Discriminative pattern discovery for the characterization of different network populations

Motivation: An interesting problem is to study how gene co-expression varies in two different populations, associated with healthy and unhealthy individuals, respectively. To this aim, two important aspects should be taken into account: (i) in some cases, pairs/groups of genes show collaborative attitudes, emerging in the study of disorders and diseases; (ii) information coming from each single individual may be crucial to capture specific details, at the basis of complex cellular mechanisms; therefore, it is important avoiding to miss potentially powerful information, associated with the single samples. Results: Here, a novel approach is proposed, such that two different input populations are considered, and represented by two datasets of edge-labeled graphs. Each graph is associated to an individual, and the edge label is the co-expression value between the two genes associated to the nodes. Discriminative patterns among graphs belonging to different sample sets are searched for, based on a statistical notion of 'relevance' able to take into account important local similarities, and also collaborative effects, involving the co-expression among multiple genes. Four different gene expression datasets have been analyzed by the proposed approach, each associated to a different disease. An extensive set of experiments show that the extracted patterns significantly characterize important differences between healthy and unhealthy samples, both in the cooperation and in the biological functionality of the involved genes/proteins. Moreover, the provided analysis confirms some results already presented in the literature on genes with a central role for the considered diseases, still allowing to identify novel and useful insights on this aspect

Evolutionary and Ecological Trees and Networks

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can also be represented as a network. In this paper we briefly show some properties of these complex networks of evolutionary and ecological relationships. First, we characterize large scale evolutionary relationships in the Tree of Life by a degree distribution. Second, we represent genetic relationships between individuals of a Mediterranean marine plant, Posidonia oceanica, in terms of a Minimum Spanning Tree. Finally, relationships among plant shoots inside populations are represented as networks of genetic similarity.Comment: 6 pages, 5 figures. To appear in Proceedings of the Medyfinol06 Conferenc

Physiological potential of the chlorophyte Caulerpa prolifera for proliferation across the Mediterranean-Atlantic basins in a warmer ocean

Ocean warming is altering the metabolic balances of organisms, favouring the expansion of thermo-tolerant individuals. The fast-growing macroalga Caulerpa prolifera is rapidly expanding in the Ria Formosa lagoon (Portugal), a connection area between Mediterranean and Atlantic basins. We investigated the metabolic capacity of C. prolifera to cope with ocean warming, to elucidate its expansion potential. The photosynthetic and respiratory plasticity of 4 populations of C. prolifera spread along the Mediterranean−Atlantic basins was assessed under a temperature range of 20 to 30°C. In addition, molecular markers were used to investigate the genetic identity of the strain found in Ria Formosa, which confirmed its Mediterranean origin. All examined populations showed large physiological thermo tolerance and metabolic plasticity to warming. The photosynthetic efficiency of C. prolifera improved by 50% with temperature, and the maximum photosynthetic production doubled along the temperature range tested. Respiration did not vary with temperature, whereas the metabolic quotient increased by more than 70%when temperature increased from 20 to 25−30°C. Minor differences in the photosynthetic descriptors were detected among populations, reflecting light- and dark-adapted physiology of Mediterranean and Atlantic populations, respectively. Our results show that all tested populations of C. prolifera have the physiological potential to cope with temperature increases up to 30°C, which indicates that ocean warming may contribute to the expansion of C. prolifera in the Mediterranean− Atlantic basins.PTDC/MAR-EST/3223/2014, PTDC/MAR-EST/4257/2014, UIDB/ 04326/2020, CCMAR/BPD/004/ 2017 , H202-MSCA-IF-EF-ST-752 250, SFRH/BPD/ 109452/2015, DL 57/ 2016/ CP1361/CT0037, SFRH/ BSAB/ 150485/2019info:eu-repo/semantics/publishedVersio

