Zika virus infection in semen: Effect on human reproduction

Unique among vector-borne flaviviruses, Zika virus can infect testis and male genital tract, can persist in semen for months after symptoms onset, and be sexually transmitted. In The Lancet Infectious Diseases, Guillaume Joguet and colleagues report alterations of sperm and testicular function in men with Zika virus infection, with potential effect on human reproduction. In this prospective longitudinal study, the authors detected viral RNA in the semen of 11 of 15 tested men, including five with persistent seminal shedding after viral clearance in blood. Notably, they were able to isolate infectious virus from motile spermatozoa obtained using semen separation methods that are generally used in assisted reproductive procedures. Semen alterations were observed, including a decreased sperm count and a concurrent increment of multiple sperm anomalies, especially in patients with Zika virus RNA-positive seminal specimens, while recovery was observed at day 120 post infection. In addition, inhibin \u3b2 concentrations decreased after infection, suggesting an impairment of Sertoli cells, which are key components of the blood\u2013testis barrier, produce immunoregulatory factors, and provide support to sperm cells during spermatogenesis. These findings suggest a direct effect of viral infection on the testis or epididymis with impairment of sperm development, in agreement with findings in animal models

Eliciting the Functional Taxonomy from protein annotations and taxa

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules

Full genome sequence-based comparative study of wild-type and vaccine strains of infectious laryngotracheitis virus from Italy

Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980,2007 and 2011, and two commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and maybe involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains

Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites. We found that the most stable G-quadruplexes were in the promoter region of genes belonging to definite functional categories. Actual G-quadruplex folding of four selected sequences was assessed by biophysical and biomolecular techniques: all molecules formed stable G-quadruplexes, which were further stabilized by two G-quadruplex ligands. These compounds inhibited Mycobacterium tuberculosis growth with minimal inhibitory concentrations in the low micromolar range. These data support formation of Mycobacterium tuberculosis G-quadruplexes in vivo and their potential regulation of gene transcription, and prompt the use of G4 ligands to develop original antitubercular agents

DNS of vertical plane channel flow with finite-size particles: Voronoi analysis, acceleration statistics and particle-conditioned averaging

We have performed a direct numerical simulation of dilute turbulent particulate flow in a vertical plane channel, fully resolving the phase interfaces. The flow conditions are the same as those in the main case of "Uhlmann, M., Phys. Fluids, vol. 20, 2008, 053305", with the exception of the computational domain length which has been doubled in the present study. The statistics of flow and particle motion are not significantly altered by the elongation of the domain. The large-scale columnar-like structures which had previously been identified do persist and they are still only marginally decorrelated in the prolonged domain. Voronoi analysis of the spatial particle distribution shows that the state of the dispersed phase can be characterized as slightly more ordered than random tending towards a homogeneous spatial distribution. It is also found that the p.d.f.'s of Lagrangian particle accelerations for wall-normal and spanwise directions follow a lognormal distribution as observed in previous experiments of homogeneous flows. The streamwise component deviates from this law presenting significant skewness. Finally, a statistical analysis of the flow in the near field around the particles reveals that particle wakes present two regions, a near wake where the velocity deficit decays as 1/x and a far wake with a decay of approximately 1/(x*x).Comment: accepted for publication in Int. J. Multiphase Flo

Noninvasive assessment of respiratory muscle strength and activity in Myotonic dystrophy

To evaluate sensitivity/specificity of the maximum relaxation rate (MRR) of inspiratory muscles, amplitude of electromyographic activity of the sternocleidomastoid (SCM), scalene (SCA), parasternal (2ndIS) and rectus abdominis (RA) muscles; lung function and respiratory muscle strength in subjects with Myotonic dystrophy type 1 (DM1) compared with healthy subjects

Identifying Lepton Reconstruction Failures in the CMS detector for a Disappearing Tracks Search

A brief overview of the CMS experiment at the LHC and of related experimental particle physics is given. A recently published search at CMS for beyond the Standard Model long lived particles that have a 'disappearing tracks' signature is summarized. A method utilized in the search, names 'fiducial maps', which addressed lepton reconstruction inefficiencies of the CMS detector is studied in more detail, and solutions are proposed to replace it for electrons and muons independently. For electrons, a deep learning classifier is developed to identify electron tracks that fail to be reconstructed as electrons by the CMS software. This is shown to improve the reach of the search by reducing the electron background by $20 \pm 5$% compared to the fiducial maps; the classifier also retains $6-15$% more signal, except for the longest Higgsino lifetime studied in the search, for which the fiducial map is shown to have slightly better performance. Similarly, a deep learning classifier is developed to identify muon tracks that fail the CMS reconstruction. The classifier identifies $28 \pm 3$% of isolated tag and probe muons that failed the reconstruction; however, this classifier is not able to identify the muons that pass the full selections of this search.No embargoAcademic Major: MathematicsAcademic Major: Physic