Complete genome sequence of a new isolate of caper latent virus in caper.

The genome of a new carlavirus isolate from asymptomatic wild Capparis spinosa L. plants in Sicily was sequenced via high-throughput sequencing (HTS) and 5'/3' RACE experiments. The complete genomic sequence was found to be 8,280 nt in length, excluding the poly(A) tail, and contained five putative open reading frames (ORFs). Molecular characterization revealed a close relationship to caper latent virus (CapLV), with 87% and 90% nucleotide sequence identity to available partial sequences of the ORFs encoding the replicase and coat protein of that virus. According to the molecular criteria for species demarcation, which is based on the ORF-1- and ORF-5-encoded proteins, the virus characterized in this study could be considered a variant of CapLV, and we have thus designated it as CapLV-W.

Candida parapsilosis Infection: A Multilocus Microsatellite Genotyping-Based Survey Demonstrating an Outbreak in Hospitalized Patients.

Microsatellite analysis identifies specific genotypes and the genetic relationship between strains. Our objective was to analyze the genotypes of C. parapsilosis strains isolated on different wards of a Tertiary-Referral University Center. We evaluated 70 C. parapsilosis strains in total, isolated from samples of patients admitted to five different wards over two years (January 2015-December 2016). Eight microsatellite markers were selected, and two multiplex PCR assays were set up for microsatellite analysis. The 70 strains, examined at eight microsatellite loci, showed 46 different multilocus genotypes profiles. A total of 74 alleles were detected, with an average of 9.25 alleles per locus. The most variable loci were CP6 and CP4, with 20 and 15 alleles, respectively. Four clusters were detected in four out of five wards. A significant cluster that involved 16 patients in the General Surgery department was also found in two patients who had been transferred to the General Medicine ward. Two multiplex PCRs allowed us to minimize costs, define genotypes and study the isolates' genetic diversity with extreme accuracy, demonstrating the high discriminative power of the microsatellite markers. Molecular epidemiology constitutes an appropriate tool for evaluating horizontal transmission of C. parapsilosis in different clinical settings. Microsatellite genotyping and the utilization of Bruvo's genetic distance are suitable for detecting and appraising nosocomial fungal infections.

First annulus formation in the European anchovy; a two-stage approach for robust validation.

The age determination in fast-growing short-living species, such as European anchovy (Engraulis encrasicolus), has been widely recognized as a difficult task and bias introduced by readers leads to bias in reconstructing the population age structure. In this context, it is worth to note that age structure of fish population represents key information in fishery ecology and for stock assessment models. The uncertainty in estimating the age of the European anchovy by otolith reading is linked to the number of false-growth increments (checks) laid down before the annulus formation. While direct validation methods (e.g. mark-recapture, rearing, radiochemical dating) are difficult to implement specially for this short living species, the use of different indirect methods, supported by a coherent statistical approach, represents a robust and easier validation tool. A statistical modeling approach has been here adopted to assess the coherence of two well-known methods, namely Edge Analysis and Marginal Increment Analysis, in order to validate the first annulus formation in European anchovy. Both methodologies in two different yearly cycles converged toward the same result, thus confirming the annulus identification for the first year class. In addition, the completion dates of the checks and the first annulus were computed in order to gain a better insight into otolith growth dynamic. According to the species spawning period, the completion date of the first annulus falls in the summer period, while the first and second checks completion dates were mostly found in summer and winter respectively. General additive models using marginal increments as dependent variable showed a significant effect of the month, highlighting the presence of only one clear minimum in July/August, as well as specific relationships with condition factor and gonadosomatic index. Modeling the otolith edge morphology, the probability to find a hyaline band displayed in both years a similar shape, characterized by a minimum in July/August and higher values between November and January. The obtained results evidenced temporally coherent patterns providing a better insight in the otolith growth dynamic as well as a more robust validation of the first annulus formation in the European anchovy.

Phylogenetic Relationship Among Wild and Cultivated Grapevine in Sicily: A Hotspot in the Middle of the Mediterranean Basin.

