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2. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Luyi Tian, Jafar S. Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L. Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei R. M. Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W. Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernández, Jin D. Chung, Timur Naim, Audrey Chan, Chi Hai Ly, Gordon S. Lynch, James G. Ryall, Casey J. A. Anttila, Hongke Peng, Mary Ann Anderson, Christoffer Flensburg, Ian Majewski, Andrew W. Roberts, David C. S. Huang, Michael B. Clark, and Matthew E. Ritchie

Subjects
Single-cell gene expression, Long-read sequencing, Splicing, Single-cell multi-omics, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.

Published
2021
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3. ICT Framework for Supporting Applied Behavior Analysis in the Social Inclusion of Children with Neurodevelopmental Disorders

Author

Sara Jayousi, Alessio Martinelli, Paolo Lucattini, and Lorenzo Mucchi

Subjects
Information and communication technologies, ICT, wireless communications, applied behavior analysis, ABA, children with neurodevelpmental disorders, Chemical technology, TP1-1185
Abstract

The applied behavior analysis (ABA) model emphasizes observable and measurable behaviors by carrying out decision making using experimental data (behavioral observation assessment strategies). In this framework, information and communication technology (ICT) becomes highly suitable for enhancing the efficiency and effectiveness of the methodology. This paper aims to delve into the potential of ICT in providing innovative solutions to support ABA applications. It focuses on how ICT can contribute to fostering social inclusion with respect to children with neurodevelopmental disorders. ICT offers advanced solutions for continuous and context-aware monitoring, as well as automatic real-time behavior assessments. Wireless sensor systems (wearable perceptual, biomedical, motion, location, and environmental sensors) facilitate real-time behavioral monitoring in various contexts, enabling the collection of behavior-related data that may not be readily evident in traditional observational studies. Moreover, the incorporation of artificial intelligence algorithms that are appropriately trained can further assist therapists throughout the different phases of ABA therapy. These algorithms can provide intervention guidelines and deliver an automatic behavioral analysis that is personalized to the child’s unique profile. By leveraging the power of ICT, ABA practitioners can benefit from cutting-edge technological advancements to optimize their therapeutic interventions and outcomes for children with neurodevelopmental disorders, ultimately contributing to their social inclusion and overall wellbeing.

Published
2023
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4. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De Novo Duplications in the ATAD3 Locus

Author

Frazier, Ann E., Compton, Alison G., Kishita, Yoshihito, Hock, Daniella H., Welch, AnneMarie E., Amarasekera, Sumudu S.C., Rius, Rocio, Formosa, Luke E., Imai-Okazaki, Atsuko, Francis, David, Wang, Min, Lake, Nicole J., Tregoning, Simone, Jabbari, Jafar S., Lucattini, Alexis, Nitta, Kazuhiro R., Ohtake, Akira, Murayama, Kei, Amor, David J., McGillivray, George, Wong, Flora Y., van der Knaap, Marjo S., Vermeulen, R. Jeroen, Wiltshire, Esko J., Fletcher, Janice M., Lewis, Barry, Baynam, Gareth, Ellaway, Carolyn, Balasubramaniam, Shanti, Bhattacharya, Kaustuv, Freckmann, Mary-Louise, Arbuckle, Susan, Rodriguez, Michael, Taft, Ryan J., Sadedin, Simon, Cowley, Mark J., Minoche, André E., Calvo, Sarah E., Mootha, Vamsi K., Ryan, Michael T., Okazaki, Yasushi, Stroud, David A., Simons, Cas, Christodoulou, John, and Thorburn, David R.

Published
2021
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6. Social Inclusion for Children with Disabilities: The Role of ICT in Play and Entertainment Activities

Author

Lucattini, Paolo, Jayousi, Sara, Martinelli, Alessio, Mucchi, Lorenzo, Lombardi, Grazia, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin (Sherman), Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Mucchi, Lorenzo, editor, Hämäläinen, Matti, editor, Jayousi, Sara, editor, and Morosi, Simone, editor

Published
2019
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7. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Tian, Luyi, Jabbari, Jafar S., Thijssen, Rachel, Gouil, Quentin, Amarasinghe, Shanika L., Voogd, Oliver, Kariyawasam, Hasaru, Du, Mei R. M., Schuster, Jakob, Wang, Changqing, Su, Shian, Dong, Xueyi, Law, Charity W., Lucattini, Alexis, Prawer, Yair David Joseph, Collar-Fernández, Coralina, Chung, Jin D., Naim, Timur, Chan, Audrey, Ly, Chi Hai, Lynch, Gordon S., Ryall, James G., Anttila, Casey J. A., Peng, Hongke, Anderson, Mary Ann, Flensburg, Christoffer, Majewski, Ian, Roberts, Andrew W., Huang, David C. S., Clark, Michael B., and Ritchie, Matthew E.

Published
2021
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12. Pedagogia e Vita: Sport e Educazione

Author

Francesco Bonini, Antonella Stelitano, Angela Teja, Domenico F.A.Elia, Giuseppe Mari, Raniero Regni, Cosimo Costa, Alba G.A.Naccari, Onorina del Vecchio, Pierluigi Palmieri, Paolo Lucattini, Mario Salisci, Nicoletta Rosati, Antonietta Panella, Edio Costantini

Published
2017

13. Children and Context-aware Inclusive Tuning of Cartoons. Design of multimedia contents in an inclusive perspective

Author

Cosimo Di Bari, Sara Jayousi, Paolo Lucattini, and Lorenzo Mucchi

Abstract

Thanks to the specific characteristics of multimedia language, cartoons can transmit significant messages to viewers, both emotionally and rationally: this contribution reflects on the potential of cartoons to facilitate and support inclusive processes (also) regarding children with disabilities. In addition to examining functional strategies for promoting a more aware and more active use by all subjects, the article proposes a possible use of Artificial Intelligence to support the dialogue between Media Education and inclusive processes. On one level, the adult (educator, teacher or parent) has the task of observing the child during viewing, interacting with the child and encouraging verbalization about what has been seen: technologies can offer additional data compared to what has been observed, allowing for an even more targeted way of acting with respect to the specific needs of each child. On another level, one can use the same data to create even more interactive content that allows the narration to adapt to the specific wishes, attitudes and needs of each child. Striving in the direction of educating the media, with the media and for the media, the article promotes a conscious and critical use of technologies: useful tools for both education professionals and family members.

Published
2022

20. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Shanika L. Amarasinghe, Mei R. M. Du, Jakob Schuster, Michael B. Clark, Changqing Wang, Yair David Joseph Prawer, Xueyi Dong, Audrey S. M. Chan, Mary Ann Anderson, Casey J. A. Anttila, James G. Ryall, Gordon S. Lynch, Hasaru Kariyawasam, Ian J. Majewski, Jafar S. Jabbari, Christoffer Flensburg, Andrew W. Roberts, Charity W. Law, Shian Su, Luyi Tian, Hongke Peng, Quentin Gouil, Chi Hai Ly, Coralina Collar-Fernández, Timur Naim, Alexis Lucattini, David C.S. Huang, Rachel Thijssen, Oliver Voogd, Matthew E. Ritchie, and Jin D. Chung

Subjects
Gene isoform, Cell type, QH301-705.5, RNA Splicing, Ribosome biogenesis, Method, Computational biology, QH426-470, Biology, Splicing, Transcriptome, Mice, Genetics, Animals, Humans, Protein Isoforms, RNA, Messenger, Biology (General), Long-read sequencing, Gene, Single-cell gene expression, Single-cell multi-omics, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Promoter, Exons, Alternative Splicing, Nanopore Sequencing, RNA splicing, Human genome
Abstract

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02525-6.

Published
2021

21. Metabolic syndrome and drug discontinuation in schizophrenia: a randomized trial comparing aripiprazole olanzapine and haloperidol

Author

Parabiaghi, A., Tettamanti, M., DʼAvanzo, B., Barbato, A., Aguglia, Eugenio, Bassi, Mariano, Breviario, Giancarlo, Casacchia, Massimo, Colotto, Antonio, Corrivetti, Giulio, Erlicher, Arcadio, Ferrannini, Luigi, Ferrato, Farida, Francomano, Antonio, Marcenaro, Maurizio, Mastroeni, Antonino, Mauri, Massimo C, Percudani, Mauro, Picci, Rocco, Pioli, Rosaria, Smerieri, Giovanni, Vaggi, Marco, Visani, Enrico, Buratti, Grazia, Buratti, Lucia, De Micheli, Andrea, Furlato, Karin, DʼOnofrio, Simona, Mariannantoni, Ilaria, Rapisarda, Filippo, Riccardi, Francesca, Ruberto, Alessandra, Ruggirello, Irene, Santini, Ilaria, Trivelli, Federica, Ullo, Angelida, Agnetti, Germana, Bignotti, Stefano, Bufalino, Chiara, Cannavò, Dario, Cattaneo, Carlo I., Caverzasi, Edgardo, Cervetti, Alice, Colombo, Roberto, Comino, Laura, DʼAloise, Angela, De Gaspari, Ilaria F., Parise, Vincenzo Fricchione, Florio, Vincenzo, Gandolfo, Liliana, Ghinaglia, Emanuela, Ghio, Lucio, Groppi, Christian, Hadjichristos, Aristotele, La Placa, Maddalena, Lucattini, Adelia, Manfrinati, Samuele, Natta, Werner, Paschetta, Elena, Pinto, Gaetano, Pollice, Rocco, Pomero, Paolo, and Rigamonti, Danilo

Published
2016
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22. Retention in Care of Adult HIV Patients Initiating Antiretroviral Therapy in Tigray, Ethiopia: A Prospective Observational Cohort Study.

