Differential protein expression profile in gastrointestinal stromal tumors

Summary. Gastrointestinal stromal tumors (GISTs) arise from the interstitial cells of Cajal through gain of function mutations of the oncogene KIT. Imatinib offers the first effective treatment for patients with GISTs, but the therapeutic outcome strongly depends on the type of KIT mutation. We used ProteinChip technology to investigate whether GISTs with different KIT mutations express different proteins. In total, 154 proteins were significantly differentially expressed in GISTs with exon 9 KIT mutation compared to GISTs with exon 11 KIT mutation.     

Differential proteomic analysis of proteins in wheat spikes induced by Fusarium graminearum

Scab, caused by Fusarium graminearum, is a serious spike disease in wheat. To identify proteins in resistant wheat cultivar Wangshuibai induced by F. graminearum infection, proteins extracted from spikes 6, 12 and 24 h after inoculation were separated by 2-DE. Thirty protein spots showing 3-fold change in abundance when compared with treatment without inoculation were characterized by MALDI-TOF MS and matched to proteins by querying the mass spectra in protein databases or the Triticeae EST translation database. Based on their volume profiles, these proteins were classified into four categories. The first one fell off rapidly at the initial inoculation and then rose at 12 or 24 hai, the second one decreased considerably after inoculation and remained at low level, the third one rose at the initial inoculation and then declined at 12 or 24 hai, the forth one showed steady increase after inoculation and maintained at a high level. Many of the proteins identified in the first two categories are related to carbon metabolism and photosynthesis. While most of proteins identified in the last two categories are related to stress defense of plants, indicating that proteins associated with the defense reactions were activated or translated shortly after inoculation.     

Proteomics analysis of mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritional, and allergenic proteins

Profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nESI-LC–MS/MS). Two-dimensional gels stained with silver nitrate revealed a total of 457, 516, 556, and 530 protein spots in NM Valencia C, Tamspan 90, Georgia Green, and NC-7, respectively. Twenty abundant protein spots showing differences in relative abundance among these cultivars were analyzed by nESI-LC–MS/MS, resulting in identification of 14 non-redundant proteins. The majority of these proteins belonged to the globulin fraction consisting of arachin (glycinin and Arah3/4) and conarachin seed storage proteins as well as other allergen proteins. The expression of some of these identified protein spots was cultivar-specific. For example, allergen Arah3/Arah4 and conarachin protein spots were only detected in Tamspan 90 and NC-7, whereas the Gly1 protein spot was detected only in NM Valencia C and NC-7. Moreover, a galactose-binding lectin protein spot with anti-nutritive properties was only present in Tamspan 90. Other proteins showing differences in relative abundance among the four cultivars included 13-lipoxygenase, fructose-biphosphate aldolase, and glyceraldehyde 3-phosphate dehydrogenase. Together, these results suggest that identified proteins might serve as potential markers for cultivar differentiation and may be associated with underlying sensory and nutritional traits of peanut cultivars.     

Plasma marker proteins associated with the progression of lung cancer in obese mice fed a high-fat diet

Recent studies have indicated that obesity increases the risk of developing several types of cancers including lung cancer, which is the leading cause of cancer death worldwide. In the present study, we attempted to discover marker proteins associated with lung cancer progression mediated by treatment of a high-fat diet (HFD) using 2DE combined with MALDI-TOF-MS. Image analysis and further statistical analysis allowed for the detection and identification of 14 proteins, which consequently were classified into two groups based on their regulation patterns in response to diet and tumor. Interestingly, the protein abundances of ten proteins exhibited a synergistic effect when treated with HFD in tumor-bearing mice (Group I). Proteins that had a higher abundance in the plasma of tumor-bearing mice included FGB, Tf, Hpx, Cp, and Hp and the proteins that had a lower abundance included A1AT precursor, PON1, TTRt, and α2-M. These proteins can be used as molecular markers that contribute simultaneously to both obesity and cancer. Four other proteins showed an increase (complement C3 and FGA) or decrease (Apo H and AT III precursor) in the only tumor-bearing mice independently of diet (Group II). The marker proteins identified here may lead to the development of new therapeutics for obesity-causative treatment of lung cancer.     

