RNAseq of total, soluble and insoluble fraction of WT and mutant yeast cells after 10 minutes at 30, 40 or 42°C
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE141029 | GEO | 2019/11/26
REPOSITORIES: GEO
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Project description:RNAseq of total, soluble and insoluble fraction of WT and mutant yeast cells after 10 minutes at 30, 40 or 42°C
| PRJNA591797 | ENA
Project description:BackgroundDespite the high sensitivity of cerebrospinal fluid (CSF) amyloid beta (Aβ)42 to detect amyloid pathology, the Aβ42/Aβ40 ratio (amyR) better estimates amyloid load, with higher specificity for Alzheimer's disease (AD). However, whether Aβ42 and amyR have different meanings and whether Aβ40 represents more than an Aβ42-corrective factor remain to be clarified. Our study aimed to compare the ability of Aβ42 and amyR to detect AD pathology in terms of p-tau/Aβ42 ratio and brain glucose metabolic patterns using fluorodeoxyglucose-positron emission tomography (FDG-PET).MethodsCSF biomarkers were analyzed with EUROIMMUN ELISA. We included 163 patients showing pathological CSF Aβ42 and normal p-tau (A + T - = 98) or pathological p-tau levels (A + T + = 65) and 36 control subjects (A - T -). A + T - patients were further stratified into those with normal (CSFAβ42 + /amyR - = 46) and pathological amyR (CSFAβ42 + /amyR + = 52). We used two distinct cut-offs to determine pathological values of p-tau/Aβ42: (1) ≥ 0.086 and (2) ≥ 0.122. FDG-PET patterns were evaluated in a subsample of patients (n = 46) and compared to 24 controls.ResultsCSF Aβ40 levels were the lowest in A - T - and in CSFAβ42 + /amyR - , higher in CSFAβ42 + /amyR + and highest in A + T + (F = 50.75; p < 0.001), resembling CSF levels of p-tau (F = 192; p < 0.001). We found a positive association between Aβ40 and p-tau in A - T - (β = 0.58; p < 0.001), CSFAβ42 + /amyR - (β = 0.47; p < 0.001), and CSFAβ42 + /amyR + patients (β = 0.48; p < 0.001) but not in A + T + . Investigating biomarker changes as a function of amyR, we observed a weak variation in CSF p-tau (+ 2 z-scores) and Aβ40 (+ 0.8 z-scores) in the normal amyR range, becoming steeper over the pathological threshold of amyR (p-tau: + 5 z-scores, Aβ40: + 4.5 z-score). CSFAβ42 + /amyR + patients showed a significantly higher probability of having pathological p-tau/Aβ42 than CSFAβ42 + /amyR - (cut-off ≥ 0.086: OR 23.3; cut-off ≥ 0.122: OR 8.8), which however still showed pathological values of p-tau/Aβ42 in some cases (cut-off ≥ 0.086: 35.7%; cut-off ≥ 0.122: 17.3%) unlike A - T - . Accordingly, we found reduced FDG metabolism in the temporoparietal regions of CSFAβ42 + /amyR - compared to controls, and further reduction in frontal areas in CSFAβ42 + /amyR + , like in A + T + .ConclusionsPathological p-tau/Aβ42 and FDG hypometabolism typical of AD can be found in patients with decreased CSF Aβ42 levels alone. AmyR positivity, associated with higher Aβ40 levels, is accompanied by higher CSF p-tau and widespread FDG hypometabolism.
