Monthly Archives: March 2011

Traps of carnivorous pitcher plants as habitats (Review)

Traps of carnivorous pitcher plants as habitats
Traps of carnivorous pitcher plants as habitats

A great diversity of organisms, ranging from bacteria to vertebrates, survive and propagate in the otherwise deadly traps of carnivorous pitcher plants. Adlassnig et al. review the diversity of trap inquilines and the data on their environment, the pitcher fluid. Nepenthes and Cephalotus produce acidic, toxic or digestive fluids and host a limited diversity of inquilines, whereas genera without efficient enzymes show more diversity and depend to a large extent on their symbionts for prey utilization.

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The New Face of Science in the World

I remember sometime ago when I opened a journal to read a scientific paper, most papers were authored by two or three people from the same laboratory, less often from different laboratories of the same country and rarely from different countries. However the scientific age has been changing like the global climate and nowadays most of the scientific papers are authored by many researchers from different places around the world, particularly those concerning big challenges like genome organization, or global climate change, not to say particle physics or astrophysical observations. Is this is only an illusion, as a mirage on a desert, or in fact Science is a real network?

According to a new report published by The Royal Society UK: Yes! “Over a third of all articles published in international journals are internationally collaborative”. The report emphasizes that Science is a global enterprise with more than 7 million researchers around the world and a combined R&D spend around 1 trillion dollars, publishing papers in almost 25 thousand scientific journals and thousands of patents.

However, the global participation is not equitable. Despite the fact of an impressive growth of China, followed by India, Brazil and other emerging countries, the participation of these countries in big projects and the impact of their research are still shy of others. G7 countries and their internal network make most of the papers published in the recognized high impact journals, while the rest the world needs to make science by themselves for many different reasons.

This situation does not characterize a real network, so what then is needed to build a real one? How can the rest of the world be included? These questions are important, certainly, because the science network will drive discussions about questions, affecting mainly the developing world. At least, does it mean the three highlighted countries, China, Brazil and India, are not mature enough to participate in big challenge research projects?

The report makes five major recommendations but my suspicion is that these will develop even more highly the well-established network among the G7 countries, without giving directions to include developing countries. At least, one good example of inclusion may be given, where FAPESP (State of São Paulo Research Foundation-Brazil) and RCUK (UK Research Councils) signed a memorandum of understanding where joint research projects will be funded by each part, facilitating collaborative projects and making a new branch to the network.

Most of the questions remain without an answer, but the recognition this report gives makes one think about how to construct a real Global Science Network.

Guest blog by Mateus Mondin
Department of Genetics, “Luiz de Queiroz” College of Agriculture – ESALQ, University of São Paulo – Brazil

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Information overload and links: blogs, social networks and scholarly journals

 

Information, links and networks

Information, links and networks

Next week, a virtual conference is addressing some very pertinent questions of universal relevance to science. In fact, CIARD (Coherence in Information for Agricultural Research for Development) is asking more specifically about e-agriculture and their e-agriculture platform, but I expect the answers will be of wider value:

+ What are we sharing and what needs to be shared?

+ What are the prospects for interoperability in the future?

+ What are the emerging tools, standards and infrastructures?

+ What actions should now be facilitated?

Their background briefing makes clear the information overload problem. It looks like 2011 will be the first year when 1,000,000 MEDLINE-indexed peer-reviewed articles will be published.

I’ve copied part of their vision for the solution in the image above: “Peer reviewed journals and scientific conferences are still the basis of scholarly communication, but science blogs and social community platforms become increasingly important.”

For me, another part of the solution is development of powerful, natural language, search algorithms. Where would we be without Google in research today? If I want to find which wheat line carries Ug99 rust resistance, I don’t go to a genebank database, nor even Theoretical and Applied Genetics TAG on the shelf behind me and where I saw the relevant article. I Google the phrase. The importance of this searchability is re-emphasized every time I look for a reference on one subject: I happen to work on a type of transposable element, Long Interspersed Nuclear Elements, and their acronym, LINE, is found in a majority of those million papers!

I’m now getting my information from browsing half-a-dozen journals and magazines, but much that is new and directly related to my main research is from links which reach me through several keyword and citations search engines which scan new publications, as well as various news feeds which appear on my internet homepage. For this year at least, many other links come from the social and scientific networks and my ‘friends’ and ‘likes’ there. Mendeley suggests papers which I am sure I would not have found otherwise; Twitter finds articles in regional country newspapers; even the AnnBot Daily newspaper provides links of a lighter set of articles about plant science and the environment.

