Two-dimensional Polyacrylamide Gel Electrophoresis Research Articles

Key Proteins in Rat Cerebral Cortex: Application of Cornu aspersum Extract as a Neuroprotective Agent in Alzheimer’s Type Dementia

Alzheimer’s disease (AD) is the most widespread neurodegenerative disorder. Recently, it was found that mucus extract from Cornu aspersum has beneficial effects on memory and cognitive processes in a rat scopolamine model of AD. The present study elucidated the mechanisms of action of standardized mucus snail extract (SE) enriched with a fraction above 20 kDa on Alzheimer-type dementia in rats. Using proteomic analysis on two-dimensional polyacrylamide gel electrophoresis (2D–PAGE) on rat cortex extracts, we compared protein expression in both groups: the first group was treated intraperitoneally with scopolamine (Sco, 2 mg/kg, 11 days) and the second (Sco + SE) group was treated intraperitoneally with Sco (Sco, 2 mg/kg) and protected by SE (0.5 mL/100 g bw) applied daily orally for 11 days. Brain cortex was separated and the expressions of various proteins related to memory and cognitive functions were identified. We found that the expression of Ubiquitin carboxyl-terminal hydrolase isozyme L1, Calbindin, Vacuolar ATP synthase catalytic subunit A, Tropomyosin beta chain, 14-3-3 zeta/delta, Kinesin-1 heavy chain, and Stathmin-4 significantly differs in SE-protected rats as compared to dement animals treated only by Sco, and these brain proteins might be potential therapeutic targets for Alzheimer’s-type dementia treatment.

Proteomic analysis of storage proteins in Phaseolus vulgaris associated with resistance to water stress

The common bean (Phaseolus vulgaris), a widely consumed legume in Ecuador, boasts low economic value, significant nutritional contributions, and a remarkable capacity to enhance soil fertility. Despite these attributes, its field productivity often needs to improve, with the water deficit emerging as a primary hindrance. Consequently, genetic enhancements have been incorporated into select varieties, conferring tolerance to specific levels of water scarcity stress. This study aimed to elucidate the distinctions in protein expression patterns responding to water deficiency stress across nine bean varieties. Protein patterns were scrutinized through two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and selected protein spots were subjected to mass spectrometry analysis (MALDI-TOF MS/RP-LC-MS/MS). A comprehensive identification of 111 proteins was achieved and categorized based on their respective functions. Noteworthy among these were the desiccation-protectant protein (LEA14) and Desiccation-related protein PCC13–62, identified as proteins associated with the response to abiotic stress, particularly prevalent in the INIAP_473 cultivar. These findings underscore the potential for targeted genetic improvements to mitigate the impact of water deficit stress on common bean cultivation, contributing to enhanced agricultural resilience and productivity.

Proteomic Analysis of Gingival Crevicular Fluid During Tooth Eruption

Objective: Gingival crevicular fluid (GCF) is a biological fluid that has the unique capacity to reflect changes in periodontium to its protein composition, making it ideal for potential biomarkers. There is limited information about the mechanism of tooth eruption, for which GCF might provide valuable knowledge. This study aimed to provide a proteomic approach to investigate the composition of GCF obtained from two different supraosseous tooth eruption stages of permanent molars changes.
 Methods: GCF samples were taken from a total of 26 healthy children, whose permanent molar just emerged from the gingiva (5-8 years old) and the occlusal equilibrium stage (9-13 years old). Proteins were extracted with Bio-Rad Rehydration Buffer followed by ZebaTM Spin Desalting Column. GCF samples were separated with two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) followed by mass spectrometry- based protein identification.
 Results: A new optimized protocol with enriched protein extraction from GCF samples was developed. Several proteins related to tooth eruption were detected. It was determined that keratin type II cytoskeletal 4 and keratin type I cytoskeletal 9 decreased and albumin increased in GCF protein content in erupting teeth compared to those in the occlusal equilibrium phase.
 Conclusion: This methodology, which we have applied for 2D-PAGE of GCF, can also be a source for other studies. There is huge diagnostic potential in mass spectrometry technologies, this study can be carried forward by using other approaches.

Holo/apo conversion two-dimensional urea PAGE for speciation of Fe3+-bound transferrin in serum.

