Tag Archives: Plant Cell

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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Chloroplasts are how old???

Image: Mariana Ruiz Villarreal/Wikimedia Commons.

Image: Mariana Ruiz Villarreal/Wikimedia Commons.

It is widely acknowledged that eukaryotic cells (you know, the ones with a membrane-bound nucleus and a variety of other membrane-bound organelles (cf. prokaryotes)) came to be so complex by a series of ‘mergers and acquisitions’ that saw a prokaryote-like cell internalise other, smaller ‘cells’ to gain organelles such as mitochondria and chloroplasts. That is the essence of the Serial Endosymbiotic Hypothesis/Theory. But have you ever wondered how long ago such events took place? Well, Patrick Shih and Nicholas Matzke have done so on our behalf .

Using ‘cross-calibrated phylogenetic dating of duplicated ATPase proteins’ (which are retained by mitochondria and chloroplasts and involved in energy production in both), the duo’s results suggest that primary plastid endosymbiosis (which eventually gave us plant cells) occurred approximately 900 Mya (millions of years ago), whereas mitochondrial endosymbiosis occurred around 1200 Mya. Interestingly, both authors contributed equally to this work, and both were PhD students at the time! I’d so like one of the authors to have done the mitochondria work, and the other to have been ‘responsible’ for chloroplasts; that would make for a pleasingly symmetrical, modern-day parallel to the 19th century’s Cell Theory, largely attributed to Schleiden (‘botanist’) and Schwann (‘zoologist’). Way to go, gentlemen!

[Please don’t construe Mr Cuttings’ comments about putative parallels with Schleiden and Schwann to mean that only animal cells have mitochondria, and only plant cells have chloroplasts; plant cells can contain both (yes, so they are better than animals…)! – Ed.]

 

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The Repressive ER

Image: Magnus Manske/Wikimedia Commons.

Image: Magnus Manske/Wikimedia Commons.

Often over-shadowed by other organelles such as the nucleus, chloroplast or vacuole, the endoplasmic reticulum (ER) – ‘an organelle of cells in eukaryotic organisms that forms an interconnected network of membrane vesicles’ – is slowly revealing its secrets (John Runions).

As a major component of the cell’s secretory pathway, the ER is intimately involved in protein synthesis via the ribosomes that are studded along its cytoplasmic surface (and which give rise to RER – rough endoplasmic reticulum). The process of protein synthesis is known as translation as it involves ‘translation’ of the message encoded in the m(essenger)RNA (which is itself made within the nucleus and carries the information for a particular protein originally contained within a gene in the cell’s DNA). However, once made, the ‘proteins’ – strictly speaking they are polypeptides: protein is a name that should be reserved for the fully functional, final product – are often altered to produce the protein, a process called post-translational modification.

While the details are beyond the scope of this item, the controls over gene expression – which include transcription, mRNA processing, and translation – are numerous. But one such system uses micro-ribonucleic acids (miRNAs), short-lengths of RNA that interact with mRNA thereby preventing its subsequent translation into protein. Now, here’s the take-home message: Shengben Li et al. have demonstrated that translation-inhibition activity by miRNAs occurs on the ER, and requires ALTERED MERISTEM PROGRAM1 (AMP1), which encodes an integral membrane protein associated with ER. But! Not only is this study important in identifying a previously unknown function of the ER, the work was performed in arabidopsis (i.e. a plant!), and, according to Xuemei Chen (lead researcher of the work), ‘as AMP1 has counterparts in animals, our findings in plants could have broader implications’. How refreshing to see plant work paving the way for animal/biomedical studies!

[For more on the world of small RNA, timely news that the Plant Cell’s Teaching Tools in Plant Biology on that topic has just been revised. This FREE resource – which includes a ready-made PowerPoint presentation, lecture notes, and teaching guide – can be accessed at http://www.plantcell.org/site/teachingtools/TTPB5.xhtml. – Ed.]

 

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Roles for calcium: numero uno

Image: Wikimedia Commons.

Image: Wikimedia Commons.

As an essential macronutrient calcium participates in many aspects of plant biology, e.g. structural roles in the cell wall, as a counter-cation for anions in the vacuole and as a so-called ‘secondary messenger’, where calcium signals participate in many developmental processes. But one function that has passed me by until now is the part it plays in the water-splitting reaction of photosynthesis.

Although all parts of photosynthesis are important, arguably the photolysis of water is the most important reaction in the process since it generates the hydrogen ions (protons) and electrons that participate in the ATP- and NADPH-generating activities of the light-dependent reactions of photosynthesis, which are fundamental to subsequent carbon-fixation in the light-independent stages (‘dark reactions’) of the process. Oh! And this photolysis also releases oxygen that accumulates in the atmosphere, and which is so essential to all aerobic life forms.

