Flow regulation by dams affects ecosystem metabolism in Mediterranean rivers

相似文献   

A preliminary report on the distribution of lizards in Qatar

We have updated the list of the lizard species present in Qatar and produced the first distribution maps based on two field surveys in 2012 and 2013. We used the QND95/Qatar National Grid with a grid of 10 × 10 km squares for mapping. Our results show the occurrence of 21 lizard species in Qatar, from the 15 species indicated in the last biodiversity report conducted in 2004. The most abundant family found in Qatar is Gekkonidae with nine species (Bunopus tuberculatus, Cyrtopodion scabrum, Hemidactylus robustus, H. flaviviridis, H. persicus, Stenodactylus arabicus, S. slevini, S. doriae, Pseudoceramodactylus khobarensis), followed by Lacertidae with four species (Acanthodactylus schmidti, A. opheodurus, Mesalina brevirostris, M. adramitana), Agamidae with three species (Trapelus flavimaculatus, Uromastyx aegyptia, Phrynocephalus arabicus), Scincidae with two species (Scincus mitranus, Trachylepis septemtaeniata), and Varanidae (Varanus griseus), Sphaerodactylidae (Pristurus rupestris) and Trogonophiidae (Diplometopon zarudnyi) with one species each. The species richness fluctuated largely across Qatar between one and eleven species per grid square. We believe that the lizard fauna records in Qatar are still incomplete and that additional studies are required. However, our study here fills a gap concerning lizard biodiversity knowledge in the Gulf Region.     

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.     

Feature Selection for Speech Emotion Recognition in Spanish and Basque: On the Use of Machine Learning to Improve Human-Computer Interaction

Study of emotions in human–computer interaction is a growing research area. This paper shows an attempt to select the most significant features for emotion recognition in spoken Basque and Spanish Languages using different methods for feature selection. RekEmozio database was used as the experimental data set. Several Machine Learning paradigms were used for the emotion classification task. Experiments were executed in three phases, using different sets of features as classification variables in each phase. Moreover, feature subset selection was applied at each phase in order to seek for the most relevant feature subset. The three phases approach was selected to check the validity of the proposed approach. Achieved results show that an instance-based learning algorithm using feature subset selection techniques based on evolutionary algorithms is the best Machine Learning paradigm in automatic emotion recognition, with all different feature sets, obtaining a mean of 80,05% emotion recognition rate in Basque and a 74,82% in Spanish. In order to check the goodness of the proposed process, a greedy searching approach (FSS-Forward) has been applied and a comparison between them is provided. Based on achieved results, a set of most relevant non-speaker dependent features is proposed for both languages and new perspectives are suggested.     

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over‐exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded F_ST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between‐ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17‐SNP panel was developed in Atlantic BFT by cross‐species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (F_ST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.     

CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea

The use of carbon monoxide (CO) as a biological energy source is widespread in microbes. In recent years, the role of CO oxidation in superficial ocean waters has been shown to be an important energy supplement for heterotrophs (carboxydovores). The key enzyme CO dehydrogenase was found in both isolates and metagenomes from the ocean''s photic zone, where CO is continuously generated by organic matter photolysis. We have also found genes that code for both forms I (low affinity) and II (high affinity) in fosmids from a metagenomic library generated from a 3,000-m depth in the Mediterranean Sea. Analysis of other metagenomic databases indicates that similar genes are also found in the mesopelagic and bathypelagic North Pacific and on the surfaces of this and other oceanic locations (in lower proportions and similarities). The frequency with which this gene was found indicates that this energy-generating metabolism would be at least as important in the bathypelagic habitat as it is in the photic zone. Although there are no data about CO concentrations or origins deep in the ocean, it could have a geothermal origin or be associated with anaerobic metabolism of organic matter. The identities of the microbes that carry out these processes were not established, but they seem to be representatives of either Bacteroidetes or Chloroflexi.Carbon monoxide (CO) oxidation is a source of energy for a wide diversity of prokaryotes and is an important process within the global carbon cycle. There is a wide diversity of CO oxidation pathways among both archaea and bacteria (27, 28), and their wide distribution attests to both the ecological importance and ancient origin of CO oxidation. Most of these pathways are anaerobic (31, 40) and have been reported in both archaea and bacteria. However, aerobic CO oxidation is found only in a few groups of bacteria, specifically in many Actinobacteria and Proteobacteria spp. and in at least one Firmicutes sp. (for examples, see references 16, 17, 26, 35, 46, and 47). Classically, aerobic oxidation of CO has been known to be carried out in soils where, in addition to geological or anthropogenic emissions, there are local biological sources connected to plant roots and animals (15, 18, 19). However, more recently, the relevance of CO oxidation processes in the marine environment has also become clear, mostly from evidence from the fields of genomics and metagenomics (26, 42, 43).The aerobic oxidation of CO is very amenable to genomic analysis, since the genes involved are very characteristic, and their presence in marine bacterial genomes and in metagenomic databases can be considered diagnostic. The genes required for aerobic CO oxidation were first described in detail in chemolithoautotrophic Oligotropha carboxidovorans OM5 (10, 35, 36). The enzyme CO dehydrogenase (CODH) catalyzes the oxidation of CO and water to produce carbon dioxide, two electrons, and two protons (8, 11). The electrons are transferred to an electron transfer chain and used to generate a proton gradient across the membrane. Three genes, coxL, coxM, and coxS (for large, medium, and small subunits, respectively), encode the polypeptides for the CODH enzyme. Two heterotrimers, each composed of one CoxL, CoxM, and CoxS subunit, combine to form a functional aerobic CODH enzyme. The large subunit contains the molybdenum cofactor, the medium subunit binds flavin adenine dinucleotide, and the small subunit has two iron-sulfur clusters (13). In addition to these three genes, a number of other accessory genes have also been identified (CoxB, CoxC, CoxH, CoxD, CoxE, CoxF, CoxG, CoxI, and CoxK) that are believed to be required in the processes of regulation, posttranslational modification, and anchorage of the CODH complex to the cytoplasmic membrane. A number of these accessory genes are membrane-bound proteins themselves (CoxB, CoxC, CoxH, and CoxK), containing several transmembrane helices, and indeed, in O. carboxidovorans OM5, the CODH enzyme itself has been observed to associate with the inner cytoplasmic membrane.Based on sequence differences, genome organization, and catalytic properties, there are two types of aerobic molybdenum-based CODH (the anaerobic enzymes are a different class of genes) (20). Both forms can be readily differentiated from other molybdenum hydroxylases by phylogenetic analysis. Form I CODH (also called OMS, named after Oligotropha, Mycobacterium, and Pseudomonas) has been conclusively proven by mutagenesis experiments and X-ray crystallography (8, 32, 35) to be the key enzyme in aerobic CO oxidation by carboxydotrophic bacteria, i.e., those that can grow on CO as the sole carbon and energy source (at >10% CO concentration). The reaction mechanism has also been clearly defined. Form I CODH large-subunit CoxL can be readily diagnosed by its characteristic catalytic site motif AYXCSFR. Moreover, in all the organisms in which form I CODH genes have been identified so far, the genomic organization of the three subunits is always M→S→L. The organization of the accessory genes, however, may vary from organism to organism.There is much less known about the other form, form II CODH (or BMS, after Bradyrhizobium, Mesorhizobium, and Sinorhizobium), which was first described in Bradyrhizobium japonicum USDA 110 (23), a gram-negative bacterial strain and a nitrogen-fixing symbiont of soybeans. Form II CODH enables these bacteria to grow, albeit slowly, in the presence of CO as the sole carbon and energy source, but the rate of CO oxidation by form II CODH of B. japonicum USDA 110 is 10 to 1,000 times lower than that for form I CODH in O. carboxidovorans OM5 and Pseudomonas carboxydohydrogena OM5. The catalytic site of the form II CoxL large subunit is AYRGAGR. The genome organization of the form II subunits is S→L→M, different from that of form I. The number of accessory genes present along with these genes is also variable (20). Form II is often found as a paralogous copy of three subunits of form I, but without the accompanying set of CODH-related genes. This is not surprising, since in most cases, the genes appear to be already associated with the form I cluster elsewhere in the genome, like in Rhodothermus marinus DSM 4252, Dinoroseobacter shibae DFL 12, and Bradyrhizobium sp. strain BTAi1.The discovery of the role played by CODH in marine waters is relatively recent. First, it was found in the genome of Silicibacter pomeroyi DSS-3, a marine alphaproteobacterium of the Roseobacter cluster (26), which was concomitantly proven to be able to oxidize CO at low concentrations (as should be expected in marine waters). Later on the process, it was also found in metagenomic studies of surface waters for the Sargasso Sea metagenome project (26, 45). It has been proposed that many heterotrophic bacteria in surface waters are lithoheterotrophs and take advantage of the CO released by organic matter photolysis as an alternative energy source to supplement the scarce dissolved organic matter in a way akin to the photoheterotrophy mediated by proteorhodopsin or anoxygenic photosynthesis.We recently found evidence of a CODH presence deep in the Mediterranean Sea by the end sequencing of fosmids from a metagenomic library from a 3,000-m depth in the Ionian Sea (southeast of Sicily, Italy) (24). Here we present the analysis of nine fully sequenced fosmids that were chosen on the basis of the presence of CODH cluster genes at their ends. The results confirm the presence of complete CODH clusters, including one that has the gene sequence and cluster structure of a form I CODH. Although the source of CO deep in the ocean is unclear, the frequency in which these genes were found and the retrieval of similar sequences from the deep-ocean metagenomic database of the Hawaii Ocean Time-Series (HOT) station (7, 21) point toward an important contribution of this lithotrophic metabolism deep in the ocean, similarly relevant to that found in the surface waters.     

