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Project description:Primary objectives: percentuale di pazienti che saranno sottoposti a resezione completa
Primary endpoints: Lo Studio si propone di aumentare la percentuale di resecabilita’ di pazienti con metastasi epatiche da carcinoma del colon retto.
| 2517634 | ecrin-mdr-crc
Project description:C-di-AMP is primarily associated with the regulation of carbon utilization as well as other central traits, central metabolism, and bacterial stringent response to environmental changes. Elevated c-di-AMP levels result in aberrant physiology for most c-di-AMP synthesizing organisms, drawing particular attention to the importance of the c-di-AMP homeostasis and the molecular mechanisms pertaining to nucleotide metabolism and signal transduction. Here we show that c-di-AMP binds the GntR-family regulator DasR, uncovering a direct link between c-di-AMP and GlcNAc signaling. Further, we show c-di-AMP functions as an allosteric activator of DasR activity. GlcNAc is necessary for cell-surface structure from bacteria to humans, as well as a signal for bacterial development and antibiotic production. DasR is a global repressor that oversees GlcNAc metabolism and antibiotic production, which enables Actinobacteria to cope with stress and starvation. Our in vivo studies reveal the important biological role of allosteric regulation by c-di-AMP in metabolic imbalance and the transduction of a series of signals. Notably, DasR also controls intracellular c-di-AMP level through direct repression on disA. Overall, we identify a function of allosteric regulation between c-di-AMP and DasR in global signal integration and c-di-AMP homeostasis in bacteria, which is likely widespread in Actinobacteria.
2024-03-31 | GSE229938 | GEO
Project description:The dimerization and binding of DNA by BldD is affected by its interaction with cyclic di-GMP. The D116A mutant of BldD is partially impaired in its biding of cyclic di-GMP. ChIP-Seq was carried out to determine the difference in the degree of DNA binding by the wild type and D116A mutated BldD in Streptomyces venezuelae.
2017-11-01 | E-MTAB-5328 | biostudies-arrayexpress
Project description:Correct chromosome segregation requires that sister chromatids are held together by the protein complex cohesin, from S phase until anaphase. This S phase established cohesion is, together with DSB recruitment of cohesin and formation of damage induced (DI) cohesion, also important for repair of DSBs. Eco1 is a common essential factor for S phase and DI-cohesion. The fission yeast Eco1ortholog, Eso1, is important both for S phase cohesion and for bypass of UV induced lesions, and is expressed as a fusion protein with Polη. The cohesion function has been attributed solely to Eso1 and the lesion bypass function to the Polη part of the protein. As we found the interaction between the two proteins intriguing we decided to look for a functional connection also in budding yeast. Indeed, despite being dispensable for S phase cohesion, budding yeast Polη is required for formation of DI genome-wide cohesion. However, Polη deficient cells are DSB repair competent, revealing differential regulation of DI-cohesion at the break and genome-wide. This finding challenges the importance of DI genome-wide cohesion for DSB repair, and based on our findings we suggest that S phase cohesion is not sufficient for correct chromosome segregation in the presence of DNA damage. Whole Genome binding of G2 expressed Scc1 in the presence and absence of Rad30.
2013-01-15 | E-GEOD-42655 | biostudies-arrayexpress
Project description:affy_agro-bi_medicago - Identification of genes from the model legume Medicago truncatula whose expression is affected by the plant nitrogen status, with or without inoculation with the symbiotic bacteria Sinorhizobium meliloti. - Comparison of the supernodulant, nitrogen-insensitive, sunn-2 mutant with the A17 wild type genotype.-The plant root systems of plants were split into two parts, each one being installed in a separate compartment. For the â??Sâ?? treatment, one part was supplied with 10 mM NH4NO3 while the other part was supplied with a nitrogen-free nutrient solution. For the â??Lâ?? treatment, one part was supplied 0.5mM NO3- and the other part was supplied with the nitrogen free solution. Eight biological materials (designated AL, AS, SL, SS, IL, IS, NIL, NIS), with three biological repeats for each, were collected and analyzed. The effects of the S and L conditions were investigated on wild-type A17 (AL vs. AS) and sunn-2 mutant plants (SL vs. SS); one set of A17 plants was inoculated with Sinorhizobium meliloti (IL vs. IS), harvested at four days post inoculation and compared to non-inoculated plants (NIL vs. NIS). Keywords: growth in nitrogen-sufficient (s) vs. nitrogen-limited (l) conditions 18 arrays - Medicago
2010-10-28 | E-GEOD-17253 | biostudies-arrayexpress
Project description:affy_agro-bi_medicago - Identification of genes from the model legume Medicago truncatula whose expression is affected by the plant nitrogen status, with or without inoculation with the symbiotic bacteria Sinorhizobium meliloti. - Comparison of the supernodulant, nitrogen-insensitive, sunn-2 mutant with the A17 wild type genotype.-The plant root systems of plants were split into two parts, each one being installed in a separate compartment. For the “S” treatment, one part was supplied with 10 mM NH4NO3 while the other part was supplied with a nitrogen-free nutrient solution. For the “L” treatment, one part was supplied 0.5mM NO3- and the other part was supplied with the nitrogen free solution. Eight biological materials (designated AL, AS, SL, SS, IL, IS, NIL, NIS), with three biological repeats for each, were collected and analyzed. The effects of the S and L conditions were investigated on wild-type A17 (AL vs. AS) and sunn-2 mutant plants (SL vs. SS); one set of A17 plants was inoculated with Sinorhizobium meliloti (IL vs. IS), harvested at four days post inoculation and compared to non-inoculated plants (NIL vs. NIS). Keywords: growth in nitrogen-sufficient (s) vs. nitrogen-limited (l) conditions
2010-10-28 | GSE17253 | GEO
Project description:To examine the effects of cyclic-di-GMP on DNA binding by BldD in vivo, we manipulated the levels of c-di-GMP in Streptomyces venezuelae and monitored the effect on BldD binding to its target promoters in vivo by ChIP-seq, using a polyclonal BldD antibody. The degree of BldD binding was assayed at a single time point in wild-type (wt) S. venezuelae and the wt overexpressing either the diguanylate cyclase CdgB or the phosphodiesterase YhjH. A bldD null mutant was used a negative control.
