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University of California at Berkeley I or UCB-1 pistachio rootstock is propagated from the cross between Pistacia integerrima male × Pistacia atlantica female. So far, no report has been presented on the proteomic profile of Pistacia genus. In this research, 7-month-old UCB-1 rootstocks that were produced by tissue culture method and grown in pots containing 1/3 perlite, 1/3 clay and 1/3 sand were exposed to the three different concentrations of NaCl including 0, 100 and 200 mM for 30 days in the controlled conditions in the greenhouse. In the first step, under these three different concentrations of NaCl, the content of malondialdehyde and activities of guaiacol peroxidase, superoxide dismutase, catalase and peroxidase were evaluated. Malondialdehyde content increased up to 100 mM NaCl and then decreased. Activities of guaiacol peroxidase, superoxide dismutase and catalase increased with increasing concentration of NaCl, while peroxidase activity reduced. In the second step, 0 and 100 mM NaCl were selected to evaluate changes in the proteomic profile of this rootstock using MALDI-TOF/TOF method. In this study, ribonucleoside-diphosphate reductase small chain, polcalcin Phl p 7-like and golgin subfamily A member 5 were identified for the first time in response to salinity stress and have not been previously reported to be involved in the response of plant under abiotic stresses. Moreover, in this study, five unknown proteins were identified in UCB-1 pistachio under salinity stress. [ABSTRACT FROM AUTHOR]

Background: Marine medaka is among the most popular models of fish species for ecotoxicology and environmental research and proteomic studies are useful tools for understanding the molecular responses of medaka upon exposure to different environmental stressors. The preparation of high-quality protein samples is the key to producing high-quality two-dimensional gel electrophoresis (2-DE) results for proteomic analysis. In recent years, Trizol-based protein extraction has been gaining popularity because of its promising performance in producing high-quality 2-DE as well as the convenience of the method. Methods: Three Trizol-based approaches (Trizol method, Aliquot Trizol method and Trizol method with a commercial clean-up kit) were used to extract proteins from a marine medaka sample and 2-DE profiles were produced. Quality of the 2-DE profiles and effectiveness of the extraction methods were evaluated. For comparison, two common protein extraction methods (lysis buffer method and trichloroacetic acid (TCA)/acetone precipitation extraction) were also applied in parallel to Trizol-based approaches. Results: Any of the three Trizol-based approaches produced a high-quality 2-DE profile of marine medaka compared with both lysis buffer method and TCA/acetone precipitation extraction. In addition, Trizol method with a commercial clean-up kit produced the best 2-DE profile in terms of background clarity, number of spots and resolution of proteins. Conclusions: Trizol-based approaches offered better choices than traditional protein extraction methods for 2-DE analysis of marine medaka. The modified version of Trizol method with a commercial clean-up kit was shown to produce the best 2-DE profile. [ABSTRACT FROM AUTHOR]

Characterization of the uterine proteome before the entry of the conceptus to the uterus is essential to know the factors involved in the physiological events of gestation. The objective of the study was to compare proteomic profile of uterine fluid collected on day 5 post ovulation of cyclic and inseminated mares. Samples of endometrial secretion were recovered over 2 cycles during the fifth day post ovulation. The first cycle constituted the Cyclic group and in the following cycle, the same mares were inseminated and considered as the Inseminated group. All the samples were subjected to two-dimensional electrophoresis (2D-PAGE). A total of 107 spots were visualized by 2D-PAGE. Three spots with differences in abundance between the inseminated and cyclic mares and with presence in at least 80% in one of the groups were selected and identified. The selected spots were extracted, digested by trypsin and analyzed by matrix assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometry (MS) for protein identification. Three proteins were identified: ceruloplasmin (CP) serotransferrin (TF) and albumin (ALB). The identified proteins in this study were related to iron metabolism and immunological tolerance suggesting that changes in their abundance during the 5 days after ovulation are probably a signaling mechanism of the potential equine conceptus to the maternal immune system for its immunological recognition. Probably changes in abundance of CP, ALB and TF represent a mechanism of endometrial preparation for the maternal recognition, attachment and development of a potential equine embryo. There is also evidence to support an alternative hypothesis suggesting that protein changes are inflammatory events, resulting from a previous inflammation due to residual seminal effects. • Ceruloplasmin was more abundant in inseminated mares than in cyclic on day 5. • Serotransferrin was more abundant in cyclic mares than inseminated on day 5. • Albumin was more abundant in cyclic mares than inseminated on day 5. • Changes occurred in endometrium fluid before the entry of the embryo into the uterus. [ABSTRACT FROM AUTHOR]

Background and aims: Avicennia marina is a pioneer mangrove species widely distributed along the southeast coast of China. It suffers, especially in the seedling stage, from the tidal flooding and anaerobic surroundings as it closes to the seaward side. The aim of this study is to assess the ability of A. marina seedlings to withstand different tidal inundations by physiological and proteomic approaches. Methods: To accomplish this, the artificial tidal inundations were mimicked as 0, 4, and 8 h per tidal cycle about 1 week. The physiological approaches and two-dimensional electrophoresis coupled with MALDI-TOF/TOF-MS technology were used to reveal the adaptive alterations of A. marina seedlings to tidal inundation. Results: There were profound changes in photosynthesis and chlorophyll fluorescence characteristics of A. marina seedling leaves under inundation treatment. Particularly, photosynthetic rate increased at 4 h inundation, while decreasing at 8 h inundation treatment compared with control (0 h). The results highlighted that A. marina seedlings could greatly upregulate the abundances of photosynthesis-related proteins, activate antioxidant and defense systems to efficiently suppress the reactive oxygen species (ROS) burst and cell damages, mobilize carbohydrate metabolism associated proteins, and then maintain cellular homeostasis, resulting in well adaptation to short-term tidal inundation. Conclusion: Overall, our results demonstrated that short-term inundation is beneficial, while long-term inundation is detrimental to A. marina. The results allow us to recognize the roles of specific proteins in molecular tolerance to tidal inundation in mangrove plants. [ABSTRACT FROM AUTHOR]

