Effects of Music Therapy on Mood in Stroke Patients

PURPOSE: To investigate the effects of music therapy on depressive mood and anxiety in post-stroke patients and evaluate satisfaction levels of patients and caregivers. MATERIALS AND METHODS: Eighteen post-stroke patients, within six months of onset and mini mental status examination score of over 20, participated in this study. Patients were divided into music and control groups. The experimental group participated in the music therapy program for four weeks. Psychological status was evaluated with the Beck Anxiety Inventory (BAI) and Beck Depression Inventory (BDI) before and after music therapy. Satisfaction with music therapy was evaluated by a questionnaire. RESULTS: BAI and BDI scores showed a greater decrease in the music group than the control group after music therapy, but only the decrease of BDI scores were statistically significant (p=0.048). Music therapy satisfaction in patients and caregivers was affirmative. CONCLUSION: Music therapy has a positive effect on mood in post-stroke patients and may be beneficial for mood improvement with stroke. These results are encouraging, but further studies are needed in this field.ope

Standardized benchmarking in the quest for orthologs

Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.This work was supported by Swiss National Science Foundation grant PP00P3_150654 (to C.D.), UK Biotechnology and Biological Sciences Research Council grant BB/L018241/1 (to C.D.), Spanish Ministry of Economy and Competitiveness grant BIO2012-37161 (to T.G.), Qatar National Research Fund NPRP 5-298-3-086 (to T.G.), European Research Council grant ERC-2012-StG-310325 (to T.G.), National Institutes of Health (NIH) grant R24 OD011883 (to S.E.L.), U41 HG002273 (to S.E.L. and P.D.T.), U41 HG007822 (to M.J.M. and I.X.), Swiss State Secretariat for Education, Research and Innovation (SERI) funding (to I.X. and C.D.), US National Science Foundation EAGER Award #1355632 (to K.S.) and ANR project BIP-BIP ANR-10-BINF-03-02 (to O.L.). Furthermore, A.S.d.S., J.H.-C., M.J.M., M.M. and P.B. acknowledge support from the European Molecular Biology Laboratory, M.M. acknowledges support from the Wellcome Trust (WT095908), S.E.L. acknowledges support from Lawrence Berkeley National Laboratory core funds (Office of Basic Energy Sciences and US Department of Energy Contract No. DE-AC02-05CH11231), L.J.J. acknowledges support from the Novo Nordisk Foundation (Grant No. NNF14CC0001) and L.P.P. acknowledges support from the La Caixa–CRG International Fellowship Program

Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the Baker's yeast lineage

Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies have focused on establishing when these events occurred and on elucidating their functional and evolutionary consequences, but we still lack sufficient understanding of how genome duplications first originated. We used phylogenomics to study the ancient genome duplication occurred in the yeast Saccharomyces cerevisiae lineage and found compelling evidence for the existence of a contemporaneous interspecies hybridization. We propose that the genome doubling was a direct consequence of this hybridization and that it served to provide stability to the recently formed allopolyploid. This scenario provides a mechanism for the origin of this ancient duplication and the lineage that originated from it and brings a new perspective to the interpretation of the origin and consequences of whole-genome duplications.TG group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), which includes FEDER structural funds, a grant from the Qatar National Research Fund (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC (Grant Agreement n. ERC-2012-StG-310325). The funders had no role in study/ndesign, data collection and analysis, decision to publish, or preparation of the manuscript

