A Naturally Heteroplasmic Clam Provides Clues about the Effects of Genetic Bottleneck on Paternal mtDNA

Mitochondrial DNA (mtDNA) is present in multiple copies within an organism. Since these copies are not identical, a single individual carries a heterogeneous population of mtDNAs, a condition known as heteroplasmy. Several factors play a role in the dynamics of the within-organism mtDNA population: among them, genetic bottlenecks, selection, and strictly maternal inheritance are known to shape the levels of heteroplasmy across mtDNAs. In Metazoa, the only evolutionarily stable exception to the strictly maternal inheritance of mitochondria is the doubly uniparental inheritance (DUI), reported in 100+ bivalve species. In DUI species, there are two highly divergent mtDNA lineages, one inherited through oocyte mitochondria (F-type) and the other through sperm mitochondria (M-type). Having both parents contributing to the mtDNA pool of the progeny makes DUI a unique system to study the dynamics of mtDNA populations. Since, in bivalves, the spermatozoon has few mitochondria (4-5), M-type mtDNA faces a tight bottleneck during embryo segregation, one of the narrowest mitochondrial bottlenecks investigated so far. Here, we analyzed the F- and M-type mtDNA variability within individuals of the DUI species Ruditapes philippinarum and investigated for the first time the effects of such a narrow bottleneck affecting mtDNA populations. As a potential consequence of this narrow bottleneck, the M-type mtDNA shows a large variability in different tissues, a condition so pronounced that it leads to genotypes from different tissues of the same individual not to cluster together. We believe that such results may help understanding the effect of low population size on mtDNA bottleneck

Very large ensemble ocean forecasting experiment using the Grid computing infrastructure

Atmospheric and oceanic ensemble forecasting is a way to deal with uncertainty related to inaccurate knowledge of the initial state of the atmosphere and the ocean, the lateral and vertical boundary condition errors and the model physics shortfalls (Lewis, 2005, Epstein, 1969). Since the atmosphere and the ocean are extremely non-linear systems (Lorenz, 1993, Saravanan et al., 2000) initial uncertainties can amplify and limit the predictability of short term forecasts (Kleeman and Majda, 2005). For the ocean, ensemble forecasting is a novel field. Ensemble methods are used to compute the background error covariance matrix in data assimilation schemes (Evensen, 2003) but are not used yet to quantify the forecast uncertainty in short term ocean forecasting systems. Initial conditions uncertainty is a major source of unpredictability for ocean currents due to the limited observations available for nowcasting and the highly non-linear physics. In this study we explore the short term ensemble forecast variance generated by perturbing the initial conditions using a new computational facility, so-called Grid infrastructure (http://grid.infn.it/), distributed over the Italian territory. This infrastructure allowed us to perform several ensemble forecast experiments with 1000 members: they are completed within 5 hours of wall-clock time after their submission and the ensemble variance peaks at the mesoscales

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics.Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived similar to 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads.Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes

Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics

Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with doubly uniparental inheritance (DUI) of mtDNA. However, the link between DUI and sex determination remains obscure. In this study, we performed a comparative gonad transcriptomics analysis for two DUI-possessing freshwater mussel species to better understand the mechanisms underlying sex determination and DUI in these bivalves. We used a BLAST reciprocal analysis to identify orthologs between Venustaconcha ellipsiformis and Utterbackia peninsularis and compared our results with previously published sex-specific bivalve transcriptomes to identify conserved sex-determining genes. We also compared our data with other DUI species to identify candidate genes possibly involved in the regulation of DUI. A total of 3c12,000 orthologous relationships were found, with 2,583 genes differentially expressed in both species. Among these genes, key sex-determining factors previously reported in vertebrates and in bivalves (e.g., Sry, Dmrt1, Foxl2) were identified, suggesting that some steps of the sex-determination pathway may be deeply conserved in metazoans. Our results also support the hypothesis that a modified ubiquitination mechanism could be responsible for the retention of the paternal mtDNA in male bivalves, and revealed that DNA methylation could also be involved in the regulation of DUI. Globally, our results suggest that sets of genes associated with sex determination and DUI are similar in distantly-related DUI species

Cochlear implantation in post-lingually deafened adults and elderly patients: analysis of audiometric and speech perception outcomes during the first year of use

Questo studio è volto alla valutazione degli outcomes audiometrici e logopedici dei pazienti anziani portatori di impianto cocleare durante il primo anno di utilizzo del dispositivo. Sono stati valutati 42 pazienti impiantati tra marzo 2010 e settembre 2014 presso lUO ORL dellAzienda Ospedaliera Universitaria di Padova. Sono stati inclusi nello studio pazienti affetti da sordità bilaterale postlinguale di grado severo-profondo impiantati unilateralmente. I soggetti sono stati divisi in tre gruppi in base allepoca della chirurgia: 14 soggetti con impianto fra i 35 e i 49 anni, 14 fra i 50 e i 64 anni e 14 impiantati a unetà superiore di 65 anni. Tutti i pazienti sono stati valutati prima e dopo la chirurgia (a 1, 3, 6 e 12 mesi di follow-up) attraverso lesecuzione di: audiometria tonale, audiometria vocale, test logopedici e somministrazione del questionario delle categorie percettive (CAP). Lanalisi statistica è stata effettuata attraverso il Students t-test. La totalità dei soggetti nei tre gruppi hanno dimostrato significativi miglioramenti allaudiometria tonale e vocale ai controlli post chirurgici rispetto alle performance ottenute precedentemente allimpianto. In particolare si sono verificati miglioramenti della soglia audiometrica media (PTA) senza differenze statisticamente significative tra i tre gruppi. risultati ottenuti nei test logopedici e dalla somministrazione del CAP hanno dimostrato evidenti miglioramenti in tutti i tre gruppi in studio. Abbiamo riscontrato, però, che i soggetti più giovani hanno raggiunto maggiori punteggi ai controlli post impianto rispetto a quelli più anziani. Concludendo, possiamo affermare che limpianto cocleare è un trattamento efficace per soggetti affetti da ipoacusia severa-profonda senza differenze significative nelle performance audiologiche e logopediche in relazione alletà di impianto. Anche se più lentamente, i pazienti impiantati dopo i 65 anni di età raggiungono performance ottimali e possono essere ritenuti dei candidati ottimali allintervento

