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Citizen science blog

7 Posts tagged with the schools tag
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This week Dr. Della Hopkins tells us about how the Decoding Nature project takes school students out on field trips and involves them in the Museum's science research.

 

In June, a group of ‘scientists in the making’ from Pimlico Academy joined up with a small band of research scientists from the Museum as part of a long running project called Decoding Nature. Decoding Nature is a Museum-run venture which delivers residential science courses to school children aged 8-18.

 

The courses take place at The Old Malthouse School near Wareham in Dorset, and combine learning with original, ongoing scientific research. Over the years the project has evolved and included a wide range of scientists with varied areas of expertise. Each course is different, ensuring that the children are taking part in cutting edge research that will be used for publication.

 

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Amazing lichen communities on Dorset trees - a winning photo from the photography competition. Image credit: Coco from Pimlico.

 

For this particular course our budding scientists from Pimlico Academy were set several tasks, to aid renowned Lichenologist Holger Thues with several important research questions. The week began with an introduction to lichens and a recap on classification and how to use keys, before launching into investigations into the species composition of spice lichens; bags of mixed lichen species sold as cooking ingredients in many Asian supermarkets.

 

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Recording the lichens on coastal trees. Image Credit: Annabel Crookshank, The Old Malthouse.

 

Next we took to the fields to carry out an air quality survey (designed by the OPAL project), using nine target lichen species growing on tree branches to give an indication of pollution levels. Three of these lichens are very sensitive to pollution, three are ‘intermediate’ and the final three are nitrogen-tolerant. The children’s findings were of great interest, showing that the presence of sheep dramatically altered the lichen community, with the nitrogen sensitive species nowhere to be found. Less than a mile away, by the coast, these species were flourishing.

 

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Comparing the lichen species on trees in grazed fields. Image credit: Annabel Crookshank, The Old Malthouse.

 

Once they had honed their lichen-identification skills we headed out to Dancing Ledge, a beautiful area on the coast where the cliffs meet the sea. The students carried out a series of transects to answer questions about the habitat preferences of the coastal lichens, such as whether the rocks were sea- or land-facing, vertical or horizontal, and how close to the sea they were. We made some surprising discoveries, and were able to make some collections to take back to the Natural History Museum.

 

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Making a (permitted!) lichen collection at Dancing Ledge.

 

Finally we used DNA barcoding techniques on a number of European and British samples of the lichen Verrucaria pachyderma. This involved working in the laboratory to extract DNA, and amplify it to a level which could be taken to the museum for the sequences to be read. This was very important work, and great care was needed with the samples. Everyone managed the task superbly, and we were successful in extracting the DNA.

 

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Ready and prepared for DNA extraction.

 

Once we left Dorset, and returned to the museum, the DNA samples were sequenced. Genetic analysis of the lichens collected from Europe show that the British collections may in fact represent an entirely separate species. The next step is to expand the collection range and analyse more genetic markers, but the results so far are already a big surprise and wonderfully exciting.

 

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Holger Thues explaining the different habitat preferences of the lichens. Image credit: Annabel Crookshank, The Old Malthouse.

 

The week was full of games to encourage learning, especially with the more tricky subjects such as DNA barcoding. The children entered each challenge with enthusiasm, whether they were in the lab extracting DNA, or buzzing around the field as worker bees collecting their sand pollen. We also found time to learn about other techniques used by scientists in botany (plants) and entomology (invertebrates).

 

To find out more, visit our Decoding Nature webpage.

You can also find out how to participate in OPAL surveys here.

 

Della Hopkins

 

Dr Della Hopkins has worked at the NHM for 6 years, and has managed the Decoding Nature project for the past 5. She previously worked on seed conservation with the Millennium Seed Bank at Kew. She studied Environmental Biology at Royal Holloway University of London, followed by an MSc in Ecology (Bangor) and her PhD from London investigated heathland conservation and restoration.

 

Della runs the Decoding Nature project with Dr Robert Dyer (molecular laboratory assistant).

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This week we hear from Freya Bolton and Emily Stearn, students at Bedford Girls' School, about their experience of visiting the Museum to meet with the Angela Marmont Centre for UK Biodiversity team and Dr Anne Jungblut who leads the Microverse project.

 

On 30 April, we (eleven International Baccalaureate students from Bedford Girls' School) had the opportunity to come and visit the Natural History Museum, having participated in the Museum's exciting project 'The Microverse'. For many of us, despite the fact we'd visited many times previously, we knew this time it was going to be something slightly different, being able to explore the Museum in a new, unique and fascinating light. Having spoken to Jade Cawthray, she kindly agreed to arrange a behind the scenes tour especially for us!

