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Biodiversity initiative

Musca domestica

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Mar 29, 2015 Filipa amplifying DNA in the lab | The Microverse

Hello! I'm Filipa, the laboratory assistant in the Microverse project. My role is to prepare all the samples that arrive from schools and community groups for DNA sequencing.

 

Each group collected 10 samples from three different locations, which they labelled A, B and C. I select one sample from each location and I set up my lab bench with everything I need, including micropippetes, tubes and the reagents necessary for DNA extraction.

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Filipa's workbench, ready to extract DNA from the samples.

 

Then I label all the tubes I'm going to use with the respective sample code, so that none of the samples gets mixed up, otherwise that would lead to misleading results. Then I extract the cotton wool, where all microorganisms are, from the wooden stick with the help of a pair of forceps and I use the reagents - following a specific protocol - to extract the DNA from the microorganisms. Finally I get a tube with DNA in it!

 

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DNA extracted from the microorganisms.

 

We then use this DNA to carry out a PCR (Polimerase Chain Reaction) - a process through which we are able to amplify a specific DNA region, by producing millions of copies. We chose to sequence the gene for the 16S rRNA, which is regarded to be an excellent genetic marker for microbial community biodiversity studies due to it being an essential component of the protein synthesis machinery. That will enable us to identify which microorganisms are present in the sample. We amplify each sample three times (with different DNA concentrations), plus a negative control (with no DNA) to make sure that there isn't any contamination in the reaction.

 

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This is the machine to visualise PCR products on an agarose gel using electrophoresis.

 

Then we run the PCR products on an agarose gel to see whether we have amplified the right size fragment - we expect our gene (16S rRNA) to be a 300-350 base pair fragment, which we compare with the ladder on the left - and that the control sample does not show up at all. The result is something like this:

 

PCR image.jpg

A photograph of the PCR products after gel electrophoresis.

 

Everything worked! For each sample we have three bright bands in the position for 300-350 base pairs and a blank one, where we put the control.

 

Lets imagine that this was not the case and some things hadn't worked so well. For instance, if we didn't get a bright band from our samples it would mean that the DNA fragment wasn't amplified. In this case it would mean that an error occurred during the PCR set up and as a result we would need to repeat it.

 

It could also happen that we found a band in one of our negative controls, this would reveal a contamination in the PCR reagents, which are not supposed to have any DNA. To solve this, we would need to start again with brand new reagents (and be more careful!).

 

In the control sample, and in some of the samples with DNA, we see a short faint fragment, this is a by-product of the reaction called a primer-dimer. To remove this we do a PCR clean-up. When that is done the samples are almost ready to be sent for sequencing, and soon after we will find out what microorganisms inhabit the surfaces you've been swabbing!

 

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Filipa Leao Sampaio, laboratory assistant.

 

Filipa is a laboratory assistant at the Museum, she began her career with an undergraduate degree in Biology and then a masters in Biodiversity, Genetics and Evolution in the University of Porto, in Portugal. For her dissertation she worked on a project where she studied phylogenetic relationships and patterns of genetic diversity in reptiles from the Mediterranean Basin.

 

Since September 2013 she has been working at the Museum carrying out molecular lab work on different projects - snake vision evolution, Antarctic soil microbial diversity and UK urban microbial diversity. Later this year she starts a PhD in London where she will receive training in different areas of environmental sciences.

 

Jade Lauren

Mar 20, 2015 A big welcome to our new trainees | ID Trainers for the Future

Welcome to the first blog post for the Museums Identification Trainers for the Future project! This exciting new project centers around 15 work-based traineeship positions that will be hosted at the Museum and has been designed to address the growing skills gap in species identification in the UK. We will be doing this by targeting species groups where there is a lack, or loss, of ID skills in biological recording.

 

Our first group of trainees started with us this month, having come through a very competitive selection process, and were selected from over 400 applications. Choosing our first cohort has meant we have had to make some difficult decisions: certainly by the standard of the 25 we invited to selection day back in January, there are some very capable and enthusiastic people out there, with everyone who came along performing extremely well. Hopefully that, of course, means great things for UK biodiversity and biological recording!

 

http://www.nhm.ac.uk/resources/natureplus/images/life-sciences/id-trainers/Our-first-cohort-of-trainees.jpg

Our first trainees taking part in the Identification Trainers for the Future project

L-R Sally Hyslop, Michael Waller, Katy Potts, Anthony Roach and Chloe Rose

 

Sally, Katy, Michael, Chloe and Anthony will be introducing themselves in their own blog posts which will appear here over the next few weeks, so I will save mentioning more about their backgrounds here. They have a very busy year in front of them getting involved in our work in the Angela Marmont Centre for UK Biodiversity as well as working with our specialist curation teams and helping out at Field Studies Council centres across the country.

 

They will be building their own species identification skills through a wide range of workshops, field visits and private study and later on we will be looking at building their communication and teaching skills so they can pass on to others what they have learnt, which is the priniciple purpose of our new project. In the mean time they will also be out and about at various Museum events throughout the year, and we will be reporting back on those too as soon as we can.

 

For now that leaves me only needing to say a big welcome to all our trainees, I look forward to working with you over the next 12 months!

 

Steph West

Project Manager - Identification Trainers for the Future

 

The ID Trainers for the Future project is sponsored through the Heritage Lottery Fund’s Skills for the Future programme and is supported by the Field Studies Council and National Biodiversity Network Trust.

 

For more information, see our website

Mar 9, 2015 South Georgia’s glaciers and microbial diversity

Our team went on a one month field expedition to South Georgia at the beginning of this year, funded by the National Geographic Society to collect water, sediment, ice and snow samples from glaciers around South Georgia.

 

South Georgia is located south of the Antarctic Convergence and its mountainous landscapes are dominated by glaciers. More than 150 glaciers can be found on South Georgia, and until recently glaciers have been seen as abiotic features, but now it is known that they contain diverse ecosystems with rich communities of bacteria, cyanobacteria, microbial eukaryotes, Archaea, fungi and microfauna even sometimes insects.

 

South Georgia is located in a zone that will likely be affected by climatic change, which could lead to a further decline of glacial ecosystems. In our project we will therefore do a detailed documentation of the biology and biodiversity found on glaciers on South Georgia using a combination of environmental (eDNA), culture isolation and sequencing. The project is a collaboration between Dr Arwyn Edwards and Tris Irvine-Fynn (Abyerystwyth University), Dr David Pearce (Northumbria University) and me based at the Natural History Museum.

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Heaney Glacier.

 

IMG_1467.jpg    Nordenskjöld Glacier.

 

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Calving glacier front.

Biodiversity staff

Research

Alfried Vogler (lead)

Paul Eggleton (tropical entomology)

Alex Monro (tropical botany)

Neil Brummitt (spatial biodiversity)

Martijn Timmermans (genomics)

 

Collections

Max Barclay (entomology)

Beulah Garner (entomology)

Jackie Mackenzie-Dodds (molecular collections facility)

 

UK Biodiversity

Angela Marmont Centre

John Tweddle (citizen science)

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