Author

Raffaella Bucciardini, Vincenzo Fragola, Teshome Abegaz, Stefano Lucattini, Atakilt Halifom, Eskedar Tadesse, Micheal Berhe, Katherina Pugliese, Andrea Binelli, Paola De Castro, Roberta Terlizzi, Luca Fucili, Massimiliano Di Gregorio, Marco Mirra, Erika Olivieri, Tsigemariam Teklu, Teame Zegeye, Amanuel Haile, Stefano Vella, Loko Abraham, Hagos Godefay, and CASA-project Health Facilities

Subjects
Medicine, Science
Abstract

Although Ethiopia has been scaling up the antiretroviral therapy (ART) services, low retention in care of patients remains one of the main obstacles to treatment success. We report data on retention in care and its associated determinants in Tigray, Ethiopia.We used data from the CASA project, a prospective observational and multi-site study of a cohort of HIV-infected patients who initiated ART for the first time in Tigray. Four participating health facilities (HFs) located in the South of Tigray were considered for this study. Patients were followed for one year after ART initiation. The main outcome measure was represented by the current retention in care, defined as the proportion of patients who were alive and receiving ART at the same HF one year after ART initiation. Patients who started ART between January 1, 2013 and December 31, 2013 were included in this analysis. Patients were followed for one year after ART initiation. The determinants of retention were analysed using univariate and multivariate Cox Proportional Hazards model with robust sandwich estimates to account for within HF correlation.The four participating HFs in Tigray were able to retain overall 85.1% of their patients after one year from starting ART. Loss to follow-up (5.5%) and transfers to other HF (6.6) were the main determinant of attrition. A multivariate analysis shows that the factors significantly associated with retention were the type of HF, gender and active TB. Alamata health center was the HF with the highest attrition rate (HR 2.99, 95% CI: 2.77-3.23). Active TB (HR 1.72, 95% CI: 1.23-2.41) and gender (HR 1.64, 95% CI: 1.10-2.56) were also significantly associated with attrition.Although Ethiopia has significantly improved access to the ART program, achieving and maintaining a satisfactory long-term retention rate is a future goal. This is difficult because of different retention rates among HFs. Moreover specific interventions should be directed to people of different sex to improve retention in care in male population.

Published
2015
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23. Fatal perinatal mitochondrial cardiac failure caused by recurrent

Author

Ann E, Frazier, Alison G, Compton, Yoshihito, Kishita, Daniella H, Hock, AnneMarie E, Welch, Sumudu S C, Amarasekera, Rocio, Rius, Luke E, Formosa, Atsuko, Imai-Okazaki, David, Francis, Min, Wang, Nicole J, Lake, Simone, Tregoning, Jafar S, Jabbari, Alexis, Lucattini, Kazuhiro R, Nitta, Akira, Ohtake, Kei, Murayama, David J, Amor, George, McGillivray, Flora Y, Wong, Marjo S, van der Knaap, R, Jeroen Vermeulen, Esko J, Wiltshire, Janice M, Fletcher, Barry, Lewis, Gareth, Baynam, Carolyn, Ellaway, Shanti, Balasubramaniam, Kaustuv, Bhattacharya, Mary-Louise, Freckmann, Susan, Arbuckle, Michael, Rodriguez, Ryan J, Taft, Simon, Sadedin, Mark J, Cowley, André E, Minoche, Sarah E, Calvo, Vamsi K, Mootha, Michael T, Ryan, Yasushi, Okazaki, David A, Stroud, Cas, Simons, John, Christodoulou, and David R, Thorburn

Subjects
Heart Failure, Mitochondrial Proteins, Mitochondrial Diseases, Australia, ATPases Associated with Diverse Cellular Activities, Humans, Membrane Proteins, Cardiomyopathies, Child, United States
Abstract

In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. TheWhole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease.We report six differentAustralian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.

Published
2021

24. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De Novo Duplications in the ATAD3 Locus

Author

Flora Y. Wong, Nicole J. Lake, Michael T. Ryan, Anne Marie E. Welch, Kazuhiro R. Nitta, Sarah E. Calvo, Yoshihito Kishita, Daniella H Hock, David A. Stroud, Simone Tregoning, Gareth Baynam, Michael Rodriguez, André E. Minoche, Susan Arbuckle, Kaustuv Bhattacharya, Yasushi Okazaki, David J. Amor, Akira Ohtake, George McGillivray, John Christodoulou, R. Jeroen Vermeulen, Mary Louise Freckmann, Atsuko Imai-Okazaki, Shanti Balasubramaniam, Carolyn Ellaway, Luke E. Formosa, David R. Thorburn, Marjo S van der Knaap, Alison G. Compton, Rocio Rius, Janice M. Fletcher, Mark J. Cowley, Cas Simons, Ann E. Frazier, Kei Murayama, Alexis Lucattini, Ryan J. Taft, Barry Lewis, David Francis, Simon Sadedin, Sumudu S.C. Amarasekera, Jafar S. Jabbari, Vamsi K. Mootha, Min Wang, Esko Wiltshire, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Pediatric surgery, Functional Genomics, Klinische Neurowetenschappen, MUMC+: MA Med Staf Spec Neurologie (9), and RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience

Subjects
quantitative proteomics, COMPUTATIONAL PLATFORM, Translation to Patients, Mitochondrial disease, Pontocerebellar hypoplasia, segmental duplication, Locus (genetics), Biology, HIGH-THROUGHPUT, Genome, GENOMIC DISORDERS, SDG 3 - Good Health and Well-being, medicine, de novo duplication, genomics, Copy-number variation, COPY-NUMBER VARIANTS, ATAD3, Exome sequencing, Segmental duplication, Genetics, ARCHITECTURE, MEMBRANE-PROTEIN, MUTATIONS, CHOLESTEROL, General Medicine, DNA, medicine.disease, COMPLEX I DEFICIENCY, mitochondrial disease, perinatal death, Human genome, cardiomyopathy
Abstract

Summary Background In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. Methods Whole-exome, whole-genome, and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. Findings We report 6 different de novo duplications in the ATAD3 gene locus causing a distinctive presentation, including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently, corneal clouding or cataracts and encephalopathy. The recurrent 68-kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes, and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. Conclusions ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience, the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease, but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. Funding Australian NHMRC, US Department of Defense, US National Institutes of Health, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance, and Australian Mito Foundation.

Published
2021

25. Traduire l’inconscient

Author

Lucattini, Adelia

Subjects
Psychoanalyse, Écriture, Interprétation herméneutique, Assonance, Transformation
Abstract

Cette réflexion porte sur l’Avertissement d’André Pézard, introduction à sa traduction des Œuvres complètes de Dante (Paris, 1965). Dans ce traité de traductologie, Pézard justifie ses choix. D’un point de vue psychanalytique, il y soulève des problèmes de méthode et de technique, concernant « le langage de l’inconscient », communs à la traduction et à la psychanalyse. Le traducteur s’identifie à Dante pour traduire ce que le poète « avait l’intention de dire », et ce qu’il a inconsciemment dit.

Published
2021
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26. Additional file 6 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Tian, Luyi, Jabbari, Jafar S., Thijssen, Rachel, Gouil, Quentin, Amarasinghe, Shanika L., Voogd, Oliver, Kariyawasam, Hasaru, Du, Mei R. M., Schuster, Jakob, Wang, Changqing, Su, Shian, Dong, Xueyi, Law, Charity W., Lucattini, Alexis, Prawer, Yair David Joseph, Collar-Fern��ndez, Coralina, Chung, Jin D., Naim, Timur, Chan, Audrey, Ly, Chi Hai, Lynch, Gordon S., Ryall, James G., Anttila, Casey J. A., Peng, Hongke, Anderson, Mary Ann, Flensburg, Christoffer, Majewski, Ian, Roberts, Andrew W., Huang, David C. S., Clark, Michael B., and Ritchie, Matthew E.

Abstract

Additional file 6. Review history.

Published
2021
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27. Additional file 2 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Tian, Luyi, Jabbari, Jafar S., Thijssen, Rachel, Gouil, Quentin, Amarasinghe, Shanika L., Voogd, Oliver, Kariyawasam, Hasaru, Du, Mei R. M., Schuster, Jakob, Wang, Changqing, Su, Shian, Dong, Xueyi, Law, Charity W., Lucattini, Alexis, Prawer, Yair David Joseph, Collar-Fern��ndez, Coralina, Chung, Jin D., Naim, Timur, Chan, Audrey, Ly, Chi Hai, Lynch, Gordon S., Ryall, James G., Anttila, Casey J. A., Peng, Hongke, Anderson, Mary Ann, Flensburg, Christoffer, Majewski, Ian, Roberts, Andrew W., Huang, David C. S., Clark, Michael B., and Ritchie, Matthew E.

