Biodiversity Beermats

A group of Irish biologists have produced a set of eight biodiversity beermats which aim to raise awareness of biodiversity issues in Ireland.

The postgraduate students from the School of Natural Sciences in Trinity College Dublin under the banner of the Trinity Centre for Biodiversity Research  have produced the beermats as an innovative way of sharing their work with the Dublin public.

The beermats were designed and illustrated by Aileen Crossley and can be found in 10 pubs around Dublin. The group are also hosting 2-3 minute long pop-up pub talks on biodiversity.

The beermats have also been featured in the Irish Times and Science magazine in recent months. I'll drink to that!

More info: Biodiversity in our lives website

Fascination of Plants Day

Image: Wageningen UR/Fascination of Plants Day

Today, May 18, the fascination and importance of having plants on our planet will be in the spotlight worldwide.

Launched under the umbrella of the European Plant Science Organization (EPSO, Brussels), the Fascination of Plants Day has been adopted by 39 countries, 29 from Europe and 10 from North- and South America, Asia, Australasia and Africa.

More than 580 institutions - ranging from botanical gardens to plant research centres - are hosting different kinds of public and media events which are all closely related to basic plant science, agricultural research, environmental conservation, biodiversity, education and arts.

The public as well as journalists and the media are invited to attend press conferences, to explore laboratories or to visit greenhouses, field stations or field sites, museums, and other exhibitions. People will have the opportunity to talk with plant scientists and discuss basic and applied research in plant biology.

For information on Irish Events for Fascination of Plants Day - see here

Australian organisers have been running a Youtube video competition on the theme. Here's one of the entries-

World’s first night flowering orchid discovered on the island of New Britain

B. nocturnum (Image: J. Vermeulen)

Botanists from the Royal Botanic Gardens, Kew, and the Netherlands Centre for Biodiversity Naturalis have described the first night-flowering orchid known to science. The discovery is published in the Botanical Journal of the Linnean Society.

The new night flowering species, Bulbophyllum nocturnum, from the island of New Britain near Papua New Guinea, is the first known example of an orchid species with flowers that consistently open after dark and close in the morning. Its flowers last one night only.

A relatively small number of plant species have flowers that open at night and close during the day. Until now, no orchids were known among them. This in spite of the fact that many orchids are pollinated by moths. But these moth-pollinated orchids all have flowers that remain open during the day, even if they are mainly pollinated after dark.

Bulbophyllum nocturnum was discovered by Dutch orchid specialist Ed de Vogel on a field trip to the island of New Britain, where he was allowed to collect some orchids in a logging area for cultivation at the Hortus Botanicus in Leiden, the Netherlands.

Under the care of garden manager Art Vogel one of these plant soon produced buds. Their opening was eagerly anticipated as de Vogel and his colleagues had already established that this plant was a member of the Epicrianthes group of orchids of the genus Bulbophyllum. Epicrianthes contains many rare and bizarre species, most of which have only been discovered recently as they occur in some of the remotest jungle habitats on earth.

Frustratingly, however, the buds all withered once they had seemingly reached the size at which they should open. Wanting to get to the bottom of this, de Vogel took the plant home with him one evening in order to find out exactly what happened to the buds.

B. nocturnum (Image: A. Schuiteman)

To his surprise, the bud that was then present opened up at ten in the evening, long after dark, revealing the flower of an undescribed species.

Observations on subsequent buds confirmed that they all opened around 10pm, and closed the next morning around 10am. The flowers lasted only one night, which explained why the buds were seemingly about to open one day and withered the next.

Royal Botanic Gardens, Kew orchid specialist, André Schuiteman, and Leiden Bulbophyllum expert, Jaap Vermeulen, teamed up with de Vogel to investigate and describe this remarkable new species.

Says André Schuiteman of the discovery, “This is another reminder that surprising discoveries can still be made. But it is a race against time to find species like this that only occur in primeval tropical forests. As we all know, such forests are disappearing fast. It is therefore increasingly important to obtain funding for the fieldwork required to make such discoveries.”

Why Bulbophyllum nocturnum has adopted a night flowering habit is unknown and requires further investigation. However, it may be speculated that its pollinators are midges that forage at night.

In February 2012 Kew’s Tropical Extravaganza festival (4 February – 4 March 2012) will celebrate the beauty and diversity of orchids. Orchids make up what is probably the largest plant family on earth, with an estimated 25,000 species. Their flowers show a tremendous range of variation in size, colour and shape.

