced to G. mellonella larvae. These include force-feeding, injection, and burn models. The lower half (B) shows example interactions described in the literature within the G. mellonella model, including antagonistic, competitive, and cooperative co-infection outcomes.

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Freya Harrison @friendlymicrobe.bsky.social · 01/09/2026

The social lives of bacteria as revealed through CLASI-FISH - thank you @jmarkwelch.bsky.social for this lovely review, covering the structure of bacterial communities in the human mouth, mouse gut and associated with kelp portlandpress.com/essaysbioche... #MicroSky

Bacteria in a cross-section of the mouse colon. The colonic epithelium (gray) is at right and at the bottom of the image; bacterial cells appear as colored dots, and food particles appear bright yellow. Some regions are rich in Bacteroides spp.; others have all five labeled cell types, but in all regions, bacteria are mixed.

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Freya Harrison @friendlymicrobe.bsky.social · 11/08/2026

How do phages maintain or increase the diversity of plant-associated microbiomes? Thanks Renée Smith & @dholtappels.bsky.social for contributing this review to Essays in Biochem #MicroSky portlandpress.com/essaysbioche...

Phages impact microbial communities from individual interactions to ecosystem-level functions. At the individual level (top, individual host represented by the dark blue color), phages infect single bacterial hosts, resulting in co-evolutionary arms races and the dispersal of genetic information through phage-mediated HGT. At the population level (closely related host bacteria as represented by various blue shades), phages and their bacterial hosts are intertwined with predator-prey dynamics and KtW dynamics, which support microbiome diversity and community structure effects. By influencing bacteria at the individual and population levels, phageomes are hypothesized to play important roles at the ecosystem level (including distantly related non-host bacteria, as represented by different colors and morphologies) in both function and resilience

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Freya Harrison @friendlymicrobe.bsky.social · 11/08/2026

One of the best summaries I’ve seen of the whole sorry Arday situation. From Reddit.

A post from user PeterRum. It reads as follows. “ How about this. I've been fascinated by the story, as an Oxford and LJMU graduate who is a disabled person.

It has made me doubt myself, despite the fact I usually downplay my academic record. I want to be judged for my work. Still, I feel inherited shame over this whole affair.

First hand I have seen academics being racist to felloow students in a casual way (not at Oxford tho). How much worse to be held back and told you were pushed forward.

Yes, it seems in this case they tried to rectify things by allocating a poster boy to show things had changed. But they made it worse for all of us by casting doubt on our achievements by allowing him to fake his.

I've got enough imposter syndrome without this shit.

Also, that poor, sad, delusional clown who spouted nonsense everyone pretended to believe. How much of it did he believe? Was he clinically delusional?”

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Freya Harrison @friendlymicrobe.bsky.social · 10/08/2026

How much do we currently know about the influence of bacterial-fungal interactions: on community function in environmental, health & industrial contexts? Thanks @halllab.bsky.social & @katherine-baxter.bsky.social for this review for Essays in Biochem! #MicroSky portlandpress.com/essaysbioche...

Example bacterial-fungal interactions in three different niches. Plant niches: synergistic interactions to promote plant growth by enhancing nutrient uptake, and antagonistic interactions where a bacterium prevents fungal infection. Human niches. Examples of C. albicans interactions across four different body niches showing synergy with bacteria in oral plaque formation, the CF lung and gut microbiome dysbiosis, and antagonism where bacteria prevent fungal infection in the vaginal microbiome. The built environment: co-occurrence of fungal species increases the resistance of Legionella to UV disinfection.

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Freya Harrison @friendlymicrobe.bsky.social · 10/08/2026

Absolutely stunning dual RNAseq/imaging work by @andresfloto.bsky.social & colleagues: subpopulations of P. aeruginosa with different transcriptomes exist in different niches (airway lumen, glands, blood vessels) in explanted #CysticFibrosis lungs 🤯 #MicroSky www.biorxiv.org/content/10.6...