Abstract

Additional file 2. Supplementary Figures.

Published
2021
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29. Recurrent de novo ATAD3 duplications cause fatal perinatal mitochondrial cardiomyopathy, persistent hyperlactacidemia, encephalopathy and heart-specific mitochondrial oxidative phosphorylation complex i deficiency.

Author

Calvo S.E., Ohtake A., Murayama K., Sadedin S., Cowley M.J., Minoche A.E., Mootha V.K., Ryan M.T., Okazaki Y., Stroud D.A., Simons C., Christodoulou J., Thorburn D.R., Frazier A.E., Compton A.G., Kishita Y., Hock D.H., Welch A.E., Amarasekera S.S.C., Rius R., Formosa L.E., Imai-Okazaki A., Francis D., Wang M., Lake N.J., Tregoning S., Jabbari J.S., Lucattini A., Nitta K.R., Amor D.J., McGillivray G., Wong F.Y., Van Der Knaap M.S., Vermeulen R.J., Wiltshire E.J., Fletcher J.M., Lewis B., Baynam G., Ellaway C., Balasubramaniam S., Bhattacharya K., Freckmann M.L., Taft R.J., Calvo S.E., Ohtake A., Murayama K., Sadedin S., Cowley M.J., Minoche A.E., Mootha V.K., Ryan M.T., Okazaki Y., Stroud D.A., Simons C., Christodoulou J., Thorburn D.R., Frazier A.E., Compton A.G., Kishita Y., Hock D.H., Welch A.E., Amarasekera S.S.C., Rius R., Formosa L.E., Imai-Okazaki A., Francis D., Wang M., Lake N.J., Tregoning S., Jabbari J.S., Lucattini A., Nitta K.R., Amor D.J., McGillivray G., Wong F.Y., Van Der Knaap M.S., Vermeulen R.J., Wiltshire E.J., Fletcher J.M., Lewis B., Baynam G., Ellaway C., Balasubramaniam S., Bhattacharya K., Freckmann M.L., and Taft R.J.

Abstract

Mitochondrial disorders are clinically heterogeneous and comprise over 350 different genetic conditions. However, the molecular diagnosis is unknown in ~50% of cases, partly due to some genomic regions being refractory to standard genomic analysis. One such region is the ATAD3 locus consisting of 3 highly homologous tandemly arrayed genes (ATAD3C, ATAD3B and ATAD3A) encoding mitochondrial proteins implicated in processes including cholesterol metabolism, and mitochondrial replication, dynamics and morphology. Recessive deletions and dominant duplications in this locus have recently been reported to cause rare, lethal perinatal mitochondrial disorders characterised by pontocerebellar hypoplasia or cardiomyopathy, respectively. We report 17 subjects from 16 unrelated families with cardiomyopathy, persistent hyperlactacidemia, encephalopathy and frequently corneal clouding or cataracts due to de novo ATAD3 duplications. The six different 68 Kb duplications were consistently identifiable from whole genome and exome sequencing, but usually missed on microarray. The duplications all resulted in the formation of an identical chimeric ATAD3A/ATAD3C fusion protein, which appears to act in a dominant manner causing altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. In our experience, the ATAD3 locus is one of the five most common causes of nuclear-encoded paediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies.

Published
2021

30. Fatal Perinatal Mitochondrial Cardiac Failure Caused by Recurrent De Novo Duplications in the ATAD3 Locus

Author

Frazier, AE, Compton, AG, Kishita, Y, Hock, DH, Welch, AE, Amarasekera, SSC, Rius, R, Formosa, LE, Imai-Okazaki, A, Francis, D, Wang, M, Lake, NJ, Tregoning, S, Jabbari, JS, Lucattini, A, Nitta, KR, Ohtake, A, Murayama, K, Amor, DJ, McGillivray, G, Wong, FY, van der Knaap, MS, Vermeulen, RJ, Wiltshire, EJ, Fletcher, JM, Lewis, B, Baynam, G, Ellaway, C, Balasubramaniam, S, Bhattacharya, K, Freckmann, M-L, Arbuckle, S, Rodriguez, M, Taft, RJ, Sadedin, S, Cowley, MJ, Minoche, AE, Calvo, SE, Mootha, VK, Ryan, MT, Okazaki, Y, Stroud, DA, Simons, C, Christodoulou, J, Thorburn, DR, Frazier, AE, Compton, AG, Kishita, Y, Hock, DH, Welch, AE, Amarasekera, SSC, Rius, R, Formosa, LE, Imai-Okazaki, A, Francis, D, Wang, M, Lake, NJ, Tregoning, S, Jabbari, JS, Lucattini, A, Nitta, KR, Ohtake, A, Murayama, K, Amor, DJ, McGillivray, G, Wong, FY, van der Knaap, MS, Vermeulen, RJ, Wiltshire, EJ, Fletcher, JM, Lewis, B, Baynam, G, Ellaway, C, Balasubramaniam, S, Bhattacharya, K, Freckmann, M-L, Arbuckle, S, Rodriguez, M, Taft, RJ, Sadedin, S, Cowley, MJ, Minoche, AE, Calvo, SE, Mootha, VK, Ryan, MT, Okazaki, Y, Stroud, DA, Simons, C, Christodoulou, J, and Thorburn, DR

Abstract

BACKGROUND: In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications. The ATAD3 locus is one such region, in which recessive deletions and dominant duplications have recently been reported to cause lethal perinatal mitochondrial diseases characterized by pontocerebellar hypoplasia or cardiomyopathy, respectively. METHODS: Whole exome, whole genome and long-read DNA sequencing techniques combined with studies of RNA and quantitative proteomics were used to investigate 17 subjects from 16 unrelated families with suspected mitochondrial disease. FINDINGS: We report six different de novo duplications in the ATAD3 gene locus causing a distinctive presentation including lethal perinatal cardiomyopathy, persistent hyperlactacidemia, and frequently corneal clouding or cataracts and encephalopathy. The recurrent 68 Kb ATAD3 duplications are identifiable from genome and exome sequencing but usually missed by microarrays. The ATAD3 duplications result in the formation of identical chimeric ATAD3A/ATAD3C proteins, altered ATAD3 complexes and a striking reduction in mitochondrial oxidative phosphorylation complex I and its activity in heart tissue. CONCLUSIONS: ATAD3 duplications appear to act in a dominant-negative manner and the de novo inheritance infers a low recurrence risk for families, unlike most pediatric mitochondrial diseases. More than 350 genes underlie mitochondrial diseases. In our experience the ATAD3 locus is now one of the five most common causes of nuclear-encoded pediatric mitochondrial disease but the repetitive nature of the locus means ATAD3 diagnoses may be frequently missed by current genomic strategies. FUNDING: Australian NHMRC, US Department of Defense, Japanese AMED and JSPS agencies, Australian Genomics Health Alliance and Australian Mito Foundation.

Published
2021

31. Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Author

Tian, L, Jabbari, JS, Thijssen, R, Gouil, Q, Amarasinghe, SL, Voogd, O, Kariyawasam, H, Du, MRM, Schuster, J, Wang, C, Su, S, Dong, X, Law, CW, Lucattini, A, Prawer, YDJ, Collar-Fernandez, C, Chung, JD, Naim, T, Chan, A, Ly, CH, Lynch, GS, Ryall, JG, Anttila, CJA, Peng, H, Anderson, MA, Flensburg, C, Majewski, I, Roberts, AW, Huang, DCS, Clark, MB, Ritchie, ME, Tian, L, Jabbari, JS, Thijssen, R, Gouil, Q, Amarasinghe, SL, Voogd, O, Kariyawasam, H, Du, MRM, Schuster, J, Wang, C, Su, S, Dong, X, Law, CW, Lucattini, A, Prawer, YDJ, Collar-Fernandez, C, Chung, JD, Naim, T, Chan, A, Ly, CH, Lynch, GS, Ryall, JG, Anttila, CJA, Peng, H, Anderson, MA, Flensburg, C, Majewski, I, Roberts, AW, Huang, DCS, Clark, MB, and Ritchie, ME

Abstract

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.

Published
2021

32. Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Author

Audrey S. M. Chan, Quentin Gouil, Matthew E. Ritchie, Luyi Tian, Chi Hai Ly, Shanika L. Amarasinghe, Timur Naim, Mary Ann Anderson, Gordon S. Lynch, Rachel Thijssen, Andrew W. Roberts, Shian Su, Casey J. A. Anttila, Alexis Lucattini, David C.S. Huang, Jin D. Chung, Charity W. Law, Jafar S. Jabbari, James G. Ryall, Hongke Peng, Hasaru Kariyawasam, Xueyi Dong, and Michael B. Clark

Subjects
Transcriptome, Gene isoform, medicine.anatomical_structure, RNA splicing, Alternative splicing, Cell, medicine, Ribosome biogenesis, Promoter, Computational biology, Biology, Phenotype
Abstract

Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipeline FLAMES to overcome these issues and perform isoform discovery and quantification, splicing analysis and mutation detection in single cells. With FLT-seq and FLAMES, we performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms. We found conserved functional modules that were enriched for alternative transcript usage in different cell populations, including ribosome biogenesis and mRNA splicing. Analysis at the transcript-level allowed data integration with scATAC-seq on individual promoters, improved correlation with protein expression data and linked mutations known to confer drug resistance to transcriptome heterogeneity. Our methods reveal previously unseen isoform complexity and provide a better framework for multi-omics data integration.

