Loss of heterozygosity is related to p53 mutations and smoking in lung cancer

Carcinogenesis results from an accumulation of several genetic alterations. Mutations in the p53 gene are frequent and occur at an early stage of lung carcinogenesis. Loss of multiple chromosomal regions is another genetic alteration frequently found in lung tumours. We have examined the association between p53 mutations, loss of heterozygosity (LOH) at frequently deleted loci in lung cancer, and tobacco exposure in 165 tumours from non-small cell lung cancer (NSCLC) patients. A highly significant association between p53 mutations and deletions on 3p, 5q, 9p, 11p and 17p was found. There was also a significant correlation between deletions at these loci. 86% of the tumours with concordant deletion in the 4 most involved loci (3p21, 5q11–13, 9p21 and 17p13) had p53 mutations as compared to only 8% of the tumours without deletions at the corresponding loci (P< 0.0001). Data were also examined in relation to smoking status of the patients and histology of the tumours. The frequency of deletions was significantly higher among smokers as compared to non-smokers. This difference was significant for the 3p21.3 (hMLH1 locus), 3p14.2 (FHIT locus), 5q11–13 (hMSH3 locus) and 9p21 (D9S157 locus). Tumours with deletions at the hMLH1 locus had higher levels of hydrophobic DNA adducts. Deletions were more common in squamous cell carcinomas than in adenocarcinomas. Covariate analysis revealed that histological type and p53 mutations were significant and independent parameters for predicting LOH status at several loci. In the pathogenesis of NSCLC exposure to tobacco carcinogens in addition to clonal selection may be the driving force in these alterations. © 2001 Cancer Research Campaign http://www.bjcancer.co

Taxonomy and evolutionary relationships within species of section Rimosae (Inocybe) based on ITS, LSU and mtSSU sequence data

The present study aimed at elucidating the structure of Inocybe subg. Inosperma sect. Rimosae but included also representatives from subg. Mallocybe and the genus Auritella. Phylogenetic relationships were inferred using ITS, LSU and mtSSU sequence data. The analyses recovered the ingroup as a monophyletic, strongly supported clade. The results indicate that recognizing Auritella on the genus level renders Inocybe paraphyletic. The species traditionally placed in sect. Rimosae were found to be distributed over two strongly supported clades, Maculata and Rimosae s.s. The Maculata clade clusters with sect. Cervicolores and the two represent subg. Inosperma in a strict sense. Rimosae s.s. emerges as an independent, supported clade well separated from Inosperma s.s. Twenty-one terminal groups were correlated with morphologically distinct species. In addition several taxa on single branches and minor less supported clades were recovered. A key to the identified species of the Maculata and Rimosae s.s. clades which occur in Northwest Europe is provided

Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Combined seismic and borehole investigation of the deep granite weathering structure—Santa Gracia Reserve case in Chile

Imaging the critical zone at depth, where intact bedrock transforms into regolith, is critical in understanding the interaction between geological and biological processes. We acquired a 500 m‐long near‐surface seismic profile to investigate the weathering structure in the Santa Gracia National Reserve, Chile, which is located in a granitic environment in an arid climate. Data processing comprised the combination of two seismic approaches: (1) body wave tomography and (2) multichannel analysis of surface wave (MASW) with Bayesian inversion. This allowed us to derive P‐wave and S‐wave velocity models down to 90 and 70 m depth, respectively. By calibrating the seismic results with those from an 87 m‐deep borehole that is crossed by the profile. We identified the boundaries of saprolite, weathered bedrock, and bedrock. These divisions are indicated in the seismic velocity variations and refer to weathering effects at depth. The thereby determined weathering front in the borehole location can be traced down to 30 m depth. The modelled lateral extent of the weathering front, however, cannot be described by an established weathering front model. The discrepancies suggest a more complex interaction between different aspects such as precipitation and topography in controlling the weathering front depth

Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.RHN acknowledges financial support from FORMAS (215-2011- 498) and from Stiftelsen Olle Engkvist Byggmästare. MPM was partially supported by Plan Nacional I+D+i project CGL2012-35559. CW acknowledges a Marie Skłodowska-Curie post doc grant (660122, CRYPTRANS)Peer reviewe

South Atlantic opening: A plume-induced breakup?

