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Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of Key words: bacterial taxonomy, bioinformatics, nucleotide identity, nomenclature. De maniere routiniere, les populations bacteriennes sont examinees au microscope, evaluees pour la formation de colonies et font l'objet de tests biochimiques. Cependant, depuis peu, l'identification, la classification etla nomenclature des bacteries ont ete largement influencees par les informations genomiques. Les avancees en bioinformatique et la croissance des bases de donnees genomiques ont fourni aux chercheurs des outils d'analyse de metadonnees genomiques, lesquels pourront faire appel a leur experience en taxonomie pour resoudre des differences subtiles. Pour y arriver, differents outils sont maintenant disponibles pour mesurer de maniere quantitative le degre de proximite entre membres d'une même espece. La moyenne globale d'identite nucleotidique (gANI, pour << genome-wide average nucleotide identity >>) est l'un de ces outils pour mesurer de maniere fiable la similarite des genomes. A l'echelle d'un genome, un score gANI Mots-cles : taxonomie bacterienne, bioinformatique, identite nucleotidique, nomenclature., Introduction Accurate bacterial classification is essential to identify potential genes to understand genetic mechanisms, diagnose disease, and provide better treatment, especially during infectious disease spread, outbreaks, and progression (Fricke and [...]

Highlights • The size of styrene-maleic acid copolymer-lipid nanoparticles (SMALPs) were characterized using Dynamic Light Scattering. • EPR spectra showed the incorporation of a membrane protein into the nanoparticles and liposomes. • TEM images show the size and distribution of the SMALPs. Abstract Membrane proteins play an important role in maintaining the structure and physiology of an organism. Despite their significance, spectroscopic studies involving membrane proteins remain challenging due to the difficulties in mimicking their native lipid bilayer environment. Membrane mimetic systems such as detergent micelles, liposomes, bicelles, nanodiscs, lipodisqs have improved the solubility and folding properties of the membrane proteins for structural studies, however, each mimetic system suffers from its own limitations. In this study, using three different lipid environments, vesicles were titrated with styrene-maleic acid (StMA) copolymer leading to a homogeneous SMALP system (∼10 nm) at a weight ratio of 1:1.5 (vesicle: StMA solution). A combination of Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM) was used to characterize these SMALPs. We used a controlled synthesis mechanism to synthesize StMA based block copolymers called reversible addition-fragmentation chain transfer polymerization (RAFT) SMALPs. Incorporation of the Voltage Sensor Domain of KCNQ1 (Q1-VSD) into RAFT SMALPs indicates that this is a promising application of this system to study membrane proteins using different biophysical techniques. V165C in Q1-VSD corresponding to the hydrophobic region was incorporated into the SMALP system. Continuous Wave-Electron Paramagnetic Resonance (CW-EPR) line shape analysis showed line shape broadening, exposing a lower rigid component and a faster component of the spin label. [ABSTRACT FROM AUTHOR]

The clinical association between atrial fibrillation (AF), coronary microvascular disease (CMD) and heart failure with preserved ejection fraction (HFpEF) is highly prevalent, however the mechanism behind this association is not known. We hypothesized that plasma proteomic analysis can identify novel biomarkers and the mechanistic pathways in concomitant AF, CMD and HFpEF. To discover circulating biomarkers for the association between AF, CMD and HFpEF, an unbiased label-free quantitative proteomics approach was used in plasma derived from patients who underwent coronary physiology studies (n=18). Circulating proteins were analyzed by liquid chromatography-mass spectrometry and screened to determine candidate biomarkers of the concomitant AF, CMD and HFpEF. We identified 130 dysregulated proteins across the groups with the independent patient replicates. Among those, 35 proteins were candidate biomarkers of the association between AF, CMD and HFpEF. We found significantly elevated SAA1, LRG1 and APOC3 proteins in the coexistence of AF, CMD and HFpEF, whereas LCP1, PON1 and C1S were markedly downregulated in their associations. AF was associated with reduced LCP1, KLKB1 and C4A in these patients. Combined downregulation of PON1 and C1S was a marker of concurrent HFpEF and CMD. PON1 was associated with HFpEF while C1S was a marker of CMD. These proteins are related to inflammation, extra cellular remodeling, oxidative stress, and coagulation. In conclusion, plasma proteomic profile provides biomarkers and mechanistic insight into the association of AF, CMD and HFpEF. SAA1, LRG1, APOC3, LCP1, PON1 and C1S are candidate markers for the risk stratification of their associations and potential underlying mechanistic pathways., Competing Interests: None., (AJCD Copyright © 2022.)

Pinholins are a family of lytic membrane proteins responsible for the lysis of the cytosolic membrane in host cells of double stranded DNA bacteriophages. Protein-lipid interactions have been shown to influence membrane protein topology as well as its function. This work investigated the interactions of pinholin with the phospholipid bilayer while in active and inactive confirmations to elucidate the different interactions the two forms have with the bilayer. Pinholin incorporated into deuterated DMPC-d 54 lipid bilayers, along with 31 P and 2 H solid state NMR (SS-NMR) spectroscopy were used to probe the protein-lipid interactions with the phosphorus head group at the surface of the bilayer while interactions with the 2 H nuclei were used to study the hydrophobic core. A comparison of the 31 P chemical shift anisotropy (CSA) values of the active S 21 68 pinholin and inactive S 21 IRS pinholin indicated stronger head group interactions for the pinholin in its active form when compared to that of the inactive form supporting the model of a partially externalized peripheral transmembrane domain (TMD) of the active S 21 68 instead of complete externalized TMD1 as suggested by Ahammad et al. JPC B 2019. The 2 H quadrupolar splitting analysis showed a decrease in spectral width for both forms of the pinholin when compared to the empty bilayers at all temperatures. In this case the decrease in the spectral width of the inactive S 21 IRS form of the pinholin showed stronger interactions with the acyl chains of the bilayer. The presence of the inactive form's additional TMD within the membrane was supported by the loss of peak resolution observed in the 2 H NMR spectra., (Copyright © 2020 Elsevier B.V. All rights reserved.)