Published
2020

33. Genetic susceptibility to hydroxychloroquine retinal toxicity

Author

Ian P. Wicks, Anthony J. Hall, Rc Andrew Symons, Alexis Lucattini, Heather G Mack, and Tanya Kowalski

Subjects
0301 basic medicine, Adult, Genetic Markers, Male, medicine.medical_specialty, 030105 genetics & heredity, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Retinal Diseases, Risk Factors, Internal medicine, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Genetics (clinical), Exome sequencing, Aged, Polymorphism, Genetic, business.industry, Case-control study, Australia, Hydroxychloroquine, Retinal, Macular degeneration, Middle Aged, medicine.disease, Ophthalmology, chemistry, Antirheumatic Agents, Case-Control Studies, Pediatrics, Perinatology and Child Health, Cohort, Toxicity, 030221 ophthalmology & optometry, Female, business, medicine.drug
Abstract

Background: Hydroxychloroquine retinal toxicity can occur in up to 7.5% of patients receiving treatment; however, possible genetic risk factors are poorly understood. The main objective of the study was to explore candidate genetic risk factors for retinal toxicity.Materials and Methods: Case-control study of patients with confirmed hydroxychloroquine retinal toxicity identified through ophthalmology departments of tertiary care hospitals and private ophthalmic practice in Australia. Participants were 26 Caucasian patients with hydroxychloroquine retinal toxicity who were matched with control subjects for age, gender, treatment duration and indication for hydroxychloroquine treatment. Participants underwent clinical examination, optical coherence tomographic scanning, automated field testing and whole exome sequencing of DNA extracted from saliva or blood. Outcome measures were grade of hydroxychloroquine toxicity and mutations in a panel of 40 candidate genes.Results: No susceptibility or protective factors were identified in either the cohort as a whole or any subset of patients.Conclusions and relevance: Further larger studies, with whole-exome analysis and consideration of additional modifying genes are needed.

Published
2020

36. Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Author

Tian, Luyi, primary, Jabbari, Jafar S., additional, Thijssen, Rachel, additional, Gouil, Quentin, additional, Amarasinghe, Shanika L., additional, Kariyawasam, Hasaru, additional, Su, Shian, additional, Dong, Xueyi, additional, Law, Charity W., additional, Lucattini, Alexis, additional, Chung, Jin D., additional, Naim, Timur, additional, Chan, Audrey, additional, Ly, Chi Hai, additional, Lynch, Gordon S., additional, Ryall, James G., additional, Anttila, Casey J.A., additional, Peng, Hongke, additional, Anderson, Mary Ann, additional, Roberts, Andrew W., additional, Huang, David C.S., additional, Clark, Michael B., additional, and Ritchie, Matthew E., additional

Published
2020
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38. Harnessing Sliding-Window Execution Semantics for Parallel Stream Processing

Author

Fabio Lucattini, Massimo Torquati, Salvatore Cuomo, Gabriele Mencagli, Marco Aldinucci, Mencagli, Gabriele, Torquati, Massimo, Lucattini, Fabio, Cuomo, Salvatore, and Aldinucci, Marco

Subjects
Parallel computing, Continuous queries, Data stream processing, Internet of Things, Sliding windows, Software, Theoretical Computer Science, Hardware and Architecture, Computer Networks and Communications, Artificial Intelligence, Computer science, Semantics (computer science), Big data, 02 engineering and technology, Stream processing, Continuous querie, Data acquisition, 020204 information systems, Sliding window protocol, 0202 electrical engineering, electronic engineering, information engineering, Data Stream Processing, Internet of Things, Continuous Queries, Sliding Windows, Parallel Computing, Representation (mathematics), 020203 distributed computing, business.industry, Concurrent data structure, Sliding window, Computer Networks and Communication, Internet of Thing, business
Abstract

According to the recent trend in data acquisition and processing technology, big data are increasingly available in the form of unbounded streams of elementary data items to be processed in real-time. In this paper we study in detail the paradigm of sliding windows, a well-known technique for approximated queries that update their results continuously as new fresh data arrive from the stream. In this work we focus on the relationship between the various existing sliding window semantics and the way the query processing is performed from the parallelism perspective. From this study two alternative parallel models are identified, each covering semantics with very precise properties. Each model is described in terms of its pros and cons, and parallel implementations in the FastFlow framework are analyzed by discussing the layout of the concurrent data structures used for the efficient windows representation in each model.

Published
2018
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39. Estimating human exposure to perfluoroalkyl acids via solid food and drinks: Implementation and comparison of different dietary assessment methods

Author

Margaretha Haugen, Luisa Lucattini, Pim E.G. Leonards, Somrutai Poothong, Eleni Papadopoulou, Line Småstuen Haug, Ian T. Cousins, Dorte Herzke, Stig Valdersnes, Jacco Koekkoek, Juan Antonio Padilla-Sánchez, Amund Maage, E&H: Environmental Chemistry and Toxicology, AIMMS, and E&H: Environmental Bioanalytical Chemistry

Subjects
Adult, Dietary assessment, Food diary, Food Contamination, 010501 environmental sciences, 01 natural sciences, Biochemistry, Beverages, Tandem Mass Spectrometry, PFOS, Humans, Food science, 0105 earth and related environmental sciences, General Environmental Science, Fluorocarbons, Human studies, Norway, Chemistry, Dietary exposure, PFOA, 010401 analytical chemistry, Environmental Exposure, Middle Aged, Human exposure, Diet, 0104 chemical sciences, Nutrition Assessment, Food, Solid food, Assessment methods, Environmental Pollutants, Female, Chromatography, Liquid, Environmental Monitoring, Food contaminant
Abstract

Background Diet is a major source of human exposure to hazardous environmental chemicals, including many perfluoroalkyl acids (PFAAs). Several assessment methods of dietary exposure to PFAAs have been used previously, but there is a lack of comparisons between methods. Aim To assess human exposure to PFAAs through diet by different methods and compare the results. Methods We studied the dietary exposure to PFAAs in 61 Norwegian adults (74% women, average age: 42 years) using three methods: i) by measuring daily PFAA intakes through a 1-day duplicate diet study (separately in solid and liquid foods), ii) by estimating intake after combining food contamination with food consumption data, as assessed by 2-day weighted food diaries and iii) by a Food Frequency Questionnaire (FFQ). We used existing food contamination data mainly from samples purchased in Norway and if not available, data from food purchased in other European countries were used. Duplicate diet samples (n=122) were analysed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to quantify 15 PFAAs (11 perfluoroalkyl carboxylates and 4 perfluoroalkyl sulfonates). Differences and correlations between measured and estimated intakes were assessed. Results The most abundant PFAAs in the duplicate diet samples were PFOA, PFOS and PFHxS and the median total intakes were 5.6 ng/day, 11 ng/day and 0.78 ng/day, respectively. PFOS and PFOA concentrations were higher in solid than liquid samples. PFOS was the main contributor to the contamination in the solid samples (median concentration 14 pg/g food), while it was PFOA in the liquid samples (median concentrations: 0.72 pg/g food). High intakes of fats, oils, and eggs were statistically significantly related to high intakes of PFOS and PFOA from solid foods. High intake of milk and consumption of alcoholic beverages, as well as food in paper container were related to high PFOA intakes from liquid foods. PFOA intakes derived from food diary and FFQ were significantly higher than those derived from duplicate diet, but intakes of PFOS derived from food diary and FFQ were significantly lower than those derived from duplicate diet. We found a positive and statistically significant correlation between the PFOS intakes derived from duplicate diet with those using the food diary (rho=0.26, p-value=0.041), but not with the FFQ. Additionally, PFOA intakes derived by duplicate diet were significantly correlated with estimated intakes from liquid food derived from the food diary (rho=0.34, p=0.008) and estimated intakes from the FFQ (rho=0.25, p-value=0.055). Conclusions We provide evidence that a food diary or a FFQ-based method can provide comparable intake estimates to PFOS and PFOA intakes derived from a duplicate diet study. These less burdensome methods are valuable and reliable tools to assess dietary exposure to PFASs in human studies.

