GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a 'mean' human protein-coding gene is 67 kbp long, has eleven 309\u2009bp long exons and ten 6355\u2009bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/

Comparison between crown thinning and girdling to enhance sporadic tree species in a coppice stand in Central Italy

Sporadic valuable tree species and especially Sorbus species have gained importance in forest management as they increase tree biodiversity, ensure a higher resilience of the stand to climate change, and enhance valuable timber production. This paper reports the first results of a trial carried out in Central Italy in a Turkey oak coppice stand (aged 17 years) where three different silvicultural treatments (crown thinning, girdling and unthinned control) were applied to favour sporadic tree species. The monitoring was carried out for 5 years and showed the limits of girdling application as Mediterranean species like Turkey oak form easily scar cords and epicormic sprouting. Furthermore, the progressive reduction of canopy cover of the competitors resulted from girdling and the effect of the thinning and girdling on the growth of selected service trees (Sorbus domestica L.) were evaluated. The first results of this research have pointed out some difficulties in the girdling application and a higher effect of crown thinning in stimulating the growth of selected service trees

Systematic reanalysis of partial trisomy 21 cases with or without Down syndrome suggests a small region on 21q22.13 as critical to the phenotype

A "Down Syndrome critical region" (DSCR) sufficient to induce the most constant phenotypes of Down syndrome (DS) had been identified by studying partial (segmental) trisomy 21 (PT21) as an interval of 0.6-8.3 Mb within human chromosome 21 (Hsa21), although its existence was later questioned. We propose an innovative, systematic reanalysis of all described PT21 cases (from 1973 to 2015). In particular, we built an integrated, comparative map from 125 cases with or without DS fulfilling stringent cytogenetic and clinical criteria. The map allowed to define or exclude as candidates for DS fine Hsa21 sequence intervals, also integrating duplication copy number variants (CNVs) data. A highly restricted DSCR (HR-DSCR) of only 34 kb on distal 21q22.13 has been identified as the minimal region whose duplication is shared by all DS subjects and is absent in all non-DS subjects. Also being spared by any duplication CNV in healthy subjects, HR-DSCR is proposed as a candidate for the typical DS features, the intellectual disability and some facial phenotypes. HR-DSCR contains no known gene and has relevant homology only to the chimpanzee genome. Searching for HR-DSCR functional loci might become a priority for understanding the fundamental genotype-phenotype relationships in DS

Tree Species Composition in Mixed Plantations Influences Plant Growth, Intrinsic Water Use Efficiency and Soil Carbon Stock

Species interactions in mixed plantations can influence tree growth, resources capture and soil fertility of the stands. A combined approach of tree-ring analyses and carbon stable isotope was used to check tree growth and water use efficiency of two species, Populus alba L. and Juglans regia L., intercropped with each other and with N-fixing or competitive production species. Furthermore, soil analyses were performed to understand how the different intercropping systems can influence soil characteristics, in particular soil carbon stock. Dendrochronological data showed that during the first years, the growth of principal species was favored by intercropping. This positive effect decreased in the following years in most of intercropped stands, due to light competition with the crown of companion species. Carbon isotope data showed that P. alba and J. regia had the highest intrinsic water use efficiency when growing with Elaeagnus umbellata Thunb, a shrubby species with a shallow root system that favors a non-competitive exploitation of soil water resources. Finally, the intercropping of the principal species with Corylus avellana L. promoted the highest soil C stock. Our findings confirmed the importance to consider the plantation dynamics and wood formation in the long-run and to apply appropriate thinning and pruning interventions to counteract interspecific competition

The GIS database of WOODnat project for the inventory and monitoring of walnut plantations in Italy and Spain

