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

Comparing population trend estimates of migratory birds from breeding censuses and capture data at a spring migration bottleneck

Europe has a well-established network of breeding bird monitoring that is used to produce supranational indices of population trends for many species. However, a comparison of breeding bird censuses with other methods may be beneficial to confirm the validity of such indices. The aim of this study was to assess the value of standardized capture data of migratory birds at migration bottlenecks as an indicator of the effective breeding populations. One limitation to this method is that several populations are co-occurring at these bottlenecks and their catchment areas need to be clearly identified to allow extrapolation of population indices. Here, we used standardized trends in capture numbers of 30 species on the island of Ponza, a migration bottleneck in the central Mediterranean, and compared them to population trends estimated in the putative catchment breeding areas between 2005 and 2016. The catchment areas were identified through the analysis of ring recoveries during the breeding season of birds passing through Ponza. Our results show an agreement between the population trends observed on Ponza and those in the breeding areas in 15 out of 30 species. The correlations were strongest in species with a more robust definition of the catchment areas, that is, species with more than 10 recoveries, and for which the recoveries were most likely of breeding birds. The main reason for disagreement between the two indices in the remaining species might be related to different intensity of sampling in different areas. This issue can be solved by further developing monitoring projects in underrepresented countries, as well as by intensifying monitoring through ringing, both in the breeding grounds and at migration bottlenecks. These results show that spring migration monitoring at bottlenecks has the potential to provide a valuable complement and an independent control of breeding bird surveys, allowing raising early warnings of population declines and contributing to their conservation

"A green sloping surface". Concorso internazionale di idee "PISA CONFERENCE HALL Costruire nella storia" 2017, Start for Talents.

La proposta progettuale si inserisce all'interno dei temi di ricerca riguardanti la costruzione di architetture ipogee, soprattutto all’interno di contesti urbani storicizzati, sviluppati presso l’Università di Pisa, e come continuo dei risultati ottenuti nel PRIN 2007 “Progettare il sottosuolo – creazione di Linee Guida alla progettazione architettonica per il recupero e la valorizzazione del sottosuolo urbano ed extraurbano” e nel PRIN 2009 “Modelli ipogei: il progetto del sottosuolo tra benessere ed architettura”

Short- and long-distance avian migrants differ in exercise endurance but not aerobic capacity

Background: Migratory birds differ markedly in their migration strategies, particularly those performing short- versus long-distance migrations. In preparation for migration, all birds undergo physiological and morphological modifications including enlargement of fat stores and pectoral muscles to fuel and power their flights, as well as cardiovascular and biochemical adjustments that improve lipid and oxygen delivery and uptake by flight muscles. While the magnitude of these changes varies in relation to migration strategy, the consequence of these variations on aerobic performance is unknown. We tested whether the aerobic performance of four Old-world flycatcher species (Muscicapidae) varied according to migration strategy by comparing minimum resting metabolic rates (RMRmin), exercise-induced maximum metabolic rates (MMR), and exercise endurance times of short-distance and long-distance migratory birds. Results: As expected, RMRmin did not vary between short-distance and long-distance migrants but differed between the species within a migration strategy and between sexes. Unexpectedly, MMR did not vary with migration strategy, but MMR and blood haemoglobin content were positively related among the birds tested. Exercise endurance times differed substantially between migration strategies with long-distance migrants sustaining exercise for \u3e 60% longer than short-distance migrants. Blood haemoglobin content had a significant positive effect on endurance among all birds examined. Conclusions: The lack of difference in RMRmin and MMR between long- and short-distance migrants during this stage of migration suggests that the attributes favouring the greater aerobic endurance of long-distance migrants did not come at the expense of increased maintenance costs or require greater aerobic capacity

Direct and Indirect Role of Migratory Birds in Spreading CCHFV and WNV: A Multidisciplinary Study on Three Stop-Over Islands in Italy

The annual movements of migratory birds can contribute to the spread of African ticks and tick-borne pathogens of potential public health concern across Europe. The aim of the study was to investigate their role in the possible introduction of African ticks and tick-borne pathogens into European countries during spring migration. A total of 2344 ticks were collected during three spring seasons from 1079 birds captured on three Italian stop-over islands during their northbound migration. Once identified, each tick was tested by RT-PCR for the presence of Crimean-Congo hemorrhagic fever (CCHFV), West Nile (WNV), and Usutu (USUV) viruses. Moreover, carcasses of birds found dead were collected and tested for the possible presence of WNV and USUV. Results confirmed a higher contribution of trans-Saharan migrants compared to intra-Palearctic ones and the prevalence of African tick species in the sample. CCHFV was detected for the second time in Italy in a Hyalomma rufipes, and WNV was found in two ticks of the same genus, all carried by trans-Saharan birds. WNV lineage 1 was also found in the organs of a Garden warbler. These results confirm the role of migratory birds in carrying African ticks, as well as viruses of zoonotic importance, from Africa into Europe