Introduction: Drug-resistance is a major hindrance to successful treatment of AML. Current predictive biomarkers are mainly genetic aberrations and insufficient in foretelling treatment outcome in all acute myeloid leukaemia (AML) due to its heterogeneous and aggressive nature. Proteins are stable and reliable. Secreted proteins in AML may have predictive or prognostic values for early intervention. Proteomic studies on AML are few and further investigations will benefit in selection of best markers. The aim of the study was to identify differentially expressed plasma proteins in AML with different treatment outcome. Methods: Two-dimensional electrophoresis (2-DE) technique was utilised to identify proteins differentially expressed in chemo-sensitive/chemo-resistant AML. Plasma and peripheral blood mononuclear cell (PBMC) lysate proteome analysis were performed on six chemo-resistant, four chemo-sensitive and six healthy controls and seven chemo-resistant, three chemo-sensitive and six healthy controls, respectively. Each experiment was conducted in duplicate or triplicate. Images were captured and protein spots detected by software. Differentially expressed protein spots were excised from gel and proteins were identified using LC/MS/MS. Proteins spots that were also detected in healthy controls were excluded. Results: Comparing mean % volume of each spot demonstrated significantly enhanced expression of apoliprotein-E (APO-E) and haptoglobin (HP) (p<0.05) in plasma and HNRNP H1 (p=0.049) in cell lysate of chemo-sensitive group. Serotransferrin (STF) from plasma and DNA-PK from cell lysate (p=0.01) were associated with chemo-resistance. Conclusion: This preliminary study identified several potential predictive biomarkers associated with chemo-resistance/chemo-sensitivity to treatment in AML. Further studies with a larger number of samples are required to validate the results. [ABSTRACT FROM AUTHOR]

Background: Malignant pleural mesothelioma (MPM) a rare neoplasm linked to asbestos exposure is characterized by a poor prognosis. Soluble mesothelin is currently considered the most specific diagnostic biomarker. The aim of the study was to identify novel biomarkers by proteomic analysis of two MPM cell lines secretome. Materials and Methods: The protein patterns of MPM cells secretome were examined and compared to a non-malignant mesothelial cell line using two-dimensional gel electrophoresis coupled to mass spectrometry. Serum levels of candidate biomarkers were determined in MPM patients and control subjects. Results: Two up-regulated proteins involved in cancer biology, prosaposin and quiescin Q6 sulfhydryl oxidase 1, were considered candidate biomarkers. Serum levels of both proteins were significantly higher in MPM patients than control subjects. Combining the data of each receiveroperating characteristic analysis predicted a good diagnostic accuracy. Conclusion: A panel of the putative biomarkers represents a promising tool for MPM diagnosis. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Ascaris roundworms are the parasitic nematodes responsible for causing human and porcine ascariasis. Whereas A. lumbricoides is the most common soil-transmitted helminth infecting humans in the world, A. suum causes important economic losses in the porcine industry. The latter has been proposed as a model for the study of A. lumbricoides since both species are closely related. The third larval stage of these parasites carries out an intriguing and complex hepatopulmonary route through the bloodstream of its hosts. This allows the interaction between larvae and the physiological mechanisms of the hosts circulatory system, such as the fibrinolytic system. Parasite migration has been widely linked to the activation of this system by pathogens that are able to bind plasminogen and enhance plasmin generation. Therefore, the aim of this study was to examine the interaction between the infective third larval stage of A. suum and the host fibrinolytic system as a model of the host-Ascaris spp. relationships. Methods: Infective larvae were obtained after incubating and hatching fertile eggs of A. suum in order to extract their cuticle and excretory/secretory antigens. The ability of both extracts to bind and activate plasminogen, as well as promote plasmin generation were assayed by ELISA and western blot. The location of plasminogen binding on the larval surface was revealed by immunofluorescence. The plasminogen-binding proteins from both antigenic extracts were revealed by two-dimensional electrophoresis and plasminogen-ligand blotting, and identified by mass spectrometry. Results: Cuticle and excretory/secretory antigens from infective larvae of A. suum were able to bind plasminogen and promote plasmin generation in the presence of plasminogen activators. Plasminogen binding was located on the larval surface. Twelve plasminogen-binding proteins were identified in both antigenic extracts. Conclusions: To the best of our knowledge, the present results showed for the first time, the pro-fibrinolytic potential of infective larvae of Ascaris spp., which suggests a novel parasite survival mechanism by facilitating the migration through host tissues. [ABSTRACT FROM AUTHOR]

Adipose derived stem cells (ADSCs) are multipotent and can transdifferentiate into neural stem cells. We investigated the transdifferentiation of ADSCs to neural phenotype (NP) cells using selegiline and two-dimensional electrophoresis (2-DE). The perinephric and inguinal fat of rats was collected and used to isolate ADSCs that were characterized by immunophenotyping using flow cytometry. The ADSCs were differentiated into osteogenic and lipogenic cells. The NP cells were generated using 10−9 mM selegiline and characterized by immunocytochemical staining of nestin and neurofilament 68 (NF-68), and by qRT-PCR of nestin, neurod1 and NF68. Total protein of ADSCs and NP cells was extracted and their proteome patterns were examined using 2-DE. ADSCs carried CD73, CD44 and CD90 cell markers, but not CD34. ADSCs were differentiated into osteocyte and adipocyte lineages. The differentiated NP cells expressed nestin, neuro d1 and NF-68. The proteome pattern of ADSCs was compared with that of NP cells and eight spots showed more than a two fold increase in protein expression. The molecular weights and isoelectric points of these highly expressed proteins were estimated using Melanie software. We compared these results with those of the mouse proteomic database using the protein isoelectric point database, and the functions of the eight proteins in differentiation of NP cells were predicted using the UniProt database. The probable identities of the proteins that showed higher expression in NP cells included cholinesterase, GFRa2, protein kinase C (PKC-eta) and RING finger protein 121. The sequences of the proteins identified from mouse database were aligned by comparing them with similar proteins in rat database using the Basic Local Alignment Search Tool (BLAST). The E values of all aligned proteins were zero, which indicates consistency of the matched protein. These proteins participate in differentiation of the neuron and their overexpression causes ADSCs transdifferentiation into NP cells. [ABSTRACT FROM AUTHOR]

