Star-planet interactions: I. Stellar rotation and planetary orbits

Context. As a star evolves, the planet orbits change with time due to tidal interactions, stellar mass losses, friction and gravitational drag forces, mass accretion and evaporation on/by the planet. Stellar rotation modifies the structure of the star and therefore the way these different processes occur. Changes of the orbits, at their turn, have an impact on the rotation of the star. Aims. Models accounting in a consistent way for these interactions between the orbital evolution of the planet and the evolution of the rotation of the star are still missing. The present work is a first attempt to fill this gap. Methods. We compute the evolution of stellar models including a comprehensive treatment of rotational effects together with the evolution of planetary orbits, so that the exchanges of angular momentum between the star and the planetary orbit are treated in a self-consistent way. The evolution of the rotation of the star accounts for the angular momentum exchange with the planet and also follows the effects of the internal transport of angular momentum and chemicals. Results. We show that rotating stellar models without tidal interactions can well reproduce the surface rotations of the bulk of the red giants. However, models without any interactions cannot account for fast rotating red giants in the upper part of the red giant branch, where, such models, whatever the initial rotation considered on the ZAMS, always predict very low velocities. For those stars some interaction with a companion is highly probable and the present rotating stellar models with planets confirm that tidal interaction can reproduce their high surface velocities. We show also that the minimum distance between the planet and the star on the ZAMS that will allow the planet to avoid engulfment and survive is decreased around faster rotating stars. [abridged]Comment: 14 pages, abstract abridged for arXiv submission, accepted for publication in Astronomy & Astrophysic

Toward NZEB by optimizing HVAC system configuration in different climates

Finding the most appropriate matching between envelope features and HVAC system configurations in function of different climates results fundamental for minimizing buildings’ energy consumptions. The research aims at presenting the most energy-performing HVAC system configurations for high-performing buildings. Different configurations were modeled for new non-residential Reference Buildings in seven European cities, using dynamic simulation software EnergyPlus and some evaluation tools specifically set to emulate the energy performance of some specific HVAC technologies. Finally, the results obtained were compared in order to outline some conclusions, useful as guidelines for optimizing the choice of HVAC systems in function of climate conditions

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors

Transcriptomic analysis of the polyploid Adriatic sturgeon (Acipenser naccarii)

