| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Barretina, Jordi, et al.
(författare)
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Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy.
- 2010
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:8, s. 715-21
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Tidskriftsartikel (refereegranskat)abstract
- Soft-tissue sarcomas, which result in approximately 10,700 diagnoses and 3,800 deaths per year in the United States, show remarkable histologic diversity, with more than 50 recognized subtypes. However, knowledge of their genomic alterations is limited. We describe an integrative analysis of DNA sequence, copy number and mRNA expression in 207 samples encompassing seven major subtypes. Frequently mutated genes included TP53 (17% of pleomorphic liposarcomas), NF1 (10.5% of myxofibrosarcomas and 8% of pleomorphic liposarcomas) and PIK3CA (18% of myxoid/round-cell liposarcomas, or MRCs). PIK3CA mutations in MRCs were associated with Akt activation and poor clinical outcomes. In myxofibrosarcomas and pleomorphic liposarcomas, we found both point mutations and genomic deletions affecting the tumor suppressor NF1. Finally, we found that short hairpin RNA (shRNA)-based knockdown of several genes amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields a detailed map of molecular alterations across diverse sarcoma subtypes and suggests potential subtype-specific targets for therapy.
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| 3. |
- Cvijovic, Marija, 1977, et al.
(författare)
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Bridging the gaps in systems biology
- 2014
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Ingår i: Molecular Genetics and Genomics. - : Springer Science and Business Media LLC. - 1617-4615 .- 1617-4623. ; 289:5, s. 727-734
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Tidskriftsartikel (refereegranskat)abstract
- Systems biology aims at creating mathematical models, i.e., computational reconstructions of biological systems and processes that will result in a new level of understanding-the elucidation of the basic and presumably conserved "design" and "engineering" principles of biomolecular systems. Thus, systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved our understanding of many cellular processes. However, given the massive amount of qualitative and quantitative data currently produced and number of burning questions in health care and biotechnology needed to be solved is still in its early phases. The field requires novel approaches for abstraction, for modeling bioprocesses that follow different biochemical and biophysical rules, and for combining different modules into larger models that still allow realistic simulation with the computational power available today. We have identified and discussed currently most prominent problems in systems biology: (1) how to bridge different scales of modeling abstraction, (2) how to bridge the gap between topological and mechanistic modeling, and (3) how to bridge the wet and dry laboratory gap. The future success of systems biology largely depends on bridging the recognized gaps.
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| 4. |
- Andersen, J, et al.
(författare)
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Communication: THz absorption spectrum of the CO2-H2O complex: Observation and assignment of intermolecular van der Waals vibrations.
- 2014
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 140:9
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Tidskriftsartikel (refereegranskat)abstract
- Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm(-1) from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm(-1) for the dissociation energy D0.
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| 5. |
- Ceponkus, J, et al.
(författare)
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Acceptor switching and axial rotation of the water dimer in matrices, observed by infrared spectroscopy.
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:7
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Tidskriftsartikel (refereegranskat)abstract
- Several isotopologues of the water dimer have been studied in different matrices (Ne, Ar, Kr, and p-H(2)) at very low temperatures. A fine structure, which is more or less matrix independent and very similar for different intramolecular fundamentals of the same isotopologic dimer, is present on the high wavenumber side of the main component. The bound OD (OH) stretches of the donor have temperature dependent components. The fine structure and temperature dependency is interpreted as evidence for acceptor switching and rotation of the water dimer around its O-O axis in the matrices studied here. The slow nuclear spin equilibration in H(2)O inhibits the thermal equilibration between the acceptor switching states in H(2)O-DOH and H(2)O-DOD. The condensed environment slows down the acceptor switching rate compared to the gas phase. The antisymmetric stretch of the proton acceptor is assigned by combining information from different matrices with the rotation-acceptor switching model.
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| 6. |
- Ceponkus, J, et al.
(författare)
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Complex Formation of Small Molecules during Isolation in Low Temperature Matrices: Water Dimers in p-H-2 and Ne Matrices
- 2010
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 114:25, s. 6829-6831
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Tidskriftsartikel (refereegranskat)abstract
- The concentrations of water dimer are compared in Ne and p-H-2 matrices at low temperatures, using infrared spectroscopy. Additional data are given for o-D-2 and Ar matrices. For a given monomer concentration, the dimer concentration is significantly higher in solid Ne (or Ar) than in solid p-H-2. In p-H-2, the dimer concentration is only slightly higher than expected for a random distribution of water in the matrix. The dimer concentration in o-D-2 matrices is intermediate between p-H-2 and noble gas matrices. This strongly suggests that most dimers form on the surface of the growing matrix, and not as the result of diffusion in the bulk of the matrix.
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| 7. |
- Ceponkus, J, et al.
