Presence, Location and Conservation of Putative G-Quadruplex Forming Sequences in Arboviruses Infecting Humans

Guanine quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich tracts that assemble into a core of stacked planar tetrads. G4s are found in the human genome and in the genomes of human pathogens, where they are involved in the regulation of gene expression and genome replication. G4s have been proposed as novel pharmacological targets in humans and their exploitation for antiviral therapy is an emerging research topic. Here, we report on the presence, conservation and localization of putative G4-forming sequences (PQSs) in human arboviruses. The prediction of PQSs was performed on more than twelve thousand viral genomes, belonging to forty different arboviruses that infect humans, and revealed that the abundance of PQSs in arboviruses is not related to the genomic GC content, but depends on the type of nucleic acid that constitutes the viral genome. Positive-strand ssRNA arboviruses, especially Flaviviruses, are significantly enriched in highly conserved PQSs, located in coding sequences (CDSs) or untranslated regions (UTRs). In contrast, negative-strand ssRNA and dsRNA arboviruses contain few conserved PQSs. Our analyses also revealed the presence of bulged PQSs, accounting for 17-26% of the total predicted PQSs. The data presented highlight the presence of highly conserved PQS in human arboviruses and present non-canonical nucleic acid-structures as promising therapeutic targets in arbovirus infections

Application of Building Typologies for Modelling the Energy Balance of the Residential Building Stock

Building typologies can serve as a basis for analysing the national housing sector. During the TABULA project which was introducing or further developing building typologies in thirteen EU countries, six of the European partners have carried out model calculations which aim at imaging the energy consumption and estimating the energy saving potentials of their national residential building stocks (IWU / Germany, NOA / Greece, POLITO / Italy, VITO / Belgium, STU-K / Czech Republic, SBi / Denmark). The results show that the model calculations can provide plausible projections of the energy consumption of the national residential buildings stock. The fit of model calculations and national energy statistics is satisfactory, deviations can often be explained and corrected by adapting standard boundary conditions of the applied calculation models to more realistic values. In general, the analysis shows that building typologies can be a helpful tool for modelling the energy consumption of national building stocks and for carrying out scenario analysis beyond the TABULA project. The consideration of a set of representative buildings makes it possible to have a detailed view on various packages of measures for the complete buildings stock or for its sub-categories. The effects of different insulation measures at the respective construction elements as well as different heat supply measures including renewable energies can be considered in detail. The quality of future model calculations will depend very much on the availability of statistical data. For reliable scenario analysis information is necessary about the current state of the building stock (How many buildings and heating systems have been refurbished until now?) and about the current trends (How many buildings and heating systems are being refurbished every year?). The availability and regular update of the relevant statistical data will be an important basis for the development and evaluation of national climate protection strategies in the building secto

Formation of a Unique Cluster of G-Quadruplex Structures in the HIV-1 nef Coding Region: Implications for Antiviral Activity

G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment. © 2013 Perrone et al

microRNAs combined to radiomic features as a predictor of complete clinical response after neoadjuvant radio-chemotherapy for locally advanced rectal cancer: a preliminary study

Objective: To define a predictive Artificial Intelligence (AI) algorithm based on the integration of a set of biopsy-based microRNAs expression data and radiomic features to understand their potential impact in predicting clinical response (CR) to neoadjuvant radio-chemotherapy (nRCT). The identification of patients who would truly benefit from nRCT for Locally Advanced Rectal Cancer (LARC) could be crucial for an improvement in a tailored therapy. Methods: Forty patients with LARC were retrospectively analyzed. An MRI of the pelvis before and after nRCT was performed. In the diagnostic biopsy, the expression levels of 7 miRNAs were measured and correlated with the tumor response rate (TRG), assessed on the surgical sample. The accuracy of complete CR (cCR) prediction was compared for i) clinical predictors; ii) radiomic features; iii) miRNAs levels; and iv) combination of radiomics and miRNAs. Results: Clinical predictors showed the lowest accuracy. The best performing model was based on the integration of radiomic features with miR-145 expression level (AUC-ROC = 0.90). AI algorithm, based on radiomics features and the overexpression of miR-145, showed an association with the TRG class and demonstrated a significant impact on the outcome. Conclusion: The pre-treatment identification of responders/NON-responders to nRCT could address patients to a personalized strategy, such as total neoadjuvant therapy (TNT) for responders and upfront surgery for non-responders. The combination of radiomic features and miRNAs expression data from images and biopsy obtained through standard of care has the potential to accelerate the discovery of a noninvasive multimodal approach to predict the cCR after nRCT for LARC

Real-time on-board condition monitoring of train axle bearings

Premature failure of rail axle bearings causes a significant increase in train operating costs and can impact train safety. A new on-board condition monitoring approach provided by Perpetuum Ltd is fitted on passenger trains to provide the operator with real-time information on bearing health. This new technology allows the detection of early bearing damage.This paper reports an initial study to understand the source of vibrations. The final aim of the project is to connect the increasing vibration data to the bearing surface damage, measured with surface profilometr

Mechanisms of HIV-1 Nucleocapsid Protein Inhibition by Lysyl-Peptidyl-Anthraquinone Conjugates

