What We’re Reading: May 5

Why we’re writing What We’re Reading and how you can contribute…. (more)

Nature Outlook Supplement: Food Security (OA)

Nature has published an Outlook feature on the topic of Food Security with the following overview articles, all useful for teaching:

Food security,   Nutrition: A world of insecurity,   Agrobiodiversity: The living library,   Bioengineering: Solar upgrade,  Egypt: Space to grow,  Perspective: Look beyond production,   Sustainability: A meaty issue,  and Technology: The future of agriculture   (Tags: Education and Outreach, Food Security)

Review: Light-harvesting antenna complexes in the moss Physcomitrella patens: implications for the evolutionary transition from green algae to land plants ($)

The ancestors of land plants were aquatic. Myriad changes accompanied the transition from aquatic to terrestrial life, including changes necessitated by the difference in light intensity and quality. Bryophytes, the earliest diverging land plants, have some characteristics that reveal how plants transitioned from aquatic algae. The moss Physcomitrella patens has become a model for the bryophytes, with a sequenced genome and many genetic tools available. Iwai and Yokono review the moss light-harvesting complex (Lhc) proteins, which are more diverse than those of the angiosperm Arabidopsis or the alga Chlamydomonas, and appear to facilitate additional photoprotection and electron transport pathways. Curr. Opin. Plant Biol. 10.1016/j.pbi.2017.04.002 Tags: Botany, Evolution, Bioenergetics

Review: Phytochrome diversification in cyanobacteria and eukaryotic algae ($)

Phytochromes were first characterized in classic studies of plants, in which their contributions to seed germination and initiation of flowering were described. Subsequently, phytochromes were identified in cyanobacteria and in non-photosynthetic organisms including fungi. Rockwell and Lagarias review the structure and function of phytochromes in diverse organisms, describe current models for the origin of plant phytochromes, and summarize unanswered questions. Curr. Opin. Plant Biol. 10.1016/j.pbi.2017.04.003 Tags: Botany, Evolution, Signals and Responses

Review: Insights into grassland ecosystem responses to global environmental change – NutNet  ($)

Environmental changes affect the biodiversity (variety of life forms) and productivity (conversion of sunlight energy and carbon into plant biomass) of ecological communities. The collaborative Nutrient Network (NutNet) was created 10 years ago with the goal of synthesizing studies of ecosystem environmental responses (mainly of grasslands) and tackling their shortcomings. This review by Borer et al. summarizes the results of this global experiment with over 100 study sites from all over the world, focusing on advances in productivity-diversity relationships, and interactive effects of multiple nutrients, nutrient supply and herbivory. NutNet data have shown that variation in environmental factors (climate, soil fertility, herbivory and light) explains most of the variation in plant diversity within and among grasslands, more than productivity alone. Further, variation in the balance of many nutrients, not only N and P, influences diversity. Specifically, there is a decline in species richness in fertilized or more productive plots, as well as an increase in dominance of exotic species and loss of natives. However, this latter effect can be overcome by the presence of vertebrate herbivores, as grazing increases diversity which favors native flowering plants. Fortunately for us, NutNet’s dataset keeps growing, and our capacity to understand ecosystem dynamics in response to climate change grows along with it. “A decade of NutNet research has demonstrated that a multi-continental, distributed, experimental approach, if designed well, can be a sustainable approach for generating high-quality, large-scale, long-term ecological datasets.” (Summary by Gaby Auge) Nature Ecol.  Evol.  10.1038/s41559-017-0118 Tags: Botany, Ecology, Environmental Plant Biology

Breakthrough Technologies: Hydroxyproline-rich glycoproteins – bioinformatics and evolution

A pair of Breakthrough Technology papers in Plant Physiology discusses new tools to identify hydroxyproline-rich glycoproteins and insights into their evolution. Hydroxyproline-rich glycoproteins (HRGPs) are repeat-rich cell wall proteins that have been described as falling into three large families: arabinogalactan-proteins (AGPs), extensins (EXTs), and proline-rich proteins (PRPs).  In the first paper (10.1104/pp.17.00294), Johnson et al. describe a motif and amino acid bias (MAAB) approach to classify HRGPs, which they now describe as falling into 23 sub-classes. Using these insights, Johnson et al. (10.1104/pp.17.00295) examine the phylogenetic distribution and evolution of HRGPs using data from the 1000 plant transcriptome project (www.onekp.com).  They also describe the many remaining challenges to understand the contributions of these diverse proteins to cell wall structure and function. Plant Physiol.  Tags: Biochemistry, Bioenergy, Cell Biology, Computational Biology

Technical Advance: Quantification of near attomole gibberellins in floral organs dissected froma single Arabidopsis flower ($)

