11 results on '"Oliver, Thomas"'
Search Results
2. Clonal diversification and histogenesis of malignant germ cell tumours
- Author
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Oliver, Thomas R. W., Chappell, Lia, Sanghvi, Rashesh, Deighton, Lauren, Ansari-Pour, Naser, Dentro, Stefan C., Young, Matthew D., Coorens, Tim H. H., Jung, Hyunchul, Butler, Tim, Neville, Matthew D. C., Leongamornlert, Daniel, Sanders, Mathijs A., Hooks, Yvette, Cagan, Alex, Mitchell, Thomas J., Cortes-Ciriano, Isidro, Warren, Anne Y., Wedge, David C., Heer, Rakesh, Coleman, Nicholas, Murray, Matthew J., Campbell, Peter J., Rahbari, Raheleh, and Behjati, Sam
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- 2022
- Full Text
- View/download PDF
3. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours
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Custers, Lars, Khabirova, Eleonora, Coorens, Tim H. H., Oliver, Thomas R. W., Calandrini, Camilla, Young, Matthew D., Vieira Braga, Felipe A., Ellis, Peter, Mamanova, Lira, Segers, Heidi, Maat, Arie, Kool, Marcel, Hoving, Eelco W., van den Heuvel-Eibrink, Marry M., Nicholson, James, Straathof, Karin, Hook, Liz, de Krijger, Ronald R., Trayers, Claire, Allinson, Kieren, Behjati, Sam, and Drost, Jarno
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- 2021
- Full Text
- View/download PDF
4. Single cell derived mRNA signals across human kidney tumors
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Young, Matthew D., Mitchell, Thomas J., Custers, Lars, Margaritis, Thanasis, Morales-Rodriguez, Francisco, Kwakwa, Kwasi, Khabirova, Eleonora, Kildisiute, Gerda, Oliver, Thomas R. W., de Krijger, Ronald R., van den Heuvel-Eibrink, Marry M., Comitani, Federico, Piapi, Alice, Bugallo-Blanco, Eva, Thevanesan, Christine, Burke, Christina, Prigmore, Elena, Ambridge, Kirsty, Roberts, Kenny, Braga, Felipe A. Vieira, Coorens, Tim H. H., Del Valle, Ignacio, Wilbrey-Clark, Anna, Mamanova, Lira, Stewart, Grant D., Gnanapragasam, Vincent J., Rampling, Dyanne, Sebire, Neil, Coleman, Nicholas, Hook, Liz, Warren, Anne, Haniffa, Muzlifah, Kool, Marcel, Pfister, Stefan M., Achermann, John C., He, Xiaoling, Barker, Roger A., Shlien, Adam, Bayraktar, Omer A., Teichmann, Sarah A., Holstege, Frank C., Meyer, Kerstin B., Drost, Jarno, Straathof, Karin, and Behjati, Sam
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- 2021
- Full Text
- View/download PDF
5. Observation of pendular butterfly Rydberg molecules
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Thomas Niederprüm, Oliver Thomas, Tanita Eichert, Carsten Lippe, Jesús Pérez-Ríos, Chris H. Greene, and Herwig Ott
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Science - Abstract
Rydberg molecules have potential for ultracold chemistry applications in light of their unconventional binding mechanism that provides high tunability. Here the authors observe and control butterfly Rydberg molecules, which are bound by a shape resonance in the electron-perturber scattering.
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- 2016
- Full Text
- View/download PDF
6. Experimental realization of a Rydberg optical Feshbach resonance in a quantum many-body system
- Author
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Herwig Ott, Carsten Lippe, Oliver Thomas, and Tanita Eichert
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Bose gas ,Science ,General Physics and Astronomy ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,010305 fluids & plasmas ,Physics - Atomic Physics ,symbols.namesake ,0103 physical sciences ,Physics::Atomic Physics ,lcsh:Science ,010306 general physics ,Feshbach resonance ,Quantum ,Physics ,Condensed Matter::Quantum Gases ,Optical lattice ,Quantum Physics ,Multidisciplinary ,Condensed Matter::Other ,Degenerate energy levels ,General Chemistry ,Rydberg formula ,symbols ,lcsh:Q ,Atomic physics ,Rydberg state ,Condensed Matter - Quantum Gases ,Realization (systems) - Abstract
Feshbach resonances are a powerful tool to tune the interaction in an ultracold atomic gas. The commonly used magnetic Feshbach resonances are specific for each species and are restricted with respect to their temporal and spatial modulation. Optical Feshbach resonances are an alternative which can overcome this limitation. Here, we show that ultra-long-range Rydberg molecules can be used to implement an optical Feshbach resonance. Tuning the on-site interaction of a degenerate Bose gas in a 3D optical lattice, we demonstrate a similar performance compared to recent realizations of optical Feshbach resonances using intercombination transitions. Our results open up a class of optical Feshbach resonances with a plenitude of available lines for many atomic species and the possibility to further increase the performance by carefully selecting the underlying Rydberg state., Ultracold Rydberg molecules have characteristic properties that can be exploited for quantum control and applications. Here the authors demonstrate a Rydberg optical Feshbach resonance, which is based on ultra-long-range Rydberg molecules.
