Tag Archives: Science

Science: for the sheer fun of it!

Image: Robert Hooke, 1665. Micrographia. Jo. Martyn and Ja. Allestry, London.

Image: Robert Hooke, 1665. Micrographia. Jo. Martyn and Ja. Allestry, London.

Despite frequently expressed assumptions to the contrary, science – whether it’s botany or some lesser intellectual pursuit – isn’t always about having an idea and undertaking an experiment to test it. Anyway, that type of investigation can be hard work. Fortunately, there is an alternative approach that basically studies ‘what’s there’ and muses on why that might be (or not…), so-called blue skies research.  Sadly, the latter type of science – which I think is much more fun and interesting – is less likely to get financed than the ‘there’s a definite question that we aim to answer’ type of study, and is generally much less common. Nice then to see that, in conversation with Sarah Williams in the Howard Hughes’ Medical Institute’s Fall 2013 issue of the HHMI BulletinDr Richard Flavell (Sterling Professor of Immunobiology at Yale School of Medicine) promotes the view that observation-driven studies have a place in science. He goes further in saying that, ‘there’s nothing wrong with a lab team doing observational study after observational study. They are still helping advance the science, and likely providing fodder for hypothesis-driven studies to come…’. Now that is my kind of science. I do hope those who fund research are listening to – and heeding – this!

Unfortunately, I suspect the more usual reaction to requests to finance such work from the grant-awarding bodies would be similar to that which prompted this acknowledgement in a scientific paper: ‘I thank the National Science Foundation for regularly rejecting my (honest) grant applications for work on real organisms (cf. Szent-Gyorgyi, 1972)…’ (from Leigh Van Valen’s* paper, ‘A new Evolutionary Law’). But occasionally studies along the lines of ‘let’s just see what turns up’ do appear. Take, for example, Michael Proctor and Margaret Bradshaw’s first in a planned series of papers on scanning electron microscopy (SEM) examination of leaves of British sedges in New Journal of Botany**. Acknowledging that the ability to identify sedges in the field is important to many vegetation studies but recognising that inflorescences are available for only a short period each year, the pair have concentrated on SEM studies of leaf surfaces to assist those identification endeavours. Whilst the duo don’t advocate taking a SEM into the field, they do believe that such SEM studies will be ‘useful in putting leaf characters on a firmer footing, and drawing attention to characters which could be useful for identification with a hand-lens or low power microscope’ (which can be taken into the field…). The images need to be seen to be properly appreciated, but the imaging of epicuticular waxes in, for example, Figure 1f attests to their high quality. Bring on Part 2!

[For those expecting to read about ‘botanist’ Richard Flavell PhD, FRS, CBE, former Director of the John Innes Centre, etc, I’m sorry to ‘disappoint’ – Ed.]

* Leigh van Valen is an American evolutionary biologist probably best known for the Red Queen Hypothesis.

** this is the official organ of the BSBI,  the leading society in Britain and Ireland for the study of plant distribution and taxonomy. The Botanical Society of Britain and Ireland was formerly called the Botanical Society of the British Isles, and represents a name change every bit as slick as that of the WWF (which changed from World Wildlife Fund to World Wide Fund for Nature in 1986), and which also allows it to keep its abbreviation of BSBI (which is an initialism not an acronym) the same. The New Journal of Botany is itself the successor to the BSBI’s Watsonia journal, named in honour of Hewett Cottrell Watson (one of the “most colourful figures in the annals of British botany”) who developed the vice-county system in 1852 that currently divides up the United Kingdom and the Republic of Ireland into 152 geographical units for vegetation recording purposes.]

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Picture perfect vs. perfect genuine…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It has been oft-claimed that a picture is worth a thousand words. In the space-constricted world of science publishing a well-executed image can indeed save valuable text and convey often complicated information in a ‘much-more-easily-comprehended’ way. But in this digital-imagery age ‘building a convincing figure is a demanding task that covers different steps ranging from content acquisition to figure assembly in editing software’. Furthermore, it can get rather technical and ‘notions of image processing are required when it comes to even simple tasks such as cropping or resizing images and assembling them in a single figure’. A Franco-German co-operation between Jérôme Mutterer (Bio-Image facility, Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France) and Edda Zinck (International Media and Computing, HTW, Berlin, Germany) aims to help this with the creation of ‘FigureJ’ – an ImageJ plugin – which is dedicated to the preparation of figures for scientific articles and is described in their recent ‘Hot Topic – fast-tracked short communication’. FigureJ is free and open-source software, can be obtained from http://www.figurej.org/, and – amongst other benefits – produces pixel-precise panel arrangements.