This paper presents holo/apo conversion two-dimensional urea polyacrylamide gel electrophoresis (HAC-2D urea PAGE) as a novel method for speciating Fe3+-bound transferrin (Tf) species in biological samples, with a combination of metal ion contaminant sweeping (MICS) technique and Fe3+ detection PAGE. In the HAC-2D urea MICS-PAGE approach, HAC was performed to dissociate all the Fe3+ ions bound to Tf from the Fe-Tf species, during a two-step urea PAGE. Using this method, Fe2-Tf, FeN-Tf, and FeC-Tf (holo-Tf, Fe3+-bound Tf attached to N-lobe, and Fe3+-bound Tf attached C-lobe, respectively) were completely isolated based on the difference in the higher-order structure of Tf, visible as horizontally aligned spots off the diagonal. The Fe3+ ions bound to Tf in each gel fraction were determined using PAGE with a fluorescent probe. Without the MICS technique, which electrophoretically removes all contaminant Fe3+ ions from the gel medium to ensure accurate determination of the Fe3+ concentration, it becomes challenging to precisely measure the distribution of metalloprotein species owing to the contaminants. Finally, the distribution of each Fe-bound Tf in a standard human serum sample was successfully determined by complete separation from large amounts of coexisting proteins, and the free Fe3+ concentration in the serum was estimated.

Junctional Adhesion Molecule a (JAM-A) Associates with CD36 upon Platelet Activation and Cytoskeleton in a Phosphorylation-Dependent Manner to Promote Platelet-Platelet Contacts

Background: Platelets play a fundamental role inmaintaining hemostasis. Stability of hemostatic plug is crucial for arresting blood loss during vascular breach. JAM-A is a member of the immunoglobulin superfamily that restricts α IIbβ 3 to its low affinity state by recruiting CSK to the α IIbβ 3-c-Src complex in resting platelets. Agonist-induced inside-out signaling causes JAM-A to dissociate from the α IIbβ 3-Src complex, thus facilitating activation of α IIbβ 3 and outside-in signaling. However, the function of JAM-A in the process of hemostasis is poorly understood. Aim: To evaluate the role of JAM-A in activated platelets and on hemostasis. Methods: Washed human platelets were used in these studies. Full-length cytoplasmic domain of JAM-A (cyto JAM-A) and JAM-A cytoplasmic domain lacking C-terminal PDZ-domain-binding motif (ΔPDZ cyto JAM-A) were expressed as GST-fusion proteins in bacteria using pGEX4T-1 vector. GST-fusion proteins were purified using glutathione beads. Pull-down assays were performed by incubating glutathione GST-fusion proteins beads with lysates of washed human platelets (4×10 8/mL). GST beads alone without the fusion proteins were used as a control. Immunoprecipitation studies were performed using washed human platelets (4x10 8/mL) lysed with CHAPS lysis buffer and precleared by using Protein G Sepharose beads. Specific primary antibodies and isotype specific IgGs (control) were used for immunoprecipitation followed by western blotting. To identify protein complexes two-dimensional blue-native polyacrylamide gel electrophoresis was performed in which protein complexes were first separated based on their size (1 st dimension) and individual proteins in each complex were separated using SDS PAGE (2 nd dimension). JAM-A S 284 phosphorylation was detected using anti-Phospho-S 284. Rap1 activation assay was performed by pull-down GTP-bound Rap1 following the manufacturer's instructions. Results: CD9 and α IIbβ 3 co-immunoprecipitated with JAM-A from resting platelet lysates suggesting that CD9 is a part of the JAM-A/α IIbβ 3 complex. In a pull-down assay recombinant full-length JAM-A cytoplasmic tail fused with GST, but not JAM-A tail lacking the PDZ domain motif fused with GST pull-down CD9 and α IIbβ 3 from resting platelet lysates suggesting that PDZ-domain binding motif of JAM-A is responsible for its interaction with CD9/α IIbβ 3 complex. Interestingly, platelet activation resulted in the dissociation of JAM-A from the CD9/α IIbβ 3 complex as seen by loss of interaction between JAM-A and CD9/α IIbβ 3 in co-immunoprecipitation and blue-native PAGE assays. It is reported that platelet activation results in rapid phosphorylation of JAM-A on S 284 in a PKC-dependent manner. We found that S 284 phosphorylated JAM-A associates with CD36 and this complex moves to the Triton X-100 insoluble cytoskeletal fraction upon platelet activation suggesting that phosphorylation of JAM-A may assist its localization to cytoskeleton. Interestingly, we found that induction of conformational change in α IIbβ 3 using Mn 2+ (10μM) activates JAM-A S 284 phosphorylation. Furthermore, Mn 2+ also induced a robust activation of Rap1, a key signaling molecule involved in junctional assembly. Both JAM-A phosphorylation and Rap1 activation were significantly ( P<0.05) inhibited by a pan PKC inhibitor, bisindolylmaleimide (10μM) suggesting that S 284 phosphorylated JAM-A/CD36 complex may support junctional assembly within the platelet plug. Conclusion: JAM-A, through its cytoplasmic domain, associates with α IIbβ 3 and CD9 in resting platelets. Upon platelet activation JAM-A rapidly dissociates from this complex and is phosphorylated on S 284. Phosphorylated JAM-A then associates with CD36 and cytoskeleton leading to activation of Rap1, a protein important in junctional assembly between platelets within a hemostatic plug.

