Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

No evidence for an intragenomic arms race under paternal genome elimination in <i>Planococcus</i> mealybugs

Genomic conflicts arising during reproduction might play an important role in shaping the striking diversity of reproductive strategies across life. Among these is paternal genome elimination (PGE), a form of haplodiploidy which has independently evolved several times in arthropods. PGE males are diploid but transmit maternally inherited chromosomes only, whereas paternal homologues are excluded from sperm. Mothers thereby effectively monopolize the parentage of sons, at the cost of the father's reproductive success. This creates striking conflict between the sexes that could result in a co-evolutionary arms race between paternal and maternal genomes over gene transmission, yet empirical evidence that such an arms race indeed takes place under PGE is scarce. This study addresses this by testing whether PGE is complete when paternal genotypes are exposed to divergent maternal backgrounds in intraspecific and hybrid crosses of the citrus mealybug, Planococcus citri, and the closely related Planococcus ficus. We determined whether males can transmit genetic information through their sons by tracking inheritance of two traits in a three-generation pedigree: microsatellite markers and sex-specific pheromone preferences. Our results suggest leakages of single paternal chromosomes through males occurring at a low frequency, but we find no evidence for transmission of paternal pheromone preferences from fathers to sons. The absence of differences between hybrid and intraspecific crosses in leakage rate of paternal alleles suggests that a co-evolutionary arms race cannot be demonstrated on this evolutionary timescale, but we conclude that there is scope for intragenomic conflict between parental genomes in mealybugs. Finally, we discuss how these paternal escapes can occur and what these findings may reveal about the evolutionary dynamics of this bizarre genetic system

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Abstract: Background: Bovine Spastic Paresis (BSP) is a neuromuscular disorder which affects both male and female cattle. BSP is characterized by spastic contraction and overextension of the gastrocnemious muscle of one or both limbs and is associated with a scarce increase in body weight. This disease seems to be caused by an autosomal and recessive gene, with incomplete penetration, although no genes clearly involved with its onset have been so far identified. We employed cDNA microarrays to identify metabolic pathways affected by BSP in Romagnola cattle breed. Investigation of those pathways at the genome level can help to understand this disease. Results: Microarray analysis of control and affected individuals resulted in 268 differentially expressed genes. These genes were subjected to KEGG pathway functional clustering analysis, revealing that they are predominantly involved in Cell Communication, Signalling Molecules and Interaction and Signal Transduction, Diseases and Nervous System classes. Significantly enriched KEGG pathway's classes for the differentially expressed genes were calculated; interestingly, all those significantly under-expressed in the affected samples are included in Neurodegenerative Diseases. To identify genome locations possibly harbouring gene(s) involved in the disease, the chromosome distribution of the differentially expressed genes was also investigated. Conclusions: The cDNA microarray we used in this study contains a brain library and, even if carrying an incomplete transcriptome representation, it has proven to be a valuable tool allowing us to add useful and new information to a poorly studied disease. By using this tool, we examined nearly 15000 transcripts and analysed gene pathways affected by the disease. Particularly, our data suggest also a defective glycinergic synaptic transmission in the development of the disease and an alteration of calcium signalling proteins. We provide data to acquire knowledge of a genetic disease for which literature still presents poor results and that could be further and specifically analysed in the next future. Moreover this study, performed in livestock, may also harbour molecular information useful for understanding human diseases

Spatio-temporal variability in Mediterranean rocky shore microphytobenthos

Knowledge of spatio-temporal variability of assemblages is the first step in identifying key factors affecting the abundance and distribution of organisms. Despite a long history of ecological studies on rocky intertidal habitats, there is still a lack of basic knowledge about the microphytobenthic components. We investigated the spatio-temporal variability of microphytobenthos in the northwest Mediterranean at multiple scales, including both seasonal and daily observations, as well as its composition. Spatial variability of microphytobenthic biomass varied significantly with season, with an increase in small-scale variance from cold to warm periods. Furthermore, during warmer months, small-scale variances (tens to hundreds of centimeters) were larger than large-scale components (tens to thousands of meters). These results suggest large spatiotemporal variation in the processes driving variation in microphytobenthic assemblages, including interactive effects among stressful abiotic conditions, substratum topography and grazing. In addition, observed variability on a daily scale suggested that microphytobenthos at the study site (dominated by cyanobacteria) might cope with stressful environmental conditions through both physiological and behavioral strategies at micro-spatial scales, including small movements within the substratum. Additional research on ecological and physiological aspects of rocky shore microphytobenthos is needed to better understand its role within interaction webs and primary productivity processes

An Osteosarcoma Model by 3D Printed Polyurethane Scaffold and In Vitro Generated Bone Extracellular Matrix