Grapevine (Vitis vinifera ssp. sativa) is a perennial crop especially important for wine and fruit production. The species is highly polymorphic with thousands of different varieties selected by farmers and clonally propagated. However, it is still debated whether grapevine domestication from its wild ancestor (V. vinifera ssp. sylvestris) has been a single event or rather it occurred on multiple occasions during the diffusion of its cultivation across the Mediterranean. Located in the center of the Basin, Sicily is its largest island and has served as a hotspot for all civilizations that have crossed the Mediterranean throughout history. Hundreds of unique grapevine cultivars are still cultivated in Sicily and its surrounding minor islands, though most of them are menaced by extinction. Wild grapevine is also present with isolated populations thriving along riverbanks. With the aim to evaluate the phylogenetic relationships among Sicilian varieties, and to assess the possible contribution of indigenous wild populations to the genetic makeup of cultivated grapevine, we analyzed 170 domestic cultivars and 125 wild plants, collected from 10 different populations, with 23 SSR markers. We also compared our data with published dataset from Eurasia. Results show that Sicilian wild populations are related to the cultivated Sicilian and Italian germplasm, suggesting events of introgression and/or domestication of local varieties.

Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value.

Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.

Detection of the IncX3 plasmid carrying blaKPC-3 in a Serratia marcescens strain isolated from a kidney-liver transplanted patient.

Dissemination of resistance to carbapenems among Enterobacteriaceae through plasmids is an increasingly important concern in health care worldwide. Here we report the first description of an IncX3 plasmid carrying the blaKPC-3 gene in a strain of Serratia marcescens isolated from a kidney-liver transplanted patient at the transplantation centre ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, Palermo, Italy). To localize the transposable element containing the resistance-associated gene Next-Generation Sequencing of the bacterial DNA was performed. S. marcescens was positive for blaKPC-3 and blaSHV-11 genes. The molecular analysis demonstrated that the blaKPC-3 gene of this bacterial strain was located in one copy of the Tn-3-like element Tn4401-a carried in a plasmid that is 53 392 bp in size and showed the typical IncX3 scaffold. Our data demonstrated the presence of a new blaKPC-3 harbouring the IncX3 plasmid in S. marcescens. The possible dissemination among Enterobacteriaceae of this type of plasmid should be monitored and evaluated in terms of clinical risk.

Habitat selection response of small pelagic fish in different environments. Two examples from the oligotrophic Mediterranean Sea.

A number of scientific papers in the last few years singled out the influence of environmental conditions on the spatial distribution of fish species, highlighting the need for the fisheries scientific community to investigate, besides biomass estimates, also the habitat selection of commercially important fish species. The Mediterranean Sea, although generally oligotrophic, is characterized by high habitat variability and represents an ideal study area to investigate the adaptive behavior of small pelagics under different environmental conditions. In this study the habitat selection of European anchovy Engraulis encrasicolus and European sardine Sardina pilchardus is analyzed in two areas of the Mediterranean Sea that largely differentiate in terms of environmental regimes: the Strait of Sicily and the North Aegean Sea. A number of environmental parameters were used to investigate factors influencing anchovy and sardine habitat selection. Acoustic surveys data, collected during the summer period 2002-2010, were used for this purpose. The quotient analysis was used to identify the association between high density values and environmental variables; it was applied to the entire dataset in each area in order to identify similarities or differences in the "mean" spatial behavioral pattern for each species. Principal component analysis was applied to selected environmental variables in order to identify those environmental regimes which drive each of the two ecosystems. The analysis revealed the effect of food availability along with bottom depth selection on the spatial distribution of both species. Furthermore PCA results highlighted that observed selectivity for shallower waters is mainly associated to specific environmental processes that locally increase productivity. The common trends in habitat selection of the two species, as observed in the two regions although they present marked differences in hydrodynamics, seem to be driven by the oligotrophic character of the study areas, highlighting the role of areas where the local environmental regimes meet 'the ocean triad hypothesis'.