I do wonder now if I spend too much time reading while the e-mails pile up unanswered, and the chase letters asking for the reviews pile in, but without these links I think I would not have the knowledge to give opinions. I’m sure I will be advocating more and different tools in a few months time, but I don’t think I will be going back to delving into specialist databases or many dozens of journals.

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The Rhizosphere of wild barley across Evolution Canyon

Bacteria and other microorganisms contribute greatly to the Earth’s biomass as they form the bottom of the food chain and orchestrate the cycling of carbon, nitrogen, and flow of other nutrients through the ecosystem. They are the ‘dark matter’ of life and may also hold the key to various global problems facing our society e.g. generating sources of nutrition and energy, developing powerful new pharmaceuticals, and cleaning up the environmental disorder. To date, there are a limited number of microbial species that have been studied in the laboratory. The most well-known of these are perhaps E. coli and B. subtilis. However even their wild relatives differ substantially from the highly subcultured laboratory representatives.

In the study reported in this manuscript, samples were collected from the ecological laboratory called Evolution Canyon (EC) which is found in northern Israel. The ‘African’ or south-facing slopes in canyons north of the equator receive higher solar radiation than on the adjacent ‘European’ or north-facing slopes. This difference in solar radiation is associated with higher maximal and average temperatures and evapotranspirations on the more stressful ‘African’ slope. It causes dramatic physical and biotic interslope divergence, which may have originated several million years ago after mountain uplifts. These canyons are extraordinary, natural, evolutionary laboratories. Rocks, soils, and topography are similar on the opposite slopes (50–100 m apart at the bottom); microclimate remains the major interslope divergent factor. So far the intraspecific interslope divergence has been compared in 2500 species across various life forms from prokaryotes through eukaryotic lower and higher plants, fungi, and animals, unraveling the link between environmental stress and genome evolution in adaptation. This unique ecological situation facilitates the generation of theoretical testable and predictable models of biodiversity and genome evolution.

Evolution Canyon

Timmusk S, Paalme V, Pavlicek T, Bergquist J, Vangala A, et al. 2011 Bacterial Distribution in the Rhizosphere of Wild Barley under Contrasting Microclimates. PLoS ONE 6(3): e17968. doi:10.1371/journal.pone.0017968
Background – All plants in nature harbor a diverse community of rhizosphere bacteria which can affect the plant growth. Our samples are isolated from the rhizosphere of wild barley Hordeum spontaneum at the Evolution Canyon (‘EC’), Israel. The bacteria which have been living in close relationship with the plant root under the stressful conditions over millennia are likely to have developed strategies to alleviate plant stress.
Methodology/Principal Findings – We studied distribution of culturable bacteria in the rhizosphere of H. spontaneum and characterized the bacterial 1-aminocyclopropane-1-carboxylate deaminase (ACCd) production, biofilm production, phosphorus solubilization and halophilic behavior. We have shown that the H. spontaneum rhizosphere at the stressful South Facing Slope (SFS) harbors significantly higher population of ACCd producing biofilm forming phosphorus solubilizing osmotic stress tolerant bacteria.
Conclusions/Significance – The long-lived natural laboratory ‘EC’ facilitates the generation of theoretical testable and predictable models of biodiversity and genome evolution on the area of plant microbe interactions. It is likely that the bacteria isolated at the stressful SFS offer new opportunities for the biotechnological applications in our agro-ecological systems.

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Cadmium and hypodermal periderm formation in roots

Cadmium and hypodermal periderm formation in roots
Cadmium and hypodermal periderm formation in roots

Periderm as a result of secondary meristem activity is not usually formed in monocot species. Lux et al.  describe periclinal cell division in the hypodermal layer of Merwilla plumbea, an African medicinal species often found on contaminated soils, which results in formation of multilayered suberized tissue when roots are treated with cadmium. This may be a novel defence reaction of young plants, protecting the roots from radial uptake of Cd ions.

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Open Access in Annals of Botany – low costs allowing more pages

 

Open Access in Annals of Botany

Open Access in Annals of Botany

I’m delighted to say that we have reduced the Annals of Botany Open Access charges to £1000 GBP/ $1615 USD/ €1160 EURO for all papers. Open Access papers are freely accessible to everybody over the web, and all rights for reuse, republication and dissemination lie with the authors. Our discussions suggest that the high charges are a major limitation to wider uptake of open access across the whole plant research community, and this 40% reduction makes our charges substantially lower than those of all the major on-line/open-access-only subject journals. We have the additional advantages that our open-access papers are distributed not just on-line but in the printed journal. Like all our authors, the open access authors have no charges for full-colour in their papers and receive free reprints. For authors from low-income developing countries, we completely waive the open access charge so these authors can distribute their papers more widely. Full details are given at  http://www.oxfordjournals.org/annbot/oxfordopen/article . Our Annals of Botany subscription costs will be reduced in line with the open-access content in the journal, so this will allow us to increase the number of papers we publish without increasing the subscription. Authors make a decision about open-access after acceptance of their manuscript so editorial processes are not changed.