Whilst I was familiar with the idea that manganese (an essential micronutrient) is a major component of the water-splitting complex, I didn’t realise that calcium was too. However, although its presence there was known to others, its role was not (so I don’t feel so bad about my state of comparative ignorance…). But work by Emily Tsui et al. has revealed that calcium plays an important supportive role in allowing the manganese to transfer electrons away from the oxygen thereby facilitating the subsequent production of molecular oxygen.

Fascinating as this is in adding yet another role to the already extensive catalogue of calcium’s competencies, it is also hoped that this insight might help in the construction of artificial photosynthesis systems, with promises of renewable, cleaner energy. New light on an old topic: we like that!

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Sex inequality in science: skirting around the issue?

Image: Illumination from Scivias, by Hildegard von Bingen, ca. 1152.

Image: Illumination from Scivias, by Hildegard von Bingen, ca. 1152.

Recognising the under-representation of women in the science arena (including botany, which is a science – see David Chamovitz’s Daily Plant blog on this point), the European Commission (EC, Brussels-based overlords of a Greater European political entity), have decided to do something about it. Launched in June 2012 the premise of its ‘Science: it’s a girl thing!’ campaign is that, ‘There is a growing pool of female talent in Europe from which research and innovation should benefit… There are many factors at work explaining the lack of women in research in general and in some sectors in particular… The campaign intends to address these stereotypes’. Its straightforward goal is to ‘attract young women to research careers in order to increase the total number of researchers in Europe’. Nobel aims, and at a time when plant scientists (OK, botanists) will be at the forefront of solving many of the most urgent global problems (e.g. Claire Grierson et al.), what employment initiative could be more apt, and timely? Well – and you really couldn’t make it up – the EC campaign has not been without its ‘knockers’ (UK English colloquial term for detractors). It’s not that the idea is bad, but there were serious ‘issues’ with the video that accompanied the initiative’s launch. In the interests of balanced reporting I watched the video. I concur with the outraged news item which starts, ‘A man with a chiseled face dons his horn rims for a better look as three barely adult women in micromini dresses and stilettos catwalk toward him. As he stares in shock, lust, and awe, each woman strikes a pose as a bass beat throbs in the background’. Widely denounced on various social media sites and in respected news media, and satirised on YouTube, the video has since been removed on the grounds that the EC ‘does want it to distract from the main campaign’. I think – hope! – that a ‘not’ has been inadvertently omitted from that sentence in Mark Peplow’s article on the usually unimpeachable Nature news blog site. And hot on the, err, high heels of the furore over that video is Katherine O’Brien and Karen Hapgood’s timely academic study entitled ‘The academic jungle: ecosystem modelling reveals why women are driven out of research’. Applying ecological methodology normally reserved for investigating how species battle to sustain themselves in challenging habitats, the duo have investigated why women are being driven out of science. Interestingly, the study not only identifies how a gender imbalance in science and academia is maintained by institutional barriers, it also offers advice on strategies to enable part-timers – predominantly women who’ve taken career breaks to have children – to do better in the career progression and advancement stakes. Amongst its recommendations are measures under the following categories: ‘For women working in part-time roles in academia: how to survive’; ‘For women after a career break: how to re-enter academia’; ‘For university managers: how to help part-time staff thrive’; and ‘For university administrators: how to encourage a productive, diverse workforce’. Ladies (and lads…), if you’re not completely put off the idea of pursuing science as a career, welcome news of 66 new post-docs in… PLANT SCIENCE for you to apply for. Termed ‘PLANT FELLOWS’, it is a new international post-doc fellowship programme in the field of plant sciences co-funded by the EC’s (!) Seventh Framework Programme (FP7) Marie Curie Actions – People, Co-funding of Regional, National and International Programmes (COFUND). Co-ordinated by the Zurich-based Plant Science Center, the scheme is open to applicants from all over the world to work within 14 European and seven international universities and research institutes and three industry partners selected as host organisations on the basis of their excellence in higher education and plant research. And if you’re stuck for ideas of what to study and put in your application, look no further than Irene Lavagi et al.’s Open Access Commentary article on a road map for the next decade of Arabidopsis research (The Plant Cell, in press, 2012). Drawn up by the Multinational Arabidopsis Steering Committee (MASC), this 10-year ‘plan’ is intended to inform scientists and decision makers on the future foci of Arabidopsis research within the wider plant science landscape. Bon voyage, as the worthies in Brussels might say. [Please, no jokes about ‘have you got the map the right way up?’! – Ed. No, because it is well known that it is men who never ask for directions! – Mrs P. Cuttings]

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Hard-up botanist, please give generously

Image: Sidney Paget, Strand Magazine, 1891.

Image: Sidney Paget, Strand Magazine, 1891.