 

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So much to identify so little time. Florin Feneru with a draw of specimens for identification.

Photo credit: Aarti Bhogaita

 

We were greeted by Lucy Robinson, who explained to us, as we travelled through the Museum, that within there were over 80 million different plant, animal, fossil and mineral specimens. After this, we were introduced to Dr Florin Feneru at the Angela Marmont Centre for UK Biodiversity, who confessed that he would receive specimens sent in from thousands of people each year, from the UK and abroad, in the hope that he could identify what exactly they were.

 

He explained that the most common specimen query was the "meteorite" (or as he would like to call them "meteo-wrongs") from members of the public who wanted validation for the rocks they believed to have mysteriously entered from outer space. Dr Feneru did however then excitedly show us, an ACTUAL meteorite received earlier this year, letting us hold it. It was extremely heavy for its size - not surprisingly as it was composed of mainly iron.

 

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An actual meterorite, and not a "meteo-wrong!"

Photo credit: Aarti Bhogaita

 

He then led us into the Cocoon: an eight storey building with 3 metre thick walls, containing just over 22 million specimens. The building was kept at a particular humidity and temperature in order to keep the specimens in good condition. The storey we entered was maintained at 14°C - 16°C and kept at 45 percent relative humidity. We were shown by Dr Feneru a range of butterfly species on the ground floor, and he explained that, before the Cocoon was built, the curators had to use mothballs to prevent infestations with pest insects.

 

After we'd visited the Cocoon, we were shown to a workshop area, where we met Dr Anne Jungblut, one of the founders of the project we have been participating in. She gave us a brief talk about her other current projects, including an expedition to Antarctica, and we had the opportunity to ask her about The Microverse and what inspired her to create this project. We were informed that one hundred and fifty four schools had taken part, and that Dr Jungblut was looking for a difference in diversity of microscopic life in different urban environments.

 

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A group photo with Dr Anne Jungblut.

Photo credit: Aarti Bhogaita

 

Following this talk, we had two hours remaining to ourselves, before it was time to depart back to sunny Bedford. Instinctively, we headed first to the cafes and shops before exploring the more scientific parts of the Museum. Full stomachs and emptier purses in hand we chose to explore the Marine Biology and Dinosaur galleries (naturally). One of the pupils explained that she hadn't been to the Dinosaur exhibition since she was 5 years old, as a consequence of being absolutely terrified of the animatronic Tyrannosaurus rex (she had many nightmares apparently). She confirmed that he definitely was not as scary as she thought he was at the time - that being said, she is now 17.

 

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Sophie the Stegosaurus, looking very friendly.

Photo credit: Aarti Bhogaita

 

Returning back to Bedford with new knowledge of both 'The Microverse' project, marine biology, and dinosaurs, as a whole group we would like to thank the Museum staff members and the teachers at Bedford Girls' School who made this amazing experience possible.

 

Freya Bolton and Emily Stearn

 

Thank you to Freya and Emily for writing their blog post and to Bedford Girls' School for coming to visit. It was an absolute pleasure to have them with us!

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Advances in DNA sequencing technology are occurring at an incredible speed and Kevin Hopkins is one of the Museum's Next Generation Sequencing Specialists working with the sequencing technologies used at the Museum to produce relevant data for our Microverse research.

 

"The challenge is being able to bring together the technology, often developed in biomedical settings, and the samples at the Museum, where limited and often damaged DNA from specimens is the only chance we have of sequencing them. My job involves designing methods that work for our unusual samples, extracting DNA and producing sequencing ready samples from it, and running our MiSeq and NextSeq next generation sequencing platforms."

 

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Kevin Hopkins is a Next Generation Sequencing Specialist at the Museum.

 

What is DNA sequencing?

DNA sequencing is the process of reading the order of nucleotide bases (adenine, guanine, cytosine and thymine) in a particular strand of DNA. Sequencing can be used for many different applications, such as defining a specific gene or a whole genome. The best way to sequence DNA is in sections; this is because there are a number of challenges to sampling the whole genome of a species in one go.

 

There is so much data within a genome that it takes an incredibly long time for any sequencing machine to process the information. In the Microverse project we are analysing short strands of DNA. At least 60 samples are loaded into the sequencer at a time and the analysis takes a total of 65 hours. If we were to analyse the whole genome rather than smaller parts, it would take a considerably greater amount of time, but luckily we don't need to do it for The Microverse project.

 

Another challenge for sequencing can be old DNA that has been degraded into very short sections, in this situation it is difficult to gain enough DNA from all the microorganism in the samples, to study the community composition. To avoid this in The Microverse project, we asked the schools to return the biofilm samples in a DNA preservative to minimise the degradation of the DNA.

