Tag: DNAPage 1 of 3

RBGE’s Silica-dried Collections

We have been working towards protocols for the management and storage of the RBGE specimens dried in silica gel. The bulk of this material is collected by RBGE…

Polytrichum baits: cutting cleaned mosses

Following on from the rather unpredictable results we obtained from fragmenting duplicate aliquots of CTAB-extracted Polytrichum DNA in the Bioruptor, Isuru cleaned aliquots of IK31 and IK53 using…

Hybrid capture from degraded DNA: the mysterious case of the vanishing libraries

When we’re working out a protocol or troubleshooting, we spend a lot of time quantifying small quantities of fluids, looking at DNA concentrations on the DeNovix, running tapes…

Polytrichum baits: Cutting mosses

We started our lab work on the Polytrichum hybrid baits project on the 1st of October, by normalising some CTAB-extracted DNA with 0.1X TE to 55 µL of…

Hybrid capture from degraded DNA: bead-cleaning away the adaptor peaks

After testing bead-to-sample ratios of 30:50, 35:50, 40:50, 50:50 and 60:50 on a Thermo Scientific™ GeneRuler™ 50 bp DNA Ladder, using Beckman Coulter AMPure XP beads, we focused…

Hybrid capture from degraded DNA: testing bead cleaning on a 50bp ladder

When we made our Begonia libraries, working with (in some cases) relatively small quantities of very degraded DNA, we should have diluted the adaptors. We didn’t. Consequently, we…

Hybrid capture from degraded DNA: quality metrics for duplicate extractions

For one of the taxa in our study set, Begonia scottii (living collection no. 20170076), we made a few replicate DNA extractions using Qiagen DNeasy plant mini-kits, and…

How much liverwort do you need to get 50 μg of DNA?

There’s an exciting project, The 10KP (10,000 Plants) Genome Sequencing Project, that aims to sequence and characterize representative genomes from every major clade of embryophytes, green algae, and…

Alternative Methods for Collecting Plant Material for Future DNA Extraction – Part I

Quality and quantity of DNA recovered from stored plant material is becoming more important as DNA sequencing technologies change from the relatively simple Sanger sequencing, to next generation…

Hybrid capture from degraded DNA: test Begonia sample quality

Keen to see the effects of different specimen preservation techniques on DNA quantity and quality, we have assessed extractions of DNA from nine Begonia accessions x seven preservation…

Hybrid capture from degraded DNA: stockpiling Begonia DNA for protocol testing

When working out new protocols, it’s very useful to have a big stash of DNA to test them on. Just now, in a collaborative project with Dr Michelle…

Unlocking the power of poo

A short video by Dr Linda Neaves about the challenges of finding giant panda poo in the mountains of China, and how poo samples can unlock the mystery…

Nuclear internal transcribed spacer (ITS) primers

There are lots of different primers that sit in slightly different parts of the ITS locus, some forward and some reverse. There’s a very well-worn printout stored on…

Testing extractions – comparing DNA on agarose gels

Looking at the capture plates from the two DNA extraction protocols that were tested on our QIAcube, it was fairly obvious that a lot more plant fragments and…

Describing your DNA

One of the amazing things about the polymerase chain reaction, PCR, is how little starting DNA is needed, with an exponential increase in the number of copies of…

Letting the robot do its job

Having got together two plates of tubes with little bits of plant and lichen tissue in them, and pulverised them with tungsten beads in a TissueLyser for a…

Dealing with DNA extraction protocol changes

It’s a horrible and unwelcome upheaval to have to change a protocol that works, but that’s the situation in which we have found ourselves with our semi-robotic DNA…

Santos & Stech’s phylogeny of Octoblepharum

As far as our 2013 RBGE MSc project proposal to generate a phylogeny of Octoblepharum goes, Juan Carlos Villarreal, Noris Salazar Allen and I were clearly not the…

Only 12 Seconds To Poop – But Enough Information To Understand An Ecosystem

It may only take a mammal 12 seconds to poop – but poo contains a treasure trove of information about the animal and its environment that can take…

Telaranea murphyae: The non-native endemic that wasn’t

Murphy’s threadwort (Telaranea murphyae) has had a singular position in the British flora. The species was described by renowned bryologist Jean Paton in 1965, from plants collected in…