A study of Virus-induced changes in mRNA secondary structure uncover cis-regulatory elements that directly control gene expression. Mizrahi et al.
Contributors: Orel Mizrahi
... Unraveling cis-regulatory elements by mapping changes in mRNA structure for that reason, we measure the changes in mRNA structure using DMS-MaPseq libraries between uninfected and HCMV infected cells, and found dozens of regions in mRNAs that significantly change their structure, and have a direct role in gene expression regulation.
Contributors: Sergey Ananyev
... Numerical simulation of the motion of the plasma current sheath (PCS) of the plasma-focus discharge, dynamics of pinching and subsequent pinch decay is carried out using various working gases in the PF-3 facility – the Filippov’s type plasma focus. For calculations, a one-component magnetohydrodynamic model was used taking into account the Hall-effect near the electrodes. On the basis of the simulation, the previously predicted key role of the Hall-effect in the phenomenon of PCS “runaway” along the anode has been confirmed. The simulation of PCS motion is in good agreement with the experimental results for the heavy gases (Ne, Ar) and the light ones (hydrogen and deuterium). The influence of the addition of heavy gas (Xe) to deuterium on the structure of the sheath and the dynamics of compression was simulated, previously observed in experiments.
Raw, not cropped supporting Western blot files for: Mavrommati, I., ... Pagano, M., D'Angiolella, V.: β-TrCP- and Casein Kinase II-Mediated Degradation of Cyclin F Controls Timely Mitotic Progression. Cell Rep. (2018)
Contributors: Michele Pagano
... Raw, not cropped supporting Western blot files for: Mavrommati I, Faedda R, Galasso G, Li J, Burdova K, Fischer R, Kessler BM, Carrero ZI, Guardavaccaro D, Pagano M, D'Angiolella V. β-TrCP- and Casein Kinase II-Mediated Degradation of Cyclin F Controls Timely Mitotic Progression. Cell Rep. 2018 Sep 25;24(13):3404-3412. doi: 10.1016/j.celrep.2018.08.076. PMID: 30257202 PMCID: PMC6172692 DOI: 10.1016/j.celrep.2018.08.076
Contributors: Philipp Keller
... Guide's software and data repository- compact version
Contributors: Philipp Keller
... Guide's software and data repository- full version
Data for: An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network
Contributors: Ying Liang, Peng Xu, Huaibing Luo, Wenqiang Yu, zou qingping
... Fig.1. Differential and conserved nucleosome occupancy at NSR and NDR during the cell cycle. In the upper panel, a model describing NDR and NSR. In the lower panel, signal-plots showing nucleosome occupancy spanning 3kb at NSR and NDR identified in G0/G1, S2, and G2/M phases. 0 indicates the middle of the NSR and NDR. Fig.2. miRNAs genome loci are overlapped with enhancers. Among 1871 annotated human miRNA precursor loci, 1263 miRNA genome loci are overlapped with enhancer marked by H3K4me1, and 1217 miRNA genome loci are overlapped with enhancer marked by H3K27ac, 1076 miRNA precursor loci partially or absolutely overlapped with the corresponding enhancer regions which are marked by both H3K27ac and H3K4me1. The blue circle means there are 478 highly conserved miRNA precursors marked by both markers. Fig.3. Tissue-specific enhancer marked in genome loci. The tissue-specific enhancer region is defined by the H3K27ac ChIP-seq peaks from Roadmap Data with macs2.0 default parameters. The top three lines of graphics mark the tissue-specific enhancer region and the miRNAs locus, such as miR-122 in liver, let-7g-5p in lung, miR-1-5P in skeletal muscle. The X axis shows the genome position; and the Y axis indicates H3K27ac ChIP-seq reads per million/base pair. The bottom line pictures show the miRNA expression in different tissues. The X axis presents the miRNAs expression level, meanwhile, the Y axis displays different tissue. Fig.4. NamiRNA miR-339 activates GPER1 expression in T47D cell. miR-339 were successfully transfected in breast cancer cell line T47D (Left panel). miR-339 can upregulates expression of targeted gene GPER1 compared to the negative control group (Right panel). Fig.5. NamiRNA ‒ enhancer ‒ gene activation network and cell identity loss The upper left panel indicates NSRs and NDRs are formed by the selective exclusion of histone during cell cycle. In the NDR regions, NamiRNA-enhancer-gene activation network exerts their function to govern the cell-specific gene expression pattern, in which Ago2 may serve as a guide. The upper right panel indicates the altered NSR-NDR distribution and NamiRNA-enhancer-gene activation network in a cancer cell, which drives the cell identity transition from normal cell to cancer cell during the cell cycle (the lower panel).
Contributors: Rikke Meyer
... Inorganic fouling is one of the challenging problems in heat exchanger applications. One approach to mitigate fouling is to employ surface coatings. In this study, we evaluated the feasibility of surface initiated polymerization (SIP) as thin coating technology to mitigate CaCO3 formation for heat transfer applications. The extent of formation of CaCO3 on different types of poly(oligoethyleneglycol) methacrylate brushes (POEGMA) was investigated under stagnant and flow heat-exchanging conditions. Polymer brushes of high graft density reduced the surface coverage of CaCO3 more effectively than the low graft density brushes. By contrast, the thickness of the brush did not correlate with the surface coverage of CaCO3. The comparison of stagnant and flow experiments revealed that the antiscaling effect of POEGMA brushes originate due to reduced adhesion of CaCO3. Finally, the SIP process was successfully scaled-up to coat commercial heat exchanger plates with thickness and homogeneity comparable to lab-scale surfaces. Under industrial testing, the POEGMA brushes extended the performance by 50 h before the commencement of complete blockage.
Contributors: Yuliang Tan
... Nuclear receptors induce both transcriptional activation and repression programs responsible for development, homeostasis, and disease. Here, we report a previously overlooked enhancer decommissioning strategy underlying a large estrogen receptor alpha (ERα)-dependent transcriptional repression program. The unexpected signature for this E2-induced program resides in indirect recruitment of ERα to a large cohort of pioneer factor basally active FOXA1-bound enhancers that lack cognate ERα DNA-binding elements. Surprisingly, these basally active estrogen-repressed (BAER) enhancers are decommissioned by ERα-dependent recruitment of the histone demethylase KDM2A, functioning independently of its demethylase activity. Rather, KDM2A tethers the E3 ubiquitin-protein ligase NEDD4 to ubiquitylate/dismiss Pol II to abrogate eRNA transcription, with consequent target gene downregulation. Thus, our data reveal that Pol II ubiquitylation/dismissal may serve as a potentially broad strategy utilized by indirectly bound nuclear receptors to abrogate large programs of pioneer factor-mediated, eRNA-producing enhancers.
Contributors: Gabriel Fiorin, Andrea Sanchez-Vallet , Daniela Thomazella, Paula Prado, Leandro Nascimento, Antonio Figueira, Bart Thomma, Goncalo Pereira, Paulo Teixeira
... Source data of the paper "Suppression of plant immunity by fungal chitinase-like effectors".
Contributors: Eran Halfi, Asher Brenner, David Katoshevski
... This video, filmed with Go-Pro Hero2, is an overview of the grouping process in a laboratory experiment conducted in a 2 Liter beaker with initial turbidity of 50 NTU. The time shown in the down right corner of the presentation is in minutes (high speed editing). The experiment consisted of 30 minutes of oscillations. The white sedimentation which accumulates in the bottom of the beaker are the aggregates which are formed and settle due to the oscillation process in distinct settling zones. The shape of "lungs" formed by the aggregates sedimentation is representative for all experiments.