Project description:This dataset has been used to establish GroEL-SIP, coupling a targeted proteotyping approach for assessing bacterial community compositions using the taxonomic marker protein GroEL with stable isotope probing to link the identified taxa to substrate assimilation. This dataset contains raw data of four experiments: 1.) Pure cultures of T. aromatica cultivated with 13C or 12C benzoate mixed in defined ratios. 2.) Pure cultures of P. putida cultivated with 13C or 12C benzoate mixed in a 1:1 ratio. 3.) Pure cultures of E. coli cultivated with 12C acetate and 13C or 12C benzoate mixed in a 1:1 ratio. 4.) Co-cultivated biculture of T. aromatica and P. putida cultivated with 13C or 12C benzoate and mixed in a 1:1 ratio. 5.) Co-cultivated biculture of T. aromatica and E. coli cultivated with 12c acetate and 13C or 12C benzoate and mixed in a 1:1 ratio. 1)-3) were analyzed after in-solution digestion 4)-5) were analyzed after in-gel digestion of the 60 kDa band
Project description:Therapeutic neo-vasculogenesis in vivo can be achieved by the co-transplantation of human endothelial colony-forming progenitor cells (ECFCs) with mesenchymal stem/progenitor cells (MSPCs).The underlying mechanism is not completely understood thus hampering the development of novel stem cell therapies.We hypothesized that proteomic profiling could be used to retrieve the in vivo signaling signature during the initial phase of human neo-vasculogenesis. ECFCs and MSPCs were therefore either transplanted alone or co-transplanted subcutaneously into immune deficient mice. Early cell signaling, occurring within the first 24 hours in vivo, was analyzed using antibody microarray proteomic profiling.Vessel formation and persistence were verified in parallel transplants for up to 24 weeks. Proteomic analysis revealed significant alteration of regulatory components including caspases, calcium/calmodulin-dependent protein kinase, DNA protein kinase,human ErbB2 receptor-tyrosine kinase as well as mitogen-activated protein kinases.Therapeutic candidate caspase-4 was selected from array results for targeting vascular network formation in vitro as well as modulating therapeutic vasculogenesis in vivo. As a proof-of-principle, caspase-4 and general caspase-blocking led to diminished endothelial network formation in vitro and significantly decreased vasculogenesis in vivo. Proteomic profiling ex vivo thus unraveled a signaling signature which can be targeted to modulate neo-vasculogenesis in vivo.
Project description:To investigate the role of eosinophils on osteoclast differentiation from bone marrow-derived monocytes (BMMs), BMMs were cultivated in the presence or absence of eosinophils and eosinophil supernatant as compared with unstimulated control.
Project description:Differential gene expression analysis of C. glutamicum ATCC 13032 in presence of 2.5 mM indole compared to control conditions without indole. C. glutamicum ATCC 13032 cells were cultivated in CGXII minimal medium with 40 g per litre glucose in presence of 2.5 mM indole and harvested during exponential phase (o.d.600 4).
Project description:Serum Proteomic Analysis of patients with Hidradenitis Suppurativa treated with 15mg daily of Upadacitinib. Samples from Week 0 and Week 4 of therapy, Straficied by clinical response.
Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.
Project description:Differential gene expression analysis of C. glutamicum C1 in presence of 3 mM indole-alanine dipeptide compared to control conditions without indole-alanine dipeptide. C. glutamicum C1 cells were cultivated in CGXII minimal medium with 40 g per litre glucose in presence or absence of 3 mM indole-alanine dipeptide and harvested during exponential phase (o.d.600 6).