We all learned the series milli-, micro-, nano-, pico-,  femto-, but I didn’t learn atto- (10^-18), as it’s rarely used in biology, representing such a tiny number (FYI, atto- is followed by zepto- and yocto-).  Li et al provide a method for quantifying gibberellin (GA) hormones at “near attomole” amounts from a single Arabidopsis flower. Any molecule is hard to isolate in attomolar amounts, but gibberellins provide a particular challenge as they are a family of closely-related compounds that are difficult to separate. By reacting the GAs with a positively-charged moiety [N-(3-dimethylaminopropyl)-N’-ethylcarbodiimide (EDC)] in ethanol, the authors were able to use an ultra-high-performance liquid chromatography (UHPLC)-ESI-MS/MS method to detect tiny amounts of different GAs from the dissected organs of a single Arabidopsis flower. Plant J. 10.1111/tpj.13580 Tags: Biochemistry, Signals and Responses

Young inversion with multiple linked QTLs under selection in a hybrid zone

Chromosomal inversions are chromosomal rearrangements that can span several Mb and have been described in several organisms from Drosophila to maize. Inversions suppress recombination and can favor local adaptation and speciation if they capture favorable alleles. It’s not clear though if favorable alleles accumulate in older inversions or, as the Kirkpatrick–Barton model proposes, inversions capture chromosomal blocks that contain pre-existing adaptive alleles.  Lee et al. show that in a hybrid speciation zone with ecologically different subspecies (East and West) of Boechera stricta (a wild-growing brassica)  a young inversion arose after the last glaciation, quickly reached high frequency and shows signs of positive selection. The authors used a cross of collinear haplotypes to show that the inversion carries several QTLs that influence several phenological and developmental traits and controls high percentages of the phenological differences between the two subspecies. In summary this paper shows that inversions can capture pre-existing, favorable, linked QTLs during initial steps of speciation. (Summary by Rubén Rellán-Álverez) Nature Ecol. Evol. 10.1038/s41559-017-0119 Tags: Botany, Genetics, Evolution

A chromosome conformation capture ordered sequence of the barley genome

Cereal grasses are of course economically important, but they also have large repetitive genomes with large pericentromeric regions that have been difficult to map and sequence. Barley (Hordeum vulgare L.) is used for human and animal food and fermented to produce beer and whisky. A barley sequence assembly was published in 2012, but now Mascher et al. have used chromosome conformation capture mapping to produce a much more complete barley genome sequence, including sequences across the pericentromeric region. Their data reveal significant differences in gene density, recombination rates and retrotransposon distribution in the distal versus proximal regions of the chromosome. They also observe low levels of variation within elite germplasms, presumably due to intense selection. Nature 10.1038/nature22043 Tags: Genomics

Cell-size dependent progression of the cell cycle for homeostasis and flexibility of cell size

Cell size is determined by growth rate and frequency of division. Studies in yeast revealed mechanisms that coordinate these processes, as well as the crucial checkpoint controls that ensure the cell is “ready” to divide, but can models from single-celled organisms be applied to multicellular ones that have intrinsic differences including mechanical constraints? Jones et al. investigate the linkage between growth and division in the shoot apical meristem. Through imaging, modeling and mutant analysis, they show that the size of the call at birth is correlated with the length of time to division, which serves to normalize variations in cell size. They also found that the cell cycle length is determined by the activity of cyclin-dependent kinase (CDK), that the lengths of the G1 phase and the S-G2-M phase are size dependent, and that cell size is dependent on metabolic status. Overall, they conclude that cell size control regulation is similar in Arabidopsis and yeast.  Nature Comms.  10.1038/ncomms15060 Tags: Cell Biology, Genetics, Growth Regulation

Nanoscale movements of cellulose microfibrils in primary cell walls ($)

Cell walls are complex mixtures of cellulose microfibrils, proteins and other materials. Their mechanical properties can be measured and modeled, but it is not always simple to translate these measurements to changes at the molecular level. Zhang et al. used atomic force microscopy to provide an unprecedented view of how cellulose microfibrils respond to stress and strain (if you are a bit fuzzy on the difference between stress and strain see Baskin’s excellent News and Views ). The authors imaged the microfibrils while the cell wall was subjected to plastic and elastic extension and stress relaxation by the addition of a cell-wall loosening enzyme. A key finding is that in some conditions the microfibrils are able to slip relative to the surrounding matrix. The authors also describe new insights into microfibril connections and anchoring. Nature Plants 10.1038/nplants.2017.56 Tags: Bioenergy, Cell Biology, Growth Regulation

