Proteomic analysis of Saccharomyces cerevisiae to study the effects of red wine polyphenols on oxidative stress.

Understanding the molecular mechanisms underlying the "French paradox" has contributed to a growing interest in the investigation of the biological activity of red wine polyphenols (RWP). The main goal of this research is to provide valuable information on how RWP could exert their biological action at the cellular level. So, we report a proteomic analysis of S. cerevisiae exposed to both pro-oxidant (H2O2) and antioxidant (wine) agents. Cellular proteome analysis shows that RWP modify the level of certain proteins. Under both normal conditions (Wine treatment) and oxidative stress situations (Wine + H2O2 treatment), the proteins involved in the metabolism and biosynthesis of biomolecules were down-regulated, while one ribosomal protein was up-regulated, probably performing its ribosome-independent functions, and so contributing to the stress defense system. Considering this action mechanism, we suggest that RWP may be acting as mild pro-oxidants and, therefore, exerting a hormetic effect that leads to the strengthening of cells' antioxidant capacity.

Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis.

Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.

Identification of Clostridium difficile Immunoreactive Spore Proteins of the Epidemic Strain R20291.

PURPOSE: Clostridium difficile infections are the leading cause of diarrhea associated with the use of antibiotics. During infection, C. difficile initiates a sporulation cycle leading to the persistence of C. difficile spores in the host and disease dissemination. The development of vaccine and passive immunization therapies against C. difficile has focused on toxins A and B. In this study, an immunoproteome-based approach to identify immunogenic proteins located on the outer layers of C. difficile spores as potential candidates for the development of immunotherapy and/or diagnostic methods against this devastating infection is used. EXPERIMENTAL DESIGN: To identify potential immunogenic proteins on the surface of C. difficile R20291, spore coat/exosporium extracts are separated by 2D electrophoresis (2-DE) and analyzed for reactivity against C. difficile spore-specific goat sera. Finally, the selected spots are in-gel digested with chymotrypsin, peptides generated are separated by nanoUPLC followed by MS/MS using Quad-TOF-MS, corroborated by Ultimate 3000RS-nano-UHPLC coupled to Q-Exactive-Plus-Orbitrap MS. RESULTS: The analysis identify five immunoreactive proteins: spore coat proteins CotE, CotA, and CotCB; exosporium protein CdeC; and a cytosolic methyltransferase. CONCLUSION: This data provides a list of spore surface protein candidates as antigens for vaccine development against C. difficile infections.

Origin and Processing Methods Slightly Affect Allergenic Characteristics of Cashew Nuts (Anacardium occidentale).

The protein content and allergen composition was studied of cashews from 8 different origins (Benin, Brazil, Ghana, India, Ivory Coast, Mozambique, Tanzania, Vietnam), subjected to different in-shell heat treatments (steamed, fried, drum-roasted). On 2D electrophoresis, 9 isoforms of Ana o 1, 29 isoforms of Ana o 2 (11 of the acidic subunit, 18 of the basic subunit), and 8 isoforms of the large subunit of Ana o 3 were tentatively identified. Based on 1D and 2D electrophoresis, no difference in allergen content (Ana o 1, 2, 3) was detected between the cashews of different origins (P > 0.5), some small but significant differences were detected in allergen solubility between differently heated cashews. No major differences in N- and C-terminal microheterogeneity of Ana o 3 were detected between cashews of different origins. Between the different heat treatments, no difference was detected in glycation, pepsin digestibility, or IgE binding of the cashew proteins.