Times are hard; everybody wants more (but seems to be getting less…), many demands are placed upon the flimsy, finite finances of states and their funding agencies. But if future food and energy supplies are to be secured – for all of us – it has been estimated that expenditure of US$100 billion is needed over a 10-year period. Or such is the claim of Wolf Frommer (Carnegie Institution for Science, USA) and Tom Brutnell (Danforth Plant Science Center, USA) in their ‘Food for thought’ opinion piece in The Scientist. As the pair note, ‘Today, we face growing and economically empowered nations, energy-intensive global economies, and major shifts in global climate that together constitute the perfect storm for agriculture. Yet plant-science research has been underfunded for decades—and funding is projected to shrink’. Key to much of this is exploitation of new and emerging 21st century technologies in the plant sciences – particularly molecular and imaging ones – a topic developed in a Plant Cell ‘Perspective’ paper by David Ehrhardt and Frommer. But the sum of US$100 billion is just for the USA: how much more is needed for a truly global commitment to end food poverty, etc? As an encouragement to stumping up the dosh, the pair conclude that ‘If we [the USA] do nothing, we may return to our pre-1776 role as colonists who simply provide food to more strategically minded nations’. Or, alternatively and even more unthinkably, ‘The risks for failing to meet this challenge are great: in an overpopulated, food-limited world we will inevitably witness more social unrest and, potentially, food and climate wars’. Now, what red-blooded American Congressman/woman would risk that in this US presidential (re?)election year? Let those ‘green’ dollars roll! [Ehrhardt and Frommer’s article is a modified version of the paper generated for the Plant Science Research Summit in 2011. For more information, visit its webpage– Ed.].

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New methodologies…

Image: Wikimedia Commons

Image: Wikimedia Commons

In the olden days – e.g. the 19th Century – science was severely hampered by the lack of technology to perform the experiments that those gentlemen (sorry, gentlewomen…) of the 20th and 21st Centuries of great vision and imagination conjured up. Today, we have access to an unparalleled arsenal of techniques and equipment to test our hypotheses (it is often our imagination that lets us down…). But that is not to say that we can’t use even more new methods and kit. So, here’s a bit of a catalogue of recent developments/break-through technologies in plant biology.

Whilst hormones (plant growth regulators?…) don’t control everything botanical, they are major players in co-ordinating growth and development. So, it would be useful to be able to see where they are in planta. Well, Géraldine Brunoud et al. report a ‘novel sensor to map auxin response and distribution at high spatio-temporal resolution’. Amongst other things, this method ‘provides a map of relative auxin distribution at cellular resolution in different tissues’. The method was exploited to very good effect in demonstrating that ‘root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism’. Fed-up with the tedium of weekly subculture of plant cell suspensions? Well, fret no more: Anne-Marie Boisson et al. report ‘a simple and efficient method for the long-term preservation of plant cell suspension cultures’.

Too busy searching for your next post-doc position to solve protein structures yourself? Crowd-source it! This is how the still-unsolved-after-more-than-10-years-of-study problem of the folding of a protein was tackled, by an army of virtual lab assistants playing the ‘protein folding game’, Foldit – ‘an online puzzle video game about protein folding’. OK, so this work was actually done with ‘a retroviral protease of the Mason–Pfizer monkey virus, which causes an AIDS-like disease in monkeys’, but surely the principle’s the same for plant proteins. Envious of the ease with which your colleagues working with Nicotiana benthamiana can perform Agrobacterium-mediated transient transformation by leaf infiltration? Not any more! Kenichi Tsuda et al. present a protocol for an ‘efficient Agrobacterium-mediated transient transformation of Arabidopsis’. I know, and you thought we could do EVERYTHING with Arabidopsis, already. Well, looks like we can now! And many high-resolution methodologies and measurement techniques are showcased/reviewed in a special issue of our favourite journal about plants [second-favourite, surely? – Ed.], and a useful editorial overview is provided by Asaph Aharoni and Federica Brandizzi. One contribution that caught my eye was Ljudmilla Borisjuk et al.’s ‘Surveying the plant’s world by magnetic resonance imaging’, which shows the ingenuity of the botanist in adopting and adapting a technique more usually associated with biomedical applications.

Penultimately, Guido Grossmann et al. present the RootChip – ‘an integrated microfluidic chip for plant science’, which aims to overcome the acknowledged problems of studying development and physiology of growing roots. The RootChip integrates live-cell imaging of growth and metabolism of Arabidopsis thaliana roots with rapid modulation of environmental conditions, and can cope with multiple roots from multiple seedlings in parallel. As presented it sounds impressive, but am I wrong in thinking that roots tend to grow in the dark, in soil? Well, the image accompanying the article shows roots in transparent plastic tubes, in a well-lit lab. Maybe that’s just for purposes of illustration and the meaningful measurements, etc, are made when the roots are in their native darkened state.

Finally, recognising that the ability to quantify the geometry of plant organs at the cellular scale can provide novel insights into their structural organisation, Andrew French et al. present a tool to count and measure individual neighbouring cells along a defined file in confocal laser scanning microscope images. Amongst other uses, the Cell-o-Tape tool can be used to provide an estimate of the position of transition into the elongation zone of an Arabidopsis root – a location apparently ‘sensitive’ to the subjectivity of the experimenter. Quite a list – which is by no means exhaustive! – but, my personal favourite is… Cell-o-Tape. And I’m sticking to it!

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