Project description:Background: Systemic light chain amyloidosis is a protein misfolding disorder characterized by deposition of clonal immunoglobulin light chains in vital organs. To date, little is known about the contribution of light chain constant domain mutations in thermodynamic stability and amyloidogenicity.Methods: In 89 patients, RNA-based full-length light chain repertoire sequencing with Oxford Nanopore was performed, in addition to Illumina sequencing and mass spectrometric detection of light chain protein in serum and amyloid deposits. Computational methods for conservation, free energy calculation, and molecular dynamics simulations were applied to investigate the thermodynamic stability.Results: Monoclonal light chain detection rate was 95.4%, and sequences showed 100% identity with Illumina in all patients. Light chain protein was specifically detectable by mass spectrometry in serum and amyloid deposits. Lambda constant domain mutations were present in 10%, while no kappa constant domain mutations were detected. Fold free energy change and molecular dynamics simulations indicate potential light chain stabilizing or destabilizing effects of detected constant domain mutations.Conclusion: Current findings highlight the importance of routinely implementing full-length light chain sequencing in plasma cell dyscrasias, particularly light chain amyloidosis to account for the potential impact of constant domain mutations on light chain stability and amyloidogenicity.
Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
Project description:Over the last 20 years, the advances in sequencing technologies highlighted the unique composition of the salivary glands of blood-feeding arthropods. Further biochemical and structural data demonstrated that salivary proteins can disrupt host hemostasis, inflammation and immune response in addition to favor pathogen transmission. Previously, a Sanger-based sialome of the adult Ochlerotatus. triseriatus female salivary glands was published based on 731 ESTs. Here we revisited O. triseriatus salivary glands contents using an Illumina-sequencing approach of both male and female tissues. In the current data set we report 10,317 coding DNA sequences classified into several functional classes. The translated transcripts also served as reference database for the proteomic analysis of O. triseriatus female saliva, in which unique peptides of 101 proteins were found. Finally, comparison of male and female libraries allowed the identification of female-enriched transcripts that are potentially related to blood acquisition and virus transmission.
Project description:Compound 4, an antileishmanial compound identified in a GSK phenotypic-screen against Leishmania donovani (Leish-box)1 and not currently being actively researched for drug discovery, was investigated with the aim of elucidated its mode-of-action (MoA) in L. major and L. mexicana (two causative agents of cutaneous leishmaniasis). A novel pipeline approach was developed and utilised for this purpose; it included (1) characterising the mode-of-resistance of in vitro evolution-derived mutants via Illumina sequencing and cross-resistance studies against clinical antileishmanials and (2) investigating compound protein targets via thermal proteome profiling (TPP). TPP indicated differences between the two species in terms of the number and type of proteins being targeted by compound 4.