双孢蘑菇子实体发育后期差异表达蛋白质分析

为探讨双孢蘑菇子实体发育后期的蛋白质表达变化,对双孢蘑菇As2796子实体采收期、成熟期和开伞期的蛋白质组进行了双向电泳(2-DE)分析,发现了16个表达差异明显的蛋白质。通过质谱分析(MALDI-TOF/TOF MS)和数据库检索,有14个差异蛋白质获得鉴定。其中磷酸烯醇式丙酮酸水合酶与能量代谢相关,T-蛋白复合体1、蛋白酶体、5-甲基四氢三谷氨酸-同型半胱氨酸甲基转移酶、1-吡咯琳-5-羧酸脱氢酶、精氨酸酶与氨基酸或蛋白质代谢直接相关,而GTP结合蛋白则参与细胞的多种生命活动,在细胞的生长发育过程中起着重要的作用。另外7个为功能未知的蛋白质。     

Redox regulation of heat shock protein expression in aging and neurodegenerative disorders associated with oxidative stress: A nutritional approach

Summary. Oxidative stress has been implicated in mechanisms leading to neuronal cell injury in various pathological states of the brain. Alzheimers disease (AD) is a progressive disorder with cognitive and memory decline, speech loss, personality changes and synapse loss. Many approaches have been undertaken to understand AD, but the heterogeneity of the etiologic factors makes it difficult to define the clinically most important factor determining the onset and progression of the disease. However, increasing evidence indicates that factors such as oxidative stress and disturbed protein metabolism and their interaction in a vicious cycle are central to AD pathogenesis.Brains of AD patients undergo many changes, such as disruption of protein synthesis and degradation, classically associated with the heat shock response, which is one form of stress response. Heat shock proteins are proteins serving as molecular chaperones involved in the protection of cells from various forms of stress.Recently, the involvement of the heme oxygenase (HO) pathway in anti-degenerative mechanisms operating in AD has received considerable attention, as it has been demonstrated that the expression of HO is closely related to that of amyloid precursor protein (APP). HO induction occurs together with the induction of other HSPs during various physiopathological conditions. The vasoactive molecule carbon monoxide and the potent antioxidant bilirubin, products of HO-catalyzed reaction, represent a protective system potentially active against brain oxidative injury. Given the broad cytoprotective properties of the heat shock response there is now strong interest in discovering and developing pharmacological agents capable of inducing the heat shock response.Increasing interest has been focused on identifying dietary compounds that can inhibit, retard or reverse the multi-stage pathophysiological events underlying AD pathology. Alzheimers disease, in fact, involves a chronic inflammatory response associated with both brain injury and -amyloid associated pathology. All of the above evidence suggests that stimulation of various repair pathways by mild stress has significant effects on delaying the onset of various age-associated alterations in cells, tissues and organisms. Spice and herbs contain phenolic substances with potent antioxidative and chemopreventive properties, and it is generally assumed that the phenol moiety is responsible for the antioxidant activity. In particular, curcumin, a powerful antioxidant derived from the curry spice turmeric, has emerged as a strong inducer of the heat shock response. In light of this finding, curcumin supplementation has been recently considered as an alternative, nutritional approach to reduce oxidative damage and amyloid pathology associated with AD. Here we review the importance of the heme oxygenase pathway in brain stress tolerance and its significance as an antidegenerative mechanism potentially important in AD pathogenesis. These findings have offered new perspectives in medicine and pharmacology, as molecules inducing this defense mechanism appear to be possible candidates for novel cytoprotective strategies. In particular, manipulation of endogenous cellular defense mechanisms such as the heat shock response, through nutritional antioxidants or pharmacological compounds, represents an innovative approach to therapeutic intervention in diseases causing tissue damage, such as neurodegeneration. Consistent with this notion, maintenance or recovery of the activity of vitagenes, such as the HO gene, conceivably may delay the aging process and decrease the occurrence of age-related neurodegenerative diseases.     

