Matched Protein Spots Research Articles

Identification of peroxiredoxin 6 as a potential lung-adenocarcinoma biomarker for predicting chemotherapy response by proteomic analysis.

The prognosis of lung cancer remains poor due to the limited biomarker selection for treating patients with optimal chemotherapy. The aim of this study is to discover and identify new biomarkers with the value of predicting chemotherapy responses in a lung adenocarcinoma (AD) specimen. In this study, six pairs of pre-treatment fresh primary lung AD-cancer tumors with varied chemotherapy responses were used to discover new biomarkers by two-dimensional difference gel electrophoresis (2D DIGE). Among the matched protein spots, 19 were up-regulated and 18 were down-regulated in chemo-sensitive tumors versus chemo-resistant tissues. These differentially expressed proteins could be divided into five classes: redox regulation protein, the cytoskeletal protein, cell metabolism enzymes or proteins, apoptosis, signal transduction mediated molecules, and other functional proteins. Proteins of interest, including PRDX2, PRDX6, and Gelsolin, were differentially expressed in chemo-sensitive tumors versus chemo-resistant tissues and these observations were validated by immunohistochemistry in 92 formalin-fixed and paraffin-embedded (FFPE) specimens. Our results demonstrated that PRDX6 protein expression was closely related to tumor response (cc2 = 5.57, P < 0.05), whereas no relationship of PRDX2 and Gelsolin were obtained with tumor response (cc2 = 0.51 P > 0.05, cc2 = 0.41 P > 0.05). This tissue proteomics study provides evidence that PRDX6 may be regarded as a predictive biomarker for poor chemotherapy response, which can be helpful in guiding pretreatment protocols.

Proteomics approach to identify serum biomarkers associated with the progression of diabetes in Korean patients with abdominal obesity.

Type 2 diabetes is a metabolic disease with a group of metabolic derangements and inflammatory reactants in the serum. Despite the substantial public health implications, markers of diabetes progression with abdominal obesity are still needed to facilitate early detection and treatment. In this study, we performed a proteomic approach to identify differential target proteins underlying diabetes progression in patients with abdominal obesity. Proteomic differences were investigated in the serum of controls and patients with prediabetes or diabetes with or without abdominal obesity by 2-DE combined with MALDI-TOF-MS. Proteomics data were validated by western blot analyses and major protein-protein interactions were assessed using a network analysis with String database. Among 245 matched protein spots, 36 exhibited marked differences in normal patients with abdominal obesity, prediabetes, and diabetes compared to levels in normal patients without abdominal obesity. Seven (Alpha-1-antichymotrypsin, Alpha-1-antitrypsin, Apolipoprotein A-I, haptoglobin, retinol-binding protein 4, transthyretin, and zinc-alpha2-glycoprotein) of these spots exhibited significant differences between normal and prediabetes/diabetes patients. After a network analysis, functional annotation using Gene Ontology indicated that most of the identified proteins were involved in lipid transport, lipid localization, and the regulation of serum lipoprotein particle levels. Our results indicated that variation in the levels of these identified protein biomarkers has been reported in normal, prediabetes and diabetic Assessment of the levels of these biomarkers may contribute to the development of biomarkers for not only early diagnosis but also in prognosis of diabetes mellitus type 2.

Comparison of protein expression pattern between the Plasmodium falciparum chloroquine-resistant RKL9 and chloroquine-sensitive MRC2 strains.

