Selection and phenotypic characterization of a core collection of <i>Brachypodium distachyon</i> inbred lines

BACKGROUND: The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. RESULTS: We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, growth habit, stem density, flowering time, and seed weight. We also surveyed differences in cell wall composition using near infrared spectroscopy (NIR) and comprehensive microarray polymer profiling (CoMPP). In all cases, we observed extensive natural variation including a two-fold variation in stem density, four-fold variation in ferulic acid bound to hemicellulose, and 1.7-fold variation in seed mass. CONCLUSION: These characterizations can provide the criteria for selecting diverse lines for future investigations of the genetic basis of the observed phenotypic variation

Indications for thyroid FNA and pre-FNA requirements: A synopsis of the National Cancer Institute Thyroid Fine-Needle Aspiration State of the Science Conference

The National Cancer Institute (NCI) sponsored the NCI Thyroid Fine-Needle Aspiration (FNA) State of the Science Conference on October 22–23, 2007 in Bethesda, MD. The 2-day meeting was accompanied by a permanent informational website and several on-line discussions between May 1 and December 15, 2007 ( http://thyroidfna.cancer.gov ). This document summarizes the indications for performing an FNA of a nodule discovered by physical examination or an imaging study; the indications for using ultrasound versus palpation for guidance when performing a thyroid FNA; the issues surrounding informed consent for thyroid FNA; and the information required on a requisition form that accompanies a thyroid FNA specimen. ( http://thyroidfna.cancer.gov/pages/info/agenda/ ) Diagn. Cytopathol. 2008;36:390–399. © 2008 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58658/1/20827_ftp.pd

Reduction of iron (III) and humic substances plays a major role in anaerobic respiration in an Arctic peat soil

Arctic peat soils contain vast reserves of organic C and are largely anaerobic. However, anaerobic respiration, particularly the role of Fe(III) and humic substances as electron acceptors, is not well understood in such ecosystems. We investigated these processes in a drained thaw lake basin on the Arctic coastal plain near Barrow, Alaska. We measured concentrations of soluble Fe and other potential electron acceptors, described the microbial community, and performed experiments in the laboratory and field to measure net rates of Fe(III) reduction and the relationship of this process to C cycling. In most areas within the basin, aerobic conditions existed only in the upper few centimeters of soil, though oxygen penetrated deeper in raised areas, such as rims of ice wedge polygons. Concentrations of nitrate and sulfate in soil pore water were low or negligible. Soil pore water contained surprisingly high concentrations of Fe(II) and Fe(III), in the range of hundreds of μM, suggesting the presence of organic chelators. The solid phase contained substantial amounts of iron minerals, with a progressively reduced oxidation state throughout the growing season. The most abundant 16S rRNA sequence in our gene survey was closely related to the Fe(III)-reducing bacterium, Rhodoferax ferrireducens, and other sequences closely related to Fe-transforming bacteria were found. Field and laboratory incubations with soluble Fe(III) and the quinonic compound, AQDS (a common humic analog), stimulated respiration and verified that Fe(III) reduction occurs in these soils. We conclude that reduction of Fe(III) and humic substances are major metabolic pathways in this ecosystem

Planta �2001) 213: 881±887 DOI 10.1007/s004250100554 ORIGINAL ARTICLE

Visualizing rhizosphere chemistry of legumes with mid-infrared synchrotron radiatio

PMR6, a Pectate Lyase–Like Gene Required for Powdery Mildew Susceptibility in Arabidopsis

The plant genes required for the growth and reproduction of plant pathogens are largely unknown. In an effort to identify these genes, we isolated Arabidopsis mutants that do not support the normal growth of the powdery mildew pathogen Erysiphe cichoracearum. Here, we report on the cloning and characterization of one of these genes, PMR6. PMR6 encodes a pectate lyase–like protein with a novel C-terminal domain. Consistent with its predicted gene function, mutations in PMR6 alter the composition of the plant cell wall, as shown by Fourier transform infrared spectroscopy. pmr6-mediated resistance requires neither salicylic acid nor the ability to perceive jasmonic acid or ethylene, indicating that the resistance mechanism does not require the activation of well-described defense pathways. Thus, pmr6 resistance represents a novel form of disease resistance based on the loss of a gene required during a compatible interaction rather than the activation of known host defense pathways

Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes: they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study

Comparison of Barrow soil metagenomes presented in this study (all layers combined) with published Waseca farm soil metagenome [6].

a<p>Pearson chi-squared statistic (χ², and corresponding P value) compares proportions of sequences between the two soils.</p