Perfluorinated alcohol induced coacervates as extraction media for proteomic analysis

Compounding Achromobacter Phages for Therapeutic Applications

Achromobacter species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by Achromobacter xylosoxidans CF418 or Achromobacter ruhlandii CF116 experienced fatal exacerbations. Achromobacter spp. are naturally resistant to several antibiotics. Therefore, phages could be valuable as therapeutics for the control of Achromobacter. In this study, thirteen lytic phages were isolated and characterized at the morphological and genomic levels for potential future use in phage therapy. They are presented here as the Achromobacter Kumeyaay phage collection. Six distinct Achromobacter phage genome clusters were identified based on a comprehensive phylogenetic analysis of the Kumeyaay collection as well as the publicly available Achromobacter phages. The infectivity of all phages in the Kumeyaay collection was tested in 23 Achromobacter clinical isolates; 78% of these isolates were lysed by at least one phage. A cryptic prophage was induced in Achromobacter xylosoxidans CF418 when infected with some of the lytic phages. This prophage genome was characterized and is presented as Achromobacter phage CF418-P1. Prophage induction during lytic phage preparation for therapy interventions require further exploration. Large-scale production of phages and removal of endotoxins using an octanol-based procedure resulted in a phage concentrate of 1 × 109 plaque-forming units per milliliter with an endotoxin concentration of 65 endotoxin units per milliliter, which is below the Food and Drugs Administration recommended maximum threshold for human administration. This study provides a comprehensive framework for the isolation, bioinformatic characterization, and safe production of phages to kill Achromobacter spp. in order to potentially manage Cystic Fibrosis (CF) pulmonary infections.

Double-headed amphiphile-based sponge droplets: synthesis, characterization and potential for the extraction of compounds over a wide polarity range

Supramolecular solvents (SUPRASs) are gaining momentum in the multi-residue analysis of liquid samples thanks to the delimited hydrophilic and hydrophobic microenvironments in their nanostructures. In this work, SUPRASs with increased hydrophilicity were synthesized with the aim of enhancing the extractability of polar compounds. For this purpose, a double-headed amphiphile, 1,2-decanediol, was self-assembled in hydro-organic media in the presence and absence of sodium chloride. The SUPRASs formed, characterized by scanning electron microscopy, consisted of sponge droplets made up of a highly convoluted three-dimensional (3D) network of amphiphile. The network contained interconnected bilayers that were intersected by similarly interconnected aqueous channels with high and nearly constant water content (∼30%, w/w). Both the inherently open structure of the sponge morphology and the increased hydrophilic-hydrophobic balance of the amphiphile, provided highly hydrophilic microenvironments into the aggregates that rendered in increased recovery factors for 15 perfluorinated compounds (PFCs, C₄-C₁₈, log P_ow values from 0.4 to 11.6) in natural waters. Extraction took 15 min without further clean-up or evaporation of extracts which were readily compatible with LC-MS/MS quantitation. Absolute recoveries for PFCs, at the level of a few ng L^-1, were in the range 70-120%, except for perfluoropentanoic acid (40%) and perfluorobutane sulfonic acid (51%). Detection limits for PFCs in water were in the range 0.01-0.02 ng L^-1, which allowed their determination in slightly polluted waters (0.07-2.33 ng L^-1). This work proves that hydrophilicity in SUPRASs can be tailored through the amphiphile and the morphology of their aggregates, and that this characteristic improves compound extractability in multi-residue analysis.

Improving identification of low abundance and hydrophobic proteins using fluoroalcohol mediated supramolecular biphasic systems with quaternary ammonium salts

In this study, a newly discovered Supramolecular Biphasic System (S-BPS) was used in bottom-up proteomics of the Saccharomyces cerevisiae strain of yeast. We took advantage of S-BPS in bottom-up proteomics of this strain of yeast as the protein sample, while the results were compared to routinely used solubilizing reagents, such as urea, and sodium dodecyl sulfate (SDS). With the S-BPS, we identified 3043 proteins as compared to 2653 proteins that were identified in the control system. Interestingly, of the additional 390 proteins characterized by the S-BPS, 300 proteins were low abundance (less than 4000 molecules/cell). Remarkably, the identification of proteins at very low abundance (less than 2000 molecule/cell) was improved by 106%. This suggests that the S-BPS is particularly advantageous for detecting low abundance proteins. Gene Ontology (GO) analysis was conducted to find fractionation pattern of proteins in our two-phase system, and in nearly every gene ontology category, the S-BPS provided greater coverage than the control experiment, i.e., coverage for integral membrane proteins and mitochondrial ribosome proteins are improved by 18% and 58%, respectively. The improvements in proteins coverage for low abundance and membrane proteins can be attributed to the strong solubilizing power of the amphiphile-rich phase of this S-BPS and its capability for concomitant extraction, fractionation, and enrichment of the complex proteomics samples. Each phase has selectivity towards specific yeast protein groups, this selectivity is generally based on pI and hydrophobicity of proteins. Therefore, more hydrophobic proteins and acidic proteins exhibit greater affinities for the amphiphile-rich phase due to the hydrophobic effect and electrostatic interactions.

