Archaeal Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The archaeal composition of permafrost samples taken during the drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. This study is based on an analysis of the V4 region of the 16S rRNA gene, carried out using next-generation sequencing. The general phyla of the Archaea domain are Euryarchaeota, Bathyarchaeota, Thaumarchaeota, and Asgardarchaea. As a result of a phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic and methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea, are found. The methanogenic archaea of Euryarchaeota phylum, Methanobacteria class, are found in permafrost with controversial genesis, while the methane-oxidizing archaea of Methanomicrobia class Methanosarcinales order are found in the marine permafrost at Cape Finneset: the ANME-2a, -2b group in layers of 8.6 and 11.7 m and the ANME-2d group (Candidatus Methanoperedens) in a layer of 6.5 m. Ammonium-oxidizing archaea of phylum Thaumarchaeota is present in all types of permafrost, while the order of Nitrososphaerales is found in permafrost with controversial genesis and the order Nitrosopumilales is in permafrost with marine and controversial genesis. Representatives of phylum Bathyarchaeota are found stratigraphically in the most ancient samples under study. Asgardarchaeota superfylum is excluded in the layers of permafrost with marine genesis and is represented by the phyla Lokiarchaeota, Thorarchaeota, and an unclassified group belonging to this superphylum. The presence of methane, ethylene, and ethane in the permafrost of the first sea terrace of Cape Finneset at a depth of 11.7 m, as well as the composition of the archaeal community, give us reason to assume that, before freezing, microbiological processes of anaerobic methane oxidation took place in it, probably received from Tertiary rocks. The results of both this and previous works present the Spitsbergen permafrost as a rich archive of genetic information of little-studied prokaryotic groups

Bacterial Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The bacterial composition of permafrost samples taken during drilling of frozen marine sediments in the area of Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. The study was based on the analysis of the V4 region of the 16S rRNA gene, carried out using next generation sequencing, as well as using classical microbiological methods (direct luminescence microscopy and aerobic cultivation).The total cell number in permafrost samples ranges from 6.73 ± 0.73 × 106 to 3.37 ± 0.19 107 cells per g. The number of cultivable aerobic bacteria in frozen samples on 1/5 TSA and R2A media ranges from 0 to 6.20 ± 0.45 × 104 CFU/g. Isolates of aerobic bacteria were identified by 16S rRNA gene analysis as representatives of the genera Arthrobacter, Pseudarthrobacter, Psychrobacter, and Rhodoferax. The dominant phyla of the domain Bacteria were Actinobacteria, Proteobacteria, Chloroflexi, Nitrospirae and Firmicutes. As a result of phylogenetic analysis of the dominant operational taxonomic units, representatives of methane oxidizing, sulfate reducing bacteria, as well as heterotrophic bacteria involved in the transformation of organic matter were found

Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction

none7Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor−lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol’s retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators.openCiancetta, Antonella; Gill, Amandeep Kaur; Ding, Tianyi; Karlov, Dmitry S.; Chalhoub, George; McCormick, Peter J.; Tikhonova, Irina G.Ciancetta, Antonella; Gill, Amandeep Kaur; Ding, Tianyi; Karlov, Dmitry S.; Chalhoub, George; Mccormick, Peter J.; Tikhonova, Irina G