Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. ...[more]
Project description:Anaplastic Lymphoma Kinase (ALK) is a tyrosine kinase receptor which is a clinical target of major interest in cancer, including neuroblastoma. To better understand ALK signaling, three different neuroblastoma cell lines (CLB-BAR, CLB-GE and SK-N-AS) were cultured for 1hr and 24hrs in control conditions or after treatment with the ALK inhibitors crizotinib or lorlatinib. RNA-Seq experiments were performed to determine the expression changes resulting from ALK inhibition. Together with parallel phosphoproteomic experiments, these data unveil several important conserved oncogenic pathways in neuroblastoma.
Project description:Objective: We analyzed changes in A. fumigatus gene expression profile at various stages of an in vitro model of aspergillosis to study the adaptation of A. fumigatus to the blood environment. Results: Most of virulence factors described to be involved in aspergillosis were not activated during the blood phase. We found three active processes to be activated in the later phase that may help to the adaptation: Iron homeostasis, a partial secondary metabolite cluster and the formation of detoxification enzymes. Conclusions: We propose that A. fumigatus is unable to grow in blood and it requires a metabolic change that allows the organism to shut down all uptake and energy-consume mechanisms, resulting in a resting mycelial stage. We performed gene expression profile by sequencing mRNA of A. fumigatus that were growm under two conditions, Minimal Medium (M) and human blood (B), and at different times: before placing the fungus in the final medium (pre), at 30' and at 180', with 2 biological replicates per condition.
Project description:We investigated the transcriptome of the eye imaginal discs and retinae in wild type (GMR/+) and DeIF6 overexpressing (GMR>DeIF6) flies at the third instar larva stage and pupa 40 hours after puparium formation.
Project description:For RNA sequencing, 3 days seedlings were moved to agar plates supplemented with 1/4 B&D media and susceptible zone of 14 days-old plants was harvested after specific treatment with water (Mock treated) or M.loti Nod factor 10-8M (NF). The total RNA was isolated from the susceptible zone (15 mm root pieces) using Nucleo spin RNA plant (Macherey-Nagel). Total RNA (> 0.8 g) from two biological replicas per sample was used by GATC Biotech (Germany) to prepare random primed cDNA library and for sequencing with Illumina HiSeq: read length 1 x 50bp. Gifu- L. japonicus wild-type, 4820- nfre-1 allele of Nfre, 38534- nfre-2 allele of Nfre.
Project description:GA2OX::PLA1 transgenic plants and their none-transgenic siblings were grown in the field in Wetteren and in the growth chamber. In the field, we sampled three plants per plot (three plots were sown per genotype), resulting in three pools each consisting of three plants. Every pool represented a different subplot. In the growth chamber, the plants were sampled randomly across the population, with three pools, each consisting of three plants. For each plant, the day of leaf 4 appearance was marked and the samples were taken two days after leaf 4 appeared (DALA). The seedlings were cut just above soil level and the growing fourth leaf was dissected out and the younger leaves inside leaf 4 were removed. Using a ruler we sampled the basal cm of leaf 4 (division zone) for RNA preparation. The samples were snap frozen and transported to the lab for storage at -80 degrees and further processing. One time point was sampled, two days after leaf 4 appearance.
Project description:GA2OX::PLA1 transgenic plants and their none-transgenic siblings were grown in the field in Wetteren and in the growth chamber. In the field, we sampled three plants per plot (three plots were sown per genotype), resulting in three pools each consisting of three plants. Every pool represented a different subplot. In the growth chamber, the plants were sampled randomly across the population, with three pools, each consisting of three plants. For each plant, the day of leaf 4 appearance was marked and the samples were taken two days after leaf 4 appeared. The seedlings were cut just above soil level and the growing fourth leaf was dissected out and the younger leaves inside leaf 4 were removed. Using a ruler we sampled the basal cm of leaf 4 (division zone) for RNA preparation. The samples were snap frozen and transported to the lab for storage at -80 degrees and further processing. Two time points were sampled, two days after leaf 4 appearance as well as six days after leaf appearance.
Project description:Transcriptomic analyses are particularly powerful in research when they are based on detailed underlying knowledge of developmental processes, morphological/anatomical features and biochemical/metabolic processes. Our work is based on our detailed knowledge of grain development and provides an invaluable resource for both Brachypodium grain development specifically and for comparative analyses to other species, including cereal crops. Grain development includes several transition points in addition to being preceded and succeeded by the fundamental developmental switches of fertilization and germination. Such complex process requires a larger sets of genes expressed in a highly-controlled manner. We have selected eight stages of developmental in Brachypodium distachyon encompassing these transitions and conducted comprehensive transcriptomic analyses to generate a valuable resource of the developmental transitions and the distinctive biological processes that are activated and/or repressed during grain development and germination. Comparison of the data generated in this project to other grasses, including the important crop species, and beyond will also shed light on the conservation and/or diversification in gene expression and function in an evolutionary context. Brachypodium distachyon grains (Bd-21 accession) were germinated on moist filter paper after stratification at 4°C for 48h. Five-day old seedlings were transferred to 9cm square pots with a 2:2:1 multipurpose compost: vermiculite: sand mix and grown under controlled environment conditions with a 18h photoperiod at 20°-22°C and light intensity of 180-200 umol/m/s. Tissue samples were collected from eight distinct developmental stages; pre-anthesis ovaries, young grains (1-3 DAA), middle length grains (3-8 DAA), full length grains (8-15 DAA), mature grains (15-20 DAA), mature grains without embryo, germinating grains and seedlings at 3-4 days after germination (Fig.1). Tissues were frozen in liquid nitrogen immediately after collection and were kept at -80°C until further analyses. Total RNA was isolated from frozen tissue samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions. Three biological replicates were used for each stage of development. The RNA samples were treated with DNase I (New England Biolabs) in order to eliminate DNA contamination and their concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
Project description:White fat browning is a highly variable genetic trait in mice (Guerra et al., 1998). To gain an overview of strain variations in browning capacities, we performed transcriptome analysis of white fat browning in (1) 5 inbred mouse strains (C57BL/6J, 129S6sv/ev, A/J, AKR/J, and SWR/J) with distinct browning propensities in WAT, and (2) F1 hybrids derived from a high (129S6sv/ev) and low browning strain (C57BL/6J) cross. From our analyses, several transcription factors emerged as novel regulators of white fat browning, including the TFs Zfp521, Fhl1, and Mxd1. We further validated the role of these TFs and performed 3' RNA-seq experiments upon their knockdown, in order to characterize their mechanism of action.