Neochloris oleoabundans RNA sequencing of 5 growth conditions, 8 samples
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ABSTRACT: Growth conditions with different light and nitrogen supply, to understand the transcriptional response caused by the environmental conditions.
Project description:This SuperSeries is composed of the following subset Series: GSE27245: Expression data from Top2β KO cells as well ICRF-193 treatment of in vitro derived neurons and cortical glutamatergic neurons GSE27246: Top2β ChIP-chip Refer to individual Series
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
Project description:Non-canonical small open reading frames (smORFs) that encode microproteins (miPs; <100 amino acids) are present in the genome. However, the study of smORF-encoded miPs has been hampered by technical challenges associated with the detection of small peptides by mass spectrometry. Here we combined deep RNA sequencing of ribosome-associated transcripts and optimized bioinformatic pipelines for downstream proteomic studies to identify thousands of smORF-derived miPs in endothelial cells (human 2,256, murine 7,597). Profound alterations in smORF/miP expression were detected following human endothelial cell activation by interleukin 1beat (IL-1beta) in vitro and by hypercholesterolemia and altered blood flow in vivo (in mice). Genome-wide homology analyses revealed that human smORFs are highly conserved among primates, and poorly in rodents or zebrafish. Functional characterization of selected miPs demonstrated their physical interaction with proteins in different subcellular compartments and their involvement in the regulation of proliferation, cell death, gene expression and inflammation. Moreover, it was possible to demonstrate that miPs can be released into the blood stream following cellular damage in humans. These findings demonstrate the value of this proteo-genomic pipeline for smORF and miP identification and highlight that the potential impact of miPs on cell and tissue function is much larger than previously presumed.
Project description:Non-canonical small open reading frames (smORFs) that encode microproteins (miPs; <100 amino acids) are present in the genome. However, the study of smORF-encoded miPs has been hampered by technical challenges associated with the detection of small peptides by mass spectrometry. Here we combined deep RNA sequencing of ribosome-associated transcripts and optimized bioinformatic pipelines for downstream proteomic studies to identify thousands of smORF-derived miPs in endothelial cells (human 2,256, murine 7,597). Profound alterations in smORF/miP expression were detected following human endothelial cell activation by interleukin 1beat (IL-1beta) in vitro and by hypercholesterolemia and altered blood flow in vivo (in mice). Genome-wide homology analyses revealed that human smORFs are highly conserved among primates, and poorly in rodents or zebrafish. Functional characterization of selected miPs demonstrated their physical interaction with proteins in different subcellular compartments and their involvement in the regulation of proliferation, cell death, gene expression and inflammation. Moreover, it was possible to demonstrate that miPs can be released into the blood stream following cellular damage in humans. These findings demonstrate the value of this proteo-genomic pipeline for smORF and miP identification and highlight that the potential impact of miPs on cell and tissue function is much larger than previously presumed.
Project description:The layered structure of the cerebral cortex is formed through a complicated sequence of highly controlled stages. During this process, the perturbations of neuronal migration and cell division can result in a rare disorder called cortical heterotopia. Heterotopia patients can have recurrent epileptic seizures, developmental delays, and mild intellectual disabilities. Studying heterotopia has been challenging because human mutations linked to the disease often do not result in heterotopia formation in mouse models. EML1 is a microtubule-binding protein, and it stands out as the first heterotopia-associated gene where mutations lead to heterotopia formation in both humans and mice. In this study, we conducted a comparative proteomic analysis of the Eml1 cKO heterotopic mice cortices and neuronal progenitor primary cells during cerebral cortex development. We performed label-free and dimethyl labeling-based quantitative proteomic approaches, and microtubule pelleting assays to understand how Eml1 depletion disrupts protein networks in cortical tissue and neuronal progenitor primary cells during cerebral cortex development.
Project description:The use of cell factories to convert sugars from lignocellulosic biomass into chemicals in which oleochemicals and food additives, such as carotenoids, play an important role is essential for the shift towards sustainable processes. Rhodotorula toruloides is a yeast that naturally metabolises a wide range of substrates, including lignocellulosic hydrolysates, and converts them into lipids and carotenoids. In this study, xylose, the main component of hemicellulose, was used as the sole substrate for R. toruloides, and a detailed physiology characterisation combined with absolute proteomics and genome-scale metabolic models was carried out to understand the regulation of lipid and carotenoid production. To improve these productions, oxidative stress was induced by hydrogen peroxide and light irradiation and further enhanced by adaptive laboratory evolution. Based on the online measurements of growth and CO2 excretion, three distinct growth phases were identified during batch cultivations. The intracellular flux estimations correlated well with the measured protein levels and demonstrated improved NADPH regeneration and phosphoketolase activity and reduced beta-oxidation, correlating with increasing lipid yields. Light irradiation conditions resulted in 70% higher carotenoid and 40% higher lipid yields. The presence of hydrogen peroxide did not affect the carotenoid yield but culminated in the highest lipid yield of 0.65 ± 0.06 g/gDCW. The adapted strain showed improved fitness and 130% higher carotenoid yield than the parental strain. This work presented a holistic view of xylose conversion into microbial oil and carotenoids by R. toruloides for further cost-effective and renewable production of these molecules.
Project description:We tested the inhibitory effects of hydroalcoholic extracts from grape leaves in breast cancer malignancy using MCF-7 and SKBR-3 cell lines.
Project description:We aim to test how SMARCA4 restoration impacts p300 occupancy distribution. To this aim we generated ChIP-seq samples in BIN-67 with or without A-485 treatment (1 μM, 24h), as a proxy for p300 acetylatransferase inhibition, and BIN-67 with inducible SMARCA4 restoration (1 μg/ml Doxycycline for 24h). We pulled down p300 and H3K27ac as a marker for p300 acetyltransferase activity on the chromatin.