Control of polymorphism in coronene by the application of magnetic fields

Coronene, a polyaromatic hydrocarbon, has been crystallized for the first time in a different polymorph using a crystal growth method that utilizes magnetic fields to access a unit cell configuration that was hitherto unknown. Crystals grown in magnetic field of 1 T are larger, have a different appearance to those grown in zero field and retain their structure in ambient conditions. We identify the new form, beta-coronene, as the most stable at low temperatures. As a result of the new supramolecular configuration we report significantly altered electronic, optical and mechanical properties.Comment: 32 pages, 17 figure

Analysis of the melanocortin receptor 1 (MC1R) gene in Sicilian goat breeds

AbstractMammalian coat colour is mainly determined by the distribution of two different types of melanins: pheomelanin (red/yellow pigments) and eumelanin (black pigments). Their synthesis is regulated by the melanocortin 1 receptor (MC1R/Extension locus) that binds the α-melanocyte-stimulating hormone (α-MSH) and the agouti signalling protein (ASIP, coded by the Agouti locus). In mammals, several studies have reported that loss-of-function mutations in MC1R lead to red/yellow pigmentation, while gain-of-function mutations lead to black/dark colours. Mutations at the Agouti locus exert, in general, epistatic interactions on the Extension locus. In goats, classical genetic studies have indicated that variations at the Agouti locus may be the main source of colour variability within and between breeds, while the effect of the Extension locus on this phenotypic trait has been only partially deduced. In order to better understand the role of the Extension locus on coat colour in this species, here we analysed..

PANI-Based Stacked Ferromagnetic Systems: Electrochemical Preparation and Characterization

In this work, the electropolymerization of polyaniline (PANI) is explored for its action as either a suitable coating or as a substrate for Nickel (Ni) and Magnetite (Fe3O4) surfaces. PANI electropolymerization has been achieved through cyclic voltammetry (CV), potentiostatic and galvanostatic electrochemical methods. The interaction between the obtained surfaces and the ferromagnetic layers (Ni and Fe3O4) has been investigated as a function of the pH of the electrolytic PANI solution, and also a variety of experimental parameters have been optimized in order to achieve the synthesis of PANI coatings (solvent, substrate, concentrations, and cell set-up). Thus, we obtained stable and consistent PANI thick films at the interface of both the nickel and the magnetite ferromagnetic materials

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity

Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels

Nero Siciliano pig: analysis of coat colour affecting genes and perspectives for breed traceability

Nero Siciliano is an autochthonous pig breed reared in the internal areas of Sicily region mainly in the Nebrodi mountains. The animals are usually completely black with a dorsal stripe but a few present white portions mainly in the face or in the fore legs. According to the increased requests of the consumers for local and typical products, meat and cured products of Nero Siciliano pigs are sold at a higher price compared to other pig products. Thus there is the need to guarantee both consumers and the whole Nero Siciliano production chain from possible frauds. The identification and/or use of DNA markers that may be breed specific could make it possible to establish breed traceability and authenticity systems for the products obtained with this local pig breed. Mutations in coat colour genes have been already described and utilized for porcine breed traceability. In this trial we analysed mutations identified in two coat colour affecting genes, the melanocortin 1 receptor (MC1R) and the v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene (KIT), with the aim to characterize the Nero Siciliano pig at these loci and provide useful information to establish authenticity systems for the meat products. Fragment analysis of PCR products and PCRRFLP methods were used to identify the polymorphic sites that can distinguish known alleles at these two loci in 104 Nero Siciliano pigs. Four alleles were identified at the MC1R locus: the two dominant black alleles (ED2, frequency of 0.673; ED1, 0.187), allele EP (0.106) and the recessive e allele (0.034). The results showed that different alleles were observed at this locus, polymorphisms at the MC1R gene cannot be used for product traceability and authentication of this breed. As regards the KIT locus, all the animals were negative for the splice site mutation of exon/intron 17. Thus, meat of Nero Siciliano pigs can be distinguished from meat of white pigs that are positive for this polymorphic site. Moreover, at this locus only 4 pigs showed the 3'-5' duplication breakpoint suggesting that they carried the Ip allele. Studies are in progress to evaluate the effect of this allele on coat colour phenotypes in Nero Siciliano pig