Within the activity of the H2020 ‘WOODnat’ project (“Second generation of planted hardwood forests in the European Union”) the growth parameters, yield and sanitary conditions of the most important walnut (Juglans spp.) plantations, established in Italy in the 1990s and in Spain starting from 1996, were recorded. One of the objectives of the project was to evaluate tree growth and stem quality to derive insight on the main environmental factors affecting the production of this valuable specie. An inventory of walnut plantations in the area of interest was necessary due to the relevance of this tree species in the EU timber market. In this paper the final dataset is presented and available with DOI: 10.5281/zenodo.3769940. The database is finalized to narrow the knowledge gap between growers and processing industry with the aim to relaunching the market for this valuable species. Data were collected in the spring 2017 and winter 2017-2018 on 27 stands established in Northern Italy (Piemonte and Lombardia), on 51 stands in Central Italy (Toscana and Marche) and on 17 stands in Spain for a total of 95 plantations. In each plantation, general information was collected such as the planting layout, spacing, age, environment conditions as well as tree-level dendrometric data and phytosanitary information. The sampled stands have been georeferenced in WGS84 reference system (EPSG 4326). These data can be exploited to assess potential wood volume obtainable and quality of raw material, and to identify the weaknesses and errors, strengths and opportunities of the experiences conducted to plan future plantings with greater awareness

Partial trisomy 21 with or without highly restricted Down syndrome critical region (HR-DSCR): report of two new cases and reanalysis of the genotype-phenotype association

Background: Down syndrome (DS) is caused by the presence of an extra copy of full or partial human chromosome 21 (Hsa21). Partial (segmental) trisomy 21 (PT21) is the duplication of only a delimited region of Hsa21 and can be associated or not to DS: the study of PT21 cases is an invaluable model for addressing genotype-phenotype correlation in DS. Previous works reported systematic reanalyses of 132 subjects with PT21 and allowed the identification of a 34-kb highly restricted DS critical region (HR-DSCR) as the minimal region whose duplication is shared by all PT21 subjects diagnosed with DS. Methods: We report clinical data and cytogenetic analysis of two children with PT21, one with DS and the other without DS. Moreover, we performed a systematic bibliographic search for any new PT21 report. Results: Clinical and cytogenetic analyses of the two PT21 children have been reported: in Case 1 the duplication involves the whole long arm of Hsa21, except for the last 2.7 Mb, which are deleted as a consequence of an isodicentric 21: the HR-DSCR is within the duplicated regions and the child is diagnosed with DS. In Case 2 the duplication involves 7.1 Mb of distal 21q22, with a deletion of 2.1 Mb of proximal 20p, as a consequence of an unbalanced translocation: the HR-DSCR is not duplicated and the child presents with psychomotor development delay but no clinical signs of DS. Furthermore, two PT21 reports recently published (named Case 3 and 4) have been discussed: Case 3 has DS diagnosis, nearly full trisomy for Hsa21 and a monosomy for the 21q22.3 region. Case 4 is a baby without DS and a 0.56-Mb duplication of 21q22.3. Genotype-phenotype correlation confirmed the presence of three copies of the HR-DSCR in all DS subjects and two copies in all non-DS individuals. Conclusions: The results presented here are fully consistent with the hypothesis that the HR-DSCR is critically associated with DS diagnosis. No exception to this pathogenetic model was found. Further studies are needed to detect genetic determinants likely located in the HR-DSCR and possibly responsible for core DS features, in particular intellectual disability

Enhancing chestnut coppices: silvicultural management and socio-economic context.