(författare)
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Observations of Host Guest Interactions Specific to Molecular Matrices: Water Monomers and Dimers in Hydrogen Matrices.
- 2011
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Ingår i: Journal of physical chemistry. A. - : American Chemical Society (ACS). - 1520-5215 .- 1089-5639. ; 115:27, s. 7921-7927
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Tidskriftsartikel (refereegranskat)abstract
- Water monomers and dimers have been studied at low temperatures in matrices of solid p-H(2), o-D(2), n-H(2), and n-D(2) using infrared spectroscopy. Our data demonstrate interaction mechanisms between host matrix and guest molecules that are different from the ones observed in atomic noble gas matrices. Notably both guest/host rotational-rotational interaction and matrix induced modifications of the guest libration modes are observed. We also show that different types of interaction influence the relaxation times of some of guest modes. Water rotates freely in p-H(2) and o-D(2) but librates in n-H(2) and n-D(2). Rotational relaxation is faster in o-D(2) than in p-H(2) and faster in p-H(2) than in Ne. This is attributed to interactions between water rotation and matrix molecule rotation in p-H(2) and o-D(2). In n-H(2) and n-D(2), a strong water libration band is observed in the far-infrared, and strong water monomer vibration bands have libration satellites. Water dimer bands, close to matrix rotation bands, are perturbed by the matrix motions. The H-bonded isomer H(2)O-HOD rapidly converts to the D-bonded form H(2)O-DOH in p-H(2) and in o-D(2) but slowly in n-H(2) and n-D(2).
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| 8. |
- Ceponkus, J, et al.
(författare)
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On the structure of the matrix isolated water trimer.
- 2011
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 134:6
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Tidskriftsartikel (refereegranskat)abstract
- Infrared spectra of partially deuterated water trimers have been investigated. It is found that HDO(H(2)O)(2) has a single, bound OD stretching fundamental, (HDO)(2)H(2)O two bound OD stretches. (HDO)(3) has a single, bound OD stretch and (H(2)O)(3) has a pair of bound OH stretches. Ab initio and discrete Fourier transform (DFT) calculations predict that the water trimer has C(1) symmetry with six different, isoenergetic minima. These calculations consequently give three numerically different OD stretches for HDO(H(2)O)(2), six for (HDO)(2)H(2)O, three for (HDO)(3), and three bound OH stretches for (H(2)O)(3). The connection between the observations and the pseudorotation of the trimer is discussed with the help of Wales' pseudorotation model. It is found that pseudorotation is sufficiently fast to average the effective symmetry of the A(3) trimer to C(3h) and to eliminate the difference between the different ab initio minima for A(2)B. The only exception is (H(2)O)(3) where the splitting between the different bound OH stretches is largest. Here a doublet is observed due to incomplete averaging. DFT calculations indicate that the D-bonded form of HDO(H(2)O)(2) is between 50 and 60 cm(-1) more stable than the H-bonded form. The energy difference is determined by differences in zero point vibration energy of intermolecular librations of the two forms. Attempts to measure the energy difference indicate that the energy difference is larger, of the order of 100 cm(-1).
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| 9. |
- Ceponkus, J, et al.
(författare)
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Rotation of Water in Solid Parahydrogen and Orthodeuterium.
- 2010
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Ingår i: Journal of physical chemistry. A. - : American Chemical Society (ACS). - 1520-5215 .- 1089-5639. ; 114, s. 12979-12985
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Tidskriftsartikel (refereegranskat)abstract
- The far-infrared spectra of solid orthodeuterium and solid normal deuterium are presented and compared to the corresponding spectra of solid parahydrogen and solid normal hydrogen. Spectra of water in orthodeuterium are compared to spectra of water in parahydrogen. The water rotation constants in orthodeuterium are approximately 80% of the rotation constants of water in parahydrogen. The S(0)(0) band of orthodeuterium gets a strong satellite in the presence of water. The position and width of the satellite depends on the isotopic composition of the water present. If there is a corresponding satellite in parahydrogen it is weak and closer to the S(0)(0) band of the matrix. The conclusion of the paper is that interaction between guest rotation and the rotation of matrix molecules must be taken into account to explain the reduction of the rotation constants in orthodeuterium.
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| 10. |
- Ceponkus, J., et al.
(författare)
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Structure and dynamics of small water clusters, trapped in inert matrices
- 2013
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 581, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- Recent matrix isolation (p-H-2, Ne, Ar, Kr) studies of water clusters made in Lund are reviewed. Gas phase positions of water cluster bands are estimated from matrix data. Intermolecular spectra of several isotopomers of the water dimer have been obtained, and approximate band strengths have been measured. Acceptor switching of the water dimer has been observed in matrices. A few intermolecular vibrations of (H2O)(3), (D2O)(3), (H2O)(4), and (D2O)(4) have been measured. The pseudorotation of the water trimer is not quenched in matrices, and pentamer pseudorotation appears to be fast as well. Spectra of partially deuterated water tetramers support a rigid cyclic tetramer structure. The hydrogen rotation in p-H-2 may interfere with guest vibrations at frequencies near the J = 2 <- J = 0 band of solid parahydrogen. (C) 2013 Elsevier B.V. All rights reserved.
