Exploring the Anti-Inflammatory Effect of Inulin by Integrating Transcriptomic and Proteomic Analyses in a Murine Macrophage Cell Model.

Inulin is a natural polysaccharide classified as a soluble fiber with demonstrated prebiotic activity. Prebiotics can reduce intestinal and systemic inflammation through modulation of the gut microflora and their metabolites. Additionally, extensive research is illuminating the role of macrophages in the interaction between gut microbiota and many systemic inflammatory diseases. In this study, the anti-inflammatory properties of inulin were evaluated using a murine macrophage cell model (RAW 264.7) of inflammation, and the immunomodulatory mechanism was investigated using omics technologies. The cells underwent comprehensive transcriptomic and proteomic analyses to identify the mechanisms responsible for the observed anti-inflammatory phenotype. Functional analyses of these omics results revealed two potential mechanisms that may lead to an overall reduction in cytokine and chemokine transcription: the inhibition of the NF-κB signaling pathway, leading to the downregulation of proinflammatory factors such as COX2, and the promotion of the phase II defense protein Hmox1 via the Nrf2 pathway. This study provides promising targets for research on immune modulation by dietary fibers and offers new strategies for the design of functional ingredients, foods, and nutraceutical products, which could ultimately lead to personalized nutrition and improved consumer health.

Fast Real-Time PCR for the Detection of Crustacean Allergens in Foods.

Crustaceans are one of the most common allergens causing severe food reaction. Hypersensitivity reactions associated with seafood intake are one of the most common food allergies in adults. Crustaceans including shrimps, prawns, crabs, lobster, and crayfish are a common cause of anaphylaxis or hypersensitivity, with shrimps and crabs being the most common causes of allergy. Symptoms occur most often when food or cooking water are ingested.These food allergens are a health problem, and they have become very important; as evidenced by the existence of several regulations that establish that labeling must be present regarding these allergens to warn consumers.The methodology herein exposed allows the detection of crustaceans in any type of product, including those where very aggressive treatments of temperature and pressure are used during the manufacturing process.The main features of this method are its high sensitivity and specificity, and reduced analysis time of real-time PCR (40 min). This assay is a potential tool in issues related to the labeling of products and food security to protect the allergic consumer.

Fast Real-Time PCR Method for Detection of Soy in Foods.

Soy is used as an additive in the manufacturing of diverse products, because of their ability of emulsification, water and fat absorption, contributing to the consistency of food products. Moreover, soy is recognized as a potential allergen, so its presence should be indicated in all the food products.These issues highlight the need for techniques that allow the detection of soy in foods. This work describes a real-time PCR method for the detection of soy in a wide range of foodstuffs. The main features of this technique are its reliability and sensitivity, allowing the detection of trace amounts of soybean in processed products. TaqMan real-time PCR is one of the simplest and fastest molecular biology techniques, with a high potential for automation. Therefore, it is one of the techniques most used for screening a variety of substances.The methodology herein described is of great value in issues regarding the presence of soy protein in processed products, especially in verifying labeling and security regulations to protect consumer's rights.

Assessment of global DNA methylation in peripheral blood cell subpopulations of early rheumatoid arthritis before and after methotrexate.