Irish Scientists Search for New Species in the mid-Atlantic

A group of Irish scientists will today lead a mission to the mid-Atlantic in search of strange new species at the bottom of the ocean.

The VENTURE mission is led by Dr. Andy Wheeler from the School of Biological, Earth and Environmental Sciences at UCC and includes a host of scientists from that institution, along with colleagues from NUIGalway, the Marine Institute and the UK's National Oceanography Centre.

The scientists leave Galway this morning aboard the Marine Institute's research vessel, the RV Celtic Explorer. The mission is being filmed by the National Geographic Channel.

The mission will investigate life 3,000 metres below the surface of the sea and seek out hydrothermal vents using the ship's Remotely Operated Vehicle, the Holland 1.

The Holland 1 is named for the Irish scientist and inventor John Philip Holland who invented the first modern submarines. I've written extensively about Holland on this blog already.

Patrick Collins of NUI Galway says this mission will allow him to find some new marine species: "We hope to find a whole community of previously unknown species, increasing our understanding of deep sea biogeography. There is potential here to put Ireland on the global map as a serious player in deep sea science. This is all the more timely with the exploitation of deep sea and hydrothermal vents for precious metals and rare earth minerals now a reality.”

You can find more information on the VENTURE mission here.
For a Q&A on the mission, see here.
The scientists will be maintaining a blog of their activities during the trip here.
Aaron Lim, a 4th year Earth Science student from UCC is also blogging from the mission here.

A sticky problem?

White's Tree Frog (Pic: Diana Samuel)

Frogs that use their sticky feet to cling to trees could have practical applications in medicine.

That's according to University of Glasgow-based scientist Niall Crawford who presented this work yesterday.

"Tree frog feet may provide a design for self-cleaning sticky surfaces, which could be useful for a wide range of products especially in contaminating environments - medical bandages, tyre performance, and even long lasting adhesives," says Crawford.

Tree frogs have sticky pads on their toes that they use to cling on in difficult situations, but until now it was unclear how they prevent these pads from picking up dirt.

"Interestingly the same factors that allow tree frogs to cling on also provide a self cleaning service. To make their feet sticky tree frogs secrete mucus, they can then increase their adhesion by moving their feet against the surface to create friction. We have now shown that the mucus combined with this movement allows the frogs to clean their feet as they walk," says Crawford.

The work is part of a European-wide project on biological and technological adhesives which aims to "provide more elegant solutions to contemporary engineering and biomedical adhesive requirements and will additionally provide a platform for future technological innovation that requires adhesion in hostile conditions as a prerequisite".

The researchers put White's tree frogs (Litoria caerulea) on a rotating platform and measured the angel at which they lost their grip.

When the experiment was repeated with frogs whose feet were contaminated with dust they initially lost grip but if they took a few steps their adhesive forces were recovered. "When the frogs did not move the adhesive forces recovered much more slowly," says Mr. Crawford. "This shows that just taking a step enables frogs to clean their feet and restore their adhesion ability."

White's tree frogs have tiny hexagonal patterns on their feet, which allow some parts of the pad to remain in contact with the surface and create friction, whilst the channels between allow the mucus to spread throughout the pad. This mucus at once allows the frog to stick and then, when they move, also carries away any dirt. If this can be translated into a man-made design it could provide a re-useable, effective adhesive.

Fancy getting to name a new marine species?

Image: (c)Patrick Collins

A team of Irish and UK scientists will shortly embark on a 25-day trip to the depths of the Atlantic ocean as part of a National Geographic-funded study to examine a previously uncharted hydrothermal vent ecosystem.

The work will be filmed by National Geographic and the campaign will be led by Chief Scientist Dr. Andy Wheeler of the School of Biological, Earth and Environmental Sciences, UCC.

The Marine Institute's research vessel, Celtic Explorer will travel to the mid-Atlantic ridge to examine the unique ecosystem in July. "It is literally, an alien world", according to Andy Wheeler.

UCC scientists Prof. John Gamble, Dr. Jens Carlsson, Prof. John Benzie Prof. Tom Cross, Dr. Boris Dorschel will all contribute to the study, alongside a number of scientists from NUI Galway, National Oceanography Centre (UK) in Southampton, University of Southampton and the Geological Survey of Ireland.