| S-EPMC10466826 | biostudies-literature
Project description:DEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5’ end or subsequent scanning of the 5’UTR, but whether they perform distinct functions or act redundantly in vivo is poorly understood. We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in yeast by ribosome footprint profiling. Despite similar reductions in bulk translation, inactivation of a cold-sensitive Ded1 mutant substantially reduced the TEs of >600 mRNAs, whereas inactivation of a temperature-sensitive eIF4A mutant yielded <40 similarly impaired mRNAs. The broader requirement for Ded1 did not reflect more pervasive secondary structures at low temperature, as inactivation of temperature-sensitive and cold-sensitive ded1 mutants gave highly correlated results. Interestingly, Ded1-dependent mRNAs exhibit greater than average 5’UTR length and propensity for secondary structure, implicating Ded1 in scanning though structured 5' UTRs. Reporter assays confirmed that cap- distal stem-loop insertions increase dependence on Ded1 but not eIF4A for efficient translation. While only a small fraction of mRNAs is strongly dependent on eIF4A, this dependence is significantly correlated with requirements for Ded1 and 5’UTR features characteristic of Ded1- dependent mRNAs. Our findings suggest that Ded1 is critically required to promote scanning through secondary structures within 5’UTRs; and while eIF4A cooperates with Ded1 in this function, it also promotes a step of initiation common to virtually all yeast mRNAs. We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in yeast by ribosome footprint profiling.The study includes 32 samples, comprised of 16 mRNA-Seq samples and 16 ribosome footprint profiling samples, derived from biological replicates of 3 mutant strains, ded1-cs, ded1-ts and tif1-ts, and the corresponding wild-type strains. The tif1-ts mutant and its wild-type counterpart were analyzed at 30°C and 37°C.
2015-03-02 | E-GEOD-66411 | biostudies-arrayexpress
Project description:Cryptand-containing alternative copolymers were first made from copolymerization of styrenic derivatives and maleic anhydride and then chemically modified in this work by grafting methoxy poly(ethylene glycol) (MPEG) onto the maleic functional groups. These graft copolymers show interesting multistep soluble-insoluble-soluble (S-I-S) transitions in acidic aqueous media at a cloud point (T cp) and a subsequent mixing temperature (T mix). Turbidity measurements and dynamic light scattering studies indicate that such complex transitions may be attributed to the entropic contribution associated with the dehydration and aggregation of the MPEG groups and then the enthalpic contribution associated with the hydrogen bonding between ethylene glycol and carboxylic acid groups. More importantly, the phase transition temperatures and insoluble temperature ranges are very sensitive to changes in subtle hydrophobic-hydrophilic balance of the copolymers, such as the variation of pH, the cryptand size, and the length of the MPEG graft. The understanding of the S-I-S transition in relation to the structure of the copolymers and the external conditions may be useful in the design of smart materials and sensors.
| S-EPMC6645115 | biostudies-literature
Project description:We use ribosome footprinting to assess the gene expression changes occuring after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C). We find that between 40°C and 42°C there is a shift in gene expression from the expression of genes harboring long and structured 5'UTRs to the expression of genes harboring thranscripts with short and unstructure 5'UTRs. We performed these experiments for WT yeast cells as well as for mutant yeast cells in which the RNA helicase Ded1 condensates at lower temperatures (Ded1-IDRm). We find upon comparing mutant and WT cells at 42°C, that Ded1-IDRm has increased expression of genes harboring unstructured 5'UTRs and decreased expression of genes harboring structured 5'UTRs.
2020-04-30 | GSE131176 | GEO
Project description:Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eIF2. However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a ~4.5-fold general translational repression, the protein coding ORFs of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated uORF that repress translation of the main coding ORF under normal conditions. Site specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely in SLC35A4 and MIEF1) encode functional protein products.
2015-01-27 | GSE55195 | GEO
Project description:One of the most applied reaction types to synthesize shape-persistent organic cage compounds is the imine condensation reaction and it is assumed that the formed cages are thermodynamically controlled products due to the reversibility of the imine condensation. However, most of the synthesized imine cages reported are formed as precipitate from the reaction mixture and therefore rather may be kinetically controlled products. There are even examples in literature, where resulting cages are not soluble at all in common organic solvents to characterize or study their formation by NMR spectroscopy in solution. Here, a triptycene triamine containing three solubilizing n-hexyloxy chains has been used to synthesize soluble congeners of prior insoluble cages. This allowed us to study the formation as well as the reversibility of cage formation in solution by investigating exchange of building blocks between the cages and deuterated derivatives thereof.