Images of H&E stained slices through bronchiole and surrounding tissue, overlaid with coloured spots showing where expression of different P. aeruginosa transcripts was detected. Transcripts are detected throughout the large mucus plug in the lumen, and also to a lesser extent in the surrounding tissue.

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Freya Harrison @friendlymicrobe.bsky.social · 31/07/2026

Excited to share this paper led by @aaroncurtismicro.bsky.social @medmycology.bsky.social! Coinfection of Pseudomonas aeruginosa & Aspergillus fumigatus in an ex vivo lung model leads to competition and changes in both pathogen & host proteomes #MicroSky www.microbiologyresearch.org/content/jour...

A graphical abstract. Pseudomonas infection leads to increased fibrosis and NK cytotoxicity in pig tissue, while A. fumigatus infection leads to increased fibrosis and activation of the complement cascade. In coinfections, several aspects of pathogen metabolism and virulence are altered.

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Freya Harrison @friendlymicrobe.bsky.social · 03/06/2026

Imaging of #biofilms using cryo-scanning electron microscopy - a superb review and how-to guide from Saskia Bakker, our resident EM wizard here at Warwick #MicroSky portlandpress.com/essaysbioche... Image: S. aureus #biofilm, with clusters of bacteria (white arrows) on a background of matrix.

Biofilm of Staphylococcus aureus, showing clusters of bacteria (indicated with solid white arrows) on a background of EPS (outline arrows) and hydrogel matrix (arrowheads). Scale bar 1 μm.

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Freya Harrison @friendlymicrobe.bsky.social · 04/05/2026

Had a super time at Flag Fen’s Viking Festival this weekend. A friend wanted a walk-through of early medieval bookbinding, so I improvised a jig and we each got a new book sewn. I love the diversity of crafty hobbies and skills that reenactment has introduced me to.

An early medieval encampment, with tents, wooden tables and various tools and items of daily life. In the foreground, two people stand either side of a table. Between, them, and upside-down stool is being used to hold vertical jute cords taut. Each is bent over a stack of folden manuscript pages on the table in front of them. They are sewing the stacks of pages together and attaching them to the jute cords as they sew.

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Freya Harrison @friendlymicrobe.bsky.social · 01/05/2026

Super poster from Simran on her PhD work and plans at today’s student symposium! She’s co-infecting our CF lung model with Pseudomonas & Burkholderia species to see how they interact #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 27/04/2026

Another lab presentation success - well done @kadeayomikun.bsky.social for winning "best talk" at the Warwick Respiratory Infections Sparking Chronic Diseases symposium 🎉

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Freya Harrison @friendlymicrobe.bsky.social · 15/04/2026

Find out about how different host-mimicking environments alter P. aeruginosa biofilm from @kadeayomikun.bsky.social at poster 169 at #Microbio26

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Freya Harrison @friendlymicrobe.bsky.social · 15/04/2026

@c-cornbill.bsky.social has has TWO posters at #Microbio26! find out about antibiotic resistance evolution in our cystic fibrosis lung infection model at no. 124

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Freya Harrison @friendlymicrobe.bsky.social · 15/04/2026

Saskia is presenting her MBio project on optimising our cystic fibrosis lung model for working with Aspergillus - no. 141 at #MicroBio26 @warwicklifesci.bsky.social

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Freya Harrison @friendlymicrobe.bsky.social · 14/04/2026

Come to #Microbio26 poster 192 to hear how @charisthompson.bsky.social is sensitising mycobacteria to beta-lactams by making them flip their wall-building strategy #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 14/04/2026

Cracking talk from @nreddy.bsky.social about her PhD work - designing polymers based on AMPs to kill troublesome biofilm bacteria, or to help antibiotics kill these bacteria #Microbio26

A woman talking in front of a projected slide. The slide shows a synergy plot - for a narrow range of polymyxin concentrations, any concentration of our polymer synergises with the polymyxin when used to co-treat Pseudomonas aeruginosa.

