Method for rapid removal of sodium dodecyl sulfate from polyacrylamide gels

Photodegradable Polyacrylamide Gels for Dynamic Control of Cell Functions

Cross-linked polyacrylamide hydrogels are commonly used in biotechnology and cell culture applications due to advantageous properties, such as the precise control of material stiffness and the attachment of cell adhesive ligands. However, the chemical and physical properties of polyacrylamide gels cannot be altered once fabricated. Here, we develop a photodegradable polyacrylamide gel system that allows for a dynamic control of polyacrylamide gel stiffness with exposure to light. Photodegradable polyacrylamide hydrogel networks are produced by copolymerizing acrylamide and a photocleavable ortho-nitrobenzyl (o-NB) bis-acrylate cross-linker. When the hydrogels are exposed to light, the o-NB cross-links cleave and the stiffness of the photodegradable polyacrylamide gels decreases. Further examination of the effect of dynamic stiffness changes on cell behavior reveals that in situ softening of the culture substrate leads to changes in cell behavior that are not observed when cells are cultured on presoftened gels, indicating that both dynamic and static mechanical environments influence cell fate. Notably, we observe significant changes in nuclear localization of YAP and cytoskeletal organization after in situ softening; these changes further depend on the type and concentration of cell adhesive proteins attached to the gel surface. By incorporating the simplicity and well-established protocols of standard polyacrylamide gel fabrication with the dynamic control of photodegradable systems, we can enhance the capability of polyacrylamide gels, thereby enabling cell biologists and engineers to study more complex cellular behaviors that were previously inaccessible using regular polyacrylamide gels.

Intact proteome fractionation strategies compatible with mass spectrometry

Proteome fractionation refers to separation at the level of intact proteins. Proteome fractionation may precede sample digestion and subsequent peptide-level separation and detection (i.e., bottom-up mass spectrometry [MS]). For top-down MS, proteome fractionation acts as a stand-alone separation platform, since intact proteins are directly analyzed by the mass spectrometer. Regardless of the MS identification strategy, separation of intact proteins has clear benefits as a result of decreasing sample complexity. However, this stage of the workflow also creates considerable challenges, which are generally absent from the counterpart peptide separation experiment. For example, maintaining protein solubility is a key concern before, during and after separation. To this end, surfactants such as sodium dodecyl sulfate may be employed during fractionation, so long as they are eliminated prior to MS. In this article, current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.

First report on purification of the predominant acidic coagulum protein of human semen prior to liquefaction

The predominant acidic coagulum protein of freshly ejaculated human semen under reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was purified for the first time from washed seminal coagulum keeping urea throughout the entire procedure. Washed seminal coagulum was isolated from fresh semen sample in acetate buffer at pH 4.5 at 0 degrees C, solubilized rapidly in deionized 4 M urea followed by reduction and carboxymethylation of disulfide bonds. By CM-Sephadex and Sephacryl S-300 high-resolution chromatography in presence of urea at room temperature, the predominant acidic coagulum protein was highly purified (99.1%) with a yield of 2.7% of the coagulum protein. The molecular weight of the purified protein in reducing SDS-PAGE was 162 kD.

Collective isolation of two major, close molecular weight coagulum proteins occurring in human semen before liquefaction

Two major, close molecular weight basic coagulum proteins of freshly ejaculated human semen identifiable on reducing SDS-PAGE, have been isolated together from washed seminal coagulum. The latter was solubilized in urea, followed by reduction and carboxymethylation of disulphide bonds. By high-resolution chromatography on carboxymethy-Sephadex and Sephacryl S-300 using 8 M urea in 0.1M Tris-HCl (pH 7.4) as eluate these proteins were isolated together (purity 99%) with a yield of 10.5%. The molecular weights of the isolated proteins on SDS-PAGE were 75 and 79 kD.

Deficiency in major high molecular-weight seminal proteins in men producing poorly coagulating and alkaline liquid ejaculates

Using SDS-PAGE three major high molecular-weight coagulum proteins (57, 75 and 79 kD) were identified in unliquefied human ejaculates. Washed coagulum was prepared at pH 4.5 and demonstrated negligible proteolysis as determined by a highly sensitive fluorescamine-based method. Laser densitometric scanning of these high molecular-weight proteins in unliquefied ejaculates in relation to their coagulational failure revealed that the total content of 57, 75 and 79 kD proteins in whole semen represented approximately 44% of levels in the normally coagulated, approximately 24% in poorly coagulated (P less than 0.005) and approximately 3% in the non-coagulated (alkaline liquid, P less than 0.001) samples. The findings imply that these predominant high molecular-weight proteins play a major role in human seminal coagulum formation.

Detection of dextransucrase and levansucrase on polyacrylamide gels by the periodic acid-Schiff stain: staining artifacts and their prevention

One use of the periodic acid-Schiff (PAS) stain is to detect dextransucrase and levansucrase activities on polyacrylamide gels by staining their polysaccharide products, dextran and levan. When gels with heavy dextran or levan bands were PAS stained, proteins other than dextransucrase and levansucrase also were stained, and a high background developed during storage. The staining of proteins other than dextransucrase and levansucrase is caused by the diffusion of the periodate-oxidized carbohydrate before and after staining. This diffusion could be greatly slowed, and the staining artifact decreased, by following the PAS stain by a crosslinking treatment of the carbohydrate-dye complex. Protein staining artifacts could be prevented by using chymotrypsin to remove the protein from the gel at the stage after polysaccharide synthesis but before the PAS stain.

Staining of alkali-labile phosphoproteins and alkaline phosphatases on polyacrylamide gels

A sensitive staining method for alkali-labile phosphoproteins has been developed. As little as 0.2 nmol bound P/mm2 can be detected. The procedure is based on alkaline hydrolysis, phosphate capture, and formation of an insoluble rhodamine B-phosphomolybdate complex. A further modification for the qualitative detection of alkaline phosphatase activity on polyacrylamide gels is proposed. During incubation, the released Pi is precipitated as lead phosphate and subsequently stained with rhodamine B.