| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Alekeyenko, Artyom A., et al.
(författare)
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Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context
- 2012
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Ingår i: PLoS Genetics. - San Francisco : Public Library of Science. - 1553-7390 .- 1553-7404. ; 8:4, s. e1002646-
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Tidskriftsartikel (refereegranskat)abstract
- The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at "entry sites" that contain a consensus sequence motif ("MSL recognition element" or MRE). However, this motif is only similar to 2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome.
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| 3. |
- 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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| 4. |
- Girardelli, Davide, 1973, et al.
(författare)
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Gamifying impromptu speech for ESL/EFL students
- 2016
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Ingår i: Proceedings of the 2nd International Conference on Higher Education Advances (HEAd’16), Valencia, Spain. - 9788490484753
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Konferensbidrag (refereegranskat)abstract
- This paper outlines an impromptu speech activity entitled “Dented Helmet vs. Spambot” intended as part of any introductory public speaking course. The activity is designed to overcome specific affective and cognitive challenges of ESL/EFL students, in particular Chinese learners, and is inspired by the principles of gamification (Kapp, 2012) with core gaming elements such as “freedom to fail”, “rapid feedback”, and “storytelling”, The activity requires “Rory’s Story Cubes” (a set of nine six-sided dice designed to spark creativity) and a special set of slides. An exploratory assessment of the effectiveness of our proposed activity was conducted on a sample of Chinese EFL sophomores enrolled in an international branch campus of a U.S. university in China, with 81 students completing our questionnaire. Overall, our findings provided some initial support to the effectiveness of our activity in terms of strenghtening students’ ability to communicate orally “off the cuff”, promoting students’ understanding of the role of storytelling in effective presentations, fostering students’ understanding of the major organizational formats used in organizing speeches, and increasing students’ awareness of their nonverbal communication during oral presentations.
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| 5. |
- 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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| 6. |
- Huang, Xin, 1982-, et al.
(författare)
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Sensor Aided Authentication
- 2010
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Ingår i: Communications in Computer and Information Science Volume 76 CCIS, 2010. - Berlin, Heidelberg : Springer. - 3642133649 - 9783642133640 ; , s. 265-277
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Konferensbidrag (refereegranskat)abstract
- The sharing of sensor data globally becomes possible by the development of wireless sensor network, cloud computing, and other related technologies. These new trends can also benefit information security. In this paper, the sensor data is involved in the authentication procedure which is one main component of security systems. Sensor aided password is proposed. In addition, the architecture for sensor aided authentication corresponding to the simple authentication scenario is also designed. Sensor data aided password generation and utilization bring convenience to users without weakening the password strength.
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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. |
- Li, Qizhao, et al.
(författare)
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Regioselectively Halogenated Expanded Porphyrinoids as Building Blocks for Constructing Porphyrin-Porphyrinoid Heterodyads with Tunable Energy Transfer
- 2019
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 141:13, s. 5294-5302
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Tidskriftsartikel (refereegranskat)abstract
- Expanded porphyrins have been attracting increasing attention owing to their unique optical and electrochemical properties as well as switchable aromaticity. Toward material applications, regioselective functionalization of the expanded porphyrins at their periphery is indeed challenging due to the presence of multiple reactive sites. Herein, a set of regioselective halogenated isomers (L5-Br-A/B/C) of neo-confused isosmaragdyrin (L5) are synthesized by a combination of the halogenation reaction of L5 and sequential macrocycleto-macrocycle transformation reactions of its halogenated isomers. On this basis, the regioselectively functionalized isosmaragdyrins are utilized as building blocks for constructing multichromophoric porphyrinoids, specifically, heterodyads L5-ZnP-A/B/C, in which a common zinc porphyrin is linked at three different pyrrolic positions of isosmaragdyrins, respectively, by Sonogashira coupling reactions. The highly efficient energy cascade from porphyrin to isosmaragdyrin is elucidated using steady-state/time-resolved spectroscopies and theoretical calculations. Notably, the energy transfer processes from the porphyrin to the isosmaragdyrin moieties as well as the excitation energy transfer rates in L5-ZnP-A/B/C are highly dependent on the linking sites by through-bond and Forster-type resonance energy transfer mechanisms. The site-selective functionalization and subsequent construction of a set of heterodyads of the expanded porphyrinoid would provide opportunities for developing new materials for optoelectronic applications.
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| 9. |
- Li, Qizhao, et al.
(författare)
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Skeletal Rearrangement of Twisted Thia-Norhexaphyrin : Multiply Annulated Polypyrrolic Aromatic Macrocycles
- 2019
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Ingår i: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 58:18, s. 5925-5929
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Tidskriftsartikel (refereegranskat)abstract
- A hybrid thia-norhexaphyrin comprising a directly linked N-confused pyrrole and thiophene unit (1) revealed unique macrocycle transformations to afford multiply inner-annulated aromatic macrocycles. Oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone triggered a cleavage of the C-S bond of the thiophene unit, accompanied with skeletal rearrangement to afford unique pi-conjugated products: a thiopyrrolo-pentaphyrin embedded with a pyrrolo[1,2]isothiazole (2), a sulfur-free pentaphyrin incorporating an indolizine moiety (3), and a thiopyranyltriphyrinoid containing a 2H-thiopyran unit (4). Furthermore, 2 underwent desulfurization reactions to afford a fused pentaphyrin containing a pyrrolizine moiety (5) under mild conditions. Using expanded porphyrin scaffolds, oxidative thiophene cleavage and desulfurization of the hitherto unknown N-confused core-modified macrocycles would be a practical approach for developing unique polypyrrolic aromatic macrocycles.
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| 10. |
- Li, Qizhao, et al.
(författare)
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Twisted-Planar-Twisted expanded porphyrinoid dimer as a rudimentary reaction-based methanol indicator
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Directly linked porphyrin dimers have attracted considerable attention because of their intriguing electronic features. Most emphasis has been placed on either dimers with large dihedral angles between the constituent planar monomeric subunits or those with overall planarity, referred to as "Planar-Twisted-Planar" and "Planar-Planar-Planar", respectively. Herein, we report a "Twisted-Planar-Twisted" framework, the hexaphyrin dimer D that exists in a trans configuration. Treatment of D with MeOH affords two isomeric dimers, MD1 and MD2, both of which incorporate a methoxy moiety and exist in cis orientations with respect to the tethering linkage. The methanol-promoted conversion is accompanied by a readily discernible color change from green to brown and is not induced to an appreciable level by other alcohols. Dimer D thus acts as a rudimentary, albeit highly selective, reaction-based methanol indicator. This work provides a promising approach for constructing reaction-based chemosensors using porphyrinoid dimers of nonplanar subunits with biased reactivity. Directly linked porphyrin dimers show intriguing electronic features but emphasis has been placed on planar monomeric units. Here, the authors report a Twisted-Planar-Twisted framework which can undergo a cis-trans transformation accompanied by a colour change in presence of methanol, making this framework applicable as a methanol sensor.
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