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Concept: Gel electrophoresis

173

The microaerophilic parasite Trichomonas vaginalis is a causative agent of painful vaginitis or urethritis, termed trichomoniasis, and can also cause preterm delivery or stillbirth. Treatment of trichomoniasis is almost exclusively based on the nitroimidazole drugs metronidazole and tinidazole. Metronidazole resistance in T. vaginalis does occur and is often associated with treatment failure. In most cases, metronidazole-resistant isolates remain susceptible to tinidazole, but cross resistance between the two closely related drugs can be a problem. In this study we measured activities of thioredoxin reductase and flavin reductase in four metronidazole-susceptible and five metronidazole-resistant isolates. These enzyme activities had been previously found to be downregulated in T. vaginalis with high-level metronidazole resistance induced in the laboratory. Further, we aimed at identifying factors causing metronidazole resistance and compared the protein expression profiles of all nine isolates by application of two-dimensional gel electrophoresis (2DE). Thioredoxin reductase activity was nearly equal in all strains assayed but flavin reductase activity was clearly down-regulated, or even absent, in metronidazole-resistant strains. Since flavin reductase has been shown to reduce oxygen to hydrogen peroxide, its down-regulation could significantly contribute to the impairment of oxygen scavenging as reported by others for metronidazole-resistant strains. Analysis by 2DE revealed down-regulation of alcohol dehydrogenase 1 (ADH1) in strains with reduced sensitivity to metronidazole, an enzyme that could be involved in detoxification of intracellular acetaldehyde.

Concepts: Protein, Oxygen, Alcohol, Molecular biology, Enzyme, Gel electrophoresis, Alcohol dehydrogenase, Trichomonas vaginalis

168

BACKGROUND: Many proteins form insoluble protein aggregates, called “inclusion bodies”, when overexpressed in E. coli. This is the biggest obstacle in biotechnology. Ever since the reversible denaturation of proteins by chaotropic agents such as urea or guanidinium hydrochloride had been shown, these compounds were predominantly used to dissolve inclusion bodies. Other denaturants exist but have received much less attention in protein purification. While the anionic, denaturing detergent sodiumdodecylsulphate (SDS) is used extensively in analytical SDS-PAGE, it has rarely been used in preparative purification. RESULTS: Here we present a simple and versatile method to purify insoluble, hexahistidine-tagged proteins under denaturing conditions. It is based on dissolution of overexpressing bacterial cells in a buffer containing sodiumdodecylsulfate (SDS) and whole-lysate denaturation of proteins. The excess of detergent is removed by cooling and centrifugation prior to affinity purification. Host- and overexpressed proteins do not co-precipitate with SDS and the residual concentration of detergent is compatible with affinity purification on Ni/NTA resin. We show that SDS can be replaced with another ionic detergent, Sarkosyl, during purification. Key advantages over denaturing purification in urea or guanidinium are speed, ease of use, low cost of denaturant and the compatibility of buffers with automated FPLC. CONCLUSION: Ionic, denaturing detergents are useful in breaking the solubility barrier, a major obstacle in biotechnology. The method we present yields detergent-denatured protein. Methods to refold proteins from a detergent denatured state are known and therefore we propose that the procedure presented herein will be of general application in biotechnology.

Concepts: Protein, Protein structure, Molecular biology, Escherichia coli, Biotechnology, Gel electrophoresis, Denaturation, Chaotropic agent

166

Two-dimensional gel electrophoresis (2-DE)-based proteomics approach was applied to extensively explore the molecular basis of plant development and environmental adaptation. These proteomics analyses revealed thousands of differentially expressed proteins (DEPs) closely related to different biological processes. However, little attention has been paid to how peptide mass fingerprinting (PMF) data generated by the approach can be directly utilized for the determination of protein phosphorylation. Here, we used the software tool FindMod to predict the peptides that might carry the phosphorylation modification by examining their PMF data for mass differences between the empirical and theoretical peptides and then identified phosphorylation sites using MALDI TOF/TOF according to predicted peptide data from these DEP spots in the 2-D gels. As a result, a total of 48 phosphorylation sites of 40 DEPs were successfully identified among 235 known DEPs previously revealed in the 2-D gels of elongating cotton fiber cells. The 40 phosphorylated DEPs, including important enzymes such as enolase, transketolase and UDP-L-rhamnose synthase, are presumed to participate in the functional regulation of numerous metabolic pathways, suggesting the reverse phosphorylation of these proteins might play important roles in elongating cotton fibers. The results also indicated that some different isoforms of the identical DEP revealed in our 2-DE-based proteomics analysis could be annotated by phosphorylation events. Taken together, as the first report of large-scale identification of phosphorylation sites in elongating cotton fiber cells, our study provides not only an excellent example of directly identifying phosphorylation sites from known DEPs on 2-D gels but also provides a valuable resource for future functional studies of phosphorylated proteins in this field.