Improved Protein Coverage in Bottom-Up Proteomes Analysis Using Fluoroalcohol-Mediated Supramolecular Biphasic Systems With Mixed Amphiphiles for Sample Extraction, Fractionation, and Enrichment

A new class of supramolecular biphasic systems containing fluoroalcohol-induced coacervates (FAiC) provides concomitant fractionation of complex protein mixtures, high solubilizing power for extraction of various types of proteins, especially those with high hydrophobicity (such as membrane proteins), and enrichment of low-abundance proteins. Subsequently, the use of FAiC biphasic systems (BPS) in the bottom-up proteomics workflow resulted in significantly higher coverage for the whole proteome, various subproteomes, especially those embedded or associated with membranes, post-translationally modified proteins, and low-abundance proteins (LAPs) as compared to the conventional methodologies. In this work, we used a new type of FAiC-BPS composed of mixed amphiphiles, a zwitterionic surfactant 3-(N,N-dimethylmyristyl ammonia) propane sulfonate (DMMAPS), a quaternary ammonium salt (QUATS), and hexafluoroisopropanol (HFIP) as the coacervator for extraction, fractionation, and enrichment of yeast proteome in bottom-up proteomics. The coverage of the lower-abundance proteins (abundance below 2000 molecules/cell) improved by more than 100% using DMMAPS and DMMAPS + QUATS systems as compared to the conventional methods using urea or detergent solutions for protein solubilization. Additionally, these coacervate systems show increased coverage of integral membrane proteins and proteins with α-helices by up to 24 and 555%, respectively.

Twenty years of supramolecular solvents in sample preparation for chromatography: achievements and challenges ahead

Supramolecular solvents (SUPRAS) have progressively become a suitable alternative to organic solvents for sample preparation in chromatographic analysis. The inherent properties of these nanostructured solvents (e.g. different polarity microenvironments, multiple binding sites, possibility of tailoring their properties, etc.) offer multiple opportunities for the development of innovative sample treatment platforms not approachable by conventional solvents. In this review, major achievements attained in the combination SUPRAS-chromatography in the last 20 years as well as the challenges that should be addressed in the near future are critically discussed. Among achievements, particular attention is paid to the theoretical and practical knowledge gained that has helped make substantial progress in the area. In this respect, advances in the understanding of the mechanisms involved in SUPRAS formation and SUPRAS-solute interactions driving extractions are discussed, with a view to the setting up of knowledge-based extraction procedures. Likewise, the strategies followed to improve the compatibility of SUPRAS extracts with liquid and gas chromatography and adapt SUPRAS-based extractions to different formats are presented. Ongoing efforts to apply SUPRAS in multicomponent extractions and synthesize tailored SUPRAS for the development of innovative sample treatments are highlighted. Among challenges identified, discussion is focused on the automation of SUPRAS-based sample treatment and the elucidation of SUPRAS nanostructures, which are considered essential for their acceptance in routine labs and the design of tailored SUPRAS with programmed functions. Graphical abstract.

Macro- and Microphase Separated Protein-Polyelectrolyte Complexes: Design Parameters and Current Progress

Protein-containing polyelectrolyte complexes (PECs) are a diverse class of materials, composed of two or more oppositely charged polyelectrolytes that condense and phase separate near overall charge neutrality. Such phase-separation can take on a variety of morphologies from macrophase separated liquid condensates, to solid precipitates, to monodispersed spherical micelles. In this review, we present an overview of recent advances in protein-containing PECs, with an overall goal of defining relevant design parameters for macro- and microphase separated PECs. For both classes of PECs, the influence of protein characteristics, such as surface charge and patchiness, co-polyelectrolyte characteristics, such as charge density and structure, and overall solution characteristics, such as salt concentration and pH, are considered. After overall design features are established, potential applications in food processing, biosensing, drug delivery, and protein purification are discussed and recent characterization techniques for protein-containing PECs are highlighted.