62 results on '"Silva, Ricardo R"'
Search Results
52. Propagating annotations of molecular networks using in silico fragmentation.
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Wang, Mingxun, Nothias, Louis-Félix, Caraballo-Rodríguez, Andrés Mauricio, Dorrestein, Pieter C., da Silva, Ricardo R., van der Hooft, Justin J. J., Lopes, Norberto Peporine, Fox, Evan, Klassen, Jonathan L., and Balunas, Marcy J.
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FRAGMENTATION reactions ,MASS spectrometry ,METABOLOMICS ,ANNOTATIONS ,MOLECULES - Abstract
The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when there is no match to a MS/MS spectrum in spectral libraries. This is accomplished through creating a network consensus of re-ranked structural candidates using the molecular network topology and structural similarity to improve in silico annotations. The Network Annotation Propagation (NAP) tool is accessible through the GNPS web-platform . [ABSTRACT FROM AUTHOR]
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- 2018
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53. Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupaniiand Euphobia pithyusawith MS2LDAand Combinatorial Molecular Network Annotation Propagation
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Nothias-Esposito, Mélissa, Nothias, Louis Felix, Da Silva, Ricardo R., Retailleau, Pascal, Zhang, Zheng, Leyssen, Pieter, Roussi, Fanny, Touboul, David, Paolini, Julien, Dorrestein, Pieter C., and Litaudon, Marc
- Abstract
The species Euphorbia pithyusaand Euphorbia cupaniiare two closely related Mediterranean spurges for which their taxonomic relationships are still being debated. Herein, the diterpene ester content of E. cupaniiwas investigated using liquid chromatography coupled to tandem mass spectrometry. The use of molecular networking coupled to unsupervised substructure annotation (MS2LDA) indicated the presence of new premyrsinane/myrsinane diterpene esters in the E. cupaniifractions. A structure-guided isolation procedure yielded 16 myrsinane (11a–h, 12, and 13) and premyrsinane esters (14a–cand 15a–c), along with four 4β-phorbol esters (16a–cand 17) that showed inhibitory activity against chikungunya virus replication. The structures of the 16 new compounds (11a–c, 11h, 12, 13, 14a–c, 15a–c, 16a–c, and 17) were characterized by NMR spectroscopy and X-ray crystallography. To further uncover the diterpene ester content of these two species, the concept of combinatorial network annotation propagation (C-NAP) was developed. By leveraging the fact that the diterpene esters of Euphorbiaspecies are made up of limited building blocks, a combinatorial database of theoretical structures was created and used for C-NAP that made possible the annotation of 123 premyrsinane or myrsinane esters, from which 74% are not found in any compound database.
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- 2019
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54. Improved virus purification processes for vaccines and gene therapy
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Nestola, Piergiuseppe, primary, Peixoto, Cristina, additional, Silva, Ricardo R. J. S, additional, Alves, Paula M., additional, Mota, José P. B., additional, and Carrondo, Manuel J. T., additional
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- 2015
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55. Ralstonia solanacearum em viveiros clonais de eucalipto no Brasil
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Alfenas, Acelino C., Mafia, Reginaldo G., Sartório, Robert C., Binoti, Daniel H.B., Silva, Ricardo R., Lau, Douglas, and Vanetti, Cláudia A.