A new approach to monitor expression of aldo–keto reductase proteins in mouse tissues

The aldo–keto reductase (AKR) proteins catalyze reduction of diverse aldehydes and play detoxification roles in many organisms. Since many substrates are shared among AKR, it is generally accepted that these enzymes can functionally compensate each other in response to oxidative stress. Their overall abundances are the important factor that partially reflects the capacity of antioxidant and detoxification in tissues. In this study, the strategy was proposed for generation of Pan‐AKR antibodies to recognize most AKR proteins in mouse tissues. Derived from bioinformatic analysis, several consensus peptides with different potential antigenicities were synthesized, conjugated to hemocyanin from keyhole limpets and further delivered to rabbits to generate polyclonal antibodies. Three Pan‐AKR antibodies exhibited the immune specificities and immune sensitivities, Pan‐AKR‐P1 for AKR1B and AKR1C, Pan‐AKR‐P3 for AKR1C and Pan‐AKR‐P4 for all the AKR proteins. Pan‐AKR‐P4 antibody was employed to 2‐DE Western blot to examine the AKR abundances in mouse liver and kidney, resulting in seven immune‐reactive spots from each tissue. Protein identification with MS revealed that most immune‐positive spots were the members of AKR superfamily. Furthermore, Pan‐AKR‐P4 antibody was implemented to compare the different abundances of the AKR proteins in liver and kidney between normal and diabetic mice, suggesting that diabetes did cause some abnormal changes in the AKR protein abundances.     

Differential expression of proteins induced by lead in the Dwarf Sunflower Helianthus annuus

The Dwarf Sunflower (Helianthus annuus) is a hyperaccumulator of toxic metals including cadmium (Cd), mercury (Hg), nickel (Ni), and lead (Pb). In order to identify stress response to Pb, plants were exposed to a mixture of 30 mg/l of three ions, Cd, Cr, and Ni, with and without Pb. Soluble proteins were resolved by two-dimensional gel electrophoresis. Four proteins were differentially expressed and very abundant in the leaf samples after plants were exposed to all these four metals. The first protein spot contained two proteins: chitinase and a chloroplast drought-induced stress protein CDSP-34. The second spot contained a thaumatin-like protein. Two proteins in spot 3 were identified as heat-shock cognate 70-1 and the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Several peptides were identified in spot 4 but none could be matched to any sequence in the NCBI database.     

Differentiation-dependent expression of hypothetical proteins in the neuroblastoma cell line N1E-115

Several protein cascades, including signaling, cytoskeletal, chaperones, metabolic, and antioxidant proteins, have been shown to be involved in the process of neuronal differentiation (ND) of neuroblastoma cell lines. No systematic approach to detect hitherto unknown and unnamed proteins or structures that have been predicted upon nucleic acid sequences in ND has been published so far. We therefore decided to screen hypothetical protein (HP) expression by protein profiling. Two-dimensional gel electrophoresis with subsequent matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/TOF) identification was used for expression analysis of undifferentiated and dimethylsulfoxide-induced neuronally differentiated N1E-115 cells. We unambiguously identified six HPs: Q8C520, Q99LF4, Q9CXS1, Q9DAF8, Q91WT0, and Q8C5G2. A prefoldin domain in Q91WT0, a t-SNARE domain in Q9CXS1, and a bromodomain were observed in Q8C5G2. For the three remaining proteins, no putative function using Pfam, BLOCKS, PROSITE, PRINTS, InterPro, Superfamily, CoPS, and ExPASy could be assigned. While two proteins were present in both cell lines, Q9CXS1 was switched off (i.e., undetectably low) in differentiated cells only, and Q9DAF8, Q91WT0, and Q8C5G2 were switched on in differentiated cells exclusively. Herein, using a proteomic approach suitable for screening and identification of HP, we present HP structures that have been only predicted so far based upon nucleic acid sequences. The four differentially regulated HPs may play a putative role in the process of ND.     