Objective:The objective of this study was to compare the protein expression patterns of Plasmodium falciparum extracellular and intracellular proteins separated by two-dimensional electrophoresis (2-DE) from the chloroquine-sensitive (CQS) MRC2 strain and chloroquine-resistant (CQR) RKL9 strain. Materials and Methods: Both the extracellular protein (ECP) and intracellular protein (ICP) were extracted and solubilized. The proteins were separated by 2-DE, first based on their charges using isoelectric focusing and then their sizes by electrophoresis. The separated protein spots were detected by silver staining, and further, the protein spot density was analyzed by an image analysis software.Results:2-DE separated the proteins extracted from the CQS and CQR strains based on their differentially expressed protein patterns.Extracellular Protein Analysis:A total of 109 and 77 protein spots were detected by image analysis of ECP extracted from MRC2 and RKL9 strains, respectively. There was a marked reduction in protein expression pattern in the CQR strain when compared with the CQS strain. Interestingly, 50 and 18 protein spots were uniquely expressed in MRC2 and RKL9 strains, respectively. When MRC2 strain-expressed proteins were taken as the control, 12 upregulated and 14 downregulated protein spots were observed in the RKL9 strain-extracted proteins.Intracellular Protein Analysis:ICP extracted from MRC2 and RKL9 strains showed 187 and 199 protein spots by an image analysis software, and a small enhancement of protein expression was measured when comparing the CQR strain with CQS strain. There were 67 and 79 unique protein spots detected in MRC2 and RKL9 strains, respectively. A total of 120 protein spots were similar when MRC2 proteins were taken as the control; among these protein spots, 40 upregulated and 22 downregulated protein spots were detected in RKL9 strain-expressed protein.Conclusions:Both these unique and matched protein spots might be molecularly potent drug targets for chloroquine resistance in P. falciparum. Further identification of these proteins by mass spectrometry/peptide sequencing is essential to clearly understand the mechanism of resistance.

Evaluation of protein extraction protocols for 2DE in marine ecotoxicoproteomics

In ecotoxicoproteomics, an accurate and reproducible extraction of proteins is a critical step for 2DE analysis and further protein identification using MS. The criteria for the assessment of protein extraction quality include protein yield, protein spots resolved in a 2DE gel, matched protein spots in replicate gels, reproducibility, and compatibility with MS. In this work, we evaluated three protein extraction systems, straightforward lysis buffer, trichloroacetic acid-acetone, and TRIzol reagent with some modifications, for the protein extraction from three animal species including mussel Mytilus galloprovincialis, flounder Paralichthys olivaceus, and polychaete Nereis diversicolor used in marine ecotoxicology. Our results indicated that these methods could extract significantly different protein profiles. The method using TRIzol reagent resulted in the most matched protein spots resolved in four replicate 2DE gels and highest reproducibilities for the gill of M. galloprovincialis and liver of P. olivaceus. However, a modified trichloroacetic acid-acetone solvent system was best for the whole soft tissue of N. diversicolor. This work provides the fundamental information of the extraction quality of protein extraction protocols from different marine animals, which may facilitate the selection of a suitable protein extraction protocol for ecotoxicoproteomics.

Proteomic Identification of Proteins Suggestive of Immune-Mediated Response or Neuronal Degeneration in Serum of Achalasia Patients

Background/AimsThe primary pathophysiologic abnormality in achalasia is known to be a loss of inhibitory myenteric ganglion cells, which may result from an immune-mediated response or neuronal degeneration. The aim of this study was to identify proteins suggestive of an immune-mediated response or neuronal degeneration in the serum of achalasia patients using a proteomic analysis.MethodsBlood samples were collected from five symptomatic achalasia patients and five sex- and age-matched healthy controls. Serum proteomic analysis was conducted, and the protein spots were identified using matrix-assisted laser desorption ionization/time-of-flight and a proteomics analyzer. The serum level of C3 was measured by enzyme-linked immunosorbent assay in nine patients with achalasia and 18 sex- and age-matched healthy controls.ResultsOf the 658 matched protein spots, 28 spots were up-regulated over 2-fold in the serum from achalasia patients compared with that from controls. The up-regulated proteins included complement C4B5, complement C3, cyclin-dependent kinase 5, transthyretin, and alpha 2 macroglobulin. The serum levels of C3 in achalasia patients were significantly higher than those of controls.ConclusionsThe serum proteomic analysis of achalasia patients suggests an immune-mediated response or neuronal degeneration. Further validation studies in larger samples and the esophageal tissue of achalasia patients are required.