Lab work

When Kevin receives the samples from Anne, the lead researcher on the project, he performs two quality control checks before loading them into the DNA sequencer: these are the concentration of the samples and the average DNA strand length. It is important to know both of these factors as they allow us to estimate the number of DNA fragments that are in each sample.

 

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We are using the Illumina MiSeq machine to sequence The Microverse samples.

 

The equipment that Kevin uses to sequence DNA is an Illumina MiSeq which can sequence up to 75,000 samples per year. Having equipment like this allows scientists at the Museum to carry out research such as looking at plant DNA to reveal the history of their evolution in relation to climate change, and using molecular work to benefit human health by understanding tropical diseases such as leishmaniasis, as well as exploring microbial diversity in soil, lakes and oceans.

 

During DNA sequencing the DNA double helix comprising two strands of DNA is split to give single stranded DNA. This DNA is then placed into a sequencing machine alongside chemicals that cause the free nucleotides to bind to the single stranded DNA. Within this sequencing cycle when a nucleotide, which is fluorescently charged, successfully binds to its complementary nucleotide in the DNA strand (A with T and vice versa, G with C and vice versa), a fluorescent signal is emitted. The intensity and length of this fluorescent signal determines which nucleotide base is present, and is recorded by the sequencing machine. The sequencer can read millions of strands at the same time.

 

Why is this important?

 

DNA sequencing is vitally important because it allows scientists to distinguish one species from another and determine how different organisms are related to each other. In the Microverse project we are using the sequencer to identify the taxonomic groups of the microorganisms in the samples that you have sent to the Museum.

 

Katy Potts

 

Katy Potts is one of the trainees on the Identification Trainers for the Future programme, who is based at the Angela Marmont Centre for UK Biodiversity. Alongside her work on the Microverse project she is developing her skills in insect identification, particularly Coleoptera (beetles).

 

If you are taking part in the Microverse project the deadline for sending us your samples is Fri 29 May.

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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:

 

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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

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MidKent College are one of the 140 schools and community groups to take part in The Microverse so far. We asked two of their students, studying for a BTEC Extended Diploma in Applied Science, to tell us what got them excited about microorganisms, DNA and taking part.

 

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The team at MidKent College pausing for a group photo while collecting microbial specimens for The Microverse.

 

Here's Emmanuel Shobande:

 

We were informed about the Microverse project during a lesson and a majority of the class took a keen interest in what Alison, our lecturer, was saying. On the day, every member of the class went outside to collect biological samples from one side of the college building.

 

I took interest in the project as I wish to study Biomedical Science at university, so collecting data and analysing it is something I take an interest in. The course involves lots of research and analysis of data, so this project would be a great way to enhance my CV, thus making me more employable when applying for a job/placement.

 

But what inspired me was the fact that the data that I collected was going to be published and used for DNA analysis, which could help scientists identify the types of microorganisms with potential nutrient deficiencies, those living in wet/dry conditions and those which are housed in areas of high pollution from different areas and on different buildings. For scientists to say that they are to travel the whole world and swab every building for living microorganisms would be a very time-consuming and expensive task, which is why we, as future scientists, have been given such a great opportunity to get involved in the collection of data, which could one day help identify a new form of microorganism which may not have been studied prior to the project. Who knows, our data could one day be quite essential!

 

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Emmanuel Shobande, studying for a BTEC Extended Diploma in Applied Science

 

And now for Max Squires:

 

To be part of an actual scientific project has helped me gain a range of microbiological skills which will help me with my Biomedical Science course at university. It has made me feel like an actual scientist by helping to gather data which will be analysed and be part of informative research about the microbiological life within urban ecosystems. As part of this, my class swabbed the exterior college building to hopefully identify the types of microorganisms that live in similar conditions across the UK.

 

This project has got me thinking of the life of microorganisms in urban environments. In built up environments, such as the college building which was swabbed, there are not many nutrients for microorganisms to thrive, there are high levels of pollution which can affect how microbes thrive and different weather conditions in which the microbes are exposed to (rain, hot weather, snow, etc.).

 

Could the high levels of pollution, possible lack of nutrients and harsh weather conditions inhibit microbiological life? In theory, microbes thrive in warm, moist, oxygen-rich environments and if one thinks about it, urban environments provide these factors, so it is very likely to find microbes in urban environments. Identifying specifically what microbes live in these environments will help us map out where each different microbe lives and possibly identify many new biofilms, which can give us an idea how microbes interact with each other to thrive.