Sturgeons are a group of Condrostean fishes with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent a luxury delicacy and are one of the most valuable foods of animal origin. The intense exploitation of wild stocks for the harvesting of caviar caused in the last decades a dramatic decline of their distribution and abundance leading, in 2010, the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, selective farming of females would increase the economical profits and the characterisation of genes involved in sex determination becomes a major issue. The 454 sequencing of four normalised cDNA libraries from gonads and brain of A naccarii and A. stellatus, one male and one female full-sib per species, yielded 182,066 and 167,776 reads for A. naccarii which after a strict quality control were iteratively assembled together, giving more then 55,000 high quality Expressed sequence tags (ESTs). A total of 184,374 and 169,286 raw reads were instead produced for A. stellaus male and female libraries respectively, resulting in 63,606 ESTs after two round assembly. It was estimated the joint assembly of A. naccarii was able to cover about 80% of its total transcripts expressed in both gonad and brain with a mean contigs coverage of 4X. Similarly 86% transcriptome coverage was achieved by assembling both sex specific libraries of A. stellatus, with 3.6X as mean contig coverage. The Multi-step annotation process finally results in 16% and 15% successfully annotated sequences, with GO terms, respectively in A. naccarii and A. stellatus. Both transcriptomes were screened for 32 sex related genes and highlighted 5 and 2 genes that are potentially specifically expressed in A. naccarii male and female, at the first life stage at which sex is histologically identifiable. The screening in A. stellatus is currently at preliminary stage and further filtering steps are required. Both sturgeon transcriptomes were also compared with those of other fish species for which relevant genomic informations were available. Finally, 21,791 putative EST-linked Single Nucleotide Polymorphisms (SNPs) and 5,295 Single Sequence Repeats (SSRs) were identified in A. naccarii, while 15,449 and 5,696 were putatively classified in A. stellatus assembly. This study represents the first characterisation of transcriptomes from two high endangered sturgeon species. Most of the information acquired for A. naccarii were well organised into the public database AnaccariiBase, freely available at http://compgen.bio.unipd.it/anaccariibase/, while the information obtained for A stellatus will be released soon. This study represents a precious source of information for more focussed studies aimed at characterising or comparing genes, deciphering molecular mechanisms or genetic pathways in this group of species, or discovering hundreds of EST-linked markers with several possible applications in sturgeon conservation.Gli storioni sono un gruppo di pesci Condrostei, di elevato interesse evoluzionistico, economico e di conservazione. Le uova di questi fossili viventi costituiscono uno degli alimenti di origine animale più preziosi sul mercato. L'intenso sfruttamento delle popolazioni selvatiche per la raccolta del caviale ha causato, negli ultimi decenni, un calo drammatico della loro distribuzione ed abbondanza che ha portato, nel 2010, l'Unione Internazionale per la Conservazione della Natura ad indicarli come il gruppo di specie a maggior rischio di estinzione. Come diretta conseguenza, sono stati compiuti sforzi notevoli, in tutto il mondo, per sviluppare programmi finalizzati alla produzione di caviale via acquacoltura. In questo contesto, l'allevamento selettivo delle femmine aumenterebbe i profitti economici e la caratterizzazione dei geni coinvolti nella determinazione del sesso, diventa decisiva. Il sequenziamento 454 di quattro librerie di cDNA normalizzate, costruite a partire da gonadi e cervello di A naccarii e A. stellatus, un maschio ed una femmina (fratelli) per specie, ha prodotto 182,066 e 167,776 reads grezze rispettivamente per i due sessi di A naccarii, che dopo un severo controllo di qualità sono state assemblate insieme attraverso un processo iterativo, risultando in più di 55,000 Expressed Sequence Tags (ESTs) di qualità elevata. Per la specie A. stellatus, invece, sono state prodotte 184,374 reads per la libreria maschile e 169,286 per quella femminile, allineate in 63,606 ESTs dopo due giri di assemblaggio. E’ stato stimato che, l’assemblaggio di A. naccarii contenga i tag di circa l’80% dei trascritti totali espressi in gonadi e cervello, in questa specie, con una copertura media dei contigs pari a 4X. La copertura del trascrittoma di A. stellatus è stata stimata in circa l’86%, con 3.6X come media di copertura dei contigs. Il processo di annotazione multi-fase, ha portato ad annotare correttamente, con termini GO circa 16% ed il 15% delle sequenze, rispettivamente in A. naccarii ed A. stellatus. Entrambi i trascrittomi sono stati interrogati alla ricerca di 32 geni legati al sesso e sono stati evidenziati 5 geni potenzialmente espressi in modo specifico nel maschio e 2 nella femmina di A. naccarii, nel primo stadio di sviluppo, in cui il sesso è istologicamente identificabile. La ricerca nel trascrittoma di A. stellatus è attualmente preliminare e sono necessarie ulteriori fasi di filtraggio. Entrambi i trascrittomi sono stati confrontati con quelli di altre specie di pesci, per la quali erano disponibili rilevanti informazioni genomiche. Infine, 21.791 putativi Single Nucleotide Polymorphisms (SNPs) e 5.295 Single Sequence Repeats (SSR) EST-linked sono stati identificati in A. naccarii, mentre 15.449 e 5.696 sono stati rispettivamente classificati nell’assemblaggio di A. stellatus. Questo studio rappresenta la prima caratterizzazione dei trascrittomi di due specie di storione ad elevato rischio di estinzione. Gran parte delle informazioni acquisite per la specie A. naccarii sono state organizzati all’interno della banca dati pubblica AnaccariiBase, liberamente disponibile all’indirizzo http://compgen.bio.unipd.it/anaccariibase/, mentre le informazioni ottenute per A stellatus saranno rilasciate al più presto. Questa analisi rappresenta una preziosa fonte di informazioni per ulteriori studi più mirati, volti a caratterizzare o confrontare geni, a decifrare i meccanismi molecolari o le vie genetiche in questo gruppo di specie, o a scoprire centinaia di marcatori associati ad ESTs per diverse applicazioni nella conservazione dello storione

Transcriptomic analysis of the polyploid Adriatic sturgeon (Acipenser naccarii)