Concepts: Protein, Molecular biology, Adenosine triphosphate, Mass spectrometry, Gel electrophoresis, Phosphorylation, Proteomics, Two-dimensional gel electrophoresis

166

Optic nerve atrophy caused by abnormal intraocular pressure (IOP) remains the most common cause of irreversible loss of vision worldwide. The aim of this study was to determine whether topically applied IOP-lowering eye drugs affect retinal ganglion cells (RGCs) and retinal metabolism in a rat model of optic neuropathy. IOP was elevated through cauterization of episcleral veins, and then lowered either by the daily topical application of timolol, timolol/travoprost, timolol/dorzolamide, or timolol/brimonidine, or surgically with sectorial iridectomy. RGCs were retrogradely labeled 4 days prior to enucleation, and counted. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), matrix-assisted laser desorption ionization mass spectrometry, Western blotting, and immunohistochemistry allowed the identification of IOP-dependent proteomic changes. Genomic changes were scrutinized using microarrays and qRT-PCR. The significant increase in IOP induced by episcleral vein cauterization that persisted until 8 weeks of follow-up in control animals (<0.05) was effectively lowered by the eye drops (<0.05). As anticipated, the number of RGCs decreased significantly following 8 weeks of elevated IOP (<0.05), while treatment with combination compounds markedly improved RGC survival (<0.05). 2D-PAGE and Western blot analyses revealed an IOP-dependent expression of crystallin cry-βb2. Microarray and qRT-PCR analyses verified the results at the mRNA level. IHC demonstrated that crystallins were expressed mainly in the ganglion cell layer. The data suggest that IOP and either topically applied antiglaucomatous drugs influence crystallin expression within the retina. Neuronal crystallins are thus suitable biomarkers for monitoring the progression of neuropathy and evaluating any neuroprotective effects.

Concepts: Molecular biology, Western blot, Gel electrophoresis, Retina, Eye, SDS-PAGE, Retinal ganglion cell, Southern blot

30

BACKGROUND:Prehabilitation is defined as preparing an individual to withstand a stressful event through enhancement of functional capacity. HYPOTHESIS:We hypothesized that a preoperative exercise program would enhance postoperative outcomes after anterior cruciate ligament reconstruction (ACLR). STUDY DESIGN:Randomized controlled clinical trial; Level of evidence, 1. METHODS:Twenty volunteers awaiting ACLR were randomly assigned to a control or exercise intervention group. The exercise group completed a 6-week gym- and home-based exercise program. Assessments include single-legged hop test; quadriceps and hamstring peak torque and magnetic resonance imaging cross-sectional area (CSA); Modified Cincinnati Knee Rating System score; and muscle biopsy of the vastus lateralis muscle completed at baseline, preoperatively, and 12 weeks postoperatively. Myosin heavy chain (MHC) isoforms protein and messenger RNA (mRNA) expression were determined with SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) and RT-PCR (real-time polymerase chain reaction), respectively; IGF-1 (insulin-like growth factor 1), MuRF-1 (muscle RING-finger protein-1), and MAFbx (muscle atrophy f-box) mRNA expression were determined with quantitative RT-PCR. RESULTS:Following 6 weeks of exercise intervention, the single-legged hop test results improved significantly in the exercise-injured limb compared with baseline (P = .001). Quadriceps peak torque in the injured limb improved with similar gains in CSA compared with baseline (P = .001). However, this was not significantly increased compared with the control group. Quadriceps and vastus medialis CSA were also larger in the exercise group than in controls (P = .0024 and P = .015, respectively). The modified Cincinnati score was better in the exercise-injured limb compared with baseline. At 12 weeks postoperatively, the rate of decline in the single-legged hop test was reduced in the exercise group compared with controls (P = .001). Similar trends were not seen for quadriceps peak torque and CSA. The vastus medialis CSA had regressed to similar levels as the control group (P = .008). The modified Cincinnati score continued to increase in the exercise group compared with controls (P = .004). The expression of the hypertrophic IGF-1 gene was significantly increased after the exercise intervention (P = .028), with a decrease back to baseline 12 weeks postoperatively (P = .012). Atrophic MuRF-1 gene expression was decreased after intervention compared with baseline (P = .05) but increased again at 12 weeks postoperatively (P = .03). The MAFbx levels did not change significantly in either group and within each time point. On the mRNA level, there was a shift from MHC-IIx isoform to MHC-IIa after exercise, with significant changes compared with control preoperatively (P = .028). Protein testing was able to reproduce this increase for MHC-IIa isoform expression only. CONCLUSION:The 6-week progressive prehabilitation program for subjects undergoing ACLR led to improved knee function based on the single-legged hop test and self-reported assessment using the modified Cincinnati score. These effects were sustained at 12 weeks postoperatively. This study supports prehabilitation as a consideration for patients awaiting ACLR; however, further studies are warranted.

