Showing papers by "Paul Wilmes published in 2012"

The complex exogenous RNA spectra in human plasma: an interface with human gut biota?

Abstract: Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers. Surveying human plasma for microRNA biomarkers using next generation sequencing technology, we observed that a significant fraction of the circulating RNA appear to originate from exogenous species. With careful analysis of sequence error statistics and other controls, we demonstrated that there is a wide range of RNA from many different organisms, including bacteria and fungi as well as from other species. These RNAs may be associated with protein, lipid or other molecules protecting them from RNase activity in plasma. Some of these RNAs are detected in intracellular complexes and may be able to influence cellular activities under in vitro conditions. These findings raise the possibility that plasma RNAs of exogenous origin may serve as signaling molecules mediating for example the human-microbiome interaction and may affect and/or indicate the state of human health.

Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

Abstract: "Candidatus Microthrix" bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: "Candidatus Microthrix parvicella" strain Bio17-1.

Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities.

Abstract: Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report an approach to link these data sets by coupling fluorescence in situ hybridization (FISH) with either conventional biological or cryogenic TEM. The method could fundamentally improve our understanding of the organization and functioning of microbial communities in natural systems.

Deuterium-exchange metabolomics identifies N -methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities

Abstract: Natural microbial communities are extremely diverse and contain uncharacterized but functionally important small molecules By coupling a deuterium (D) labeling technique to high mass accuracy untargeted liquid chromatography-electrospray ionization-mass spec- trometry (LC-ESI-MS) metabolomic analysis, we found that natural acidophilic microbial biofilms dominated by bacteria of the genus Leptospirillum contained unusual lyso phosphatidylethanolamine (PE) lipids in high abundance (more than 10 nmol/mg of dry biomass) The unusual polar head group structure of these lipids is similar to lipids found in phylogenetically unrelated acidophilic chemo- autolithotrophs and may be related to the affinity of these lipids for iron and calcium ions Correlations of lyso phospholipid and proteome abundance patterns suggest a link between the lyso phospholipids and the UBA-type substrain of Leptospirillum group II By combining untar- geted metabolomics with D exchange we demonstrate the ability to identify cryptic but biologically functional small molecules in mixed microbial communities

Method and Kit For The Isolation Of Genomic DNA, RNA Proteins and Metabolites From A Single Biological Sample

Abstract: The invention provides method and kit for the separation and purification of cellular components including polar and non-polar metabolites, genomic DNA, RNA and proteins from a single biological sample where two steps of lysis of the cells are performed sequentially, before and after a metabolite isolation step. The first lysis step is mechanical and performed in order to be incomplete, whereas the second is chemical or both mechanical and chemical. A sequential isolation of genomic DNA, RNA and proteins is carried out after the second lysis step.