Ecophysiological traits of grasses: resolving the effects of photosynthetic pathway and phylogeny

C4 photosynthesis is an important example of convergent evolution in plants, having arisen in eudicots, monocots and diatoms. Comparisons between such diverse groups are confounded by phylogenetic and ecological differences, so that only broad generalisations can be made about the role of C4 photosynthesis in
determining ecophysiological traits. However, 60% of C4 species occur in the grasses (Poaceae) and molecular phylogenetic techniques confirm that there are between 8 and 17 independent origins of C4 photosynthesis in the Poaceae. In a screening experiment, we compared leaf physiology and growth traits across several major
independent C3 & C4 groups within the Poaceae, asking 1) which traits differ consistently between photosynthetic
types and 2) which traits differ consistently between clades within each photosynthetic type

The Ca2+ transient as a feedback sensor controlling cardiomyocyte ionic conductances in mouse populations.

Conductances of ion channels and transporters controlling cardiac excitation may vary in a population of subjects with different cardiac gene expression patterns. However, the amount of variability and its origin are not quantitatively known. We propose a new conceptual approach to predict this variability that consists of finding combinations of conductances generating a normal intracellular Ca2+ transient without any constraint on the action potential. Furthermore, we validate experimentally its predictions using the Hybrid Mouse Diversity Panel, a model system of genetically diverse mouse strains that allows us to quantify inter-subject versus intra-subject variability. The method predicts that conductances of inward Ca2+ and outward K+ currents compensate each other to generate a normal Ca2+ transient in good quantitative agreement with current measurements in ventricular myocytes from hearts of different isogenic strains. Our results suggest that a feedback mechanism sensing the aggregate Ca2+ transient of the heart suffices to regulate ionic conductances

Structural analysis of herpes simplex virus by optical super-resolution imaging.

Herpes simplex virus type-1 (HSV-1) is one of the most widespread pathogens among humans. Although the structure of HSV-1 has been extensively investigated, the precise organization of tegument and envelope proteins remains elusive. Here we use super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) in combination with a model-based analysis of single-molecule localization data, to determine the position of protein layers within virus particles. We resolve different protein layers within individual HSV-1 particles using multi-colour dSTORM imaging and discriminate envelope-anchored glycoproteins from tegument proteins, both in purified virions and in virions present in infected cells. Precise characterization of HSV-1 structure was achieved by particle averaging of purified viruses and model-based analysis of the radial distribution of the tegument proteins VP16, VP1/2 and pUL37, and envelope protein gD. From this data, we propose a model of the protein organization inside the tegument.This work was supported by grants from the Leverhulme Trust (grant RPG-2012-793), the Royal Society (University Research Fellowship to C.M.C.), the Engineering and Physical Sciences Research Council, UK (grant EP/H018301/1) and by the Medical Research Council (grant MR/K015850/1).This is the final published version. It first appeared at http://www.nature.com/ncomms/2015/150122/ncomms6980/full/ncomms6980.html

Were Fertile Crescent crop progenitors higher yielding than other wild species that were never domesticated?

During the origin of agriculture in the Fertile Crescent, the broad spectrum of wild plant species exploited by hunter-gatherers narrowed dramatically. The mechanisms responsible for this specialization and the associated domestication of plants are intensely debated. We investigated why some species were domesticated rather than others, and which traits they shared. We tested whether the progenitors of cereal and pulse crops, grown individually, produced a higher yield and less chaff than other wild grasses and legumes, thereby maximizing the return per seed planted and minimizing processing time. We compared harvest traits of species originating from the Fertile Crescent, including those for which there is archaeological evidence of deliberate collection. Unexpectedly, wild crop progenitors in both families had neither higher grain yield nor, in grasses, less chaff, although they did have larger seeds. Moreover, small-seeded grasses actually returned a higher yield relative to the mass of seeds sown. However, cereal progenitors had threefold fewer seeds per plant, representing a major difference in how seeds are packaged on plants. These data suggest that there was no intrinsic yield advantage to adopting large-seeded progenitor species as crops. Explaining why Neolithic agriculture was founded on these species, therefore, remains an important unresolved challenge

