Tag Archives: Science

Timeless inner beauty…

Image: P. Cuttings’ personal archive.

Image: P. Cuttings’ personal archive.

When trying to appreciate something, it’s often remarked that it is the ‘inner beauty’ that’s important. In which case the plant cell biologists who probe the details within cells (and often illuminate them in all their glorious pin-point precision and fluorescent beauty with immunofluorescent techniques*) must not only, as scientists, be seekers of truth (for is it not writ, in scientia veritas?)  but also be true searchers after beauty. And if something’s really beautiful/true then it has a quality that transcends normal, mortal values and should be permanent. Is that correct? Well, the palaeopteridophytological work of Benjamin Bomfleur et al. may just be the definitive proof of that notion of transcendental permanence. Using language unusual for a serious, sober, scientific article, they describe the fossilised stem of a royal fern (family: Osmundaceae) in Lahar deposits (of putative Early Jurassic – Pliensbachian – date; 189.6–183 million years ago) from Korsaröd in Scania (southern Sweden) as having cellular details that are ‘exquisitely preserved’. Amongst the sub-cellular features discernible are parenchyma cells in the pith and cortex that show preserved membrane-bound cytoplasm, cytosol granules and putative amyloplasts (starch-bearing bodies). Furthermore, most cells contain interphase nuclei with conspicuous nucleoli! And – even more remarkably? – Supplementary Fig. S6 shows detail that is interpreted as signs of necrosis and programmed cell death(!). Whilst more importance is attached by the authors to the fact that the genome size of these reputed ‘living fossils’ has remained unchanged over at least 180 million years (and is understandably viewed as a ‘paramount example of evolutionary stasis’), the degree of internal preservation of cell contents is so good (see Figs S4 and S6 in the paper’s supplementary material!) I’m sure many extant workers could only hope to emulate such faithful preservation in their current work! So, not only is a thing of beauty a joy, it is a joy… forever (or 180 million years at least – long enough for you?). Somebody should write a poem about that!

* For a scientific haiku poem about this, may I humbly suggest the following? Page 15 at the Art Science Movement’s website.

 

[For an award-winning science journalist’s take on Bomfleur et al.’s Science paper, see Jennifer Frazer’s blog. Full-text of the paper – with supplementary pages – appears to be available in front of a paywall via the DiVA portal. And with apologies to our readers for the shameless self-advertisement by Mr P. Cuttings for his ‘poem’! – Ed.]

One hundred and twenty-five years of the Annals of Botany

The first issue of Annals of Botany, August 1887 By August 2012, the Annals of Botany had been published without a break for 125 years. In that time it has become not only the world’s oldest continuously published botanical title but one that has retained a high international standing despite the emergence of numerous popular and well-run competitors. A recent article in the journal is the first of two that, together, look back over the Journal’s long history.

The article describes how the Annals of Botany first came into being in 1887 and the evolution of its editorship and management over the 50 years to 1937. These developments are described in terms of the people involved, how they organized the starting of the Journal and how they ran and financed it on a not-for-profit basis. The article pays particular attention to the lives of the nine remarkable and mostly rather grand individuals who founded the Journal and who, for the most part, came from privileged backgrounds. Despite being a youthful group (all but one were under 40), most were already establishment figures by 1887, e.g. Fellows of the Royal Society (FRS) or directors/professors of prestigious establishments, while the others were soon to become so. The article also outlines the academic environment which allowed the founders and their vision of modern botanical science to prosper, and describes a notable clash of personalities that almost brought the Journal down after only 12 years. In addition, accounts are given of the creation of the ‘Annals of Botany Company’, the effects on the Journal of the First World War and its aftermath, and how the Journal’s managers looked to the future by planning a ‘New Series’ starting 50 years after its foundation.

Jackson, M.B. (2015) One hundred and twenty-five years of the Annals of Botany. Part 1: the first 50 years (1887–1936). Annals of Botany, 115(1), 1-18

Tinted plates used to illustrate early issues of the Annals of Botany

Tinted plates used to illustrate early issues of the Annals of Botany

 

Phylogeny and biogeography of wild roses

Phylogeny and biogeography of wild roses The genus Rosa (with 150–200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus.

The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.

Fougère-Danezan, M., Joly, S., Bruneau, A., Gao, X. F., & Zhang, L. B. (2014) Phylogeny and biogeography of wild roses with specific attention to polyploids. Annals of Botany, December 29, 2014, doi: 10.1093/aob/mcu245

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