But… with greater pressure on decisions over career-advancement by publication output, and the ease of access to all sorts of digital-pokery, has come the temptation to ‘massage’ images so that they look their best (or even better than their best…). This has been recognized for some time and instances of such ‘manipulation’ are regularly highlighted by Retraction Watch. Such tampering is quite simply wrong and unacceptable; there can be no happy ending for this form of massage. Whilst all decent, honest practitioners know this, sometimes reminders are needed. So, by way of raising awareness in terms of ‘what is and what isn’t acceptable’ in the world of image ‘enhancement’, a joint statement by the Plant Cell and Plant Physiology expands and expounds upon those journal’s existing stances on this matter. And to help in the task of picture-policing, those two journals have access to unspecified ‘forensic tools’ to analyse cases of suspected mishandling of images. You have been warned! Both Editors-in-Chief hope that this approach ‘will help strengthen the scientific community and the reliability of the data we publish’. Hear, hear! Or, rather, we’ll see…

[Right, that’s the pictures sorted, what about dodgy text and made-up results, as exemplified by recent revelations that a spoof science (both senses of the word!) paper was accepted for publication by several ‘open access’ journals leading its perpetrator – one John Bohannon – to question many aspects of the science publishing business (for such it has become…) – Ed.]

 

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Plants… chickens… children…

Encyclopedia Britannica, 9th edn, vol. 1, 1875.

Encyclopedia Britannica, 9th edn, vol. 1, 1875.

No, this post is not an animate version of ‘rock, paper, scissors’, but please bear with me… It’s an age-old question: how do plants survive the metabolic demands of the long, dark night of the cell where there is no light for photosynthesis and production of energy-rich ‘food’? Well, they can use photosynthates – such as starch – built up during the lit periods. OK, but how do they ensure that those reserves are not depleted before they can photosynthesise more?

To avoid this scenario, Antonio Scialdone et al. have shown that plants – well, our old friend arabidopsis anyway – performs ‘arithmetic division to prevent starvation at night’. ‘During the night, mechanisms inside the leaf measure the size of the starch store and estimate the length of time until dawn. Information about time comes from an internal clock, similar to our own body clock. The size of the starch store is then divided by the length of time until dawn to set the correct rate of starch consumption, so that, by dawn, around 95% of starch is used up’. Inevitably, there are detractors who say this is not intelligence or mathematical ability because plants do this without ‘thinking’. To which one must say: Wow! To do such complicated sums without even thinking about it!? How clever is that! Impressive? Yes, but even more so – surely? – is plants (and that’s all plants, not just arabidopsis!) ‘doing’ quantum physics during the wonderful process of photosynthesis.  Well, that’s what Richard Hildner et al. have demonstrated with their identification of  ‘ultrafast quantum coherent energy transfer within individual antenna complexes of a purple bacterium [as a proxy for photosynthesis in plants…] under physiological conditions’. Or, as the article’s Editor’s summary enlighteningly puts it, the team ‘observed coherence – prolonged persistence of a quantum mechanical phase relationship – at the single-molecule level in light-harvesting complexes from purple bacteria’. Sounds complicated? Yep, and consequently sure seems like quantum physics to me. Clearly, a plant must therefore be regarded as the real ‘quantum of Sol’,  ace!

Finally (you knew we’d get there eventually…): there’s been lively debate about the subject of ‘plant intelligence’, but I think the above items have settled the question once and for all. Thus: since chickens are smarter than young children (as a proxy for people generally), and plants are far cleverer than chickens (how many chickens can do quantum  physics???), plants must be more intelligent than people. QED!

[Ed. - and to infuriate people even more/put the cat amongst the pigeons/chickens, why not read about intelligent plants at Elaine Dewar's blog entitled, Shh . . . the plants are thinking?]

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Science and Plants for Schools – Biology practical demo – How do nettles sting?

This demo from Science and Plants for Schools demonstrates a quick and easy plant practical for biology labs. Using Universal Indicator paper, students investigate the pH of nettle stings. This can easily be built up into a broader investigation, or used as a quick practical to introduce the topics of plant defences, adaptations and specialised cells.

Download the full student sheet and teacher’s and technical notes free from the SAPS website:
http://www.saps.org.uk/secondary/teaching-resources/869

 

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Social media tips and tools for scientists

Researchers discussing ideas for social media use in academia. Photo by Clara Howcroft.

Researchers discussing ideas for social media use in academia. Photo by Clara Howcroft.