Previous studies have shown that both hydrogen gas (H2) and ethylene (ETH) play positive roles in plant adventitious rooting. However, the relationship between H2 and ETH during this process has not been explored and remains insufficiently understood. In this study, cucumber (Cucumis sativus L.) was used to explore the proteomic changes in ETH-H2-induced rooting. Our results show that hydrogen-rich water (HRW) and ethylene-releasing compound (ethephon) at proper concentrations promote adventitious rooting, with maximal biological responses occurring at 50% HRW or 0.5 mM ethephon. ETH inhibitors aminoethoxyvinylglycine (AVG) and AgNO3 cause partial inhibition of adventitious rooting induced by H2, suggesting that ETH might be involved in H2-induced adventitious rooting. According to two-dimensional electrophoresis (2-DE) and mass spectrometric analyses, compared with the control, 9 proteins were up-regulated while 15 proteins were down-regulated in HRW treatment; four proteins were up-regulated while 10 proteins were down-regulated in ethephon treatment; and one protein was up-regulated while nine proteins were down-regulated in HRW+AVG treatment. Six of these differentially accumulated proteins were further analyzed, including photosynthesis-related proteins (ribulose-1,5-bisphosphate carall boxylase smsubunit (Rubisco), sedoheptulose-1,7-bisphosphatase (SBPase), oxygen-evolving enhancer protein (OEE1)), amino and metabolism-related protein (threonine dehydratase (TDH)), stress response-related protein (cytosolic ascorbate peroxidase (CAPX)), and folding, modification and degradation-related protein (protein disulfide-isomerase (PDI)). Moreover, the results of real-time PCR about the mRNA levels of these genes in various treatments were consistent with the 2-DE results. Therefore, ETH may be the downstream signaling molecule during H2-induced adventitious rooting and proteins Rubisco, SBPase, OEE1, TDH, CAPX and PDI may play important roles during the process. [ABSTRACT FROM AUTHOR]

Copyright of Acta Edulis Fungi is the property of Acta Edulis Fungi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background: Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction method based on gradient interval histogram (GIH) is proposed in this paper. Results: First, GIH equalization is proposed to enhance the protein spot edges, especially the weak protein spots in the 2DE image. Second, to eliminate the overall brightness shift, GIH matching is applied to the 2DE images that need to be compared. Finally, the proposed method is verified by subjective quality evaluation and quantitative analysis of protein spots in real 2DE images. Conclusions: The experimental results show that the average error of the quantification of corresponding protein spots in the resulting image pairs is less than 3%, which is significantly superior to that of the existing methods. [ABSTRACT FROM AUTHOR]

Systemic anaplastic large cell lymphoma (ALCL) is an aggressive T-cell lymphoma most commonly seen in children and young adults. The majority of pediatric ALCLs are associated with the t(2;5)(p23;q35) translocation which fuses the Anaplastic Lymphoma Kinase (ALK) gene with the Nucleophosmin (NPM) gene. The NPM-ALK fusion protein is a constitutively-active tyrosine kinase, and plays a major role in tumor pathogenesis. In an effort to advance novel diagnostic approaches and the understanding of the function of this fusion protein in cancer cells, we expressed in E. coli, purified and characterized human NPM-ALK fusion protein to be used as a standard for estimating expression levels in cultured human ALCL cells, a key tool in ALCL pathobiology research. We estimated that NPM-ALK fusion protein is expressed at substantial levels in both Karpas 299 and SU-DHL-1 cells (ca. 4–6 million molecules or 0.5–0.7 pg protein per cell; based on our in-house developed NPM-ALK ELISA; LOD of 40 pM) as compared to the ubiquitous β-actin protein (ca. 64 million molecules or 4.5 pg per lymphocyte). We also compared NPM-ALK/ β-actin ratios determined by ELISA to those independently determined by two-dimensional electrophoresis and showed that the two methods are in good agreement. [ABSTRACT FROM AUTHOR]

Background: Traditional studies of the cardiac proteome have mainly investigated in an animal model by two-dimensional gel electrophoresis (2-DE). However, the results have not been of satisfactory quality for an understanding of the underlying mechanism. Recent quantitative proteomic methods have been improved to overcome these limitations. To comprehensively study the cardiac proteome in a rat model of ischemia-reperfusion (IR), we developed a tandem mass tag (TMT)-based quantitative proteomic strategy. Furthermore, using this strategy, we examined the molecular mechanisms underlying the prevention of myocardial infarction by the intake of Triticum aestivum L. extract (TALE), a representative dietary fiber grain. Methods: Cardiac proteomes were analyzed by 2-DE as a gel-based approach, and TMT labeling coupled with two-dimensional liquid chromatography (2D-LC) and tandem mass spectrometry (MS/MS) as a non-gel-based quantitative approach. Additionally, gene ontology annotation was conducted by PANTHER database. Several proteins of interest were verified by a Western blot analysis. Results: Total 641 proteins were identified commonly from two independent MS datasets using 2D-LC MS/MS. Among these, we identified 151 IR-related proteins that were differentially expressed between the sham-operation group and IR group, comprising 62 up-regulated proteins and 89 down-regulated proteins. Most of the reduced proteins were involved in metabolic processes. In addition, 57 of the IR-related proteins were affected by TALE intake, representing 25 up-regulated proteins and 32 down-regulated proteins. In particular, TALE intake leads to a switch in metabolism to reduce the loss of high-energy phosphates and the accumulation of harmful catabolites (especially reactive oxygen species (ROS)) and to maintain cytoskeleton balance, leading to a reduction in cardiac IR injury. Conclusions: Our study provides a comprehensive proteome map of IR-related proteins and potential target proteins and identifies mechanisms implicated in the prevention of myocardial infarction by TALE intake in a rat IR model. [ABSTRACT FROM AUTHOR]

