Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series
Project description:Gene transcription was compared in blood between noninfected mice and infected mice after 6h of intraperitoneal infection by Neisseria meningitidis
Project description:This experiment aimed at indentifying secreted proteins/enzymes from saliva of the fly Pseudolycoriella hygida. To do this, twelve-day-old Psl. hygida larvae were selected and the last segment of the larvae was tied with elastane fishing line with the help of a stereomicroscope. This was performed to avoid contamination of saliva samples with feaces. Groups of 20 tied larvae were transferred to 1.5-mL microtubes and a few holes were made in the microtube cap. Then, the microtubes were incubated at 22 °C for 3 h. After removing the larvae, the microtubes were briefly centrifuged at 15,000 g for 30 s, and the secreted saliva, usually 2-3 ul per tube, was stored at -20 °C until gel electrophoresis.
Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926A>C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5’-splice site (5’SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5’SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.
Project description:Gene transcription was compared in brain between noninfected mice and infected mice after 6h of intraperitoneal infection by Neisseria meningitidis
Project description:Expression profile of mutant cells compared to wild-type cells: Expression profile of Schizosaccharomyces pombe genome in ∆pht1, ∆ago1, ∆clr4, rik1, ∆pht1rik1, ∆pht1∆ago1 and ∆pht1∆clr4 cells. Expression profile of Schizosaccharomyces pombe genome in ∆rrp6, ∆cid14, ∆swi6, ∆swr1, ∆set1, ∆pht1∆swi6 and ∆pht1∆set1 cells. Expression profile of Schizosaccharomyces pombe genome in ∆alp13, ∆cph1, ∆set2, clr6-1 and ∆cph1∆pht1 cells. Occupancy profiling: Occupancy profiling of RNA polymerase II, histone variant H2A.Z and ClrC subunit Rik1 in fission yeast Schizosaccharomyces pombe Occupancy profiling of histone variant H2A.Z in ∆msc1 cells. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of RNA polymerase II, H2A.Z or Rik1 from asynchronous culture of fission yeast. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of histone H2A.Z from asynchronous culture of fission yeast.
Project description:Antigen processing and presentation (APP) is essential for adaptive immunosurveillance. We uncover a mechanism whereby activated T cell-derived extracellular vesicles (AT EVs ) drive a positive feedback loop that enhances antigen presentation and immune responses in normal physiology and cancer. AT EV -induced immunogenicity relies on extracellular vesicular double-stranded DNA (EV DNA ), which is notably abundant and primarily composed of genomic DNA enriched in immune-related genes, including those encoding APP machinery. Mechanistically, granzyme B (Gzmb) packaged by AT EVs disrupts the nuclear envelope of recipient cells, facilitating intranuclear transfer and subsequent transient expression of EV DNA encoding APP genes. DNase treatment removes most AT-EV DNA , abrogating APP upregulation and thus T cell activation and recruitment to tumors. Notably, AT EVs hold promise as an acellular immunotherapy, restoring APP and synergizing with checkpoint blockade in immunotherapy-refractory tumors. Collectively, our findings uncover a mechanism of transient, non-viral gene delivery by AT EVs which boosts APP and anti- tumor immunity while limiting autoimmunity.