 

It has been a great opportunity to be part of this research. It feels great knowing that an actual sample I collected will be analysed by top scientists and will be used in actual scientific research! It has got me thinking of the life in urban environments on a microscopic scale and has allowed me to develop my practical skills in science giving me a good start at university and in the future.

 

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Max Squires, studying for a BTEC Extended Diploma in Applied Science.

 

The Microverse is a citizen science project, suitable for A-level Biology students or equivalent, and also community groups. The project takes you out of the classroom to gather microorganisms for DNA analysis, as part of our cutting edge research into the biodiversity and ecology of the microbial world. Free to participate, you can find out more at: http://www.nhm.ac.uk/microverse/

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This blog post is a guest blog from the Natural History Investigators at Oxford Univeristy Natural History Museum (OUNHM).  After visiting us in London, to find out more about The Microverse research and to support us in our development of the project, museum educator Sarah Lloyd, took the project back to Oxford to involve students at both the OUNHM and the Oxford University Botanic Garden.  Here is what the Natural History Investigators got up to.

 

One snowy Saturday morning we unpacked our Microverse pack and lay out the scientific looking contents.  We are Natural History Investigators, a group of 14 to 16 year olds who meet every Saturday morning at OUNHM. We carry out our own research using Museum specimens. Before we begin our individual project work, we always spend some time doing something together. We've been into the Museum's spirit store, we have handled live tarantulas, but this week we were to collect samples to contribute to The Microverse project.

 

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Investigator, Gemma George investigating the similarities and differences between domestic and wild cats.

 

We divided the tasks amongst the group. Three of us were photographers. Six of us were keen to glove up and become swabbers and sample collectors.  We read through our instructions carefully and began collecting the grime that has accumulated on the outside of the neo-gothic museum building since 1860. We were very thorough and very efficient. Freezing temperatures definitely focus the mind!

 

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Abdullah Nassar collects samples from the north wall of the Museum.

 

With everything packaged up we eagerly wait to find out how many species exist in this special environment. Our individual projects have been based on things we can observe and hold in our hands.  So we are really keen to find out more about the process of studying life that you can't see or hold!

 

Natural History Investigators, OUNHM

 

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I can confirm that the samples from OUNHM have arrived at the Museum's laboratory.  Our lab assistant Filipa will be starting the PCR process very soon and then they will go into the sequencer.  In just a couple of weeks we'll be able to send the results back the Natural History Investigators, for them to explore.

 

Jade Lauren

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If you've joined us from our last blog post where we introduced the team, hello again! I'm really excited to be taking part in the Museum's newest citizen science project, The Microverse, that we launched at the end of 2014. This is a research project that will explore what microorganisms are living on UK buildings.

 

 

The research is being led by Dr Anne Jungblut, who studies microorganisms in extreme environments, exerting much of her research effort on the microorganisms that are found in Antarctica. Despite taking field trips to Antarctica, Anne is also very keen to explore the life that lives on buildings here in the UK, which - perhaps surprisingly - have received very little attention with respect to their microbiology to date.

 

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Cyanobacteria are the specific type of microorganism that Anne studies in Antarctica.

 

Like Antarctica, buildings are an extreme environment for life, exposing microorganims to extremes of wet and dry and - sometimes - high levels of pollution, while providing little access to nutrients. Anne approached Lucy Robinson and I to see if we could help her to recruit members of the public into collecting data (it would take Anne years if she collected the data from across the UK herself).

 

So we want to get 250 secondary schools to step out of the classroom and swab a local building.

 

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Students will find a local building and collect samples from the wall using a cotton swab.

 

Throughout January and February, A-Level Biology students from across the UK will be swabbing buildings and recording data about the building's environment and form. The students will collect the samples on cotton wool swabs and post them back to the Museum in a preservative. Once here, Anne will then extract DNA from the swabs and sequence it, to reveal what types of microorganism groups are living there and how many different types.

 

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Samples are added to labelled tubes of DNA preservative to be sent back to the museum for analysis.

 

Schools will literally be contributing the genuine scientific research and to the Museum's collection, because Anne will use the data to publish academic research in a scientific journal and the specimens will be incorporated into our Molecular Collections Facility. This research project aims to determine the diversity of microorganisms on buildings across the UK and what types of variables are impacting on that diversity. It will form a foundation of knowledge from which more detailed questions can be asked.

 

If you are an A-Level Biology student or teacher, or you know of anyone that might like to get involved in The Microverse, there is still time to join the programme, just visit our webpage to find out how to take part. It's completely free and each school receives a pack with equipment and resources guiding both teachers and students through the method and the science. Data collection has already started in January and will continue throughout February, and the results will be returned to students by the end of March 2015.

 

Jade Lauren