Using Specialist Screening Practitioners (SSPs) to increase uptake of the Bowel Scope (Flexible Sigmoidoscopy) Screening Programme: a study protocol for a feasibility single-stage phase II trial

Background: The NHS Bowel Scope Screening (BSS) programme offers men and women aged 55 years a onceonly flexible sigmoidoscopy (FS), a test that can help reduce colorectal cancer (CRC) incidence and mortality. However, the benefits of BSS are contingent on uptake. This National Institute for Health Research-funded singlestage phase II trial will test the feasibility of using patient navigation (PN), an intervention that offers support to patients to overcome barriers to healthcare, to increase BSS uptake within a socially deprived area of England. Methods/design: All individuals invited for BSS at South Tyneside NHS Foundation Trust during the 6-month recruitment period will be invited to take part in the study. Consenting participants will be randomised to receive PN or usual care in a 2:1 ratio. PN involves non-attenders receiving a phone call from a Specialist Screening Practitioner (SSP) who will elicit reasons for non-attendance and offer educational, practical, and emotional support as needed. If requested by the patient, another appointment for BSS will then be arranged. We anticipate 30 % of participants will be non-attenders. Using A’Hern single-stage design, with 20 % significance level and 80 % power, at least 35 participants who receive PN need to subsequently attend for PN to be considered worthy of further investigation in a definitive trial. The primary outcome measure will be the number of participants in the PN group who re-book and attend their BSS appointment. A qualitative analysis of the PN transcripts, and interviews with the SSPs, will also be conducted, alongside a quantitative analysis of completed patient-reported experience questionnaires. An economic analysis will calculate the costs of delivering PN. Discussion: This feasibility study will be instrumental in deciding whether to conduct the first definitive trial of PN in BSS in England. If PN is subsequently shown to be cost-effective at increasing uptake of BSS, NHS policies could be modified to implement PN as a standard service. The results will be disseminated in peer-reviewed journals and at scientific conferences. Trial registration: International Standard Randomised Controlled Trial Number, ISRCTN1331475

Characteristics of particle dispersion in the North Atlantic: An alternative interpretation of SOFAR float results

An analysis of published results on the dispersion behavior of SOFAR floats indicates a systematic depth dependence of the mixing length in the North Atlantic subtropical gyre. In contrast to the integral time scale, the length scale appears to be independent of eddy intensity in the thermocline (Lx, Ly ∼ 80, 45 km) and in the deep ocean (Lx ∼ Ly : 20 – 30 km). A similar decrease with depth is revealed by particle dispersion in an eddy-resolving circulation model and interpreted as an enhanced effect of wave behavior in the weaker, subthermocline flow. The only weak anisotropy of deep float dispersion suggests an influence of bottom roughness on the structure of eddy variability

Were Fertile Crescent crop progenitors higher yielding than other wild species that were never domesticated?

During the origin of agriculture in the Fertile Crescent, the broad spectrum of wild plant species exploited by hunter-gatherers narrowed dramatically. The mechanisms responsible for this specialization and the associated domestication of plants are intensely debated. We investigated why some species were domesticated rather than others, and which traits they shared. We tested whether the progenitors of cereal and pulse crops, grown individually, produced a higher yield and less chaff than other wild grasses and legumes, thereby maximizing the return per seed planted and minimizing processing time. We compared harvest traits of species originating from the Fertile Crescent, including those for which there is archaeological evidence of deliberate collection. Unexpectedly, wild crop progenitors in both families had neither higher grain yield nor, in grasses, less chaff, although they did have larger seeds. Moreover, small-seeded grasses actually returned a higher yield relative to the mass of seeds sown. However, cereal progenitors had threefold fewer seeds per plant, representing a major difference in how seeds are packaged on plants. These data suggest that there was no intrinsic yield advantage to adopting large-seeded progenitor species as crops. Explaining why Neolithic agriculture was founded on these species, therefore, remains an important unresolved challenge

