Suitability of PCR Fingerprinting, Infrequent-Restriction-Site PCR, and Pulsed-Field Gel Electrophoresis, Combined with Computerized Gel Analysis, in Library Typing of Salmonella enterica Serovar Enteritidis

Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate of PCR fingerprinting interassay and intercenter reproducibility was low and was only increased when DNA samples were extracted at the same time and amplified with the same reaction mixtures. Reproducibility of IRS-PCR technique reached 100%, but discrimination was low (D = 0.52). The PFGE procedure showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.0 software. Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance of Salmonella serovar Enteritidis, specially if the prevalence of genetic events that could be responsible for changes in PFGE profiles in this serovar was low.     

The Upper Eocene South Pyrenean Coastal deposits (Liedena sandstone, navarre): Sedimentary facies, benthic formanifera and avian ichnology

Summary During the 1960's and the 1970's the Liedena Sandstone was a type deposit for “flysch-like facies” (sandstone and lutite alternations) of coastal sedimentary systems. However, the depositional system of these beds was never accurately defined. The sedimentological analysis along 100 km of outcrops in the western part of the South Pyrenean Zone (Navarre) allows these peculiar facies to be assigned to a mixed intertidal flat. Furthermore, sandy beach facies, different types of heterolithic, backbarrier deposits and conglomeratic, fluviatile facies have been recognized associated with these intriguing deposits. Generally, a northwestward-facing barrier-island system or wave-dominated delta was the likely depositional environment. The benthic foraminiferal assemblage in the intertidal deposits exhibits the typical characteristics of a marginal marine environment: extremely high dominance of one species (Pararotalia inermis), low species diversity, and a hyaline dominance with discrete amounts of miliolids. Furthermore, the most abundant species indicates that the Liedena Sandstone was deposited during the Late Eocene. Abundant footprints of aquatic birds are known in the tidal flat deposits. Six morphotypes have been distinguished: two (types 1 and 2) are ciconiforme-like; type 1 is here assigned to a new ichnotaxon,Leptoptilostipus pyrenaicus and is one of the oldest occurrences of Ciconiiforme-like ischmites in the fossil record. Two other morphotypes (5 and 6) are similar to those of the Charadriiformes and are refeered to asCharadriipeda. Finally, the affinities of the two remainder morphotypes (3 and 4) are unclear, they could have been made by Charadriiformes. Synsedimentary tectonic activity controlled the evolution of the depositional system, as the area of deposition of the Liedena Sandstone was progressively incorporated into the active thrust sheets of the Pyrenean Orogen during the Late Eocene. The structural uplift and the large amount of sediments derived from the adjacent highlands induced progradation of the depositional system and the definitive retreat of the sea from the South Pyrenean Zone.     

A state-of-the-art review on nitrous oxide control from waste treatment and industrial sources

This review aims at holistically analyzing the environmental problems associated with nitrous oxide (N₂O) emissions by evaluating the most important sources of N₂O and its environmental impacts. Emissions from wastewater treatment processes and the industrial production of nitric and adipic acid represent nowadays the most important anthropogenic point sources of N₂O. Therefore, state-of-the-art strategies to mitigate the generation and release to the atmosphere of this greenhouse and O₃-depleting gas in the waste treatment and industrial sectors are also reviewed. An updated review of the end-of-the-pipe technologies for N₂O abatement, both in the waste treatment and industrial sectors, is herein presented and critically discussed for the first time. Despite the consistent efforts recently conducted in the development of cost-efficient and eco-friendly N₂O abatement technologies, physical/chemical technologies still constitute the most popular treatments for the control of industrial N₂O emissions at commercial scale. The recent advances achieved on biological N₂O abatement based on heterotrophic denitrification have opened new opportunities for the development of eco-friendly alternatives for the treatment of N₂O emissions. Finally, the main limitations and challenges faced by these novel N₂O abatement biotechnologies are identified in order to pave the way for market implementation.     

URGORRI COMPLANATUS GEN. ET SP. NOV. (CRYPTOPHYCEAE), A RED‐TIDE‐FORMING SPECIES IN BRACKISH WATERS1

The morphology, ultrastructure, phylogeny, and ecology of a new red‐tide‐forming cryptomonad, Urgorri complanatus Laza‐Martínez gen. et sp. nov., is described. U. complanatus has been collected in southwestern European estuaries, blooming in the inner reaches of several of them. The estuarine character of the species is also supported by its in vitro salinity preferences, showing a maximum growth rate at 10 psu. U. complanatus is a distinctive species and can be easily distinguished by LM from other known brackish and marine species. Cells are dorsoventrally flattened. The plastid has two anterior lobes. One pyrenoid is located in each of the lobes, and a third one on the posterior part. Thylakoids are arranged in pairs and do not penetrate pyrenoids. The plastid is reddish due to the presence of the phycoerythrin Cr‐PE545. An orange discoidal eyespot lies beneath the nucleus, in the posterior ventral face of the plastid. A long furrow runs from the vestibulum, and a gullet is lacking. The periplast is composed of an inner sheet. The nuclear 18S rDNA based molecular analysis reveals U. complanatus is not related to any of the main cryptomonad lineages. Based on ultrastructural and pigment data, the most probable relatives are those merged under the family Geminigeraceae. Its lack of derived characters, together with the presence of characters proposed in previous studies to be primitive, suggests Urgorri could be considered representative of the cryptophycean ancestral character state.     

