Project description:Interventions: Group 1: In this retrospective analysis, the following patient data are analyzed to compare the laser-assisted versus non-laser-assisted lung metastasisctomy with respect to long-term survival:
Age, sex, date of primary surgery, date of lung metastasectomy, localization of the metastasis, TNM staging, existence of extrapulmonal metastasis, neoadjuvant/adjuvant systemic treatments (chemotherapy, radiotherapy), date of recurrent surgery, surgical technique, surgical access, extent of resection, number of resected lung metastases, lung function data, number of dissected lymph nodes, resection margins, duration of hospitalisation, postoperative complications, date of recurrence, localization of recurrence, treatment at recurrence, date of death
Primary outcome(s): overall survival
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: treatment
Project description:Novel development makes remote real-time analysis with possible translation to in-vivo a reality. Remote Infrared Matrix Assisted Laser Desorption Ionization (Remote IR MALDI) system with endogenous water as matrix becomes real and allows to envisage real-time proteomics to be performed in the in-vivo context. Remote IR MALDI is demonstrated to be used to analyze peptides and proteins. Very interestingly, the corresponding mass spectra show ESI like charge states distribution, opening many applications for structural elucidation to be performed in real-time by Top-Down analysis. The charge states show no dependence toward laser wavelength or length of the transfer tube allowing for remote analyses to be perform 5 m away from the mass spectrometry (MS) instrument without modification of spectra. This brings also interesting features to the understanding of IR MALDI ionization mechanism
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments. Four samples were analysed in total. One corresponded to a pooled sample of RNA extracted from root tissues of 60 plants. The other three were biological replicates from shoot tissues, each of which contained 20 plants. Controls were used as reference and corresponded to tissues of plants grown in sterile conditions.
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.
Project description:This project aimed to explore the microbial chemical ecology of a consortium derived from a water kefir fermentation through the integration of directed culturomics, compositional metagenomics and the identification of key metabolites with biological potential, through untargeted metabolomics.
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. In order to study their metabolic potentials, samples of glacial ice were taken from several glacial ecosystems. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures.
Project description:Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. In order to study their metabolic potentials, samples of glacial ice were taken from several glacial ecosystems. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures.
Project description:Cell-free RNAs in biofluids provide opportunities to monitor cancer in a non-invasive manner. Although extracellular microRNAs are extensively characterized, fragmented cell-free long RNAs are not well investigated. Here, we developed Detector-seq (depletion-assisted multiplexing cell-free total RNA sequencing) to enable the deciphering of the cell-free transcriptome. After demonstrating the superior performance of detecting fragmented cell-free long RNAs, we applied Detector-seq to compare cell-free RNAs in human plasma and its extracellular vesicle (EV). Distinct human and microbial RNA signatures were revealed. Structured circular RNA, tRNA, and Y RNA were enriched in plasma, while mRNA and srpRNA were enriched in EV. Meanwhile, cell-free RNAs derived from the virus were more enriched in plasma than in EV. We identified RNAs that showed a selective distribution between plasma and EV and uncovered their distinct functional pathways, that is RNA splicing, antimicrobial humoral response enriched in plasma and transcriptional activity, cell migration, and antigen receptor-mediated immune signals enriched in EV. Although distinctive cancer-relevant RNA signals were identified in plasma and EV, a comparable performance of distinguishing cancer patients from normal individuals could be achieved. Compared to human RNAs, microbe-derived RNA features enabled better classification between colorectal and lung cancer. And for these microbial RNAs, plasma RNAs outperformed EV RNAs for the discrimination of cancer types. Overall, our work provides insights into the unexplored difference of cell-free RNA signals between plasma and EV, thus offering practical guidance for proper selection (with/without EV enrichment) when launching an RNA-based liquid biopsy study. Furthermore, with the ability to capture understudied cell-free long RNA fragments, Detector-seq offers new possibilities for transcriptome-wide characterization of cell-free RNAs to facilitate the understanding of extracellular RNA biology and clinical advances of liquid biopsy.