| 1311. |
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| 1312. |
- Sinha, Indranil, et al.
(författare)
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Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast
- 2010
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Ingår i: Epigenomics. - 1750-1911. ; 2:3, s. 377-393
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Tidskriftsartikel (refereegranskat)abstract
- To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. Using clustering analysis and gene ontology search tools, we identified promoter histone modification patterns that characterize several classes of gene function. For example, gene promoters of genes involved in cytokinesis have high H3K36me2 and low H3K4me2, whereas the converse pattern is found ar promoters of gene involved in positive regulation of the cell cycle. We detected acetylation of H4 preferentially at lysine 16 followed by lysine 12, 8 and 5. Our analysis shows that this H4 acetylation bias in the coding regions is dependent upon gene length and linked to gene expression. Our analysis also reveals a role for H3K36 methylation at gene promoters where it functions in a crosstalk between the histone methyltransferase Set2(KMT3) and the histone deacetylase Clr6, which removes H3K27ac leading to repression of transcription. Conclusion: Histone modification patterns could be linked to gene expression in fission yeast.
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| 1313. |
- Sinha, Indranil
(författare)
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Genome-wide patterns of histone modifications in fission yeast
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- DNA is wrapped almost two times around a group of proteins called histones to form a chromosomal structure known as the nucleosome. Both DNA and histones can be modified with different chemical tags by several enzymes to activate or suppress a particular gene or group of genes. Histones can be covalently modified at several places. Among many different types of post-translational histone modifications, histone acetylation and methylation are two important modification types that are associated with transcriptional activation and repression. Histone acetylation and methylation can be added by histone acetyltransferases (HATs) and histone methyletransferases (HMTs), whereas these modifications can be removed by histone deacetylases (HDACs) and histone demethylases (HDMs). Histone modifications are not only involved in the regulation of gene expression, but also in DNA-based processes, such as replication, repair, and the formation and maintenance of heterochromatin. Combinations of modified and unmodified states of histones can form distinct histone modification patterns. In many different genome-wide studies, it was observed that a distinctive pattern of histone modification in various organisms is important for gene regulation, DNA replication, chromosome segregation and heterochromatin-mediated silencing. In this thesis, we have conducted several genome-wide investigations to uncover different histone modification patterns and their roles in transcriptional control in fission yeast. Our analysis of six different HDACs in fission yeast showed that Clr6 and Clr3 are mainly involved in keeping repressed genes silent; Sir2 and Hst2 repress non-expressed genes, and Hst4 acts globally to reduce gene expression, whereas Hos2 is required for the activation of gene expression. By investigating the influence of each HDAC on nucleosome density, we found that all sirtuins and Hos2 enzymes are required to maintain normal nucleosome density and distribution in the S. pombe genome. We have reported that histone acetylation patterns show a 5` to 3` polarity, i.e., the modification levels peak near the ATG and gradually decrease in the coding regions. We also found that histone acetylation patterns depend on gene expression but are independent of gene length. Comparing our data with other published datasets, we observed that different HDAC mutants affect acetylation in different parts of open reading frames (ORFs). We have demonstrated that histone H4 acetylation proceeds in the direction from K16 to K5, consistent with a `zip` model that may be involved in transcriptional control. Our analysis revealed antagonistic crosstalk between H3K36me2/me3 and H3K27ac at promoter regions. We observed that histone H3 K18, K27 and K9 acetylation positively correlate with gene expression, and a conserved pattern was also reported in other organisms. Finally, we report that histone H4K20me1 is strongly linked to active genes, whereas H4K20me3 is associated with weakly expressed genes. Our analysis further shows that H4K20me1 modification levels peak at 3‟UTR regions in active genes. Thus, our analysis revealed many different aspects of histone modification patterns and their roles in transcriptional control in fission yeast.
