8 research outputs found
Uniconf: An alternative conformer generator with broad applicability
No full textThe Uniconf program aimed at conformational search/sampling in molecular clusters and isolated molecules with rotatable bonds has been developed. Unlike the other approaches, the spatial structural diversity of generated conformations is prioritized over targeting a semiempirical method or a force field minimum energy structures. The code is tested in generating of the gas-phase conformers for transition metal complexes, biologically active oligopeptides, and sodium ion microsolvated clusters. In one third of cases, either more or equally stable conformers compared to the previously found ones were generated. Energetically more diverse structures than available in the literature were obtained for practically all compounds.Prof. Vidar R. Jensen, University of Bergen, Norway, is deeply acknowledged for bringing our attention to the conformational search problem. The author gratefully acknowledges Prof. Luigi Cavallo, King Abdullah University of Science and Technology and Dr. Edrisse Chermak, SABIC, Saudi Arabia, and Dr. Arseniy A. Otlyotov, Dr. Daniil Itkis, Prof. Lada V. Yashina, and Andrey D. Moshchenkov, N. N. Semenov Federal Research Center for Chemical Physics RAS, Moscow, Russia for many insightful discussions. The anonymous reviewers of this work are gratefully acknowledged for their valuable comments and suggestions. The work was financially supported by the Russian Science Foundation (project 24-23-00301)
Clinical implementation of RNA sequencing for Mendelian disease diagnostics
No full text\ua9 2022, The Author(s). Background: Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. Methods: We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. Results: We detected on average 12,500 genes per sample including around 60% of all disease genes—a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. Conclusion: Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics
Purification Of Catalytically Produced Carbon Nanotubes For Use As Support For Fuel Cell Cathode Pt Catalyst
No full textA purification method based on HCl treatment under reflux was employed for purification of carbon nanotube (CNT) samples, obtained by the electric discharge method utilizing Zr(Co0.5Ni0.5)2, Ce3(Co0.5Ni0.5)2 and Ce(Co 0.5Ni0.5)5 as catalysts. Raman Spectroscopy provided information on the SWCNT presence in the untreated samples. Scanning Electron Microscopy (SEM) showed CNT with different diameters and lengths. Different acid treatment conditions were employed and the best results were achieved for HCl 3 mol/L aqueous solution during 24 h reflux. Transmission Electron Microscopy (TEM) images, associated with EDS, revealed the catalyst removal from the original sample and the presence of other carbon structures near the CNT formation. CNT acid functionalization for Pt nanoparticles dispersion was successful, resulting in a homogeneously dispersed system, as seen in TEM images. Temperature Programmed Oxidation (TPO) analysis of the raw and purified samples indicated that after purification there are three different carbon species present on the purified material, each one showing a different behavior towards O2 oxidation. © 2007 Springer Science+Business Media, LLC.432557567Tzitzios, V., Georgakilas, V., Oikonomou, E., Karakassidesb, M., Petridis, D., (2006) Carbon, 44, p. 848Baughman, R.H., Zakhidov, A.A., De Heer, W.A., (2002) Science, 297, p. 787Kong, J., Franklin, N.R., Zhou, C., Chapline, M.G., Peng, S., Cho, K., (2000) Science, 287, p. 622Postma, H.W.C., Teepen, T., Yao, Z., Grifoni, M., Dekker, C., (2001) Science, 293, p. 76Ajayan, P.M., Schadler, L.S., Giannaris, C., Rubio, A., (2000) Adv Mater, 12, p. 750Waje, M.M., Wang, X., Li, W., Yan, Y., (2005) Nanotechnology, 16, p. 395Ye, J.S., Wen, Y., Zhang, W.D., Gan, L.M., Xu, G.Q., Sheu, F.S., (2004) Electrochem Commun, 6, p. 66He, P.G., Dai, L.M., (2004) Chem Commun, 3, p. 348Herrera, J.E., Resasco, D.E., (2003) Chem Phys Lett, 376, p. 302Nikolaev, P., Bronikowski, M.J., Bradley, R.K., Rohmund, F., Colbert, D.T., Smith, K.A., Smalley, R.E., (1999) Chem Phys Lett, 313, p. 91Kong, J.A., Cassell, A.M., Dai, H., (1998) Chem Phys Lett, 292, p. 567Rana, R.K., Koltypin, Y., Gedanken, A., (2001) Chem Phys Lett, 344, p. 256Resasco, D.E., Alvarez, W.E., Pompeo, F., Balzano, L., Herrera, J.E., Kitiyanan, B., Borgna, A., (2002) J Nanoparticle Res, 4, p. 131Peigney, A., Coquay, P., Flahaut, E., Vandenberghe, R.E., De Grave, E., Laurent, C., (2001) J Phys Chem B, 105, p. 9699Zhao, B., Hu, H., Niyogi, S., Itkis, M.E., Hamon, M.A., Bhowmik, P., Meier, M.S., Haddon, R.C., (2001) J Am Chem Soc, 123, p. 11673Yang, C.M., Kaneko, K., Yudasaka, M., Iijima, S., (2002) Nano Lett, 2, p. 385Lobach, A.S., Spitsina, N.G., Terekhov, S.V., Obraztsova, E.D., (2002) Phys Solid State, 44, p. 475Niyogi, S., Hu, H., Hamon, M.A., Bhowmik, P., Zhao, B., Rozenzhak, S.M., Chen, J., Haddon, R.C., (2001) J