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clonal propagation ,Eucalyptus spp ,propagação clonal ,vascular wilt ,murcha bacteriana ,murcha vascular ,DNA ,PCR/RFLP ,bacterial wilt - Abstract
A incidência da murcha bacteriana, causada por Ralstonia solanacearum, em viveiros clonais de eucalipto, no período de abril a setembro de 2005, resultou no descarte de cerca de 553.991 minicepas, 6.837.691 propágulos na fase de enraizamento e 11.266.819 mudas, nos Estados da Bahia, do Espírito Santo, do Maranhão, de Minas Gerais e do Pará, totalizando um prejuízo estimado em, no mínimo, seis milhões de reais (US$ 2,7 milhões). Em minijardim clonal, a doença caracteriza-se por necrose foliar, escurecimento anelar ou completo do lenho, murcha e morte de minicepas. Os sintomas na parte aérea são similares à morte gradual de minicepas submetidas a podas drásticas ou com sistema radicular malformado. Na fase de enraizamento, miniestacas infectadas podem apresentar arroxeamento das nervuras do limbo foliar e podridão. No campo, a doença caracteriza-se por bronzeamento e necrose foliar, desfolha basal, ascendente escurecimento interno do lenho e morte da planta, geralmente a partir do quarto mês após o transplantio. Os sintomas geralmente se agravam em árvores com enovelamento de raízes e afogamento de coleto. A etiologia da doença foi confirmada por meio de testes de exsudação, microscopia de varredura, isolamento da bactéria, análises de PCR/RFLP, reação de hipersensibilidade (HR) em mudas de fumo, testes de patogenicidade em plântulas de eucalipto e tomate e re-isolamento da bactéria. Como o sistema de produção de mudas clonais de eucalipto é altamente favorável à multiplicação bacteriana e na falta de conhecimento sobre a resistência genética e de outras estratégias de controle da doença, é essencial evitar a introdução da bactéria em viveiros. The occurrence of bacterial wilt caused by Ralstonia solanacearum in eucalyptus clonal hedges in the Brazilian states of Bahia, Espírito Santo, Maranhão, Minas Gerais and Pará, from April to September, 2005 resulted in loss of 553,991 rooted cuttings, 6,837,691 cuttings at rooting stage and 11,266,819 cuttings, with a total loss estimated to be at least six million reais (US$ 2.7 M). In clonal minihedges, the disease is characterized by foliar necrosis, annular or complete wood darkening, wilt and death of rooted-cuttings. Leaf symptoms are similar to those observed during the gradual death of rooted-cuttings subjected to drastic pruning or with malformed root systems. In the rooting phase, infected minicuttings can present redning of leaf blade veins and cutting rot. In the field, the disease is characterized by leaf browning and necrosis, basal leaf loss, internal wood darkening and plant death, with onset generally occurring four months after transplant. Disease severity is generally higher in trees with entangled roots and overplanting. The causal agent of the disease was confirmed through exudate tests, scanning electron microscopy, bacterial isolation, PCR/RFLP analyses, hypersensitive reactions (HR) in tobacco seedlings, pathogenicity tests in eucalyptus and tomato plantlets and reisolation of the bacteria. The production of cuttings offers a highly favorable environment for bacterial multiplication. This, combined with the lack of knowledge on genetic resistance and other disease control strategies, makes it essential to avoid introduction of this bacterium in clonal nurseries.
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- 2006
56. Perseverative Thinking, Anxiety and Emotional Coping Effects on Determinants of Academic Success
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Rocha, Jose Carlos, primary, Moreira, Andre, primary, Veiga, Valentina, primary, Silva, Ricardo R., primary, and Teixeira, Ricardo Joao, primary
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57. CHAPTER 3. Metabolomics
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da Silva, Ricardo R., primary, Lopes, Norberto Peporine, additional, and Silva, Denise Brentan, additional
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58. Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezansUsing in SilicoMolecular Network Annotation Propagation-Based Dereplication
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Kang, Kyo Bin, Park, Eun Jin, da Silva, Ricardo R., Kim, Hyun Woo, Dorrestein, Pieter C., and Sung, Sang Hyun
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The integration of LC–MS/MS molecular networking and in silicoMS/MS fragmentation is an emerging method for dereplication of natural products. In the present study, a targeted isolation of natural products using a new in silico-based annotation tool named Network Annotation Propagation (NAP) is described. NAP improves accuracy of in silicofragmentation analyses by reranking candidate structures based on the network topology from MS/MS-based molecular networking. Annotation for the MS/MS spectral network of the Sageratia theezanstwig extract was performed using NAP, and most molecular families within the network, including the known triterpenoids 1–7, could be putatively annotated, without relying on any previous reports of molecules from this species. Based on the in silicodereplication results, molecules were prioritized for isolation. In total, six dicoumaroyl 8-O-4′ neolignans (8–13) and three dicoumaroyl lignans (14–16) were isolated from the twigs of S. theezansand structurally characterized by spectroscopic analyses. Isolates were evaluated for their neuroprotective activity, and compounds 14–16showed potent protective effects against glutamate-induced oxidative stress in mouse HT22 cells at a concentration of 12.5 μM.
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- 2018
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59. A Subspace-Projected Approximate Matrix Method for Systems of Linear Equations
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Brandts, Jan, primary and da Silva, Ricardo R., additional
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- 2013
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60. Lifestyle chemistries from phones for individual profiling.