Published
2017

40. PS-003: EVIDENCE-INFORMED POLICY MAKING: CHALLENGES AND OPPORTUNITIES

Author

Makanga, Michael, Beattie, Pauline, Breugelmans, Gabrielle, Nyirenda, Thomas, Bockarie, Moses, Tanner, Marcel, Volmink, Jimmy, Hankins, Catherine, Walzl, Gerhard, Chegou, Novel, Malherbe, Stephanus, Hatherill, Mark, Scriba, Thomas J., Zak, Daniel E., Barry, Clifton E., Kaufmann, Stefan H.E., Noor, Abdisalan, Strub-Wourgaft, Nathalie, Phillips, Patrick, Munguambe, Khátia, Ravinetto, Raffaella, Tinto, Halidou, Diro, Ermias, Mahendrahata, Yodi, Okebe, Joseph, Rijal, Suman, Garcia, Coralith, Sundar, Shyam, Ndayisaba, Gilles, Sopheak, Thai, Ngoduc, Thang, Loen, Harry Van, Jacobs, Jan, D'Alessandro, Umberto, Boelaert, Marleen, Buvé, Anne, Kamalo, Patrick, Manda-Taylor, Lucinda, Rennie, Stuart, Mokgatla, Boitumelo, Bahati, Prince, Ijsselmuiden, Carel, Afolabi, Muhammed, Mcgrath, Nuala, Kampmann, Beate, Imoukhuede, Egeruan, Alexander, Neal, Larson, Heidi, Chandramohan, Daniel, Bojang, Kalifa, Kasaro, Margaret Phiri, Muluka, Brenda, Kaunda, Kaunda, Morse, Jill, Westfall, Andrew, Kapata, Nathan, Kruuner, Annika, Henostroza, German, Reid, Stewart, Alabi, Abraham, Foguim, Francis, Sankarganesh, Jeyaraj, Bruske, Ellen, Mfoumbi, Arnault, Mevyann, Chester, Adegnika, Ayola, Lell, Bertrand, Kranzer, Katharina, Kremsner, Peter, Grobusch, Martin, Sabiiti, Wilber, Ntinginya, Nyanda, Kuchaka, Davis, Azam, Khalide, Kampira, Elizabeth, Mtafya, Bariki, Bowness, Ruth, Bhatt, Nilesh, Davies, Gerry, Kibiki, Gibson, Gillespie, Stephen, Lejon, Veerle, Ilboudo, Hamidou, Mumba, Dieudonné, Camara, Mamady, Kaba, Dramane, Lumbala, Crispin, Fèvre, Eric, Jamonneau, Vincent, Bucheton, Bruno, Büscher, Philippe, Chisenga, Caroline, Sinkala, Edford, Chilengi, Roma, Chitundu, Hellen, Zyambo, Zude, Wandeler, Gilles, Vinikoor, Michael, Emilie, Dama, Camara, Oumou, Mathurin, Koffi, Guiguigbaza-Kossigan, Dayo, Philippe, Büscher, Regassa, Fikru, Hassane, Sakande, Bienvenu, Somda Martin, Fabrice, Courtin, Ouédraogo, Elie, Kouakou, Lingue, Owusu, Michael, Mensah, Eric, Enimil, Anthony, Mutocheluh, Mohamed, Ndongo, Francis Ateba, Tejiokem, Mathurin Cyrille, Texier, Gaetan, Penda, Calixte, Ndiang, Suzie, Ndongo, Jean-Audrey, Guemkam, Georgette, Sofeu, Casimir Ledoux, Afumbom, Kfutwa, Faye, Albert, Msellati, Philippe, Warszawski, Josiane, Vos, Alinda, Devillé, Walter, Barth, Roos, Klipstein-Grobusch, Kerstin, Tempelman, Hugo, Venter, François, Coutinho, Roel, Grobbee, Diederick, Ssemwanga, Deogratius, Lyagoba, Frederick, Magambo, Brian, Kapaata, Anne, Kirangwa, Joseph, Nannyonjo, Maria, Nassolo, Faridah, Nsubuga, Rebecca, Yebra, Gonzalo, Brown, Andrew, Kaleebu, Pontiano, Nylén, Hanna, Habtewold, Abiy, Makonnen, Eyasu, Yimer, Getnet, Burhenne, Jürgen, Diczfalusy, Ulf, Aklillu, Eleni, Steele, Duncan, Walker, Richard, Simuyandi, Michelo, Beres, Laura, Bosomprah, Samuel, Ansumana, Rashid, Taitt, C., Lamin, J.M., Jacobsen, K.H., Mulvaney, S.P., Leski, T., Bangura, U., Stenger, D., Vries, Sophie De, Zinsou, Frejus Jeannot, Honkpehedji, J, Dejon, Jean Claude, Loembe, Marguerite Massinga, Bache, Bache, Pakker, Nadine, Leeuwen, Remko Van, Hounkpatin, Aurore Bouyoukou, Yazdanbakhsh, Maria, Bethony, Jeffrey, Hotez, Peter, Diemert, David, Bache, Bache Emmanuel, Fernandes, José F., Mba, Régis M Obiang, Kabwende, Anita L., Grobusch, Martin P., Krishna, Sanjeev, Kremsner, Peter G., Todagbe, Agnandji Selidji, Nambozi, Michael, Kabuya, Jean-Bertin, Hachizovu, Sebastian, Mwakazanga, David, Kasongo, Webster, Buyze, Jozefien, Mulenga, Modest, Geertruyden, Jean-Pierre, Gitaka, Jesse, Chan, Chim, Kongere, James, Kagaya, Wataru, Kaneko, Akira, Kabore, Naomie, Barry, Nouhoun, Kabre, Zachari, Werme, Karidia, Fofana, Aminata, Compaore, Daniel, Nikiema, Frederic, Some, Fabrice, Djimde, Abdoulaye, Zongo, Issaka, Ouedraogo, Bosco, Kone, Aminatou, Sagara, Issaka, Björkman, Anders, Gil, Jose Pedro, Nchinda, Godwin, Bopda, Alain, Nji, Nadesh, Ambada, Georgia, Ngu, Loveline, Tchadji, Jules, Sake, Carol, Magagoum, Suzanne, Njambe, Ghislain D., Lisom, Abel, Park, Chae Gyu, Tait, Dereck, Sibusiso, Hlatjwako, Manda, Olga, Croucher, Kristin, Westhuizen, Anja Van Der, Mshanga, Isaac, Levin, Jonathan, Nanvubya, Annet, Kibengo, Freddie, Jaoko, Walter, Pala, Pietro, Perreau, Matthieu, Namuniina, Annemarie, Kitandwe, Paul, Tapia, Gonzalo, Serwanga, Jennifer, Yates, Nicole, Fast, Pat, Mayer, Bryan, Montefiori, David, Tomaras, Georgia, Robb, Merlin, Lee, Carter, Wagner, Ralf, Sanders, Edward, Kilembe, William, Kiwanuka, Noah, Gilmour, Jill, Kuipers, Hester, Vooij, Dani, Chinyenze, Kundai, Priddy, Frances, Ding, Song, Hanke, Tom, Pantaleo, Giuseppe, Ngasala, Billy, Jovel, Irina, Malmberg, Maja, Mmbando, Bruno, Premji, Zul, Mårtensson, Andreas, Mwaiswelo, Richard, Agbor, Lenshina, Apinjoh, Tobias, Mwanza, Sydney, Chileshe, Justin, Joshi, Sudhaunshu, Malunga, Phidelis, Manyando, Christine, Laufer, Miriam, Dara, Antoine, Niangaly, Amadou, Sinha, Indranil, Brodin, David, Fofana, Bakary, Dama, Souleymane, Dembele, Demba, Sidibe, Bakary, Diallo, Nouhoum, Thera, Mahamadou, Wright, Karin, Gil, Jose, Doumbo, Ogobara, Baraka, Vito, Nabasumba, Carolyn, Francis, Filbert, Lutumba, Pascal, Mavoko, Hypolite, Alifrangis, Michael, Geertruyden, Jean-Pierre Van, Sissoko, Sekou, Sangaré, Cheick, Toure, Sekou, Sanogo, Kassim, Diakite, Hamadoun, Toure, Siaka, Doumbia, Diagassan, Haidara, Kadiatou, Julé, Amélie, Ashurst, Hazel, Merson, Laura, Olliaro, Piero, Marsh, Vicki, Lang, Trudie, Guérin, Philippe, Awuondo, Kennedy, Njenga, Daniel, Nyakarungu, Elizabeth, Titus, Pauline, Sutamihardja, Awalludin, Lowe, Brett, Ogutu, Bernhards, Billingsley, Peter, Soulama, Issiaka, Kaboré, Moïse, Coulibaly, Aboubacar, Ouattara, Maurice, Sanon, Souleymane, Diarra, Amidou, Bougouma, Edith, Ouedraogo, Alphonse, Sombie, Benjamin, Ouedraogo, Amidou, Kargougou, Désiré, Ouattara, Daouda, Issa, Nebie, Tiono, Alfred, Sirima, Sodiomon, Chaponda, Mike, Dabira, Edgard, Dao, François, Dara, Nianwalou, Sidibe, Bouran, Coulibaly, Moctar, Tolo, Allaye, Maiga, Hamma, Ouologuem, Nouhoum, Niangaly, Hamidou, Botchway, Felix, Wilson, Nana, Dickinson-Copeland, Carmen M, Adjei, Andrew A., Wilson, Michael, Stiles, Jonathan