Determination of multidrug resistance mechanisms in Clostridium perfringens type A isolates using RNA sequencing and 2D-electrophoresis

In this study, we screened differentially expressed genes in a multidrug-resistant isolate strain of Clostridium perfringens by RNA sequencing. We also separated and identified differentially expressed proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE) and mass spectrometry (MS). The RNA sequencing results showed that, compared with the control strain, 1128 genes were differentially expressed in the isolate strain, and these included 227 up-regulated genes and 901 down-regulated genes. Bioinformatics analysis identified the following genes and gene categories that are potentially involved in multidrug resistance (MDR) in the isolate strain: drug transport, drug response, hydrolase activity, transmembrane transporter, transferase activity, amidase transmembrane transporter, efflux transmembrane transporter, bacterial chemotaxis, ABC transporter, and others. The results of the 2-DE showed that 70 proteins were differentially expressed in the isolate strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs were identified by MS and these included the following protein categories: ribosome, antimicrobial peptide resistance, and ABC transporter, all of which may be involved in MDR in the isolate strain of C. perfringens. The results provide reference data for further investigations on the drug resistant molecular mechanisms of C. perfringens.

Proteomic analysis of seminal plasma from locally-adapted "Curraleiro Pé-Duro bulls" (Bos taurus): identifying biomarkers involved in sperm physiology in endangered animals for conservation of biodiversity.

The present study was aimed at evaluating the seminal plasma proteins and sperm parameters of Curraleiro Pé-Duro bulls. Semen was collected from 10 bulls by electroejaculation, and sperm parameters were evaluated in fresh and frozen-thawed semen. Seminal plasma proteins were analyzed by 2-D SDS-PAGE and mass spectrophotometry. Tools in computational biology were used to generate bioinformatic knowledge and evaluate gene ontology, protein-protein interactions, phylogenetic trees and multiple sequence alignments. Sperm motility in fresh and frozen-thawed semen was 78.8±1.8% and 21.2±1.6%, respectively. Pearson's correlations were evaluated (p<0.05). Sperm motility and vigor in fresh semen were correlated with clusterin, TIMP2 and cathepsin S (r=0.64-0.71) and sperm defects were related to inhibitor of carbonic anhydrase and BSP 5 (r=0.78-0.80). Clusterin, BSP 5, alpha-enolase, creatine kinase M-type, glyceraldehyde-3-phosphate dehydrogenase, BSP 3, albumin, and 5'-nucleotidase and legumain were correlated with acrosome intact live sperm (r=0.80-0.64). Associations were detected between sperm vigor and spermadhesin 1 (r=-0.89), and between sperm defects in fresh semen and spermadhesin 1 and clusterin (r=-0.81). Sperm motility in frozen-thawed semen was associated with BSP 1, spermadhesin 1, clusterin and spermadhesin Z13 (r=0.64-0.85). The percent of motile sperm after freeze-thawing was negatively correlated (r=-0.64) with the amount of spermadhesin 1 in the seminal plasma. Based on in silico analysis, TIMP2 interacted with BSP1, BSP3, BSP5 and metalloproteinases. Molecular functions of proteins associated with sperm parameters were binding, catalytic activity and enzymatic regulation. Amino acid sequences of spermadhesin 1 and BSP 1 from Bos taurus, and other domestic species were similar. Phylogenetic tree analysis demonstrated that clusterin from Bos taurus was related to Ovis aries and domains of clusterin, spermadhesin 1, BSP 1 and inhibitor of carbonic anhydrase were conserved as well. In summary, specific seminal proteins are associated with sperm parameters of locally-adapted bulls. Use of the endangered mammalian as a model may assist in understanding aspects of evolutionary adaptations and could improve assisted reproductive biotechnologies.

Plasma proteome of buffaloes.

The proteomic approach has aroused the interest of veterinary medicine researchers, especially regarding the production of biopharmaceuticals and diagnosis of diseases in farm animals. Water buffaloes have gained prominence in the world economy due to the quality of their milk, meat, and leather, in addition to being an important donor of blood components. This work aimed to identify and characterize the proteins present in the blood plasma of Murrah buffaloes (Bubalus bubalis) through 2D electrophoresis, in gel protein digestion followed by mass spectrometry technique and for albumin depletion, in solution protein digestion followed by shotgun analysis. Our results showed the identification of 112 protein spots and 35 individual proteins, respectively. The abundant proteins were represented by albumin, fibrinogen-α, fibrinogen-ß, fibrinogen-γ, immunoglobulins in general, α-1-antiproteinase, α-1B-glycoprotein, α-2-HS-glycoprotein, α-macroglobulin, apolipoprotein A1, antithrombin-III, endopin 2B, fetuin-B, retinol-binding protein, serotransferrin, transthyretin and vitamin D-binding protein. Most of these proteins are related to the signaling pathways of the complement system and coagulation cascade. The results allowed a better understanding of the protein composition of these blood components, thus promoting studies on animal health in the search for molecular markers of zoonotic diseases in buffaloes.