Phytoplankton Assemblages and Their Dominant Pigments in the Nervion River Estuary

In the Nervion River estuary surface samples were taken from March to September 2003 at six sites covering most of the salinity range with the aim to know the biomass and taxonomic composition of phytoplankton assemblages in the different segments. Nine groups of algae including cyanobacteria, diatoms, dinoflagellates, chlorophytes, prasinophytes, euglenophytes, chrysophytes, haptophytes, raphidophytes and cryptophytes were identified by means of a combination of pigment analysis by high-performance liquid chromatography (HPLC) and microscopic observations of live and preserved cells. Diatoms, chlorophytes and cryptophytes were the most abundant algae in terms of cells number, whereas fucoxanthin, peridinin, chlorophyll b (Chl b) and alloxanthin were the most abundant auxiliary pigments. Based on multiple regression analysis, in the outer estuary (stations 0, 1, 2 and 3) about 93% of the chlorophyll a (Chl a) could be explained by algae containing fucoxanthin and by algae containing Chl b, whereas in the rest of the estuary most of the Chl a (about 98%) was accounted for by fucoxanthin, Chl b and alloxanthin containing algae. The study period coincided with that of most active phytoplankton growth in the estuary and fucoxanthin was by far the dominant among those signature pigments. Several diatoms, chrysophytes, haptophytes and raphydophytes were responsible for fucoxanthin among identified species. Besides, dinoflagellates with a pigment pattern corresponding to chrysophytes and type 4 haptophytes were identified among fucoxanthin-bearing algae. Cryptophytes were the most abundant species among those containing alloxanthin. The maximum of Chl b registered at the seaward end in April coincided with a bloom of the prasinophytes Cymbomonas tetramitiformis, whereas the Chl b maxima in late spring and summer were accounted for by prasinophytes in the middle and outer estuary and by several species of chlorophytes in the middle and inner estuary. Other Chl b containing algae were euglenophytes and the dinoflagellate Peridinium chlorophorum. Dinoflagellates constituted generally a minor component of the phytoplankton.     

Infectious Bursal Disease Virus VP3 Upregulates VP1-Mediated RNA-Dependent RNA Replication

Genome replication is a critical step in virus life cycles. Here, we analyzed the role of the infectious bursal disease virus (IBDV) VP3, a major component of IBDV ribonucleoprotein complexes, on the regulation of VP1, the virus-encoded RNA-dependent RNA polymerase (RdRp). Data show that VP3, as well as a peptide mimicking its C-terminal domain, efficiently stimulates the ability of VP1 to replicate synthetic single-stranded RNA templates containing the 3′ untranslated regions (UTRs) from the IBDV genome segments.     

Scedosporium prolificans immunomes against human salivary immunoglobulin A

The filamentous fungus Scedosporium prolificans is an emerging multidrug resistant pathogen related to serious infections mainly affecting immunocompromised individuals. Considering that it is frequently isolated from anthropic environments and penetrates mainly through the airways, the human mucosal immune system may play an important protective role against S. prolificans. To advance in the search for biomarkers and targets both for diagnosis and treatment, we analysed the S. prolificans immunomes recognized by human salivary Immunoglobulin A. Using indirect immunofluorescence, it was observed that conidia were strongly recognized, while hyphae were not. By 2-D immunoblotting and peptide mass fingerprinting, 25 immunodominant antigens in conidia and 30 in hyphae were identified. These included catalase, putative glyceronetransferase, translation elongation factor-1α, serine/threonine protein kinase, putative superoxide dismutase, putative mitochondrial cyclophilin 1 and peptidyl-prolyl cis-trans isomerase in conidiospores, and putative Hsp60, ATP synthase β chain, 40S ribosomal protein S0, citrate synthase and putative ATP synthase in hyphae. The functional study showed that metabolism – and protein fate – related enzymes were the most abundant antigens in conidia, whereas metabolism – , translation – , or energy production – related enzymes were in hyphae. The immunogenic proteins identified are proposed as candidates for the development of novel diagnostic tools or therapeutic strategies.