Gaia Data Release 1 The Cepheid and RR Lyrae star pipeline and its application to the south ecliptic pole region

Context. The European Space Agency spacecraft Gaia is expected to observe about 10 000 Galactic Cepheids and over 100 000 Milky Way RR Lyrae stars (a large fraction of which will be new discoveries), during the five-year nominal lifetime spent scanning the whole sky to a faint limit of G = 20:7 mag, sampling their light variation on average about 70 times. Aims. We present an overview of the Specific Objects Study (SOS) pipeline developed within the Coordination Unit 7 (CU7) of the Data Processing and Analysis Consortium (DPAC), the coordination unit charged with the processing and analysis of variable sources observed by Gaia, to validate and fully characterise Cepheids and RR Lyrae stars observed by the spacecraft. The algorithms developed to classify and extract information such as the pulsation period, mode of pulsation, mean magnitude, peak-to-peak amplitude of the light variation, subclassification in type, multiplicity, secondary periodicities, and light curve Fourier decomposition parameters, as well as physical parameters such as mass, metallicity, reddening, and age (for classical Cepheids) are briefly described. Methods. The full chain of the CU7 pipeline was run on the time series photometry collected by Gaia during 28 days of ecliptic pole scanning law (EPSL) and over a year of nominal scanning law (NSL), starting from the general Variability Detection, general Characterization, proceeding through the global Classification and ending with the detailed checks and typecasting of the SOS for Cepheids and RR Lyrae stars (SOS Cep&RRL).We describe in more detail how the SOS Cep&RRL pipeline was specifically tailored to analyse Gaia’s G-band photometric time series with a south ecliptic pole (SEP) footprint, which covers an external region of the Large Magellanic Cloud (LMC), and to produce results for confirmed RR Lyrae stars and Cepheids to be published in Gaia Data Release 1 (Gaia DR1). Results. G-band time series photometry and characterisation by the SOS Cep&RRL pipeline (mean magnitude and pulsation characteristics) are published in Gaia DR1 for a total sample of 3194 variable stars (599 Cepheids and 2595 RR Lyrae stars), of which 386 (43 Cepheids and 343 RR Lyrae stars) are new discoveries by Gaia. All 3194 stars are distributed over an area extending 38 degrees on either side from a point oset from the centre of the LMC by about 3 degrees to the north and 4 degrees to the east. The vast majority are located within the LMC. The published sample also includes a few bright RR Lyrae stars that trace the outer halo of the Milky Way in front of the LMC.36 pages, 45 figures, 4 tables. Accepted for publication on A&A. A full version with higher resolution figures and the complete atlas of light curves can be found at this link: http://davide2.bo.astro.it/~felix/ The manuscript is part of the series of DPAC papers that accompany Gaia DR1status: publishe

Textiles

Ce numéro de Perspective, conçu en partenariat avec le Mobilier national et les Manufactures des Gobelins, de Beauvais et de la Savonnerie, est consacré aux textiles à différentes époques et en différents lieux de production et d’usage, comme à la notion de textilité : les avatars conceptuels, métaphoriques et matériels de l’ornement, du tissage ou encore de l’étoffe. Les articles offrent un éclairage sur les recherches récentes en archéologie, sur les textiles islamiques médiévaux, et en ce qui concerne l’architecture des XIXe et XXe siècles et le renouveau de la tapisserie à la même époque. Une Tribune, un Entretien et des débats sur la place du musée dans l’histoire du textile, la circulation des motifs et des savoir-faire à l’époque moderne ou encore la dimension textile de l’art conceptuel dans les années 1970, complètent ce numéro en phase avec le dynamisme et l’éclectisme de la recherche dans ce domaine si stimulant. Des notes plus brèves font état de recherches singulières sur les voiles ou les drapés… et, plus généralement, sur les textiles du Moyen Âge, les vêtements en Chine et au Pérou, ou encore les estampes habillées des XVIIe et XVIIIe siècles européens. Ce numéro est en vente sur le site du Comptoir des presses d'universités. Comité de rédaction du volume Marc Bayard, Marion Boudon-Machuel, Catherine Breniquet, Pascale Charron, Rossella Froissart, Charlotte Guichard, Rémi Labrusse, Philippe Malgouyres, Sara Martinetti, Nicole Pellegrin, Katie Scott, Philippe Sénéchal, Merel van Tilburg, Tristan Weddige