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Lung cancer (LC) is the most common cause of cancer death worldwide mostly due to the low survival rate: 75% of cases are identified in advanced stages. In this study, the list of useful biomarkers to make an early diagnosis using liquid biopsies was expanded. A total of 30 samples of LC were analyzed to define potential miRNA biomarkers in liquid biopsies for LC. The biomarkers have been identified in interaction networks miRNA–mRNA. The potential biomarkers have been then validated in large cohorts. A total of 15 candidate miRNAs, that regulate the repression of 30 mRNAs, have been identified as a specific functional interaction network for squamous carcinoma, while the specific functional interaction network of adenocarcinoma consists of four candidate miRNAs that seem to handle the repression of five mRNA. Inspection of expression levels in larger cohorts validates the usefulness of the 11 candidates as biomarkers in liquid biopsies. The 11 candidate miRNAs found could be utilized to form diagnostic predictive biomarkers for LC in liquid biopsies. [ABSTRACT FROM AUTHOR]

The integration of physical and high-density genetic maps is a very useful approach to achieve chromosome-level genome assemblies. Here, the genome of a male Senegalese sole (Solea senegalensis) was de novo assembled and the contigs were anchored to a high-quality genetic map for chromosome-level scaffolding. Hybrid assembled genome was 609.3 Mb long and contained 3403 contigs with a N50 of 513 kb. The linkage map was constructed using 16,287 informative SNPs derived from ddRAD sequencing in 327 sole individuals from five families. Markers were assigned to 21 linkage groups with an average number of 21.9 markers per megabase. The anchoring of the physical to the genetic map positioned 1563 contigs into 21 pseudo-chromosomes covering 548.6 Mb. Comparison of genetic and physical distances indicated that the average genome-wide recombination rate was 0.23 cM/Mb and the female-to-male ratio 1.49 (female map length: 2,698.4 cM, male: 2,036.6 cM). Genomic recombination landscapes were different between sexes with crossovers mainly concentrated toward the telomeres in males while they were more uniformly distributed in females. A GWAS analysis using seven families identified 30 significant sex-associated SNP markers located in linkage group 18. The follicle-stimulating hormone receptor appeared as the most promising locus associated with sex within a region with very low recombination rates. An incomplete penetrance of sex markers with males as the heterogametic sex was determined. An interspecific comparison with other Pleuronectiformes genomes identified a high sequence similarity between homologous chromosomes, and several chromosomal rearrangements including a lineage-specific Robertsonian fusion in S. senegalensis. [ABSTRACT FROM AUTHOR]

The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole. [ABSTRACT FROM AUTHOR]

Overview: Lung cancer is one of the deadliest cancers in the world. Its histological classification depends on early diagnosis and successful treatment. Therefore, having specific biomarkers for a quick sorting widens the successful output of lung cancer treatment. Material and methods: High-throughput sequencing (RNA-seq) was performed of small cohorts of BioBanco samples from healthy and tumour cells from lung adenocarcinoma (LUAD) and squamous cell carcinoma of the lung (lSCC). RNA-seq samples from small cell lung cancer (SCLC) were downloaded from databases. A bioinformatic workflow has been programmed for the identification of differentially expressed genes (DEGs). Results: A total of 4777 DEGs were differentially expressed in SCLC, 3676 DEGs were in lSCC, while the lowest number of DEGs, 2819, appeared in LUAD. Among them, 945 DEGs were common to the three histological types. Once validated their expression profile and their survival predictive capacity in large, public cohorts, three DEGs can be exclusively considered as diagnostic biomarkers, three as prognosis biomarkers, and other three exhibit both diagnosis and prognosis capabilities. Conclusions: This prospective study presents evidences for the diagnostic and prognostic capabilities of expression changes in CAPN8-2, TMC5 and MUC1 in LUAD, while they are non-significant in SCLC and lSCC. Their translation to clinical practice is proposed. [ABSTRACT FROM AUTHOR]