The Nucleocapsid protein NCp7 (NC) is a nucleic acid chaperone responsible for essential steps of the HIV-1 life cycle and an attractive candidate for drug development. NC destabilizes nucleic acid structures and promotes the formation of annealed substrates for HIV-1 reverse transcription elongation. Short helical nucleic acid segments bordered by bulges and loops, such as the Trans-Activation Response element (TAR) of HIV-1 and its complementary sequence (cTAR), are nucleation elements for helix destabilization by NC and also preferred recognition sites for threading intercalators. Inspired by these observations, we have recently demonstrated that 2,6-disubstituted peptidylanthraquinone-conjugates inhibit the chaperone activities of recombinant NC in vitro, and that inhibition correlates with the stabilization of TAR and cTAR stem-loop structures. We describe here enhanced NC inhibitory activity by novel conjugates that exhibit longer peptidyl chains ending with a conserved Nterminal lysine. Their efficient inhibition of TAR/cTAR annealing mediated by NC originates from the combination of at least three different mechanisms, namely, their stabilizing effects on nucleic acids dynamics by threading intercalation, their ability to target TAR RNA substrate leading to a direct competition with the protein for the same binding sites on TAR, and, finally, their effective binding to the NC protein. Our results suggest that these molecules may represent the stepping-stone for the future development of NC-inhibitors capable of targeting the protein itself and its recognition site in RNA

Laser scanning estimation of relative light interception by canopy components in different grapevine training systems

The fractional light interception by different parts of vines trained to various systems was estimated by a modified point-quadrat method using an over-row solar are positioning device equipped with a laser to simulate sunbeam position and angle at any latitude and time of the day. Laser readings were also combined with total vine light interception estimates via a line sensor to calculate the total light intercepted by specific canopy components. At each sampling date (late June and September, corresponding to fruit set and full canopy), type and position of organs were directly detected by the laser beam. Regardless of sampling date, the relative amount of light captured by the renewal-fruiting area (nodes 1 to 6) of simple cordon (SC) and double curtain (GDC) was considerably higher than that of spur-pruned cordon (SPC), whose vegetative area (distal to node 6) received about two-thirds of the incoming light. Relative light interception by main and lateral leaves was rather constant for GDC, thus reflecting the negligible regrowth after topping. By contrast, SC and SPC showed a much stronger response to topping which caused an increase of light interception by laterals (19 % for SC and +21 % for SPC). Frequencies of relative intercepted light by main leaves as a function of node position showed a peak around nodes 6-8, a zone where maximum leaf size is attained in all systems and on all dates. Instead, lateral leaves predominantly exposed to light were within the three basal nodes of the lateral shoots. Estimates of relative and total light for different vine parts at any time during the season as detected by laser scanning can objectively assess important characteristics of grapevine training systems, e.g. cluster and basal node exposure to light

Prevalence of aac(6')-Ib-cr plasmid-mediated and chromosome-encoded fluoroquinolone resistance in Enterobacteriaceae in Italy

The spread of aac(6')-Ib-cr plasmid-mediated quinolone resistance determinants was evaluated in 197 enterobacterial isolates recovered in an Italian teaching hospital. The aac(6')-Ib-cr gene was found exclusively in Escherichia coli strains. The gene was located on a plasmid which presented additional ESBL genes. Most of the clinical strains were clonally related and displayed three point mutations at the topoisomerase level which conferred high resistance to fluoroquinolones

Potential use in the treatment of inflammatory disorders and obesity of selected wild edible plants from Calabria region (Southern Italy)

Abstract The potential role of plants and their metabolites has been recently considered in the search for new well-tolerated anti-arthritic and anti-obesity drugs. This study was designed to assess the potential effectiveness of the methanolic extracts from four wild edible species from Southern Italy, Asparagus officinalis L., Bellis perennis L., Daucus carota L. and Sambucus nigra L. All these plants have a history as anti-rheumatic or anti-arthritic remedies. The chemical constituents were identified through GC–MS and HPTLC analyses and the in vitro antioxidant activity was determined by means of DPPH, ABTS, FRAP-Ferrozine and β-carotene bleaching tests. To assess the anti-inflammatory and anti-arthritic potentials, the capacity to inhibit nitric oxide production in murine macrophage RAW 264.7 cells and protein denaturation was measured. The anti-obesity potential was determined by evaluating the ability of the sample to inhibit pancreatic lipase, a key enzyme for dietary fats absorption. The raw extract of D. carota showed the best inhibitory activity on NO production (IC50 = 45.1 ± 1.0 μg/mL), followed by B. perennis and A. officinalis (IC50 equal to 193.1 ± 3.2 μg/mL and 506.3 ± 5.1 μg/mL, respectively). D. carota induced also inhibitory effects against the heat-induced denaturation of bovine serum albumin (IC50 = 878.7 ± 19.09 μg/mL) and the best lipase inhibitory potential (IC50 = 1.63 ± 0.07 mg/mL). Our findings suggest that this species could be a potential effective therapeutic agent to treat inflammation and arthritis, supporting the traditional popular use of this plant