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Freya Harrison @friendlymicrobe.bsky.social · 14/04/2026

Come to #Microbio26 poster 094 to hear all about natural product antimocrobial discovery from @tosinorababa.bsky.social and me #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 13/04/2026

En route to #Microbio26 on a very crowded train. But I have a case to sit on and a brew, so it’s not all bad.

The photographer is looking down at a take-away cup in her lap, and the surrounding floor. Lots of pairs of feet and suitcases are crowding the shot.

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Freya Harrison @friendlymicrobe.bsky.social · 06/04/2026

Who else spent Easter Sunday paddling a coracle while wearing early medieval drag?

A lake, surrounded by trees and rushes. The water surface shows that it is breezy. Two people are paddling coracles, dressed in early medieval tunics and nalbound hats. One wears a cloak, which is billowing in the breeze.

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Freya Harrison @friendlymicrobe.bsky.social · 25/03/2026

I loved the Made in the Middle exhibition, currently at mac Birmingham. 37 artists creating beautiful things with exceptional technical skills in different media. The pictured vases look like delicate hand-carved clay, but are 3D printed - by www.keeleytraae.com. Full info at craftspace.co.uk/mitm/

A collection of brightly-coloured vases and pots. Each is a single solid colour, with geometric sharp ridges covering its surfaces.

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Freya Harrison @friendlymicrobe.bsky.social · 14/03/2026

Lovely to see biological art by one of our undergraduates, Joseph Moulton, on display @warwicklifesci.bsky.social! He’s at uk.linkedin.com/in/joseph-mo... #SciArt #SciComm

A display case of various pieces in different media. There is a scuplture and drawing of a human heart, a painting showing the view through an endoscopy camera, a print of fungi and others. The style is that of detailed scientific illustration.

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Freya Harrison @friendlymicrobe.bsky.social · 06/03/2026

Our wall of women in STEM for international women’s day is growing! Set up by the @warwicklifesci.bsky.social & @warwickmed.bsky.social women’s health group and growing organically

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Freya Harrison @friendlymicrobe.bsky.social · 05/03/2026

If you check out my lab's recent work, you'll notice how much biofilm structure is destroyed by dehydration & vacuum during standard scanning electron microscopy. These are both images of P. aeruginosa PA14 #biofilm on pig lung tissue at 48h p.i: using cryoSEM retains the biofilm matrix. #MicroSky

In the standard SEM image, aggregates of bacterial cells with no visible matrix sit on top of a network of collagen fibrils. In the cryo image, interconnected aggregates are covered with a smooth coat of matrix, and no collagen is visible - it is under the aggregates, and the only tissue structures visible are patches of elastin fibres.

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Freya Harrison @friendlymicrobe.bsky.social · 05/03/2026

Paper out! We used RNAseq to track changes in P. aeruginosa gene expression over 7 days of #biofilm infection in our #CysticFibrosis lung model. www.microbiologyresearch.org/content/jour... #MicroSky (1/n)

A four-panel figure showing scanning electron micrographs of Pseudomonas biofilm on the surface of pig lung tissue. Aggregates of bacteria sit on top of a network of collagen fibrils, with some bacterial cells penetrating the collagen mesh.

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Freya Harrison @friendlymicrobe.bsky.social · 03/03/2026

The fabulous Cassandra Quave invited on to her Foodie Pharmacology podcast to talk about our #ancientbiotics and #biofilm research - there are audio (www.podbean.com/media/share/...) and video (www.youtube.com/watch?v=DCs2...) versions available #MicroSky #SciComm

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Freya Harrison @friendlymicrobe.bsky.social · 25/02/2026

Looking forward to a day in Glasgow talking bacteria with colleagues - just off the sleeper train, caffeinating and becoming vaguely human again. Here’s an arty coffee shop reflection in the drizzle

A reflection of a well-lit coffee shop counter in the dark window of an amusement arcade. The unlit Amusements sign is visible, superimposed on the glass cases of pastries.