Upwelling hot mantle plumes are thought to disintegrate continental lithosphere and are considered to be drivers of active continental breakup. The formation of the Walvis Ridge during the opening of the South Atlantic is related to a putative plume-induced breakup. We investigated the crustal structure of the Walvis Ridge (southeast Atlantic Ocean) at its intersection with the continental margin and searched for anomalies related to the possible plume head. The overall structure we identify suggests that no broad plume head existed during opening of the South Atlantic and anomalous mantle melting occurred only locally. We therefore question the importance of a plume head as a driver of continental breakup and further speculate that the hotspot was present before the rifting, leaving a track of kimberlites in the African craton

3D shear wave velocity imaging of the subsurface structure of granite rocks in the arid climate of Pan de Azúcar, Chile, revealed by Bayesian inversion of HVSR curves

Seismic methods are emerging as efficient tools for imaging the subsurface to investigate the weathering zone. The structure of the weathering zone can be identified by differing shear wave velocities as various weathering processes will alter the properties of rocks. Currently, 3D subsurface modelling of the weathering zone is gaining increasing importance as results allow the identification of the weathering imprint in the subsurface not only from top to bottom but also in three dimensions. We investigated the 3D weathering structure of monzogranite bedrock near the Pan de Azúcar National Park (Atacama Desert, northern Chile), where the weathering is weak due to the arid climate conditions. We set up an array measurement that records seismic ambient noise, which we used to extract the horizontal-to-vertical spectral ratio (HVSR) curves. The curves were then used to invert for 1D shear wave velocity (Vs) models, which we then used to compile a pseudo-3D model of the subsurface structure in our study area. To invert the 1D Vs model, we applied a transdimensional hierarchical Bayesian inversion scheme, allowing us to invert the HVSR curve with minimal prior information. The resulting 3D model allowed us to image the granite gradient from the surface down to ca. 50 m depth and confirmed the presence of dikes of mafic composition intruding the granite. We identified three main zones of fractured granite, altered granite, and the granite bedrock in addition to the mafic dikes with relatively higher Vs. The fractured granite layer was identified with Vs of 1.4 km s−1 at 30–40 m depth, while the granite bedrock was delineated with Vs of 2.5 km s−1 and a depth range between 10 and 50 m depth. We compared the resulting subsurface structure to other sites in the Chilean coastal cordillera located in various climatic conditions and found that the weathering depth and structure at a given location depend on a complex interaction between surface processes such as precipitation rate, tectonic uplift and fracturing, and erosion. Moreover, these local geological features such as the intrusion of mafic dikes can create significant spatial variations to the weathering structure and therefore emphasize the importance of 3D imaging of the weathering structure. The imaged structure of the subsurface in Pan de Azúcar provides the unique opportunity to image the heterogeneities of a rock preconditioned for weathering but one that has never experienced extensive weathering given the absence of precipitation.</p

Shear-wave velocity imaging of weathered granite in La Campana (Chile) from Bayesian inversion of micro-tremor H/V spectral ratios

Subsurface imaging of the regolith layer is an important tool for weathering zone characterization. For example, the extent of bedrock modification by weathering processes can be modelled by means of differing seismic velocities. We acquired a 360 m-long seismic profile in central Chile to characterise weathering at a semi-arid site. We used 87 3-component geophones, which continuously recorded ambient seismic noise for three days. The seismic line was centered at an 88 m deep borehole, providing core and downhole logging data for calibration. We extract Horizontal-to-Vertical Spectral Ratio (HVSR) curves along the seismic line to image the subsurface. Temporal analysis of the HVSR curves shows that the ambient noise vibrations recorded during the nighttime provide more stable HVSR curves. The trans-dimensional Bayesian Markov chain Monte Carlo (McMC) approach was used to invert the micro-tremor HVSR curves at each station to reconstruct 1D shear-wave velocity (Vs) models. The resulting individual 1D Vs models were merged to create a 2D Vs model along the linear seismic array in La Campana. The resulting Vs model shows an increase from 0.85 km/s at the surface to ca. 2.5 km/s at 100 m depth. We use the interface probability as a by-product of the Bayesian inversion to apply a more data-driven approach in identifying the different weathering layers. This method identified the boundary between saprolite and fractured bedrock at 42 m depth at the borehole, as evidenced by the interpretation of downhole logging data such as magnetic susceptibility. The resulting 2D Vs model of this site in Mediterranean climate shows a strong correlation between the interpreted weathering front at around 90-m depth and a higher precipitation rate in the study site compared to arid sites. The horizontal alignment of the weathering front indicates a correlation between the weathering front depth with topography and fractures in the bedrock