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- 2018
7. Clonal diversification and histogenesis of malignant germ cell tumours
- Author
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Thomas R. W. Oliver, Lia Chappell, Rashesh Sanghvi, Lauren Deighton, Naser Ansari-Pour, Stefan C. Dentro, Matthew D. Young, Tim H. H. Coorens, Hyunchul Jung, Tim Butler, Matthew D. C. Neville, Daniel Leongamornlert, Mathijs A. Sanders, Yvette Hooks, Alex Cagan, Thomas J. Mitchell, Isidro Cortes-Ciriano, Anne Y. Warren, David C. Wedge, Rakesh Heer, Nicholas Coleman, Matthew J. Murray, Peter J. Campbell, Raheleh Rahbari, Sam Behjati, Hematology, Oliver, Thomas RW [0000-0003-4306-0102], Chappell, Lia [0000-0002-2317-3524], Sanghvi, Rashesh [0000-0002-7703-9216], Ansari-Pour, Naser [0000-0003-0908-0484], Young, Matthew D [0000-0003-0937-5290], Coorens, Tim HH [0000-0002-5826-3554], Butler, Tim [0000-0001-5803-1035], Neville, Matthew DC [0000-0001-5816-7936], Leongamornlert, Daniel [0000-0002-3486-3168], Cagan, Alex [0000-0002-7857-4771], Mitchell, Thomas J [0000-0003-0761-9503], Cortes-Ciriano, Isidro [0000-0002-2036-494X], Wedge, David C [0000-0002-7572-3196], Murray, Matthew J [0000-0002-4480-1147], Campbell, Peter J [0000-0002-3921-0510], Rahbari, Raheleh [0000-0002-1839-7785], Behjati, Sam [0000-0002-6600-7665], Apollo - University of Cambridge Repository, Oliver, Thomas R. W. [0000-0003-4306-0102], Young, Matthew D. [0000-0003-0937-5290], Coorens, Tim H. H. [0000-0002-5826-3554], Neville, Matthew D. C. [0000-0001-5816-7936], Mitchell, Thomas J. [0000-0003-0761-9503], Wedge, David C. [0000-0002-7572-3196], Murray, Matthew J. [0000-0002-4480-1147], and Campbell, Peter J. [0000-0002-3921-0510]
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631/114/739 ,45/91 ,Male ,45/70 ,Multidisciplinary ,631/1647/514 ,article ,General Physics and Astronomy ,45/23 ,631/67/69 ,Genomics ,General Chemistry ,Neoplasms, Germ Cell and Embryonal ,631/67/1679 ,631/67/2329 ,General Biochemistry, Genetics and Molecular Biology ,Testicular Neoplasms ,13/51 ,14/63 ,Humans ,Child ,Transcriptome - Abstract
Funder: Max Williamson Fund, Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.