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum

BACKGROUND: Penicillium griseofulvum is associated in stored apples with blue mould, the most important postharvest disease of pome fruit. This pathogen can simultaneously produce both detrimental and beneficial secondary metabolites (SM). In order to gain insight into SM synthesis in P. griseofulvum in vitro and during disease development on apple, we sequenced the genome of P. griseofulvum strain PG3 and analysed important SM clusters. RESULTS: PG3 genome sequence (29.3 Mb) shows that P. griseofulvum branched off after the divergence of P. oxalicum but before the divergence of P. chrysogenum. Genome-wide analysis of P. griseofulvum revealed putative gene clusters for patulin, griseofulvin and roquefortine C biosynthesis. Furthermore, we quantified the SM production in vitro and on apples during the course of infection. The expression kinetics of key genes of SM produced in infected apple were examined. We found additional SM clusters, including those potentially responsible for the synthesis of penicillin, yanuthone D, cyclopiazonic acid and we predicted a cluster putatively responsible for the synthesis of chanoclavine I. CONCLUSIONS: These findings provide relevant information to understand the molecular basis of SM biosynthesis in P. griseofulvum, to allow further research directed to the overexpression or blocking the synthesis of specific SM.Work at the University of Torino was partially supported by the LIFE financial instrument of the European Union (Contract LIFE13 ENV/HR/000580). TG group research was partially funded by a grant from the Spanish Ministry of Economy and Competitiveness (BIO2012-37161), a grant from the Qatar National Research Fund (NPRP5-298-3-086), and a grant from the European Research Council (Grant Agreement ERC-2012-StG-310325). Work at LGC lab was partially supported by a grant from the Spanish Ministry of Economy and Innovation (AGL2011-30519-C03-01) and by the Generalitat Valenciana, Spain (PROMETEOII/2014/027). ARB is grateful to CSIC and the European Social Fund for her postdoctoral contract JAE-Do

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

Background: Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees. Results: Our results depict a complex scenario involving at least three past polyploidization events, of which two—at the bases of the family Oleaceae and the tribe Oleeae, respectively—are likely to be the result of ancient allopolyploidization. A more recent polyploidization involves specifically the olive tree and relatives. Conclusion: Our results show the power of phylogenomics to distinguish between allo- and auto polyploidization events and clarify the contributions of duplications in the evolutionary history of the olive tree.TG’s group acknowledges support from the Spanish Ministry of Economy and Competitiveness through grants “Centro de Excelencia Severo Ochoa 2013-2017” SEV-2012-0208 and BFU2015-67107, cofounded by the European Regional Development Fund; from the Catalan Research Agency (AGAUR) SGR857, from the CERCA programme/ Generalitat de Catalunya; and from the European Union’s Horizon 2020 research and innovation program under Marie Sklodowska-Curie grant agreement H2020-MSCA-ITN-2014-642095 and European Research Council grant agreement ERC-2016-CoG-724173. TG and PV acknowledge support from Banco Santander for the olive genome sequencing project. IJ was supported in part by a grant from the Peruvian Ministry of Education, “Beca Presidente de la República” (2013-III)

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

Background. Leishmaniasis is a neglected parasitic disease with diverse clinical manifestations and a complex epidemiology. It has been shown that its parasite-related traits vary between species and that they modulate infectivity, pathogenicity, and virulence. However, understanding of the species-specific adaptations responsible for these features and their evolutionary background is limited. To improve our knowledge regarding the parasite biology and adaptation mechanisms of different Leishmania species, we conducted a proteome-wide phylogenomic analysis to gain insights into Leishmania evolution./nResults. The analysis of the reconstructed phylomes (totaling 45,918 phylogenies) allowed us to detect genes that are shared in pathogenic Leishmania species, such as calpain-like cysteine peptidases and 3'a2rel-related proteins, or genes that could be associated with visceral or cutaneous development. This analysis also established the phylogenetic relationship of several hypothetical proteins whose roles remain to be characterized. Our findings demonstrated that gene duplication constitutes an important evolutionary force in Leishmania, acting on protein families that mediate host-parasite interactions, such as amastins, GP63 metallopeptidases, cathepsin L-like proteases, and our methods permitted a deeper analysis of their phylogenetic relationships./nConclusions. Our results highlight the importance of proteome wide phylogenetic analyses to detect adaptation and evolutionary processes in different organisms and underscore the need to characterize the role of expanded and species-specific proteins in the context of Leishmania evolution by providing a framework for the phylogenetic relationships of Leishmania proteins.We thank Leszek P. Pryszcz for his assistance with MetaPhOrs. DB group is funded by The National Institute of Science and Technology for Vaccines (Brazil) (MCT/CNPq, grant CNPq 573547/2008-4), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG, grant # APQ-04073-10, PPM-00219-13) and Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES, grant # 051/2013). TG group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund grant (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013) / ERC (Grant Agreement n. ERC-2012-StG-310325). GO group was funded by NIH-Fogarty (TW007012), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (REDE-56/11, RED-00014-14) and Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (309312/2012-4)