Foul brood

[Follow up to Lariocidin last Weds: launched on "5th March" in error earlier, so you may have read it already]

Was I talking about spending a life-time culturing Paenibacillus spp.? I was. It is common enough in science. You pick a final year undergraduate project at random or because you have crush on one of the post-grads and you spend the next 40 years working out minuter details of what your supervisor was interested in . . . who got there because their supervisor was. But really Paenibacillus? never 'eard of it. I used to teach microbiology at The Institute but that doesn't mean I knew anything about it!

So I looked it up. Paeni- means almost and bacillus means little stick. They are distantly related to old Blob pals like Bacillus and Lactobacillus. Perhaps the most common example with in the genus is Paenibacillus larvae the causative agent of American foul-brood a fatal infestation of honeycomb. But there is also Paenibacillus vortex which grows in such striking patterns [L] on a Petri dish. Other Paenibacillus strains are valued for the anti-microbial properties and also for making industrially useful enzymes. 

But back to foul-brood, which can pop up pretty much anywhere in the world to the despair of bee-keepers. But no surprises when it turns out that there is a lot of diversity within the species Paenibacillus larvae some more damaging than others. One of the key diagnostic signatures are variations among their ERIC sequences. Whoa! that's a rabbit hole because ERICs were discovered by my then boss Paul Sharp just about the time I started working for him in the early 90s. It's also a bit odd to continue using ERIC for species which are not even in the same Kingdom as Enterobacteria.

Bacterial genomes, in contrast to ours, have only small stretches of non-coding DNA between the genes which get translated into protein. The phrase "DNA makes [RNA and RNA makes] protein and protein make everything else" has a lot of explanatory power. All enzymes, transporters, channels,  essential for everyday life are all proteins. Enterobacterial repetitive intergenic consensus (ERIC) is a ~127bp sequence which is found between genes in multiple copies in a lot of 'enterics' include E. coli and Salmonella - here's fragment of the ERIC consensus sequence clipped from the 1991 paper:

note the funny arrows on top of the sequence - they indicate the palindromes where CTTAC - pairs anti-parallel with - GTAAG to form a stable double helix structure. There are too many ERICs around, and the palindromes are too long for this to be a noisy coincidence; and molecular biologists have spent the last 25 years trying to figure out their function. It took Paul a couple of sessions in the pub to come up with ERIC as a memorable, expressive and mildly amusing acronym.

Around about then for Paul's birthday for a jape, I commissioned The Brother of the Beloved BTB, a graphic designer, to make The Boss a pack of business cards. This was before the WWW but after e-mails, so we included name, addr, eddr, phone and fax - and round the edge the 127 As Ts Cs and Gs of the newly discovered ERIC sequence. I thought that was a clever in-joke that might jump-start a geeky conversation about mutual progress at the frontier of sequence analysis. He thought it / I was weird.

Lasso them microdogies

My correspondent G continues to scour through the interwebs looking for Blobocopy. I tell 'er she should start 'er own effin' blog but she's too busy scouring the interwebs. She did though submit The Blob's one-and-only guest blog [cw: asthma] in 2019. The latest alert concerned the discovery of a novel source of potent antibiotics in a Canadian soil sample. This happens occasionally as in the discovery of Eleftheria terrae ten years ago or more to the point discovery of Teixobactin - a chemical from that novel microbe that kills pathogens like MRSA. Back in my 2015 report, I bet that Teixobactin would give its discoverers a Nobel gong within ten years. But they haven't even got a production schedule sorted [there are technical hurdles] let alone FDA approval. Science is Hard.

Gerry Wright [L,L] has been on this line of research for at least ten years but Manoj Jangra [L.R] only came to the lab as a post-doc a tuthree years ago. He is holding [yea! 3-D printers!] a model of their novel antibiotic. If you squint, the molecule looks like a lasso = lariat hence "lariocidin". Their discovery is important because lariocidin nobbles other bacteria in a novel way - by interfering with the bacterial ribosome and preventing protein synthesis. 