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Freya Harrison @friendlymicrobe.bsky.social · 18/02/2026

In doing this research, we worked with CryoSEM wizards Chris Parmenter & Saskia Bakker to image #biofilm in our ex vivo lung model. I‘m in love with the gorgeous images they got of near native-state, hydrated biofilms. Compare panels A-D with standard SEM in E-F 😯💜 #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 18/02/2026

You can read in our new preprint how she used RNA seq to compare the responses of WT and pel-deficient PA14 to the lung environment, and to the presence of sub-inhibitory colistin. Ultimately, the only real difference was in which efflux pumps were upregulated in resonse to the antibiotic #MicroSky

Graohs showing that wild type upregulates MexXYOprM but not MexEFOprnN, while the mutant does the opposite.

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Freya Harrison @friendlymicrobe.bsky.social · 18/02/2026

During her PhD, Jenny found something unexpected: biofilm-deficient P. aeruginosa mutants were just as tolerant to antibiotics as the WT when grown in our cystic fibrosis lung model. But why? #MicroSky 1/n

Four graphs, showing the response of PA14 and an isogenic pel mutant, and PAO1 and an isogenic pel psl double mutant, to meropenem and colistin. There is no difference between the response of mutants and WTs.

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Freya Harrison @friendlymicrobe.bsky.social · 17/02/2026

Congratulations to our latest Dr, @phoebesilva.bsky.social! Phoebe has done some beautiful work optimising cystic fibrosis media & models to allow growth of NTHis so we can start to understand their role in lung disease, and exploring interactions between NTHi, P. aeruginosa and S. aureus. #MicroSky

A smiling woman kneels to cut a cake on a low table. The cake is decorated to look like a bacterial biofilm. There is a bunch of pink roses and a large gift bag on the table.

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Freya Harrison @friendlymicrobe.bsky.social · 03/02/2026

Remember the medieval remedy we reconstructed years ago? We've now dissected the various ways it attacks and kills bacteria! Preprinted & submitted, led by @tosinorababa.bsky.social & Jess Furner-Pardoe w/ many collaborators #MicroSky #Ancientbiotics www.biorxiv.org/content/10.6...

A cartoon showing the various targets of reconstructed eyesalve against Gram-positive and Gram-negative bacteria. It targets the cell membrane, as well as several intracellular targets including nucleotide biosynthesis. In S. aureus, it also affect quorum sensing.

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Freya Harrison @friendlymicrobe.bsky.social · 29/01/2026

We discuss how historical remedies are potential sources of treatments for AMR infections. We focus esp. on tests for interactions between compounds present in these complex mixtures. Fig below shows key moments in the history of human use of three NPs (artemisinin, honey, β-lactams) #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 08/01/2026

They are sending emails from an official address with the PI’s name on too - it’s a massive data scraping project, not just one PhD: knowledgelab.org/team/ Or possibly a concerted effort to anger as wide a section of academia as possible and study our responses..

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Freya Harrison @friendlymicrobe.bsky.social · 11/12/2025

Congratulations to the latest new Dr in the house, @microbescience.bsky.social! 🍾

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Freya Harrison @friendlymicrobe.bsky.social · 08/12/2025

Another new Dr in the house! Massive congratulations to @nreddy.bsky.social 🥳 Thanks to @sebperrier.bsky.social for the continuing teamwork on antimicrobial polymers & excellent PhD students, and to @correlab.bsky.social and @profjamesmason.bsky.social for examining. #MicroSky

Five happy people smiling - four are holding glasses of champagne, and one a coffee mug.

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Freya Harrison @friendlymicrobe.bsky.social · 01/12/2025

Christ on a bike, this is worse than timewasting, it's downright offensive.

An email. It reads as follows.

Dear Author,

We are emailing you from Knowledge Lab (https://knowledgelab.org/) at the University of Chicago, led by Prof. James A. Evans. We are studying how AI helps scientists extend their work in new directions. We came across your paper "Sweet and sour synergy: exploring the antibacterial and antibiofilm activity of acetic acid and vinegar combined with medical-grade honeys" and applied custom AI models on it, which generated 5 new extensions. Our pilot study indicates that up to 60% of scientists found the proposed extensions both thought-provoking and actionable.
Would you like to see these ideas? They are absolutely free and with no obligations -- although we would sincerely appreciate your thoughts on their quality. You may review these extensions and share your feedback with us at your convenience within the next 7 days.

