Mitochondrial DNA: a tool for populational genetics studies

Mitochondria are cellular organelles that have the function of the oxidative phosphorilation and the formation of ATP. In humans, the mtDNA is a double-stranded, circular, covalent closed molecule of 16.5 kb. The mtDNA is inherited as a haploid from the mother and heteroplasmy has been found rarely. From a populational perspective, it could be considered as a system of small, sexually isolated demes, or clonal lineages, with an evolutionary rate 5 to 10 times faster than the nuclear genome. All these characteristics make this molecule ideal for evolutionary studies. We present two applications of this molecule in genetical studies. One of these is referred to the Balearic Islands populations, Majorca, Minorca, Ibiza, and Chuetas. The other example is the populational dynamics of the different mitochondrial haplotypes in Drosophila subobscura. We also discuss the importance of nuclear markers to complete these studies as well as the study of the Y chromosome to compensate the bias produced by the study of only the mtDNA

Caracterització histològica i genètica de Perkinsus mediterraneus de les Illes Balears a diferents espècies de mol·luscs bivalves

[cat]Perkinsus mediterraneus infecta, sense mortalitats associades, a una gran varietat de mol·luscs bivalves a l’arxipèlag balear: Ostrea edulis, Mimachlamys varia, Arca noae, Chamelea gallina, Pinna nobilis i Venus verrucosa. La detecció de Perkinsus spp. s’ha realitzat mitjançant RFTM i la determinació de l’espècie per PCR-RFLP i seqüenciació. Els nostres resultats han indicat l’existència a Balears de 12 haplotips de P. mediterraneus amb una elevada similitud genètica. Les anàlisis filogenètiques han detectat tres grups diferents d’O. edulis a l’illa de Menorca, que es diferencien d’altres llinatges coespecífics. Les anàlisis recolzen aquesta diferenciació entre les poblacions de Menorca i Mallorca, la qual sembla, en bona part deguda a l’aïllament geogràfic del port de Maó. Malgrat això, altres factors, com la variabilitat ambiental, diferents localitats i dates de detecció, la translocació d’animals, l’activitat humana, etc. poden tenir certa influència. Malgrat que hi ha co-infeccions a l’escopinya gravada del port de Maó amb P. olseni i P. mediterraneus, no n’hem trobat cap cas, ni tampoc bivalves afectats per P. chesapeaki, espècie que recentment s’ha detectat al delta de l'Ebre. Amb aquest treball es determina la distribució geogràfica de P. mediterraneus, les espècies afectades, la seva variabilitat genètica, la seva prevalença i la dinàmica de la infecció.[eng]A wide bivalve mollusc variety is infected by Perkinsus mediterraneus in Balearic Islands: Ostrea edulis, Mimachlamys varia, Arca noae, Chamelea gallina, Pinna nobilis and Venus verrucosa. Perkinsus spp. search was performed using RFTM and species was established by PCR-RFLP and sequencing. We have found 12 P. mediterraneus haplotypes, all of them sharing a high similarity. Three groups of O. edulis from Minorca were revealed by phylogenetic analyses which are different from other co-specifics lineages. Analysis supported this differentiation among populations from Minorca and Majorca. This differentiation could be due to Mahon harbour geographic isolation. Nevertheless, other factors, such as environmental variability, different detection locations and dates, animal translocations, human activity, etc., might also have some influence. Although it is known that co-infections between P. olseni and P. mediterraneus can happen in Venus verrucosa from Mahon harbour, we have not found any occurrence. Furthermore, we have not detected infection by P. chesapeaki, although it has been found in the Ebro delta. This work establishes distribution, affected species, their genetic variability, its prevalence and the infection dynamics by P. mediterraneus

Environmental DNA: State-of-the-art of its application for fisheries assessment in marine environments

Fisheries management involves a broad and complex set of tasks that are necessary to prevent overfishing and to help the recovery of overfished stock. Monitoring fishing activities based on two main sources, landings data and scientific surveys, is a challenging task. Fisheries collection data is often limited, which compromises the accuracy of the results obtained. Therefore, several emerging applications of molecular methods have the potential to provide unique understanding of ecological processes in marine environments and to build stronger empirical underpinnings for the Ecosystem-Based Fisheries Management. Environmental DNA (eDNA) is a complex mixture of genetic material shed by those organisms that inhabit a given environment, whereby DNA is extracted from an environmental sample without accessing the target organism. eDNA studies can be categorized into two main approaches, i) eDNA metabarcoding or semi-targeted (community) approaches and ii) species-specific or targeted approaches (single). Although both categories are often discussed, they differ drastically in their methodology, interpretations and accuracy. Both approaches involve a series of steps that include eDNA capture, preservation, extraction and amplification. This detection will depend on the affinity to the targeted taxa sequences and completeness and accuracy of DNA reference collection databases. The eDNA method applied in marine environments are probably the most challenging aquatic environments for applying this technique. This is because of the extreme relationship between water-volume to biomass, dynamics and the physical and chemical properties of seawater that affect dispersion, dilution and preservation. Here, we review the present application of this novel method in fishery assessment in marine environments. To date, many studies suggest that this method offers the potential to revolutionize fisheries monitoring, which will contribute to improving the range of tasks involved in fisheries management. The compelling conclusion is that the methodological steps including in eDNA surveys should be standardized and that research efforts should focus on developing appropriately validated tests to address environmental and sampling factors that may affect eDNA detection in marine environments in order to draw reliable conclusions. This bioassessment tool can assist fisheries professionals in achieve their research, management, and conservation objectives, but not as a replacement for time-proven assessment methods

