Why genes overlap in viruses

The genomes of most virus species have overlapping genes\u2014two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length

Vulnerabilità del territorio vesuviano a fenomeni meteorologici attraverso l’analisi quantitativa di fattori geologici ed antropici.

In questo lavoro viene descritta l’applicazione al territorio vesuviano di una metodologia di analisi geomorfologico-quantitativa multiparametrica da DTM (Digital Terrain Model) di dettaglio (5x5m) in ambiente GIS, utilizzando procedure di analisi e tecniche di valutazione della vulnerabilità a fenomeni meteorologici che tengano conto della complessità dell’assetto geologico, geomorfologico, urbanistico ed economico dell’area. Il risultato del lavoro è stato la realizzazione di mappe di vulnerabilità idrogeologica prodotte tenendo conto delle mutue relazioni tra fattori territoriali ed antropici. L’obiettivo di questo studio è stato sviluppare un sistema di analisi utile alla valutazione del rischio idrogeologico ed al suo controllo e prevenzione, considerato che negli ultimi anni si e’ assistito ad incrementi rilevanti e disordinati dell’urbanizzazione nell’area vesuviana, per la maggior parte abusiva e con forti carenze strutturali, che, unitamente ad eventi piovosi particolarmente intensi nonché alle caratteristiche geologico-geomorfologiche del territorio, hanno causato eventi franosi parossistici come quelli dei comuni di Sarno, Episcopia e Bracigliano. L’area di indagine, rappresentata dal complesso vulcanico del Somma–Vesuvio in Campania, è densamente abitata (2500 abitanti per km2) ed oltre ad essere ad alto rischio vulcanico è anche esposta ad alto rischio idrogeologico come dimostrato dalle ripetute esondazioni disastrose fin dall’epoca storica (Accardo et al., 1981; Catenacci et al., 1992). La conoscenza dell’assetto geologico e geomorfologico del complesso Somma-Vesuvio è necessaria per una corretta individuazione dei parametri utili per questo studio. Un esempio è quello della caratterizzazione dei versanti del vulcano, fattore di notevole importanza per la valutazione del rischio idrogeologico, sia per la pendenza che per le loro caratteristiche morfologiche superficiali. Il primo parametro geomorfologico adottato per l’applicazione della metodologia (Tagil and Jenness, 2008) è stato l’indice di posizione topografica (TPI, Topographic Position Index) che ha consentito una classificazione del paesaggio sia in base alla distribuzione areale delle pendenze (slope position) che in classi uniformi di paesaggio (landform classes). La classificazione finale è stata adeguata al particolare paesaggio oggetto di studio, che è di tipo vulcanico. L’analisi della vulnerabilità è stata condotta tenendo conto della permeabilità del suolo e dei dati pluviometrici in quanto possibili fattori predisponenti al dissesto idrogeologico. Il GIS ha rappresentato lo strumento necessario per gestire dati di tipo diverso ed effettuarne l’analisi e la rappresentazione congiunta. Il software utilizzato è stato ArcGis (9.3) e attraverso l’applicazione Spatial Analyst è stato possibile estrarre dati ed informazioni nuove che non sarebbe stato possibile ottenere con l’analisi geomorfologica classica da cartografia su supporto cartaceo. La realizzazione di mappe di vulnerabilità idrogeologica dell’area del Somma-Vesuvio, ottenute stabilendo le relazioni tra i vari fattori incidenti con l’ausilio di metodologie note (Cherubini et al., 2006), ha rappresentato uno dei risultati del lavoro. Le interrelazioni tra i vari fattori (geologico, geomorfologico, idrogeologico, urbanistico) mostrate dalle mappe prodotte costituiscono uno strumento indispensabile per monitorare il rischio territoriale e per poter intervenire laddove venga superata una soglia di rischio ritenuta accettabile