Proteome of the rete testis fluid from tropically-adapted Morada Nova rams.

The rete testis has a close relationship with sperm development and may have other functions besides serving as an intercalated channel. The aim of this study was to identify and characterize the proteins of rete testis fluid (RTF) from tropically-adapted Morada Nova rams. Testicles obtained from six Morada Nova rams were dissected and the head of the epididymis was separated to access the efferent ducts. Rete testis fluid was obtained by gentle massage of the testis. The fluid was centrifuged to remove cell debris and sperm. RTF samples (containing 400µg protein) were separated by 2-D SDS-PAGE and gels, analyzed using PDQuest software (Bio Rad, USA). Proteins were identified using tandem mass spectrometry. Gene ontology and protein network were analyzed using the software tool for searching annotations of proteins (STRAP) and STRING database. Gels had, on average, 227±13.5 spots and 51% of the proteins were found above 40kDa, corresponding to 65% of the intensity of all spots detected. Based on gene ontology analysis, the most common biological processes associated with RTF proteins were regulation (24.3%) and cellular process (23.3%). Binding (27.3%) and catalytic activity (19.3%) corresponded to the most frequent molecular functions. Albumin, clusterin, serotransferrin, immunoglobulin gamma-1 chain and alpha-2-HS-glycoprotein were the most abundant proteins in the ram rete testis fluid. In conclusion, proteins identified in the ram rete testis fluid are linked to several physiological processes associated with sperm protection and spermatogenesis.

Two Dimensional Gel Electrophoresis of Insulin Secretory Granule Proteins from Biosynthetically-Labeled Pancreatic Islets.

Pulse-chase radiolabeling of cells with radioactive amino acids is a common method for tracking the biosynthesis of proteins. Radiolabeled newly synthesized proteins can be analyzed by a number of techniques such as two dimensional gel electrophoresis (2DE). This chapter presents a protocol for the biosynthetic labeling of pancreatic islets with 35S-methionine in the presence of basal and stimulatory concentrations of glucose, followed by subcellular fractionation to produce a secretory granule fraction and analysis of the granule protein contents by 2DE. This provides a means of determining whether or not the biosynthetic rates of the entire granule constituents are coordinately regulated.

Meat quality assessment from young goats fed for long periods with castor de-oiled cake.

Diet can influence both the qualitative and quantitative traits of ruminant meat. This study evaluated the effects of castor de-oiled cake on the meat of mixed-breed male goat kids. After 165days of diet treatment, no alterations (p>0.05) were observed in the in vivo performance, anatomic components, dissection and proximate composition of the Longissimus dorsi muscle, as well as in the color and pH of the carcasses. However, diet had an effect (p<0.05) on energy metabolites, fatty acid profile, and expression of certain proteins of the Longissimus dorsi muscle. To conclude, this study showed that the establishment of castor de-oiled cake diet for a long period to goats led to alterations in meat quality, without compromising its consumption qualities.

Proteomic profiling of liver from Elaphe taeniura, a common snake in eastern and southeastern Asia.

Snake liver has been implicated in the adaptation of snakes to a variety of habitats. However, to date, there has been no systematic analysis of snake liver proteins. In this study, we undertook a proteomic analysis of liver from the colubrid snake Elaphe taeniura using a combination of two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flightmass spectrometry (MALDI-TOF MS). We also constructed a local protein sequence database based on transcriptome sequencing to facilitate protein identification. Of the 268 protein spots revealed by 2-DE 109 gave positive MS signals, 84 of which were identified by searching the NCBInr, Swiss-Prot and local databases. The other 25 protein spots could not be identified, possibly because their transcripts were not be stable enough to be detected by transcriptome sequencing. GO analysis showed that most proteins may be involved in binding, catalysis, cellular processes and metabolic processes. Forty-two of the liver proteins identified were found in other reptiles and in amphibians. The findings of this study provide a good reference map of snake liver proteins that will be useful in molecular investigations of snake physiology and adaptation.