Density profiles of dark matter haloes: diversity and dependence on environment

(Abridged) We study the outer density profiles of dark matter haloes predicted by a generalized secondary infall model and observed in a N-body cosmological simulation of a \Lambda CDM model. We find substantial systematic variations in shapes and concentrations of the halo profiles as well as a strong correlation of the profiles with the environment. In the N-body simulation, the average outer slope of the density profiles, \beta (\rho\propto r^{-\beta}), of isolated haloes is \approx 2.9; 68% of these haloes have values of \beta between 2.5 and 3.8. Haloes in dense environments of clusters are more concentrated and exhibit a broad distribution of \beta with values larger than for isolated haloes . Contrary to what one may expect, the haloes contained within groups and galaxy systems are less concentrated and have flatter outer density profiles than the isolated haloes. The concentration decreases with M_h, but its scatter for a given mass is substantial. The mass and circular velocity of the haloes are strongly correlated: M_h \propto V_m^{\alpha} with \alpha ~ 3.3 (isolated) and ~3.5 (haloes in clusters). For M_h=10^12M_sun the rms deviations from these relations are \Delta logM_h=0.12 and 0.18, respectively. Approximately 30% of the haloes are contained within larger haloes or have massive companions (larger than ~0.3 the mass of the current halo) within 3 virial radii. The remaining 70% of the haloes are isolated objects. The distribution of \beta as well as the concentration-mass and M_h-V_m relations for the isolated haloes agree very well with the predictions of our seminumerical approach which is based on a generalization of the secondary infall model and on the extended Press-Schechter formalism.Comment: 14 pages, 11 figures included, uses mn.sty, accepted by MNRAS. Minor modifications, new and updated reference

Evolution of bias in different cosmological models

We study the evolution of the halo-halo correlation function and bias in four cosmological models (LCDM, OCDM, tauCDM, and SCDM) using very high-resolution N-body simulations. The high force and mass resolution allows dark matter (DM) halos to survive in the tidal fields of high-density regions and thus prevents the ambiguities related with the ``overmerging problem.'' This allows us to estimate for the first time the evolution of the correlation function and bias at small (down to ~100/h kpc) scales. We find that at all epochs the 2-point correlation function of galaxy-size halos xi_hh is well approximated by a power-law with slope ~1.6-1.8. The difference between the shape of xi_hh and the shape of the correlation function of matter results in the scale-dependent bias at scales <7/h Mpc, which we find to be a generic prediction of the hierarchical models. The bias evolves rapidly from a high value of ~2-5 at z~3-7 to the anti-bias of b~0.5-1 at small <5/h Mpc scales at z=0. We find that our results agree well with existing clustering data at different redshifts. Particularly, we find an excellent agreement in both slope and the amplitude between xi_hh(z=0) in our LCDM simulation and the galaxy correlation function measured using the APM galaxy survey. At high redshifts, the observed clustering of the Lyman-break galaxies is also well reproduced by the models. The agreement with the data at high and low z indicates the general success of the hierarchical models of structure formation in which galaxies form inside the host DM halos. (Abridged)Comment: submitted to the Astrophys.Journal; 21 pages, LaTeX (uses emulateapj.sty); full resolution versions of figs.1 and 2 are available at http://astro.nmsu.edu/~akravtso/GROUP/group_publications.html or at ftp://charon.nmsu.edu/pub/kravtsov/PAPERS/Bias

Estimation of peptide concentration by a modified bicinchoninic acid assay

Although biuret based protein assays are theoretically applicable to peptide measurement, there is a high level of inter-peptide variation, determined largely by peptide hydrophobicity. This variation in peptide reactivity can be significantly reduced by heat-denaturation of peptides at 95 °C for 5 minutes in the presence of 0.1 M NaOH containing 1% (w/v) SDS, prior to incubation for 30 min at 37 °C in BCA standard working reagent. This modification to the standard bicinchoninic acid (BCA) assay protocol allows for an accurate, rapid and economical estimation of the peptide concentration within an unknown sample