Analysis of Actin FLAP Dynamics in the Leading Lamella

BACKGROUND. The transport of labeled G-actin from the mid-lamella region to the leading edge in a highly motile malignant rat fibroblast line has been studied using fluorescence localization after photobleaching or FLAP, and the transit times recorded in these experiments were so fast that simple diffusion was deemed an insufficient explanation (see Zicha et al., Science, v. 300, pp. 142-145 [1]). METHODOLOGY/PRINCIPAL FINDINGS. We re-examine the Zicha FLAP experiments using a two-phase reactive interpenetrating flow formalism to model the cytoplasm and the transport dynamics of bleached and unbleached actin. By allowing an improved treatment of effects related to the retrograde flow of the cytoskeleton and of the geometry and finite thickness of the lamella, this new analysis reveals a mechanism that can realistically explain the timing and the amplitude of all the FLAP signals observed in [1] without invoking special transport modalities. CONCLUSIONS/SIGNIFICANCE. We conclude that simple diffusion is sufficent to explain the observed transport rates, and that variations in the transport of labeled actin through the lamella are minor and not likely to be the cause of the observed physiological variations among different segments of the leading edge. We find that such variations in labeling can easily arise from differences and changes in the microscopic actin dynamics inside the edge compartment, and that the key dynamical parameter in this regard is the so-called "dilatation rate" (the velocity of cytoskeletal retrograde flow divided by a characteristic dimension of the edge compartment where rapid polymerization occurs). If our dilatation hypothesis is correct, the transient kinetics of bleached actin relocalization constitute a novel and very sensitive method for probing the cytoskeletal dynamics in leading edge micro-environments which are otherwise very difficult to directly interrogate.Whitaker biomedical engineering research grant (RG-02-0714); National Institutes of Health (RO1 GM7200

Hyaluronic acid injections in post-enucleation or evisceration socket syndrome: a case series

Background: One of the primary goals of enucleation and evisceration surgery is the restoration of an adequate orbital volume through the use of appropriately sized alloplastic or autogenous tissues. In patients inadequately treated, post-enucleation or evisceration socket syndrome occurs. Fillers are an ideal alternative for eyelid and eyebrow arcade volume enhancement since their injection is easily performed in an outpatient setting avoiding several complications. The aim of this study is to report the use of hyaluronic acid (HA) fillers to treat volume deficits of the upper and lower eyelids, projecting the brow arcade and reducing the asymmetry. Methods: Thirteen patients (2 male, 11 female, mean age 32.7 years) were treated from June 2012 to May 2020. Non-surgical treatment by HA filler injection for aesthetic rehabilitation of deep superior sulcus, inferior tear trough deformity, and scleral show was performed. Results: No complications as orbital-ache and/or vasovagal response were reported during the injections. Minor complications such as light swelling at the site of injection, self-resolved within 2 days, were recorded. Stable results were observed at follow-ups. In two cases, two successive treatments were required at 3 and 6 years from the first injection. Conclusions: Hyaluronic acid fillers offer a versatile and safe method for replacing soft tissue lost from the upper eyelid/brow complex in cases of post-enucleation or evisceration socket syndrome. Level of evidence: Level IV, therapeutic study

Mapping hydrothermal and supergene alteration zones associated with carbonate-hosted Zn-Pb deposits by using PRISMA satellite imagery supported by field-based hyperspectral data, mineralogical and geochemical analysis

Delineating hydrothermal alteration and supergene caps is fundamental for mineral exploration of sulfide ores. The aim of this study is to apply a multi-scale workflow based on hyperspectral remote and proximal sensing data in order to delineate hydrothermal dolomitization and supergene alteration associated with the Mississippi Valley-Type Zn-Pb(-Ag) deposit of Jabali (Western Yemen). The area was investigated through hyperspectral images derived from the new launched Italian Space Agency's PRISMA satellite, which has a higher spectral resolution compared to multispectral sensors and covers the mineral-diagnostic wavelength regions (such as the 2100 nm to 2300 nm range) with a Signal to Noise Ratio (SNR) ≥ 100. Spectral mineral maps were produced through the band ratios method using specific feature extraction indices applied to the hyperspectral satellite data. The results were validated by using Visible Near InfraRed (VNIR) to Short Wave InfraRed (SWIR) reflectance spectra, mineralogical (XRPD) and geochemical (ICP-ES/MS) analyses on rock samples collected in the Jabali area. The dolomites footprint was mapped using a PRISMA Level 2C image, by enhancing the spectral differences between limestones and dolomites in the SWIR-2 region (major features centered at 2340 nm and 2320 nm, respectively). Gossans were detected due to the Fe3+ absorption band in the VNIR region at 900 nm. The Zn-Pb mineralized area, extended for approximately 25 km2, was thus identified by recognizing gossan occurrences in dolomites. The study demonstrates that the PRISMA satellite is effective in identifying Zn-Pb mineralized outcrops in sedimentary basins

COVID-19 Outbreak and Physical Activity in the Italian Population : A Cross-Sectional Analysis of the Underlying Psychosocial Mechanisms

