Seedling development traits in Brassica napus examined by gene expression analysis and association mapping

BACKGROUND: An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS: The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION: A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0496-3) contains supplementary material, which is available to authorized users

Wind Energy and the Turbulent Nature of the Atmospheric Boundary Layer

Wind turbines operate in the atmospheric boundary layer, where they are exposed to the turbulent atmospheric flows. As the response time of wind turbine is typically in the range of seconds, they are affected by the small scale intermittent properties of the turbulent wind. Consequently, basic features which are known for small-scale homogeneous isotropic turbulence, and in particular the well-known intermittency problem, have an important impact on the wind energy conversion process. We report on basic research results concerning the small-scale intermittent properties of atmospheric flows and their impact on the wind energy conversion process. The analysis of wind data shows strongly intermittent statistics of wind fluctuations. To achieve numerical modeling a data-driven superposition model is proposed. For the experimental reproduction and adjustment of intermittent flows a so-called active grid setup is presented. Its ability is shown to generate reproducible properties of atmospheric flows on the smaller scales of the laboratory conditions of a wind tunnel. As an application example the response dynamics of different anemometer types are tested. To achieve a proper understanding of the impact of intermittent turbulent inflow properties on wind turbines we present methods of numerical and stochastic modeling, and compare the results to measurement data. As a summarizing result we find that atmospheric turbulence imposes its intermittent features on the complete wind energy conversion process. Intermittent turbulence features are not only present in atmospheric wind, but are also dominant in the loads on the turbine, i.e. rotor torque and thrust, and in the electrical power output signal. We conclude that profound knowledge of turbulent statistics and the application of suitable numerical as well as experimental methods are necessary to grasp these unique features (...)Comment: Accepted by the Journal of Turbulence on May 17, 201

Toward neuronal current spectroscopy at Ultra-Low field NMR

Centro Studi e Ricerche "E. Fermi", Rome, Italy. Email: [email protected] Physikalish-Technische Bundesanstalt (PTB), Abbestr. 2-12, 10587 Berlin, Germany University of Leipzig, Leipzig, Germany Neurophysics Group, Dept. of Neurology, Campus Benjamin Franklin, Charite/University Medicine, Berlin, Germany Dip. di Fisica, Universita di Roma "La Sapienza", Piazzale Aldo Moro, 5, 00185, Rome, Ital

Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene

Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease gene. By whole-exome sequencing (WES) in a consanguineous family with congenital non-syndromic deafness, we unexpectedly identified a homozygous nonsense variant, p.Arg1066*, in AHI1, a gene associated with Joubert syndrome (JBTS), a severe recessive ciliopathy. None of four homozygotes expressed any signs of JBTS, and one of them had normal hearing, which also ruled out p.Arg1066* as the cause of deafness. Homozygosity mapping and WES in the only other reported JBTS family with a homozygous C-terminal truncation (p.Trp1088Leufs*16) confirmed AHI1 as disease gene, but based on a more N-terminal missense mutation impairing WD40-repeat formation. Morpholinos against N-terminal zebrafish Ahi1, orthologous to where human mutations cluster, produced a ciliopathy, but targeting near human p.Arg1066 and p.Trp1088 did not. Most AHI1 mutations in JBTS patients result in truncated protein lacking WD40-repeats and the SH3 domain; disease was hitherto attributed to loss of these protein interaction modules. Our findings indicate that normal development does not require the C-terminal SH3 domain. This has far-reaching implications, considering that variants like p.Glu984* identified by preconception screening (‘Kingsmore panel') do not necessarily indicate JBTS carriership. Genomes of individuals with consanguineous background are enriched for homozygous variants that may unmask dispensable regions of disease genes and unrecognized false positives in diagnostic large-scale sequencing and preconception carrier screenin

Quasiparticle spin susceptibility in heavy-fermion superconductors : An NMR study compared with specific heat results

Quasi-particle spin susceptibility ($\chi^{qp}$) for various heavy-fermion (HF) superconductors are discussed on the basis of the experimental results of electronic specific heat ($\gamma_{el}$), NMR Knight shift ($K$) and NMR relaxation rate ($1/T_1$) within the framework of the Fermi liquid model for a Kramers doublet crystal electric field (CEF) ground state. $\chi^{qp}_{\gamma}$ is calculated from the enhanced Sommerfeld coefficient $\gamma_{el}$ and $\chi^{qp}_{T_1}$ from the quasi-particle Korringa relation $T_1T(K^{qp}_{T_1})^2=const.$ via the relation of $\chi^{qp}_{T_1}=(N_A\mu_B/A_{hf})K^{qp}_{T_1}$ where $A_{hf}$ is the hyperfine coupling constant, $N_A$ the Abogadoro's number and $\mu_B$ the Bohr magneton. For the even-parity (spin-singlet) superconductors CeCu$_2$Si$_2$, CeCoIn$_5$ and UPd$_2$Al$_3$, the fractional decrease in the Knight shift, $\delta K^{obs}$, below the superconducting transition temperature ($T_c$) is due to the decrease of the spin susceptibility of heavy quasi-particle estimated consistently from $\chi^{qp}_{\gamma}$ and $\chi^{qp}_{T_1}$. This result allows us to conclude that the heavy quasi-particles form the spin-singlet Cooper pairs in CeCu$_2$Si$_2$, CeCoIn$_5$ and UPd$_2$Al$_3$. On the other hand, no reduction in the Knight shift is observed in UPt$_3$ and UNi$_2$Al$_3$, nevertheless the estimated values of $\chi^{qp}_{\gamma}$ and $\chi^{qp}_{T_1}$ are large enough to be probed experimentally. The odd-parity superconductivity is therefore concluded in these compounds. The NMR result provides a convincing way to classify the HF superconductors into either even- or odd- parity paring together with the identification for the gap structure, as long as the system has Kramers degeneracy.Comment: 11 pages, 3 tables, 5 figures, RevTex4(LaTex2e

Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit

Background: Mineral nutrient uptake and utilisation by plants are controlled by many traits relating to root morphology, ion transport, sequestration and translocation. The aims of this study were to determine the phenotypic diversity in root morphology and leaf and seed mineral composition of a polyploid crop species, Brassica napus L., and how these traits relate to crop habit. Traits were quantified in a diversity panel of up to 387 genotypes: 163 winter, 127 spring, and seven semiwinter oilseed rape (OSR) habits, 35 swede, 15 winter fodder, and 40 exotic/unspecified habits. Root traits of 14 d old seedlings were measured in a ‘pouch and wick’ system (n = ~24 replicates per genotype). The mineral composition of 3–6 rosette-stage leaves, and mature seeds, was determined on compost-grown plants from a designed experiment (n = 5) by inductively coupled plasma-mass spectrometry (ICP-MS). Results: Seed size explained a large proportion of the variation in root length. Winter OSR and fodder habits had longer primary and lateral roots than spring OSR habits, with generally lower mineral concentrations. A comparison of the ratios of elements in leaf and seed parts revealed differences in translocation processes between crop habits, including those likely to be associated with crop-selection for OSR seeds with lower sulphur-containing glucosinolates. Combining root, leaf and seed traits in a discriminant analysis provided the most accurate characterisation of crop habit, illustrating the interdependence of plant tissues. Conclusions: High-throughput morphological and composition phenotyping reveals complex interrelationships between mineral acquisition and accumulation linked to genetic control within and between crop types (habits) in B. napus. Despite its recent genetic ancestry (<10 ky), root morphology, and leaf and seed composition traits could potentially be used in crop improvement, if suitable markers can be identified and if these correspond with suitable agronomy and quality traits

Functional integrity of the contractile actin cortex is safeguarded by multiple Diaphanous-related formins

The contractile actin cortex is a thin layer of filamentous actin, myosin motors, and regulatory proteins beneath the plasma membrane crucial to cytokinesis, morphogenesis, and cell migration. However, the factors regulating actin assembly in this compartment are not well understood. Using the Dictyostelium model system, we show that the three Diaphanous-related formins (DRFs) ForA, ForE, and ForH are regulated by the RhoA-like GTPase RacE and synergize in the assembly of filaments in the actin cortex. Single or double formin-null mutants displayed only moderate defects in cortex function whereas the concurrent elimination of all three formins or of RacE caused massive defects in cortical rigidity and architecture as assessed by aspiration assays and electron microscopy. Consistently, the triple formin and RacE mutants encompassed large peripheral patches devoid of cortical F-actin and exhibited severe defects in cytokinesis and multicellular development. Unexpectedly, many forA−/E−/H− and racE− mutants protruded efficiently, formed multiple exaggerated fronts, and migrated with morphologies reminiscent of rapidly moving fish keratocytes. In 2D-confinement, however, these mutants failed to properly polarize and recruit myosin II to the cell rear essential for migration. Cells arrested in these conditions displayed dramatically amplified flow of cortical actin filaments, as revealed by total internal reflection fluorescence (TIRF) imaging and iterative particle image velocimetry (PIV). Consistently, individual and combined, CRISPR/Cas9-mediated disruption of genes encoding mDia1 and -3 formins in B16-F1 mouse melanoma cells revealed enhanced frequency of cells displaying multiple fronts, again accompanied by defects in cell polarization and migration. These results suggest evolutionarily conserved functions for formin-mediated actin assembly in actin cortex mechanics

Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico

Natural hydrocarbon seeps occur on the sea floor along continental margins, and account for up to 47% of the oil released into the oceans. Hydrocarbon seeps are known to support local benthic productivity, but little is known about their impact on photosynthetic organisms in the overlying water column. Here we present observations with high temporal and spatial resolution of chlorophyll concentrations in the northern Gulf of Mexico using in situ and shipboard flow-through fluorescence measurements from May to July 2012, as well as an analysis of ocean-colour satellite images from 1997 to 2007. All three methods reveal elevated chlorophyll concentrations in waters influenced by natural hydrocarbon seeps. Temperature and nutrient profiles above seep sites suggest that nutrient-rich water upwells from depth, which may facilitate phytoplankton growth and thus support the higher chlorophyll concentrations observed. Because upwelling occurs at natural seep locations around the world, we conclude that offshore hydrocarbon seeps, and perhaps other types of deep ocean vents and seeps at depths exceeding 1,000 m, may influence biogeochemistry and productivity of the overlying water column