Eletroforese bidimensional e espectrometria de massa como ferramentas proteômicas aplicadas à definição de marcadores proteicos associados à eficiência reprodutiva de caprinos / Two-dimensional electrophoresis and mass spectrometry as proteomic tools applied to the definition of protein markers associated with reproductive efficiency goats

O crescimento e desenvolvimento do rebanho caprino no Nordeste são observados com o aumento na produção da pecuária do Brasil. Esse aumento é reflexo, a princípio, das maiores exigências do mercado consumidor por produtos de melhor qualidade obtidos a partir de rebanhos de alto padrão zootécnico. As pesquisas atuais ilustram a necessidade de dispor de biomarcadores que auxiliem a indicação do potencial reprodutivo dos animais, uma vez que isso não pode ser expresso apenas com o exame andrológico. A avaliação da expressão das proteínas, tomando-as como biomarcadores, é análise potencial uma vez que estas, dentre os constituintes do plasma seminal, são encontradas em maior quantidade na forma de complexos associados, desempenhando papel crucial em todos os processos relacionados à capacidade fecundante dos espermatozoides. Essa análise é realizada por métodos de separação e detecção simultânea de proteínas utilizando técnicas como a eletroforese bidimensional (2DE) ou cromatografias, acoplados a métodos cada vez mais eficientes e sensíveis de identificação e quantificação de níveis de expressão de proteínas por espectrometria de massas. O objetivo desta revisão é abordar sobre a técnica de eletroforese bidimensional associada à espectrometria de massa como ferramenta na análise da expressão de proteínas dentro do campo da proteômica.(AU)

The growth and development of goat herds in the northeast are being observed due to the increase in livestock production in Brazil. This increase reflects demands of the consumer market for high quality product, which are obtained from flocks of high standard zootechnics. Current research illustrates the need for biomarkers that indicate an animal ́s reproductive potential, since this cannot be expressed solely with andrologic evaluation. For this reason, the expression of the proteins as biomarkers is a potential analysis. The proteins from the seminal plasma constituents are found in larger amounts in the form of associated complexes, playing a crucial role in all processes related to the fertilizing capacity of sperm. This analysis is performed by separation methods and simultaneous detection of proteins using techniques such as two-dimensional electrophoresis (2DE) or chromatography. These techniques are coupled with methods to identify and quantify expression levels of proteins by mass spectrometry that are increasingly efficient and sensitive. The aim of this review was to discuss the technique of two-dimensional electrophoresis combined with mass spectrometry as a tool in the analysis of protein expression within the field of proteomics.(AU)

Eletroforese bidimensional e espectrometria de massa como ferramentas proteômicas aplicadas à definição de marcadores proteicos associados à eficiência reprodutiva de caprinos / Two-dimensional electrophoresis and mass spectrometry as proteomic tools applied to the definition of protein markers associated with reproductive efficiency goats

O crescimento e desenvolvimento do rebanho caprino no Nordeste são observados com o aumento na produção da pecuária do Brasil. Esse aumento é reflexo, a princípio, das maiores exigências do mercado consumidor por produtos de melhor qualidade obtidos a partir de rebanhos de alto padrão zootécnico. As pesquisas atuais ilustram a necessidade de dispor de biomarcadores que auxiliem a indicação do potencial reprodutivo dos animais, uma vez que isso não pode ser expresso apenas com o exame andrológico. A avaliação da expressão das proteínas, tomando-as como biomarcadores, é análise potencial uma vez que estas, dentre os constituintes do plasma seminal, são encontradas em maior quantidade na forma de complexos associados, desempenhando papel crucial em todos os processos relacionados à capacidade fecundante dos espermatozoides. Essa análise é realizada por métodos de separação e detecção simultânea de proteínas utilizando técnicas como a eletroforese bidimensional (2DE) ou cromatografias, acoplados a métodos cada vez mais eficientes e sensíveis de identificação e quantificação de níveis de expressão de proteínas por espectrometria de massas. O objetivo desta revisão é abordar sobre a técnica de eletroforese bidimensional associada à espectrometria de massa como ferramenta na análise da expressão de proteínas dentro do campo da proteômica.