 Castanea sativa is one of the most important species for timber production in Italy but, both management system, ownership type and wood chain structure, aren’t able to  enhance enough the market value of wood assortments. Although the high demand of quality timber, the internal production is heavily  reduced, mainly as far as timber quality is concerned and because of the lack of suitable timber sizes. In this context, experimental trials  have been approached to identify and verify which silvicultural methods are best suited to reach high yields depending to the investments  needed and the local socio-economical condition. Two technical approaches were evaluated: stand silviculture and single-tree oriented silviculture. As for the socio-economical aspects, a few demographic indexes have been examined and the first-phase processing enterprises  acting in the concerned area were analyzed. The goals of this paper are to evaluate the biological response to the applied silviculture, to  analyze the problems arisen and to estimate the applicability of the proposed methods in relation to the different socio-economic contexts. The research has been carried out in Tuscany in two important forest areas - Monte Amiata and Colline Metallifere - in young chestnut  coppices characterized by an homogeneous stand density and a good site index. The two examined districts showed some similarities  but they have mainly highlighted important differences about the social structure and concerns and enterprises characteristics. The area of Monte Amiata is typified by a higher residents density then the Colline Metallifere but only 1/3 of the population is employed in the agro-forest sector. In addition, in the Monte Amiata district most concerns are sized less than 2 hectares and chestnut is the main forest  species. On the contrary, in the Colline Metallifere the agro-forest sector (57% of workers) is one of the main sources of income for the  local communities and medium-sized concerns are noteworthy present. Chestnut stands have here a marginal role, oaks are dominant  and the prevailing assortment is firewood. From a silvicultural viewpoint, both the studied areas showed a quite good potentiality, suitabl

Adoption of new silvicultural methods in Mediterranean forests: the influence of educational background and sociodemographic factors on marker decisions

Producción Científica- Key message The adoption of new silvicultural methods and approaches requires an understanding of the differences between those and “old” or “conventional” approaches, along with extensive training to break previous knowledge bias. - Context Forestry is in transition towards ecosystem-based management, and new silvicultural approaches are appearing worldwide. However, the adoption of an alternative silvicultural approach is difficult in practice. - Aims We analyzed the effect of forestry background and demographic variables (gender and age) of 24 raters on the application of the systemic approach (SA) and the conventional approach (CA) in the Northern Apennines (Italy) and compared this with tree marking performed by experts. - Methods Data were analyzed as raters’ departures from experts’ selections at the stand and the individual tree level. The probability of tree selection was also calculated. - Results At the stand level, raters with forestry background performed the SA as if they were marking for crown thinning, whereas the CA was less intense than experts’ crown thinning. Non-foresters differentiated poorly between the SA and the CA. At the individual tree level, background and gender affected tree selection. - Conclusion The adoption of the SA as a silvicultural system may be conditioned by previous knowledge. The difference between SA and CA remains unclear when it comes to non-foresters. Gender was a more important variable than age in selecting which trees would be harvested

One-carbon pathway metabolites are altered in the plasma of subjects with Down syndrome: Relation to chromosomal dosage

Introduction: Down syndrome (DS) is the most common chromosomal disorder and it is caused by trisomy of chromosome 21 (Hsa21). Subjects with DS show a large heterogeneity of phenotypes and the most constant clinical features present are typical facies and intellectual disability (ID). Several studies demonstrated that trisomy 21 causes an alteration in the metabolic profile, involving among all the one-carbon cycle. Methods: We performed enzyme-linked immunosorbent assays (ELISAs) to identify the concentration of 5 different intermediates of the one-carbon cycle in plasma samples obtained from a total of 164 subjects with DS compared to 54 euploid subjects. We investigated: tetrahydrofolate (THF; DS n = 108, control n = 41), 5-methyltetrahydrofolate (5-methyl-THF; DS n = 140, control n = 34), 5-formyltetrahydrofolate (5-formyl-THF; DS n = 80, control n = 21), S-adenosyl-homocysteine (SAH; DS n = 94, control n = 20) and S-adenosyl-methionine (SAM; DS n = 24, control n = 15). Results: Results highlight specific alterations of THF with a median concentration ratio DS/control of 2:3, a decrease of a necessary molecule perfectly consistent with a chromosomal dosage effect. Moreover, SAM and SAH show a ratio DS/control of 1.82:1 and 3.6:1, respectively. Discussion: The relevance of these results for the biology of intelligence and its impairment in trisomy 21 is discussed, leading to the final proposal of 5-methyl-THF as the best candidate for a clinical trial aimed at restoring the dysregulation of one-carbon cycle in trisomy 21, possibly improving cognitive skills of subjects with DS