Osteosarcoma is a primary bone tumor characterized by a dismal prognosis, especially in the case of recurrent disease or metastases. Therefore, tools to understand in-depth osteosarcoma progression and ultimately develop new therapeutics are urgently required. 3D in vitro models can provide an optimal option, as they are highly reproducible, yet sufficiently complex, thus reliable alternatives to 2D in vitro and in vivo models. Here, we describe 3D in vitro osteosarcoma models prepared by printing polyurethane (PU) by fused deposition modeling, further enriched with human mesenchymal stromal cell (hMSC)-secreted biomolecules. We printed scaffolds with different morphologies by changing their design (i.e., the distance between printed filaments and printed patterns) to obtain different pore geometry, size, and distribution. The printed PU scaffolds were stable during in vitro cultures, showed adequate porosity (55–67%) and tunable mechanical properties (Young’s modulus ranging in 0.5–4.0 MPa), and resulted in cytocompatible. We developed the in vitro model by seeding SAOS-2 cells on the optimal PU scaffold (i.e., 0.7 mm inter-filament distance, 60 pattern), by testing different pre-conditioning factors: none, undifferentiated hMSC-secreted, and osteo-differentiated hMSC-secreted extracellular matrix (ECM), which were obtained by cell lysis before SAOS-2 seeding. Scaffolds pre-cultured with osteo-differentiated hMSCs, subsequently lysed, and seeded with SAOS-2 cells showed optimal colonization, thus disclosing a suitable biomimetic microenvironment for osteosarcoma cells, which can be useful both in tumor biology study and, possibly, treatment

Transvenous removal of pacing and implantable cardiac defibrillating leads using single sheath mechanical dilatation and multiple venous approaches: high success rate and safety in more than 2000 leads

Abstract: The aim of the present study was to describe a 10 years single-centre experience in pacing and defibrillating leads removal using an effective and safe modified mechanical dilatation technique. We developed a single mechanical dilating sheath extraction technique with multiple venous entry site approaches. We performed a venous entry site approach (VEA) in cases of exposed leads and an alternative transvenous femoral approach (TFA) combined with an internal transjugular approach (ITA) in the presence of very tight binding sites causing failure of VEA extraction or in cases of free-floating leads. We attempted to remove 2062 leads [1825 pacing and 237 implantable cardiac defibrillating (ICD) leads; 1989 exposed at the venous entry site and 73 free-floating] in 1193 consecutive patients. The VEA was effective in 1799 leads, the TFA in 28, and the ITA in 205; in the overall population, we completely removed 2032 leads (98.4%), partially removed 18 (0.9%), and failed to remove 12 leads (0.6%). Major complications were observed in eight patients (0.7%), causing three deaths (0.3%). Mechanical single sheath extraction technique with multiple venous entry site approaches is effective, safe, and with a good cost effective profile for pacing and ICD leads removal

Viral Production, Decay Rates, and Life Strategies along a Trophic Gradient in the North Adriatic Sea

Although the relationships between trophic conditions and viral dynamics have been widely explored in different pelagic environments, there have been few attempts at independent estimates of both viral production and decay. In this study, we investigated factors controlling the balance between viral production and decay along a trophic gradient in the north Adriatic basin, providing independent estimates of these variables and determining the relative importance of nanoflagellate grazing and viral life strategies. Increasing trophic conditions induced an increase of bacterioplankton growth rates and of the burst sizes. As a result, eutrophic waters displayed highest rates of viral production, which considerably exceeded observed rates of viral decay (up to 2.9 × 109 VLP liter−1 h−1). Viral decay was also higher in eutrophic waters, where it accounted for ca. 40% of viral production, and dropped significantly to 1.3 to 10.7% in oligotrophic waters. These results suggest that viral production and decay rates may not necessarily be balanced in the short term, resulting in a net increase of viruses in the system. In eutrophic waters nanoflagellate grazing, dissolved-colloidal substances, and lysogenic infection were responsible together for the removal of ca. 66% of viral production versus 17% in oligotrophic waters. Our results suggest that different causative agents are primarily responsible for the removal of viruses from the water column in different trophic conditions. Factors other than those considered in the past might shed light on processes responsible for the removal and/or decay of viral particles from the water column

Cardiac resynchronization therapy after coronary sinus lead extraction: feasibility and mid-term outcome of transvenous reimplantation in a tertiary referral centre

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Transvenous Lead Extraction in Patients with Cardiac Implantable Device: The Impact of Systemic and Local Infection on Clinical Outcomes. An ESC‐EHRA ELECTRa (European Lead Extraction Controlled) Registry Substudy

Background: Infections of cardiac implantable devices (CIEDI) have poor outcomes despite improvement in lead extraction (TLE) procedures. Methods: To explore the influence of CIEDI on the outcomes of TLE and the differences between patients with systemic (Sy) vs. local (Lo) CIEDI, we performed a sub‐analysis of the EORP ELECTRa (European Lead Extraction ConTRolled) Registry. Results: Among 3555 patients enrolled by 73 centers in 19 Countries, the indication for TLE was CIEDI in 1850: 1170 with Lo‐CIEDI and 680 with Sy‐CIEDI. Patients with CIEDI had a worse in‐hospital prognosis in terms of major complications (3.57% vs. 1.71%; p = 0.0007) and mortality (2.27% vs. 0.49%; p &lt; 0.0001). Sy‐CIEDI was an independent predictor of in‐hospital death (H.R. 2.14; 95%CI 1.06–4.33. p = 0.0345). Patients with Sy‐CIEDI more frequently had an initial CIED implant and a higher prevalence of comorbidities, while subjects with Lo‐CIEDI had a higher prevalence of previous CIED procedures. Time from signs of CIEDI and TLE was longer for Lo‐CIEDI despite a shorter pre‐TLE antibiotic treatment. Conclusions: Patients with CIEDI have a worse in‐hospital prognosis after TLE, especially for patients with Sy‐CIEDI. These results raise the suspicion that in a relevant group of patients CIEDI can be systemic from the beginning without progression from Lo‐CIEDI. Future research is needed to characterize this subgroup of patients