Seminal Plasma Proteins Associated with The Fertility of Brahman Bulls in The Colombian Low Tropics.

The sperm interacts with seminal plasma proteins during its transport through the female reproductive tract to reach the oocyte. Seminal plasma proteins have been associated as biomarkers of fertility in bovine males, while two-dimensional electrophoresis in polyacrylamide gels under denaturing conditions (2D-PAGE) is a useful technique for their separation, allowing their subsequent analysis with the aid of specialised software. Brahman bulls are known for their tolerance to tropical conditions such as low-quality pastures, high temperatures, and relative humidity as well as moderate resistance to infestations by parasites and insects. The present study describes the two-dimensional electrophoretic profiles of the seminal plasma proteins in the rainy and dry seasons, associating them with the fertility of Brahman bulls in the Colombian Orinoquía in a 90-days breeding season and a single-sire mating system (1 bull per 50 Brahman cows) with 60 consecutive days of rest. The fertility-related seminal plasma protein spots increased in the dry season. Likewise, a meaningful relationship was found between the protein spots that possibly coincide with the Binder of Sperm Proteins. It was also found that bulls with the highest percentages of pregnancy also had similarities in their 2D seminal plasma maps. We conclude that the seminal plasma protein profile of Brahman bulls raised in the Colombian low tropic changes between rainy and dry seasons, and such changes may influence the reproductive performance of those animals.

Two-Dimensional Polyacrylamide Gel Electrophoresis Coupled with Nanoliquid Chromatography-Tandem Mass Spectrometry-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in the MCF7 Breast Cancer Cell Line Transfected for Jumping Translocation Breakpoint Protein Overexpression.

The identification of new genes/proteins involved in breast cancer (BC) occurrence is widely used to discover novel biomarkers and understand the molecular mechanisms of BC initiation and progression. The jumping translocation breakpoint (JTB) gene may act both as a tumor suppressor or oncogene in various types of tumors, including BC. Thus, the JTB protein could have the potential to be used as a biomarker in BC, but its neoplastic mechanisms still remain unknown or controversial. We previously analyzed the interacting partners of JTBhigh protein extracted from transfected MCF7 BC cell line using SDS-PAGE complemented with in-solution digestion, respectively. The previous results suggested the JTB contributed to the development of a more aggressive phenotype and behavior for the MCF7 BC cell line through synergistic upregulation of epithelial-mesenchymal transition (EMT), mitotic spindle, and fatty acid metabolism-related pathways. In this work, we aim to complement the previously reported JTB proteomics-based experiments by investigating differentially expressed proteins (DEPs) and tumorigenic pathways associated with JTB overexpression using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Statistically different gel spots were picked for protein digestion, followed by nanoliquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis. We identified six DEPs related to the JTBhigh condition vs. control that emphasize a pro-tumorigenic (PT) role. Twenty-one proteins, which are known to be usually overexpressed in cancer cells, emphasize an anti-tumorigenic (AT) role when low expression occurs. According to our previous results, proteins that have a PT role are mainly involved in the activation of the EMT process. Interestingly, JTB overexpression has been correlated here with a plethora of significant upregulated and downregulated proteins that sustain JTB tumor suppressive functions. Our present and previous results sustain the necessity of the complementary use of different proteomics-based methods (SDS-PAGE, 2D-PAGE, and in-solution digestion) followed by tandem mass spectrometry to avoid their limitations, with each method leading to the delineation of specific clusters of DEPs that may be merged for a better understanding of molecular pathways and neoplastic mechanisms related to the JTB's role in BC initiation and progression.