2016-07-03 | E-MTAB-2196 | biostudies-arrayexpress
Project description:The cholera disease bacterium V. cholerae, can adopt planktonic or biofilm lifestyles depending on the intracellular concentration of the second messenger cyclic diguanylic acid (c-di-GMP). Biofilm formation protects Vibrios from stressful conditions and facilitates disease transmission by enhancing infectivity. The histone-like nucleoid structuring protein (H-NS) is a global regulator of genes associated with pathogenicity and responses to environmental stresses. H-NS represses the transcription of genes vpsT, vpsA and vpsL, which are required for the biosynthesis of the biofilm exopolysacchide matrix. Here we demonstrate that the c-di-GMP-binding protein VpsT disrupts H-NS nucleoprotein complexes at the vpsA and vpsL promoters and that this effect is enhanced by c-di-GMP. We used ChIP coupled with Next Generation Sequencing (ChIP-Seq) and transcriptome analysis (RNA-Seq) to identify additional loci repressed by H-NS affecting biofilm formation. This study showed that H-NS directly represses the transcription of genes encoding proteins present in the biofilm matrix such as the rbmA-F cluster, hemolysin and chitinase. Similar to vpsA and vpsL, the promoter region of vpsU, rbmA and rbmF exhibited overlapping H-NS and VpsT binding motifs. Deletion of vpsT increased H-NS occupancy at the vpsU, vpsA, vpsL, rbmA and rbmF promoters. Conversely, artificially increasing the c-di-GMP pool diminished H-NS occupancy at the above promoters. Deletion of vpsT did not affect H-NS occupancy at its own promoter. However, deletion of genes encoding the regulators AphA and VpsR significantly increased H-NS occupancy at the vpsT promoter. In sum, our study shows that c-di-GMP enhances biofilm formation by acting through VpsT to activate an H-NS anti-repression cascade. The Binding profile of V. cholerae H-NS to the genome was determined by ChIP followed by Next Generation Sequencing (ChIP-Seq) using the Illumina HiSeq2000 platform. V. cholerae C7258 cells expressing H-NS-FLAG fusion protein from the hns transcription and translation signals were collected from LB cultures grown to mid-exponential phase (OD600 0.5). An anti-FLAG Immunoprecipitation (IP) and an Input samples were used for the analysis.
2015-05-13 | E-GEOD-64249 | biostudies-arrayexpress
Project description:TICAM1 knockout and wild-type (TICAM1 knockout MEFs with restored TICAM1 expression) MEFs were treated by c-di-GMP or DMSO for 4 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. Changes in gene induction, especially of interferon-stimulated genes, between c-di-GMP and DMSO treated cells were examined. Total RNA from c-di-GMP or DMSO treated wild-type MEFs, c-di-GMP or DMSO treated TICAM1 knockout MEFs were analyzed. Gene expression was compared between c-di-GMP treated and DMSO treated samples.
2016-07-29 | E-GEOD-78205 | biostudies-arrayexpress
Project description:Correct chromosome segregation requires that sister chromatids are held together by the protein complex cohesin, from S phase until anaphase. This S phase established cohesion is, together with DSB recruitment of cohesin and formation of damage induced (DI) cohesion, also important for repair of DSBs. Eco1 is a common essential factor for S phase and DI-cohesion. The fission yeast Eco1ortholog, Eso1, is important both for S phase cohesion and for bypass of UV induced lesions, and is expressed as a fusion protein with Polη. The cohesion function has been attributed solely to Eso1 and the lesion bypass function to the Polη part of the protein. As we found the interaction between the two proteins intriguing we decided to look for a functional connection also in budding yeast. Indeed, despite being dispensable for S phase cohesion, budding yeast Polη is required for formation of DI genome-wide cohesion. However, Polη deficient cells are DSB repair competent, revealing differential regulation of DI-cohesion at the break and genome-wide. This finding challenges the importance of DI genome-wide cohesion for DSB repair, and based on our findings we suggest that S phase cohesion is not sufficient for correct chromosome segregation in the presence of DNA damage.
2013-01-15 | GSE42655 | GEO