Potato tuberization is a complicated biological process regulated by multiple phytohormones, in particular cytokinins (CKs). The information available on the molecular mechanisms regulating tuber development by CKs remains largely unclear. Physiological results initially indicated that low 6‐benzylaminopurine (BAP) concentration (3 mg l−1) advanced the tuberization beginning time and promoted tuber formation. A comparative proteomics approach was applied to investigate the proteome change of tuber development by two‐dimensional gel electrophoresis in vitro, subjected to exogenous BAP treatments (0, 3, 6 and 13 mg l−1). Quantitative image analysis showed a total of 83 protein spots with significantly altered abundance (>2.5‐fold, P < 0.05), and 55 differentially abundant proteins were identified by MALDI‐TOF/TOF MS. Among these proteins, 22 proteins exhibited up‐regulation with the increase of exogenous BAP concentration, and 31 proteins were upregulated at 3 mg l−1 BAP whereas being downregulated at higher BAP concentrations. These proteins were involved in metabolism and bioenergy, storage, redox homeostasis, cell defense and rescue, transcription and translation, chaperones, signaling and transport. The favorable effects of low BAP concentrations on tuber development were found in various cellular processes, mainly including the stimulation of starch and storage protein accumulation, the enhancement of the glycolysis pathway and ATP synthesis, the cellular homeostasis maintenance, the activation of pathogen defense, the higher efficiency of transcription and translation, as well as the enhanced metabolite transport. However, higher BAP concentration, especially 13 mg l−1, showed disadvantageous effects. The proposed hypothetical model would explain the interaction of these proteins associated with CK‐induced tuber development in vitro. [ABSTRACT FROM AUTHOR]

In the present study, the mechanisms of Aspergillus niger AM1 and AM2 resistance to white phosphorus were studied. It was shown that the presence of white phosphorus (P4) at a concentration of 0.25% in the medium had a marginal impact on the ratio of living to dead cells during fungal cultivation, which indicates a high resistance of the strains to P4. Observations made with electron microscopy showed an increase in the thickness of the fungal cell wall, which is a barrier to the penetration of white phosphorus. MALDI results revealed the biosynthesis of new protein enzymes that could potentially participate in the neutralization of white phosphorus. In addition, white phosphorus caused activation of the metabolism, accompanied by an increase in the number of mitochondria in the cells. [ABSTRACT FROM AUTHOR]

Summary: A diet based on sunflower cake for lambs was assayed in order to reuse biodiesel industrial by‐products with the aim of reducing livestock costs and evaluating their influence on meat quality. To achieve these goals, sixteen male lambs were fed diets containing different levels of sunflower cake (control, 5%, 10% and 15%). Afterwards, their semimembranosus muscles were analysed by two‐dimensional electrophoresis coupled to mass spectrometry and their functional protein association was examined using STRING. Structural and metabolic proteins in the lambs' proteomes changed significantly according to their diet. Fifteen proteins showed significant changes caused by the inclusion of sunflower cake, and the most differentially abundant structural proteins were detected in 2‐DE gels from the lambs. Differentially abundant metabolic proteins such as ENO3 (enolase 3), MDH1 (malate dehydrogenase) and ALDH1A1 (retinal dehydrogenase) have been proposed as biomarkers of quality parameters in other species. [ABSTRACT FROM AUTHOR]

Objective: Liverworts possess historical adaptive strategies for abiotic stresses because they were the first plants that shifted from water to land. Proteomics is a state-of-the-art technique that can capture snapshots of events occurring at the protein level in many organisms. Herein, we highlight the comparison and optimization of an effective protein extraction and precipitation protocol for two-dimensional gel electrophoresis (2-DE) of liverworts. Results: We compared three different protein extraction methods, i.e.,1.5 M Tris–HCl (pH 8.8), 50 mM Tris–HCl (pH 7.5), and polyvinylpolypyrrolidone (PVPP) extraction, followed by three precipitation methods, i.e., 80% ethanol, 80% acetone, and 20% tricholoroacetic acid (TCA)–acetone, in a liverwort Dumortiera hirsuta. Among these methods, 50 mM Tris–HCl (pH 7.5) extraction, followed by 20% TCA–acetone precipitation, appeared to be more suitable for 2-DE. Furthermore, we performed modifications during protein washing, re-solubilization in rehydration buffer and isoelectric focusing (IEF). The modifications provided us better results in terms of protein yield, resolution, spot numbers, and intensities for 2-DE gels of D. hirsuta and other two liverworts, i.e., Marchantia paleacea and Plagiochasma appendiculatum. Furthermore, we randomly selected spots from the 2-DE gel of D. hirsuta and identified using mass spectrometry, which confirms the applicability of this protocol for liverworts proteomics. [ABSTRACT FROM AUTHOR]