Proteomics for the identification of specifically oxidized proteins in brain: Technology and application to the study of neurodegenerative disorders

Summary. Proteomics offers the opportunity elucidate the complex protein interactions of cellular systems by studying the products of genes, i.e., proteins, and their structure, function and localization. The purpose of proteomics is to explain the information contained in the genome sequences in order to provide clues on cellular events, especially related to disease.Our proteomic approach has made possible the identification of specifically oxidized proteins in Alzheimers disease (AD) brain, providing for the first time evidence on how oxidative stress plays a crucial role in AD-related neurodegeneration. This represents an example of the use of proteomics to solve biological problems related to disease. The field, which is still in its infancy, represents a very promising way to elucidate mechanism of disease at a protein level. However, the techniques that support its development present several limitations and require introduction of new tools and innovation in order to achieve a fast, reliable and sensitive method to understand normal biological processes and their regulation as well as these cellular properties in disease.     

Proteomic analysis of differentially expressed proteins in human cholangiocarcinoma cells treated with Clonorchis sinensis excretory–secretory products

Severe Clonorchis sinensis infection is a significant risk factor for malignant changes in bile ducts and surrounding liver tissues occurring as a result of direct contact with C. sinensis worms and their excretory–secretory products (ESP). However, the intrinsic molecular mechanisms involved in these processes remain obscure. To determine the effects of C. sinensis infection on protein expression in host bile duct epithelium, we examined proteomic profile changes in the human cholangiocarcinoma cell line (HuCCT1) treated with ESP at 24 h. Using a combination of 2‐DE, quantitative image and MALDI‐TOF MS analysis, we identified 83 proteins that were translationally modulated in response to ESP, among which 49 were up‐regulated and 34 down‐regulated. These proteins were classified under various biological categories, including metabolism, cell structure and architecture, proteolysis, protein modification, transport, signal transduction, and reactive oxygen species (ROS) detoxification. In particular, ESP induced the expression of redox‐regulating proteins, including peroxiredoxins (Prdx 2, 3, and 6) and thioredoxin 1 (Trx 1), possibly via intracellular ROS generation. Application of the proteomic approach to identify ESP response proteins should be a prerequisite before further investigation to clarify the molecular pathways and mechanisms involved in C. sinensis infection of host cells. J. Cell. Biochem. 108: 1376–1388, 2009. © 2009 Wiley‐Liss, Inc.     

About three‐fourths of mouse proteins unexpectedly appear at a low position of SDS‐PAGE,often as additional isoforms,questioning whether all protein isoforms have been eliminated in gene‐knockout cells or organisms

Most genes in evolutionarily complex genomes are expressed to multiple protein isoforms, but there is not yet any simple high‐throughput approach to identify these isoforms. Using an oversimplified top‐down LC–MS/MS strategy, we detected, around the 26‐kD position of SDS‐PAGE, proteins produced from 782 genes in a Cdk4?/? mouse embryonic fibroblast cell line. Interestingly, only 213 (27.24%, about one‐fourth) of these 782 genes have their proteins with a theoretical molecular mass (TMM) 10% smaller or larger than 26 kD, that is, between 23 and 29 kD, the range set as allowed variation in SDS‐PAGE. These 213 proteins are considered as the wild type (WT). The remaining three‐fourths includes proteins from 66 (9.44%) genes with a TMM smaller than 23 kD and proteins from 503 (64.32%, nearly two‐thirds) genes with a TMM larger than 29 kD; these proteins are categorized into a larger‐group or a smaller‐group, respectively, for their appearance at a higher or lower position of SDS‐PAGE. For instance, at this 26‐kD position we detected proteins from the Rps27a, Snrpf, Hist1h4a, and Rps25 genes whose proteins' TMM is 8.6, 9.7, 11.4, and 13.7 kD, respectively, and detected proteins from the Plelc1 and Prkdc genes, whose largest isoform is 533.9 and 471.1 kD, respectively. We extrapolate that many of those proteins migrating unexpectedly in SDS‐PAGE may be isoforms besides the WT protein. Moreover, we also detected a Cdk4 protein in this Cdk4?/? cell line, thus wondering whether some of other gene‐knockout cells or organisms show similar incompleteness of the knockout.     