INTRODUCTION: DNA methylation is an epigenetic mechanism regulating gene expression that has been insufficiently studied in the blood of rheumatoid arthritis (RA) patients, as only T cells and total peripheral blood mononuclear cells (PBMCs) from patients with established RA have been studied and with conflicting results. METHOD: Five major blood cell subpopulations: T, B and NK cells, monocytes, and polymorphonuclear leukocytes, were isolated from 19 early RA patients and 17 healthy controls. Patient samples were taken before and 1 month after the start of treatment with methotrexate (MTX). Analysis included DNA methylation with high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry-selected reaction monitoring (HPLC-ESI-MS/MS-SRM) and expression levels of seven methylation-specific enzymes by quantitative polymerase chain reaction (qPCR). RESULTS: Disease-modifying anti-rheumatic drug (DMARD)-naïve early RA patients showed global DNA hypomethylation in T cells and monocytes, together with a lower expression of DNA methyltrasnferase 1 (DNMT1), the maintenance DNA methyltransferase, which was also decreased in B cells. Furthermore, significantly increased expression of ten-eleven translocation1 (TET1), TET2 and TET3, enzymes involved in demethylation, was found in monocytes and of TET2 in T cells. There was also modest decreased expression of DNMT3A in B cells and of growth arrest and DNA-damage-inducible protein 45A (GADD45A) in T and B cells. Treatment with MTX reverted hypomethylation in T cells and monocytes, which were no longer different from controls, and increased global methylation in B cells. In addition, DNMT1 and DNMT3A showed a trend to reversion of their decreased expression. CONCLUSIONS: Our results confirm global DNA hypomethylation in patients with RA with specificity for some blood cell subpopulations and their reversal with methotrexate treatment. These changes are accompanied by parallel changes in the levels of enzymes involved in methylation, suggesting the possibility of regulation at this level.

Development of a multiplex PCR-ELISA method for the genetic authentication of Thunnus species and Katsuwonus pelamis in food products.

In the present work a PCR-ELISA technique for the authentication of Thunnus species was developed. This method is composed by four systems that can be used in a hierarchical way allowing the identification of several scombroids species; or each individual system independently. The hierarchical strategy, proposes a first step, to assign one sample to the Thunnus genus. Next, if the result is positive, several tests can be applied to assign the sample to some particular species of the Thunnus genus. In the case that the result is negative (absence of Thunnus species), it is possible to verify if Katsuwonus pelamis is included in the sample. The method even allows the detection of mixtures of these species in relatively low amounts (up to 1%). Finally, this method was applied to 11 commercial samples to verify the labelling status of tuna products in the market, detecting that 18% were mislabelling.

Identification of Atlantic cod (Gadus morhua), ling (Molva molva), and Alaska pollock (Gadus chalcogrammus) by PCR-ELISA using duplex PCR.

Species-specific PCR-ELISA assays for the identification of Atlantic cod (Gadus morhua), Alaska pollock (Gadus chalcogrammus), and ling (Molva molva) in food products have been developed. The method, comprising a set of primers common to the first two species, a set of primers for M. molva, and a probe for each species, was designed using ND4 and cytochrome b genes as molecular markers. The sensitivity and selectivity were then determined for each assay. These assays were afterward used to analyze DNA extracted from commercial fish products. The presence of the target species was successfully detected in all analyzed samples, demonstrating the applicability of this method to the analysis of food products.

Developed of a method for the genetic identification of ling species (Genypterus spp.) in seafood products by FINS methodology.

In the present work a method of authentication of Genypterus and their substitute species was developed, by means of Polymerase Chain Reaction (PCR) technique followed by phylogenetic analysis (FINS, Forensically Informative Nucleotide Sequencing). The methodology developed allows the identification of all the studied species using the mitochondrial cytochrome oxidase subunit I gene (COXI) as molecular marker. Substitutions of the species belonging to Genypterus genera by other species with minor value can take place, since in a lot of seafood products , is not possible the assignation to a particular species based on morphological traits, because it are removed in the transformation process. In this work several methodological strategies were developed and all of them allow the authentication of the studied species in any kind of products, from fresh or frozen fish, to ready-cooked meal. Therefore, the proposed methodology can be used as a routine method to avoid the mislabelling in the marketing of Genypterus species. Also this methodological approximation is suitable to assess the correct seafood traceability of the products elaborated from the mentioned species.

Development of a real-time PCR method for the identification of Atlantic mackerel (Scomber scombrus).