When bacteria become resistant to antibiotics, researchers tend to modify [add a bell, drop a whistle] the antibiotic chemically, so that the bacteria no longer recognise the cause of their own demise. But that tends to buy only a few years until the bacteria develop their own modification in the arms-race. It is hoped that, by presenting a completely new method of attack, the effective life of lariocidin (and its inevitable derivatives) will be longer. And lariocidin's structure is radically different from existing antibiotics, so that will pose an extra challenge for the target pathogens. On the safety-side, bacterial ribosomes are functionally equivalent [make proteins] but structurally different from mammalian ribosomes; so there is not going to be cross-toxicity to both pathogen and patient.

Seems that the soil sample from which the lariocidin-producing Paenibacillus was isolated came from the garden of one of the lab techs in Wright's lab at McMasters U. But that's the easy bit, it only needs a trowel. I assured G that her garden was full of bacteria killing each other but even the a silver plated trowel isn't going to get her a Nobel. Wright sensibly enlisted the help of a team from University of Illinois Chicago UIC, who provided complementary expertise.

Wright seems to have a thing about Paenibacillus: in 2016 he was scrabbling about in the bowels of the New Mexico earth to find an ecosystem uncontaminated by humans. There they uncovered Paenibacillus sp LC321whose genome held a number of potential target antibiotics. One of the nice threads in that tale is that Wright heard about these New Mexico caves by going to a lecture by Hazel Barton, an Akron U spelunking microbiologist.  Note to self: always go to lunchtime seminars! Like me at Aled Edwards' giving side-eye to same-old same-old research funding.

Microdogies? It's a Rawhide reference. Dogie: an orphan calf.

free pease

 Last year, just as Summer was fading, a mysterious donor flooded the local library with yellow-pack seeds. Unable to resist freebies, I snagged a packet of peas and a packet of spinach; and hoped I would remember doing so in the Spring. I did! On 11th March, I planted 9x peas in my handy everlasting set of 5cm ⌀ micro plant pots. In the same session I planted 9x black haricot beans own-self-saved from last year. Remarkably, I scored `100+100% germination and here they are on 26th March:

I think I'm probably a bit previous on this because we are a full 5 weeks from last possible frost (1st week in May hereabouts) and I can't leave them in those tiny pots that long and I really don't want to do an interim re-potting of t'buggers. I think I'll tek a chance on putting them in the ground inside the poly-tunnel this coming week. I also started another set of 9xpea + 9xbean on the 27th Mar as a backstop.

We are currently enjoying a bounteous flush of salad greens which have appeared from nowhere - or at least which re-appeared more-or-less where they were last year with no effort on my part. Rocket Eruca satica (really tasty unlike the watery stuff that's sold by Tescaldi), lettuce Lactuca saliva; mustard greens Brassica juncea; tarragon! Artemisia dracunculus (so good); wild garlic Allium triquetrum; mint Mentha spp. is impossible to kill and we have two varieties intermixed. When I'm home alone, I nip up and snip a sandwich full for lunch. Less often when anyone else is present because they will insist on rinsing the leaves and discarding any with holes - such a waste.
 

Allen the Ever-present

Hex and jiminy, it's so much easier to deal with someone else's clutter! Following the departure of Pat the Salt last October, we have undertaken to clear out The Shanty at his old gaff on the Waterford Coast. The Shanty is a 2m x 4m garden shed sold as a kit and spectacularly under-engineered. The floor and roof consisting of 10mm pressed fibre-board sheets, the former covered with roofing felt. Several years ago, the place next door was rented to a single-parent dad who worked as a chippy. We helped populate a veg garden to amuse his daughter; and he offered to fix the Shanty's sagging wind-swept roof. The installation of a new marine-ply roof cost more that the whole shed-kit, but it seemed good value if only for feeding the local-local economy. 

16 cu.m. can hold a lorra shite! It was arranged that a van-with-two-man would come on Tuesday last to whisk away anything we didn't want including a matching slightly furry matching sofa-and-chair set and the decidedly furry mattress off a day-bed. Triage was the day before.

We set off bright and early last Monday. And when I say bright, this was Met Eireann's forcast for the day: ⬤⬤⬤⬤⬤⬤⬤⬤⬤⬤⬤⬤.  But about five minutes into the trip The Beloved said "Dang, we'll need an Allen key to dismantle the day-bed, we should go back". I demurred, not least because with the ubiquity of Allen keys, I reckoned we could borrow one from the neighbours.