For more background on the Venture project, see this article from the Irish Times.

RV Celtic Explorer

Patrick Collins, a researcher at NUI Galway, also taking part in the project, has organised an exciting competition for secondary school students in Ireland. The prize? To get to put your name on one of the many newly discovered species that the team are likely to find as part of the study.

The competition is open to all secondary school students across Ireland and the UK. To enter, students must use their imaginations and understanding of biology and habitats to design their own deep sea hydrothermal vent creature.

The organisers are looking for carefully thought out illustrations along with a description of the creature’s habitat, diet, life and evolutionary history, and whatever else you think is important. The competition will close on June 15 2011, and the winner will be announced after the Celtic Explorer returns to Ireland in August.

For more details on how to enter see the BEES Research Blog.

Little water flea has big genome

Credit: Paul Hebert, University of Guelph

The little water flea used to have pride of place on the front cover of the Leaving Certificate Biology textbook when I was going to school. Little did we realise then that Daphnia would turn out to be so impressive!

Research just published in Science shows that the near-microscopic freshwater crustacean Daphnia pulex (the water flea) is the animal with most genes (about 31,000 in total).

"Daphnia's high gene number is largely because its genes are multiplying, creating copies at a higher rate than other species," said project leader and CGB (Centre for Genomics and Bioinformatics, Indiana University) genomics director John Colbourne.

"We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

Colbourne postulates that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

Much of the media coverage has centred around the fact that the water flea outstrips humans in terms of gene number (humans have around 23,000 genes). This "paradox" known as the C-value enigma or C-value paradox is based on the fact that the genome size of an organism does not correlate with the complexity of the organism.

'Daphnia is an exquisite aquatic sensor, a modern version of the mineshaft canary' - James KlaunigIt's not a new idea - the term was first used in 1971 and the solution lies in the fact that lots of DNA in eukaryotes (i.e. non-bacteria) does not code for genes. For example, only about 1.5% of the human genome codes for genes. The wheat genome, for example, is five times larger than the human genome.

Daphnia have long been studied because they can be an indicator of environmental health in freshwater bodies. "Daphnia is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary", says James Klaunig of Indiana University.

"With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

[For our Irish Readers: Does anyone have an image of the front cover of the Leaving Certificate Biology Textbook with Daphnia ? If so, let me know and I'll add it to the post]

Reference
Colbourne, J., Pfrender, M., Gilbert, D., Thomas, W., Tucker, A., Oakley, T., Tokishita, S., Aerts, A., Arnold, G., Basu, M., Bauer, D., Caceres, C., Carmel, L., Casola, C., Choi, J., Detter, J., Dong, Q., Dusheyko, S., Eads, B., Frohlich, T., Geiler-Samerotte, K., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J., Muller, J., Pangilinan, J., Patwardhan, R., Pitluck, S., Pritham, E., Rechtsteiner, A., Rho, M., Rogozin, I., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y., Yamagata, H., Yamada, T., Ye, Y., Shaw, J., Andrews, J., Crease, T., Tang, H., Lucas, S., Robertson, H., Bork, P., Koonin, E., Zdobnov, E., Grigoriev, I., Lynch, M., & Boore, J. (2011). The Ecoresponsive Genome of Daphnia pulex Science, 331 (6017), 555-561 DOI: 10.1126/science.1197761

Soil microbes make great art

PLoS (Public Library of Science) Biology have launched an important new series of articles and resources for open access life sciences education.

"The Education Series combines the philosophy of the open education movement with the unrestricted access to scientific papers and data afforded by open-access publishing to present innovative approaches to teaching critical concepts, developments, and methods in biology" says the editorial in this months edition of the open access journal.

"By enabling students to use the same tools researchers use and to explore real data, such approaches are especially valuable—it's widely acknowledged that engaging students in active research fosters their enthusiasm for and interest in science.

By mining the promise of open education and harnessing the collective imagination and talent of PLoS Biology readers and contributors, the Education Series will create a virtual biology education library."

The first article in the series demonstrates how natural products derived from the soil bacterium Streptomyces can be used as biopigments with the hope that the work can inspire others to explore the potential of biopigments in art, industry and the classroom.

Since the spread of Streptomyces on an agar plate is determined by the boundaries of the plate, the agar can be used as a canvas, where the spores of Streptomyces can be used as paint and applied in brush strokes.