The growth and development of goat herds in the northeast are being observed due to the increase in livestock production in Brazil. This increase reflects demands of the consumer market for high quality product, which are obtained from flocks of high standard zootechnics. Current research illustrates the need for biomarkers that indicate an animal ́s reproductive potential, since this cannot be expressed solely with andrologic evaluation. For this reason, the expression of the proteins as biomarkers is a potential analysis. The proteins from the seminal plasma constituents are found in larger amounts in the form of associated complexes, playing a crucial role in all processes related to the fertilizing capacity of sperm. This analysis is performed by separation methods and simultaneous detection of proteins using techniques such as two-dimensional electrophoresis (2DE) or chromatography. These techniques are coupled with methods to identify and quantify expression levels of proteins by mass spectrometry that are increasingly efficient and sensitive. The aim of this review was to discuss the technique of two-dimensional electrophoresis combined with mass spectrometry as a tool in the analysis of protein expression within the field of proteomics.

Análisis proteóiico de cultivos primarios de tiroides / Proteomic nalysiis of primary cultures from thyroid / Análiseproteómicco de culturas preliminares do thyroid

En el presente estudio se identificaron proteínas de expresión constitutiva, como vimentina, actina, tubulina, proteína de choque térmico de 60 kDa, peroxirredoxina y la ATP sintasa mitocondrial, en cultivos primarios de tiroides normales y de carcinoma papilar de tiroides. Se establecieron las condiciones de extracción, solubilización, análisis cuantitativo y cualitativo de dichas proteínas, y se buscaron las mejores condiciones de isoelectroenfoque (IEF) en la electroforesis en dos dimensiones (2D). En la extracción y solubilización de las proteínas se evaluó la presencia o ausencia de anfolitos y sales, se obtuvo un mejor resultado empleando en el amortiguador de extracción sales como Tris-HCl y acetato de magnesio que incrementan la solubilidad de las proteínas. Para la cuantificación se recomienda el uso conjunto de técnicas colorimétricas con la electroforesis SDS-PAGE tiñendo con azul de Coomassie y corroborando los resultados mediante western blot, lo cual permite, además, verificar la integridad de las proteínas. Respecto a la electroforesis en dos dimensiones, se obtuvieron geles con un mayor número de manchas (spots),resueltos, enfocados y reproducibles empleando en el IEF gradientes inmovilizados de pH de 4-7 y voltaje final de 8.000 V. Las proteínas se identificaron mediante el análisis bioinformático de los geles 2D con el programa PDQuest (PDQuest 7.2, Bio-Rad®) y MALDI-TOF.

In this paper, proteins of constitutive expression such as vimentin, actin, tubulin, heat shock protein of 60 kDa, peroxiredoxin and the mitochondrial ATP sintase were identified in primary cultures of normal thyroid and papillary carcinoma. The extraction conditions, solubilization, quantitative and qualitative analysis of such proteins were established. In addition, the best conditions for isoelectrofocusing (IEF) in the two-dimensional electrophoresis (2D) were founded. In the extraction and solubilization of proteins, the presence or absence ofampholytes or salts was evaluated. The best result in the extraction was obtained using buffer salts such as Tris-HCl and magnesium acetate, which increase the solubility of these proteins. For quantification, the recommendation is to combine colorimetric techniques with SDS-PAGE electrophoresis stained with Coomasie blue and Western blot to confirm the results, which allows verifying the integrity of these proteins. In the two-dimensional electrophoresis, resolved, focused and reproducible gels with greater number of spots were obtained using in the IEF immobilized pH gradients of 4-7 and final voltage of 8000 V. The proteins were identified by the bioinformatic analysis of the 2DE gels with the PDQuest program (PDQuest 7.2 (BioRad®) and MALDI-TOF.