K., Hamid, Muzamil Abdel, Awad-Elgeid, Mona, Nasr, Awad, Netongo, Palmer, Kamdem, Séverin, Velavan, Thirumalaisamy, Lasry, Estrella, Diarra, Modibo, Bamadio, Amadou, Traore, Aliou, Coumare, Samba, Soma, Bahonan, Dicko, Yeyia, Sangare, Boubou, Tembely, Aly, Traore, Djibril, Haidara, Aboubecrin, Dicko, Alassane, Diawara, Elisabeth, Beavogui, Abdoul, Camara, Daouda, Sylla, Malick, Yattara, Mohamed, Sow, Amadou, Camara, Gnèpou Camara, Diallo, Saliou, Mombo-Ngoma, Ghyslain, Remppis, Jonathan, Sievers, Moritz, Manego, Rella Zoleko, Endamne, Lilian, Hutchinson, David, Held, Jana, Supan, Christian, Salazar, Carmen L. Ospina, Bonkian, Léa Nadège, Nahum, Alain, Sié, Ali, Abdulla, Salim, Cantalloube, Cathy, Djeriou, Elhadj, Bouyou-Akotet, Marielle, Mordmüller, Benjamin, Siribie, Mohamadou, Sirima, Sodiomon B., Ouattara, San Maurice, Coulibaly, Sam, Kabore, Jean Moïse, Amidou, Diarra, Tekete, Mamadou, Burhenne, Juergen, Traore, Oumar, Haefeli, Walter, Borrmann, Steffen, Kaboré, Naomie, Kabré, Zachari, Nikèma, Fréderic, Compaoré, Daniel, Somé, Fabrice, Djimdé, Abdoulaye, Ouédraogo, Jean, Chalwe, Victor, Miller, John, Diakité, Hamadoun, Greco, Beatrice, Spangenberg, Thomas, Kourany-Lefoll, Elly, Oeuvray, Claude, Mulry, Jim, Tyagarajan, Kamala, Magsaam, Bettina, Barnes, Karen, Hodel, Eva Maria, Humphreys, Georgina, Pace, Cheryl, Banda, C.G, Denti, Paulo, Allen, Elizabeth, Lalloo, David, Mwapasa, Victor, Terlouw, Anja, Mwesigwa, Julia, Achan, Jane, Jawara, Musa, Ditanna, Gian, Worwui, Archibald, Affara, Muna, Koukouikila-Koussounda, Félix, Kombo, Michael, Vouvoungui, Christevy, Ntoumi, Francine, Etoka-Beka, Mandingha Kosso, Deibert, Julia, Poulain, Pierre, Kobawila, Simon, Gueye, Nerly Gampio, Koukouikila-Koussounda, Felix, Seda, Brian, Kwambai, Titus, Jangu, Phelix, Samuels, Aaron, ter Kuile, Feike, Kariuki, Simon, Barry, Aissata, Bousema, Teun, Okech, Brenda, Egwang, Thomas, Corran, Patrick, Riley, Eleanor, Ezennia, Ifeoma, Ekwunife, Obinna, Muleba, Mbanga, Stevenson, Jennifer, Mbata, Keith, Coetzee, Maureen, Norris, Douglas, Moneke-Anyanwoke, Ngozi, Momodou, Jasseh, Clarke, Ed, Scott, Susana, Tijani, Adelani, Djimde, Moussa, Vaillant, Michel, Samouda, Hanen, Mensah, Victorine, Roetynck, Sophie, Kanteh, Ebrima, Bowyer, Georgina, Ndaw, Amy, Oko, Francis, Bliss, Carly, Jagne, Ya Jankey, Cortese, Riccardo, Nicosia, Alfredo, Roberts, Rachel, D'Alessio, Flavia, Leroy, Odile, Faye, Babacar, Cisse, Badara, Gerry, Stephen, Viebig, Nicola, Lawrie, Alison, Ewer, Katie, Hill, Adrian, Nebie, Issa, Tiono, Alfred B, Sanou, Guillaume, Konate, Amadou T, Yaro, Baptiste J, Sodiomon, Sirima, Honkpehedji, Yabo, Agobe, Jean Claude Dejon, Zinsou, Frejus, Mengue, Juliana, Richie, Thomas, Hoffman, Stephen, Nouatin, Odilon, Ngoa, Ulysse Ateba, Edoa, Jean R, Homoet, Andreas, Engelhon, Julie Englhon, Massinga-Louembe, Marguerite, Esen, Meral, Theisen, Michael, Sim, Kim Lee, Luty, Adrian Jf, Moutairou, Kabirou, Dinko, Bismarck, King, Elizabeth, Targett, Geoffrey, Sutherland, Colin, Likhovole, Clement, Ouma, Collins, Vulule, John, Musau, Susan, Khayumbi, Jeremiah, Okumu, Albert, Murithi, Wilfred, Otu, Jacob, Gehre, Florian, Zingue, Dezemon, Kudzawu, Samuel, Forson, Audrey, Mane, Morto, Rabna, Paulo, Diarra, Bassirou, Kayede, Salako, Adebiyi, Emmanuel, Kehinde, Aderemi, Onyejepu, Nneka, Onubogu, Catherine, Idigbe, Emmanuel, Ba, Awa, Diallo, Aissatou, Mboup, Souleymane, Disse, Kodjo, Kadanga, Gerard, Dagnra, Yaotse, Baldeh, Ignatius, Corrah, Tumani, Jong, Bouke De, Antonio, Martin, Musanabaganwa, Clarisse, Musabyimana, Jean Pierre, Karita, Etienne, Diop, Blondin, Nambajimana, Abidan, Dushimiyimana, Valentine, Karame, Prosper, Russell, Jim, Ndoli, Jules, Hategekimana, Theobald, Sendegeya, Augustin, Condo, Jeannine, Binagwaho, Agnes, Okonko, Iheanyi, Okerentugba, Phillip, Opaleye, Oluyinka, Awujo, Ezinwanne, Frank-Peterside, Nnenna, Moyo, Sikhulile, Kotokwe, Kenanao, Mohammed, Terence, Boleo, Coretah, Mupfumi, Lucy, Chishala, Samuel, Gaseitsiwe, Simani, Tsalaile, Lesedi, Bussmann, Herman, Makhema, Joseph, Baum, Marianna, Marlink, Richard, Engelbretch, Susan, Essex, Max, Novitsky, Vladimir, Saka, Emmanuel, Kalipalire, Zex, Bhairavabhotla, Ravikiran, Midiani, Dalitso, Sherman, Judith, Mgode, Georgies, Cox, Christophe, Bwana, Dickens, Mtui, Leah, Magesa, Daniel, Kahwa, Amos, Mfinanga, Godfrey, Mulder, Christiaan, Borain, Nick, Petersen, Lizette, Plessis, Julianne Du, Theron, Grant, Holm-Hansen, Carol, Tekwu, Emmanuel Mouafo, Sidze, Larissa Kamgue, Assam, Jean Paul Assam, Eyangoh, Sarah, Niemann, Stefan, Beng, Veronique Penlap, Frank, Matthias, Atiadeve, Samuel, Hilmann, Doris, Awoniyi, Dolapo, Baumann, Ralf, Kriel, Belinda, Jacobs, Ruschca, Kidd, Martin, Loxton, Andre, Kaempfer, Susanne, Singh, Mahavir, Mwanza, Winnie, Milimo, Deborah, Moyo, Maureen, Kasese, Nkatya, Cheeba-Lengwe, Maina, Munkondya, Stembiso, Ayles, Helen, Haas, Petra De, Muyoyeta, Monde, Namuganga, Anna Ritah, Kizza, Harriet Mayanja, Mendy, Alieu, Tientcheu, Leopold, Ayorinde, Abigail, Coker, Edward, Egere, Uzochukwu, Coussens, Anna, Naude, Celeste, Chaplin, George, Noursadeghi, Mahdad, Martineau, Adrian, Jablonski, Nina, Wilkinson, Robert, Ouedraogo, Henri Gautier, Matteelli, Alberto, Regazzi, Mario, Tarnagda, Grissoum, Villani, Paola, Sulis, Giorgia, Diagbouga, Serge, Roggi, Alberto, Giorgetti, Francesco, Kouanda, Seni, Bidias, Amel, Ndjonka, Dieudonné, Olemba, Clémence, Souleymanou, Arabo, Mukonzo, Jackson, Kuteesa, Ronald, Ogwal-Okeng, Jasper, Gustafsson, Lars L., Owen, Joel, Bassi, Peter, Gashau, Wadzani, Olaf, Klungel, Dodoo, Alexander, Okonkwo, Prosper, Kanki, Phyllis, Maruapula, Dorcas, Seraise, Boitumelo, Einkauf, Kevin, Reilly, Amanda, Rowley, Christopher, Musonda, Rosemary, Framhein, Anna, Mpagama, Stella, Semvua, Hadija, Maboko, Leonard, Hoelscher, Michael, Heinrich, Norbert, Mulenga, Lloyd, Kaayunga, Callistus, Davies, Mary-Ann, Egger, Matthias, Musukuma, Kalo, Dambe, Rosalia, Usadi, Benjamin, Ngari, Moses, Thitiri, Johnstone, Mwalekwa, Laura, Fegan, Greg, Berkley, James, Nsagha, Dickson, Munamunungu, Virginia, Bolton, Carolyn, Siyunda, Alice, Shilimi, Jacinta, Bucciardini, Raffaella, Fragola, Vincenzo, Abegaz, Teshome, Lucattini, Stefano, Halifom, Atakilt, Tadesse, Eskedar, Berhe, Micheal, Pugliese, Katherina, Castro, Paola