Metroxylon sagu Rottb. or locally known as sago palm is a tropical starch crop grown for starch production in commercial plantations in Malaysia, especially in Sarawak, East Malaysia. This plant species accumulate the highest amount of edible starch compared to other starch-producing crops. However, the non-trunking phenomenon has been observed to be one of the major issues restricting the yield of sago palm starch. In this study, proteomics approach was utilised to discover differences between trunking and non-trunking proteomes in sago palm leaf tissues. Total protein from 16 years old trunking and non-trunking sago palm leaves from deep peat area were extracted with PEG fractionation extraction method and subjected to two-dimensional gel electrophoresis (2D PAGE). Differential protein spots were subjected to MALDI-ToF/ToF MS/MS. Proteomic analysis has identified 34 differentially expressed proteins between trunking and non-trunking sago samples. From these protein spots, all 19 proteins representing different enzymes and proteins have significantly increased in abundance in non-trunking sago plant when subjected to mass spectrometry. The identified proteins mostly function in metabolic pathways including photosynthesis, tricarboxylic acid cycle, glycolysis, carbon utilization and oxidative stress. The current study indicated that the several proteins identified through differentially expressed proteome contributed to physical differences in trunking and non-trunking sago palm. [ABSTRACT FROM AUTHOR]

Vibrio alginolyticus is one of the most serious causative agents of diseases in cultured marine fish and shellfish. However, the characteristics of virulence factors in pathogenic V. alginolyticus are poorly known. To gain insight into fish diseases caused by V. alginolyticus, we carried out two‐dimensional gel electrophoresis (2‐DE) combined with MALDI‐TOF mass spectrometry to identify uniquely expressed proteins in the disease‐causing V. alginolyticus. V. alginolyticus strains were isolated from marine environments and diseased fish obtained from southern Thailand. We identified seven unique proteins in the disease‐causing V. alginolyticus strain. Among those, the outer membrane protein A (OmpA) had the strongest expression. Therefore, the function of this protein was further analysed. To investigate the role of OmpA protein, an in‐frame deletion mutant of ompA was constructed using the homologous recombination method. Although the ompA mutant V. alginolyticus strain (ΔompA) grew normally, the mutant exhibited a significant defect in the swarming ability and the biofilm formation. Furthermore, Galleria mellonella larvae injected with the mutant bacteria had a significantly greater survival percentage than those injected with the wild‐type strain, demonstrating that OmpA protein is required for the pathogenicity of V. alginolyticus. Together, this study suggests a potential target for vaccine development against pathogenic V. alginolyticus strain. [ABSTRACT FROM AUTHOR]

Copyright of Forest Research is the property of Forest Research Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

As one of the main indicators of nutritional values of foxtail millet, grain protein contents (GPCs) of seeds can be affected by soil water conditions. Studies in this report indicated that intensified drought in filling stage increased the GPCs. To gain better insight into the interaction mechanism between the GPCs and soil water deficits, the proteomic profiles of mature seeds under three drought stress levels (moderate drought-W2; combined drought-W1; severe drought-W0) were conducted on two varieties, Longgu6 (LG6) and Huangjinmiao (HJM) by two-dimensional electrophoresis, with acidic (pH 4–7) gels. There were 83 protein spots in total identified successfully in two comparison groups (W1 vs W2 and W0 vs W2), associated with four major biochemical and metabolic pathways, including storage protein, amino acid and protein metabolisms, energy metabolism, response to stress and defense, and chaperones. Further analysis revealed that the increase of GPCs in LG6 under both W0 and W1 may be owing to the up-regulated storage proteins and the up-regulated protein response to drought stress. The levels of DEPs related to protein and amino acid biosynthesis and starch metabolism increased greatly in LG6 under W1, and this may also result in the high GPC level of seeds in LG6 under W1. Protein biosynthesis was up-regulated and drought stress-related pathways were enhanced in HJM under W1, thereby resulting in the increase of GPC in HJM under W1. These results will contribute to the existing knowledge on the complexity of protein changes leading to the GPC changes in response to drought. [ABSTRACT FROM AUTHOR]

Background: Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments. Results: Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source. Conclusions: Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments. [ABSTRACT FROM AUTHOR]

Ureteropelvic junction (UPJ) obstruction is a common problem in children, but its etiology remains unclear. In this study, the proteome profiles of the obstructed segment and its surrounding distal and proximal parts were comparatively evaluated. Twelve children younger than 2 years of age with unilateral intrinsic UPJ obstruction were included. The excised operational tissue was divided into three parts immediately after resection: the obstructed part (Obst), the distal normal ureteral part (Dist), and the proximal part of the obstructed segment (Prox). Proteins extracted from the tissue samples were subjected to two-dimensional gel electrophoresis analysis to identify differentially regulated proteins. Spot analysis revealed that four proteins, namely tropomyosin beta and alpha-1 chains, actin and desmin, were upregulated in Obst in comparison to Dist. A similar analysis between Obst and Prox showed that heat shock protein beta-1 and carbonic anhydrase-1 were upregulated in Obst, while tropomyosin alpha 3 chain and ATP synthase beta were upregulated in Prox. The last comparative analysis between Dist and Prox revealed upregulation of annexin-A5 and annexin-A1 in Dist and vimentin, mitochondrial ATP synthase subunit-beta, peroxiredoxin-2, and apolipoprotein-A1 in Prox. Bioinformatics analysis using the STRING server indicated that the differentially regulated proteins, altogether, point to the changes occurring in muscle filament sliding pathway. When regulations occurring in each group were mutually compared, a change in lipase inhibition activity was detected by STRING. This is the first study scrutinizing changes occurring in protein profiles in UPJ. [ABSTRACT FROM AUTHOR]