 

We maintain our other reader- and author-friendly policies for all our contributors, including no page charges for authors, authors retaining copyright on all their work, free access to many review articles, increasing amounts of editorial material including ContentSnapshots, Plant Cuttings, and book reviews, wide free distribution of Special Issues, and of course distribution and circulation through AoBBlog.com and press releases for papers of wider public interest. We are grateful to the not-for-profit charity Annals of Botany (owner of the journal) for agreeing to subsidize the costs of the open access papers, in line with their mission for promotion and dissemination of botanical sciences.

We hope and expect that the more even mix of open access and subscription access papers will make us even more attractive for publication of the best novel and substantial plant science, a feature that makes Annals of Botany among the leading broad-spectrum botanical Journals. As Chief Editor, I am very happy that we will be able to offer the best of open-access to those authors with appropriate grants or other funding, while giving other authors from around the world the opportunity to publish without any charges.

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C4 photosynthesis in genus Cleome

C<sub>4</sub> photosynthesis in genus <i>Cleome</i>
C4 photosynthesis in genus Cleome

The genus Cleome (Cleomaceae) includes more than 200 species including one, C. gynandra, that is known to be C4 and two others that are believed to be. Koteyeva et al.  show that all three have features of C4 photosynthesis in their leaves and cotyledons. They are NAD-malic enzyme-type C4 species, and two very different forms of leaf morphology and Kranz anatomy have evolved in the genus, with adaptations to different environments that are supported by biogeographical information.

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Root mechanics and chemistry in Abies

Root mechanics and chemistry in <i>Abies</i>
Root mechanics and chemistry in Abies

The mobile carbon supply to different compartments of a tree is affected by climate but its impact on cell-wall chemistry and mechanics remains unknown. Genet et al.  investigate root properties of mature Abies georgei var. smithii growing at different elevations on the Tibet–Qinghai Plateau and find that mechanical resistance, holocellulose and non-structural carbon (NSC) content all decrease with increasing altitude. Root NSC stocks at the treeline may be depleted through over-demand for carbon supply due to increased fine root production or winter root growth.

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Cone age and longevity of Banksia seeds

Cone age and longevity of <i>Banksia</i> seeds
Cone age and longevity of Banksia seeds

Serotiny, where seeds are retained in the canopy for prolonged periods, is common in the genus Banksia and hence seed collections are likely to to comprised of seeds produced in many different years. Crawford et al.  determine the degree of serotiny in three species and, contrary to expectations, find no relationship between comparative longevity and degree of serotiny. Differences in longevity between cone age classes and species is related to variation in initial viability rather than to differences in the rate of decline of viability with time.

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Life Ascending by Nick Lane

There’s a tendency to look back to at earlier times as some sort of golden age. Even scientists to this despite the fact that “2011 is the most futuristic year there’s ever been” to misquote Paul Sinha. People look back to time when Carl Sagan or David Attenborough were titans of television and, coincidentally, we were all younger. Nick Lane in his book Life Ascending harks back to Jacob Bronowski’s Ascent of Man. As good as Bronowski was, I firmly believe that the golden age of science writing is now, and Life Ascending is an prime example of why 2011 is an excellent time to visit a bookshop to read popular science.

The basic premise behind Life Ascending is that Nick Lane has chosen the ten most innovations created through evolution and given a chapter to each. His choice is personal and requires that the change be a major effect on all life and that the innovation is also still relevant today. Some of the choices are obvious like Sight, or The Complex Cell. Some less so, like the closing chapter Death or Hot Blood. Biologically they’re important, but to someone outside they’re not things that automatically come to mind. Flight doesn’t make the list as such, but there is a chapter Movement.

The spur for getting the book is that we’ll be covering it in SciReadr. I’d heard it was good, but the idea doesn’t sound that compelling. In fact it sounds like a cast-off from Channel 4, like one of those cheap TV programmes where stand-up comedians you’ve never heard of pontificate on past fads. “Antennae, remember those? They were really big in the 70s. Even my Gran had a pair.” I was utterly wrong. It was a brilliant idea.

