| 1. |
- Ho, Joshua W. K., et al.
(författare)
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Comparative analysis of metazoan chromatin organization
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 512:7515, s. 449-U507
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Tidskriftsartikel (refereegranskat)abstract
- Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms(1-3). Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths(4,5). To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.
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| 2. |
- Jana, Manoj K., et al.
(författare)
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Resolving Rotational Stacking Disorder and Electronic Level Alignment in a 2D Oligothiophene-Based Lead Iodide Perovskite
- 2019
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 31:20, s. 8523-8532
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Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) hybrid organic-inorganic perovskites (HOIPs) represent diverse quantum well heterostructures composed of alternating inorganic and organic layers. While 2D HOIPs are nominally periodic in three dimensions for X-ray scattering, the inorganic layers can orient quasi-randomly, leading to rotational stacking disorder (RSD). RSD manifests as poorly resolved, diffuse X-ray scattering along the stacking direction, limiting the structural description to an apparently disordered subcell. However, local ordering preferences can still exist between adjacent unit cells and can considerably impact the properties, particularly the electronic structure. Here, we elucidate RSD and determine the preferred local ordering in the 2D [AE2T]PbI4 HOIP (AE2T: 5,5′-bis(ethylammonium)-[2,2′-bithiophene]). We use first-principles calculations to determine energy differences between a set of systematically generated supercells with different order patterns. We show that interlayer ordering tendencies are weak, explaining the observed RSD in terms of differing in-plane rotation of PbI6 octahedra in neighboring inorganic planes. In contrast, the ordering preference within a given organic layer is strong, favoring a herringbone-type arrangement of adjacent AE2T cations. The calculated electronic level alignments of proximal organic and inorganic frontier orbitals in the valence band vary significantly with the local arrangement of AE2T cations; only the most stable AE2T configuration leads to an interfacial type-Ib band alignment consistent with observed optical properties. The present study underscores the importance of resolving local structure arrangements in 2D HOIPs for reliable structure-property prediction.
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| 3. |
- Roy, Sushmita, et al.
(författare)
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Identification of functional elements and regulatory circuits by Drosophila modENCODE.
- 2010
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 330:6012, s. 1787-1797
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Tidskriftsartikel (refereegranskat)abstract
- To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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| 4. |
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| 5. |
- Almora, Osbel, et al.
(författare)
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Device Performance of Emerging Photovoltaic Materials (Version 1)
- 2020
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Ingår i: Advanced Energy Materials. - : Wiley. - 1614-6832 .- 1614-6840. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Emerging photovoltaics (PVs) focus on a variety of applications complementing large scale electricity generation. Organic, dye-sensitized, and some perovskite solar cells are considered in building integration, greenhouses, wearable, and indoor applications, thereby motivating research on flexible, transparent, semitransparent, and multi-junction PVs. Nevertheless, it can be very time consuming to find or develop an up-to-date overview of the state-of-the-art performance for these systems and applications. Two important resources for recording research cells efficiencies are the National Renewable Energy Laboratory chart and the efficiency tables compiled biannually by Martin Green and colleagues. Both publications provide an effective coverage over the established technologies, bridging research and industry. An alternative approach is proposed here summarizing the best reports in the diverse research subjects for emerging PVs. Best performance parameters are provided as a function of the photovoltaic bandgap energy for each technology and application, and are put into perspective using, e.g., the Shockley–Queisser limit. In all cases, the reported data correspond to published and/or properly described certified results, with enough details provided for prospective data reproduction. Additionally, the stability test energy yield is included as an analysis parameter among state-of-the-art emerging PVs.
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| 6. |
- Egelhofer, Thea A, et al.
(författare)
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An assessment of histone-modification antibody quality
- 2011
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Ingår i: Nature Structural & Molecular Biology. - : Springer Science and Business Media LLC. - 1545-9993 .- 1545-9985. ; 18:1, s. 91-93
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Tidskriftsartikel (refereegranskat)abstract
- We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).
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| 7. |
- Kharchenko, Peter V, et al.
(författare)
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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 471:7339, s. 480-485
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Tidskriftsartikel (refereegranskat)abstract
- Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.
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| 8. |
- Marquez, Jose A., et al.
(författare)
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High-temperature decomposition of Cu2BaSnS4 with Sn loss reveals newly identified compound Cu2Ba3Sn2S8
- 2020
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Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 8:22, s. 11346-11353
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Tidskriftsartikel (refereegranskat)abstract
- The earth-abundant quaternary compound Cu(2)BaSnS(4)is being currently studied as a candidate for photovoltaics and as a photocathode for water splitting. However, the chemical stability of this phase during synthesis is unclear. The synthesis of other quaternary tin-sulphur-based absorbers (e.g., Cu2ZnSnS4) involves an annealing step at high temperature under sulphur gas atmosphere, which can lead to decomposition into secondary phases involving Sn loss from the sample. As the presence of secondary phases can be detrimental for device performance, it is crucial to identify secondary phase chemical, structural and optoelectronic properties. Here we used a combination ofin situEDXRD/XRF and TEM to identify a decomposition pathway for Cu2BaSnS4. Our study reveals that, while Cu(2)BaSnS(4)remains stable at high sulphur partial pressure, the material decomposes at high temperatures into Cu(4)BaS(3)and the hitherto unknown compound Cu(2)Ba(3)Sn(2)S(8)if the synthesis is performed under low partial pressure of sulphur. The presence of Cu(4)BaS(3)in devices could be harmful due to its high conductivity and relatively lower band gap compared to Cu2BaSnS4. The analysis of powder diffraction data reveals that the newly identified compound Cu(2)Ba(3)Sn(2)S(8)crystallizes in the cubic system (space groupI4x304;3d) with a lattice parameter ofa= 14.53(1) angstrom. A yellow powder of Cu(2)Ba(3)Sn(2)S(8)has been synthesized, exhibiting an absorption onset at 2.19 eV.
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