Should scientists use social media for work purposes? What types of content can researchers put online and how can they make it reach even further? How to engage students via Twitter? How do you manage information overload?

These were some of the topics and questions we addressed in our workshop ‘Linking research and teaching with social media’. In this post, like in the session, I am covering the research aspect, whereas Dr Jeremy Pritchard talked about uses of social media for teaching.I have made my slides available online and the presentation is embedded at the end of this post, so I won’t go into details about it.  It addresses basic questions such as how to find interesting people to follow and make sure that people find you, or what to be aware of when using social media. It also explains the mysterious ‘hashtag’ and describes the different tools available to bring your science online, from blogging to audio, video or Facebook pages. The presentations were followed by a group discussion and here are additional links to resources not mentioned in the talks

If you are running a meeting or a lecture, projecting all tweets that have been posted under your specific hashtag on a screen is a great way to engage participants. There are free websites available to do this. Two examples are ‘Visible Tweets‘ and ‘Twitterfall‘. Just enter your hashtag into the field and maximise the browser window to full screen display.
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How learned societies can boost your scientific career

Anne Osterrieder is a Research and Science Communication Fellow at Oxford Brookes University. 

Over the next few days I’ll be blogging from the annual meeting of the Society for Experimental Biology. This year it takes place in Valencia, Spain and as always features tons and tons of plant, cell and animal biology.

Pink Dinosaur in Valencia

A pink dinosaur shows you can take experimental biology too far in Valencia. Photo: marcp_dmoz/Flickr

I don’t think I got the point of a ‘learned society’ when I first started my PhD. My supervisors, both active in different societies, encouraged me strongly to join a couple of relevant ones. I only realised the benefits a year later, when I wanted to travel to my first international conference. I was able to apply for travel grants under the condition that I presented in form of a poster or talk, and that I’d write a short report for their magazine.

Both of these things seemed relatively unimportant at the time when my main focus was on getting data. But when it comes to writing up your PhD and putting together your CV, these are the first – and sometimes only – opportunities for young researchers to demonstrate their ability to win external funding (yes, even if it is ‘only’ £100 – everyone starts small!), write a ‘published’ article and show initiative. It doesn’t stop at travel grants. Societies also offer public engagement grants as well as funding and help to organize meetings.
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Time for some carbs, now

Image: Wikimedia Commons.

Image: Wikimedia Commons.

When carbohydrates [organic compounds consisting only of carbon, hydrogen and water, usually with a H:O ratio of 2:1, and with the empirical formula of Cm(H2O)n; e.g. glucose] and plants are mentioned, the botanically inclined amongst you should – in suitable pavlovian manner – think instantly of saccharides (a general synonym for sugars, and including mono-, di-, oligo-, and polysaccharides) such as sucrose, starch and cellulose. Well, this piece will make no further mention of sucrose (a disaccharide of glucose and fructose that is the main form in which photosynthetically fixed carbon is transported long-distance in many plants) nor of starch (a medium- to long-term polysaccharide store of fixed carbon/energy, often deposited in storage organs, e.g. tubers of potato). Cellulose does feature, but let’s build-up to that (yes, pun intended!).

First, a tale of trehalose, a disaccharide that is famously linked to feats of desiccation-tolerance in the resurrection plant Selaginella, but which – especially in its phosphorylated form trehalose-6-phosphae (T6P) – participates in a variety of roles connecting plant metabolism and development. To its list of accomplishments we now need to add a role in flowering, since loss of TREHALOSE-6-PHOSPHATE SYNTHASE 1 (which enzyme adds the phosphate group to trehalose to make T6P) causes Arabidopsis thaliana to flower extremely late – even under otherwise inductive environmental conditions. Want to find out more? Then go to the article by Vanessa Wahl et al. or either of the two summary/interpretative commentaries – by Jonas Danielson and Wolf Frommer or by Pamela Hines).