Proteome variability amongHelicobacter pyloriisolates clustered according to genomic methylation

To understand whether the variability found in the proteome of Helicobacter pylori relates to the genomic methylation, virulence and associated gastric disease. We applied the Minimum-Common-Restriction-Modification (MCRM) algorithm to genomic methylation data of 30 Portuguese H.pylori strains, obtained by genome sensitivity to Type II restriction enzymes' digestion. All the generated dendrograms presented three clusters with no association with gastric disease. Comparative analysis of two-dimensional gel electrophoresis (2DE) maps obtained for total protein extracts of 10 of these strains, representative of the three main clusters, revealed that among 70 matched protein spots (in a universe of 300), 16 were differently abundant (P<0·05) among clusters. Of these, 13 proteins appear to be related to the cagA genotype or gastric disease. The abundance of three protein species, DnaK, GlnA and HylB, appeared to be dictated by the methylation status of their gene promoter. Variations in the proteome profile of strains with common geographic origin appear to be related to differences in cagA genotype or gastric disease, rather than to clusters organized according to strain genomic methylation. The simultaneous study of the genomic methylation and proteome is important to correlate epigenetic modifications with gene expression and pathogen virulence.

Proteomic profiling of the acid tolerance response (ATR) during the enhanced biomethanation process from Taihu Blue Algae with butyrate stress on anaerobic sludge

Enhanced biomethanation with acid stress on anaerobic sludge, dehydrogenase activity, protein expression, and the primary proteomic profiling of microbial communities during the enhanced anaerobic digestion process from Taihu Blue Algae were investigated. It was found that the accumulation of organic acids and the specific biogas accumulation rate were 1.8 and 1.3 times of the control, when 10g/L and 7.5g/L of butyrate were selected for acid stress, respectively. Meanwhile, dehydrogenase activity of the 7.5g/L acid stress group exhibited an increase of 1.6 times of the control, and protein expression was also found to be enhanced sharply as revealed by 1D-PAGE. Finally, twenty of the matched protein spots through 2D-PAGE from both the control and the 7.5g/L stress groups were identified by MALDI-TOF MS, and five of which were proved to be involved in bioenergy metabolism. Significantly, ATR related proteins might be induced as the pIs of which were acidic as 5.92, 5.51 and 5.54, respectively.

Changes in Serum Protein Profiles of Chickens with Tibial Dyschondroplasia

Differences in serum protein profiles were analyzed to identify possible biomarkers associated with a poultry leg problem named tibial dyschondroplasia (TD) that can lead to lameness. A bead-based affinity matrix (ProteoMiner TM ) containing a combinatorial library of hexapeptides was used to deplete high abundant proteins and enrich the less abundant ones to compare between the sera of six-week old normal and TD affected chickens. Equal amounts of proteins in ProteoMiner depleted serum from control and TD-affected birds were subject to 2D gel electrophoresis, image analysis, and compared to identify the differentially expressed protein spots. The protein spots were characterized using in-gel trypsin digestion followed by mass spectrometry (MS). Of 46 matched protein spots in the gels, 33 were identified by peptide mass finger printing (PMF) and tandem mass spectrometry (MS/MS). Eight spots corresponding to immunoglobulins (Ig) were up-regulated in birds with TD and two spots down regulated. The up-regulated Ig proteins belonged to IgM and IgY(IgG) classes indicated by the identification of 'mu' chain and Fc fragment associated peptides respectively. Enzyme linked immunosorbent assay corroborated an increase in serum IgM levels but not IgG. Although the significance of the increase in IgM proteins in the serum of TD-affected chickens is not understood, it is likely that IgM plays some role in the removal of apoptotic chondrocytes which abound within TD lesions.

Expression and significance of skin aspartic protease in lesions of cutaneous lupus erythematosus

Objective To study the expression of skin aspartic protease (SASPase) in lesions of cutaneous lupus erythematosus (CLE) and its role in the pathogenesis of CLE.Methods Skin samples were resected from the lesions and normal skin of 9 patients with CLE,including 3 cases of subacute cutaneous lupus erythematosus (SCLE),4 cases of discoid lupus erythematosus (DLE) and 2 cases of acute cutaneous lupus erythematosus (ACLE).Keratinocytes were isolated from the tissue samples and cultured in serum-free medium.Total proteins were extracted from the keratinocytes and separated by two-dimensional gel electrophoresis.ImageMaster 2D analysis software was used to assess differentially expressed proteins in keratinocytes between the lesional and normal skin,which were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).The expression levels of SASPase were further determined by Western blot.The data were analyzed statistically by Student's t test.Results Keratinocytes were isolated from the tissue samples and successfully cultured in vitro.Two-dimensional electrophoresis profiles of proteins from the keratinocytes were obtained with high resolution and reproducibility,and the average matching protein spots were about 1200 with the matching rate higher than 80％.As Western blot showed,the relative expression level of SASPase was 0.463 ± 0.018 in keratinocytes from the lesional skin,and 0.145 ± 0.011 in those from the normal skin (P ＜ 0.05).The Western blot results were consistent with those of two-dimensional electrophoresis.Conclusion The initiation and progression of CLE seem to be associated with the abnormal activation and overexpression of SASPase. Key words: Lupus erythematosus, cutaneous; SASPase; Keratinocytes

Identification of differentially expressed biliary proteins induced by cholangiocarcinoma using 2D-DIGE

Objective To determine the probability of identification of differential expression of biliary proteins induced by cholangiocarcinoma using 2D-DIGE. Methods Bile was obtained from 12patients with obstructive jaundice (including 6 cases of cholangiocarcinoma and 6 of cholelithiasis).Each sample was labeled with three different CyDyes (y3,Cy5,Cy2) including one internal standard,pooled from all the samples, and separated with 2-D DIGE in triplicate experiments. MALDI-TOF-MS and bioinformatics were adopted to identify and elucidate the significance of differentially expressed proteins in bile induced by cholangiocarcinoma. Results 55 matched protein spots differences in abundance were detected with statistical variance of two groups(Average Volum Ratio ≥1.5, t-test, P＜0. 05). Among these proteins, 13 PMF were obtained by MALDI-TOF-MS analysis. Eight proteins were identified by searching a protein database. Conclusion The differentially displayed proteomes between the pathological bile obtained from benign and malignant obstructive jaundice indicates the potential application of 2D-DIGE to identify the biomarker of cholangiocarcinoma. Key words: Bile duct neoplasms; Bile; Fluorescence two-dimensional difference gel electrophoresis

Proteomic analysis of the metabolic adaptation of the biocontrol agent Pseudozyma flocculosa leading to glycolipid production

The yeast-like epiphytic fungus Pseudozyma flocculosa is known to antagonize powdery mildew fungi through proliferation on colonies presumably preceded by the release of an antifungal glycolipid (flocculosin). In culture conditions, P. flocculosa can be induced to produce or not flocculosin through manipulation of the culture medium nutrients. In order to characterize and understand the metabolic changes in P. flocculosa linked to glycolipid production, we conducted a 2-DE proteomic analysis and compared the proteomic profile of P. flocculosa growing under conditions favoring the development of the fungus (control) or conducive to flocculosin synthesis (stress). A large number of protein spots (771) were detected in protein extracts of the control treatment compared to only 435 matched protein spots in extracts of the stress cultures, which clearly suggests an important metabolic reorganization in slow-growing cells producing flocculosin. From the latter treatment, we were able to identify 21 protein spots that were either specific to the treatment or up-regulated significantly (2-fold increase). All of them were identified based on similarity between predicted ORF of the newly sequenced genome of P. flocculosa with Ustilago maydis' available annotated sequences. These proteins were associated with the carbon and fatty acid metabolism, and also with the filamentous change of the fungus leading to flocculosin production. This first look into the proteome of P. flocculosa suggests that flocculosin synthesis is elicited in response to specific stress or limiting conditions.