It is important to understand the molecular mechanisms that take place in muscle tissues and to predict meat quality characteristics. One of the most popular methods is two-dimensional electrophoresis, which allows us to visualize, share and identify different molecules, including meat proteins. However, the standard conditions of this method are not universal for all types of raw material, so the authors suggest a new variation of two-dimensional electrophoresis for muscle tissue analysis. Samples were tested by the classical version of isoelectric focusing (cathode buffer in the top and anode buffer in the bottom chamber of the electrophoresis cell) and its variation (anode buffer in the top and cathode buffer in the bottom chamber of the electrophoresis cell). Next, extruded gels were incubated in two different buffer systems: the first was equilibration buffer I (6 M urea, 20% w/v glycerol, 2% w/v SDS and 1% w/v Ditiothreitol in 375 mM Tris-HCl buffer, pH 8.8) followed by equilibration buffer II (6 M urea, 20% w/v glycerol, 2% w/v SDS and 4% w/v iodoacetamide in 375 mM Tris-HCl buffer pH 8.8 and the second, buffer ?, consisting of 5 M urea, 2% w/v SDS, 5% v/v mercaptoethanol, 62.5 mM Tris-HCl buffer, pH 6.8 and 0.01% w/v bromophenol blue. Electrophoretic studies of muscle tissue revealed the best protein separation after changing the direction of the current (authors' variation), while no differences were detected after changing incubation buffers. [ABSTRACT FROM AUTHOR]

The association of haptoglobin (Hp) with various cancers has been reported and also it has been documented that the Hp phenotypes/genotypes have different functional ability. So, we examined phenotypes/genotypes of Hp in newly diagnosed, untreated non-muscle invasive bladder cancer (NMIBC) patients and investigated its prognostic value for risk stratification of the cancer. In eighty NMIBC patients and 80 healthy individuals the Hp genotypes and phenotypes were analyzed using polymerase chain reaction (PCR) and two-dimensional gel electrophoresis (2D-GE), respectively. Besides, the presence of the Hpα1, α2, and β chains in the sera was confirmed by Mass Spectrometry (MS). The frequencies of the 1-1 and 2-2 genotypes/phenotypes were respectively higher and lower in healthy subjects compared to the patients. Our results revealed that the 2-2 genotype/phenotype could increase the risk of NMIBC. There was a positive association between the 2-2 genotype/phenotype with the T category/grade of cancer (p<0.05). The present study implied a strong association between the Hp phenotypes and genotypes with NMIBC. It was found that the 2-2 genotype and phenotype could be a risk factor for NMIBC incidence, as well as, progression. This study introduced Hp genotyping as a possible cost-effective and precise method for prognosis of individuals at the risk of NMIBC. [ABSTRACT FROM AUTHOR]

Many proteomics studies have been devoted to investigate the gel-based methods for separation and fractionation of complex protein mixture extracted from tissues, cells, and other biological specimens. In order to fractionate, identify, and quantify proteins when coupled with mass spectrometric identification or other immunological tests, accurate image alignment method for possible significant protein diversity under different experimental conditions is of high demand. Although lots of protein spot matching and alignment methods have been proposed for two-dimensional gel electrophoresis image, very few methods work well because of dynamic appearance changes and structure changes for gel electrophoresis images. To address these difficulties, we propose a hierarchical transformation-guided registration method to not only align the global shape changes by affine transformation but also alleviate the local structure changes between two gel electrophoresis images by no-rigid deformation registration. The non-rigid registration method is used to obtain the local displacement with shape changes. Since such initial affine transformation can alleviate the global transformation difference between two images, it becomes efficient to use non-rigid registration to refine the registration result. The visualized and quantified experimental results show that our method is more accurate and robust to identify the variability between individual proteins. [ABSTRACT FROM AUTHOR]

We extend our previous study of absorption line shapes of molecular aggregates using the Liouville space hierarchical equations of motion (HEOM) method [L. P. Chen, R. H. Zheng, Q. Shi, and Y. J. Yan, J. Chem. Phys. 131, 094502 (2009)] to calculate third order optical response functions and two-dimensional electronic spectra of model dimers. As in our previous work, we have focused on the applicability of several approximate methods related to the HEOM method. We show that while the second order perturbative quantum master equations are generally inaccurate in describing the peak shapes and solvation dynamics, they can give reasonable peak amplitude evolution even in the intermediate coupling regime. The stochastic Liouville equation results in good peak shapes, but does not properly describe the excited state dynamics due to the lack of detailed balance. A modified version of the high temperature approximation to the HEOM gives the best agreement with the exact result. [ABSTRACT FROM AUTHOR]

A method for projecting chemical reaction surface coordinates from a Hessian in curvilinear internal coordinates has recently been developed. Here we introduce a modification to this approach which allows for analytical evaluation of the necessary coordinate derivatives, thus reducing the number of ab initio calculations required. We apply this method to the determination of spectator mode frequencies and zero-point energies for the series of hydrogen abstraction reactions X+CH4→XH+CH3, X=muonium (μ), H, D, CH3. Comparison of these frequencies with those obtained using rectilinear coordinates allows us to examine how the mass of X affects the coordinate sensitivity of the spectator modes. We carry out two-dimensional quantum reactive scattering calculations for these reactions to highlight instances where the choice of coordinates may have a significant impact on the evaluated thermal rate constants. [ABSTRACT FROM AUTHOR]

A method for projecting chemical reaction surface coordinates from a Hessian in curvilinear internal coordinates has recently been developed. Here we introduce a modification to this approach which allows for analytical evaluation of the necessary coordinate derivatives, thus reducing the number of ab initio calculations required. We apply this method to the determination of spectator mode frequencies and zero-point energies for the series of hydrogen abstraction reactions X+CH4→XH+CH3, X=muonium (μ), H, D, CH3. Comparison of these frequencies with those obtained using rectilinear coordinates allows us to examine how the mass of X affects the coordinate sensitivity of the spectator modes. We carry out two-dimensional quantum reactive scattering calculations for these reactions to highlight instances where the choice of coordinates may have a significant impact on the evaluated thermal rate constants. [ABSTRACT FROM AUTHOR]

