Quantitation of polyethylene glycol by size exclusion chromatography with charged aerosol, differential refractive index, and multi-angle light scattering detectors

Polyethylene glycol (PEG) has found tremendous applications in pharmaceutical products and has played a critical role in PEGylated drug modalities to improve pharmacokinetic properties and biological efficacy. The characterization and quantitation of PEGs are essential to control manufacture process and drug product quality. However, the assay value of PEG could change dramatically depending on the structures of the PEG and the detection techniques used. In this study, we developed a size exclusion chromatographic (SEC) method for quantitative PEG analysis, and we systematically evaluated the performance of three online detectors with different operating principles: a charged aerosol detector (CAD), a differential refractive index (dRI) detector, and a multi-angle light scattering detector (MALS). Fourteen PEG compounds covering a wide range of molecular weight (MW, 1 - 40 kDa) and molecular architectures (linear, branched, Y-shaped and multi-arm geometries) were evaluated by these three detection techniques. Our study revealed that the dRI showed the most universal responses among all the PEGs regardless of their molecular weight or geometries. In the contrast, CAD and MALS detector showed MW-dependent and semi-universal geometry-dependent responses. Another key finding is that the relative response factor for each multi-arm PEG in the CAD and the MALS were inversely correlated, suggesting both can be applied to qualitatively assess polymers of different architectures, including the ones with subtle differences in their core structures. The comparison of the three detectors not only provides the fundamental and comprehensive understanding of PEG quantitation but also enables the process development and control of high-quality PEGs in producing PEGylated therapeutics in the pharmaceutical industry.

Optimization of Isolation Method for Extracellular Vesicles from Pancreatic Juice and Impact of Protease Activity

BACKGROUNDS

Pancreatic juice (PJ) is directly associated with pancreatic lesions, including pancreatic ductal cancer and intraductal papillary mucinous neoplasm-derived cancer. Therefore, EVs secreted from these lesions into PJ can be promising biomarkers for early diagnosis. However, there are limited data from analysis of EVs in PJ samples.

AIMS AND METHODS

We aimed to determine the stability of EVs in PJ collected using endoscopic naso-pancreatic drainage (ENPD) tubes as well as catheter during endoscopic retrograde cholangiography (ERCP), with or without the impact of positive protease activity, and optimize the EV isolation method.

RESULTS

Size exclusion chromatography was found to be an optimal isolation method for EVs in PJ as it achieved higher recovery and purity of EVs compared with differential ultracentrifugation and polymer-based precipitation. Approximately 40% of the PJ samples collected during ERCP and more than 90% of those collected using ENPD tubes had positive protease activity. In vitro exposure to room temperature for less than 3 h was harmless to the structure of double-membrane EVs in PJ and the expression levels of TSG101, even with positive protease activity.

CONCLUSIONS

We clarified the physiobiological status of EVs in PJ and optimized the EV isolation method using suitable PJ samples; these findings can be utilized to discover biomarkers for cancer diagnosis and elucidate their function.

Screening and Production of Recombinant Human Proteins: Protein Production in E. coli

In Chapter 3 , we described the Structural Genomics Consortium (SGC) process for generating multiple constructs of truncated versions of each protein using LIC. In this chapter we provide a step-by-step procedure of our E. coli system for test expressing intracellular (soluble) proteins in a 96-well format that enables us to identify which proteins or truncated versions are expressed in a soluble and stable form suitable for structural studies. In addition, we detail the process for scaling up cultures for large-scale protein purification. This level of production is required to obtain sufficient quantities (i.e., milligram amounts) of protein for further characterization and/or structural studies (e.g., crystallization or cryo-EM experiments). Our standard process is purification by immobilized metal affinity chromatography (IMAC) using nickel resin followed by size exclusion chromatography (SEC), with additional procedures arising from the complexity of the protein itself.

Extracellular vesicles isolated by size-exclusion chromatography present suitability for RNomics analysis in plasma

Background

Extracellular vesicles (EVs), known as cell-derived membranous structures harboring a variety of biomolecules, have been widely used in liquid biopsy. Due to the complex biological composition of plasma, plasma RNA omics analysis (RNomics) is easily affected, thus it is necessary to select an optimal strategy from exiting methods according to the performance for intended application.

Methods

In this study, four different strategies for EVs isolation were performed and compared (i.e. ultracentrifugation (UC), size exclusion chromatography (SEC), and two most frequently-used commercially available isolation kit (ExoQuick and exoEasy). We compared the yield, purity, PCR quantification of RNAs, miRNA-seq analyses and mRNA-seq analyses of RNAs from EVs isolated using four methods.

Results

The results showed that the lowest miRNA binding protein AGO2 (Argonaute-2) and the highest EVs-specific miRNA and lncRNA were observed in EVs obtained through SEC, meanwhile the content of the non-specific miRNA was the lowest. Further RNA-Seq data revealed that RNAs obtained via SEC presented more useful reads for both miRNA and mRNA. Furthermore, the mRNA delivered via SEC tended to have a concentration comparable to the ideal FPKM (Fragments Per Kilobase Million) value.