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| 1314. |
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Siri Derkert
- 2011
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)
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| 1315. |
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| 1316. |
- Sjödin, Anna-Pya, Docent, 1972-
(författare)
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Conceptualizing philosophical tradition : A reading of Wilhelm Halbfass, Daya Krishna, and Jitendranath Mohanty
- 2011
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Ingår i: Philosophy East & West. - Hawaii : University of Hawai'i Press. - 0031-8221 .- 1529-1898. ; 61:3, s. 534-546
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Tidskriftsartikel (refereegranskat)abstract
- This article takes as its point of departure the question of how Wilhelm Halbfass, Daya Krishna, and Jitendranath Mohanty have conceptualized tradition in relation to “Indian” philosophy. They have all reacted to, and criticized, homogeneous and static conceptions of Indian philosophies, and by articulating different ways of apprehending tradition they have tried to come to terms with such limiting images. My reading of their texts has been informed by a questioning of how they, in turn, conceptualize tradition. Most of all this is related to the tendency, on the one hand, to stress that tradition is open-ended and dynamic but at the same time to speak of tradition as one singular and universalizable phenomenon, sometimes even as a reified phenomenon (“it”). This discussion is connected to a concern of mine regarding how to conceptualize a plurality and heterogeneity while avoiding a reifying, generalizing language. Toward the end I present a reading of the Nyāyasūtra and how the concept of siddhānta could be understood in the light of three of its commentaries. This reading is here framed as the practical and philosophical outcome of the reflections made in the analysis of Halbfass, Krishna, and Mohanty.
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| 1317. |
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| 1318. |
- Sjödin Lindenskoug, Susanna, 1971-
(författare)
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Manlighetens bortre gräns : tidelagsrättegångar i Livland åren 1685-1709
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- There were many ways of bordering manliness during the historical period covered by my research. Borders have been metaphorically understood as those invisible, often non-enunciated limits that have safeguarded manliness. There were borders separating masculinity from femininity and from childishnes, but there is also a more distant border, separating masculinity from the bestial. The term un-manliness is a useful concept for this analysis, for it can be used to illuminate the different ways in which masculinity has been interrogated. The concept can also be used in comparative analyses of how tolerance towards men deviating from ideas of ideal masculinity has differed according to situation and culture. It has been my ambition to elucidate the particular attitudes, values, customs, knowledge and requirements that influenced the view of masculinity at both individual and the group level. The clearest-cut aspects of manliness and un-manliness expressed in court proceedings were those having to do with sexuality, relations within the household, and the subordinate and dominant masculinities displayed by different court-room actors. The latter, in turn, reflected contemporary social structures, including the social gap that divided the Livonian peasantry’s serfs or former serfs from the ruling Baltic-German elite. Records from the court proceedings have shown the subordinate masculinity of the defendants, subordinate not only to that of the officers of the court but to that of the witnesses. This subordination was an inevitable consequence of the nature of the accusations, regardless of whether they were deemed well-founded or false. The defendants were placed in a situation where they were forced constantly to be on the alert, ready to defend themselves and show their best sides. As a result, they would often give extremely clear expression to their views of proper masculinity. Such actors stressed, consciously or unconsciously, certain manly traits and behaviour patterns that characterised themselves and others. Their arguments provide insights into what they thought of each other and how they conceived a man should generally be, behave and act in different situations. By the same token, they clearly showed what kinds of behaviours were considered undesirable or outright unmanly. The positioning of the borders of manliness was linked both to time and to space. Deviations have helped different societies set the borders for what they considered acceptable behaviour. There was a clear cultural and geographical border between Sweden as such, and the Swedish province Livonia. This emerges clearly when one compares Livonian results with earlier studies on bestiality in Sweden. This shows that the view of manliness and the tolerance towards certain kinds of behaviour changed as one moved East.
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| 1319. |
- Sjöholm, Cecilia
(författare)
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Ansikten som talar : Arendts estetiska vändning
- 2011
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Ingår i: Konsten att handla – konsten att tänka. - Stockholm : Axl Books. - 9789197859875 - 9789186883171 ; , s. 183-203
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 1320. |
- Sjöholm, Cecilia
(författare)
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Beyond Pleasure : the Other History of Sexuality
- 2010
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Ingår i: Feminist readings of Antigone. - Albany : State University of New York Press. - 9781438432793 ; , s. 173-194
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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