Your contributions will be formally acknowledged in the resulting publication.

Click the link below and fill out your thoughts on them:
Take the survey
Or copy and paste the URL below into your internet browser:
https://uchicago.co1.qualtrics.com/jfe/form/SV_1yPc7XXPRcCh6Xs?Q_DL=U11HdOvG3TSWmcN_1yPc7XXPRcCh6Xs_CGC_uCvOlDC99eFZgjk&Q_CHL=email

Follow the link to opt out of future emails:
Click here to unsubscribe

We sincerely appreciate your feedback.

Warm regards,
Knowledge Lab & Data Science Institute
University of Chicago

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Freya Harrison @friendlymicrobe.bsky.social · 30/11/2025

Lottie hasn’t got the message about antibiotic stewardship, & is resisting completion of her co-amoxiclav course. The pink stains are from an attempt to smear it on her, in the hope she‘d lick it all off. Our vet, OTOH, was super keen to talk about stewardship & her prescribing decision process! 💜

A calico cat loafing on a red sofa. Her eyes are half closed and she looks slightly grumpy. There are pink stains on her white chest fur.

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Freya Harrison @friendlymicrobe.bsky.social · 28/11/2025

Congratulations to our poster prize winners at @bsacandjac.bsky.social #AntibioticResistance & Mechanisms meeting 🎉 #MicroSky

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Freya Harrison @friendlymicrobe.bsky.social · 24/11/2025

I had a little time to work on this illustration over the weekend. Disapproving expressions now added! It’s been fun to attempt a direct copy, and the owner has enjoyed the progress pics. It’ll be part of his display on maille making.

On the left is a print of a medieval illustration showing two men pointing at a third man taking off a maille hauberk. On the right is an almost-finished copy.

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Freya Harrison @friendlymicrobe.bsky.social · 19/11/2025

Here’s @tosinorababa.bsky.social & @nreddy.bsky.social showing the ways we grow bacteria in the lab to simulate conditions in an infected patient - we have models of #CysticFibrosis lung, endotracheal tube & chronic wound, all compliant with efforts to reduce & replace animals in research.

A man and a woman standing behind a table. On the table is a microscope showing an image of biofilm-infected tissue, a robotic ventilator and various items of lab equipment.

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Freya Harrison @friendlymicrobe.bsky.social · 19/11/2025

In a very interesting talk about training dogs to sniff out infection - including Pseudomonas aeruginosa in #CysticFibrosis Here’s a study link, from medicaldetectiondogs.org.uk with @janedaviescf.bsky.social & colleagues publications.ersnet.org/content/erj/5

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Freya Harrison @friendlymicrobe.bsky.social · 16/11/2025

Working on a commission a friend - the historically accurate method for removing maille, from the 13th century Maciejowski Bible (Morgan Library & Museum MS M.638, fol. 28r). Authent-ish illumination strategy with gouache on vellum. #illumination #medieval

On the left is a print of an image from the original manuscript, with test splashes of paint and notes on pigments around it. On the right is is a partially-completed copy.

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Freya Harrison @friendlymicrobe.bsky.social · 21/10/2025

On Sunday, Wantage will celebrate its most legendary figure – King Alfred the Great. I'll be there with plenty of other nerds, displaying the history and material culture of Wessex in Alfred's time. Full info at wantagetowncouncil.gov.uk/alfredfest-2...

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Freya Harrison @friendlymicrobe.bsky.social · 07/10/2025

@aaroncurtismicro.bsky.social adapted our ex-vivo pig lung infection model to conduct dual host-pathogen proteomics in response to Aspergillus infection - he’s a finalist in @microbiologysociety.org young microbiologist of the year #MicroSky www.tandfonline.com/doi/10.1080/...

A man in front of a display screen, showing images of Aspergillus growing on sections of lung tissue.

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