Sturgeons are a group of Condrostean fishes with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent a luxury delicacy and are one of the most valuable foods of animal origin. The intense exploitation of wild stocks for the harvesting of caviar caused in the last decades a dramatic decline of their distribution and abundance leading, in 2010, the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, selective farming of females would increase the economical profits and the characterisation of genes involved in sex determination becomes a major issue. The 454 sequencing of four normalised cDNA libraries from gonads and brain of A naccarii and A. stellatus, one male and one female full-sib per species, yielded 182,066 and 167,776 reads for A. naccarii which after a strict quality control were iteratively assembled together, giving more then 55,000 high quality Expressed sequence tags (ESTs). A total of 184,374 and 169,286 raw reads were instead produced for A. stellaus male and female libraries respectively, resulting in 63,606 ESTs after two round assembly. It was estimated the joint assembly of A. naccarii was able to cover about 80% of its total transcripts expressed in both gonad and brain with a mean contigs coverage of 4X. Similarly 86% transcriptome coverage was achieved by assembling both sex specific libraries of A. stellatus, with 3.6X as mean contig coverage. The Multi-step annotation process finally results in 16% and 15% successfully annotated sequences, with GO terms, respectively in A. naccarii and A. stellatus. Both transcriptomes were screened for 32 sex related genes and highlighted 5 and 2 genes that are potentially specifically expressed in A. naccarii male and female, at the first life stage at which sex is histologically identifiable. The screening in A. stellatus is currently at preliminary stage and further filtering steps are required. Both sturgeon transcriptomes were also compared with those of other fish species for which relevant genomic informations were available. Finally, 21,791 putative EST-linked Single Nucleotide Polymorphisms (SNPs) and 5,295 Single Sequence Repeats (SSRs) were identified in A. naccarii, while 15,449 and 5,696 were putatively classified in A. stellatus assembly. This study represents the first characterisation of transcriptomes from two high endangered sturgeon species. Most of the information acquired for A. naccarii were well organised into the public database AnaccariiBase, freely available at http://compgen.bio.unipd.it/anaccariibase/, while the information obtained for A stellatus will be released soon. This study represents a precious source of information for more focussed studies aimed at characterising or comparing genes, deciphering molecular mechanisms or genetic pathways in this group of species, or discovering hundreds of EST-linked markers with several possible applications in sturgeon conservation.Gli storioni sono un gruppo di pesci Condrostei, di elevato interesse evoluzionistico, economico e di conservazione. Le uova di questi fossili viventi costituiscono uno degli alimenti di origine animale più preziosi sul mercato. L'intenso sfruttamento delle popolazioni selvatiche per la raccolta del caviale ha causato, negli ultimi decenni, un calo drammatico della loro distribuzione ed abbondanza che ha portato, nel 2010, l'Unione Internazionale per la Conservazione della Natura ad indicarli come il gruppo di specie a maggior rischio di estinzione. Come diretta conseguenza, sono stati compiuti sforzi notevoli, in tutto il mondo, per sviluppare programmi finalizzati alla produzione di caviale via acquacoltura. In questo contesto, l'allevamento selettivo delle femmine aumenterebbe i profitti economici e la caratterizzazione dei geni coinvolti nella determinazione del sesso, diventa decisiva. Il sequenziamento 454 di quattro librerie di cDNA normalizzate, costruite a partire da gonadi e cervello di A naccarii e A. stellatus, un maschio ed una femmina (fratelli) per specie, ha prodotto 182,066 e 167,776 reads grezze rispettivamente per i due sessi di A naccarii, che dopo un severo controllo di qualità sono state assemblate insieme attraverso un processo iterativo, risultando in più di 55,000 Expressed Sequence Tags (ESTs) di qualità elevata. Per la specie A. stellatus, invece, sono state prodotte 184,374 reads per la libreria maschile e 169,286 per quella femminile, allineate in 63,606 ESTs dopo due giri di assemblaggio. E’ stato stimato che, l’assemblaggio di A. naccarii contenga i tag di circa l’80% dei trascritti totali espressi in gonadi e cervello, in questa specie, con una copertura media dei contigs pari a 4X. La copertura del trascrittoma di A. stellatus è stata stimata in circa l’86%, con 3.6X come media di copertura dei contigs. Il processo di annotazione multi-fase, ha portato ad annotare correttamente, con termini GO circa 16% ed il 15% delle sequenze, rispettivamente in A. naccarii ed A. stellatus. Entrambi i trascrittomi sono stati interrogati alla ricerca di 32 geni legati al sesso e sono stati evidenziati 5 geni potenzialmente espressi in modo specifico nel maschio e 2 nella femmina di A. naccarii, nel primo stadio di sviluppo, in cui il sesso è istologicamente identificabile. La ricerca nel trascrittoma di A. stellatus è attualmente preliminare e sono necessarie ulteriori fasi di filtraggio. Entrambi i trascrittomi sono stati confrontati con quelli di altre specie di pesci, per la quali erano disponibili rilevanti informazioni genomiche. Infine, 21.791 putativi Single Nucleotide Polymorphisms (SNPs) e 5.295 Single Sequence Repeats (SSR) EST-linked sono stati identificati in A. naccarii, mentre 15.449 e 5.696 sono stati rispettivamente classificati nell’assemblaggio di A. stellatus. Questo studio rappresenta la prima caratterizzazione dei trascrittomi di due specie di storione ad elevato rischio di estinzione. Gran parte delle informazioni acquisite per la specie A. naccarii sono state organizzati all’interno della banca dati pubblica AnaccariiBase, liberamente disponibile all’indirizzo http://compgen.bio.unipd.it/anaccariibase/, mentre le informazioni ottenute per A stellatus saranno rilasciate al più presto. Questa analisi rappresenta una preziosa fonte di informazioni per ulteriori studi più mirati, volti a caratterizzare o confrontare geni, a decifrare i meccanismi molecolari o le vie genetiche in questo gruppo di specie, o a scoprire centinaia di marcatori associati ad ESTs per diverse applicazioni nella conservazione dello storione