On arrival, we rolled up our sleeves, donned gloves, and set to. The first thing I picked up from the sagging Ikea shelves in the Shanty was a heavy Celebrations tin which rattled. Sure enough, in among the pot-pourri of screws, nails, hooks, spacers, scrapers and plugs, there were three Allen keys: one exactly the right size for that day-bed. 

It's a terrible thing the consumption of the planet's natural resources to make shoddy stuff that has a half-life measured in months rather than decades. We came away with a Yaris bootful  [~1 cu.m.] of stuff than can get a second life: including a brace of well-rusted club-hammers. Pat really believed in the club-hammer as a generic persuader. I concur and have several . . . when a Mummy hammer and Daddy hammer love each other very much etc. The haftless one [R above] weighs 12lb = 5½ kg which is too heavy for a) normal people b) normal handles.

yochi-yochi

That would be ヨチヨチ the tottering motion of, say, a toddler making their first steps. I guess it could be added to those tedious lists of words for which there is no equivalent in English: hiraeth and saudades , or indeed kokoro 心, looking at you. But I've been mining a deep lode of such words in Polly Barton's memoir Fifty Sounds (2019, Fitzcarraldo publ.).

Actually it's much more than a what I did in my summer hols memoir because Barton studied Philosophy at Cambridge and did a deep dive into the gnarly tortured thinking of Ludwig Wittgenstein on the nature of communication and language. Immediately after graduating she travelled to Japan as a TEFL assistante at a group of school in a remote area of that alien country. Alien to her and me and probably you too; even if you are really into manga and/or ramen.

Because of her earlier training in how to think, she didn't just try to confront and hopefully master the many examples of doing things different there. She came to appreciate and start to unpick how much of our monoglot anglophone 'lang & comms" is only partly to do with the words (which you can look up in your lexicon) but a lot to do with the gestures, pauses, emphasis and intonation. It is also an opportunity to confront the embedded certainties and warm-bath background of her native tongue: English spelinge much?

Intonation? A professor of linguistics in full flow during class announced that there is no known language in which two positives are used to indicate a negative. Voice from smart-arse at back of hall "Yeah, right!". I had something to say about phatic elements of communication back in 2019. These are all the establishing empathy and common ground that make up most of our daily interactions with other humans. All those comments about the weather, asking how d'ye do without expecting a reply - let alone a view of the stitches on the other person's hernia repair.

Barton spend 15 years in Japan learning the language, culture and customs before returning to Bristol to hang out her shingle as a translator from the Japanese of which she has a dozen books to her credit. A good translation is quite as much effort as the original book - more perhaps because the creative flow is hampered by the original author's plot line and sensibilities. Fifty Sounds is essentially 50 chapters each one riffing in a Japanese word or phrase, where she encountered it and what it made her think.

One short telling chapter is about moja-moja モジャモジャ - the adjective routinely applied to Barton's curly hair. Not the more common (loan-word?) kuru-kuru - that wouldn't do. A friend explained that her hair was beyond curly it was wild unruly electric like Struwwelpeter. The poor women's moja-moja hair [as R with a moja-moja sheep in the background] attracted A Lot of uninvited pawing and poking . . . and not only from curious pupils. This skin-crawling observation has the ring of truth because it's the frequent experience of Dau.I the Librarian who has the bestest biggest hair in the family. What is wrong with people's assessment of personal space that they feel licensed to touch other people whose work is inevitably public facing?

moja-moja? Young feller from The North comes back from college in The South raving about The Dubliners. Uncle who has seen them on the TV: "That Ronnie Drew and Luke Kelly, they look like a pair of sheep's arses." The prev jokes are the best jokes.

Beach off-limits

A lot can happen overnight, so I get out and about as soon as I've downed my first pot of tea. The key thing is to head-count the sheep: anything other than N = 15 it's Houston we have a problem.  It has happened that we have extras, as when two years ago our abutting neighbour bought in a handful of particularly jumpy sheep. But it's more likely for the count to come up short. Anything missing is dead OR has its head caught in a wire fence OR has gone on holiday. All of these are a pain in the arse. It is therefore a relief when, after repeated counts, the missing beast bursts out of the shrubbery; or is revealed cudding in plain sight exactly masked by a 'larger' sheep [not small but far away] in the foreground.