We report results of the analytical and numerical investigation of self-heating effects in GaN-based high-power field-effect transistors. The problem of heat transfer in a transistor structure has been solved both analytically, using the method of images, and numerically. Two-dimensional electrothermal simulations of the GaN metal-semiconductor field-effect transistors on SiC and sapphire substrate have been performed in a framework of the drift-diffusion model. Using the physical-based simulations, we studied the dependence of the hot-spot temperature on the gate-to-gate pitch in the transistors with multiple gate fingers. Particular attention has been paid to comparison of self-heating effects in GaN transistors on SiC and sapphire substrates. The obtained results can be used for optimization of the thermal design of the GaN-based high-power field-effect transistors. [ABSTRACT FROM AUTHOR]

Liver is responsible for 90% of lipid synthesis in poultry; thus, it plays an important role in the growth of Muscovy ducks, which have a high fat deposition ability in a time-dependent manner. Therefore, male Muscovy ducks at 14, 28, 42, and 56 days were selected for body weight (BW), carcass weight (CW), subcutaneous fat thickness (SFT), abdominal fat weight (AFW), intramuscular fat content (IMF), and breast muscle fiber (BMF) diameter and density determination. Two-dimensional electrophoresis (2-DE) combining liquid chromatography linked to tandem mass spectrometry (LC-MS/MS) was used to analyze proteomic changes in liver at each stage. The BW, CW, AFW, SFT, and BMF diameter and density were significantly increased, while IMF content was significantly decreased at 28 to 42 days of age (p < 0.05). There were 57 differentially abundant protein (DEP) spots representing 40 proteins identified among the ages, in which 17, 41 and 4 spots were differentially abundant at 14 vs. 28, 28 vs. 42, and 42 vs. 56, respectively. Gene Ontology enrichment analysis found that DEPs were mostly enriched in the oxidation-reduction process, carboxylic acid metabolism, etc. Protein–protein interaction showed that catalase (CAT), triosephosphate isomerase (TPI), and protein disulfide-isomerase (PDI) were the key proteins responsible for the growth of Muscovy duck. In conclusion, 28 to 42 days of age is the crucial period for Muscovy ducks, and the ability of metabolism and antioxidants were significantly enhanced in liver.

Abstract Background A wide range of molecules are used by tapeworm metacestodes to establish successful infection in the hostile environment of the host. Reports indicating the proteins in the cestode-host interactions are limited predominantly to taeniids, with no previous data available for non-taeniid species. A non-taeniid, Hymenolepis diminuta, represents one of the most important model species in cestode biology and exhibits an exceptional developmental plasticity in its life-cycle, which involves two phylogenetically distant hosts, arthropod and vertebrate. Results We identified H. diminuta cysticercoid proteins that were recognized by sera of H. diminuta-infected rats using two-dimensional gel electrophoresis (2DE), 2D-immunoblotting, and LC-MS/MS mass spectrometry. Proteomic analysis of 42 antigenic spots revealed 70 proteins. The largest number belonged to structural proteins and to the heat-shock protein (HSP) family. These results show a number of the antigenic proteins of the cysticercoid stage, which were present already in the insect host prior to contact with the mammal host. These are the first parasite antigens that the mammal host encounters after the infection, therefore they may represent some of the molecules important in host-parasite interactions at the early stage of infection. Conclusions These results could help in understanding how H. diminuta and other cestodes adapt to their diverse and complex parasitic life-cycles and show universal molecules used among diverse groups of cestodes to escape the host response to infection.

Abstract Background Alfalfa (Medicago sativa) is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue variations in response to salt stress, comparative physiological and proteomic analyses were made of salt responses in the roots and shoots of the alfalfa. Method A two-dimensional gel electrophoresis (2-DE)-based proteomic technique was employed to identify the differentially abundant proteins (DAPs) from salt-treated alfalfa roots and shoots of the salt tolerance cultivars Zhongmu No 1 cultivar, which was subjected to a range of salt stress concentrations for 9 days. In parallel, REL, MAD and H2O2 contents, and the activities of antioxidant enzymes of shoots and roots were determinand. Result Twenty-seven spots in the shoots and 36 spots in the roots that exhibited showed significant abundance variations were identified by MALDI-TOF-TOF MS. These DAPs are mainly involved in the biological processes of photosynthesis, stress and defense, carbohydrate and energy metabolism, second metabolism, protein metabolism, transcriptional regulation, cell wall and cytoskeleton metabolism, ion transpor, signal transduction. In parallel, physiological data were correlated well with our proteomic results. It is worth emphasizing that some novel salt-responsive proteins were identified, such as CP12, pathogenesis-related protein 2, harvest-induced protein, isoliquiritigenin 2′-O-methyltransferase. qRT-PCR was used to study the gene expression levels of the four above-mentioned proteins; four patterns are consistent with those of induced protein. Conclusion The primary mechanisms underlying the ability of alfalfa seedlings to tolerate salt stress were photosynthesis, detoxifying and antioxidant, secondary metabolism, and ion transport. And it also suggests that the different tissues responded to salt-stress in different ways.

In the study of proteomic profiles of proteins, many scientists stop at the stage of obtaining the final data of the experiment in the form of gels. They have got no information on the possibilities and prospects concerning the application of modern computer and bioinformatics resources that allow to convert the result from qualitative to quantitative form. The use of computer technology allowed to save the recorded images and carry out the calculations with chromatograms using digital video images.Densitometry with the use of video technology is characterized by high calculation speed and low cost of consumables. Digitally archived chromatograms may be used at any time for a number of applications including calculation.Thus, the “manual” bioinformatics analysis allows not only to use different densitometer software for conversion and storage of gels in digital form, but also to quantitatively interpret the results obtained.This paper presents the methods for practical application of bioinformatics tools in the interpretation of protein profiles obtained by one-dimensional and two-dimensional electrophoresis and converted into digital image. The aspects of the quantitative interpretation of electrophoretograms from one-dimensional electrophoresis (1DE) and two-dimensional electrophoresis (2DE) resulting from the studies of muscle tissue of farm animals are reviewed. Examples of various calculation software usage are given. The work in this direction will allow to considerably expand approaches for identification and quantification of protein markers related to quality, functionality and safety of food raw materials and finished products and to carry out metrological examination of the results for confirmation of product compliance.