| S-EPMC8362185 | biostudies-literature
Project description:IntroductionHuntington's disease (HD) is a rare autosomal dominant neurodegenerative disorder caused by a CAG expansion greater than 35 in the IT-15 gene. There is an inverse correlation between the number of pathological CAG and the age of onset. However, CAG repeats between 40 and 42 showed a wider onset variation. We aimed to investigate potential clinical differences between patients with age at onset ≥ 60 years (late onset-HD) and patients with age at onset between 30 and 59 years (common-onset HD) in a cohort of patients with the same CAG expansions (40-42).MethodsA retrospective analysis of 66 HD patients with 40-41-42 CAG expansion was performed. Patients were investigated with the Unified Huntington's Disease Rating Scale (subitems I-II-III and Total Functional Capacity, Functional Assessment and Stage of Disease). Data were analysed using χ2, Fisher's test, t test and Pearson's correlation coefficient. GENMOD analysis and Kaplan-Meier analysis were used to study the disease progression.ResultsThe age of onset ranged from 39 to 59 years in the CO subgroup, whereas the LO subgroup showed an age of onset from 60 to 73 years. No family history was reported in 31% of the late-onset in comparison with 20% in common-onset HD (p = 0.04). No difference emerged in symptoms of onset, in clinical manifestations and in progression of disease between the two groups.ConclusionThere were no clinical differences between CO and LO subgroups with 40-42 CAG expansion. There is a need of further studies on environmental as well genetic variables modifying the age at onset.
| S-EPMC7160095 | biostudies-literature
Project description:We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance. This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). Experiment 1 includes 8 samples, comprised of 4 RNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the dbp1Δ and ded1-ts dbp1Δ mutant strains, cultured in synthetic complete (SC) medium, following shifts in growth temperature from 30°C to 37°C for 2h. Experiment 2 examines the effect of overexpression of DBP1 in rescuing genome-wide translational defects of a ded1-cs mutant (cold-sensitive allele of DED1) and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1 (dubbed DED1-CS), ded1-cs and ded1-cs overexpressing DBP1 (ded1-cs_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 15°C for 10 min. Experiment 3 examines rescue of translational defects of ded1-ts by DBP1 overexpression and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1(DED1-TS), ded1-ts and ded1-ts overexpressing DBP1 (ded1-ts_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 37°C for 2h.
2018-03-01 | GSE111255 | GEO
Project description:BackgroundDecreased concentrations of amyloid-? 1-42 (A?42) in cerebrospinal fluid (CSF) and increased retention of A? tracers in the brain on positron emission tomography (PET) are considered the earliest biomarkers of Alzheimer's disease (AD). However, a proportion of cases show discrepancies between the results of the two biomarker modalities which may reflect inter-individual differences in A? metabolism. The CSF A?42/40 ratio seems to be a more accurate biomarker of clinical AD than CSF A?42 alone.ObjectiveWe tested whether CSF A?42 alone or the A?42/40 ratio corresponds better with amyloid PET status and analyzed the distribution of cases with discordant CSF-PET results.MethodsCSF obtained from a mixed cohort (n?=?200) of cognitively normal and abnormal research participants who had undergone amyloid PET within 12 months (n?=?150 PET-negative, n?=?50 PET-positive according to a previously published cut-off) was assayed for A?42 and A?40 using two recently developed immunoassays. Optimal CSF cut-offs for amyloid positivity were calculated, and concordance was tested by comparison of the areas under receiver operating characteristic (ROC) curves (AUC) and McNemar's test for paired proportions.ResultsCSF A?42/40 corresponded better than A?42 with PET results, with a larger proportion of concordant cases (89.4% versus 74.9%, respectively, p?<?0.0001) and a larger AUC (0.936 versus 0.814, respectively, p?<?0.0001) associated with the ratio. For both CSF biomarkers, the percentage of CSF-abnormal/PET-normal cases was larger than that of CSF-normal/PET-abnormal cases.ConclusionThe CSF A?42/40 ratio is superior to A?42 alone as a marker of amyloid-positivity by PET. We hypothesize that this increase in performance reflects the ratio compensating for general between-individual variations in CSF total A?.
| S-EPMC5147502 | biostudies-literature