Cross-Checking Different Sources of Mobility Information

International audienceThe pervasive use of new mobile devices has allowed a better characterization in space and time of human concentrations and mobility in general. Besides its theoretical interest, describing mobility is of great importance for a number of practical applications ranging from the forecast of disease spreading to the design of new spaces in urban environments. While classical data sources, such as surveys or census, have a limited level of geographical resolution (e.g., districts, municipalities, counties are typically used) or are restricted to generic workdays or weekends, the data coming from mobile devices can be precisely located both in time and space. Most previous works have used a single data source to study human mobility patterns. Here we perform instead a cross-check analysis by comparing results obtained with data collected from three different sources: Twitter, census and cell phones. The analysis is focused on the urban areas of Barcelona and Madrid, for which data of the three types is available. We assess the correlation between the datasets on different aspects: the spatial distribution of people concentration, the temporal evolution of people density and the mobility patterns of individuals. Our results show that the three data sources are providing comparable information. Even though the representativeness of Twitter geolocated data is lower than that of mobile phone and census data, the correlations between the population density profiles and mobility patterns detected by the three datasets are close to one in a grid with cells of 2 × 2 and 1 × 1 square kilometers. This level of correlation supports the feasibility of interchanging the three data sources at the spatio-temporal scales considered

Relating the outcome of HCV infection and different host SNP polymorphisms in a Majorcan population coinfected with HCV–HIV and treated with pegIFN-RBV

Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis, cirrhosis, and hepatocellular carcinoma, and the development of HCV-related disease is accelerated in individuals coinfected with human immunodeficiency-1 virus (HIV). In the present study, we correlated different host single-nucleotide polymorphisms (SNPs) in the IL28B, CTLA4, LDLr, and HFE genes and mitochondrial DNA (mtDNA) haplogroups with the outcome of HCV infection and the response to pegylated-interferon plus ribavirin (pegIFN-RBV) treatment. Our study population consisted of 63 Majorcan patients coinfected with HCV and HIV and 59 anonymous unrelated controls. Whereas the population frequency of IL28B alleles was similar to that found in a North-American cohort of European descent, the frequency of the rs12979860 C allele was lower than that determined in other cohorts from Spain. The frequencies of CTLA4 and LDLr polymorphisms were comparable to those reported in other populations. Significant differences between cases and control cohorts occurred only for the H63D mutation of the HFE gene. There were no other differences in the frequencies of other polymorphisms or mtDNA haplogroups. The IL28B rs12979860 CC genotype was shown to be associated with a rapid virological response, and the spontaneous viral clearance rate for HCV was higher in patients with the CTLA4+49 G allele. There was no relationship between SNPs in the LDLr and HFE genes and mtDNA haplogroups and the response to treatment. Our results suggest that the host genetic background plays a significant role in the pegIFN-RBV response of patients coinfected with HCV and HIV. [Int Microbiol 2014; 17(1):11-20]Keywords: HCV–HIV co-infection · mtDNA haplogroups · SNP polymorphism

Del concili de Ramon Llull, proposta d’edició crítica

[abstract not available

Ramon Llull ens ensenya la funció instrumental de la literatura: una proposta didàctica.

[cat] El present treball parteix de la qüestió de la manca de motivació que presenten els alumnes pel que fa a la literatura. Pensam que, massa sovint, els estudiants de secundària menysvaloren la literatura perquè, entre altres motius, la consideren de poca utilitat. Davant aquest fet, ens plantejam una manera per mitjà de la qual l’alumnat valori la literatura i hi dipositi la confiança per considerar-la una eina útil per a la seva vida. La resolució d’aquest propòsit, consideram adient dur-la a terme demostrant als alumnes com Ramon Llull fa de la literatura un instrument molt valuós per aconseguir el seu principal objectiu: apropar Déu als altres. D’aquesta manera, oferim una proposta didàctica que té com a finalitat aconseguir que els alumnes siguin capaços d’assolir determinats objectius quotidians a través de la literatura, amb la finalitat que es converteixin no sols en consumidors, sinó també en creadors de literatura i, així, la puguin valorar com realment es mereix