Am Chem Soc, 123, p. 733Liu, J., Rinzler, A.G., Dai, H., Hafner, J.H., Bradley, R.K., Boul, P.J., Lu, A., Smalley, R.E., (1998) Science, 280, p. 1253Holzinger, M., Hirsch, A., Bernier, P., Duesberg, G.S., Burghard, M., (2000) Appl Phys A, 70, p. 599Rao, C.N.R., Satishkumar, B.C., Govindaraj, A., Nath, M., (2001) Chem Phys Chem, 2, p. 78Rinzler, A.G., Liu, J., Dai, H., Nikolaev, P., Huffman, C.B., Rodriguez-Macias, F.J., Boul, P.J., Smalley, R.E., (1998) Appl Phys A, 67, p. 29Shi, Z., Lian, Y., Liao, F., Zhou, X., Gu, Z., Zhang, Y., Ijima, S., (1999) Solid State Commun, 112, p. 35Saito, R., Fujita, M., Dresselhaus, G., Dresselhaus, M.S., (1992) Appl Phys Lett, 60, p. 2204Alvarez, W.E., Pompeo, F., Herrera, J.E., Balzano, L., Resasco, D.E., (2002) Chem Mater, 14, p. 1853Herbst, M.H., MacÊdo, M.I.F., Rocco, A.M., (2004) Química Nova, 27, p. 986Benoit, J.M., Buisson, J.P., Chauvet, O., Godon, C., Lefrant, S., (2002) Phys Rev B, 66, p. 073417Moon, J.M., An, K.H., Lee, Y.H., Park, Y.S., Bae, D.J., Park, G.S., (2001) J Phys Chem B, 105, p. 5677Chiang, I.W., Brinson, B.E., Smalley, R.E., Margrave, J.L., Hauge, R.H., (2001) J Phys Chem B, 105, p. 1157Harutyunyan, A.R., Pradhan, B.K., Chang, J., Chen, G., Eklund, P.C., (2002) J Phys Chem B, 106, p. 8671Endo, M., Lee, B.J., Kim, Y.A., Kim, Y.J., Muramatsu, H., Yanagisawa, T., Hayashi, T., Dresselhaus, M.S., (2003) New J Phys, 5, p. 121Bandow, S., Rao, A.M., Williams, K.A., Thess, A., Smalley, R.E., Eklund, P.C., (1997) J Phys Chem B, 101, p. 8839Deng, B., Xu, A.-W., Chen, G.Y., Song, R.-Q., Chen, L., (2006) J Phys Chem B, 110, p. 11711Zhang, L., Samulski, E.T., (2004) Chem Phys Lett, 398, p. 505Kitiyanan, B., Alvarez, W.E., Harwell, J.H., Resasco, D.E., (2000) Chem Phys Lett, 317, p. 497Alvarez, W.E., Kitiyanan, B., Borona, A., Resasco, D.E., (2001) Carbon, 39, p. 54
Produção de nanotubos de carbono hidrofílicos a partir de negro de carbono tratado por plasma frio em meio líquido
No full textTese (doutorado) - Universidade Federal de Santa Catarina, Centro de Ciências Físicas e Matemáticas, Programa de Pós-Graduação em Química, Florianópolis, 2015.O principal objetivo deste trabalho foi estudar a produção de nanotubos de carbono (CNT) por plasma frio em meio líquido. O material de partida foi produzido pela degradação de metano por plasma térmico obtendo o negro de carbono (CB) e hidrogênio. Neste processo, à eficiência de degradação, rendimento de hidrogênio e identificação dos subprodutos formados também foram avaliados. Na sequência, foram apresentados detalhes sobre o método de produção de CNTS por plasma frio e o resultado de análises químicas que comprovam que um novo método de produção foi desenvolvido. Após, foi apresentado um estudo sobre as modificações químicas e estruturais que ocorreram no CB durante o tratamento por plasma frio e, consequente, a produção de CNT. Para isso, foram apresentados resultados de análises químicas comparando as estruturas do CB e do CNT. As reações químicas envolvidas no processo foram expostas e possíveis mecanismos de formação e crescimento de CNTs foram propostos, assim como modelos que descrevem como ocorreu a produção de CNTs a partir do tratamento de CB por plasma frio. Os resultados de degradação de metano mostraram que o método é eficiente para a produção de CB, chegando a uma porcentagem de degradação de 98,8% e uma seletividade para hidrogênio de 40,3% para hidrogênio. Os resultados também indicaram que um novo método de produção para CNTs foi desenvolvido e que o produto formado é composto por uma mistura de MWCNTs, SWCNTs e vestígios de CB. Análises como microscopias, energia dispersiva de raios-X, Espectroscopia Raman e difração de raios-X confirmaram a produção de CNTs. O rendimento de CNTs produzidos por plasma frio foi estimado por termogravimetria, que indicou um rendimento entre 50-60%. Resultados de espectroscopia de fotoelétrons excitados por raios-X, CHN, fisissorção e quimissorção indicaram que mudanças significativas ocorreram na superfície e na estrutura da amostra durante o tratamento por plasma frio. Os resultados das análises químicas e a identificação das espécies presentes no meio reacional possibilitaram que mecanismos de formação e crescimento de CNTs fossem sugeridos, assim como modelos que descrevem o que ocorreu durante o método de produção. As possíveis reações químicas envolvidas também foram descritas.Abstract : The main objective of this study was to detail the production of carbon nanotubes (CNT) by cold plasma, but other issues were also addressed. Initially, a study on the degradation of thermal plasma methane to produce carbon black (CB) and hydrogen was shown, as well as some additional results regarding the degradation efficiency, yield hydrogen and identification of the formed products. Further, there are details about the method of production of CNTS by cold plasma and the results of chemical analysis showing that a new production method was developed. In the sequence