Toxic moth nests
As a keen pseudo-professional photographer I am always on the look out for odd and intriguing things to photograph. In the absence of birds other than skylarks and rooks along the St Ives to Cambridge guided busway I photographed what looked like a silky nest in a blackthorn bush. It was on the left hand side of the walkway as you approach the Oakington stop (about 400m away in fact). And then another.
I posted the photo to Facebook and asked for comments (to be honest I hadn’t even noticed the caterpillars at the time I took the photo and only did so when I was “developing the print”. I had been musin...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 15, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
Classic Chords #17 – Yes, W ürm turns
The classic Yes track Starship Trooper (from 1971’s The Yes Album) comes in several parts just as any good prog rock and/or classical music should. Parts i-iii are “Life Seeker,” “Disillusion” and “Würm.” It is that latter section that is the focus of my latest Classic Chord on Sciencebase.com. The chord carries a wonderful and yet seemingly interminable jam on a mesmering progression -nominally nothing more than a G major to an Eb major to a C major and back again.
It’s not a common progression, but guitarist Steve Howe, is not known for being a common guitarist, there...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 12, 2017 Category: Science Authors: David Bradley Tags: Classic Chords Music Songs Source Type: blogs
A tree by any other name
A recent late afternoon stroll with Mrs Sciencebase around NT Anglesey Abbey in Lode, near Cambridge, led to a few revelations about various plants and statuaria that were in bloom and uncovered following the winter. There’s an avenue of trees before you leave (not the Winter Walk) but parallel to that with a tree we couldn’t identify. Picture below, tree is about 8-10 metres tall and in this zoomed in shot you can see a bee about to alight on its floral protuberances.
Tall, with both a red and yellow, rhubarb and custard, hue to its aspect overall against the blue of the sky. The curious thing though zoomin...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 11, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
Konik ponies at Wicken Fen
Hardy Konik ponies graze the Wicken Fen nature reserve, keeping the wetland grasses at bay and adding their own brand of fertiliser to the land. I snapped a clutch of photos of these beasts on a recent visit, but there were so many reeds between them and my camera lens that I had to duck and dive to try and get a shot of a head toss, or a gallop or a noisy splash in the marshy water. Of 52 photos taken from various positions along the footpath trying to capture the equine essence all but one captured a story of wild life on the fen I feel.
Of course, it was the first photo of the contact sheet. It’s often the way, t...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 8, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
Currant affairs
Quick snap of one of the many weeds growing in our garden (backyard and frontyard). Of course, it’s not really a weed, because we want it to grow there. It’s a Ribes, which a neighbour tells us his mother-in-law used to describe as smelling of cat urine (not to me it doesn’t).
Anyway, the pink “glow” around the ribes blossom in this photo confused me when I first looked at the image on the camera’s display…I couldn’t work out why the flower was out of focus until I looked again and saw that there was another floret behind the sharp one. The effect is an artefact of the shor...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 7, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
The true meaning of Easter
The Church of England, more specifically, one of its bishops complained earlier this week about how Cadbury (manufacturer of Easter eggs etc) and the UK’s National Trust (planning to run egg hunts on its properties) had dropped the word Easter and that was tantamount to spitting in the face of the founder of Cadbury and a slur against Christianity. Our Prime Minister took time out from her busy arms-dealing schedule in the Middle East to back the bishop on this. Neither of them had checked whether this dropping of Easter was anything but fake news.
Of course, it was all great free publicity for Cadbury and the Nati...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 6, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
How do non-competence genes respond to competence inducting treatment?
For the RNAseq part of the toxin-antitoxin paper, we should describe what we learn about how transfer to the competence-inducing starvation medium MIV affects genes not known to be involved in competence.The former undergrad left us with a set of Edge and DEseq2 analyses of changes in gene expression. I discussed them here last summer (http://rrresearch.fieldofscience.com/2016/08/making-sense-of-rna-seq-comparisons.html). Unfortunately I don't know how to properly interpret them. The former post-doc suggested some analyses, but I'm reluctant to dive into these until I have a better idea of what I'd be gettin...
Source: RRResearch - April 6, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
What we learned from the RNAseq data: Part 1
So, we did a massive RNAseq study, with 124 samples ofH. influenzae cultures at different growth stages, in the rich medium sBHI and the competence-inducing medium MIV, and with wildtype or mutant genes affecting competence. (You can use the Search box to find all the previous posts about this work...) Here I specifically want to think about what we learned about competence from the competence-induced cultures (cells transferred from sBHI to MIV). We sampled cultures at the T=0 point indicated by the star in the above diagram, and the 10, 30 and 10 minute times in MIV. I'll consider the results for stra...
Source: RRResearch - April 5, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
A new plan for contamination correction
The grad student and I had an intense Skype discussion with the former postdoc this morning. We realized that there's a much easier way to estimate the total Rd contamination in the uptake samples, so we're going to do this.Preamble: The former postdoc isn't convinced that this will be better than what we were doing. He likes the simplicity of using the dual-genome alignments directly to calculate uptake ratios, and doesn't think that all the missing data from multiply-mapped positions is a concern. I don't like discarding what is otherwise good data, and hope that using all the data we can will reduce the n...
Source: RRResearch - April 5, 2017 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Flying visit to Ma-in-law-on-Sea
Needed an ornithological escape on a flying visit to South-Kens-on-Sea to visit ma-in-law. Thankfully, there’s a bird hide overlooking the marshes not 10 minutes walk from ma-in-law, just up the Thorpe Road past the (in)famous Scallop sculpture on the shingle shore. Anyway, a dozen grey herons, same again little egrets on the water, a couple of shelduck (Tadorna tadorna, another tautonym), some wigeon (Anas penelope) and others waterfowl in the hazy distance, the inevitable black-headed gulls and a tiny murmuration of starlings. Much closer to the hide a male reed bunting (Emberiza schoeniclus) of which I got a quick...
Source: David Bradley Sciencebase - Songs, Snaps, Science - April 3, 2017 Category: Science Authors: David Bradley Tags: Science Source Type: blogs
