Project description:In patients with heart failure, concomitant sinus node dysfunction (SND) is an important predictor of mortality, yet its molecular underpinnings are poorly understood. Here, we acquired deep sinus node proteomes and phosphoproteomes in mice with heart failure and SND and report extensive remodelling. Intersecting the measured (phospho)proteome changes with human genomics and pharmacovigilance data highlighted downregulated proteins involved in electrical activity such as the pacemaker ion channel, Hcn4. We confirmed the importance of ion channel downregulation for sinus node physiology using computer modelling. Guided by the proteomics data, we hypothesized that an inflammatory response may drive the electrophysiological remodeling underlying SND in heart failure. In support of this, experimentally induced inflammation downregulated Hcn4 and slowed pacemaking in the isolated sinus node. From the proteomics data we identified proinflammatory cytokine-like protein galectin-3 as a potential target to mitigate the effect. Indeed, in-vivo suppression of galectin-3 in the animal model of heart failure prevented SND. Collectively, we outline the protein and phosphorylation remodeling of SND in heart failure, we highlight a role for inflammation in electrophysiological remodelling of the sinus node, and we present galectin-3 signalling as a target to ameliorate SND in heart failure.
2024-04-25 | PXD031084 | Pride
Project description:Aeration challenge
| PRJNA419321 | ENA
Project description:Combined strategy control bacterial-wilt disease
Project description:In this study, we analyzed the impact of anoxia and re-aeration on tolerant rice at a proteomic level using two-dimensional gel electrophoresis followed by mass spectrometry. Mass spectrometry revealed 82 spots corresponding to 13 and 8 unique proteins in shoots and roots, respectively. Spot-wise clusterization showed the re-aeration proteome to resemble anoxic but not control conditions. We found 4 groups of proteins displaying distinct patterns of intensities of the spots. The most notable group contained proteins whose content continually decreased during stress, such as RuBisCO and fructose-bisphosphate aldolase. The second group included proteins whose synthesis started in anoxia and reached a peak during re-aeration. It involved OEE1 (oxygen-evolving enhancer protein 1), heat shock proteins, and pathogenesis-related (PR) proteins, implying defense from oxidative damage and pathogens to which plants become vulnerable during re-aeration. Promotor regions of genes encoding these proteins were enriched with transcription factors binding sites of stress-related TFs, both well-studied (ERF, WRKY, MYB) and not as frequently discussed in such contexts (TCP, TBP, SBP). By comparing our observations with proteomic and transcriptomic research, we revealed that plant reactions to anoxia and reoxygenation are starkly similar. The results suggest that rice shoots and roots become pre-adapted to post-stress during anoxia. The experimental setup was as follows. Plants were exposed to 24 h of pure anoxia followed by 24 h of re-aeration. 2-DIGE gel figures were scanned with Typhoon, and the intensities of spots were calculated using the PDQuest software. After excision, spots were analyzed with MALDI-TOF MS/MS. Proteins were identified using MASCOT and MGSFplus utilities. Significantly different spots were identified with the limma package. Individual spots and the whole proteomes were then clustered with k-means and hierarchical clustering methods. Functional annotation of protein sequences was performed using the eggNOG standalone tool v2.0.1b-2-g816e190 (Huerta-Cepas et al., 2017a) and the topGO v.2.34.0 (Alexa and Rahnenfuhrer, 2007) package. The upstream regions of genes encoding identified proteins and the respective orthologs from A. thaliana were obtained from the EnsemblPlants (Bolser et al., 2016) database. Finally, transcription factor binding sites within the promoter regions were predicted using the PlantPAN v.3.0 (Chow et al., 2019) and AthaMap (Hehl et al., 2016) tools. Ten-day-old rice seedlings (Oryza sativa L., cv. Flagman, Federal Scientific Center of Rice, Krasnodar, Russia) were studied. Seeds were sterilized using 5% NaClO for 15 min and washed with warm distilled water. Seeds were then soaked for 1 h in hot water (50-55 °С) to induce germination in dark conditions for 3 days at 28°С. Germinated seedlings were planted on perforated plastic plates on containers filled with continuously aerated Knop nutrient solution (0.2 strength) and grown at an irradiance of 100 W/m2 with a photoperiod of 12 h at 23-25°C as described earlier (Emel’yanov et al., 2003; Yemelyanov et al., 2020). Plants were divided into control and experimental groups. For each condition (control, anoxia, and re-aeration), 3 glass beakers containing 20 mL of Knop nutrient solution (0.2 N strength) with 20 seedlings in each were used. To replicate anaerobic conditions, beakers with seedlings were placed into 1.5-liter jars (exicators). The gaseous nitrogen with less than 0.01% of oxygen oxygen was pumped to the exicators for 45 min until reaching complete anoxia. The purity of anaerobic conditions was confirmed via the Anaerotest® anaerobic indicator (Merck, Germany). Once anaerobic conditions were reached, exicators were tightly closed and put in the dark for 24 h to prevent oxygen production during photosynthesis. Control plants were exposed to the dark in aerobic conditions for 24 h. No less than three biological replicates were done for each condition. After 24 h of anoxia, the jars were opened, followed by collecting plant shoots and roots for further protein extraction in the case of anoxic proteomes and control settings. The post-anoxic beakers were exposed to 24 h of dark conditions and were then separately treated for protein extraction as well.
Project description:E. coli K12 strain W3110 was used in this study. Cells were grown anaerobically in defined medium at pH7 and 37°C in a stirred 3-liter bioreactor until the culture reached an OD (600nm) of 3. At that point the first sample was drawn and aeration was started subsequently at 1l/min. 0.5, 1, 2, 5, and 10 min after the onset of aeration additional samples were drawn.
Project description:Salmonella typhimurium 14028s Transposon library grown in M9 minimal medium (arabinose 0.4%), O/N at 37°C with aeration, compared to the initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C Keywords: Transposon tag analysis
Project description:The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.
Project description:Our research describe the influence of aeration conditions in petri dishes for A. thaliana growth. We analyze the difference between plants grown in standard Petri dish (Non-aerated) and modified Petri dish that include aeration (Aerated). To characterize the differences between those conditions the gene expression analysis was performed. We also wanted to analyze the effect of using a micropore filter, so we designed another experiment with Aerated, Non-aerated and Micropore filter conditions.