The Perigord black truffle responds to cold temperature with an extensive reprogramming of its transcriptional activity

International audienceThe Tuber melanosporum genome has been analysed with the aim of identifying and characterizing the genes involved in the environmental stress response. A whole genome array (7496 genes/probe) was used to verify the fungal transcriptional profiling upon a cold temperature period (7 days at 4 degrees C). A total of 423 genes resulted to be differentially expressed in a significant manner (>2.5-fold; p-value <0.05) in the mycelia exposed to cold, compared to the control ones: 187 of these genes were up-regulated, while 236 were down-regulated. Sixty-six and fifty-one percent, respectively, of the up- or down-regulated transcripts had no KOG classification and were clustered as unclassified proteins, which was the most abundant category in the both up- and down-regulated genes. A gene subset, containing a range of biological functions, was chosen to validate the microarray experiment through quantitative real time PCR (qRT-PCR). The analysis confirmed the array data for 16 out of 22 of the considered genes, confirming that a cold temperature period influences the truffle global gene expression. The expressed genes, which mostly resulted to be genes for heat shock proteins (HSPs) and genes involved in cell wall and lipid metabolism, could be involved in mechanisms, which are responsible for fungal adaptation. Since truffle ascomata develop during the winter period, we hypothesize that these differentially expressed genes may help the truffle to adapt to low temperatures and/or perceive environmental signals that regulate the fructification. (C) 2010 Elsevier Inc. All rights reserved

Genome-wide analysis of cell wall-related genes in Tuber melanosporum

A genome-wide inventory of proteins involved in cell wall synthesis and remodeling has been obtained by taking advantage of the recently released genome sequence of the ectomycorrhizal black truffle. Genes that encode cell wall biosynthetic enzymes, enzymes involved in cell wall polysaccharide synthesis or modification, GPI-anchored proteins and other cell wall proteins were identified in the black truffle genome. As a second step, array data were validated and the symbiotic stage was chosen as the main focus. Quantitative RT-PCR experiments were performed on 29 selected genes to verify their expression during ectomycorrhizal formation. The results confirmed the array data, and this suggests that cell wall-related genes are required for morphogenetic transition from mycelium growth to the ectomycorrhizal branched hyphae. Labeling experiments were also performed on mycelium and ectomycorrhizae to localize cell wall components

Multi-omic Analyses of Extensively Decayed Pinus contorta Reveal Expression of a Diverse Array of Lignocellulose-Degrading Enzymes.

Fungi play a key role cycling nutrients in forest ecosystems, but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, the metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to basidiomycete transcripts dominated, and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate-active enzymes (CAZymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases, including highly expressed cellulases or hemicellulases. The CAZymes also included 162 predicted redox enzymes classified within auxiliary activity (AA) families. Eighteen of these were manganese peroxidases, which are key components of ligninolytic white rot fungi. The expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radicals. These have been implicated as diffusible oxidants responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of lodgepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding the mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies

A comparison between the transpressional plate boundaries of South Island, New Zealand, and Southern California, USA: the Alpine and San Andreas fault systems

There are clear similarities in structure and tectonics between the Alpine Fault system (AF) of New Zealand’s South Island and the San Andreas Fault system (SAF) of southern California, USA. Both systems are transpressional, with similar right slip and convergence rates, similar onset ages (for the current traces), and similar total offsets. There are also notable differences, including the dips of the faults and their plate-tectonic histories. The crustal structure surrounding the AF and SAF was investigated with active and passive seismic sources along transects known as South Island Geophysical Transect (SIGHT) and Los Angeles Region Seismic Experiment (LARSE), respectively. Along the SIGHT transects, the AF appears to dip moderately southeastward (~50 deg.), toward the Pacific plate (PAC), but along the LARSE transects, the SAF dips vertically to steeply northeastward toward the North American plate (NAM). Away from the LARSE transects, the dip of the SAF changes significantly. In both locations, a midcrustal decollement is observed that connects the plate-boundary fault to thrust faults farther south in the PAC. This decollement allows upper crust to escape collision laterally and vertically, but forces the lower crust to form crustal roots, reaching maximum depths of 44 km (South Island) and 36 km (southern California). In both locations, upper-mantle bodies of high P velocity are observed extending from near the Moho to more than 200-km depth. These bodies appear to be confined to the PAC and to represent oblique downwelling of PAC mantle lithosphere along the plate boundaries

Are Predictors for Overall Mortality in COPD Patients Robust over Time?

(1) Background: Mortality is a major outcome in research on chronic obstructive pulmonary disease (COPD) with various predictors described. However, the dynamic courses of important predictors over time are disregarded. This study evaluates if longitudinal assessment of predictors provides additional information on the mortality risk in COPD when compared with a cross-sectional analysis.; (2) In a longitudinal, prospective, non-interventional cohort study including mild to very severe COPD patients, mortality and its various possible predictors were annually assessed up to seven years.; (3) Results: 297 patients were analysed. Mean (SD) age was 62.5 (7.6) years and 66% males. Mean (SD) FEV1 was 48.8 (21.4)%. A total of 105 events (35.4%) happened with a median (95% CI) survival time of 8.2 (7.2/NA) years. No evidence for a difference between the raw variable and the variable history on the predictive value for all tested variables over each visit was found. There was no evidence for changing effect estimates (coefficients) across the study visits due to the longitudinal assessment; (4) Conclusions: We found no evidence that predictors of mortality in COPD are time dependent. This implies that cross-sectional measured predictors show robust effect estimates over time and multiple assessments seem not to change the predictive value of the measure

First-principles study of orthorhombic CdTiO3 perovskite

In this work we perform an ab-initio study of CdTiO3 perovskite in its orthorhombic phase using FLAPW method. Our calculations help to decide between the different cristallographic structures proposed for this perovskite from X-Ray measurements. We compute the electric field gradient tensor (EFG) at Cd site and obtain excellent agreement with available experimental information from a perturbed angular correlation (PAC) experiment. We study EFG under an isotropic change of volume and show that in this case the widely used "point charge model approximation" to determine EFG works quite well.Comment: 4 pages, 1 figure. Accepted in Physical Review

Observational Constraints on the Formation and Evolution of Binary Stars

We present a high spatial resolution UV to NIR survey of 44 young binary stars in Taurus with separations of 10-1000 AU. The primary results include: (1) The relative ages of binary star components are more similar than the relative ages of randomly paired single stars, supporting coeval formation. (2) Only one of the companion masses is substellar, and hence the apparent overabundance of T Tauri star companions relative to main-sequence star companions can not be explained by a wealth of substellar secondaries that would have been missed in main-sequence surveys. (3) Roughly 10% of T Tauri binary star components have very red NIR colors (K-L > 1.4) and unusually high mass accretion rates. This phenomenon does not appear to be restricted to binary systems, however, since a comparable fraction of single T Tauri stars exhibit the same properties. (4) Although the disk lifetimes of single stars are roughly equal to their stellar ages, the disk lifetimes of binary stars are an order of magnitude less than their ages. (5) The accretion rates for both single and binary T Tauri stars appear to be moderately mass dependent. (6) Although most classical T Tauri star binaries retain both a circumprimary and a circumsecondary disk, there are several systems with only a circumprimary disk. Together with the relative accretion rates, this suggests that circumprimary disks survive longer, on average, than circumsecondary disks. (7) The disk lifetimes, mass ratios, and relative accretion signatures of the closest binaries (10-100 AU) suggest that they are being replenished from a circumbinary reservoir with low angular momentum. Overall, these results support fragmentation as the dominant binary star formation mechanism.Comment: 67 pages including 11 figures, LaTeX2e, accepted for publication in Ap