Comparative genome-wide analysis of repetitive DNA in the genus Populus L.

Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novák et al. BMC Bioinformatics 11:378 2010). The repetitive portion of the genome ranged from 33.8 in Populus nigra to 46.5% in Populus tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7:1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeat types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analysed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species, and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving

No efficacy of transcranial direct current stimulation on chronic migraine with medication overuse : a double blind, randomised clinical trial

Background: Transcranial direct current stimulation was suggested to provide beneficial effects in chronic migraine, a condition often associated with medication overuse for which no long-term therapy is available. Methods: We conducted a randomised controlled trial to assess long-term efficacy of transcranial direct current stimulation. Adults diagnosed with chronic migraine and medication overuse were assigned to receive in a 1:1:1 ratio anodal, cathodal, or sham transcranial direct current stimulation daily for five consecutive days, along with standardised drug withdrawal protocol. Primary outcome was 50% reduction of days of headache per month at 12 months. Co-secondary outcomes were 50% reduction of days of headache per month at 6 months, reduction of analgesic intake per month, and change in disability and quality of life, catastrophising, depression, state and trait anxiety, dependence attitude and allodynia intensity. Patients were not allowed to take any migraine prophylaxis drug for the entire study period. Results: We randomly allocated 135 patients to anodal (44), cathodal (45), and sham (46) transcranial direct current stimulation. At 6 and 12 months, the percentage of reduction of days of headache and number of analgesics per month ranged between 48.5% and 64.7%, without differences between transcranial direct current stimulation (cathodal, anodal, or the results obtained from the two arms of treatment, anodal plus cathodal) and sham. Catastrophising attitude significantly reduced at 12 months in all groups. There was no difference for the other secondary outcomes. Conclusions: Transcranial direct current stimulation did not influence the short and long-term course of chronic migraine with medication overuse after acute drug withdrawal. Behavioral and educational measures and support for patients' pain management could provide long-term improvement and low relapse rate. Trial registration number NCT04228809

Decoding the Genomic Landscape of Pomegranate: A Genome-Wide Analysis of Transposable Elements and Their Structural Proximity to Functional Genes

Transposable elements (TEs) significantly drive dynamic changes that characterize genome evolution. However, understanding the variability associated with TE insertions among different cultivars remains challenging. The pomegranate (Punica granatum L.) has yet to be extensively studied regarding the roles of TEs in the diversification of cultivars. Herein, we explored the genome distribution of TEs and its potential functional implications among four pomegranate cultivars, ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’ and ‘Tunisia’, whose genome sequences are available. A total of 8404 full-length TEs were isolated. The content of TEs varied among the cultivars, ranging from 41.67% of ‘Taishanhong’ to 52.45% of ‘Bhagwa’. In all cultivars, the Gypsy superfamily of retrotransposons accounted for a larger genome proportion than the Copia superfamily. Seventy-three full-length TEs were found at the same genomic loci in all four cultivars. By contrast, 947, 297, 311, and 874 TEs were found exclusively in ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’, and ‘Tunisia’ cultivars, respectively. Phylogenetic clustering based on the presence of TE insertions in specific loci reflected the geographic origins of the cultivars. The insertion time profiles of LTR-REs were studied in the four cultivars. Shared elements across the four cultivars exhibited, on average, a more ancient insertion date than those exclusive to three, two, or one cultivars. The majority of TEs were located within 1000 bp from the nearest gene. This localization was observed for 57% of DNA TEs and 55% of long-terminal repeat retrotransposons (LTR-RE). More than 10% of TEs resulted inserted within genes. Concerning DNA TEs, 3.91% of insertions occurred in introns, while 2.42% occurred in exons. As to LTR-REs, 4% of insertions occurred in exons and 1.98% in introns. Functional analysis of the genes lying close to TEs was performed to infer if differences in TE insertion can affect the fruit quality. Two TE insertions were found close to two genes encoding 4-coumarate--CoA ligase, an enzyme involved in the phenylpropanoid pathway. Moreover, a TIR/Mariner element was found within the exon of a gene encoding anthocyanidin reductase in the ‘Tunisia’ genotype, crucial in the biosynthesis of flavan-3-ols and proanthocyanidins, strictly correlated with the nutraceutical properties of pomegranate. Although functional and metabolomic studies are essential to elucidate the consequences of TE insertions, these results contribute to advancing our comprehension of the role of TEs in pomegranate genomics, providing insights for crop breeding