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- 2022
8. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours
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Heidi Segers, James Nicholson, Marry M. van den Heuvel-Eibrink, Liz Hook, Thomas R. W. Oliver, Arie Maat, Matthew D. Young, Lira Mamanova, Tim H. H. Coorens, Karin Straathof, Claire Trayers, Felipe A. Vieira Braga, Eleonora Khabirova, Lars Custers, Marcel Kool, Sam Behjati, Ronald R. de Krijger, Eelco W. Hoving, Camilla Calandrini, Kieren Allinson, Jarno Drost, Peter R. Ellis, Custers, Lars [0000-0003-0252-7714], Khabirova, Eleonora [0000-0002-5891-6789], Coorens, Tim H. H. [0000-0002-5826-3554], Oliver, Thomas R. W. [0000-0003-4306-0102], Vieira Braga, Felipe A. [0000-0003-0206-9258], Mamanova, Lira [0000-0003-1463-8622], Segers, Heidi [0000-0002-3604-7850], Hoving, Eelco W. [0000-0002-5587-0439], van den Heuvel-Eibrink, Marry M. [0000-0002-7760-879X], Straathof, Karin [0000-0001-9673-8568], Trayers, Claire [0000-0003-0236-6041], Behjati, Sam [0000-0002-6600-7665], Drost, Jarno [0000-0002-2941-6179], Apollo - University of Cambridge Repository, Coorens, Tim HH [0000-0002-5826-3554], Oliver, Thomas RW [0000-0003-4306-0102], Vieira Braga, Felipe A [0000-0003-0206-9258], Hoving, Eelco W [0000-0002-5587-0439], van den Heuvel-Eibrink, Marry M [0000-0002-7760-879X], Center of Experimental and Molecular Medicine, and AGEM - Amsterdam Gastroenterology Endocrinology Metabolism
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0301 basic medicine ,Somatic cell ,General Physics and Astronomy ,13 ,medicine.disease_cause ,Genomic analysis ,Tissue Culture Techniques ,631/1647/767/70 ,0302 clinical medicine ,631/1647/2217 ,38/23 ,Phylogeny ,Mutation ,Multidisciplinary ,TOR Serine-Threonine Kinases ,article ,Cell Differentiation ,SMARCB1 Protein ,3. Good health ,Gene Expression Regulation, Neoplastic ,Malignant rhabdoid tumour ,medicine.anatomical_structure ,Neural Crest ,030220 oncology & carcinogenesis ,embryonic structures ,DNA methylation ,38/39 ,Single-Cell Analysis ,animal structures ,Science ,Mesenchyme ,631/337/2019 ,13/106 ,631/67/1678 ,Biology ,General Biochemistry, Genetics and Molecular Biology ,38/91 ,03 medical and health sciences ,Embryonal neoplasms ,medicine ,Humans ,Cancer models ,Transcriptomics ,Rhabdoid Tumor ,PI3K/AKT/mTOR pathway ,45 ,Gene Expression Profiling ,General Chemistry ,DNA Methylation ,medicine.disease ,Embryonic stem cell ,Histone Deacetylase Inhibitors ,Gene expression profiling ,030104 developmental biology ,Cancer research ,Drug Screening Assays, Antitumor - Abstract
Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies., Malignant rhabdoid tumours (MRT) have been suggested to originate in the ectoderm-derived neural crest. Here, the authors analyse MRTs using phylogenetics, scRNA-seq, and patient-derived organoids; they find evidence for an MRT origin in the neural crest lineage and suggest differentiation treatment with HDAC/mTOR inhibitors.
- Published
- 2021
9. Single cell derived mRNA signals across human kidney tumors
- Author
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Eleonora Khabirova, Vincent J. Gnanapragasam, Tim H. H. Coorens, Adam Shlien, Nicholas Coleman, Omer Ali Bayraktar, Gerda Kildisiute, Muzlifah Haniffa, Federico Comitani, Roger A. Barker, Neil J. Sebire, Christine Thevanesan, Christina Burke, Kerstin B. Meyer, Stefan M. Pfister, Lars Custers, Dyanne Rampling, Karin Straathof, Elena Prigmore, Sarah A. Teichmann, Eva Bugallo-Blanco, Sam Behjati, Anne Y. Warren, Marry M. van den Heuvel-Eibrink, Thomas Rw Oliver, Ronald R. de Krijger, Ignacio del Valle, John Achermann, Anna Wilbrey-Clark, Kenny Roberts, Xiaoling He, Marcel Kool, Alice Piapi, Thanasis Margaritis, Jarno Drost, Felipe A. Vieira Braga, Kwasi Kwakwa, Kirsty Ambridge, Frank C. P. Holstege, Francisco Morales, Matthew D. Young, Thomas J. Mitchell, Grant D. Stewart, Liz Hook, Lira Mamanova, Young, Matthew D [0000-0003-0937-5290], Mitchell, Thomas J [0000-0003-0761-9503], Custers, Lars [0000-0003-0252-7714], Khabirova, Eleonora [0000-0002-5891-6789], Kildisiute, Gerda [0000-0002-5314-2294], Oliver, Thomas RW [0000-0003-4306-0102], van den Heuvel-Eibrink, Marry M [0000-0002-7760-879X], Comitani, Federico [0000-0003-3226-1179], Piapi, Alice [0000-0001-8251-3309], Burke, Christina [0000-0001-5381-3185], Roberts, Kenny [0000-0001-6155-0821], Coorens, Tim HH [0000-0002-5826-3554], Mamanova, Lira [0000-0003-1463-8622], Stewart, Grant D [0000-0003-3188-9140], Warren, Anne [0000-0002-1170-7867], Haniffa, Muzlifah [0000-0002-3927-2084], Achermann, John C [0000-0001-8787-6272], Bayraktar, Omer A [0000-0001-6055-277X], Teichmann, Sarah A [0000-0002-6294-6366], Holstege, Frank C [0000-0002-8090-5146], Meyer, Kerstin B [0000-0001-5906-1498], Drost, Jarno [0000-0002-2941-6179], Straathof, Karin [0000-0001-9673-8568], Behjati, Sam [0000-0002-6600-7665], Apollo - University of Cambridge Repository, Oliver, Thomas R W [0000-0003-4306-0102], Coorens, Tim H H [0000-0002-5826-3554], and Sebire, Neil [0000-0001-5348-9063]