Reproductive traits associated with species turnover of amphibians in Amazonia and its Andean slopes

Assembly of ecological communities is important for the conservation of ecosystems, predicting perturbation impacts, and understanding the origin and loss of biodiversity. We tested how amphibian communities are assembled by neutral and niche‐based mechanisms, such as habitat filtering. Species richness, β‐diversities, and reproductive traits of amphibians were evaluated at local scale in seven habitats at different elevation and disturbance levels in Wisui Biological Station, Morona‐Santiago, Ecuador, on the foothills of the Cordillera del Kutukú; and at regional scale using 109 localities across evergreen forests of Amazonia and its Andean slopes (0–3,900 m a.s.l.). At local scale, species composition showed strong differences among habitats, explained mainly by turnover. Reproductive modes occurred differently across habitats (e.g., prevalence of direct developers at high elevation, where breeding in ground level water disappears). At regional scale, elevation was the most important factor explaining the changes in species richness, reproductive trait occurrences, and biotic dissimilarities. Species number in all groups decreased with elevation except for those with lotic tadpoles and terrestrial reproduction stages. Seasonality, annual precipitation, and relative humidity partially explained the occurrence of some reproductive traits. Biotic dissimilarities were also mostly caused by turnover rather than nestedness and were particularly high in montane and foothill sites. Within lowlands, geographic distance explained more variability than elevation. Habitat filtering was supported by the different occurrence of reproductive traits according to elevation, water availability, and breeding microhabitats at both scales, as well as other assembly mechanisms based in biotic interactions at local scale. Human‐generated land use changes in Amazonia and its Andean slopes reduce local amphibian biodiversity by alteration of primary forests and loss of their microhabitats and the interaction network that maintains their unique amphibian assemblages with different reproductive strategies.     

Concentration dependence of luminescence efficiency of Dy3+ ions in strontium zinc phosphate glasses mixed with Pb3O4

In this work we synthesized SrO–ZnO–P₂O₅ glasses mixed with Pb₃O₄ (heavy metal oxide) and doped with different amounts of Dy₂O₃ (0.1 to 1.0 mol%). Subsequently their emission and decay characteristics were investigated as a function of Dy₂O₃ concentration. The emission spectra exhibited three principal emission bands in the visible region corresponding to ⁴F_9/2 → ⁶H_15/2 (482 nm), ⁶H_13/2 (574 nm) and ⁶H_11/2 (663 nm) transitions. With increase in the concentration of Dy₂O₃ (upto 0.8 mol%) a considerable increase in the intensity of these bands was observed and, for further increase, quenching of photoluminescence (PL) output was observed. Using emission spectra, various radiative parameters were evaluated and all these parameters were found to increase with increase in Dy₂O₃ concentration. The Y/B integral emission intensity ratio of Dy³⁺ ions evaluated from these spectra exhibited a decreasing trend with increase in the Dy₂O₃ concentration up to 0.8 mol%. Quenching of luminescence observed in the case of the glasses doped with 1.0 mol% is attributed to clustering of Dy³⁺ ions. The quantitative analysis of these results together with infra‐red (IR) spectral studies indicated that 0.8 mol% is the optimum concentration of Dy³⁺ ions needed to achieve maximum luminescence efficiency. Copyright © 2016 John Wiley & Sons, Ltd.