08:00 last Wednesday it was N = 14 again and I set off à la BoPeep. I say again because one of the sheep has been persistently AWOL over the Winter. She had a bad case of The Itch, lost chunks of fleece and looked quite wretched altogether. It was as if the poor creature had been sent to Coventry or the sheep equivalent of Leperstown. Despite expecting any day to discover her stiff with her legs in the air, she has survived two rounds of treatment and the worst of Winter. When she is away feeling mizz, she is often to be found in or around The Skunch. The Field Over The River is so called because beyond its Eastern edge the land falls abruptly 10m to the river stream which bounds our farm. This cliff tapers off along our field immediately N. Between this gentle slope and the cliff is a bosky dell or 'skunch'. There has always been a low wall parallel to the river in the Skunch and beyond it is a tiny beach covered in willow and shade-loving woodland plants. The kids used to have picnic-and-paddle down there when they were tots, but it's gotten jungly and briar-grown since the girls left home.

And that's where I found the errant sheep. In her earlier lonely sojourns she'd eaten her way through to wall and now was hopped over to the beach. Thence is but a short paddle to Wexford and the neighbour's meadow. Which would never do, so I hooshed her out of it, and spent the rest of the morning running a fence along the dwarf wall. Running a fence requires the assembly of a measured length of sheep-wire + stakes, pry-bar, shovel, staples, sledge-hammer, claw-hammer, pliers, secateurs, gloves, chain-saw + PPE. Then pushing a wheel-barrow full of kit 300m down-hill on a 1:10 slope. Down is easy, but you really don't want to push 40m = 20kg of off-cut sheep wire UP hill. 

We'll have to see what happens but the beach is now officially off-limits. ↑ indicating the two more-or-less vertical trees which book-end and support the wire. Dry-stone walls are the very devil for driving fence-posts unless they are tall enough and wide enough to have two faces back-filled with small stones and sod. Not the case here, so three (3) posts will have serve for the 11m run of fence.

Enniscorthy Co Kerry

I'm quite the fanboi for Colm Tóibín. I thought The Heather Blazing was the best history of this our Republic despite being fiction from beginning to end. I can't swear that I read his Brooklyn, but I saw the Saoirse Ronan vehicle of a film. Maybe I'm getting ahead of myself to earbook the sequel Long Island (2024) on Borrowbox. Maybe I'm lucky to have found a copy of last year's best seller available for download. Maybe Tóibín is now a drug on the market and nobody wants to read such stuff.

In Long Island, Eilis Lacey has married into a Brooklyn Italian clan which made good and made it ut to the 'burbs in Lindenhurst, Suffolk County, NY. For reasons, she leaves New York and returns home to Enniscorthy [R 1970] for the first time in 20 years. Her two teenage children have never been to visit that side of their family. Tóibín grew up in Enniscorthy and his presentation of small-town busybody snob and gossip is unsettling. As for the story, the unfolding tragedy hinges on a series of coincidences worthy of Dickens and deductive powers worth of Sherlock Holmes - so I guess it will take its place in The Canon. I reserve judgment on the moral and social failings of the cast of characters, but don't let that hold you back.

The audiobook is read by Jessie Buckley, award-winning actor from Kerry via Thurles. Buckley has a) unnecessarily, decided to render direct speech in different accents b) unaccountably, given up on the nuance of regional Irish accents to voice everyone from Enniscorthy as if they're from deepest Munster. A disconcerting cross between Martin's Life and Healy-Rae. And a lot of the proper names [Buncloddy, Curraghcloo, Clonrosh] are mangled because . . . who cares? 

~~≋~~

For the record, I've also knocked of a history of the British communications intelligence CommInt service GCHQ (2019) by Richard Aldrich. It runs to 19 hours of political and historical detail of phone-taps and radio-traffic capture. The stuff from the 1970s tinkled a distant bell because I lived in England then and read newspapers. But the more recent material was revelatory. Every email I've ever sent has been processed by GCHQ software, for example. That's the same GCHQ that put out a puzzle book for Christmas 2016