MicroRNA-145-5p suppresses cell proliferation, migration, and invasion in upper tract urothelial carcinoma by targeting 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase.

Upper tract urothelial carcinoma (UTUC), including renal, pelvic, and ureteral carcinoma, has a high incidence rate in Taiwan, which is different from that in Western countries. Therefore, it is imperative to elucidate the mechanisms underlying UTUC growth and metastasis. To explore the function of miR-145-5p in UTUC, we transfected the BFTC909 cell line with miR-145-5p mimics and analyzed the differences in protein levels by performing two-dimensional polyacrylamide gel electrophoresis. Real-time polymerase chain reaction and Western blot analysis were used to analyze 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inositol monophosphate cyclohydrolase (ATIC) messenger RNA and protein levels. A dual-luciferase assay was performed to identify the target of miR-145-5p in ATIC. The effects of miR-145-5p and ATIC expression by cell transfection on cell proliferation, migration, and invasion were also assessed. miR-145-5p downregulated ATIC protein expression. High ATIC expression is associated with tumor stage, metastasis, recurrence, and a poor prognosis in patients with UTUC. Cell function assays revealed that ATIC knockdown inhibited the proliferation, migration, and invasive abilities of UTUC cells. In contrast, miR-145-5p affected the proliferation, migration, and invasive abilities of UTUC cells by directly targeting the 3'-untranslated regions of ATIC. Furthermore, we used RNA sequencing and Ingenuity Pathway Analysis to identify possible downstream genes regulated by ATIC and found that miR-145-5p regulated the protein levels of fibronectin 1, Slug, cyclin A2, cyclin B1, P57, and interferon-induced transmembrane 1 via ATIC. ATIC may be a valuable predictor of prognosis and a potential therapeutic target for UTUC.

Protein profiles identified by LC-MS/MS demonstrate change in beta oxidation, ketogenesis, and propionate metabolism in rumen epithelium with different additives

Replacement of ionophore feed additives by essential oils demonstrates differences in energy metabolism. The mechanism of action of essential oils depends on the ruminal pH, therefore, feedlot diets with high starch inclusions tend to show greater effectiveness of these natural additives. The aim of this study is to map the proteome of the ruminal epithelium of feedlot Nellore cattle (n = 60) with different additives (monensin, blend of essential oils + exogenous α-amylase) and varying levels of starch (25% and 45%) Two-dimensional polyacrylamide gel electrophoresis was used to separate the proteome of ruminal epithelium. The differentially expressed protein spots were characterized by isoelectric point, molecular mass, volume, and intensity of the spots and identified by liquid chromatography tandem mass spectrometry (LC-MS/MS). Diets using an essential oil blend associated with exogenous amylase promoted greater expression of macromolecules from the degradation of carbohydrates through the glycolytic and ketogenesis pathway. Fourteen proteins were identified in upregulation and the presence of proteins involved in glucose oxidation as well as HydroxymethylglutarylCoA lyase (HMGCL), which catalyzes part of the metabolic intermediate metabolism—a key step in ketogenesis. Our results suggest that there was an increase in glycolysis from the oxidation of Glyceraldehyde-3-phosphate dehydrogenase (GAPDH GAPD), which participates in the first step of acetate and butyrate production and the oxidative decarboxylation of the ruminal epithelium of feedlot Nellore cattle. Monensin increased precursors of propionate, such as methylmalonyl-CoA mutase (MUT), which suggests greater synthesis of propionate via propionyl-CoA upon entry into the citric acid cycle as succinyl-CoA, which can increase feed efficiency and reduces feed intake.

Proteomics analysis of human breast milk by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) coupled with mass spectrometry to assess breast cancer risk.

