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- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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- Ramilowski, JA, et al.
(author)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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In: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Journal article (peer-reviewed)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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- Gomez, P.F., et al.
(author)
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Heavy metal biosorption by Rhizopus sp. biomass immobilized on textiles
- 2014
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In: Water, Air and Soil Pollution. - : Springer. - 0049-6979 .- 1573-2932. ; 225:2
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Journal article (peer-reviewed)abstract
- Pollution by heavy metals is at present one of the major environmental concerns. In the present study, the potential of the filamentous zygomycete fungus Rhizopus sp. to absorb/adsorb metal ions from solution was investigated. With the aim to develop a feasible process, the fungus was immobilized on 10 different textile materials during the cultivation. All immobilized biosorbents reduced the Cu2+ concentrations initially from 20 to 3.1–5.6 mg/l within 150 min, with the exception of the biomass immobilized on wool, which reduced the Cu2+ level to 10.2 mg/l. The immobilized biomass (with the exception of wool) fitted well into a pseudo-second-order model. The uptake of copper showed a slight dependence on initial metal concentration. By reapplying immobilized Rhizopus sp. to a solution containing a low concentration of Cu2+ after going through a first step of biosorption, a decrease of the concentration to below 2 mg/l was accomplished, meeting the stipulated level for Cu2+ in human drinking water. Immobilization of fungal biomass in a cushion was also successfully applied in the biosorption process. The positive results obtained in a two-step biosorption indicate that a sequential arrangement could be the foundation for a commercial product.
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- Jacobson, L., et al.
(author)
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Mechanisms compensating for visual field restriction in adolescents with damage to the retro-geniculate visual system
- 2012
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In: Eye (London. 1987). - : Springer Science and Business Media LLC. - 0950-222X .- 1476-5454. ; 26:11, s. 1437-1445
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Journal article (peer-reviewed)abstract
- Background To describe visual field (VF) outcome in three adolescents with damage to the optic radiation and to focus on mechanisms that may compensate the practical functional limitations of VF defects. Design Descriptive, prospective multi-case study in a hospital setting. Participants Three teenagers with cerebral visual dysfunction because of damage to the retro-geniculate visual pathways. Methods Best-corrected visual acuity and eye alignment were assessed. Visual field function was tested with Goldmann perimetry, and with Rarebit, Humphrey Visual Field Analyzer and Esterman computerized techniques. Fixation was registered with video oculography during Rarebit examination. Magnetic resonance imaging of the brain illustrated brain damage and its relation to the posterior visual system. Results One of the three subjects had bilateral asymmetric white matter damage of immaturity, early-onset exotropia, and a relative homonymous VF defect, but normal binocular VF. The second subject also had bilateral asymmetric white matter damage of immaturity and showed an inferior right quadrantanopia, confirmed by the binocular field. Registration of fixation revealed automatic scanning during perimetry. The third subject had an almost total left homonymous hemianopia after resection of a brain tumour in the right temporal lobe. The hemianopia could be compensated for by fast voluntary scanning. Conclusion Congenital and later-acquired homonymous VF defects may, at least in young subjects, be compensated for by scanning. Exotropia may compensate VF defects and, therefore, the VF should be tested before strabismus surgery. Eye (2012) 26, 1437-1445; doi:10.1038/eye.2012.190; published online 21 September 2012
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| 12. |
- Lennartsson, Anders, 1980, et al.
(author)
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Reversible Guest Binding in a Non-Porous FeII Coordination Polymer Host Toggles Spin Crossover
- 2015
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In: Chemistry - A European Journal. - : Wiley. - 1521-3765 .- 0947-6539. ; 21:45, s. 16066-16072
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Journal article (peer-reviewed)abstract
- Formation of either a dimetallic compound or a 1D coordination polymer of adiponitrile adducts of [Fe(bpte)]2+ (bpte=[1,2-bis(pyridin-2-ylmethyl)thio]ethane) can be controlled by the choice of counteranion. The iron(II) atoms of the bis(adiponitrile)-bridged dimeric complex [Fe2(bpte)2(μ2-(NC(CH2)4CN)2](SbF6)4 (2) are low spin at room temperature, as are those in the polymeric adiponitrile-linked acetone solvate polymer {[Fe(bpte)(μ2-NC(CH2)4CN)](BPh4)2 Me2CO} (3Me2CO). On heating 3Me2CO to 80°C, the acetone is abruptly removed with an accompanying purple to dull lavender colour change corresponding to a conversion to a high-spin compound. Cooling reveals that the desolvate 3 shows hysteretic and abrupt spin crossover (SCO) S=0虠S=2 behaviour centred at 205K. Non-porous 3 can reversibly absorb one equivalent of acetone per iron centre to regenerate the same crystalline phase of 3Me2CO concurrently reinstating a low-spin state.
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- Nore, Beston F, et al.
(author)
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Identification of phosphorylation sites within the SH3 domains of Tec family tyrosine kinases
- 2003
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In: Biochimica et Biophysica Acta. - 0006-3002 .- 1878-2434. ; 1645:2, s. 123-132
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Journal article (peer-reviewed)abstract
- Tec family protein tyrosine kinases (TFKs) play a central role in hematopoietic cellular signaling. Initial activation takes place through specific tyrosine phosphorylation situated in the activation loop. Further activation occurs within the SH3 domain via a transphosphorylation mechanism, which for Bruton's tyrosine kinase (Btk) affects tyrosine 223. We found that TFKs phosphorylate preferentially their own SH3 domains, but differentially phosphorylate other member family SH3 domains, whereas non-related SH3 domains are not phosphorylated. We demonstrate that SH3 domains are good and reliable substrates. We observe that transphosphorylation is selective not only for SH3 domains, but also for dual SH3SH2 domains. However, the dual domain is phosphorylated more effectively. The major phosphorylation sites were identified as conserved tyrosines, for Itk Y180 and for Bmx Y215, both sites being homologous to the Y223 site in Btk. There is, however, one exception because the Tec-SH3 domain is phosphorylated at a non-homologous site, nevertheless a conserved tyrosine, Y206. Consistent with these findings, the 3D structures for SH3 domains point out that these phosphorylated tyrosines are located on the ligand-binding surface. Because a number of Tec family kinases are coexpressed in cells, it is possible that they could regulate the activity of each other through transphosphorylation.
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- Theorell, Töres, et al.
(author)
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Predictors of continued playing or singing - from childhood and adolescence to adult years
- 2015
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In: Acta Paediatrica. - : Wiley. - 0803-5253 .- 1651-2227. ; 104:3, s. 274-284
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Journal article (peer-reviewed)abstract
- Aim: Many individuals play an instrument or sing during childhood, but they often stop later in life. This study surveyed adults representative of the Swedish population about musical activities during childhood.Methods: We asked 3820 adults (65% women) aged from 27 to 54 from the Swedish Twin Registry, who took extra music lessons to those provided at school, to fill in a web-based questionnaire. Factors analysed were the age they started studying music, the instrument they played, kind of teaching, institution and educational content, number of lessons and perceived characteristics of the lessons, the music environment during their childhood years and their preferred music genre. All variables were dichotomised.Results: Factors strongly associated with continued playing or singing were male sex, young starting age, cultural family background, self-selected instrument, attending music classes and more than once a week, church-related or private education, pop, rock or classical music, playing by ear and improvisation.Conclusion: Several significant predictors determined whether a child continued to sing or play an instrument as an adult and many could be externally influenced, such as starting at a young age, taking music classes more than once a week, improvisation and the type of music they played.
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