A Raf-like protein kinase BHP mediates blue light-dependent stomatal opening

How do stomata open in response to blue light?  Blue light is perceived by phototropin receptor kinases that activate BLUE LIGHT SIGNALING1 (BLUS1), type 1 protein phosphatase (PP1), and the plasma membrane (PM) H⁺-ATPase.  Hayashi et al. screened a commercial kinase inhibitor library to identify the kinases that phosphorylate PM H⁺-ATPase in response to blue light.  Inhibitors that blocked blue light-stimulated phosphorylation of PM H⁺-ATPase share targets from members of the Raf-like kinase subfamily of MAPKKK enzymes.  A mutant of a Raf-like kinase that is highly-expressed in guard cells could not open stomata in response to blue light.  This gene was named BLUE LIGHT-DEPENDENT H⁺-ATPASE PHOSPHORYLATION (BHP), and its kinase activity is necessary for stomatal opening in response to blue light. BHP localizes to the guard cell cytoplasm.  BHP binds to BLUS1 & PP1 in vitro, but not phototropins or PM H⁺-ATPase.  Hayashi et al. identified BHP as a kinase that interacts with BLUS1 to indirectly regulate the PM H⁺-ATPase and stomatal movement.  (Summary by Daniel Czerny) Sci. Reports 10.1038/srep45586 Tags: Cell Biology, Signals and Responses

Ethylene regulates differential growth via BIG ARF-GEF-dependent post-Golgi secretory trafficking in Arabidopsis

Regulated movement to and from the plasma membrane (PM) has emerged as an important strategy for controlling the activity of plasma membrane proteins such as transporters and receptors. Jonsson et al. investigated the cellular machinery required for the insertion of the auxin-transport protein AUX1 into the plasma membrane from the trans-Golgi network. AUX1 is necessary for the ethylene-induced enhancement of the apical hook that protects the shoot as seedlings emerge from the soil. The authors address the contributions of ARFs and ARF-GEFs, proteins previously shown to be required for movement of vesicles from the trans-Golgi network. The authors found that different subtypes of ARF-GEFs (GNOMs and BIGs) act non-redundantly in apical hook formation. They also showed that BIGs and another protein, ECHIDNA (ECH) are both required for trafficking of AUX1 to the plasma membrane and maintenance of the apical hook. Plant Cell 10.​1105/​tpc.​16.​00743 Tags: Cell Biology, Growth Regulation, Signals and Responses

Interspecies hormonal control of host root morphology by parasitic plants ($)

Parasitic plants draw nutrients from their hosts. Spallek et al. explored the molecular interaction between the parasitic plant Phtheirospermum japonicum (in the Orobranchaceae family) and the model plant Arabidopsis thaliana. They demonstrated movement of tracers from the host to the parasite through the xylem. They also showed that cytokinin hormone synthesis is induced in the parasite upon attachment, and that these hormones move into the host and direct changes in morphology. Specifically, the parasite induced a swelling in the host tissue (hypertrophy) above the site of attachment, which included an increase in the area of the xylem. Mutant analysis showed that hypertrophy required host cytokinin response genes but not cytokinin synthesis genes, indicating that it is a response to parasite-synthesized and transported hormones. Proc. Natl. Acad. Sci. USA 10.1073/pnas.1619078114 Tags: Biotic Interactions, Botany, Growth Regulation, Signals and Responses

Biofuel blending reduces particle emissions from aircraft engines at cruise conditions ($)

Aircraft engines release CO₂ into the atmosphere, but particles produced from aircraft emissions can also affect climate through aerosol production that leads to cloud formation. Moore et al. examined how incorporating plant-based biofuels (Camelina oil) affected the production of aerosols. They found that particle number and mass were reduced when biofuels were incorporated into the fuel, revealing another positive benefit of plant-derived biofuels to climate mitigation. Nature 10.1038/nature21420 Tags: Bioenergy, Environmental Plant Science

How do research faculty in the biosciences evaluate paper authorship criteria?

Kassis asked biology, biomedical engineering and bioengineering faculty how important they considered several criteria for recognition as an author and rank on authorship list. A key finding is that, “Overall, there seemed to be a consensus that the time spent conducting experiments, coming up with a hypothesis, analyzing data, and writing the manuscript were the four most important criteria for both determining one’s authorship status and rank.” However, there was wide variation in the relative importance of several other criteria (including contributing a reagent or code, or conducting a literature review), indicating some inconsistency in how authorship decisions are made. The author suggests that these findings will help students navigate “the discrepancy between official policies for authorship and the contributions that faculty truly value.” [For more on authorship policies see Defining the role of authors and contributors (International Committee of Medical Journal Editors) and How to handle authorship disputes:a guide for new researchers  (Tim Albert and Liz Wager)]. bioRxiv 10.1101/069468 Tags: Education and Outreach, Policy