Project description:Giant ragweed (Ambrosia trifida) is an economically disruptive weed in US corn and soybean production. Populations of this species have evolved a unique glyphosate resistance mechanism involving rapid cell death in mature leaves, also known as rapid necrosis. This abiotic stress resistance mechanism may be due to utilization of stress response pathways typically associated with biotic stresses such as pathogens. To study the genetic basis of this rapid response, an RNA-Seq time course study was conducted on young and mature leaves of glyphosate-resistant and -susceptible individuals, before and after glyphosate treatment. A major difference in gene regulation following glyphosate application was observed between young and mature leaves in the glyphosate-resistant individuals. Many differentially expressed genes were related to broad plant pathways with cross-functionality including plant stress and cell death pathways, phytohormone synthesis, response to oxidative stress, cellular metabolism, and pathogen defense pathways. Metabolic network analysis revealed that most of the genes involved in jasmonate biosynthesis were up regulated in response to glyphosate treatment in resistant mature leaves whereas this pathway was not induced in susceptible plants. The glyphosate-resistant plants appear to perceive glyphosate differently than susceptible plants, pointing to the potential role of a yet to be characterized receptor that senses glyphosate or its action and triggers the rapid necrosis response in mature leaves. Additional steps are needed for functional validation to test the hypothesis of causal relationship between function of these candidate genes of interest and the glyphosate resistance rapid response phenotype.
Project description:Neoadjuvant treated patients were selected from the Genomstudy of the University Women`s Clinic Heidelberg (2009-2016). This study includes primary breast cancer cases that were newly diagnosed at the University women's clinic of Heidelberg and had given their informed consent for participating in this study. This study was approved by the Ethical Committee of the Medical Faculty in Heidelberg. All cases were female and Caucasian. Fresh core needle biopsies and fresh tumor tissue were examined by a pathologist, snap-frozen in liquid nitrogen and stored at -80C within 15 min after sampling. Total RNA as well as DNA and protein were extracted by applying the QIAGEN All Prep Kit. All eluates were stored at -80C until usage. A sample swap most probably occurred for patient 207, so 207-S is actually in the T condition and 207-T in the S condition.
Project description:Little is known about the lung microbiome dynamics and host-microbiome interactions in relation to chronic obstructive pulmonary disease (COPD) exacerbations and in patient subgroups based on smoking status and disease severity. Here we performed a 16S ribosomal RNA survey on sputum microbiome from 16 healthy and 43 COPD subjects. For COPD subjects, a longitudinal sampling was performed from stable state to exacerbations, at two and six weeks post-exacerbations and at six months from first stable visit. Host sputum transcriptome were characterized for a subset of COPD patient samples.
Project description:The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence. Experimental Design: Whole blood collected in tempus tubes from patients with different spectra of TB disease. All patients were sampled prior to the initiation of any antimycobacterial therapy. Active Pulmonary TB: PTB - All patients confirmed by isolation of Mycobacterium Tuberculosis on culture of sputum. Latent TB: LTB - All patients were screened at a tuberculosis clinic. All were positive by Interferon-Gamma Release assay(IGRA); specifically Quantiferon Gold In-Tube Assay (Cellestis, Australia). Latent patients had no clinical, or microbiological evidence of active infection and were asymptomatic. Experimental Variables: Patient group: Active PTB; Latent TB. There are no healthy controls in this dataset as it was being used for validation only. Controls: Latent TB individuals are used as a control for PTB in this dataset since there are few to no unexposed adult controls in Cape Town.
Project description:Gene expression profiling using oligonucleotide microarrays performed on tumor samples obtained before and after imatinib mesylate (IM) therapy. Rapid responding (to IM) samples were compared to non-responding/stable disease samples as measured by CT scan measurements to identify a gene signature that can predict rapid response to IM. Experiment Overall Design: 54 samples, 29 pre-treatment biopsy samples, 25 post-treatment/post-surgery tumor samples from Gastrointestinal Stromal Tumors