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An EBNA2 binding website down-handles CIITA and you will activates the newest neighboring DEXI gene

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(A) Heat map of RNA-seq and ATAC-Seq data from EBV infection of primary B-cells for two independent donors. HLA-II and CIITA genes are shown that have associated changes in both transcription levels and chromatin accessibility during primary infection (r > 0.5). The intensity of purple color for column r is proportional to correlation coefficient. Intensity for gene expression and ATAC signal is a z-score calculated among samples at each experiment (lower right). (B) Proteomic analysis of HLA protein changes in EBV infected LCLs relative to uninfected primary B-cells averaged for 2 donors using label-free quantification. Color is proportional to magnitude of fold change. (C) RT-qPCR analysis of HLA-DRA, -DRB1, -DPA1, -DPB1, -DMA, -DMB, -DOA, and -DOB in B cells (Day 0) and LCLs derived from the B cells (Day 21). Statistical analysis was performed in GraphPad Prism 9. Error bars are standard deviation from mean (SDM) and *** indicates p-values <0.001 using 2-tailed student t-test.

(A-B) The surface expression of HLA-DR proteins on Akata T1 or T2 cells -/+E2 was determined by FACS. Representative FACS profile of Akata T1 -/+E2 (A) or mean fluorescence intensity values of Akata T1 or T2 cells -/+E2 (B) of surface HLA-DR expression are shown. Error bars are SDM and *p<0.05, *** p<0.001 using student 2-tailed t-test. (C) Freshly isolated human CD4+ T cells were incubated without stimulation as Negative (Neg) control, incubated with anti-CD3/CD28 beads as Positive (Pos) control, or cocultured with Akata T1 or T2 cells with (+) or without (-) estradiol (E2) and assayed for ATP levels by CellTiterGlo at day 6. Luminescence of Neg was set as 0, and Pos set as 100. Error bars are SDM, *** p<0.001 using 2-tailed student t-test.

Chromatin compartments covered by CTCF separate EBNA2 triggered https://datingranking.net/pl/ardent-recenzja/ DEXI out of stifled CIITA

EBV primary disease and you may B-telephone immortalization contributes to brand new off regulation of all of the HLA classification II gene transcripts. We show that it correlates that have a loss of HLA category II necessary protein expression to the cellphone epidermis and you will death of T-cell stimulatory passion. This new off regulation off HLA-class II try influenced by EBNA2 expression that will become recapitulated in structure one conditionally share EBNA2 just like the simply induced viral necessary protein. We examined a prospective head apparatus and discovered you to EBNA2 sure directly to several web sites inside the HLA locus and you will colocalized partly with CIITA binding internet sites. This suggests one EBNA2 may also antagonize CIITA transcriptional co-activator mode at the HLA locus. not, we had been struggling to have demostrated an effect out-of EBNA2 in the the brand new HLA-II locus, neither one communication ranging from EBNA2 and you can CIITA. But not, knock-down regarding CIITA revealed that EBNA2 control away from HLA-II would depend strongly on CIITA. We therefore investigated the fresh secondary method from EBNA2 regulating HLA by way of transcriptional controls away from CIITA. We learned that EBNA2 localizes so you can the right position downstream of one’s CIITA gene, and you will turns on a good downstream booster for the next gene, DEXI, that is based regarding the reverse assistance and you will direct-so you’re able to head towards the CIITA transcript. Activation out of DEXI by the EBNA2 happened as a result of antique increase in H3K27ac on enhancement and you will H3K4me3 and you can RNAPII at supporter region. Alternatively, EBNA2 induced the alternative impact on CIITA booster and supporter regions, add up to a decrease in CIITA transcription. Study of one’s chromosome domain structure revealed from the HiC within the EBV+ LCLs implies that DEXI and you will CIITA enhancers come into some other, but nearby TADs, and therefore a strong border can be acquired anywhere between this type of gene enhancers. Mutation of an excellent CTCF site throughout the border area changed the effect of EBNA2 with the CIITA enhancers, causing them to react just like the DEXI booster. Such conclusions recommend that CTCF segregates EBNA2 address family genes, and this EBNA2 normally repress some address family genes because of a competitor having surrounding enhancers and chromosome cabins for RNAPII (Fig 9).

50% of one’s instances [70,71]. Ergo, EBNA2 down regulation of CIITA are phone-style of particular, depending on chromatin website name design and you will enhancer wiring style of so you’re able to B-cells however, possibly various other from inside the EBV epithelial disease.

Combined lymphocyte reactions

gRNAs targeting CTCF binding motif or EBNA2 joining website was cloned to your lentiCRISPRv2 (Addgene 52961) playing with typed standards . Lentiviruses have been produced and you may EREB2.5 cells was in fact transduced once the described above. Genomic DNA out-of tissue is remote having Genomic DNA purification kit (Promega), gRNA address sites was in fact increased because of the PCR, examined by agarose gel electrophoresis, and the PCR affairs were Sanger sequenced from the Wistar Institute sequencing facility. The fresh new succession shade is examined because of the Wave algorithm (offered by .

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