A Real Time-PCR method based on TaqMan technology for the identification of Scomber scombrus has been developed. A system of specific primers and a Minor Groove Binding (MGB) TaqMan probe based on sequences of the mitochondrial cytochrome b region was designed. The method was successfully tested in 81 specimens of S. scombrus and related species and validated in 26 different commercial samples. An average Threshold Cycle (Ct) value of 15.3 was obtained with S. scombrus DNA. With the other species tested fluorescence signal was not detected or Ct was significantly higher (P<0.001). The efficiency of the assay was estimated to be 92.41%, with 100% specificity, and no cross reactivity was detected with any other species. These results reveal that the developed method is a rapid and efficient tool to unequivocally identify S. scombrus and may aid in the prevention of fraud or mislabelling in mackerel products.

Validation of end-point and real-time PCR methods for the rapid detection of soy allergen in processed products.

This work describes the development and validation of two PCR methods, end-point and real-time PCR, for the detection of soy protein in a wide rage of foodstuffs. These techniques are reliable and sensitive, allowing detection of trace amounts of soybean in processed products. TaqMan real-time PCR was the simpler and more rapid process, with a higher potential for automation and, therefore, currently the most suitable screening method. To verify correct operation of the proposed methodology, ELISA was used for quantitative determination of soy protein. In addition, 35 meat, fish and bakery processed products, which could potentially contain soy but was not declared on the label, were tested for the presence of soy DNA using the proposed methods. The methodologies will be valuable in issues regarding the presence of soy protein in processed products, especially in verifying labelling and security regulations to protect consumer's rights.

Validation of a method for the detection of five species, serogroups, biotypes and virulence factors of Vibrio by multiplex PCR in fish and seafood.

In this work a sequential multiplex PCR system was designed and validated for the detection of most frequent foodborne pathogen Vibrio species in fish and seafood (Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio alginoliticus and Vibrio mimicus). The method proposed functions in a hierarchical way, being composed of an end-point multiplex PCR to detect the presence of DNA belonging to the studied species, followed by multiplex PCR and fragment analysis allowing the viability assessment of the detected strains. The final multiplex PCR step of the method may be applied if identification of the serogroup, biotype and/or virulence factor level is necessary. Forty samples of commercial fish and seafood products were used at the method validation stage. Sixty three marine organism samples obtained from various estuarine areas of Spain including shrimps, crabs, bivalve mollusks and fishes were screened for presence of Vibrio species and 2 mussel samples were found positive for V. parahaemolyticus. On the whole, the proposed method is robust and readily adaptable in routine molecular diagnostic laboratories, allowing monitoring and simultaneous detection of all these bacterial pathogens in seafood samples, reducing the expenses and time consumed by other analytical methods.

Development of a method for the genetic identification of commercial bivalve species based on mitochondrial 18S rRNA sequences.

In this study a genetic methodology based on the amplification of an 18S rRNA fragment by PCR and phylogenetic analysis of the obtained DNA sequences was developed. This technique allows the genetic identification of more than 50 bivalve species in fresh, frozen, precooked and canned products. The developed method was applied to 30 commercial samples to check their labeling, showing that 12 samples were incorrectly labeled (40%). Therefore, the proposed methodology is appropriate to study questions related to the correct labeling and traceability of commercial products and the control of imported bivalves and fisheries in order to guarantee the protection of consumers' rights and verify the transparency of the extractive and transforming industries.

Authentication of anglerfish species (Lophius spp) by means of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) methodologies.

Lophius represents the most important genus of the family Lophiidae from a commercial point of view. The main marketing formats of the species included in this genus are tails and cheeks, making impossible the species identification on the basis of their morphological characters. In the present study, two methods based on the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and phylogenetic analysis of DNA sequences [forensically informative nucleotide sequencing (FINS)] were developed to differentiate the seven species contained in the genus Lophius. In both cases, the molecular marker studied was the cytochrome oxidase subunit I gene (COI). The RFLP analysis of the PCR products digested with the endonuclease Mbo I generated species-specific restriction profiles, and the phylogenetic analysis showing a neighbor-joining tree with independent nodes was strongly supported for all of the studied species. These methods were applied to 40 commercial samples, allowing us to detect the samples incorrectly labeled. The fraudulent labeling ratio was higher in processed products (68.75%) than whole fish (31.25%). The species subjected to mislabeling were L. budegassa (68.75%), L. vomerinus (18.75%), and L. piscatorius (12.5%). Therefore, both methodologies can be independently used to authenticate the species belonging to the genus Lophius, being useful to check the fulfillment of labeling regulations of seafood products and to verify the correct traceability of commercial trade and the control of fisheries.

Development of a method for the genetic identification of flatfish species on the basis of mitochondrial DNA sequences.

In the present study a method for genetic identification of flatfish species was developed. The technique is based on DNA sequencing of amplified DNA by PCR and subsequent phylogenetic analysis ( FINS). A phylogenetic tree using the cytochrome oxidase subunit I (COI) was constructed and the bootstrap values calculated. The mentioned technique allows the genetic identification of more than 50 flatfish species in fresh, frozen, and precooked products. This analytical system was validated and subsequently applied to 30 commercial samples, obtaining 13 that were incorrectly labeled (43%). Four of the mislabeled samples were whole fish (31%), and nine were fillets (69%). The species with the higher rate of incorrect labeling were Pleuronectes platessa (17%) and Solea solea (10%). Other species incorrectly labeled were Hipoglossus hipoglossus (7%), Reinharditus hippoglossoides, Limanda ferruginea, and Microstomus kitt (3% each species). Therefore, this molecular tool is appropriate to clarify questions related with the correct labeling of commercial products, the traceability of raw materials, and the control of imported flatfish, and also can be applied to questions linked to the control of fisheries.

Genetic identification of squids (families Ommastrephidae and Loliginidae) by PCR-RFLP and FINS methodologies.

Cephalopods are a taxonomic group that contains a great number of families, genera and species, with many of them very important at the commercial level. The existence of very similar species in this class added up to the transformation process applied to them makes it difficult or even impossible for species identification based on morphological characterization. Moreover, the global commerce makes it possible that one determined species can be marketed in its antipodes. These questions suggest the necessity of molecular techniques to solve this situation. In the present work, a genetic method was developed on the basis of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forensically informative nucleotide sequencing (FINS) technique and makes possible the identification of more than 20 species belonging to the families Ommastrephidae and Loliginidae, as well as some octopus and sepia species. The PCR was employed to amplify 651 and 208 bp fragments of the mitochondrial cytochrome b gene. These molecular systems were applied to fresh, frozen, precooked, even canned cephalopods, allowing for the identification of the species included in these products. Therefore, these molecular tools could be applied in questions related to correct labeling, traceability, and importation controls of squids, sepias, and octopuses.

Molecular detection of Xenostrobus securis and Mytillus galloprovincialis larvae in Galician Coast (Spain).

The mussel species Xenostrobus securis from New Zealand was detected in the Spanish coast recently, in the mouth of the Verdugo River into the Vigo Ria. In view of the great importance of the farm mussel sector in this region, the presence of this alien species greatly concerned producers and administration authorities, because of its potential medium- or long-term effects on the autochthonous species, Mytilus galloprovincialis, an important marine resource widely exploited in this location. The goal of this study was to develop a DNA-based technique to identify X. securis and M. galloprovincialis larvae in plankton samples, which would allow monitoring for the presence of X. securis in different points of the Vigo Ria. The techniques used were simplex and multiplex polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and fragment analysis. The application of this system to planktonic samples could be an effective means to assess the presence of the alien species, allowing monitoring if its dispersion is increasing, or on the contrary, if its distribution is restricted to the mouth of the Verdugo River, where X. securis was first detected. In addition, the application of this system at different times could be useful to assess the presence of larvae of these two species in the plankton.

Detection of land animal remains in fish meals by the polymerase chain reaction-restriction fragment length polymorphism technique.

In the present study a technique was developed with the aim of guaranteeing the composition and security of fish meals, since it allows verification of whether these meals contain land animal remains. The method is based on polymerase chain reaction (PCR) and length polymorphism, followed by a restriction fragment length polymorphism (RFLP). Specific primers for every species were designed and calibrated, generating exclusively a PCR product with a specific size when DNA for each species was present in the sample. This technique allows the detection of land animal remains in fish meals, specifically cow, chicken, pig, horse, sheep, and goat. The identity of the PCR products can be confirmed by RFLP analysis using only one restriction enzyme. The selected restrictase generated one characteristic restriction profile for every species included in this study. The detection limit of this method was calculated by using mixtures of fish meals in different proportions and meal that exclusively contained remains of one of these land species studied. The analytical strategy herein proposed was applied to fish and meat meals, giving good results, both in the analyzed standards and in commercial samples.

Development of a method for the genetic identification of mussel species belonging to Mytilus, Perna, Aulacomya, and other genera.

Legislation regarding the labeling of processed products is an important issue in the protection of consumer rights. This labeling is especially important in products that cannot be identified on the basis of their morphological characters, because these are removed from the animal in the transformation process. The goal of this study was the identification of mussel species using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Forensically Informative Nucleotide Sequencing (FINS) methodologies. The molecular marker selected was 18S rDNA (nuclear small-subunit rDNA gene), which allows identification at the genus level and at the species level in some cases. The genera included in this study were Mytilus, Perna, Aulacomya, Semimytilus, Brachidontes, Choromytilus, and Perumytilus. Different markers were used for genetic identification at the species level. To identify the species included in the genus Perna and Choromytilus, a fragment of ITS 1 (Internal Transcribed Spacer 1) was amplified by multiplex PCR and digested with restrictases. The species of Mytilus were identified by length polymorphism and RFLP of the polyphenolic adhesive protein gene. This methodology was validated with products manufactured in the authors' pilot plant and applied to commercial samples. Therefore, this sequential method can be completely or partially used to determine the mussel genus or species present in any food product.

Collapse of mitochondrial membrane potential and caspases activation are early events in okadaic acid-treated Caco-2 cells.

Diarrhetic Shellfish Poisoning (DSP) results from the consumption of shellfish contaminated with okadaic acid (OA) or one of the dinophysistoxins (DTX). It has been reported that this toxin induces apoptosis in several cell models, but the molecular events involved in this process have not been clarified. In this report we studied intracellular signals induced by OA in Caco-2 cells: mitochondrial membrane potential, F-actin depolymerization, caspases activation, cell proliferation and cell membrane integrity. Results indicate that caspases-8 and -9 increased their activity after 30 min of OA treatment according to their role as initiator caspases. In contrast, activation of the downstream caspase-3 is a later event in the execution phase of apoptosis. Mitochondrial membrane potential changes are detected at 30 min of OA exposure indicating that this is an early response in the apoptotic cascade. F-actin depolymerization occurs after 24h of incubation with OA and this effect is significant at low doses of the toxin. LDH is released into the culture medium, although there is not PI uptake, indicative of a significant cell death in addition to apoptosis. Moreover, OA led to a dose- and time-dependent decrease in cellular proliferation.

Effect of okadaic acid on integrins and structural proteins in BE(2)-M17 cells.

Okadaic acid (OA), an algal toxin, is known to induce Diarrhetic Shellfish Poisoning and apoptosis in a variety of cell lines. One of the main targets of OA is the actin cytoskeleton which can be modulated by integrins and other structural proteins. In this paper we studied the role of these proteins and skeletal structures on OA-induced apoptosis in neuroblastoma cells. Results show that beta1 integrin and vinculin are down-regulated when cells were exposed to OA. We observed an interaction between talin and beta1 integrin that is impaired in OA treated cells.