Analysis of Protein Expression Patterns of Silkworm Jinqiu and Its Cross Parents

The differences of protein expression between the improved cross breeding race Jinqiu and its parents were analyzed to discuss the gene construction, and to form a base for illuminating the molecular mechanisms of successful cross breeding in silkworm. Protein samples from silk gland, hemolymph, and midgut were separated by 2-dimensional gel electrophoresis (2-DE). In the three tissues the matched protein spots between Jinqiu and its cross parents were approximately 70% with approximately 30% specific protein spots. In the matched protein spots, 9-24% was differentially expressed representing up- and down-regulated expression. These specific protein spots might be either the newly appeared, which were produced from the genic interaction of cross parents' genes in cross breeding, or posttranscriptionally modified, which were produced from the different modifications on the same original proteins. These results indicate that it is important for a new successful breed, by cross breeding, relying on the actions of some newly produced functional proteins from genic interaction, in addition to marshaling excellent genes of cross parents.

Detection of autoantibodies against cyclophilin A and triosephosphate isomerase in sera from breast cancer patients by proteomic analysis

Much interest is presently being shown toward identifying markers for the detection of breast cancer. To detect autoantibodies that could represent diagnostic markers for breast cancer, we comprehensively analyzed serum autoantibodies showing immunoreactivity to proteins in tumor tissues of breast cancer. Tumor tissues were obtained from 40 patients with breast cancer, along with sera from 30 other patients with breast cancer and 22 healthy donors. Proteins from tumor tissues were separated by 2-DE. After blotting onto PVDF membranes, tissue proteins were immunoblotted with sera from patients or healthy donors. By comparing each immunoblot pattern, three immunoreactive spots displayed stronger staining intensity with patient sera than with sera from healthy donors. The matched protein spots on 2-DE gels were digested and used for LC-MS/MS analysis, and identified as cyclophilin A (peptidyl-prolyl cis-trans isomerase A), triosephosphate isomerase and ubiquitin-conjugating enzyme E2N. Immunoblot analysis was then performed using commercially available purified proteins, confirming the specificity of anti-cyclophilin A and anti-triosephosphate isomerase antibodies in sera from patients.

Differences in Pig Muscle Proteome According to HAL Genotype: Implications for Meat Quality Defects

Bidimensional electrophoresis was used to compare sarcoplasmic protein profiles of early post-mortem pig semimembranosus muscles, sampled from pigs of different HAL genotypes (RYR1 mutation 1841T/C): 6 NN, 6 Nn, 6 nn. ANOVA showed that 55 (18%) of the total of 300 matched protein spots were influenced by genotype, and hierarchical clustering analysis identified 31 (10% of the matched proteins) additional proteins coregulated with these proteins. Fold-changes of differentially expressed proteins were between 1.3 and 21.8. Peptide mass fingerprinting identification of 78 of these 86 proteins indicates that faster pH decline of nn pigs was not explained by higher abundance of glycolytic enzymes. Results indicate further that nn muscles contained fewer proteins of the oxidative metabolic pathway, fewer antioxidants, and more protein fragments. Lower abundance of small heat shock proteins and myofibrillar proteins in nn muscles may at least partly be explained by the effect of pH on their extractability. Possible consequences of lower levels of antioxidants and repair capacities, increased protein fragmentation, and lower extractability of certain proteins in nn muscles on meat quality are discussed.

