Résultats de l'expérimentation italienne sur les principales provenances de pins de la section halepensis dix ans après la plantation

Comparaison du comportement des principales provenances de ces 3 espèces, en utilisant des graines récoltées dans les peuplements les plus intéressants des différentes régions

Opportunities for coppice management at the landscape level: the Italian experience

Coppice silviculture has a long tradition in Italy. Societal demands have led to the development of forest management techniques for integrating wood production with other kinds of forest uses and regulations have been issued to limit forest degradation. In Italy, 35% of the national forest cover is currently managed under coppice silvicultural systems that provide 66% of the annual wood production. Fuel-wood demand is increasing and a large amount of fuelwood is currently imported in Italy. Modern coppice practices differ from those adopted in the past and may have a reduced impact on ecosystem characteristics and processes. Nevertheless, coppice silviculture has a bad reputation mostly on grounds that are beyond economic, technical and ecological rationales. Neither cessation of use nor a generalized conversion from coppice to high forest are likely to respond simultaneously to the many demands deriving from complex and articulated political and economic perspectives operating at global, European, national, regional and forest stand-level scales. Different approaches of modern silviculture to coppice successfully tested in Italy for more than a decade are illustrated. We propose to combine different options at the stand and sub-stand level, including either development without human interference or conversion to high forest, and to apply these approaches within the framework of novel forest management plans and regionally consistent administrative procedures. This bottom-up approach represents a potential solution to the socio-economic and environmental challenges affecting coppicing as a silvicultural system

Structural Characterization of the Highly Restricted Down Syndrome Critical Region on 21q22.13: New KCNJ6 and DSCR4 Transcript Isoforms

Down syndrome (DS) is caused by trisomy of chromosome 21 and it is the most common genetic cause of intellectual disability (ID) in humans. Subjects with DS show a typical phenotype marked by facial dysmorphisms and ID. Partial trisomy 21 (PT21) is a rare genotype characterized by the duplication of a delimited chromosome 21 (Hsa21) portion and it may or may not be associated with DS diagnosis. The highly restricted Down syndrome critical region (HR-DSCR) is a region of Hsa21 present in three copies in all individuals with PT21 and a diagnosis of DS. This region, located on distal 21q22.13, is 34 kbp long and does not include characterized genes. The HR-DSCR is annotated as an intergenic region between KCNJ6-201 transcript encoding for potassium inwardly rectifying channel subfamily J member 6 and DSCR4-201 transcript encoding Down syndrome critical region 4. Two transcripts recently identified by massive RNA-sequencing (RNA-Seq) and automatically annotated on Ensembl database reveal that the HR-DSCR seems to be partially crossed by KCNJ6-202 and DSCR4-202 isoforms. KCNJ6-202 shares the coding sequence with KCNJ6-201 which is involved in many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells. DSCR4-202 transcript has the first two exons in common with DSCR4-201, the only experimentally verified gene uniquely present in Hominidae. In this study, we performed in silico and in vitro analyses of the HR-DSCR. Bioinformatic data, obtained using Sequence Read Archive (SRA) and SRA-BLAST software, were confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing on a panel of human tissues. Our data demonstrate that the HR-DSCR cannot be defined as an intergenic region. Further studies are needed to investigate the functional role of the new transcripts, likely involved in DS phenotypes

MTHFR C677T polymorphism analysis: A simple, effective restriction enzyme-based method improving previous protocols

Background: 5,10-Methylentetrahydrofolate reductase (MTHFR) C677T polymorphism is one of the most studied genetic variations in the human genome. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is one of the most used techniques to characterize the point mutations in genomic sequences because of its suitability and low cost. The most widely used method for the MTHFR C677T polymorphism characterization was developed by Frosst et al. (1995) but appears to have some technical limitations. The aim of this study was to propose a novel PCR-RFLP method for the detection of this polymorphism. Methods: In order to retrieve all published articles possibly describing any PCR-RFLP methods useful to analyze MTHFR C677T polymorphism, we performed systematic queries on PubMed, using a combination of Boolean operators (AND/OR) and MeSH terms. Amplify software was used in order to design a new primer pair following the optimal standard criteria. Primer-BLAST software was used to check primer pair's biological specificity. Results: The analysis of previous literature showed that PCR-RFLP method remains the most used technique. None of the 108 primer pairs described was ideal with regard to main accepted primer pair biochemical technical parameters. The new primer pair amplifies a DNA-fragment of 513 base pair (bp) that, in the presence of the polymorphism, is cut by Hinf I enzyme in two pieces of 146 bp and 367 bp and clearly visible on 2% agarose gel. The level of expertise and the materials required are minimal and the protocol takes one day to carry out. Conclusion: Our original PCR-RFLP strategy, specifically designed to make the analysis optimal with respect to PCR primers and gel analysis, fits the ideal criteria compared to the widely used strategy by Frosst et al (1995) as well as any other PCR-RFLP strategies proposed for MTHFR C677T polymorphism genotyping to date

Boschi di neoformazione in Italia: approfondimenti conoscitivi e orientamenti gestionali

Nelle regioni meridionali, e in Sicilia in particolare, la fisionomia della vegetazione forestale post-abbandono è quella della macchia o arbusteto che difficilmente evolve verso un bosco propriamente detto. Il processo evolutivo della vegetazione spesso non raggiunge lo stadio di bosco non perché le condizioni ambientali non lo consentano ma per due ragioni fondamentali: i disturbi, in particolare gli incendi e il pascolo, e le limitazioni nell’arrivo di propaguli, causate dalla mancanza di piante madri, dei dispersori dei semi o entrambi. Infatti, in contesti favorevoli (assenza di disturbi e arrivo dei propaguli) la vegetazione evolve sino al bosco. Le formazioni preforestali frutto dei processi di successione secondaria occupano superfici significative e sono conseguenza del fenomeno dell’abbandono dell’agricoltura iniziato alla seconda metà del secolo scorso e che ha interessato tutta l’Europa. Alcune azioni per ridurre i fattori negativi ed esaltare invece i vantaggi ambientali sono possibili per i boschi degli ambienti mediterranei. Tra queste, la trasformazione dei boschi di neoformazione in sistemi agroforestali, e più propriamente silvopastorali, utilizzando la parte aerea delle specie arboree e arbustive e mantenendo piccoli nuclei di specie spontanee utili alla fauna selvatica (a esempio, specie con frutti carnosi) senza lasciare che esse dominino la vegetazione erbacea. Ciò consentirebbe una valorizzazione delle superfici innanzitutto come pascoli, ma non si esclude l’utilizzazione come legna da ardere della componente arborea e, in certi casi, dei prodotti ottenibili (a esempio, manna, mandorle, carrube, nocciole). Altra possibilità per non disperdere i vantaggi consisterebbe nel mettere a coltura gli ex coltivi adottando tecniche alternative che non disperdano il carbonio accumulato. Su questo aspetto esistono già esperienze: ciò potrebbe inoltre ridurre la conflittualità tra gli enti gestori delle aree protette, restii a consentire un ritorno alla coltivazione, e gli agricoltori nonché i sostenitori della necessità di tutelare i paesaggi agrari

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

<p>Abstract</p> <p>Background</p> <p>Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input.</p> <p>Results</p> <p>TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified.</p> <p>Conclusions</p> <p>TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at <url>http://apollo11.isto.unibo.it/software/</url>, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.</p

Complexity of Bidirectional Transcription and Alternative Splicing at Human RCAN3 Locus

Human RCAN3 (regulator of calcineurin 3) belongs to the human RCAN gene family

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research