Breast cancer (BC) is one of the most common cancers and one of the most common causes for cancer-related mortality. Discovery of protein biomarkers associated with cancer is considered important for early diagnosis and prediction of the cancer risk. Protein biomarkers could be investigated by large-scale protein investigation or proteomics, using mass spectrometry (MS)-based techniques. Our group applies MS-based proteomics to study the protein pattern in human breast milk from women with BC and controls and investigates the alterations and dysregulations of breast milk proteins in comparison pairs of BC versus control. These dysregulated proteins might be considered potential future biomarkers of BC. Identification of potential biomarkers in breast milk may benefit young women without BC, but who could collect the milk for future assessment of BC risk. Previously we identified several dysregulated proteins in different sets of human breast milk samples from BC patients and controls using gel-based protein separation coupled with MS. Here, we performed 2D-PAGE coupled with nano-liquid chromatography-tandem MS (nanoLC-MS/MS) in a small-scale study on a set of six human breast milk pairs (three BC samples vs. three controls) and we identified several dysregulated proteins that have potential roles in cancer progression and might be considered potential BC biomarkers in the future.

A novel rubber tree PR-10 protein involved in host-defense response against the white root rot fungus Rigidoporus microporus

BackgroundWhite root rot disease in rubber trees, caused by the pathogenic fungi Rigidoporus microporus, is currently considered a major problem in rubber tree plantations worldwide. Only a few reports have mentioned the response of rubber trees occurring at the non-infection sites, which is crucial for the disease understanding and protecting the yield losses.ResultsThrough a comparative proteomic study using the two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique, the present study reveals some distal-responsive proteins in rubber tree leaves during the plant-fungal pathogen interaction. From a total of 12 selected differentially expressed protein spots, several defense-related proteins such as molecular chaperones and ROS-detoxifying enzymes were identified. The expression of 6 candidate proteins was investigated at the transcript level by Reverse Transcription Quantitative PCR (RT-qPCR). In silico, a highly-expressed uncharacterized protein LOC110648447 found in rubber trees was predicted to be a protein in the pathogenesis-related protein 10 (PR-10) class. In silico promoter analysis and structural-related characterization of this novel PR-10 protein suggest that it plays a potential role in defending rubber trees against R. microporus infection. The promoter contains WRKY-, MYB-, and other defense-related cis-acting elements. The structural model of the novel PR-10 protein predicted by I-TASSER showed a topology of the Bet v 1 protein family, including a conserved active site and a ligand-binding hydrophobic cavity.ConclusionsA novel protein in the PR-10 group increased sharply in rubber tree leaves during interaction with the white root rot pathogen, potentially contributing to host defense. The results of this study provide information useful for white root rot disease management of rubber trees in the future.

New insights into the role of microheterogeneity of ZP3 during structural maturation of the avian equivalent of mammalian zona pellucida.

The egg coat including mammalian zona pellucida (ZP) and the avian equivalent, i.e., inner-perivitelline layer (IPVL), is a specialized extracellular matrix being composed of the ZP glycoproteins and surrounds both pre-ovulatory oocytes and ovulated egg cells in vertebrates. The egg coat is well known for its potential importance in both the reproduction and early development, although the underlying molecular mechanisms remain to be fully elucidated. Interestingly, ZP3, one of the ZP-glycoprotein family members forming scaffolds of the egg-coat matrices with other ZP glycoproteins, exhibits extreme but distinctive microheterogeneity to form a large number of isoelectric-point isoforms at least in the chicken IPVL. In the present study, we performed three-dimensional confocal imaging and two-dimensional polyacrylamide-gel electrophoresis (2D-PAGE) of chicken IPVLs that were isolated from the ovarian follicles at different growth stages before ovulation. The results suggest that the relative proportions of the ZP3 isoforms are differentially altered during the structural maturation of the egg-coat matrices. Furthermore, tandem mass spectrometry (MS/MS) analyses and ZP1 binding assays against separated ZP3 isoforms demonstrated that each ZP3 isoform contains characteristic modifications, and there are large differences among ZP3 isoforms in the ZP1 binding affinities. These results suggest that the microheterogeneity of chicken ZP3 might be regulated to be associated with the formation of egg-coat matrices during the structural maturation of chicken IPVL. Our findings may provide new insights into molecular mechanisms of egg-coat assembly processes.

The Discovery of Ribosomal Protein bL31 from Escherichia coli: A Long Story Revisited.