How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis

Although Ficus carica L. (fig) is one of the most resistant fruit tree species to salinity, no comprehensive studies are currently available on its molecular responses to salinity. Here we report a transcriptome analysis of F. carica cv. Dottato exposed to 100 mM sodium chloride for 7 weeks, where RNA-seq analysis was performed on leaf samples at 24 and 48 days after the beginning of salinization; a genomederived fig transcriptome was used as a reference. At day 24, 224 transcripts were significantly upregulated and 585 were down-regulated, while at day 48, 409 genes were activated and 285 genes were repressed. Relatively small transcriptome changes were observed after 24 days of salt treatment, showing that fig plants initially tolerate salt stress. However, after an early down-regulation of some cell functions, major transcriptome changes were observed after 48 days of salinity. Seven weeks of 100 mM NaCl dramatically changed the repertoire of expressed genes, leading to activation or reactivation of many cell functions. We also identified salt-regulated genes, some of which had not been previously reported to be involved in plant salinity responses. These genes could be potential targets for the selection of favourable genotypes, through breeding or biotechnology, to improve salt tolerance in fig or other crops

An automated system for the objective evaluation of human gustatory sensitivity using tongue biopotential recordings

The goal of this work is to develop an automatic system for the evaluation of the gustatory sensitivity of patients using an electrophysiological recording of the response of bud cells to taste stimuli. In particular, the study aims to evaluate the effectiveness and limitations of supervised classifiers in the discrimination between subjects belonging to the three 6-n-pro-pylthiouracil (PROP) taster categories (supertasters, medium tasters, and non-tasters), exploiting features extracted from electrophysiological recordings of the tongue. Thirty-nine subjects (equally divided into the three PROP status classes by standard non-objective scaling methods) underwent a non-invasive, differential, biopotential recording of their tongues during stimulation with PROP by using a custom-made, flexible, silver electrode. Two different classifiers were trained to recognize up to seven different features extracted from the recorded depolarization signal. The classification results indicate that the identified set of features allows to distinguish between PROP tasters and non-tasters (average accuracy of 80% ± 18% and up to 94% ± 15% when only supertasters and non-tasters are considered), but medium tasters were difficult to identify. However, these apparent classification errors are related to uncertainty in the labeling procedures, which are based on non-objective tests, in which the subjects provided borderline evaluations. Thus, using the proposed method, it is possible, for the first time, to automatically achieve objective PROP taster status identification with high accuracy. The simplicity of the recording technique allows for easy reproduction of the experimental setting; thus the technique can be used in future studies to evaluate other gustatory stimuli. The proposed approach represents the first objective and automatic method to directly measure human gustatory responses and a milestone for physiological taste studies, with applications ranging from basic science to food tasting evaluations

intra varietal agronomical variability in vitis vinifera l cv cannonau investigated by fluorescence texture and colorimetric analysis