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| 11. |
- Ceponkus, J., et al.
(författare)
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The coupling between translation and rotation for monomeric water in noble gas matrices.
- 2013
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 138:24
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Tidskriftsartikel (refereegranskat)abstract
- The rotation of water in noble gas matrices has been studied. It is shown that the rotation-translation coupling model of Friedmann and Kimel predicts rotation line spacings, which are close to the experimental observations for H2O, D2O, and HDO, when gas phase rotation constants are used. The model gives intensity estimates in reasonable agreement with the observations for the local oscillator bands, which accompany the rotation spectrum. It also predicts the intensity variations in the bending region of H2O between neon, argon, and krypton matrices.
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| 12. |
- Ceponkus, J., et al.
(författare)
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Water Tetramer, Pentamer, and Hexamer in Inert Matrices
- 2012
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 116:20, s. 4842-4850
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Tidskriftsartikel (refereegranskat)abstract
- The infrared spectrum of water, isolated in inert matrices, has been studied in the interval from 60 to 4000 cm(-1). Experiments with partially deuterated water combined with DFT (density functional theory) calculations have been used to investigate the structure of matrix-isolated water tetramer. A few, strong intermolecular fundamentals of the water tetramer have been observed. Mid-infrared bands due to deuterated pentamers and hexamers have been observed and are used to discuss the assignments of these water clusters.
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| 13. |
- Ganat, Yosif M., et al.
(författare)
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Identification of embryonic stem cell-derived midbrain dopaminergic neurons for engraftment
- 2012
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Ingår i: Journal of Clinical Investigation. - 0021-9738. ; 122:8, s. 2928-2939
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Tidskriftsartikel (refereegranskat)abstract
- Embryonic stem cells (ESCs) represent a promising source of midbrain dopaminergic (DA) neurons for applications in Parkinson disease. However, ESC-based transplantation paradigms carry a risk of introducing inappropriate or tumorigenic cells. Cell purification before transplantation may alleviate these concerns and enable identification of the specific DA neuron stage most suitable for cell therapy. Here, we used 3 transgenic mouse ESC reporter lines to mark DA neurons at 3 stages of differentiation (early, middle, and late) following induction of differentiation using Hes5::GFP, Nurr1::GFP, and Pitx3::YFP transgenes, respectively. Transplantation of FACS-purified cells from each line resulted in DA neuron engraftment, with the mid-stage and late-stage neuron grafts being composed almost exclusively of midbrain DA neurons. Mid-stage neuron cell grafts had the greatest amount of DA neuron survival and robustly induced recovery of motor deficits in hemiparkinsonian mice. Our data suggest that the Nurrl(+) stage (middle stage) of neuronal differentiation is particularly suitable for grafting ESC-derived DA neurons. Moreover, global transcriptome analysis of progeny from each of the ESC reporter lines revealed expression of known midbrain DA neuron genes and also uncovered previously uncharacterized midbrain genes. These data demonstrate remarkable fate specificity of ESC-derived DA neurons and outline a sequential stage-specific ESC reporter line paradigm for in vivo gene discovery.
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| 14. |
- Kitambi, Satish Srinivas, et al.
(författare)
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Vulnerability of Glioblastoma Cells to Catastrophic Vacuolization and Death Induced by a Small Molecule
- 2014
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 157:2, s. 313-328
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Tidskriftsartikel (refereegranskat)abstract
- Glioblastoma multiforme (GBM) is the most aggressive form of brain cancer with marginal life expectancy. Based on the assumption that GBM cells gain functions not necessarily involved in the cancerous process, patient-derived glioblastoma cells (GCs) were screened to identify cellular processes amenable for development of targeted treatments. The quinine-derivative NSC13316 reliably and selectively compromised viability. Synthetic chemical expansion reveals delicate structure-activity relationship and analogs with increased potency, termed Vacquinols. Vacquinols stimulate death by membrane ruffling, cell rounding, massive macropinocytic vacuole accumulation, ATP depletion, and cytoplasmic membrane rupture of GCs. The MAP kinase MKK4, identified by a shRNA screen, represents a critical signaling node. Vacquinol-1 displays excellent in vivo pharmacokinetics and brain exposure, attenuates disease progression, and prolongs survival in a GBM animal model. These results identify a vulnerability to massive vacuolization that can be targeted by small molecules and point to the possible exploitation of this process in the design of anticancer therapies.
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