State of the Art Review of Environmental DNA Genomics

In recent years, environmental DNA (eDNA) coupled with metabarcoding methodologies has emerged as a promising tool with the potential to improve biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics, and ecosystem functional analysis (Bohmann et al., 2014; Goldberg et al., 2015). eDNA is a complex mixture of genomic DNA from many organisms found in an environment, wherefore DNA is extracted from an environmental sample without accessing the target organism (Lodge et al., 2012; Taberlet et al., 2012a). In general, the eDNA approach involves a series of steps that include eDNA capture, preservation, extraction, amplification, and sequencing to ensure match to target species. Several types of samples have already been used to recover eDNA, including water, soil, feces, pollen, and air (Taberlet et al., 2012a; Deiner et al., 2015). Nevertheless, marine environments are probably the most challenging and difficult aquatic environments for applying the eDNA method. This is because of the extreme water-volume to biomass ratio, the effects of sea currents and wave action on dispersion and dilution of eDNA, and the impact of salinity on the preservation and extraction of eDNA (Thomsen et al., 2012a). eDNA detection features create uncertainty; hence its characterization and appropriate use requires better understanding of eDNA in four domains: origin, state, transport, and fate (Turner et al., 2015). DNA in environmental samples is typically highly degraded into fragments of often less than 150 base pairs (Deagle et al., 2006) and is not always easy to extract. Degradation of eDNA in the environment limits the scope of eDNA studies, as often only small segments of genetic material remain (Turner et al., 2014). eDNA concentration is dependent on biomass, age, and feeding activity of organisms, as well as physiology, life history, and space use (Barnes et al., 2014; Goldberg et al., 2016). Mitochondrial DNA is typically targeted because there are a great number of copies compared to nuclear DNA, its effectiveness in identifying organism to the species level by means of DNA barcoding, including in fish, and its accessibility via universal sequence databases on public servers (e.g. GENBANK and Bold Systems) (Rees et al., 2014). Amplified mitochondrial eDNA may originate from extracellular DNA fragments, mitochondria, cells, excretion, or eggs, and the amount of eDNA quantified is likely to vary depending on the genetic matter being targeted (Herder et al., 2014; Goldberg et al., 2016). A crucial step in the eDNA workflow is DNA capture. Several studies focus on optimization of sampling design and eDNA capture and extraction methods (e.g. Turner et al., 2014; Deiner et al., 2015, Eichmiller et al., 2016). Collection methods typically seek to identify organisms at low densities and, thus, should be optimized for detection sensitivity. Because of this, multiple protocols have been developed in the literature and may be applied to different types of samples (e.g. Turner et al., 2014; Deiner et al., 2015); however, protocol election needs to be carefully considered depending on the goals of the study and the type of sample being analyzed. eDNA extraction protocols that are being optimized within the frame of the FishGenome project target three main applications: single species detection, estimation of abundance and biomass of target species, and biodiversity assessment. The FishGenome project will use two main methods to analyze eDNA: High-Throughput Sequencing (HTS) for biodiversity assessment, and quantitative Polymerase Chain Reaction (qPCR) for the quantification of a target species. For the HTS method, both universal and species-specific primers may be used, but this will depend on the goal of the study. Power of detection will depend on the affinity to the targeted taxa sequences and the availability of DNA reference collection databases needed for species identification. HTS is mostly used to detect multiple species and for biodiversity assessment. Meanwhile, qPCR is widely used for gene expression analysis due to its large dynamic range, tremendous sensitivity, high sequence specificity, little to no postamplification processing, and sample throughput (Lodge et al., 2012). This method is usually performed for species detection and involves the use of species-specific primer sets; it also allows the quantification of target species DNA, which has been shown to correlate with species abundance and biomass in the environment (Lodge et al., 2012; Thomsen et al., 2012a). Since eDNA is a sensitive method, there are many potential sources of “errors”. Some of these errors, which are associated to collecting, laboratory, and bioinformatic procedures, are: contamination, inhibition, amplification and sequencing errors, computational artifacts, and inaccurate taxonomic assignment (Thomsen et al., 2016; Barnes and Turner 2016). Out of these errors, the most serious is probably the risk of contamination and hence the possibility of false positive results. The use and sensitivity of HTS has further complicated the contamination issue, as a very high throughput of DNA sequences is produced (Ficetola et al. 2016). Thus, understanding potential sources of errors and translating these into methodological protocols and interpretations of the results is crucial for reliable outcomes. Along these lines, eDNA offers a potential method to revolutionize marine biomonitoring by significantly augmenting spatial and temporal biological monitoring in aquatic ecosystems due to the ease of collecting water samples (Thomsen and Willerslev, 2015; Sassoubre et al., 2016). eDNA also has the potential to advance fisheries monitoring and conservation by improving detection-probabilities for rare fishes that often comprise a large proportion of the total species richness found in species assemblages. The non-invasive nature of eDNA analysis may provide advantages over traditional capture-based sampling by making it possible to determine the presence or absence of species without disturbance to the fish or their environment. This approach could be especially beneficial in situations of endangered species, where there is significant risk of injury to fishes or damage to their critical habitat (Evans and Lamberti, 2018). More investigations are required in order to understand how well the eDNA method will work for aquatic species, to evaluate the effect of species abundance on detection efficiency, and to upscale species detection from local water samples to larger spatial areas, such as drainage basins. However, it is challenging to work with such small amounts of DNA.N