The reason it works is because of the execution. The list isn’t randomly ordered and the choices work to build up more information and context for the later choices. The start is The Origin of Life and the discussion of energy and the chemical environment of deep sea vents is carried through to the next chapter on DNA. Here the chemistry is used to discuss the development of DNA and RNA and their relationship to the building of complex biochemical structures. This is expanded on further in Photosynthesis which shows how a small change in two biochemical units can dramatically change what is possible. By the time you get to chapter four, The Complex Cell, you’re drawing on information from the three prior chapters. This makes the book a far more satisfying read than if the chapters were each self-contained units on one innovation. It allows ideas to develop and mature, rather than stay perpetually basic. It makes the book harder work. Some adolescents might be frustrated that you can’t just flip ahead to the chapter on Sex and understand it. But all the effort and preparation is worth it because you’ll find Sex a much more meaningful experience than if you’d rushed headlong into it.

Another key feature which you can’t escape with books are the words, and Nick Lane has them. I struggle with opening sentences. Once I’m going I’m fine, but a good opening is a skill. Here’s the opening for Life Ascending which beats “It was a dark and stormy night“:

Night followed day in swift succession. On earth at that time a day lasted for only five or six hours. The planet spun madly on its axis. The moon hung heavy and threatening in the sky, far closer, and so looking much bigger, than today. Stars rarely shone, for the atmosphere was full of smog and dust, but spectacular shooting stars regularly threaded the night sky. The sun, when it could be seen at all through the dull red smog, was watery and weak, lacking the vigour of its prime. Humans could not survive here. Our eyes would not bulge and burst, as they may on Mars; but our lungs could find no breath of oxygen. We ’d fight for a desperate minute, and asphyxiate.

The earth was named badly. ‘Sea’ would have been better. Even today, oceans cover two-thirds of our planet, dominating views from space. Back then, the earth was virtually all water, with a few small volcanic islands poking through the turbulent waves. In thrall to that looming moon, the tides were colossal, ranging perhaps hundreds of feet. Impacts of asteroids and comets were less common than they had been earlier, when the largest of them flung off the moon; but even in this period of relative tranquillity, the oceans regularly boiled and churned. From underneath, too, they seethed. The crust was riddled with cracks, magma welled and coiled, and volcanoes made the underworld a constant presence. It was a world out of equilibrium, a world of restless activity, a feverish infant of a planet.

I knew all this before I started reading, but it’s still powerfully evocative. This tempestuous birth is in striking contrast to Darwin’s warm little pond. Whatever the origin of life, it had to be able to cope with what we would call extreme environments from the outset.

If the origin of life was not tranquil, then neither is its study. Nick Land refers to recent research throughout the book but also repeatedly refers to the fact that many of these ideas are contested. Most strikingly in Hot Blood he notes:

The other major source of rancour in the avian world is feathers. Feduccia and others have long maintained that feathers evolved for flight in birds, imparting to them a disturbingly miraculous sense of perfection. But if feathers evolved for flight, they certainly should not be found among non-avian theropods like T. rex. According to Feduccia, they’re not; but a parade of feathered dinosaurs has marched out of China over the last decade.”

A similar situation occurs in Consciousness:

I should say at the outset that this chapter is different from the other chapters in this book, in that not only does science not (yet) know the answer, but at present we can barely conceive of how that answer might look in terms of the known laws of physics or biology or information. There is no agreement among scholars of the mind about exactly how the firing of neurons could give rise to intense personal sensations.

The book isn’t just about the delivery of facts, it’s about how we know these facts. I find Consciousness the weakest chapter, the other chapters have at least a strong scaffold to hang the discussion of details on. Consciousness doesn’t really have this, but even so the focus on How do we know what we know, means it isn’t bad as such. Just not as focussed as the rest of the book. In its favour it does show that the book is about scientific practice as well as evolution.

I think another reason Consciousness reads a bit oddly is that elsewhere Nick Lane is masterly at drawing together diverse disciplines into one coherent narrative. The conclusion is brief, but in it he underscores that the Biological findings correlate with what we know independently from Geology and Astronomy. Evolution works because it makes sense, and the same can be said of Life Ascending. Collectively the chapters work with each other to emphatically and stylishly make sense. This book isn’t one where you’re impressed and dazzled but slightly at sea when you try and work out what the author is saying. With this book, I know if I forget details I can flip back and see the answer laid out clearly. Reading this I now know what the correct answer to the evolutionary riddle “What use is half an eye?” is not that it’s half as good as a full eye, but that sometimes it can be a lot more useful than a full eye.

If you want to know why, research shrimps or read this book.

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