Italy is one of the first European epicenters of the COVID-19 pandemic. In attempts to hinder the spread of the novel coronavirus disease, Italian government hardened protective measures, from quarantine to lockdown, impacting millions of lives dramatically. Amongst the enacted restrictions, all non-essential activities were prohibited as well as all outdoor activities banned. However, at the first spur of the outbreak, for about a dozen of days, physical and sports activities were permitted, while maintaining social distancing. In this timeframe, by administering measures coming from self-determination theory and theory of planned behavior and anxiety state, in an integrated approach, we investigated the prevalence of these activities by testing, via a Structural Equation Model, the influence of such psychosocial variables on the intention to preserve physical fitness during the healthcare emergency. Through an adequate fit of the hypothesized model and a multi-group analysis, we compared the most COVID-19 hit Italian region \u2013 Lombardy \u2013 to the rest of Italy, finding that anxiety was significantly higher in the Lombardy region than the rest of the country. In addition, anxiety negatively influenced the intention to do physical activity. Giving the potential deleterious effects of physical inactivity due to personal restrictions, these data may increase preparedness of public health measures and attractiveness of recommendations, including on the beneficial effects of exercise, under circumstances of social distancing to control an outbreak of a novel infectious disease

Bosentan and macitentan prevent the endothelial-to-mesenchymal transition (EndoMT) in systemic sclerosis: in vitro study.

Background: Systemic sclerosis (SSc) is characterized by early vascular abnormalities and subsequent fibroblast activation to myofibroblasts, leading to fibrosis. Recently, endothelial-to-mesenchymal transition (EndoMT), a complex biological process in which endothelial cells lose their specific markers and acquire a mesenchymal or myofibroblastic phenotype, has been reported in SSc. In the present study, we evaluated the ability of endothelin-1 (ET-1) dual receptor antagonists bosentan (BOS) and macitentan (MAC) to antagonize EndoMT in vitro. Methods: Ten women with limited SSc were enrolled. They underwent double skin biopsy (affected and nonaffected skin). Fibroblasts and microvascular endothelial cells (MVECs) were isolated from biopsies. We performed mono- or coculture of MVECs (isolated from nonaffected skin) with fibroblasts (isolated from affected skin and stimulated with ET-1 and transforming growth factor beta [TGF-\u3b2]). In cocultures, the MVEC layer was left undisturbed or was preincubated with BOS or MAC. After 48 h of coculture, MVECs were analyzed for their tube formation ability and for messenger RNA and protein expression of different vascular (CD31, vascular endothelial growth factor-A [VEGF-A], VEGF-A165b) and profibrotic (alpha-smooth muscle actin [\u3b1-SMA], collagen type I [Col I], TGF-\u3b2) molecules. Results: After 48 h, MVECs showed a reduced tube formation ability when cocultured with SSc fibroblasts. CD31 and VEGF-A resulted in downregulation, while VEGF-A165b, the antiangiogenic isoform, resulted in upregulation. At the same time, mesenchymal markers \u3b1-SMA, Col I, and TGF-\u3b2 resulted in overexpression in MVECs. Tube formation ability was restored when MVECs were preincubated with BOS or MAC, also reducing the expression of mesenchymal markers and restoring CD31 expression and the imbalance between VEGF-A and VEGF-A165b. Conclusions: With this innovative EndoMT in vitro model realized by coculturing nonaffected MVECs with affected SSc fibroblasts, we show that the presence of a myofibroblast phenotype in the fibroblast layer, coupled with an ET-1-TGF-\u3b2 synergic effect, is responsible for EndoMT. BOS and MAC seem able to antagonize this phenomenon in vitro, confirming previous evidence of endothelium-derived fibrosis in SSc and possible pharmacological interferenc

Investigations of primary and secondary particulate matter of different wood combustion appliances with a high-resolution time-of-flight aerosol mass spectrometer