Physical and genetic maps of chickpea a QTL related to Ascochyta blight resistance and located in LG2 (QTL) have been constructed. Single-copy markers based on candidate genes located in the Ca2 pseudomolecule were for the first time obtained and found to be useful for refining the QTL position. The location of the QTL peak was linked to an ethylene insensitive 3-like gene ( Ein3). The Ein3 gene explained the highest percentage of the total phenotypic variation for resistance to blight (44.3 %) with a confidence interval of 16.3 cM. This genomic region was predicted to be at the Ca2 physical position 32-33 Mb, comprising 42 genes. Candidate genes located in this region include Ein3, Avr9/Cf9 and Argonaute 4, directly involved in disease resistance mechanisms. However, there are other genes outside the confidence interval that may play a role in the blight resistance pathway. The information reported in this paper will facilitate the development of functional markers to be used in the screening of germplasm collections or breeding materials, improving the efficiency and effectiveness of conventional breeding methods. [ABSTRACT FROM AUTHOR]

The shoots of young conifer trees represent an interesting model to study the development and growth of conifers from meristematic cells in the shoot apex to differentiated tissues at the shoot base. In this work, microarray analysis was used to monitor contrasting patterns of gene expression between the apex and the base of maritime pine shoots. A group of differentially expressed genes were selected and validated by examining their relative expression levels in different sections along the stem, from the top to the bottom. After validation of the microarray data, additional gene expression analyses were also performed in the shoots of young maritime pine trees exposed to different levels of ammonium nutrition. Our results show that the apex of maritime pine trees is extremely sensitive to conditions of ammonium excess or deficiency, as revealed by the observed changes in the expression of stress-responsive genes. This new knowledge may be used to precocious detection of early symptoms of nitrogen nutritional stresses, thereby increasing survival and growth rates of young trees in managed forests. [ABSTRACT FROM AUTHOR]

This work describes an easy alkaline lysis method for isolatating bacterial artificial chromosome (BAC) DNA in sufficient quantity and quality for further manipulation without the need to use a kit. The method starts with 10 mL of culture and, by alkaline lysis only, renders up to 150 ng of DNA per milliliter of culture. This BAC DNA was successfully digested with restriction enzymes, sequenced, and subjected to PCR. [ABSTRACT FROM AUTHOR]

The sequence of 12 SCAR markers obtained for olive-tree was analysed in the seek of information about the nature of the RAPD polymorphisms in olive-tree. The absence of internal repetitions of the RAPD primer corroborates that the polymorphisms were not obtained by alternative priming nor by rearrangements. We have found a high degree repetition within each sequence which is a reflect of the repetitive nature of the RAPD polymorphisms. Most the sequence corresponded to unknown DNA sequences, although some of the SCAR markers like GH1, PH2 or PF84 present clear homology or identity to other repetitive sequences (mainly microsatellites) from other plants or animals. This suggests that repetitive sequences could be more conserved among species than initially thought. As expected, none of the markers presented any open reading frame, although PJ65 revealed a significant homology to the gene and pseudogene of a lectin receptor in Arabidopsis. Taken together, the results described in this paper demonstrate that the polymorphisms detected by SCAR/RAPD methods are mainly repetitive in olive-tree, and that most of these repetitions corresponded to microsatellite DNA. [ABSTRACT FROM AUTHOR]

There is an urgent need for the development of early identification techniques in olive-trees due to the economic importance of cultivar identification in periods of expansion like now. We have been able to identify 22 olive-tree cultivars using only 10 different, specific, repeatable markers. These markers were designed by the cloning of significant RAPD bands obtained in PCR performed on bulked DNA to retain the genetic variability of each cultivar. Clones were partially or totally sequenced and new primers derived from these sequences were used to obtain Sequence Characterised Amplified Region (SCAR) fragments. We have demonstrated that the use of the 10 SCAR markers is enough to provide a simple, cheap, and reliable procedure to identify 22 geographically related olive-tree cultivars. [ABSTRACT FROM AUTHOR]