Ribosomal protein bL31 in Escherichia coli was initially detected as a short form (62 amino acids) using Kaltschmidt and Wittmann's two-dimensional polyacrylamide gel electrophoresis (2D PAGE), but the intact form (70 amino acids) was subsequently identified by means of Wada's improved radical-free and highly reducing (RFHR) 2D PAGE, which was consistent with the analysis of its encoding gene rpmE. Ribosomes routinely prepared from the K12 wild-type strain contained both forms of bL31. ΔompT cells, which lack protease 7, only contained intact bL31, suggesting that protease 7 cleaves intact bL31 and generates short bL31 during ribosome preparation from wild-type cells. Intact bL31 was required for subunit association, and its eight cleaved C-terminal amino acids contributed to this function. 70S ribosomes protected bL31 from cleavage by protease 7, but free 50S did not. In vitro translation was assayed using three systems. The translational activities of wild-type and ΔrpmE ribosomes were 20% and 40% lower than those of ΔompT ribosomes, which contained one copy of intact bL31. The deletion of bL31 reduces cell growth. A structural analysis predicted that bL31 spans the 30S and 50S subunits, consistent with its functions in 70S association and translation. It is important to re-analyze in vitro translation with ribosomes containing only intact bL31.

Selective Cytotoxicity and Changes in Protein Expression of T24 Bladder Carcinoma Permanent Cell Line after Treatment with Hemocyanins.

Some molluscan hemocyanins (Hcs) have significant immunological and antitumor potential, enabling their application in oncology. The antitumor activity of Hcs from marine snails Rapana venosa (RvH), giant keyhole limpet Megathura crenulata (KLH) and garden snails Helix lucorum (HlH), as well as their different derivatives, were studied in vitro on a permanent T24 cell line of bladder cancer and normal urothelial cell line HL 10/29 compared to doxorubicin. The antiproliferative activity of the tested Hcs was determined using the WST-1 assay and BrdU ELISA assay. Morphological changes in both urothelial cell lines were confirmed by fluorescence microscopy. The proteomic analysis of a bladder cancer cell line before and after treatment with functional unit (FU) βc-HlH-h using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry revealed differences in the expression of some proteins. Studies prove that the T24 tumor cell line is dose- and time-dependent, sensitive to the action of the tested isoforms, and it glycosylated FU of these hemocyanins. Selective inhibition of T24 cell growth was observed after incubation with structural subunits (βc-HlH, RvHI and RvHII) and FUs (βc-HlH-h and RvHII-e). Additionally, fluorescent microphotographs did not show apoptotic or necrotic alterations in the normal urothelial cell line HL 10/29. The FU βc-HlH-h demonstrated the highest antiproliferative effect (similarly to doxorubicin), in which predominantly apoptotic and less late apoptotic or necrotic changes in the tumor cells were observed. Several downand up-regulated proteins identified by proteome analysis may be associated with the apoptosis pathway. The present study illustrated the selectivity of the cytotoxic effect of Hcs against the Т24 cancer cell line. This is the first report of protein expression in T24 human bladder cancer cells under the influence of FU βc-HlH-h. That is probably due to the specific oligosaccharide structures rich in methylated hexoses exposed on the surface of βc-HlH-h.

Two-Dimensional Gel Electrophoresis and 2D-DIGE.

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to be one of the most versatile and widely used techniques to study the proteome of a biological system, particularly in the separation of intact proteins. A modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labeling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE gels for differential quantitative analysis of protein expression between experimental groups. Both these methods have distinct advantages in the separation and identification of thousands of individual protein species including protein isoforms and post-translational modifications. This chapter discusses the principles of 2D-PAGE and 2D-DIGE including limitations to the methods. 2D-PAGE and 2D-DIGE continue to be popular methods in bioprocessing-related research, particularly on recombinant Chinese hamster ovary cells, which are also discussed in this chapter.

Proteo-Molecular Investigation of Cultivated Rice, Wild Rice, and Barley Provides Clues of Defense Responses against Rhizoctonia solani Infection.