What makes Aspergillus fumigatus a successful pathogen? Genes and molecules involved in invasive aspergillosis

Aspergillus fumigatus is an opportunistic pathogen that causes 90% of invasive aspergillosis (IA) due to Aspergillus genus, with a 50-95% mortality rate. It has been postulated that certain virulence factors are characteristic of A. fumigatus, but the "non-classical" virulence factors seem to be highly variable. Overall, published studies have demonstrated that the virulence of this fungus is multifactorial, associated with its structure, its capacity for growth and adaptation to stress conditions, its mechanisms for evading the immune system and its ability to cause damage to the host. In this review we intend to give a general overview of the genes and molecules involved in the development of IA. The thermotolerance section focuses on five genes related with the capacity of the fungus to grow at temperatures above 30°C (thtA, cgrA, afpmt1, kre2/afmnt1, and hsp1/asp f 12). The following sections discuss molecules and genes related to interaction with the host and with the immune responses. These sections include β-glucan, α-glucan, chitin, galactomannan, galactomannoproteins (afmp1/asp f 17 and afmp2), hydrophobins (rodA/hyp1 and rodB), DHN-melanin, their respective synthases (fks1, rho1-4, ags1-3, chsA-G, och1-4, mnn9, van1, anp1, glfA, pksP/alb1, arp1, arp2, abr1, abr2, and ayg1), and modifying enzymes (gel1-7, bgt1, eng1, ecm33, afpigA, afpmt1-2, afpmt4, kre2/afmnt1, afmnt2-3, afcwh41 and pmi); several enzymes related to oxidative stress protection such as catalases (catA, cat1/catB, cat2/katG, catC, and catE), superoxide dismutases (sod1, sod2, sod3/asp f 6, and sod4), fatty acid oxygenases (ppoA-C), glutathione tranferases (gstA-E), and others (afyap1, skn7, and pes1); and efflux transporters (mdr1-4, atrF, abcA-E, and msfA-E). In addition, this review considers toxins and related genes, such as a diffusible toxic substance from conidia, gliotoxin (gliP and gliZ), mitogillin (res/mitF/asp f 1), hemolysin (aspHS), festuclavine and fumigaclavine A-C, fumitremorgin A-C, verruculogen, fumagillin, helvolic acid, aflatoxin B1 and G1, and laeA. Two sections cover genes and molecules related with nutrient uptake, signaling and metabolic regulations involved in virulence, including enzymes, such as serine proteases (alp/asp f 13, alp2, and asp f 18), metalloproteases (mep/asp f 5, mepB, and mep20), aspartic proteases (pep/asp f 10, pep2, and ctsD), dipeptidylpeptidases (dppIV and dppV), and phospholipases (plb1-3 and phospholipase C); siderophores and iron acquisition (sidA-G, sreA, ftrA, fetC, mirB-C, and amcA); zinc acquisition (zrfA-H, zafA, and pacC); amino acid biosynthesis, nitrogen uptake, and cross-pathways control (areA, rhbA, mcsA, lysF, cpcA/gcn4p, and cpcC/gcn2p); general biosynthetic pathway (pyrG, hcsA, and pabaA), trehalose biosynthesis (tpsA and tpsB), and other regulation pathways such as those of the MAP kinases (sakA/hogA, mpkA-C, ste7, pbs2, mkk2, steC/ste11, bck1, ssk2, and sho1), G-proteins (gpaA, sfaD, and cpgA), cAMP-PKA signaling (acyA, gpaB, pkaC1, and pkaR), His kinases (fos1 and tcsB), Ca(2+) signaling (calA/cnaA, crzA, gprC and gprD), and Ras family (rasA, rasB, and rhbA), and others (ace2, medA, and srbA). Finally, we also comment on the effect of A. fumigatus allergens (Asp f 1-Asp f 34) on IA. The data gathered generate a complex puzzle, the pieces representing virulence factors or the different activities of the fungus, and these need to be arranged to obtain a comprehensive vision of the virulence of A. fumigatus. The most recent gene expression studies using DNA-microarrays may be help us to understand this complex virulence, and to detect targets to develop rapid diagnostic methods and new antifungal agents.