The use of resistant cultivars is one of the safest and most profitable methods of controlling post including alfalfa weevil. After farm and greenhouse evaluating, Tafresh 42 genotype for molecular studies selected and evaluated to examine the pattern of protein expression in stress and non-stress conditions to alfalfa weevil. The Changes in protein expression were investigated using two-dimensional electrophoresis gels. Clustering analysis, principal component analysis and discriminant analysis were used in statistic studies. The results showed that 11 protein spots had expression changes among 218 protein spots. The most expression pattern of proteins with a similar increase in Tafresh 42, was related to a specific group of proteins which had 45.46% variations in the expression response to the stress. From the point of protein expression, cluster analysis caused a dividing of proteins into three main clusters indicating the presence of proteins with a similar performance in each cluster. Therefore, the presence of these proteins in a common biologic pathway is confirmed. The analysis of discriminant function confirmed 100% the results from clustering that indicated protein conformity with the conditions of the experiment. It is concluded that by using statistical analysis and software, it is possible to evaluate significant expression changes induced damage alfalfa weevil in proteome level and determine the index changes, and after that genetic engineering is utilized for enhancing the level of resistance in the plant under studying.

This work is devoted to pig spleen proteome study. Spleens were taken from Duroc pigs (females, 145 – 160 days old) and typical two-dimensional electrophoregrams were obtained. On proteomic maps after visualization and image analysis there were detected 600 fractions, including organ-specific proteins – 3 62 fractions. Among the identified constitutive fractions, the highest expression was observed (Vol spots more than 3.0E + 07) four protein spots S1, S9, S12 and S21, which are supposedly Annexin A1 (MW 38.76 kDa), Ectonucleoside triphosphate diphosphohydrolase 1 (MW 57.75 kDa) Pro-cathepsin H CD59 (MW 37.45 kDa) and glycoprotein (MW 13.79 kDa), respectively. Obtained electrophoregrams analysis using information resources made it possible to identify different active compounds in spleen with various functions, mainly immunoregulatory – glycoprotein CD59 (Mm 13.79 kDa) and ATP-dependent RNA helicase (Mm 107.58 kDa); the intensely expressed LIM-domain of the actin-binding protein (Mm 83.99 kDa). The results obtained are a prospect for immunomodulating biologic development based on animal raw materials for farm animals.

The prevalence of diet-related obesity is increasing dramatically worldwide, making it important to understand the associated metabolic alterations in the liver. It is well known that obesity is a multifactorial condition that is the result of complex integration between many gene expressions and dietary factors. Obesity alone or in conjunction with other chronic diseases such as diabetes and insulin resistance causes many health problems and is considered a major risk factor for developing non-alcoholic steatohepatitis (NASH) and cirrhosis. In this study, we aimed to understand the molecular mechanisms underlying early hepatic changes in the pathophysiology of high-fat diet (HFD)-induced abdominal obesity in rats. Hepatic protein profiles of normal diet and HFD-induced obesity for 24 weeks were analysed using two-dimensional differential gel electrophoresis (DIGE) and protein identification by MS. Fifty-two proteins were identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), and computer-assisted DIGE image software analysis showed that eighteen major proteins were significantly differentially expressed between comparable groups, with 2·0–4·0-fold change/more ( P < 0·01). These proteins are regulated in response to a HFD, and differentially expressed proteins are involved in key metabolic pathways such as lipid metabolism, energy metabolism, detoxification, urea cycle and hepatic Ca homoeostasis. In addition, Western blot and immunohistochemistry of liver-specific arginase-1 (Arg-1) showed significant increased expression in the liver of high-fat-fed rats ( P < 0·01). Further, Arg-1 expression was correlated with NASH patients with obesity-related fibrosis (F0–F4). It is concluded that high-fat content may affect changes in liver pathways and may be a therapeutic target for obesity-related liver disease. Arg-1 expressions may be a potential pathological marker for assessing the progression of the disease.

This study investigated the changes in Weissella koreensis (WK) protein expression levels during fermentation in MRS medium supplemented with garlic of WK. WK was first discovered as lactic acid bacteria (LAB) in a Korean fermented cabbage dish known as kimchi. The number of WK cells in MRS medium with garlic (MBCG) and without (MB) after 7 days was 3.55 × 1010 and 2.55 × 1010 CFU/mL, respectively. To observe the changes in the carbon sources in the media, we measured the glucose, sucrose, lactic acid, and acetic acid levels in each medium (MB and MBCG). Thus, 67.2 ± 2.4 (MB) and 64.2 ± 4.7 (MBCG) mmol−1 of glucose were consumed. For sucrose, the level was 3.5 ± 2.2 (MB), and 3.4 ± 2.5 (MBCG) mmol−1. There was not much difference in the lactic acid and acetic acid levels at 160.8 ± 0.4 (MB) and 159.2 ± 0.2 (MBCG) and 2.4 ± 0.4 (MB) and 2.2 ± 8.1 (MBCG) mmol−1, respectively. After the 7-day fermentation period, two-dimensional electrophoresis (2DE) was used to confirm the protein expression pattern in the WK strain. The results show that the fusA and ssb1 proteins were reduced, and the clpP protein was increased. Afterwards, the expression patterns of the above proteins were confirmed through qRT-PCR. Thus, this study confirms the changes in protein expression levels in Weissella koreensis when garlic was added to the media. This study provides basic data for future studies on the major biosynthetic pathways of WK.