Conclusions

SEC shall be used as an optimal strategy for the isolation of EVs in plasma RNomics analysis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02775-9.

(Hyper)Thermophilic Enzymes: Production and Purification

The discovery of thermophilic and hyperthermophilic microorganisms, thriving at environmental temperatures near or above 100 °C, has revolutionized our ideas about the upper temperature limit at which life can exist. The characterization of (hyper)thermostable proteins has broadened our understanding and presented new opportunities for solving one of the most challenging problems in biophysics: how are structural stability and biological function maintained at high temperatures where "normal" proteins undergo dramatic structural changes? In our laboratory, we have purified and studied many thermostable and hyperthermostable proteins in an attempt to determine the molecular basis of heat stability. Here, we present methods to express such proteins and enzymes in E. coli and provide a general protocol for overproduction and purification. The ability to produce enzymes that retain their stability and activity at elevated temperatures creates exciting opportunities for a wide range of biocatalytic applications.

Organic carbon source-dependent properties of soluble microbial products in sequencing batch reactors and its effects on membrane fouling

This study investigated the influence of three different organic carbon sources including sodium acetate (SOD), glucose (GLU), and starch (STAR), on soluble microbial products (SMP), which presumably have dissimilar uptake rates and metabolic pathways, in sequencing batch reactors (SBR) and their subsequent effects on membrane fouling of ultrafiltration (UF). SMP were mainly characterized by fluorescence excitation emission matrix coupled with parallel factor analysis (EEM-PARAFAC) and size exclusion chromatography (SEC). SMP produced in SOD-fed SBR showed higher abundances of protein-like fluorescent component and large sized aliphatic biopolymer (BP) than GLU- or STAR-fed counterpart did, while the STAR-based operation resulted in more SMP enriched with humic-like fluorescence. The differences in SMP exerted marked effects on UF membrane fouling as indicated by the highest fouling potential with reversibility shown for the SMP from the SOD-fed reactor. Regardless of the carbon source, BP fraction and protein-like component exhibited the greatest extent of reversible fouling, suggesting that size exclusion plays a critical role. However, notable differences in the reversible fouling propensity of relatively smaller size fractions among the three SBRs signified the possible involvement of chemical interactions as a secondary fouling mechanism and its dependency on different carbon sources. Our results provide a new insight into the roles of carbon sources in the characteristics of SMP in biological treatment systems and their effects on the post-treatment using membrane filtration, which is ultimately beneficial to the optimization of biological treatment design and membrane filtration operation.

A new molecular weight (MW) descriptor of dissolved organic matter to represent the MW-dependent distribution of aromatic condensation: Insights from biodegradation and pyrene binding experiments

In this study, we utilized a size exclusion chromatography (SEC) system that was equipped with a fluorescence emission scanning mode to explore the heterogeneous distribution of the humification index (HIX) values within bulk dissolved organic matter (DOM). The HIX-based SEC chromatograms showed that the molecular weight (MW)-dependent distribution of aromatic condensation was heavily affected by the DOM sources and the progress of biodegradation. The HIX heterogeneity across different MW was more pronounced for terrestrial versus aquatic DOM sources. Microbial incubation of leaf litter DOM led to the initial enhancement of the HIX at a relatively low MW, followed by a gradual increase at larger MW values. The dynamic changes of the HIX can be attributed to (1) the preferential removal of non-aromatic or less-aromatic molecules by microorganisms, (2) the production of microbial metabolites, (3) microbial humification, and (4) self-assemblage of humic-like molecules. From the SEC chromatograms, the HIX-based average molecular weight (or MW_HIX) was proposed as a unifying surrogate to represent an MW that was highly associated with aromatic condensation. The MW_HIX discriminated four different DOM sources and described well the biodegradation-induced changes. The MW_HIX also presented a good positive correlation with pyrene organic carbon-normalized binding coefficients (K_oc). The prediction capability of the MW_HIX for pyrene K_oc was higher than those based on the single descriptors of bulk DOM, such as HIX and MW, which revealed its superior linkage with the DOM reactivity related to both MW and HIX.

Effects of COD/N ratio on soluble microbial products in effluent from sequencing batch reactors and subsequent membrane fouling

The relative ratios of chemical oxygen demand (COD) to nitrogen (N) in wastewater are known to have profound effects on the characteristics of soluble microbial products (SMP) from activated sludge. In this study, the changes in the SMP characteristics upon different COD/N ratios and the subsequent effects on ultrafiltration (UF) membrane fouling potentials were examined in sequencing batch reactors (SBR) using excitation emission matrix-parallel factor analysis (EEM-PARAFAC) and size exclusion chromatography (SEC). Three unique fluorescent components were identified from the SMP samples in the bioreactors operated at the COD/N ratios of 100/10 (N rich), 100/5 (N medium), and 100/2 (N deficient). The tryptophan-like component (C1) was the most depleted at the N medium condition. Fulvic-like (C2) and humic-like (C3) components were more abundant with N rich wastewater. Greater abundances of large size biopolymer (BP) and low molecular weight neutrals (LMWN) were found under the N deficient and N rich conditions, respectively. SMPs from various COD/N exhibited a greater degree on membrane fouling following the order of 100/2 > 100/10 > 100/5. C1 and C2 had close associations with reversible and irreversible fouling, respectively, while the reversible fouling potential of C3 depended on the COD/N ratios. No significant impact of COD/N ratio was observed on the relative contributions of SMP size fractions to either reversible or irreversible fouling potential. However, the COD/N ratios likely altered the BP foulants' composition with greater contribution of proteinaceous substances to reversible fouling under the N deficient condition than at other N richer conditions. The opposite trend was observed for irreversible fouling. Our results provided further insight into changes in different SMP constitutes and their membrane fouling in response to microbial activities under different COD/N ratios.