De, Terlizzi, Roberta, Fucili, Luca, Gregorio, Massimiliano Di, Mirra, Marco, Zegeye, Teame, Binelli, Andrea, Vella, Stefano, Abraham, Loko, Godefay, Hagos, Rakotoarivelo, Rivo, Raberahona, Mihaja, Randriamampionona, Njary, Andriamihaja, Rabezanahary, Rasamoelina, Tahinamandranto, Cornet, Muriel, Randria, Mamy Jean De Dieu, Benet, Thomas, Vanhems, Philippe, Andrianarivelo, Mala Rakoto, Chirwa, Uchizi, Michelo, Charles, Hamoonga, Raymond, Wandiga, Steve, Oduor, Patience, Agaya, Janet, Sharma, Aditya, Cavanaugh, Sean, Cain, Kevin, Mukisa, John, Mupere, Ezekiel, Worodria, William, Ngom, Justice Trésor, Koro, Francioli, Godwe, Celestin, Adande, Clemence, Ateugieu, Romaric, Onana, Tatiana, Ngono, Annie, Kamdem, Yannick, Ngo-Niobe, Sara, Etoa, François-Xavier, Kanengoni, Muchineripi, Ruzario, Sithembile, Ndebele, Paul, Shana, Melody, Tarumbiswa, Fadzai, Musesengwa, Rosemary, Gutsire, Rutendo, Fisher, Kevin, Thyagarajan, Bargavi, Akanbi, Olusola, Binuyo, Michael, Ssengooba, Willy, Respeito, Durval, Mambuque, Edson, Blanco, Silvia, Mandomando, Inacio, Cobelens, Frank, Garcia-Basteiro, Alberto, Tamene, Ayele, Topp, Stephanie, Mwamba, Chanda, Padian, Nancy, Sikazwe, Izukanji, Geng, Elvin, Holmes, Charles, Sikombe, Kombatende, Hantuba, Cardinal, Czaicki, Nancy, Simbeza, Sandra, Somwe, Paul, Umulisa, Michele, Ilo, Jennifer, Kestelyn, Evelyne, Uwineza, Mireille, Agaba, Stephen, Delvaux, Therese, Wijgert, Janneke, Gethi, Dickson, Odeny, Lazarus, Tamandjou, Cynthia, Kaindjee-Tjituka, Francina, Brandt, Laura, Cotton, Mark, Nel, Etienne, Preiser, Wolfgang, Andersson, Monique, Adepoju, Abiola, Magana, Musa, Etsetowaghan, Andrew, Chilikwazi, Mutinta, Sutcliffe, Catherine, Thuma, Philip, Sinywimaanzi, Kathy, Matakala, Hellen, Munachoonga, Passwell, Moss, William, Masenza, Issa Sabi, Geisenberger, Otto, Agrea, Peter, Rwegoshora, France, Mahiga, Hellen, Olomi, Willyhelmina, Kroidl, Arne, Kayode, Gbenga, Amoakoh-Coleman, Mary, Ansah, Evelyn, Uthman, Olalekan, Fokam, Joseph, Santoro, Maria-Mercedes, Musolo, Chrissie, Chimbiri, Isabel, Chikwenga, Gloria, Deula, Ruth, Massari, Riccardo, Lungu, Agness, Perno, Carlo-Federico, Ndzengue, Georgia, Loveline, Ngu, Lissom, Abel, Flaurent, Tchouangueu, Sosso, Samuel, Essomba, Claudine, Kpeli, Grace, Otchere, Isaac, Lamelas, Araceli, Buultjens, Andrew, Bulach, Dieter, Baines, Sarah, Seemann, Torsten, Giulieri, Stefano, Nakobu, Zuliehatu, Aboagye, Samuel, Owusu-Mireku, Evelyn, Danso, Emelia, Hauser, Julia, Hinic, Vladimira, Pluschke, Gerd, Stinear, Timothy, Yeboah-Manu, Dorothy, Elshayeb, Ayman, Siddig, Marmar El, Ahmed, Abdel Azim, Hussien, Adil El, Kabwe, Mwila, Tembo, John, Chilukutu, Lophina, Chilufya, Moses, Ngulube, Francis, Lukwesa, Chileshe, Enne, Virve, Wexner, Hannah, Mwananyanda, Lawrence, Hamer, Davidson, Sinyangwe, Sylvester, Ahmed, Yusuf, Klein, Nigel, Maeurer, Markus, Zumla, Ali, Bates, Matthew, Beyala, Landry, Etienne, Guenou, Anthony, Njimbia, Benjamin, Azike, Ateudjieu, Jerome, Chibwe, Bertha, Ojok, David, Tarr, Christine Attia, Perez, Guillermo Martinez, Omeonga, Senga, Kibungu, Fanta, Meyer, Ana, Lansana, Peter, Mayor, Alfredo, Onyango, Peter, Loggerenberg, François Van, Furtado, Tamzin, Boggs, Liam, Segrt, Alexis, Dochez, Carine, Burnett, Rosemary, Mphahlele, M. Jeffrey, Miiro, George, Mbidde, Edward, Peshu, Norbert, Kivaya, Esther, Ngowi, Bernard, Kavishe, Reginald, Maowia, Mukhtar, Sandstrom, Eric, Ayuo, Elizabeth, Mmbaga, Blandina, Leisegang, Cordelia, Thorpe, Marie, Batchilly, Elizabeth, N'Guessan, Jean-Pierre, Kanteh, Dembo, Søfteland, Solrun, Sebitloane, Motshedisi, Vwalika, Bellington, Taylor, Myra, Galappaththi-Arachchige, Hashini, Holmen, Sigve, Gundersen, Svein Gunnar, Ndhlovu, Patricia, Kjetland, Eyrun Floerecke, Kombe, Francis, Toohey, Jacintha, Pienaar, Elizabeth, Kredo, Tamara, Cham, Pa Modou, Abubakar, Ismaela, Dondeh, Bai Lamin, Vischer, Nerina, Pfeiffer, Constanze, Burri, Christian, Musukwa, Kalo, Zürcher, Samuel, Mwandu, Temwani, Bauer, Sophie, Adriko, Moses, Mwaura, Peter, Omolloh, Kevin, Jones, Clarer, Malecela, Mwelecele, Hamidu, Buhari Adamu, Jenner, Tettevi Edward, Asiedu, Larbi John, Osei-Atweneboana, Mike, Afeke, Innocent, Addo, Phyllis, Newman, Mercy, Durnez, Lies, Eddyani, Miriam, Ammisah, Nana, Abas, Mona, Quartey, Maxwell, Ablordey, Anthony, Akinwale, Olaoluwa, Adeneye, Adeniyi, Ezeugwu, Sylvanus, Olukosi, Yetunde, Adewale, Babatunde, Sulyman, Medinat, Mafe, Margaret, Okwuzu, Jane, Gyang, Pam, Nwafor, Timothy, Henry, Uzoma, Musa, Bilkisu, Ujah, Innocent, Agobé, Jean Claude Dejon, Grau-Pujol, Berta, Sacoor, Charfudin, Nhabomba, Augusto, Casellas, Aina, Quintó, Llorenç, Subirà, Carme, Giné, Ricard, Valentín, Antònia, Muñoz, Jose, Nikiema, Marguerite, Ky-Ba, Absatou, Comapore, Kiswendsida Abdou Muller, Traore, Alfred, Sangare, Lassana, Oluremi, Adeolu, Michel, Mandro, Camara, Yaya, Sanneh, Bakary, Cuamba, Inocencia, Gutiérrez, Jose, Lázaro, Carlota, Mejia, Rojelio, Adedeji, Abimbola, Folorunsho, Sola, Demehin, Pelumi, Akinsanya, Bamidele, Cowley, Giovanna, Silva, Eunice Teixeira Da, Nabicassa, Meno, Barros, Pedrozinho Duarte Pereira De, Blif, Milena Mbote, Bailey, Robin, Last, Anna, Mahendradhata, Yodi, Gotuzzo, Eduardo, Nys, Kateljine De, Casteels, Minnes, Nona, Sylvie Kwedi, Lumeka, Kabwende, Todagbe, Agnandji, Djima, Mariam Mama, Ukpong, Morenike, Sagay, Atiene, Khamofu, Hadiza, Torpey, Kwasi, Afiadigwe, Evaristus, Anenih, James, Ezechi, Oliver, Nweneka, Chidi, Idoko, John, Muhumuza, Simon, Katahoire, Anne, Nuwaha, Fred, Olsen, Annette, Okeyo, Seth, Omollo, Raymond, Kimutai, Robert, Ochieng, Michael, Egondi, Thaddaeus, Moonga, Clement, Chileshe, Chisele, Magwende, George, Anumudu, Chiaka, Onile, Olugbenga, Oladele, Victoria, Adebayo, Adewale, Awobode, Henrietta, Oyeyemi, Oyetunde, Odaibo, Alexander, Kabuye, Emily, Lutalo, Tom, Njua-Yafi, Clarisse, Nkuo-Akenji, Theresa, Anchang-Kimbi, Judith, Mugri, Regina, Chi, Hanesh, Tata, Rolland, Njumkeng, Charles, Dodoo, Daniel, Achidi, Eric, Fernandes, José, Bache, Emmanuel B., Matakala, Kalumbu, Searle, Kelly, Greenman, Michelle, and Rainwater-Lovett, Kaitlin