Key determinants of target DNA recognition by retroviral intasomes

BACKGROUND: Retroviral integration favors weakly conserved palindrome sequences at the sites of viral DNA joining and generates a short (4–6 bp) duplication of host DNA flanking the provirus. We previously determined two key parameters that underlie the target DNA preference for prototype foamy virus (PFV) and human immunodeficiency virus type 1 (HIV-1) integration: flexible pyrimidine (Y)/purine (R) dinucleotide steps at the centers of the integration sites, and base contacts with specific integrase residues, such as Ala188 in PFV integrase and Ser119 in HIV-1 integrase. Here we examined the dinucleotide preference profiles of a range of retroviruses and correlated these findings with respect to length of target site duplication (TSD). RESULTS: Integration datasets covering six viral genera and the three lengths of TSD were accessed from the literature or generated in this work. All viruses exhibited significant enrichments of flexible YR and/or selection against rigid RY dinucleotide steps at the centers of integration sites, and the magnitude of this enrichment inversely correlated with TSD length. The DNA sequence environments of in vivo-generated HIV-1 and PFV sites were consistent with integration into nucleosomes, however, the local sequence preferences were largely independent of target DNA chromatinization. Integration sites derived from cells infected with the gammaretrovirus reticuloendotheliosis virus strain A (Rev-A), which yields a 5 bp TSD, revealed the targeting of global chromatin features most similar to those of Moloney murine leukemia virus, which yields a 4 bp duplication. In vitro assays revealed that Rev-A integrase interacts with and is catalytically stimulated by cellular bromodomain containing 4 protein. CONCLUSIONS: Retroviral integrases have likely evolved to bend target DNA to fit scissile phosphodiester bonds into two active sites for integration, and viruses that cut target DNA with a 6 bp stagger may not need to bend DNA as sharply as viruses that cleave with 4 bp or 5 bp staggers. For PFV and HIV-1, the selection of signature bases and central flexibility at sites of integration is largely independent of chromatin structure. Furthermore, global Rev-A integration is likely directed to chromatin features by bromodomain and extraterminal domain proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12977-015-0167-3) contains supplementary material, which is available to authorized users

Biogeographic population structure of chimeric blades of porphyra in the northeast atlantic reveals southern rich gene pools, introgression and cryptic plasticity

The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis, both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica, microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history.info:eu-repo/semantics/publishedVersio

Network analysis identifies weak and strong links in a metapopulation system

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system by using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and from the usual underlying hypotheses required for the interpretation of classical analyses, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial

Endovascular stenting of the ascending aorta for type A aortic dissections in patients at high risk for open surgery

Background: Open repair is the gold standard for type A aortic dissection (TAAD). Endovascular option has been proposed in very limited and selected TAAD patients. We report our experience with endovascular TAAD repair. Methods: Inclusion criteria were: (1) entry tear in the ascending aorta; (2) proximal landing zone of at least 2 cm; (3) distance between entry tear and brachio-cephalic trunk of at least 0.5 cm; (4) no signs of cardiac tamponade or severe aortic regurgitation and (5) no signs of aortic branches ischaemia. Patients with cardiac revascularisation from ascending aorta were excluded. Results: From April 2009 to June 2012, 37 patients with TAAD were admitted to our hospital. As many as 28 underwent surgical repair and 9 were considered at high surgical risk in a multidisciplinary meeting. Four met our inclusion criteria for an endovascular approach. Two of them had previous ascending aortic repair for TAAD and one had aortic valve replacement. Technical success was achieved in 100% of the patients. No mortality was registered during a median follow-up of 15 months (range 4-39 months), no migration of the graft and complete false lumen thrombosis of the ascending aorta in three patients. Conclusion: Endovascular treatment of TAAD is challenging but feasible in a selected subset of patients. Further research remains mandatory. © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved

Botulinum toxin A modifies nociceptive withdrawal reflex in subacute stroke patients

Objectives: The aims of this study were to evaluate the pattern of the nociceptive withdrawal reflex (NWR) of the upper limb at rest and after injection of Botulinum toxin type A (BoNT-A) in poststroke subacute hemiparetic patients. Methods: Fourteen patients with poststroke subacute hemiparesis underwent clinical and instrumental evaluation and BoNT-A injection. Painful electrical stimulation was applied to induce the NWR. Baseline EMG activity and NWR recordings (EMG and kinematic response) were performed at T0, one month (T1), and three months (T2) after the BoNT-A injection, as were Modified Ashworth Scale (MAS) and Functional Independence Measure (FIM) scores. Results: Comparison of results at T0, T1, and T2 revealed significant changes in the MAS score for the elbow (p < 0.001) and wrist joints (p < 0.001) and in the FIM score at T0 and T2. BoNT-A injection had a significant effect on both NWR amplitude and baseline EMG activity in the posterior deltoid (PD) and flexor carpi radialis (FCR) muscles as well as in all averaged muscles. Analysis of elbow kinematics before and after treatment revealed that the reflex probability rates were significantly higher at T1 and T2 than at T0. Conclusion: Injection of BoNT-A in the subacute phase of stroke can modify both the baseline EMG activity and the NWR-related EMG responses in the upper limb muscles irrespective of the site of injection; furthermore, the reflex-mediated defensive mechanical responses, that is, shoulder extension and abduction and elbow flexion, increased after treatment. BoNT-A injection may be a useful treatment in poststroke spasticity with a potential indirect effect on spinal neurons