Rhizoctonia solani is a soil-borne fungus causing sheath blight disease in cereal crops including rice. Genetic resistance to sheath blight disease in cereal crops is not well understood in most of the host(s). Aside from this, a comparative study on the different hosts at the biochemical and proteomic level upon R. solani infection was not reported earlier. Here, we performed proteomic based analysis and studied defense pathways among cultivated rice (cv. Pusa Basmati-1), wild rice accession (Oryza grandiglumis), and barley (cv. NDB-1445) after inoculation with R. solani. Increased levels of phenol, peroxidase, and β-1, 3-glucanase were observed in infected tissue as compared to the control in all of the hosts. Wild rice accession O. grandiglumis showed a higher level of biochemical signals than barley cv. NDB 1445 and cultivated rice cv. Pusa Basmati-1. Using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS), differently expressed proteins were also studied in control and after inoculation with R. solani. Wild rice accession O. grandiglumis induced a cysteine protease inhibitor and zinc finger proteins, which have defense functions and resistance against fungal pathogens. On the other hand, barley cv. NDB-1445 and cultivated rice cv. Pusa Basmati-1 mainly induce energy metabolism-related proteins/signals after inoculation with R. solani in comparison to wild rice accession O. grandiglumis. The present comprehensive study of R. solani interaction using three hosts, namely, Pusa Basmati-1 (cultivated rice), O. grandiglumis (wild rice), and NDB-1445 (barley) would interpret wider possibilities in the dissection of the protein(s) induced during the infection process. These proteins may further be correlated to the gene(s) and other related molecular tools that will help for the marker-assisted breeding and/or gene editing for this distressing disease among the major cereal crops.

Cofilin-1 and profilin-1 expression in lung microvascular endothelial cells exposed to titanium dioxide nanoparticles

Air pollutants exacerbate chronic airway diseases, such as asthma and chronic obstructive pulmonary disease (COPD). However, the underlying mechanisms are yet to be determined. While a number of studies have reported adverse effects of nanoparticles on humans, little is known about their effects on the respiratory system. To examine the protein expression in human lung microvascular endothelial cells (HMVEC-L) exposed to titanium dioxide (TiO2) nanoparticles, a common air pollutant. A proteomics approach using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) was used to determine the differences in protein expression at 8 h and 24 h, following the treatment of HMVEC-L with 20-μM or 40-μM TiO2 nanoparticles. Human lung microvascular endothelial cells treated with 20-μM TiO2 nanoparticles showed alterations of 7 protein spots, including molecules related to calcium regulation, transport, cytoskeleton, and muscle contraction. The treatment of HMVEC-L with 40-μM TiO2 nanoparticles resulted in alterations of 4 protein spots, with molecular functions related to the cytoskeleton, myosin regulation, actin modulation, as well as guanosine diphosphate (GDP) and guanosine triphosphate (GTP) regulation. To validate these results, immunohistochemical staining and western blotting analyses were performed on lung tissues collected from mice exposed to TiO2 nanoparticles. Cofilin-1 and profilin-1 were expressed in the endothelium, epithelium and inflammatory cells, and decreased in lung tissues of TiO2 nanoparticle-exposed mice compared to sham-treated controls. These results suggest that some of the differentially expressed proteins may play important roles in airway diseases caused by TiO2 nanoparticle exposure.

Evaluation of indirect-ELISA using eluted antigens from Trichinella spiralis muscle larvae for diagnosis of swine trichinellosis

Trichinellosis is caused by Trichinella spiralis muscle larvae (TsML), which is transmitted to human when they eat infected raw or undercooked meat. T. spiralis infection is detected by an enzyme-linked immunosorbent assay (ELISA) using excretory–secretory antigens (ESAg); however, the preparation of ESAg is challenging, and yields are low, which hampers screening efforts. In this study, crude somatic antigens (CSAg) of TsML with molecular weights (MWs) of 43, 79 and 101 kDa have been identified in swine trichinellosis sera with less cross-reaction with uninfected sera and other parasitic infected sera. After that, the CSAg at MWs of 43, 79 and 101 kDa (TsCSAg-43, TsCSAg-79, and TsCSAg-101, respectively) were isolated from sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The eluted antigens were analyzed by IgG-ELISA for sensitivity and specificity, and specific antigens from the three regions were identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS-MS). The sensitivity of IgG-ELISA using the three eluted antigens was 100% with specificities of 97.77%, 95.54%, 90.63% and for TsCSAg-43, TsCSAg-79, and TsCSAg-101, respectively. The LC-MS-MS results of immunomics showed that 18/20 spots of the antigens with MWs of 43, 79, and 101 kDa represent 11 different proteins identified. TsCSAg-43 showed the highest specificity, indicating that the specific proteins identified, including 45 kDa antigen–trichina [fragment], DNA topoisomerase 2-alpha antigen targeted by protective antibodies, and a conserved hypothetical protein (gi339234223), should be developed and produced in large volumes for further immunodiagnostic studies.