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Amir, Amnon, Bouslimani, Amina, Melnik, Alexey V., da Silva, Ricardo R., Dorrestein, Pieter C., Alexandrov, Theodore, Zhenjiang Xu, Knight, Rob, Mingxun Wang, and Bandeira, Nuno
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LIFESTYLES ,PERSONAL belongings ,CELL phones ,PROFILE portraits ,MASS spectrometry - Abstract
Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available. Here, we develop an approach to translate chemistries recovered from personal objects such as phones into a lifestyle sketch of the owner, using mass spectrometry and informatics approaches. Our results show that phones' chemistries reflect a personalized lifestyle profile. The collective repertoire of molecules found on these objects provides a sketch of the lifestyle of an individual by highlighting the type of hygiene/beauty products the person uses, diet, medical status, and even the location where this person may have been. These findings introduce an additional form of trace evidence from skin-associated lifestyle chemicals found on personal belongings. Such information could help a criminal investigator narrowing down the owner of an object found at a crime scene, such as a suspect or missing person. [ABSTRACT FROM AUTHOR]
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- 2016
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61. Ralstonia solanacearum em viveiros clonais de eucalipto no Brasil
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Alfenas, Acelino C., primary, Mafia, Reginaldo G., additional, Sartório, Robert C., additional, Binoti, Daniel H.B., additional, Silva, Ricardo R., additional, Lau, Douglas, additional, and Vanetti, Cláudia A., additional
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- 2006
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62. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
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Waters, Katrina M., Peng, Yao, McPhail, Kerry L., Zhang, Lixin, Dorrestein, Kathleen, Shi, Wenyuan, Allard, Pierre-Marie, Gerwick, Lena, Torres-Mendoza, Daniel, Pogliano, Kit, Moore, Bradley S., Houson, Hailey, Kleigrewe, Karin, Kyle, Jennifer E., Hsu, Cheng-Chih, Silva, Denise B., Boya, Cristopher A.P., Litaudon, Marc, Charusanti, Pep, Pace, Laura A., Sedio, Brian E., Shinn, Paul, Liu, Xueting, Sims, Amy C., Pevzner, Pavel, Gurr, Joshua, Aigle, Bertrand, Pociute, Egle, Rodríguez, Andrés M. C., Gavilan, Ronnie G., Metz, Thomas O., Maansson, Maria, Quinn, Robert A., Palsson, Bernhard Ø, Dai, Jingqui, Carlson, Erin E., Crüsemann, Max, Ryffel, Florian, Vuong, Lisa, Nothias, Louis-Felix, Linington, Roger G., Alexandrov, Theodore, Phelan, Vanessa V., Kharbush, Jenan J., Zhang, Chen, Müller, Rolf, Lopes, Norberto P., Phapale, Prasad, Bouslimani, Amina, Dorrestein, Pieter C., Yang, Yu-Liang, Engene, Niclas, Elfeki, Maryam, McLean, Jeffrey, Neupane, Ram, O'Neill, Ellis C., Murphy, Brian T., Garg, Neha, Almaliti, Jehad, Helfrich, Eric J. N., Dutton, Rachel J., Wolfender, Jean-Luc, Melnik, Alexey V., Marques, Lucas M., Jelsbak, Lars, Baric, Ralph, Koyama, Nobuhiro, Nielsen, Kristian Fog, Johnson, Andrew R., Klitgaard, Andreas, Esquenazi, Eduardo, Duggan, Brendan M., Northen, Trent, Wang, Mingxun, Boudreau, Paul D., Gutiérrez, Marcelino, Williams, Philip G., Edlund, Anna, Michelsen, Charlotte F., Demarque, Daniel P., Mascuch, Samantha J., Mohimani, Hosein, Lamsa, Anne, Tomasi, Sophie, Glukhov, Evgenia, Larson, Charles B., Macherla, Venkat, Sandoval-Calderón, Mario, Jensen, Paul R., Gerwick, William H., Nguyen, Dac-Trung, Jadhav, Ajit, Meehan, Michael J., Porto, Carla, Parrot, Delphine, Sidebottom, Ashley M., Peryea, Tyler, Floros, Dimitrios J., Vining, Oliver B., Hoffman, Thomas, Sanchez, Laura M., Gonzalez, David J., VanLeer, Danielle, Vorholt, Julia A., Briand, Enora, Sohlenkamp, Christian, Watrous, Jeramie, Kurita, Kenji L., Kersten, Roland D., Knight, Rob, Granatosky, Eve A., Luzzatto-Knaan, Tal, Keyzers, Robert A., Jenkins, Stefan, Liu, Wei-Ting, Traxler, Matthew F., Silva, Ricardo R., Piel, Jörn, Duncan, Katherine R., Kapono, Clifford A., Humpf, Hans-Ulrich, Nguyen, Don Duy, Bandeira, Nuno, Carver, Jeremy J., Liaw, Chih-Chuang, Agarwal, Vinayak, and Zeng, Yi
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3. Good health - Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data.
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