Linking forest diversity and tree health: preliminary insights from a large-scale survey in Italy

Forest health is currently assessed in Europe (ICP Forests monitoring program). Crown defoliation and dieback, tree mortality, and pathogenic damage are the main aspects considered in tree health assessment. The worsening of environmental conditions (i.e., increase of temperature and drought events) may cause large-spatial scale tree mortality and forest decline. However, the role of stand features, including tree species assemblage and diversity as factors that modify environmental impacts, is poorly considered. The present contribution reanalyses the historical dataset of crown conditions in Italian forests from 1997 to 2014 to identify ecological and structural factors that influence tree crown defoliation, highlighting in a special manner the role of tree diversity. The effects of tree diversity were explored using the entire data set through multivariate cluster analyses and on individual trees, analysing the influence of the neighbouring tree diversity and identity at the local (neighbour) level. Preliminary results suggest that each tree species shows a specific behaviour in relation to crown defoliation, and the distribution of crown defoliation across Italian forests reflects the distribution of the main forest types and their ecological equilibrium with the environment. The potentiality and the problems connected to the possible extension of this analysis at a more general level (European and North American) were discussed

The MoVIN server for the analysis of protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produced several large-scale protein-protein interaction data sets for various organisms. It is important to develop tools for dissecting their content and analyse the information they embed by data-integration and computational methods.</p> <p>Results</p> <p>Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains. The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins in common biological processes.</p> <p>We present here a publicly available server that allows the user to investigate protein interaction data in light of other biological information, such as their sequences, presence of specific domains, process and component ontologies. The server can be effectively used to construct a high-confidence set of mutually exclusive interactions by identifying similar features in groups of proteins sharing a common interaction partner. As an example, we describe here the identification of common motifs, function, cellular localization and domains in different datasets of yeast interactions.</p> <p>Conclusions</p> <p>The server can be used to analyse user-supplied datasets, it contains pre-processed data for four yeast Protein Protein interaction datasets and the results of their statistical analysis. These show that the presence of common motifs in proteins interacting with the same partner is a valuable source of information, it can be used to investigate the properties of the interacting proteins and provides information that can be effectively integrated with other sources. As more experimental interaction data become available, this tool will become more and more useful to gain a more detailed picture of the interactome.</p

Detecting and comparing non-coding RNAs in the high-throughput era.

In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes and of the finding that many of these transcripts are involved in key cellular functions. In this context, accurately detecting and comparing RNA sequences has become important. Aligning nucleotide sequences is a key requisite when searching for homologous genes. Accurate alignments reveal evolutionary relationships, conserved regions and more generally any biologically relevant pattern. Comparing RNA molecules is, however, a challenging task. The nucleotide alphabet is simpler and therefore less informative than that of amino-acids. Moreover for many non-coding RNAs, evolution is likely to be mostly constrained at the structural level and not at the sequence level. This results in very poor sequence conservation impeding comparison of these molecules. These difficulties define a context where new methods are urgently needed in order to exploit experimental results to their full potential. This review focuses on the comparative genomics of non-coding RNAs in the context of new sequencing technologies and especially dealing with two extremely important and timely research aspects: the development of new methods to align RNAs and the analysis of high-throughput data

BlastR—fast and accurate database searches for non-coding RNAs

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.htm

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Long non-coding RNAs (lncRNAs) can often function in the regulation of gene expression during development; however, their generality as essential regulators in developmental processes and organismal phenotypes remains unclear. Here, we performed a tailored investigation of lncRNA expression and function during Drosophila embryogenesis, interrogating multiple stages, tissue specificity, nuclear localization, and genetic backgrounds. Our results almost double the number of annotated lncRNAs expressed at these embryonic stages. lncRNA levels are generally positively correlated with those of their neighboring genes, with little evidence of transcriptional interference. Using fluorescent in situ hybridization, we report the spatiotemporal expression of 15 new lncRNAs, revealing very dynamic tissue-specific patterns. Despite this, deletion of selected lncRNA genes had no obvious developmental defects or effects on viability under standard and stressed conditions. However, two lncRNA deletions resulted in modest expression changes of a small number of genes, suggesting that they fine-tune expression of non-essential genes. Several lncRNAs have strain-specific expression, indicating that they are not fixed within the population. This intra-species variation across genetic backgrounds may thereby be a useful tool to distinguish rapidly evolving lncRNAs with as yet non-essential roles.Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. European Molecular Biology Laboratory; AlemaniaFil: Bussotti, Giovanni. European Bioinformatics Institute; Reino UnidoFil: Maleš, Matilda. European Molecular Biology Laboratory; AlemaniaFil: Forneris, Mattia. European Molecular Biology Laboratory; AlemaniaFil: Viales, Rebecca R.. European Molecular Biology Laboratory; AlemaniaFil: Enright, Anton J.. European Bioinformatics Institute; Reino UnidoFil: Furlong, Eileen E. M.. European Molecular Biology Laboratory; Alemani

Defoliation, Recovery and Increasing Mortality in Italian Forests: Levels, Patterns and Possible Consequences for Forest Multifunctionality

Forest health and multifunctionality are threatened by global challenges such as climate change. Forest health is currently assessed within the pan-European ICP Forests (International Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests) programme through the evaluation of tree crown conditions (defoliation). This paper analyses the results of a 24-year assessment carried out in Italy on 253 permanent plots distributed across the whole forested area. The results evidenced a substantial stability of crown conditions at the national level, according to the usual defoliation thresholds Defoliation > 25% and Defoliation > 60%, albeit with species-specific patterns. Within this apparent temporal stability, an increased fraction of extremely defoliated and dead trees was observed. Extreme defoliation mostly occurred in years with severe summer drought, whereas mortality was higher in the years after the drought. The results for singular species evidenced critical conditions for Castanea sativa Mill. and Pinus species, whereas Quercus species showed a progressive decrease in defoliation. Deciduous species, such as Fagus sylvatica L., Ostrya carpinifolia Scop. and Quercus pubescens Willd. suffer the loss of leaves in dry years as a strategy to limit water loss by transpiration but recover their crown in the following years. The recurrence of extreme heat waves and drought from the beginning of the XXI century may increase the vulnerability of forests, and increased tree mortality can be expected in the future

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis.

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art 'HPV integrated site capture' (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a 'looping' mechanism by which flanking host regions become amplified. Furthermore, using our 'HPV16-specific Region Capture Hi-C' technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a 'cancer-causing gene' is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.This work was supported by Cancer Research UK (www.cancerresearchuk.org) Programme Award (A13080) to NC. ELAD was supported by a PhD studentship from The Pathological Society of GB & NI (www.pathsoc. org) awarded to IJG and NC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Trans-Atlantic spill over: deconstructing the ecological adaptation of Leishmania infantum in the Americas

Pathogen fitness landscapes change when transmission cycles establish in non-native environments or spill over into new vectors and hosts. The introduction of Leishmania infantum in the Americas into the Neotropics during European colonization represents a unique case study to investigate the mechanisms of ecological adaptation of this important parasite. Defining the evolutionary trajectories that drive L. infantum fitness in this new environment are of great public health importance as they will allow unique insight into pathways of host/pathogen co-evolution and their consequences for region-specific changes in disease manifestation. This review summarizes current knowledge on L. infantum genetic and phenotypic diversity in the Americas and its possible role in the unique epidemiology of visceral leishmaniasis (VL) in the New World. We highlight the importance of appreciating adaptive molecular mechanisms in L. infantum to understand the parasites’ successful establishment on the continent