Proteomic analysis of Burkholderia zhejiangensis CEIB S4–3 during the methyl parathion degradation process

Methyl parathion is an organophosphorus pesticide widely employed worldwide to control pests in agricultural and domestic environments. However, due to its intensive use, high toxicity, and environmental persistence, methyl parathion is recognized as an important ecosystem and human health threat, causing severe environmental pollution events and numerous human poisoning and deaths each year. Therefore, identifying and characterizing microorganisms capable of fully degrading methyl parathion and its degradation metabolites is a crucial environmental task for the bioremediation of pesticide-polluted sites. Burkholderia zhejiangensis CEIB S4–3 is a bacterial strain isolated from agricultural soils capable of immediately hydrolyzing methyl parathion at a concentration of 50 mg/L and degrading the 100% of the released p-nitrophenol in a 12-hour lapse when cultured in minimal salt medium. In this study, a comparative proteomic analysis was conducted in the presence and absence of methyl parathion to evaluate the biological mechanisms implicated in the methyl parathion biodegradation and resistance by the strain B. zhejiangensis CEIB S4–3. In each treatment, the changes in the protein expression patterns were evaluated at three sampling times, zero, three, and nine hours through the use of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and the differentially expressed proteins were identified by mass spectrometry (MALDI-TOF). The proteomic analysis allowed the identification of 72 proteins with differential expression, 35 proteins in the absence of the pesticide, and 37 proteins in the experimental condition in the presence of methyl parathion. The identified proteins are involved in different metabolic processes such as the carbohydrate and amino acids metabolism, carbon metabolism and energy production, fatty acids β-oxidation, and the aromatic compounds catabolism, including enzymes of the both p-nitrophenol degradation pathways (Hydroquinone dioxygenase and Hydroxyquinol 1,2 dioxygenase), as well as the overexpression of proteins implicated in cellular damage defense mechanisms such as the response and protection of the oxidative stress, reactive oxygen species defense, detoxification of xenobiotics, and DNA repair processes. According to these data, B. zhejiangensis CEIB S4–3 overexpress different proteins related to aromatic compounds catabolism and with the p-nitrophenol degradation pathways, the higher expression levels observed in the two subunits of the enzyme Hydroquinone dioxygenase, suggest a preferential use of the Hydroquinone metabolic pathway in the p-nitrophenol degradation process. Moreover the overexpression of several proteins implicated in the oxidative stress response, xenobiotics detoxification, and DNA damage repair reveals the mechanisms employed by B. zhejiangensis CEIB S4–3 to counteract the adverse effects caused by the methyl parathion and p-nitrophenol exposure.

Comparative Analysis of Proteomic of Curcumin Reversing Multidrug Resistance in HCT-8/VCR Cells.

To further explore the mechanisms of curcumin reversing multidrug resistance (MDR) in HCT8/VCR cells. Here, we employed comparative analysis of proteomic of essential proteins of human colon carcinoma HCT8/VCR cells with or without treatment of curcumin by separating and quantifying the essential protein posttranslational modification through radical-free two-dimensional polyacrylamide gel electrophoresis with strong reductant. The reverse impact of curcumin on multidrug resistance of HCT8/VCR and HCT8/VCR cells was evaluated using MTT assay. After adding curcumin 25 μM for 72 h, by 2-DE and mass spectrometry, twenty proteins were certified with changed expression levels. Three protein sites were upregulated and seventeen protein sites were downregulated in curcumin-treated HCT-8/VCR. Verification analyses were conducted using RT-PCR and Western blotting for downregulated proteins including GSTP1 and PRDX6. The proteins might have a direct or indirect contact with multidrug resistance. The finding of the research would provide novel sights for systematically comprehending the mechanisms of the reversal impacts of curcumin on MDR in HCT8/VCR cells and contribute to the recognition and application of new markers in clinical practice.