Neste estudo, se identificaram proteínas da expressão constitutiva, como vimentina, actina, tubulina, proteína de choque do calor do kDa 60, peroxiredoxinaeasintase mitocondrial do ATP, em cultivos primários de tireóide normal e de carcinoma papilar de tireóide. Se estabeleceram as condições de extração e de solubilization, assim como a análise quantitativaeaqualitativa de tais proteínas, e procuraram-se asmelhores condições para isoeletroenfoque (IEF) na eletroforese bidimensional (2D). Na extração e no solubilization das proteínas, se avaliou a presença ou a ausência de anfolitos ou de sais. O melhor resultado foi obtido usando sais como Tris-HCl e acetato do magnésio no amortecedor da extração, as quais aumentam a solubilida-de das proteínas. Na quantificação, se recomenda o uso de técnicas colorimétricas com eletroforese SDS-PAGE, tingindo com azul de Coomasie. Os resultados se confirmam com Western blot, o qual permite também verificar a integridade das proteínas. Quanto à eletroforese bidimensional, se obtiveram géis com um maior número de pontos (spots) determinados, enfocados e reprodutíveis no IEF usando gradientes imobilizados de pH 4-7 e tensão final de 8000 V. As proteínas foram identificadas por análise bioinformática de géis 2D com o programa PDQuest (PDQuest 7.2 (Bio-Rad®) e MALDITOF.

La proteomica n la era postgenómica / The Proteomics In The Postgenomic Era

El principal desafío de la biología moderna es entender la expresión, función y regulación del conjunto completo de proteínas codificadas por un organismo, lo cual describe el objetivo del nuevo campo de la proteómica. Las proteínas son las efectoras del trabajo celular, por ello el estudio de sus perfiles globales de expresión y de sus cambios bajo determinadas condiciones fisiológicas o patológicas, permite entender la red compleja de interacciones en que se basa el funcionamiento de una célula. La electroforesis en dos dimensiones (2D-PAGE) es la técnica central de la proteómica. En la actualidad no existe otro método con la capacidad para resolver simultáneamente miles de proteínas en un solo procedimiento y para detectar modificaciones post y co-traduccionales imposibles de predecir a partir de la secuencia genómica. Sus aplicaciones incluyen el análisis de proteomas, señalización, detección de marcadores de enfermedades y cáncer.

The main challenge of modern biology is to understand the expression, function and regulation of the whole set of proteins codified by an organism, which is the objective of the new field of proteomics. Proteins are the effectors of cellular work and the knowledge of their global expression profiles and changes under physiological and pathological conditions can help us to understand the complex network of interactions involved in cellular function. Two-dimensional electrophoresis (2-DE) is the central technology in proteomics. At present no other technique has the throughput and high resolution of 2-DE for the separation of thousands of proteins in one procedure and for the analysis of post-and co-translation modifications, not predictable from the genome sequence. The scope of applications extends from proteome analysis, to cell signaling, disease markers and cancer.

Some aspects of the venom proteome of the Colubridae snake Philodryas olfersii revealed from a Duvernoy's (venom) gland transcriptome

We investigated the putative toxins of Philodryas olfersii (Colubridae), a representative of a family of snakes neglected in venom studies despite their growing medical importance. Transcriptomic data of the venom gland complemented by proteomic analysis of the gland secretion revealed the presence of major toxin classes from the Viperidae family, including serine proteases, metalloproteases, C-type lectins, Crisps, and a C-type natriuretic peptide (CNP). Interestingly, the phylogenetic analysis of the CNP precursor showed it as a linker between two related precursors found in Viperidae and Elapidae snakes. We suggest that these precursors constitute a monophyletic group derived from the vertebrate CNPs.