Concepts: Protein, Polymerase chain reaction, Molecular biology, Messenger RNA, Muscle, Gel electrophoresis, Knee, Anterior cruciate ligament

28

Milk and cheese are expensive foodstuffs, and their consumption is spread among the population because of their high nutritional value; for this reason they are often subjected to adulterations. Among the common illegal practices, the addition of powdered derivatives seems very difficult to detect because the adulterant materials have almost the same chemical composition of liquid milk. However, the high temperatures (180-200 °C) used for milk powder production could imply the occurrence of some protein modifications (e.g., glycation, lactosylation, oxidation, deamidation, dehydration). The modified proteins or peptides could then be used as markers for the presence of powdered milk. In this work, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was employed to analyze tryptic digests relevant to samples of raw liquid (without heat treatment), commercial liquid, and powdered cow’s milk. Samples were subjected to two-dimensional gel electrophoresis (2-DE); differences among liquid and powder milk were detected at this stage and eventually confirmed by MALDI analysis of the in gel digested proteins. Some diagnostic peptides of powdered milk, attributed to modified whey proteins and/or caseins, were identified. Then, a faster procedure was optimized, consisting of the separation of caseins from milk whey and the subsequent in-solution digestion of the two fractions, with the advantage of obtaining almost the same information in a limited amount of time. Finally, analyses were carried out with the fast procedure on liquid milk samples adulterated with powdered milk at different percentages, and diagnostic peptides were detected down to 1% of adulteration level.

Concepts: Protein, Mass spectrometry, Milk, Gel electrophoresis, In-gel digestion, Matrix-assisted laser desorption/ionization, Two-dimensional gel electrophoresis, Powdered milk

28

High resolution digital imaging systems were recently introduced to capture and visualize serum protein electrophoresis results. In this study, we compared the performance of five, experienced interpreters using digital images and physical gels to identify and characterize monoclonal gammopathies by immunofixation.

Concepts: Gel electrophoresis, Computer graphics, Electrophoresis, Digital photography, Monoclonal gammopathy of undetermined significance, Protein electrophoresis, Digital image, Serum protein electrophoresis

28

The camel seminal plasma contains a diverse array of components including lipids, carbohydrates, peptides, ions and proteins. These are essential for maintaining normal physiology of spermatozoa and are secreted mainly from the prostrate, epidydimis and bulbo-urethral glands of reproductive system. The protein profiles of camel seminal plasma were resolved by two-dimensional gel electrophoresis (2D-PAGE). The majority of the protein was found in acidic regions below pI 7.0 and the 19 brightly stained proteins were identified by MALDI-TOF/MS analysis. On the basis of proteomic profiles, β-nerve growth factor (β-NGF) was purified by ion-exchange and gel filtration chromatography and identified by SDS-PAGE and MALDI-TOF/MS analysis. It was further confirmed by western blotting experiments using rabbit anti-β-NGF primary antibody.

Concepts: Protein, Molecular biology, Western blot, Gel electrophoresis, Electrophoresis, Laboratory techniques, Two-dimensional gel electrophoresis, Isoelectric focusing

28

The freshwater zebra mussel (Dreissena polymorpha) is a notorious biofouling organism. It adheres to a variety of substrata underwater by means of a proteinaceous structure called the byssus, which consists of a number of threads with adhesive plaques at the tips. The byssal proteins are difficult to characterize due to extensive cross-linking of 3,4-dihydroxyphenylalanine (DOPA), which renders the mature structure largely resistant to protein extraction and immunolocalization. By inducing secretion of fresh threads and plaques in which cross-linking is minimized, three novel zebra mussel byssal proteins were identified following extraction and separation by gel electrophoresis. Peptide fragment fingerprinting was used to match tryptic digests of several gel bands against a cDNA library of genes expressed uniquely in the mussel foot, the organ which secretes the byssus. This allowed identification of a more complete sequence of Dpfp2 (D. polymorpha foot protein 2), a known DOPA-containing byssal protein, and a partial sequence of Dpfp5, a novel protein with several typical characteristics of mussel adhesive proteins.

Concepts: DNA, Protein, Gene, Cell, Amino acid, Molecular biology, Gel electrophoresis, Zebra mussel

28

We present a comprehensive review and comparison of the methodologies for increasing sensitivity and resolution of capillary electrophoresis (CE) using online transient isotachophoresis (tITP). We categorize the diverse set of coupled tITP and CE (tITP-CE) methods based on their fundamental principles for disrupting isotachophoretic preconcentration and triggering electrophoretic separation. Based on this classification, we discuss important features, advantages, limitations, and optimization principles of various tITP-CE methods. We substantiate our discussion with original simulations, instructive examples, and published experimental results.

Concepts: Sensitivity and specificity, Gel electrophoresis, Debate, Capillary electrophoresis, Electrophoresis, Binary classification, Affinity electrophoresis, Isotachophoresis