Tag Archives: Science

One of a kind…

Image: Scott Zona/Wikimedia Commons.

Image: Scott Zona/Wikimedia Commons.

These articles have been going long enough(!) to be able now to report a successful outcome to a research project whose initiation was announced in a former news item entitled ‘Old meets new’. The project is the elucidation of the genome of Amborella trichopoda. “Amborella is a monotypic genus of rare understory [sic! What ever happened to understorEy??? - Ed.] shrubs or small trees endemic to… New Caledonia”.

Not only is this plant rare and monotypic – truly ‘one of a kind’! – but it is also probably the living – extant – flowering plant [angiosperm] that is closest evolutionarily to the earliest true first member of the angiosperm plant group, and may therefore be “the last survivor of a lineage that branched off during the dynasty’s earliest days, before the rest of the 350,000 or so angiosperm species diversified”. Given Amborella’s exalted status (which “represents the equivalent of the duck-billed platypus in mammals”), it is hoped that understanding its genetics will shed light on the evolution of the angiosperms as a whole. Indeed, the University of Bonn’s Dietmar Quandt is reported as describing Amborella as a more worthy model organism than Arabidopsis(!!!).

Since the angiosperms are probably the most ‘successful’ of all the groups in the Plant Kingdom (‘the land plants’, the Plantae), hopes are understandably high that unravelling the genome of Amborella – reported by the aptly named Amborella Genome Project – will lead to the identification of “the molecular basis of biological innovations that contributed to their geologically near-instantaneous rise to ecological dominance”. And accompanying the main nuclear genome article, Danny Rice et al. report on Amborella’s mitochondrial genome (mitochondria have some of their own DNA additional to that located in the nucleus) and find that numerous genes were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. So, as ancient as it is, Amborella was still prepared to ‘learn’ from the experiences of even older land plants – mosses – and plant-like algae (which are in a different kingdom entirely to the land plants, the Protista). Adopt and adapt: a life lesson for all living things, I suggest.

[For more on this fascinating story, visit the home of the Amborella genome database. And if you still need some ‘proper’ botany (after all this genomery), you need look no further than Paula Rudall and Emma Knowles’ paper examining ultrastructure of stomatal development in early-divergent angiosperms (including Amborella…).  Notwithstanding all of this understandable present-day excitement, I can’t help but think that the importance of Amborella was foretold many decades ago, as "popular-in-the-mid-1970s" British-based pop band Fox seemingly declared: "things can get much better, under your Amborella…". Indeed! So, arabidopsis had better watch out! – Ed.]

Spotlight on macronutrients (Part 2): Nitrogen, in a bit of a fix…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

In this and my next few posts we conclude our look at essential plant macronutrients that started in some previous articles, and this time concentrate on the last four of the nine elements – C, H, O, P, K, N, S, Ca and Mg – in that category (and try to bring a Cuttings-esque twist to that quartet).

 

Nitrogen, in a bit of a fix…

Nitrogen (N) is a major component of many compounds in plants, e.g. it is present in all amino acids, which are the building blocks of proteins – and hence cell membranesenzymes and nutritionally important storage or reserve proteins; and it is an important constituent of nucleotides, which are major components of nucleic acids, such as RNA (ribonucleic acid) and DNA (deoxyribonucleic acid), and of the ‘energy molecule’ ATP (adenosine triphosphate). As a major component of plants, N is needed in relatively large amounts – which is why it is termed a macronutrient. Fortunate then, you might think, that plants are virtually surrounded by an unlimited amount of nitrogen in the atmosphere,  which consists of approx. 78% of this gaseous element in the form of dinitrogen, N2. Sadly, in that state plants cannot use it; it must be converted to forms that they can use, such as the ammonium (NH4+, from ammonia – NH3) and nitrate (NO3) ions.

 

Whilst plants cannot themselves convert N2 into NH3, many groups of plants – e.g. famously, the legumes – have teamed up with bacteria that can undertake that chemical reaction in the process known as nitrogen fixation. Some of that fixed nitrogen is used by the plant that hosts the mutualistic microbe, as a sort of rent for the home that the plant provides for the bacteria within root-sited nodules.

 

Unfortunately, many more plants are not blessed with this in-built nitrogen-fixing partnership and are reliant on appropriate forms of fixed nitrogen from the environment, e.g. NO3. Since N is frequently in short supply in the soil, it is often referred to as a limiting nutrient – an essential nutrient whose amount limits overall plant growth and development. In agricultural settings this deficiency is usually remedied by the addition of chemical fertilisers, often containing phosphorus (P) and potassium (K) in addition to the N. Whilst desired increases in crop growth/yield are obtained by this human intervention, not all of that added nitrogen – and frequently phosphorus, too – is taken up by the crop; substantial amounts of N and P end up in freshwater systems where they can cause highly undesirable problems such as eutrophication. Not only is that damaging to the environment, it is costly – ‘Nitrogen fertilizer costs US farmers approximately US$8 billion each year…’.

Wouldn’t it be great if non-legumes could be persuaded to develop N-fixing bacterial partnerships? Yes, and work by Yan Liang et al. (Science 341: 1384–1387, 2013) encourages that view. The team from The Plant Molecular Biology and Biotechnology Research Center (South Korea) and University of Missouri (USA) have demonstrated that non-legumes – in this instance good old Arabidopsis thaliana, Zea mays (‘corn’) and Solanum lycopersicum (tomato) – do have the ability to respond to the rhizobial lipo-chitin Nod factors that are released by the would-be symbiotic rhizobial bacteria, and which are signal molecules that trigger nodulation in legumes. Although we are still some time away from nodulating N-fixing non-legume crops such as maize and tomato, this discovery does at least show that the rhizobia are recognized as ‘friendly bacteria’ – the plants just have to be trained to let them accept invasion of their tissues by the microbe, and build the nodule, etc, etc…

 

[Although there are generally recognised to be 17 essential plant nutrientscobalt (Co) is additionally required by the bacteria of the N-fixing nodules,  so indirectly Co is an 18th essential nutrient in those cases – Ed.]

The fruit, the whole fruit, and everything about the fruit

The opium poppy Fruits come in an impressive array of shapes, sizes, and consistencies, and also display a huge diversity in biochemical/metabolite profiles, wherein lies their value as rich sources of food, nutrition, and pharmaceuticals. This is in addition to their fundamental function in supporting and dispersing the developing and mature seeds for the next generation.

Understanding developmental processes such as fruit development and ripening, particularly at the genetic level, was once largely restricted to model and crop systems for practical and commercial reasons, but with the expansion of developmental genetic and evo-devo tools/analyses we can now investigate and compare aspects of fruit development in species spanning the angiosperms. We can superimpose recent genetic discoveries onto the detailed characterization of fruit development and ripening conducted with primary considerations such as yield and harvesting efficiency in mind, as well as on the detailed description of taxonomically relevant characters.

This free review article focuses on two very morphologically distinct and evolutionary distant fruits: the capsule of opium poppy, and the grain or caryopsis of cereals. Both are of massive economic value, but because of very different constituents; alkaloids of varied pharmaceutical value derived from secondary metabolism in opium poppy capsules, and calorific energy fuel derived from primary metabolism in cereal grains. Through comparative analyses in these and other fruit types, interesting patterns of regulatory gene function diversification and conservation are beginning to emerge.

Sofia Kourmpetli and Sinéad Drea. The fruit, the whole fruit, and everything about the fruit. J Exp Bot. Apr 10 2014.

 

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.]

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.]

 

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?]

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

 

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.]