Bacterial cellulose nanofibers for albumin depletion from human serum

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

p(HEMA)-RR241 hydrogel membranes with micron network for IgG depletion in proteomic studies

Serum proteins can generally be considered a good source for the illness' indication and are precious resources to detect diseases such as inflammation, cancer, diabetes, malnutrition, cardiovascular diseases, Alzheimer's, other autoimmune diseases, and infections. However, one of the biggest difficulties for proteomic studies is that the majority of serum protein mass consists of only a few proteins. Albumin and Immunoglobulin (IgG) constitute 80% of total serum protein. In this study, dye ligand affinity-based hydrogel membranes were proposed as new materials with micron mesh structures. Micron mesh p(HEMA) hydrogel membranes were synthesized by using the UV-photopolymerization method, then modified with Reactive Red 241 (RR241) dye ligand to increase the affinity towards IgG. Characterizations of synthesized micron mesh p(HEMA)-RR241 hydrogel membranes were also performed. It was demonstrated by the characterization studies that; the dye was successfully incorporated into the membrane structure with the amount of 119.38 mg/g. The hydrophilic property of the hydrogel membrane was demonstrated by swelling tests and the swelling value of dye modified membrane was found to be 8 times higher than that of the plain membrane. Micron network structure, as well as the porosity, were demonstrated with SEM/ESEM studies. Optimization of IgG adsorption conditions was also studied at different parameters (pH, temperature, ion strength, initial IgG concentration). Optimum pH, temperature, and ionic strength were found to be 6.5, 25 °C, 0.05 M, respectively, and the maximum IgG absorption value was 10.27 mg/g. Finally, it was shown that the proposed materials can be used repeatedly by 5 adsorption-desorption cycles.

Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.

Molecularly imprinted composite cryogels for hemoglobin depletion from human blood

A molecularly imprinted composite cryogel (MICC) was prepared for depletion of hemoglobin from human blood prior to use in proteome applications. Poly(hydroxyethyl methacrylate) based MICC was prepared with high gel fraction yields up to 90%, and characterized by Fourier transform infrared spectrophotometer, scanning electron microscopy, swelling studies, flow dynamics and surface area measurements. MICC exhibited a high binding capacity and selectivity for hemoglobin in the presence of immunoglobulin G, albumin and myoglobin. MICC column was successfully applied in fast protein liquid chromatography system for selective depletion of hemoglobin for human blood. The depletion ratio was highly increased by embedding microspheres into the cryogel (93.2%). Finally, MICC can be reused many times with no apparent decrease in hemoglobin adsorption capacity.

Applications of bacterial cellulose and its composites in biomedicine

Bacterial cellulose produced by few but specific microbial genera is an extremely pure natural exopolysaccharide. Besides providing adhesive properties and a competitive advantage to the cellulose over-producer, bacterial cellulose confers UV protection, ensures maintenance of an aerobic environment, retains moisture, protects against heavy metal stress, etc. This unique nanostructured matrix is being widely explored for various medical and nonmedical applications. It can be produced in various shapes and forms because of which it finds varied uses in biomedicine. The attributes of bacterial cellulose such as biocompatibility, haemocompatibility, mechanical strength, microporosity and biodegradability with its unique surface chemistry make it ideally suited for a plethora of biomedical applications. This review highlights these qualities of bacterial cellulose in detail with emphasis on reports that prove its utility in biomedicine. It also gives an in-depth account of various biomedical applications ranging from implants and scaffolds for tissue engineering, carriers for drug delivery, wound-dressing materials, etc. that are reported until date. Besides, perspectives on limitations of commercialisation of bacterial cellulose have been presented. This review is also an update on the variety of low-cost substrates used for production of bacterial cellulose and its nonmedical applications and includes patents and commercial products based on bacterial cellulose.

Bio-functionalized nanofibrous membranes as a hybrid platform for selective antibody recognition and capturing

PVA-co-PE nanofibers were activatedviaversatile surface chemistries to achieve protein ligand couplings and subsequent antibody recognition and capturing.

Affinity-recognition-based polymeric cryogels for protein depletion studies

Supermacroporous cryogels can be used for the depletion of highly abundant proteins prior to proteome investigations.

Dye-attached magnetic poly(hydroxyethyl methacrylate) nanospheres for albumin depletion from human plasma

The selective binding of albumin on dye-affinity nanospheres was combined with magnetic properties as an alternative approach for albumin depletion from human plasma. Magnetic poly(hydroxyethyl methacrylate) (mPHEMA) nanospheres were synthesized using mini-emulsion polymerization method in the presence of magnetite powder. The specific surface area of the mPHEMA nanospheres was found to be 1302 m(2)/g. Subsequent to Cibacron Blue F3GA (CB) immobilization onto mPHEMA nanospheres, a serial characterization processing was implemented. The quantity of immobilized CB was calculated as 800 μmol/g. Ultimately, albumin adsorption performance of the CB-attached mPHEMA nanospheres from both aqueous dissolving medium and human plasma were explored.

Metabolic flux analysis of Gluconacetobacter xylinus for bacterial cellulose production

Metabolic flux analysis was used to reveal the metabolic distributions in Gluconacetobacter xylinus (CGMCC no. 2955) cultured on different carbon sources. Compared with other sources, glucose, fructose, and glycerol could achieve much higher bacterial cellulose (BC) yields from G. xylinus (CGMCC no. 2955). The glycerol led to the highest BC production with a metabolic yield of 14.7 g/mol C, which was approximately 1.69-fold and 2.38-fold greater than that produced using fructose and glucose medium, respectively. The highest BC productivity from G. xylinus CGMCC 2955 was 5.97 g BC/L (dry weight) when using glycerol as the sole carbon source. Metabolic flux analysis for the central carbon metabolism revealed that about 47.96 % of glycerol was transformed into BC, while only 19.05 % of glucose and 24.78 % of fructose were transformed into BC. Instead, when glucose was used as the sole carbon source, 40.03 % of glucose was turned into the by-product gluconic acid. Compared with BC from glucose and fructose, BC from the glycerol medium showed the highest tensile strength at 83.5 MPa, with thinner fibers and lower porosity. As a main byproduct of biodiesel production, glycerol holds great potential to produce BC with superior mechanical and microstructural characteristics.