A series of photo-oxidation smog chamber experiments were performed to investigate the primary emissions and secondary aerosol formation from two different log wood burners and a residential pellet burner under different burning conditions: starting and flaming phase. Emissions were sampled from the chimney and injected into the smog chamber leading to primary organic aerosol (POA) concentrations comparable to ambient levels. The composition of the aerosol was measured by an Aerodyne high resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) and black carbon (BC) instrumentation. The primary emissions were then exposed to xenon light to initiate photo-chemistry and subsequent secondary organic aerosol (SOA) production. After correcting for wall losses, the average increase in organic matter (OM) concentrations by SOA formation for the starting and flaming phase experiments with the two log wood burners was found to be a factor of 4.1±1.4 after five hours of aging. No SOA formation was observed for the stable burning phase of the pellet burner. The startup emissions of the pellet burner showed an increase in OM concentration by a factor of 3.3. Including the measured SOA formation potential, average emission factors of BC+POA+SOA, calculated from CO<sub>2</sub> emission, were found to be in the range of 0.04 to 3.9 g/kg wood for the stable burning pellet burner and an old log wood burner during startup respectively. SOA contributed significantly to the ion C<sub>2</sub>H<sub>4</sub>O<sub>2</sub><sup>+</sup> at mass to charge ratio <i>m/z</i> 60, a commonly used marker for primary emissions of wood burning. This contribution at <i>m/z</i> 60 can overcompensate for the degradation of levoglucosan leading to an overestimation of the contribution of wood burning or biomass burning to the total OM. The primary organic emissions from the three different burners showed a wide range in O:C atomic ratio (0.19−0.60) for the starting and flaming conditions, which also increased during aging. Primary wood burning emissions have a rather low relative contribution at <i>m/z</i> 43 (<i>f</i> 43) to the total organic mass spectrum. The non-oxidized fragment C<sub>3</sub>H<sub>7</sub><sup>+</sup> has a considerable contribution at <i>m/z</i> 43 for the fresh OA with an increasing contribution of the oxygenated ion C<sub>2</sub>H<sub>3</sub>O<sup>+</sup> during aging. After five hours of aging, the OA has a rather low C<sub>2</sub>H<sub>3</sub>O<sup>+</sup> signal for a given CO<sub>2</sub><sup>+</sup> fraction, possibly indicating a higher ratio of acid to non-acid oxygenated compounds in wood burning OA compared to other oxygenated organic aerosol (OOA)

A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat

In Triticeae endosperm (e.g. wheat and barley), starch granules have a bimodal size distribution (with A- and B-type granules) whereas in other grasses the endosperm contains starch granules with a unimodal size distribution. Here, we identify the gene, BGC1 (B-GRANULE CONTENT 1), responsible for B-type starch granule content in Aegilops and wheat. Orthologues of this gene are known to influence starch synthesis in diploids such as rice, Arabidopsis, and barley. However, using polyploid Triticeae species, we uncovered a more complex biological role for BGC1 in starch granule initiation: BGC1 represses the initiation of A-granules in early grain development but promotes the initiation of B-granules in mid grain development. We provide evidence that the influence of BGC1 on starch synthesis is dose dependent and show that three very different starch phenotypes are conditioned by the gene dose of BGC1 in polyploid wheat: normal bimodal starch granule morphology; A-granules with few or no B-granules; or polymorphous starch with few normal A- or B-granules. We conclude from this work that BGC1 participates in controlling B-type starch granule initiation in Triticeae endosperm and that its precise effect on granule size and number varies with gene dose and stage of development

Impact of aftertreatment devices on primary emissions and secondary organic aerosol formation potential from in-use diesel vehicles: results from smog chamber experiments

Diesel particulate matter (DPM) is a significant source of aerosol in urban areas and has been linked to adverse health effects. Although newer European directives have introduced increasingly stringent standards for primary PM emissions, gaseous organics emitted from diesel cars can still lead to large amounts of secondary organic aerosol (SOA) in the atmosphere. Here we present results from smog chamber investigations characterizing the primary organic aerosol (POA) and the corresponding SOA formation at atmospherically relevant concentrations for three in-use diesel vehicles with different exhaust aftertreatment systems. One vehicle lacked exhaust aftertreatment devices, one vehicle was equipped with a diesel oxidation catalyst (DOC) and the third vehicle used both a DOC and diesel particulate filter (DPF). The experiments presented here were obtained from the vehicles at conditions representative of idle mode, and for one car in addition at a speed of 60 km/h. An Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) was used to measure the organic aerosol (OA) concentration and to obtain information on the chemical composition. For the conditions explored in this paper, primary aerosols from vehicles without a particulate filter consisted mainly of black carbon (BC) with a low fraction of organic matter (OM, OM/BC < 0.5), while the subsequent aging by photooxidation resulted in a consistent production of SOA only for the vehicles without a DOC and with a deactivated DOC. After 5 h of aging ~80% of the total organic aerosol was on average secondary and the estimated "emission factor" for SOA was 0.23–0.56 g/kg fuel burned. In presence of both a DOC and a DPF, only 0.01 g SOA per kg fuel burned was produced within 5 h after lights on. The mass spectra indicate that POA was mostly a non-oxidized OA with an oxygen to carbon atomic ratio (O/C) ranging from 0.10 to 0.19. Five hours of oxidation led to a more oxidized OA with an O/C range of 0.21 to 0.37