Background: We investigated an outbreak of Serratia marcescens in the neonatal intensive care unit (NICU) and the pediatric intensive care unit (ICU) of the University Children's Hospital Leipzig, Germany. Patients and Methods: From September to November 1998 15 patients were infected or colonized by S. marcescens. During the outbreak swabs from eye, blood, throat and nose were taken from every patient hospitalized in the ICUs. Results: In 15 cases (14 from the NICU and one from the pediatric ICU) the cultures yielded S. marcescens. All strains were investigated by pulsed field gel electrophoresis (PFGE) as well as by polymerase chain reaction (PCR) fingerprinting. Both molecular typing methods revealed corresponding fingerprint patterns in all of the 15 isolates. Typing results of the outbreak-related isolates demonstrated that two epidemic strains of distinct genotypes were associated with cross-infections of a group of five and a group of ten patients, respectively. The three invasive and seven of the colonizing isolates were related genotypically. Conclusion: This survey shows that PCR and PFGE are comparable in respect to the discrimination and reproducibility for epidemiological studies of S. marcescens strains in nosocomial outbreaks. Genotypic fingerprinting of bacterial isolates is useful and important to limit nosocomial infections. Fingerprinting sources of nosocomial infections can be traced both by PFGE and PCR. All patients infected recovered completely and the nosocomial outbreak could be stopped rapidly. [ABSTRACT FROM AUTHOR]

Málaga is a province of Spain where olive-trees are cultivated in a large range of environments, climates and soils. We have developed a reliable and reproducible method to detect RAPD and AP-PCR polymorphisms, using DNA from olive-tree ( Olea europaea L.) leaves. Starting from their natural orchards, fifty-six olive-tree cultivars throughout Málaga province, including oil and table olive cultivars, were screened and grouped into 22 varieties. A total of 62 informative polymorphic loci that provide 601 conspicuous bands were enough to differentiate the varieties. Clustering analyses managing 3 different pairwise distances, as well as phylogenetic analyses, led to the same result: olive-trees in Málaga can be divided into three main groups. Group I (90% of certainty) contains wild type and two introduced varieties, group II (83% of certainty) covers some native olive-trees, and group III (58% of certainty) is an heterogeneous cluster that includes varieties originating and cultivated in a number of Andalusian locations. Geographic location seems to be the first responsible of this classification, and morphological traits are needed to justify the group III subclustering. These results are consistent with the hypothesis of autochthonic origin of most olive-tree cultivars, and have been used to support a Label of Origin for the olive oil produced by the varieties included in group II. [ABSTRACT FROM AUTHOR]

The antimicrobial activity of moxifloxacin and seven other antibiotics (four of them quinolones) against 292 strains of obligately anaerobic bacteria was assessed employing a broth microdilution technique performed in Wilkens-Chalgren broth. MIC50/MIC90 values (mg/l) for moxifloxacin were as follows: Bacteroides fragilis (n=62) 0.25/2, Bacteroides ovatus (n=70) 1/4, Bacteroides vulgatus (n=29) 0.25/1, Bacteroides thetaiotaomicron (n=17) 2/2, Bacteroides caccae (n=11) 1/2, Prevotella spp. (n=11) 0.25/2, Fusobacterium spp. (n=17) 1/4, Bilophila wadsworthia (n=29) 0.5/1, and Clostridium spp. (n=29) 0.125/0.5, respectively. MIC50 values (mg/l) for Bacteroides distasonis (n=8) and Peptostreptococcus spp. (n=9) were 0.25. The results indicated that moxifloxacin was almost as active as trovafloxacin, as active as gatifloxacin, and more active than levofloxacin and ciprofloxacin against the anaerobes tested. [ABSTRACT FROM AUTHOR]

Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two "raw" transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture. [ABSTRACT FROM AUTHOR]

Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.

The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N 2 , which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.