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0301 basic medicine ,Cell of origin ,Cell ,General Physics and Astronomy ,Kidney ,Transcriptome ,0302 clinical medicine ,Gene expression ,Cancer genomics ,RNA-Seq ,Child ,Regulation of gene expression ,0303 health sciences ,Multidisciplinary ,Gene Expression Regulation, Developmental ,Kidney Neoplasms ,3. Good health ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Single-Cell Analysis ,Algorithms ,Signal Transduction ,Adult ,Science ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Fetus ,medicine ,Humans ,RNA, Messenger ,Transcriptomics ,030304 developmental biology ,Messenger RNA ,Models, Genetic ,Mesenchymal stem cell ,RNA ,Kidney metabolism ,Cancer ,General Chemistry ,medicine.disease ,Clear cell renal cell carcinoma ,030104 developmental biology ,Cancer research ,030217 neurology & neurosurgery - Abstract
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference “cellular signals” in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of “fetalness” with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer., Transcriptomic analysis may provide information about the differentiation state and cell of origin of a cancer. Here, the authors assess mRNA signals in 1300 childhood and adult renal tumors and report a fetal origin of childhood tumors and no dedifferentiation of adult tumors.
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- 2020
10. Continuous injection synthesis of indium arsenide quantum dots emissive in the short-wavelength infrared
- Author
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Ou Chen, Daniel Franke, Moungi G. Bawendi, Oliver T. Bruns, Jessica A. Carr, Mark W. Wilson, Daniel K. Harris, Massachusetts Institute of Technology. Department of Chemistry, Franke, Daniel, Bruns, Oliver Thomas, Carr, Jessica Ann, Bawendi, Moungi G, Harris, Daniel Kelly, Wilson, Mark William Brennan, and Chen, Ou
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Materials science ,Infrared ,Orders of magnitude (temperature) ,Infrared Rays ,Science ,Physics::Optics ,General Physics and Astronomy ,chemistry.chemical_element ,Metal Nanoparticles ,Nanotechnology ,Astrophysics::Cosmology and Extragalactic Astrophysics ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Indium ,General Biochemistry, Genetics and Molecular Biology ,Article ,Arsenicals ,Nanomaterials ,chemistry.chemical_compound ,Condensed Matter::Materials Science ,Mice ,Quantum Dots ,Animals ,Quantum ,Astrophysics::Galaxy Astrophysics ,Multidisciplinary ,business.industry ,Optical Imaging ,Brain ,General Chemistry ,Condensed Matter::Mesoscopic Systems and Quantum Hall Effect ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,3. Good health ,chemistry ,Nanocrystal ,Quantum dot ,Optoelectronics ,Indium arsenide ,0210 nano-technology ,business - Abstract
With the emergence of applications based on short-wavelength infrared light, indium arsenide quantum dots are promising candidates to address existing shortcomings of other infrared-emissive nanomaterials. However, III–V quantum dots have historically struggled to match the high-quality optical properties of II–VI quantum dots. Here we present an extensive investigation of the kinetics that govern indium arsenide nanocrystal growth. Based on these insights, we design a synthesis of large indium arsenide quantum dots with narrow emission linewidths. We further synthesize indium arsenide-based core-shell-shell nanocrystals with quantum yields up to 82% and improved photo- and long-term storage stability. We then demonstrate non-invasive through-skull fluorescence imaging of the brain vasculature of murine models, and show that our probes exhibit 2–3 orders of magnitude higher quantum yields than commonly employed infrared emitters across the entire infrared camera sensitivity range. We anticipate that these probes will not only enable new biomedical imaging applications, but also improved infrared nanocrystal-LEDs and photon-upconversion technology., National Science Foundation (U.S.) (EECS-1449291), National Institutes of Health (U.S.) (Massachusetts Institute of Technology. Laser Biomedical Research Center. 9-P41-EB015871-26A1), Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (W911NF-13-D-0001), Boehringer Ingelheim Fonds, European Molecular Biology Organization (Long-term Fellowship), National Science Foundation (U.S.). Graduate Research Fellowship Program, American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship, United States. Dept. of Energy. Center for Excitonics (DE- SC0001088).