Comparison of mycelial proteomes of two Verticillium albo-atrum pathotypes from hop

Verticillium wilt diseases caused by Verticillium spp. are known in many important crops and can seriously threaten their production. We studied Verticillium albo-atrum by comparative analysis of the proteome of four hop isolates, classified by the severity of wilt symptoms as mild and lethal pathotypes, from two geographic origins. A two-dimensional electrophoresis reference map of mycelium proteins was first established, resolving up to 650 protein spots on Coomassie-stained gels in a range of pH 4–7 and MW 14 – 116 kDa. The average coefficient of variance for the 268 matched protein spots was 16% and 15%, respectively, for technical and biological variability. Principal component analysis (PCA) discriminated the geographic origin of the isolates and between the two pathotypes and showed a closer relationship among English isolates than Slovene ones. The two-dimensional electrophoresis patterns of one mild (PG1) with one lethal pathotype (PG2) from Slovenia and one mild (M) with one lethal pathotype (PV1) from England were compared. A total of 27 and 30 spots were found differentially expressed between the pathotypes, which were analysed by tandem mass spectrometry. Fifty-three proteins were identified, of which 17 matched proteins with annotated functions. The lethal pathotypes showed increased expression of peroxiredoxine and ascorbate peroxidase, a higher level of cytoskeleton components and regulators, and a higher rate of protein synthesis and energy metabolism. These results reveal differences in the expression level of the identified proteins between the two pathotypes and are discussed in relation to virulence.

Differential analysis of protein profiles of vesicular phase and micellar phase of gallbladder bile from cholesterol gallstone patients

To identify the proteins which play key roles during the formation of cholesterol gallstone, differential analysis was carried out that the proteome of vesicular phase and micellar phase of gallbladder bile from cholesterol gallstone patients. Vesicular and micellar phases were isolated by the density gradient ultracentrifugation method. Total proteins from the two phases were extracted, and the protein expressional profiles were established by two-dimensional electrophoresis respectively. The differentially expressed protein spots analyzed by ImageMaster two-dimensional electrophoresis analysis software were identified with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The concentrations of proteins from vesicular phase and micellar phase of gallbladder bile from cholesterol gallstone patients were (1.5358 +/- 0.0682) mg/ml and (7.1222 +/- 0.2022) mg/ml (P < 0.01) respectively. The average matched protein spots were 120 +/- 24 and 198 +/- 37 in the two groups respectively. There were 72 +/- 16 matched spots in the two representative gels maps and the matched rate was 45.30%. Eight differentially expressed protein spots were identified from the two cholesterol-carrier phases. Among them, 6 were up-regulated with 2 down-regulated in vesicular phase compared with micellar phase. The abundance differentiation of RBP and HSA was confirmed by immunoblotting. The differential protein profiles of vesicular phase and micellar phase of gallbladder bile from cholesterol gallstone patients were established and 8 differential protein spots were identified successfully. The data may be a basis for further screening the key regulators of formation of cholesterol gallstone.

Differential analysis of protein profiles of gallbladder bile from patients with cholesterol cholelithiasis and controls

Objective To elucidate the mechanism of formation of cholesterol cholelithiasis, thisstudy is designed to establish two-dimensional polyacrylamide gel electrophoresis system for differenti-al analysis of the proteome of gallbladder bile from cholesterol cholelithiasis patients and control ones.Methods Total proteins of gallbladder bile were extracted from the subjects in two groups and the protein profiles were established by using the immobilized pH gradient two-dimensional electrophoresis respectively. These maps were analyzed by ImageMaster two-dimensional eleetrophoresis analysis software. Results The concentrations of bile proteins from cholesterol cholelithiasis patients and con-trol ones were (6.4824±0.3403)mg/ml and (2.3156±0.3064)mg/ml(P<0.01), respectively. The average matched protein spots were 465±71 and 407±85 in the two groups, respectively. The matched rates were 71.70% and 68.38% correspondingly. There were 269 matched spots in the two reference gels maps and the matched rate was 61.70%. A total of 34 differential protein spots were i-dentified, 16 expressed highly in cholesterol cholelithiasis patients but lowly in the control ones, while 18 expressed just in the opposite way. Conclusion The differential protein profiles of gallbladder bile between cholesterol cholelithiasis patients and controls have been established and several differential protein spots are found. The data may be a basis for further screening the key regulators of formation of cholesterol eholelithiasis. Key words: Cholelithiasis; Two-dimensional gel electrophoresis; Proteome; Bile

Proteomics Analysis Identifies Molecular Targets Related to Diabetes Mellitus-associated Bladder Dysfunction