Subjects
Abstracts of Poster Presentations, Abstracts of Oral Presentations, Author Index, Abstracts of Presentations in Plenary Sessions, Article, Abstracts of the Eighth Edctp Forum, 6–9 November 2016
Published
2017

43. Social Inclusion for Children with Disabilities: The Role of ICT in Play and Entertainment Activities

Author

Alessio Martinelli, Grazia Lombardi, Paolo Lucattini, Sara Jayousi, and Lorenzo Mucchi

Subjects
030506 rehabilitation, business.industry, Computer science, 05 social sciences, ComputingMilieux_PERSONALCOMPUTING, Context (language use), Public relations, Entertainment, 03 medical and health sciences, Politics, Game design, Information and Communications Technology, 0501 psychology and cognitive sciences, 0305 other medical science, business, 050107 human factors, Healthcare system
Abstract

Family associations, educational and university institutions, political and health systems, companies and local agencies, and third sector organizations are involved in and committed to consolidate the historical and cultural path of children’s right to play, including children with disabilities. The objective of this paper is to explore the potential role of Information and Communication Technologies (ICT) and in particular of the digital games to create opportunities for social inclusion through playful and entertainment activities for children with disabilities. Starting from the analysis on the role of “play” in the life of children, the main goals and requirements of entertainment are presented with the aim to highlight how the adoption of digital technological solutions can enable social inclusion for disabled children. Guidelines for digital game design are presented together with advanced digital solutions for engaging children with disabilities and increasing their participation and communication capabilities. Robotics, interactive platforms and devices and artificial intelligence algorithms are considered in this analysis. Finally, ICT challenges, innovative approaches and future applications in the context of social inclusion are reported.

Published
2019

44. Mass spectrometric identification of in vitro-generated metabolites of two emerging organophosphate flame retardants: V6 and BDP

Author

Matthias Cuykx, Ana Ballesteros-Gómez, Luisa Lucattini, Adrian Covaci, Andreia Alves, Pim E.G. Leonards, Stefan Voorspoels, Claudio Erratico, AIMMS, E&H: Environmental Bioanalytical Chemistry, Faculty of Medicine and Pharmacy, Pharmaceutical and Pharmacological Sciences, Experimental in vitro toxicology and dermato-cosmetology, and Biology

Subjects
0301 basic medicine, BDP, Chemistry(all), Metabolite, Health, Toxicology and Mutagenesis, Environmental engineering, 010501 environmental sciences, Secondary metabolite, 01 natural sciences, Mass Spectrometry, 03 medical and health sciences, chemistry.chemical_compound, Sulfation, Cytochrome P-450 Enzyme System, medicine, Humans, Environmental Chemistry, In vitro metabolism, Human liver fractions, Biology, 0105 earth and related environmental sciences, Flame Retardants, chemistry.chemical_classification, biology, Aryldialkylphosphatase, Public Health, Environmental and Occupational Health, Cytochrome P450, General Medicine, General Chemistry, Metabolism, respiratory system, V6, Pollution, Organophosphates, 3. Good health, Chemistry, 030104 developmental biology, Enzyme, chemistry, Biochemistry, Recombinant CYPs, Microsome, biology.protein, Microsomes, Liver, LC-QTOF-MS, Drug metabolism, medicine.drug, Environmental Monitoring
Abstract

The aim of the present study was to investigate the in vitro metabolism of two emerging organophosphate flame retardants, namely tetrekis(2-chlorethyl)dichloroisopentyldiphosphate (V6) and bisphenol-A bis-diphenyl phosphate (BDP) in human liver microsomes (HLMs), HLM S9 fractions and in human serum. In particular, the role of cytochrome P450 (CYPs) enzymes and/or paraoxonases (PONs) in the formation of V6 and BDP phase I metabolites was studied. Mono-, di-hydroxylated and hydrolytic phase I metabolites of V6 were mainly formed by CYPs in HLMs, while hydrolytic and O-dealkylated phase I metabolites of BDP were generated by PONs mainly in serum experiments. Limited number of glucuronidated and sulfated phase II metabolites were also identified for the two chemicals. The activity of seven recombinant CYPs (rCYPs) including rCYP1A2, rCYP2B6, rCYP2C9, rCYP2C19, rCYP2D6, rCYP2E1 and rCYP3A4 in the in vitro phase I metabolism of V6 and BDP was investigated. The formation of V6 metabolites was catalyzed by several enzymes, especially rCYP1A2 that was responsible for the exclusive formation of two metabolites, one primary (M1) and its secondary metabolite (M9). For BDP, only one phase I metabolite (MM1) was catalyzed by the seven rCYPs. Collectively, these results indicate that CYPs have a predominant role in the metabolism of V6, while PONs have a predominant role in BDP in vitro metabolism. These results are a starting point for future studies involving the study of the toxicity, bioaccumulation and in vivo biomonitoring of V6 and BDP.

Published
2018

46. Using long-read sequencing to detect imprinted DNA methylation

Author

Gigante, S, Gouil, Q, Lucattini, A, Keniry, A, Beck, T, Tinning, M, Gordon, L, Woodruff, C, Speed, TP, Blewitt, ME, Ritchie, ME, Gigante, S, Gouil, Q, Lucattini, A, Keniry, A, Beck, T, Tinning, M, Gordon, L, Woodruff, C, Speed, TP, Blewitt, ME, and Ritchie, ME

Abstract

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of ∼10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs.

Published
2019

48. Using long-read sequencing to detect imprinted DNA methylation

Author

Lavinia Gordon, Alexis Lucattini, Quentin Gouil, Chris Woodruff, Marnie E. Blewitt, Scott Gigante, Matthew Tinning, Andrew Keniry, Matthew E. Ritchie, Terence P. Speed, and Tamara Beck

Subjects
Male, Genotyping Techniques, Placenta, 0206 medical engineering, Genomics, 02 engineering and technology, Computational biology, Biology, 03 medical and health sciences, symbols.namesake, Genomic Imprinting, Mice, 0302 clinical medicine, Pregnancy, Genetics, Animals, Alleles, 030304 developmental biology, Sanger sequencing, 0303 health sciences, Genome, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Methylation, Sequence Analysis, DNA, DNA Methylation, Embryo, Mammalian, Differentially methylated regions, CpG site, Haplotypes, Reduced representation bisulfite sequencing, DNA methylation, symbols, Methods Online, CpG Islands, Female, Nanopore sequencing, Genomic imprinting, 030217 neurology & neurosurgery, 020602 bioinformatics
Abstract

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of approximately ten, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterise, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data.Our analysis successfully identifies known imprinting control regions as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new imprinting control regions.

Published
2018
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49. A review of semi-volatile organic compounds (SVOCs) in the indoor environment occurrence in consumer products, indoor air and dust

Author

Jacob de Boer, Luisa Lucattini, Adrian Covaci, Pim E.G. Leonards, Marja H. Lamoree, and Giulia Poma

Subjects
Environmental Engineering, 010504 meteorology & atmospheric sciences, Indoor air, Health, Toxicology and Mutagenesis, 010501 environmental sciences, 01 natural sciences, Indoor air quality, Air Pollution, Floors and Floorcoverings, Humans, Environmental Chemistry, SVOCs, Biology, 0105 earth and related environmental sciences, Volatile Organic Compounds, Schools, Waste management, Construction Materials, Public Health, Environmental and Occupational Health, Dust, General Medicine, General Chemistry, Pesticide, Contamination, Pollution, Chemistry, Indoor dust, Consumer Product Safety, 13. Climate action, Human exposure, Air Pollution, Indoor, Environmental science, SDG 4 - Quality Education, Consumer products
Abstract

As many people spend a large part of their life indoors, the quality of the indoor environment is important. Data on contaminants such as flame retardants, pesticides and plasticizers are available for indoor air and dust but are scarce for consumer products such as computers, televisions, furniture, carpets, etc. This review presents information on semi-volatile organic compounds (SVOCs) in consumer products in an attempt to link the information available for chemicals in indoor air and dust with their indoor sources. A number of 256 papers were selected and divided among SVOCs found in consumer products (n = 57), indoor dust (n =104) and air (n = 95). Concentrations of SVOCs in consumer products, indoor dust and air are reported (e.g. PFASs max: 13.9 lig/g in textiles, 5.8 ggikg in building materials, 121 ng/g in house dust and 6.4 ng/m(3) in indoor air). Most of the studies show common aims, such as human exposure and risk assessment. The main micro-environments investigated (houses, offices and schools) reflect the relevance of indoor air quality. Most of the studies show a lack of data on concentrations of chemicals in consumer goods and often only the presence of chemicals is reported. At the moment this is the largest obstacle linking chemicals in products to chemicals detected in indoor air and dust. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.

Published
2018

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