The paintbrush is first sterilised completely before being used to apply spores from another petri dish to the freshly prepared 'canvas'. If multiple strains are used, multiple colours can be achieved.

The image shown here: "Elvis Lives!" was painted on R5 media plates using S.coelicolor.

The authors (or artists?) believe that this endeavour has "the potential to lead us toward a fertile nexus between art and science" and that it is an "outstanding tool to engage students of varying academic interests across multiple age groups".



References:

Charkoudian, L., Fitzgerald, J., Khosla, C., & Champlin, A. (2010). In Living Color: Bacterial Pigments as an Untapped Resource in the Classroom and Beyond PLoS Biology, 8 (10) DOI: 10.1371/journal.pbio.1000510

Kerfeld, C., & Gross, L. (2010). Open Education, Open Minds PLoS Biology, 8 (10) DOI: 10.1371/journal.pbio.1000508

Communicate Science @ Science.ie

My recent guest blog on Frogblog.ie has been picked up as news piece by Science.ie - a website produced by Discover Science and Engineering (DSE).

DSE aim to increase the numbers of students studying Engineering and Science; to promote a positive attitute towards careers in science, technology, engineering and mathematics and to foster a greater understanding of science and its value to Irish society.

You can read the Science.ie article here.

You can read the original guest post on the Frog Blog here.

I'll have two killer whales and a bottle of milk please...

The idea of adding a barcode to a product in a shop for making the life of a checkout operator easier is one of those inventions which we now hardly think about but has revolutionised the way we shop.

Retailers no longer need to price every individual item but need only place one large display price for the consumer to refer to. It makes things easier for the consumer too, knowing that we will almost certainly not be overcharged at the till due to a human error.

Barcodes were originally developed for labelling railroad cars but only took off when supermarkets saw their advantages and began to use them widely. It was two Americans, Bernard Silver and Joseph Woodland who patented the technology in 1949 and described both the linear type of barcode which we are still familiar with, as well as a 'bullseye' circular design.

However the two men were ahead of the technology available to them at the time, with IBM reporting that while the idea was very interesting, the technology to process the information wasn't yet available in the early 1950's. It wasn't until the early 1980's that the technology began to be rolled out in supermarkets across the US. Unfortunately, Bernard Silver never got to see the success of his invention as he died in a car crash in 1963.

Nowadays, barcoding has become almost universal. Sitting at my desk, I can see that my computer is barcoded by the manufacturer and contains a unique product number. Internally, most of the components from the disk drive to the memory is all barcoded for ease of tracking.

If I decide to take a break later, I can drive to the supermarket in a car which is barcoded and pick up a barcoded lunch. I can pay for my barcoded sandwich and barcoded chocolate bar at the self service checkout, where I get to scan my own barcoded product, as well as my unique supermarket loyalty card. This allows the supermarket to record what I like to purchase and target marketing at me specifically.
Going back to the office, I could pop into the library where my unique membership card will be scanned along with the books I want to borrow. In short, my whole life is a series of barcoded events. From airline tickets to identity cards, the conspiracy theorist could have a field-day.

Some of the uses to which barcodes are now put would surely surprise the original inventors. Scientists currently meeting in Mexico City at the 3rd International Barcode of Life Conference are putting the finishing touches to an agreement which aims to give every organism on Earth a unique barcode based upon its genetic fingerprint.
Organisers at the Barcode of Life Initiative (BOLI) say that the technology will aid researchers in a host of areas which rely on accurate identification of species of plants and animals, as well as other organisms. This includes identifying and protecting endangered species, sustaining natural resources including fish stocks, understanding marine biodiversity, carrying out basic research in taxonomy (identifying and labelling distinct species), controlling agricultural pests, stopping vectors of human disease such as mosquitoes and monitoring environmental quality.

While not exactly barcoding in the sense that Silver and Woodland imagined it, the initiative aims to use a relatively minute stretch of DNA (about 648 DNA "base-pairs" compared to the billions of such base pairs which make up many organisms) called a barcode sequence.

This barcode sequence will be tracked in a range of organisms. Subtle differences within this 648 letter code will give the researchers a unique label for every species. This particular barcode sequence, while excellent for use with most animal, butterfly, bird and fish groups isn't suitable for use with plants. The meeting in Mexico this week aims to propose a plant barcode sequence so that the work can continue.

With the information now available online, researchers are hoping that the job of identifying species has now become a whole lot easier.