From a new role for a disaccharide to a new spin on a long-standing application of the polysaccharide cellulose. Although probably better known as the main structural component of plant cell walls in vivo, cellulose – a polysaccharide with the formula (C6H10O5)n, consisting of a linear chain of several hundred to more than ten thousand β(1→4) linked D-glucose units – is also commercially important in the walls of fibres (e.g. hemp) and hairs (e.g. cotton) that are extracted from plants and used as a variety of textiles, etc. Extending the uses of such natural materials in humankind’s age-old war against microbes, a team at KTH Royal Institute of Technology (Denmark) have developed an antibacterial polymer that attaches stably to cellulose in textiles, nappies, bandages, etc. Whilst antibacterial chemicals are not new, a danger inherent in their use is that they may ‘escape’ into the environment, creating selection pressure that encourages the development and spread of antibiotic-resistant bacteria. However, the Danish product is so tightly bonded to the cellulose that it does not leak, thereby minimising such dangers and concerns. Furthermore, the positively charged polymer actually draws the negatively charged bacteria to itself! Now, that is attractive, and reminds me somewhat of Ning Liu et al.’s work on ‘self-cleaning cotton’. Incorporating photosensitive 2-anthraquinone carboxylic acid (2-AQC) onto cellulose fibres, those workers demonstrated decomposition of 90 % aldicarb (an insecticide and nematicide, implicated in affecting human health) in 3 hours of UVA exposure, and inactivation of over 99 % of both Escherichia coli and Staphylococcus aureus (bacteria that are well-known human pathogens) with 1 hour of light exposure. In this instance, the self-cleaning functions result from formation of reactive oxygen species (ROS) upon light irradiation of the 2-AQC-treated cotton. Talking of ROS… Oops, out of space for this item!

[For an update on progress on photo-induced antimicrobial and decontaminating agents in polymer and textile applications, see this review by Gang Sun and Kyung Hwa Hong  – Ed.]

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There’s a lot less sperm around than most people realise

Misconceptions about plants have more lives, and much longer lives, than a cat.

 

Man sneezing in a canola/oil seed rape field.

A misunderstanding gets up his nose. Photo: Bigstockphoto

As AoB Blog’s non-botanist, I’m used to there being plenty of things I don’t know about plants. I’m usually good for a “Wow!” if anyone mentions that a line of plants has been around since the age of the dinosaurs, regardless of how many times I’m told this about plants. But there’s another problem. Sometimes I can learn a fact and be completely unhindered by any understanding of it.

An example is the post from the Phytophactor Pollen is not plant sperm. I should know this. I read about the alternation of generations when reading up about mosses, and pollen is a perfect example of this. I know some people reading will know almost as little about plants as me, so I’ll try to explain this below (or just demonstrate my misunderstanding) while botanists can skip to the next bit where I ask why should this be news?

Plant reproduction is weird

…or at least weird by human terms. Humans are dipolid. We have pairs of chromosomes. We produce a gamete which is haploid. These are cells that carry single chromosomes. They combine and make a new diploid human. So one diploid human produces another diploid human. Plants do not do this.

We’ll start by looking at angiosperms, flowering plants. Let’s imagine an oak tree. An oak tree is diploid, if we ignore the ones that aren’t. If pollen is sperm then we’d expect them to produce lots of the stuff and for some of it to fall on eggs to fertilise them. But when you look closely that’s not what happens.

Pollen is not a gamete.

It’s a spore. It grows into haploid pollen grain that can produce gametes, but it’s not just the gamete. The pollen travels to a pistile and develops a pollen tube to deliver the gametes. This can be quite complex. The seed is produced and this becomes a diploid plant that starts over again. Something like a tree that produces pollen and ovules is called a sporophyte because it produces spores as pollen or ovules. The pollen or ovule is called a gametophyte because they produce gametes.

So it’s complex, but is it so bad to think of pollen as sperm? It’s effectively doing the same job. Maybe, but things like mosses complicate things further.

Mosses alternate generations too, but the mosses you see are the gametophyte stage. The sporophyte stage, the equivalent of a tree, is tiny and only lives off the gametophyte. As the Phytophactor points out, it’s the same process but the other way round.

Why does the idea of pollen as sperm persist?

“TPP wonders how many times he’s explained this during his career and seemingly with no impact what so ever except perhaps on a case by case basis.” says the Phytophactor.

My first thought was that we don’t experience the word on a microscopic basis. It sounds like a good reason, but it can’t be right. We take germs seriously, but they’re microscopic. So the hidden nature of pollen and ovules isn’t enough to explain why we get them so badly wrong. I think it’s also that our senses tell us a different story. Seeds are produced on the tree and these become plants. It’s not simply that we don’t see the alternation of generations, it’s also that we see apparently contradictory evidence with our own eyes.

The evidence is only apparently contradictory and it would be clear that something different is happening if we looked closely, but why would we? Our thoughts about reproduction are dominated by how our own bodies work and what we erroneously think about plants is consistent with that. Even with weird sex, when Captain Kirk decides it’s time to kiss the alien’s daughter he might notice how green she is, or be surprised by an extra tentacle, but he never discovers she’s microscopic and one of thousands.

The token romance element of sci-fi films could be a lot more complex.

