Tag: molecular lab

DNA Sequencing Natural History Specimens Using New Sequencing Platforms and Protocols: a 1-day meeting at RBGE 11/07/2017

Rapid developments in high-throughput sequencing platforms are providing a step change in the recoverability of DNA sequence data from natural history collections. Short-read massively parallel sequencers are intrinsically…

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…

Bits of bamboo

In the Herbarium at RBGE, we store a huge number of sheets of archival quality paper with squashed and dried plant specimens stuck to them. These have been…

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…

Panamanian mosses from the back of the freezer

Several years back, I postdocced in Barbara Crandall-Stotler’s lab in Southern Illinois University, Carbondale. In the late Autumn of 2003, Panamanian bryologist Noris Salazar Allen spent a few…

Cleaning the Schistidium PCRs

Once we realised that most of our plate of Schistidium ITS2 amplifications had been successful, it was an easy decision to process them all for DNA sequencing. If…

Gel electrophoresis of Schistidium ITS DNA

  Once the polymerase chain reaction is over, it’s time to Run The Gel; this is make-or-break time, when we¬†find out if our PCR amplification has actually worked….

Copying moss DNA in the molecular lab

After we extracted a plate’s worth (12 columns by 8 rows, or 96 samples) of Schistidium DNA, the next step in our process is to copy a preselected…

The trials and tribulations of a moss in the lab: DNA extraction

Just over a week into our current Synthesys-funded Schistidium project, and Wolfgang has picked through piles of packets of mosses, selecting the 96 that we would most like…

Student projects at RBGE: DNA barcoding of the leafy liverwort genus Herbertus Gray in Europe and a review of the taxonomic status of Herbertus borealis Crundw.

University of Edinburgh/RBGE student David Bell, studying for the Masters degree in the Biodiversity and Taxonomy of Plants; thesis submitted August 2009. Supervisors: Dr David Long and Dr…

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…

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…

Sparkling additions in the Molecular Lab

It’s a confusing world out there – betaine, DMSO, bovine serum albumin (BSA), trehalose, glycerol, formamide – the list of things that you can throw into a PCR…