Protein expression profiles in rat bladder smooth muscle were compared between animal models of streptozotocin-induced diabetes mellitus (STZ-DM) and age-matched controls at 1 week and 2 months after induction of hyperglycemia with STZ treatment. At each time point, protein samples from four STZ-DM and four age-matched control rat bladder tissues were prepared independently and analyzed together across multiple DIGE gels using a pooled internal standard sample to quantify expression changes with statistical confidence. A total of 100 spots were determined to be significantly changing among the four experimental groups. A subsequent mass spectrometry analysis of the 100 spots identified a total of 56 unique proteins. Of the proteins identified by two-dimensional DIGE/MS, 10 exhibited significant changes 1 week after STZ-induced hyperglycemia, whereas the rest showed differential expression after 2 months. A network analysis of these proteins using MetaCore suggested induction of transcriptional factors that are too low to be detected by two-dimensional DIGE and identified an enriched cluster of down-regulated proteins that are involved in cell adhesion, cell shape control, and motility, including vinculin, intermediate filaments, Ppp2r1a, and extracellular matrix proteins. The proteins that were up-regulated include proteins involved in muscle contraction (e.g. Mrlcb and Ly-GDI), in glycolysis (e.g. alpha-enolase and Taldo1), in mRNA processing (e.g. heterogeneous nuclear ribonucleoprotein A2/B1), in inflammatory response (e.g. S100A9, Annexin 1, and apoA-I), and in chromosome segregation and migration (e.g. Tuba1 and Vil2). Our results suggest that the development of diabetes-related complications in this model involves the down-regulation of structural and extracellular matrix proteins in smooth muscle that are essential for normal muscle contraction and relaxation but also induces proteins that are associated with cell proliferation and inflammation that may account for some of the functional deficits known to occur in diabetic complications of bladder.

Pig Longissimus lumborum proteome: Part II: Relationships between protein content and meat quality

Gender, rearing environment and breed of sire influenced 50.5% of the matched protein spots of the soluble fraction and some meat quality traits [Kwasiborski, A., Sayd, T., Chambon, C., Santé-Lhoutellier, V., Rocha, D., & Terlouw, C. (2008). Muscle proteome in pigs: Part I: Effects of genetic background, rearing environment and gender. Meat Science]. Multiple regression analyses determined that 1 or 2 proteins explained between 24% and 85% of variability in Longissimus meat quality. Regression models differed between treatment groups, but relationships between proteins and meat quality traits seemed to be related to common underlying mechanisms. Thus, proteins retained in models for ultimate pH, lightness, drip, thawing and cooking loss were related to the glycolytic pathway, phosphate transfer, or fibre type composition. Another model for thawing loss retained proteins related to denaturation of myofibrils or lipid content. The models for redness involved proteins related to post-mortem oxidative activity. Thus, proteins correlated with meat quality traits were related to biochemical mechanisms known to be involved in meat quality. Relative contributions of these mechanisms may vary according to gender, sire breed or rearing environment.

An image analysis suite for spot detection and spot matching in two‐dimensional electrophoresis gels

We propose a suite of novel algorithms for image analysis of protein expression images obtained from 2-D electrophoresis. These algorithms are a segmentation algorithm for protein spot identification, and an algorithm for matching protein spots from two corresponding images for differential expression study. The proposed segmentation algorithm employs the watershed transformation, k-means analysis, and distance transform to locate the centroids and to extract the regions of the proteins spots. The proposed spot matching algorithm is an integration of the hierarchical-based and optimization-based methods. The hierarchical method is first used to find corresponding pairs of protein spots satisfying the local cross-correlation and overlapping constraints. The matching energy function based on local structure similarity, image similarity, and spatial constraints is then formulated and optimized. Our new algorithm suite has been extensively tested on synthetic and actual 2-D gel images from various biological experiments, and in quantitative comparisons with ImageMaster2D Platinum the proposed algorithms exhibit better spot detection and spot matching.