To date, innovative, rapid and non-invasive techniques have been used to assess variations in morphological and technological characteristics between grape cultivars. In order to improve knowledge of the qualitative expression of the genetic traits of cv. Cannonau (syn. Grenache), fluorescence, texture and colorimetric analyses were performed on 85 biotypes attributable to this variety. Eighty-five Cannonau biotypes cultivated in the same vineyard were analysed in order to evaluate their morphological and agronomical characteristics. As regards the morphological traits, of the six descriptors observed, five were able to discriminate the Cannonau population according to different expression levels. Must composition, berry colour (using the Minolta tristimulus colorimeter), texture (assessed using the TaxT2i plus texturimeter) and fluorescence (using the Multiplex III detector) were determined on clusters harvested at the same time. Cluster analysis was able to separate the Cannonau population into five groups, characterised by differences in the following criteria: L*, a* and b*, berry skin thickness, FERARI, TSS, pH and titratable acidity, total polyphenols and total anthocyanins. The FERARI index was highly and positively correlated with total anthocyanins and negatively correlated with grape colour, while berry weight and berry skin thickness were not correlated with any variable assessed. The remarkable intra-variability encountered for the qualitative and quantitative characters in the Cannonau variety suggests that new biotypes could be selected for different oenological purposes, using techniques such as the measure of fluorescence and colorimetry. This is the first study carried out within the cv. Cannonau using innovative and classical techniques suitable to investigate intra-varietal variability

Seminal fluid metabolomic markers of oligozoospermic infertility in humans

Infertility affects 12–15% of couples worldwide, and male factors are the cause of nearly half of all cases. Studying seminal fluid composition could lead to additional diagnostic accuracy and a better understanding of the pathophysiology of male factor infertility. Metabolomics offers a new opportunity to evaluate biomarkers and better understand pathological mechanisms. The aim of the study was to identify new markers or therapeutic targets to improve outcomes in male factor or idiopathic infertility patients. Semen samples were obtained from 29 men with a normal spermogram test, and from 18 oligozoospermic men. Samples were processed and analyzed by Nuclear Magnetic Resonance spectroscopy and, subsequently, multivariate and univariate statistical analyses. Receiving Operator Curves (ROC) and Spearman correlations were also performed. An Orthogonal Partial Least Square Discriminant Analysis supervised multivariate model was devised to compare the groups. The levels of fructose, myo‐inositol, aspartate and choline were altered. Moreover, Spearman Correlation associated fructose, aspartate and myo‐inositol with the total amount of spermatozoa, total motile spermatozoa, % of immotility and % of “in situ” spermatozoic motility respectively. NMR‐based metabolomics allowed the identification of a specific metabolic fingerprint of the seminal fluids of patients affected by oligozoospermia

Characterisation of LTR-Retrotransposons of Stevia rebaudiana and Their Use for the Analysis of Genetic Variability

Stevia rebaudiana is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The Gypsy retrotransposons were twice as abundant as the Copia ones. A disproportionate abundance of elements belonging to the Chromovirus/Tekay lineage was observed among the Gypsy elements. Only the SIRE and Angela lineages represented significant portions of the genome among the Copia elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage Angela was used to analyse the genetic variability in 25 accessions of S. rebaudiana using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding

Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in this species, we decided to study another fig genotype, the Italian cv. Dottato, in order to perform comparative studies between the two cultivars and extend the pan genome of this species. We isolated, sequenced and assembled fig genomic DNA from young fruits of cv. Dottato. Then, putative gene sequences were predicted and annotated. Finally, a comparison was performed between cvs. Dottato and Horaishi predicted transcriptomes. Our data provide a resource (available at the Sequence Read Archive database under SRP109082) to be used for functional genomics of fig, in order to fill the gap of knowledge still existing in this species concerning plant development, defense and adaptation to the environment

NA60 results on pTp_T spectra and the ρ\rho spectral function in In-In collisions

The NA60 experiment at the CERN SPS has studied low-mass muon pairs in 158 AGeV In-In collisions. A strong excess of pairs is observed above the yield expected from neutral meson decays. The unprecedented sample size of close to 400K events and the good mass resolution of about 2% have made it possible to isolate the excess by subtraction of the decay sources (keeping the $\rho$). The shape of the resulting mass spectrum exhibits considerable broadening, but essentially no shift in mass. The acceptance-corrected transverse-momentum spectra have a shape atypical for radial flow and show a significant mass dependence, pointing to different sources in different mass regions.Comment: 4 pages, 4 figures, Quark Matter 2006 conference proceeding