- Published
- 2016
11. Magneto-fluorescent core-shell supernanoparticles
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Dai Fukumura, Christian T. Farrar, Oliver T. Bruns, Jing Zhao, Mathieu Coppey, Rakesh K. Jain, He Wei, Fred Etoc, Maxime Dahan, Moungi G. Bawendi, Lars Riedemann, Peng Guo, Daniel K. Harris, Russ Jensen, Mariya Barch, Yue Chen, Jose M. Cordero, Rudolph Reimer, Hendrik Herrmann, Ou Chen, Zhongwu Wang, Jian Cui, Alan Jasanoff, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Chen, Ou, Barch, Mariya, Zhao, Jing, Bruns, Oliver Thomas, Wei, He, Cui, Jian, Jensen, Russ, Chen, Yue, Harris, Daniel K., Cordero Hernandez, Jose M., Jasanoff, Alan Pradip, and Bawendi, Moungi G.
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Materials science ,Fluorophore ,Silicon dioxide ,Shell (structure) ,General Physics and Astronomy ,Nanoparticle ,Nanotechnology ,7. Clean energy ,General Biochemistry, Genetics and Molecular Biology ,Fluorescence ,Article ,Nanomaterials ,chemistry.chemical_compound ,Quantum Dots ,Magnetite Nanoparticles ,Fluorescent Dyes ,Multidisciplinary ,General Chemistry ,equipment and supplies ,Silicon Dioxide ,Magnetic Resonance Imaging ,3. Good health ,chemistry ,Quantum dot ,Magnetic nanoparticles - Abstract
Magneto-fluorescent particles have been recognized as an emerging class of materials that exhibit great potential in advanced applications. However, synthesizing such magneto-fluorescent nanomaterials that simultaneously exhibit uniform and tunable sizes, high magnetic content loading, maximized fluorophore coverage at the surface and a versatile surface functionality has proven challenging. Here we report a simple approach for co-assembling magnetic nanoparticles with fluorescent quantum dots to form colloidal magneto-fluorescent supernanoparticles. Importantly, these supernanoparticles exhibit a superstructure consisting of a close-packed magnetic nanoparticle ‘core’, which is fully surrounded by a ‘shell’ of fluorescent quantum dots. A thin layer of silica coating provides high colloidal stability and biocompatibility, and a versatile surface functionality. We demonstrate that after surface pegylation, these silica-coated magneto-fluorescent supernanoparticles can be magnetically manipulated inside living cells while being optically tracked. Moreover, our silica-coated magneto-fluorescent supernanoparticles can also serve as an in vivo multi-photon and magnetic resonance dual-modal imaging probe., National Institutes of Health (U.S.) (5-U54-CA151884), National Institutes of Health (U.S.) (R01-CA126642), Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (W911NF-13-D-0001)), United States. Dept. of Energy (DE-FG02-07ER46454), National Institutes of Health (U.S.) (Massachusetts Institute of Technology. Laser Biomedical Research Center 9-P41-EB015871-26A1), United States. Dept. of Energy. Office of Basic Energy Sciences (Award DE-SC0001088), United States. Dept. of Defense (Breast Cancer Research Innovator Award W81XWH-10-1-0016)), Human Frontier Science Program (Strasbourg, France) (Grant RGP0005/2007), National Institutes of Health (U.S.) (R01-DA028299), National Institutes of Health (U.S.) (R01-NS076462), European Molecular Biology Organization (Long-term Fellowship)
- Published
- 2014
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