…and maybe that’s the biggest barrier of all. We like to see ourselves as the height of complexity. Really grasping what the alternation of generations means doesn’t just run counter to experience. It also challenges our chauvinism. Yet plant reproduction is not passive or simple. Clearly people can understand it, but it’s not an easy tale to sell. It’s also something that plants are very good at handling for themselves. Most people don’t intervene in their plants’ sex lives they way they would for a dog or a cat so it’s not a tale we necessarily need to know.

If leaving your gametophytes un-neutered meant you woke up one morning and your kitchen was a small forest that needed toilet training then I bet people would become staggeringly well-informed about plant reproduction. That sounds like a challenge for the GM people to sort out.

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Techniques used to modify a plant genome also affect its epigenome

Rice Rice is one of the most important food crops and is estimated to provide more than a fifth of the calories consumed by the world’s population. For several decades, rice has been modified by conventional breeding methods to produce plants with increased yields and greater resistance to pests and harsh weather conditions. Efforts are also being made to create rice plants with superior yield traits and resistance to biotic and abiotic stresses using genetic engineering techniques.

Genetically modified plants are usually produced using tissue culture. New genes are introduced into plant cells that are growing in a dish, and each cell then replicates to form a mass of genetically identical cells. The application of plant hormones triggers the tissue to produce roots and shoots, giving rise to plantlet clones.

In addition to the genes that comprise its genome, the genetic make-up of an organism also includes its epigenome—a collection of chemical modifications that influence whether or not a given gene is expressed as a protein. The addition of methyl groups to specific sequences within the DNA, for example, acts as an epigenetic signal to reduce the transcription, and thus expression, of the genes concerned.

The techniques used to modify a plant’s genome—in particular, the process of tissue culture—also affect its epigenome. They prepared high-resolution maps of DNA methylation in several regenerated rice lines, and found that regenerated plants produced in culture showed less methylation than control plants. The changes were relatively over-represented around the promoter sequences of genes—regions of DNA that act as binding sites for the enzymes that transcribe DNA into RNA—and were accompanied by changes in gene expression. Crucially, the plants’ descendants frequently also inherited the changes in methylation status. These results are likely part of the explanation for a phenomenon called somaclonal variation, first observed before the era of modern biotechnology, in which plants regenerated from tissue culture sometimes show heritable alterations in the phenotype of the plant.

 

Plants regenerated from tissue culture contain stable epigenome changes in rice. (2013) Elife 2: e00354. doi: 10.7554/eLife.00354.
Abstract

Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.

 

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Plant Identification Skills

Plant Identification Skills Taxonomic education and botany are increasingly neglected in schools and universities, leading to a ‘missed generation’ of adults that cannot identify organisms, especially plants.

The ‘taxonomic illiteracy’ of Western cultures has been recognised but limited research exists on the most effective methods for teaching species identification, especially in adults. A recent House of Lords inquiry described the state of taxonomy and systematics in the UK as ‘unsatisfactory’ and a shortage of trained taxonomists, especially for less charismatic taxa, has resulted in a ‘taxonomic impediment’ to effectively monitoring and managing biodiversity. Taxonomy is one of the science areas where ‘citizen scientists’ can most meaningfully participate but there is a need for more training in identification skills and novel training methods to raise both interest and awareness.

Botany has long been a neglected aspect of biological education in curricula, textbooks and courses from school to university level. The cycle is self-perpetuating, with biology teachers neglecting botany because of its absence in their own education. In a study of A-level biology students for example, 86% could recognise only three or fewer native plant species – which is not surprising, as their teachers’ botanical identification skills were also poor. Botanical education is an integral component of ecology, and the rapid loss of plant life and its implications for mankind deserves a more prominent role in education.

In the School of Biological Sciences at Leicester we have been aware of these problems for some time and working to mitigate them. The University Botanic Garden offers the public an opportunity to study for an Advanced Certificate in Plant Identification, and students on our Biological Sciences degrees can also take a similar Plant Identification Skills module for academic credit.

A new paper in the Journal of Biological Education makes a strong case for the importance of such public and academic courses, and the contribution that ‘Citizen Scientists’ can make in this area, which does not require any expensive equipment, only knowledge and enthusiasm (Bethan Stagg & Maria Donkin (2013) Teaching botanical identification to adults: experiences of the UK participatory science project ‘Open Air Laboratories’, Journal of Biological Education, http://dx.doi.org/10.1080/00219266.2013.764341).

Teaching people about plants does not rival the glamour aspects of medical research, but is possibly no less important in terms of the contribution that academic education can make to society.

 

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