cranial nerve abnormalities in oculo auriculo vertebral spectrum

BACKGROUND AND PURPOSE: Cranial nerve abnormalities might be observed in hemifacial microsomia and microtia (oculo-auriculo-vertebral spectrum), but the rate, features, and relationship with functional impairment or phenotype severity have not yet been defined. This study aimed at investigating absence/asymmetry, abnormal origin, morphology and course of cranial nerves, and presence/asymmetry of the foramen ovale and inferior alveolar nerve canal in a cohort of oculo-auriculo-vertebral spectrum patients. MATERIALS AND METHODS: Twenty-nine patients with oculo-auriculo-vertebral spectrum (mean age, 7 years; age range, 0.2–31 years; 12 females) underwent brain MR imaging, CT, and neurologic evaluation; 19 patients had a more severe phenotype (Goldenhar syndrome). RESULTS: Cranial nerve abnormalities were detected only in patients with Goldenhar syndrome (17/19, bilaterally in 8) and were involved the second (4/19), third (1/18), fifth (11/19), sixth (8/16), seventh (11/18), and eighth (8/18) cranial nerves. Multiple cranial nerve abnormalities were common (11/17). Eleven patients showed bone foramina abnormalities. Trigeminal and facial nerve dysfunctions were common (44% and 58%, respectively), especially in patients with Goldenhar syndrome. Trigeminal abnormalities showed a good correlation with ipsilateral dysfunction ( P = .018), which further increased when bone foramina abnormalities were included. The facial nerve showed a trend toward correlation with ipsilateral dysfunction ( P = .081). Diplopia was found only in patients with Goldenhar syndrome and was associated with third and sixth cranial nerve abnormalities ( P = .006). CONCLUSIONS: Among patients with oculo-auriculo-vertebral spectrum, cranial nerve morphologic abnormalities are common, correlate with phenotype severity, and often entail a functional impairment. The spectrum of cranial nerve abnormalities appears wider than simple hypo-/aplasia and includes an anomalous cisternal course and partial/complete fusion of diverse cranial nerves. CN : cranial nerve OAVS : oculo-auriculo-vertebral spectru

Attention to speech and music in young children with bilateral cochlear implants: a pupillometry study

Early bilateral cochlear implants (CIs) may enhance attention to speech, and reduce cognitive load in noisy environments. However, it is sometimes difficult to measure speech perception and listening effort, especially in very young children. Behavioral measures cannot always be obtained in young/uncooperative children, whereas objective measures are either difficult to assess or do not reliably correlate with behavioral measures. Recent studies have thus explored pupillometry as a possible objective measure. Here, pupillometry is introduced to assess attention to speech and music in noise in very young children with bilateral CIs (N = 14, age: 17–47 months), and in the age-matched group of normally-hearing (NH) children (N = 14, age: 22–48 months). The results show that the response to speech was affected by the presence of background noise only in children with CIs, but not NH children. Conversely, the presence of background noise altered pupil response to music only in in NH children. We conclude that whereas speech and music may receive comparable attention in comparable listening conditions, in young children with CIs, controlling for background noise affects attention to speech and speech processing more than in NH children. Potential implementations of the results for rehabilitation procedures are discussed

Agronomic, nutritional and nutraceutical aspects of durum wheat (Triticum durum Desf.) cultivars under low input agricultural management

Among cereals, durum wheat has a central role in the Italian diet and economy, where there is a historical tradition of pasta making. In the present study, we evaluated the nutrient and nutraceutical properties of 2 old and 6 modern durum wheat varieties grown under low input agricultural management. Considering the lack of available data on the adaptability of existing durum wheat varieties to the low input and organic sectors, the research aimed at providing a complete description of the investigated genotypes, considering the agronomic performance as well as the nutrient and phytochemical composition. The experimental trials were carried out at the same location (Bologna, Northern Italy) for two consecutive growing seasons (2006/2007, 2007/2008). No clear distinction between old and modern varieties was observed in terms of grain yield (mean values ranging from 2.5 to 4.0 t/ha), highlighting that the divergence in productivity, normally found between dwarf and non-dwarf genotypes, is strongly reduced when they are cropped under low input management. All durum wheat varieties presented high protein levels and, in addition, provided remarkable amounts of phytochemicals such as dietary fibre, polyphenols, flavonoids and carotenoids. Some of the investigated genotypes, such as Senatore Cappelli, Solex, Svevo and Orobel, emerged with intriguing nutritional and phytochemical profiles, with the highest levels of dietary fibre and antioxidant compounds. The study provided the basis for further investigations into the adaptability of the durum wheat genotypes to low input management, for the selection of genotypes characterised by higher yield and valuable nutrient and nutraceutical quality