Organic matter quality structures benthic fatty acid patterns and the abundance of fungi and bacteria in temperate lakes

Benthic microbial communities (BMCs) play important roles in the carbon cycle of lakes, and benthic littoral zones in particular have been previously highlighted as biogeochemical hotspots. Dissolved organic matter (DOM) presents the major carbon pool in lakes, and although the effect of DOM composition on the pelagic microbial community composition is widely accepted, little is known about its effect on BMCs, particularly aquatic fungi. Therefore, we investigated the composition of benthic littoral microbial communities in twenty highly diverse lakes in northeast Germany. DOM quality was analyzed via size exclusion chromatography (SEC), fluorescence parallel factor analyses (PRAFACs) and UV-Vis spectroscopy. We determined the BMC composition and biomass using phospholipid-derived fatty acids (PLFA) and extended the interpretation to the analysis of fungi by applying a Bayesian mixed model. We present evidence that the quality of DOM structures the BMCs, which are dominated by heterotrophic bacteria and show low fungal biomass. The fungal biomass increases when the DOM pool is processed by microorganisms of allochthonous origin, whereas the opposite is true for bacteria.

Using two-dimensional correlation size exclusion chromatography (2D-CoSEC) to explore the size-dependent heterogeneity of humic substances for copper binding

Knowledge of the heterogeneous distribution of humic substances (HS) reactivities along a continuum of molecular weight (MW) is crucial for the systems where the HS MW is subject to change. In this study, two dimensional correlation spectroscopy combined with size exclusion chromatography (2D-CoSEC) was first utilized to obtain a continuous and heterogeneous presence of copper binding characteristics within bulk HS with respect to MW. HS solutions with varying copper concentrations were directly injected into a size exclusion chromatography (SEC) system with Tris-HCl buffer as a mobile phase. Several validation tests confirmed neither structural disruption of HS nor competition effect of the mobile phase used. Similar to batch systems, fluorescence quenching was observed in the chromatograms over a wide range of HS MW. 2D-CoSEC maps of a soil-derived HS (Elliot soil humic acid) showed the greater fluorescence quenching degrees with respect to the apparent MW on the order of 12500 Da > 10600 Da > 7000 Da > 15800 Da. The binding constants calculated based on modified Stern-Volmer equation were consistent with the 2D-CoSEC results. More heterogeneity of copper binding affinities within bulk HS was found for the soil-derived HS versus an aquatic HS. The traditional fluorescence quenching titration method using ultrafiltered HS size fractions failed to delineate detailed distribution of the copper binding characteristics, exhibiting a much shorter range of the binding constants than those obtained from the 2D-CoSEC. Our proposed technique demonstrated a great potential to describe metal binding characteristics of HS at high MW resolution, providing a clear picture of the size-dependent metal-HS interactions.

Superficially porous particles with 1000Å pores for large biomolecule high performance liquid chromatography and polymer size exclusion chromatography

To facilitate mass transport and column efficiency, solutes must have free access to particle pores to facilitate interactions with the stationary phase. To ensure this feature, particles should be used for HPLC separations which have pores sufficiently large to accommodate the solute without restricted diffusion. This paper describes the design and properties of superficially porous (also called Fused-Core^®, core shell or porous shell) particles with very large (1000Å) pores specifically developed for separating very large biomolecules and polymers. Separations of DNA fragments, monoclonal antibodies, large proteins and large polystyrene standards are used to illustrate the utility of these particles for efficient, high-resolution applications.

The effect of pH on solubilization of organic matter and microbial community structures in sludge fermentation

Sludge fermentation between pH 4 and 11 was investigated to generate volatile fatty acids (VFA). Despite the highest sludge solubilization of 25.9% at pH 11, VFA accumulation was optimized at pH 8 (12.5% out of 13.1% sludge solubilization). 454 pyrosequencing identified wide diversity of acidogens in bioreactors operated at the various pHs, with Tissierella, Petrimonas, Proteiniphilum, Levilinea, Proteiniborus and Sedimentibacter enriched and contributing to the enhanced fermentation at pH 8. Hydrolytic enzymatic assays determined abiotic effect to be the leading cause for improved solubilization under high alkaline condition but the environmental stress at pH 9 and above might lead to disrupt biological activities and eventually VFA production. Furthermore, molecular weight (MW) characterization of the soluble fractions found large MW aromatic substances at pH 9 and above, that is normally associated with poor biodegradability, making them disadvantageous for subsequent bioprocesses. The findings provided information to better understand and control sludge fermentation.