Tag: DNA Page 1 of 2

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…

Sphaerocarpos, preview to a monograph

The Sphaerocarpales (or “Bottle Liverworts”) form a very distinct group in the complex thalloid liverworts, with ca. 30 species in five genera: originally the group just included Geothallus…

The RBGE DNA bank

Over the years, many different people have used the molecular laboratories at RBGE, to work on a multitude of projects on a multitude of plants and fungi. Some…

The RBGE DNA database – how an EDNA number is assigned to a DNA extraction

When people extract DNA in the RBGE molecular lab, we insist that it’s given something we call an EDNA (Edinburgh DNA) number. This links to a database that…

Capturing Genes from Herbaria. XI. Some metagenomics of a herbarium specimen

As part of our hybrid capture project, we sampled from an Inga umbellifera specimen that was collected about 180 years ago, by Andrew Mathews, in Peru in 1835….

Capturing Genes from Herbaria. X. An update.

Last May (the 15th, to be precise), we sent three eppendorf tubes containing Illumina Tru-Seq and NEB-Next libraries constructed from Inga DNAs, most of which had been extracted…

Using DNA to investigate Giant panda diet

What do Giant panda eat?  The answer might seem obvious but the reality is far from simplistic. The diet of the Giant panda (Ailuropoda melanoleuca) is highly specialised…

A mixed message on PCR additives in Aneura

This last week I’ve actually managed to spend a bit of time in the lab, trying to get some gaps filled in a DNA barcoding matrix for simple…

Delongia, a new moss genus named after David Long

The relative structural simplicity of some groups of mosses can disguise their uniqueness, especially when simplified features have evolved multiple times within the same family from ancestors with…

Oh blast – there’s more to life than Marchantia polymorpha

One of the earliest plastid genomes to be sequenced, in the late 1980s (Ohyama et al.), was that of Marchantia polymorpha, one of the commonest liverworts around town,…

Capturing Genes from Herbaria. IX. Hybrid capture

By mid-May 2015, we had 32 separate Inga umbellifera libraries, 15 generated using the Illumina Tru-Seq Nano library preparation kits, and 17 with the NEBNext Ultra library preparation…

Finding Monocarpus, in the herbarium

At the Royal Botanic Garden Edinburgh we’ve been working on the phylogeny of the complex thalloid liverworts for rather a while now. David Long presented a poster on…

Capturing Genes from Herbaria. VIII. Amplification

Both the Tru-Seq and NEB libraries were amplified pre-hybrid capture – another step at which modifications were made, according to how much DNA there was in each library….

Capturing Genes from Herbaria. VII. Comparisons.

As previously mentioned, we tested two different kits in our NBAF project. The first is the Illumina Tru-Seq Nano library preparation kit (FC-121-4001), which recommends a starting DNA…