Fear of Cockroaches Questionnaire

The aim of this study was to validate the Fear of Cockroaches Questionnaire (FCQ) in general Italian population. The FCQ is an 18-item self-report questionnaire assessing fear of cockroaches. It was translated in Italian and modified as a cockroach adaption of the Fear of Spiders Questionnaire. Data obtained from 329 (mean age 24.21 \ub1 4.08 years) undergraduates revealed that the FCQ allowed discrimination between high fear and low fear subjects. Exploratory Factor Analysis revealed a mono-factorial structure. The FCQ has a good test-retest reliability (r=.95) and a good internal consistency (\u3b1=.95). The FCQ correlates with other measures related to fear of small animals, showing good concurrent validity. Finally, the FCQ score seems to be a measure of the fear free from disgust and anxiety caused by the cockroach exposition

Fear of Cockroaches Questionnaire

The aim of this study was to validate the Fear of Cockroaches Questionnaire (FCQ) in general Italian population. The FCQ is an 18-item self-report questionnaire assessing fear of cockroaches. It was translated in Italian and modified as a cockroach adaption of the Fear of Spiders Questionnaire. Data obtained from 329 (mean age 24.21 ± 4.08 years) undergraduates revealed that the FCQ allowed discrimination between high fear and low fear subjects. Exploratory Factor Analysis revealed a mono-factorial structure. The FCQ has a good test-retest reliability (r=.95) and a good internal consistency (α=.95). The FCQ correlates with other measures related to fear of small animals, showing good concurrent validity. Finally, the FCQ score seems to be a measure of the fear free from disgust and anxiety caused by the cockroach exposition

The Fear of Cockroaches Questionnaire (FCQ)

The aim of this study was to validate the Fear of Cockroaches Questionnaire (FCQ) in general Italian population. The FCQ is an 18-item self-report questionnaire assessing fear of cockroaches. It was translated in Italian and modified as a cockroach adaption of the Fear of Spiders Questionnaire. Data obtained from 329 (mean age 24.21 ± 4.08 years) undergraduates revealed that the FCQ allowed discrimination between high fear and low fear subjects. Exploratory Factor Analysis revealed a mono-factorial structure. The FCQ has a good test-retest reliability (r=0.95) and a good internal consistency (α=0.95). The FCQ correlates with other measures related to fear of small animals, showing good concurrent validity. Finally, the FCQ score seems to be a measure of the fear free from disgust and anxiety caused by the cockroach exposition

make_repeated_assembly

Python script to perform iterative assemblies using MIRA 3.2 assemble

Data from: "Transcriptomic resources for the critically endangered stellate sturgeon Acipenser stellatus" in Genomic Resources Notes accepted 1 April 2015 – 31 May 2015

This article documents the public availability of transcriptomic resources of the non-model and critically endangered starlet sturgeon Acipenser stellatus