there s a study of the chemical and structural changes that occurred in the CB during treatment by cold plasma and, consequently, the production of CNT, through results of chemical analyzes that compared the structures of the CNTs and CB. The chemical reactions involved in the process were exposed and possible mechanisms of formation and growth of CNTs have been proposed, as well as models that describe the production of CNTs from CB treatment by cold plasma. The results of methane degradation showed that the method is efficient for the production of CB, reaching a percentage of degradation of 98.8% and a selectivity of 40.3% for hydrogen to hydrogen. The results also indicated that a new method for production of CNTs has been developed and the product formed comprises a mixture of MWCNTs, SWCNTs and traces of CB. Analyses such as microscopy, energy dispersive X-ray, Raman spectroscopy and X-ray diffraction confirmed the production of CNTs. The yield of CNTs produced by cold plasma was estimated by thermogravimetry, which indicated a yield of 50-60%. Results from excited photoelectron spectroscopy by CHN, chemisorption and physisorption X-ray indicated that significant changes occurred on the surface and structure of the sample during treatment by cold plasma. The results of chemical analyzes and the identification of the species present in the reaction medium enabled that the formation and growth mechanisms of CNTs could be suggested, as well as models that describe what happened during the production method. Possible chemical reactions involved are also described
Impaired complex I repair causes recessive Leber's hereditary optic neuropathy
No full textLeber's hereditary optic neuropathy (LHON) is the most frequent mitochondrial disease and was the first to be genetically defined by a point mutation in mitochondrial DNA (mtDNA). A molecular diagnosis is achieved in up to 95% of cases, the vast majority of which are accounted for by 3 mutations within mitochondrial complex I subunit-encoding genes in the mtDNA (mtLHON). Here, we resolve the enigma of LHON in the absence of pathogenic mtDNA mutations. We describe biallelic mutations in a nuclear encoded gene, DNAJC30, in 33 unsolved patients from 29 families and establish an autosomal recessive mode of inheritance for LHON (arLHON), which to date has been a prime example of a maternally inherited disorder. Remarkably, all hallmarks of mtLHON were recapitulated, including incomplete penetrance, male predominance, and significant idebenone responsivity. Moreover, by tracking protein turnover in patient-derived cell lines and a DNAJC30-knockout cellular model, we measured reduced turnover of specific complex I N-module subunits and a resultant impairment of complex I function. These results demonstrate that DNAJC30 is a chaperone protein needed for the efficient exchange of complex I subunits exposed to reactive oxygen species and integral to a mitochondrial complex I repair mechanism, thereby providing the first example to our knowledge of a disease resulting from impaired exchange of assembled respiratory chain subunits
Impaired complex I repair causes recessive Leber's hereditary optic neuropathy
No full textLeber's hereditary optic neuropathy (LHON) is the most frequent mitochondrial disease and was the first to be genetically defined by a point mutation in mitochondrial DNA (mtDNA). A molecular diagnosis is achieved in up to 95% of cases, the vast majority of which are accounted for by 3 mutations within mitochondrial complex I subunit-encoding genes in the mtDNA (mtLHON). Here, we resolve the enigma of LHON in the absence of pathogenic mtDNA mutations. We describe biallelic mutations in a nuclear encoded gene, DNAJC30, in 33 unsolved patients from 29 families and establish an autosomal recessive mode of inheritance for LHON (arLHON), which to date has been a prime example of a maternally inherited disorder. Remarkably, all hallmarks of mtLHON were recapitulated, including incomplete penetrance, male predominance, and significant idebenone responsivity. Moreover, by tracking protein turnover in patient-derived cell lines and a DNAJC30-knockout cellular model, we measured reduced turnover of specific complex I N-module subunits and a resultant impairment of complex I function. These results demonstrate that DNAJC30 is a chaperone protein needed for the efficient exchange of complex I subunits exposed to reactive oxygen species and integral to a mitochondrial complex I repair mechanism, thereby providing the first example to our knowledge of a disease resulting from impaired exchange of assembled respiratory chain subunits
Clinical implementation of RNA sequencing for Mendelian disease diagnostics.
No full textBACKGROUND: Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS: We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS: We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION: Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics
