Exophiala chapopotensis sp. nov., an extremotolerant black yeast from an oil-polluted soil in Mexico; phylophenetic approach to species hypothesis in the Herpotrichiellaceae family.

Exophiala is a black fungi of the family Herpotrichiellaceae that can be found in a wide range of environments like soil, water and the human body as potential opportunistic pathogen. Some species are known to be extremophiles, thriving in harsh conditions such as deserts, glaciers, and polluted habitats. The identification of novel Exophiala species across diverse environments underlines the remarkable biodiversity within the genus. However, its classification using traditional phenotypic and phylogenetic analyses has posed a challenges. Here we describe a novel taxon, Exophiala chapopotensis sp. nov., strain LBMH1013, isolated from oil-polluted soil in Mexico, delimited according to combined morphological, molecular, evolutionary and statistics criteria. This species possesses the characteristic dark mycelia growing on PDA and tends to be darker in the presence of hydrocarbons. Its growth is dual with both yeast-like and hyphal forms. LBMH1013 differs from closely related species such as E. nidicola due to its larger aseptate conidia and could be distinguished from E. dermatitidis and E. heteromorpha by its inability to thrive above 37°C or 10% of NaCl. A comprehensive genomic analyses using up-to-date overall genome relatedness indices, several multigene phylogenies and molecular evolutionary analyzes using Bayesian speciation models, further validate its species-specific transition from all current Exophiala/Capronia species. Additionally, we applied the phylophenetic conceptual framework to delineate the species-specific hypothesis in order to incorporate this proposal within an integrative taxonomic framework. We believe that this approach to delimit fungal species will also be useful to our peers.

Study of the immunologic response of marine-derived collagen and gelatin extracts for tissue engineering applications.

The host immunologic response to a specific material is a critical aspect when considering it for clinical implementation. Collagen and gelatin extracted from marine sources have been proposed as biomaterials for tissue engineering applications, but there is a lack of information in the literature about their immunogenicity. In this work, we evaluated the immune response to collagen and/or gelatin from blue shark and codfish, previously extracted and characterized. After endotoxin evaluation, bone marrow-derived macrophages were exposed to the materials and a panel of pro- and anti-inflammatory cytokines were evaluated both for protein quantification and gene expression. Then, the impact of those materials in the host was evaluated through peritoneal injection in C57BL/6 mice. The results suggested shark collagen as the less immunogenic material, inducing low expression of pro-inflammatory cytokines as well as inducible nitric oxide synthase (encoded by Nos2) and high expression of Arginase 1 (encoded by Arg1). Although shark gelatin appeared to be the material with higher pro-inflammatory expression, it also presents a high expression of IL-10 (anti-inflammatory cytokine) and Arginase (both markers for M2-like macrophages). When injected in the peritoneal cavity of mice, our materials demonstrated a transient recruitment of neutrophil, being almost non-existent after 24 hours of injection. Based on these findings, the studied collagenous materials can be considered interesting biomaterial candidates for regenerative medicine as they may induce an activation of the M2-like macrophage population, which is involved in suppressing the inflammatory processes promoting tissue remodeling. STATEMENT OF SIGNIFICANCE: Marine-origin biomaterials are emerging in the biomedical arena, namely the ones based in marine-derived collagen/gelatin proposed as cell templates for tissue regeneration. Nevertheless, although the major cause of implant rejection in clinical practice is the host's negative immune response, there is a lack of information in the literature about the immunological impact of these marine collagenous materials. This work aims to contribute with knowledge about the immunologic response to collagen/gelatin extracted from blue shark and codfish skins. The results demonstrated that despite some differences observed, all the materials can induce a macrophage phenotype related with anti-inflammation resolution and then act as immuno-modulators and anti-inflammatory inducible materials.

Aromatic Hydrocarbon Removal by Novel Extremotolerant Exophiala and Rhodotorula Spp. from an Oil Polluted Site in Mexico.

Since Aromatic hydrocarbons are recalcitrant and toxic, strategies to remove them are needed. The aim of this work was to isolate fungi capable of using aromatic hydrocarbons as carbon sources. Two isolates from an oil polluted site in Mexico were identified through morphological and molecular markers as a novel Rhodotorula sp. and an Exophiala sp. Both strains were able to grow in a wide range of pH media, from 4 to 12, showing their optimal growth at alkaline pH's and are both halotolerant. The Exophiala strain switched from hyphae to yeast morphotype in high salinity conditions. To the best of our knowledge, this is the first report of salt triggering dimorphism. The Rhodotorula strain, which is likely a new undescribed species, was capable of removing singled ringed aromatic compounds such as benzene, xylene, and toluene, but could not remove benzo[a] pyrene nor phenanthrene. Nevertheless, these hydrocarbons did not impair its growth. The Exophiala strain showed a different removal capacity. It could remove the polyaromatic hydrocarbons but performed poorly at removing toluene and xylene. Nevertheless, it still could grow well in the presence of the aromatic compounds. These strains could have a potential for aromatic compounds removal.

Comparison of real-time PCR methods for quantification of European hake (Merluccius merluccius) in processed food samples.

The quantification of species in commercial products is limited by analytical shortcomings, as most of them provide semiquantitative results. An exception is real-time PCR, which can provide quantitative results using hybridization probes. In the present work, this technique has been applied to the absolute, absolute-relative and relative quantification of the most valued hake species in European markets, Merluccius merluccius (European Hake). The best quantification results for this species in binary mixtures with non-target species (Merluccius capensis) and using a species-specific real-time PCR MMER_VIC system was achieved using a relative quantification approach (MLL as reference system). Absolute quantification using the MLL nuclear system has been demonstrated as appropriate for the quantification of the Merluccius genus in food model samples. This study reveals the impact of different reference systems (MLL and HAKE) in the absolute-relative and relative quantification approaches, showing that the nuclear MLL system performed better than the mitochondrial HAKE system.

Valorization of recurrently discarded fish species in trawler fisheries in North-West Spain.

The progressive elimination of fish discards established by the European Union Council in 2013 has stimulated the valorization of flesh from discarded high-quality species with good protein functional properties but which frequently have excessive fish-bones, fat, strange flavours, soft texture, etc. The present study therefore focuses on valorization of the extracted muscle (minced muscle), from several fish species frequently discarded in north-western Spanish fisheries (Atlantic Ocean): Blue whiting (Micromesistius poutassou), Mackerel (Scomber scombrus), Red scorpionfish (Scorpaena scrofa), Pouting (Trisoreptus luscus) and Gurnard (Trigla spp.). Valorization of these discarded fish resources is a key objective for the survival of the fishery sector in this area. In this regard present study was planned to examine the behaviour of the mince during 6 months of frozen storage by means of physicochemical and sensory analyses, and to test consumer acceptance of three technologically different products (burgers, nuggets and structured fingers) prepared with fish mince from different species. Results indicated that protein aggregation started at the outset of frozen storage but progressed very slowly, with the exception of non-washed blue whiting and red scorpionfish minces. Moreover, during frozen storage lipid oxidation increased in all samples; the increase was with two objectives highest in minced mackerel, a fatty fish, but no rancid flavour was detected. All mince samples presented acceptable physicochemical properties and good sensory acceptability after 6 months of frozen storage. Acceptability of final products made with these minces was high in all cases. Burgers were more acceptable for consumers aged over 40 and fingers and nuggets more for younger people.

Identification of European Hake species (Merluccius merluccius) using real-time PCR.

A rapid and precise method for identifying European hake (Merluccius merluccius) based on TaqMan technology is presented. The method can be applied to fresh, frozen, and processed fish products to detect the fraudulent or unintentional mislabeling of this species. Specific primers and a minor groove binding (MGB) TaqMan probe were designed for this purpose based on partial sequences of the mitochondrial DNA control region. Combinations of primers and probe concentrations that gave the lowest Ct value and the highest final fluorescence value were selected to carry out efficiency, specificity, and cross-reactivity assays. The method was successfully tested on 31 commercial hake samples. A Ct value of about 16 was obtained when Merluccius merluccius was present; however, the fluorescence signal was not detected most of the time (Ct value 40) or presented significantly higher Ct values (38.2 +/- 0.96) for the nonhake species.

Identification of shark species in seafood products by forensically informative nucleotide sequencing (FINS).

The identification of commercial shark species is a relevant issue to ensure the correct labeling of seafood products, to maintain consumer confidence in seafood, and to enhance the knowledge of the species and volumes that are at present being captured, thus improving the management of shark fisheries. The polymerase chain reaction was employed to obtain a 423 bp amplicon from the mitochondrial cytochrome b gene. The sequences from this fragment, belonging to 63 authentic individuals of 23 species, were analyzed using a genetic distance method. Nine different samples of commercial fresh, frozen, and convenience food were obtained in local and international markets to validate the methodology. These samples were analyzed, and sequences were employed for species identification, showing that forensically informative nucleotide sequencing (FINS) is a suitable technique for identification of processed seafood containing shark as an ingredient. The results also showed that incorrect labeling practices may occur regarding shark products, probably because of incorrect labeling at the production point.

Rotura espontánea de bazo. A propósito de un caso / Spontaneous splenic rupture. A case report

La rotura esplénica espontánea en bazo normal es poco frecuente. Se trata el caso de una mujer de 38 años que presentó dolor de inicio brusco en tórax y epigastrio con signos de inestabilidad hemodinámica. La ecografía abdominal objetivó líquido libre intraperitoneal y la tomografía axial computarizada (TAC) mostró rotura esplénica, por lo que se indicó esplenectomía urgente. La anatomía patológica confirmó un parénquima esplénico de características normales

Spontaneous splenic rupture in a normal spleen is uncommon. The case of a 38-year old woman with sudden thoracic and epigastric pain and hemodynamic instability signs is presented. Abdominal ultrasound revealed free intraperitoneal fluid and computed tomography (CT scan) showed splenic rupture, for which an emergency splenectomy was indicated. The pathological study confirmed a normal splenic parenchyma

Identification of Hake species (Merluccius Genus) using sequencing and PCR-RFLP analysis of mitochondrial DNA control region sequences.

The use of DNA-based methodologies in identification of hake species belonging to the Merluccius genus was shown to be successful. A short fragment of the left hypervariable domain of the mitochondrial control region was amplified, sequenced, and digested from 11 hake species. The hake-specific PCR product, due to its limited size, was obtained in a variety of tissue samples with different levels of DNA concentration and degradation, including sterilized food products. On the basis of this phylogenetically informative 156-bp sequence were selected four restriction enzymes (ApoI, DdeI, DraIII, and MboII) that allow the hake species discrimination. Species identification by phylogenetic analysis of sequences or by PCR-RFLP methodologies is useful in a variety of scenarios including authentication of thermally processed food, detection of food components, and species determination of individuals whose morphological characters are removed.

Identification of flatfish (Pleuronectiforme) species using DNA-based techniques.

Identification of flatfish species using a DNA-based methodology was studied. The polymerase chain reaction was employed to obtain a 464 bp amplicon from mitochondrial cytochrome b gene. The sequences from this fragment belonging to 24 species were analyzed using a genetic distance method, and polymorphic sites were determined. The fragment was found to be highly polymorphic (231 sites), and this permitted the differentiation of most of the species. Phylogenetic tree construction was employed to allow the identification of flatfish species. As a result, each species was grouped in a well-differentiated clade, except for two pairs: Limanda ferruginea and L. limanda, and Solea impar and S. lascaris, which could not be differentiated. On the basis of the sequences obtained, restriction enzymes were selected to provide specific restriction profiles, which allow the differentiation of 21 species of flatfish in a faster and less expensive manner than sequencing. This polymerase chain reaction-restriction fragment length polymorphism methodology (PCR-RFLP) was tested using commercial samples.

Development of a DNA-based method aimed at identifying the fish species present in food products.

Analysis of restriction fragment length polymorphism (RFLP) profiles of a 464 bp amplicon obtained from the mitochondrial cytochrome b gene was used to differentiate between several different fish species. The method was tested by a collaborative study in which 12 European laboratories participated to ascertain whether the method was reproducible. Each laboratory was required to identify 10 unknown samples by comparison with RFLP profiles from authentic species. From a total of 120 tests performed, unknown samples were correctly identified in 96% of cases. Further work attempting to use the method to analyze mixed and processed fish samples was also performed. In all cases the species contained within mixed samples were correctly identified, indicating the efficacy of the method for detecting fraudulent substitution of fish species in food products.

Use of restriction fragment length polymorphism to distinguish between salmon species.

Identification of 10 salmon species using DNA-based methodology was investigated. Amplification of DNA was carried out using a primer set which amplified a region of the mitochondrial cytochrome b gene. Sequences of PCR-amplified DNA from the salmon species were used to select six restriction enzymes allowing species to be uniquely classified. RFLP patterns generated following analysis with each enzyme were resolved using polyacrylamide gel electrophoresis and visualized by silver staining. Results indicate that it is possible to differentiate between all 10 salmon species and that the technique could be easily adopted by the food industry for analysis of processed salmon products.

Identification of fish species after cooking by SDS-PAGE and urea IEF: a collaborative study.

A collaborative study, to validate the use of SDS-PAGE and urea IEF, for the identification of fish species after cooking has been performed by nine laboratories. By following optimized standard operation procedures, 10 commercially important species (Atlantic salmon, sea trout, rainbow trout, turbot, Alaska pollock, pollack, pink salmon, Arctic char, chum salmon, and New Zealand hake) had to be identified by comparison with 22 reference samples. Some differences in the recoveries of proteins from cooked fish flesh were noted between the urea and the SDS extraction procedures used. Generally, the urea extraction procedure appears to be less efficient than the SDS extraction for protein solubilization. Except for some species belonging to the Salmonidae family (Salmo, Oncorhynchus), both of the analytical techniques tested (urea IEF, SDS-PAGE) enabled identification of the species of the samples to be established. With urea IEF, two laboratories could not differentiate Salmo salar from Salmo trutta. The same difficulties were noted for differentiation between Oncorhynchus gorbuscha and Oncorhynchus keta samples. With SDS-PAGE, three laboratories had some difficulties in identifying the S. trutta samples. However, in the contrast with the previous technique, SDS-PAGE allows the characterization of most of the Oncorhynchus species tested. Only Oncorhynchus mykiss was not clearly recognized by one laboratory. Therefore, SDS-PAGE (Excel gel homogeneous 15%) appears to be better for the identification, after cooking, of fish such as the tuna and salmon species which are characterized by neutral and basic protein bands, and urea IEF (CleanGel) is better for the gadoid species, which are characterized by acid protein bands (parvalbumins). Nevertheless, in contentious cases it is preferable to use both analytical methods.

Fish muscle parvalbumins as marker proteins for native and urea isoelectric focusing.

An isoelectric point (pI) calibration kit containing fish muscle parvalbumins was prepared and tested for its suitability for isoelectric focusing (IEF) in the presence of 8 M urea. The pattern obtained by urea CleanGel IEF consisted of nine bands covering the pI range 4.96-5.64. This range is relevant for species identification of heated fish by urea IEF. The kit may also be used for native IEF in the low pH range, as demonstrated by running an extract made from the kit together with water-soluble fish muscle proteins on Servalyt Precotes 3-6.

Development of a sodium dodecyl sulfate-polyacrylamide gel electrophoresis reference method for the analysis and identification of fish species in raw and heat-processed samples: a collaborative study.

A collaborative study was carried out in seven European labs with the aim of achieving a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) standard operation procedure to identify fish species in raw and cooked samples. Urea and SDS-containing solutions were evaluated as extractants. Several preelectrophoretic operations--such as treatment with RNase/DNase, ultrafiltration and desalting--and up to ten types of gels and three SDS-PAGE systems were considered. The SDS-containing solution allowed a higher protein extractability than urea. Unlike urea extraction, SDS extraction seemed not to be influenced so much by the state of the sample (raw, cooked at 60 degrees C, cooked at 85 degrees C). Desalting, ultrafiltration or treatment with RNase/DNase did not improve the discriminatory power of the protein patterns. Commercial homogeneous 15% ExcelGels, especially when they were silver stained, yielded good results and afforded higher reproducibility, thus allowing a better matching of results among the laboratories participating in this collaborative study. Under the optimized technical conditions described above, all the fish species tested, either raw and cooked, yielded reproducible and discriminant species-specific protein patterns.

Comparison of different methods to produce single-strand DNA for identification of canned tuna by single-strand conformation polymorphism analysis.

By using single-strand conformation polymorphism (SSCP) analysis of three amplicons of the cytochrome b gene obtained by the polymerase chain reaction (PCR) it was possible to differentiate between various species of tunas and bonitos processed as canned fish. Four different techniques were used to produce single-strand DNA (ssDNA): (i) Denaturation of double-strand DNA (dsDNA) by formamide and alkali, (ii) two-step asymmetrical PCR, (iii) one-step asymmetrical PCR, and (iv) exonuclease digestion of the phosphorylated strand of dsDNA. The technique rendering optimal results depended on the type of amplicon (i.e. the sequence).

Composition of phospholipids of white muscle of six tuna species.

A comparative study of the phospholipids of white muscle of six of the commercially utilized tuna species, including quantitative analyses of phospholipid classes and studies of the acyl composition of the major components. Plasmalogen compounds also were identified and quantified. Choline and ethanolamine glycerophospholipids were the most abundant classes in all the samples, as well as the only molecules containing plasmalogens (16:0, 18:0, and 18:1 alkenylether chains). The patterns of fatty acid distribution within each of the phospholipid classes showed general similarities in the species analyzed. However, ratios between certain saturated and polyunsaturated fatty acids in different phospholipid classes showed remarkable differences. The high content of n-3 polyunsaturated fatty acids in the principal phospholipids, such as the plasmalogens, and taking into account the fatty acids possible importance in human nutrition, indicates that the white muscle of tuna species may be a potentially important dietary item.