Analysis of melanocortin 1 receptor (MC1R) gene polymorphisms in some cattle breeds: their usefulness and application for breed traceability and authentication of Parmigiano Reggiano cheese

l legame tra un prodotto di origine animale e la razza da cui questo \ue8 originato rappresenta un aspetto importante per la valorizzazione di alcune produzioni. Il maggior prezzo che questi prodotti spuntano sul mercato fa emergere l\u2019esigenza di poter autenticare o tracciare i prodotti mono-razza per smascherare e scoraggiare possibili frodi. A questo scopo sono stati proposti sistemi di analisi del DNA, alcuni dei quali utilizzano marcatori in geni che determinano il colore del mantello, che \ue8 uno dei principali caratteri che differenziano tra di loro le razze. Diverse mutazioni nel gene melanocortin 1 receptor (MC1R) sono gi\ue0 state associate a particolari effetti sul colore del mantello nella specie bovina. In questa ricerca abbiamo studiato la presenza dei principali alleli al locus MC1R, per valutare la possibilit\ue0 di utilizzare questo gene per l\u2019autenticazione e la tracciabilit\ue0 di razza dei prodotti lattiero-caseari. Le mutazioni che permettono di distinguere questi alleli sono state analizzate utilizzando protocolli di PCR-RFLP e PCR-APLP su un totale di 1360 animali appartenenti a 18 razze bovine. Per ognuna delle seguenti razze, Frisona Italiana, Bruna Italiana, Pezzata Rossa Italiana, Jersey, Rendena, Reggiana e Modenese, \ue8 stato possibile analizzare pi\uf9 di 70 animali. L\u2019allele Ed \ue8 stato identificato nella razza Frisona Italiana con una frequenza dello 0,886. L\u2019allele E (nomenclatura che include tutti gli alleli tranne che e, Ed e E1) \ue8 stato identificato con alta frequenza nella Bruna Italiana (0,591), Rendena (0,738), Jersey (0,955) e Modenese (0,961) e con bassa frequenza nella Pezzata Rossa Italiana (0,029). Inoltre, questo allele \ue8 stato osservato nella Rossa Svedese, Rossa Danese, Grigio Alpina, Piemontese, Romagnola, Marchigiana e Chianina. In alcune di queste razze (Bruna Italiana, Rendena, Grigio Alpina, Piemontese, Rossa Svedese e Rossa Danese) \ue8 stato identificato anche l\u2019allele E1. L\u2019allele e \ue8 risultato fissato nella razza Reggiana e quasi fissato nella razza Pezzata Rossa Italiana. Inoltre, con bassa frequenza, \ue8 stato identificato in tutte le altre razze analizzate, tranne che nella Marchigiana. Le differenze osservate tra razze esaminate indicano che, almeno in alcuni casi, \ue8 possibile utilizzare i polimorfismi del gene MC1R per escludere o confermare l\u2019impiego di latte di una determinata razza nella produzione di un prodotto lattiero-caseario. Il caso pi\uf9 interessante \ue8 quello del formaggio Parmigiano Reggiano prodotto con l\u2019uso esclusivo di latte di bovine di razza Reggiana. Infatti, essendo presente in questa razza soltanto l\u2019allele e il rilievo analitico di qualsiasi altro allele nel DNA estratto dal formaggio rivela l\u2019uso di latte proveniente da altre razze. La messa a punto di un metodo PCR-RFLP per l\u2019analisi del DNA estratto da prodotti lattiero caseari, incluso il Parmigiano Reggiano di oltre 24 mesi di stagionatura, rappresenta uno strumento importante per la difesa di questo prodotto mono-razza da eventuali frodi. I risultati ottenuti su 10 forme di formaggio prodotto esclusivamente con latte di bovine di razza Reggiana e su 15 forme di Parmigiano Reggiano commerciale ottenuto senza restrizione della razza di origine del latte hanno mostrato la validit\ue0 del metodo del quale \ue8 stata valutata anche la sensibilit\ue0n cattle, the MC1R gene has been the subject of several studies with the aim to elucidate the biology of coat colour. Then, polymorphisms of this gene have been proposed as tools for breed identification and animal products authentication. As a first step to identify breed specific DNA markers that can be used for the traceability of mono-breed dairy cattle products we investigated, using PCR-RFLP and PCR-APLP protocols, the presence and distribution of some alleles at the MC1R locus in 18 cattle breeds for a total of 1360 animals. For each of seven breeds (Italian Holstein, Italian Brown, Italian Simmental, Rendena, Jersey, Reggiana and Modenese) a large number of animals (>70) was genotyped so the obtained results can be considered with more confidence. Allele Ed was identified only in black pied cattle (Italian Holstein and Black Pied Valdostana). Allele E (this nomenclature includes all alleles except Ed, E1 and e) was observed in Italian Brown, Rendena, Jersey, Modenese, Italian Simmental, Grigio Alpina, Piedmontese, Chianina, Romagnola, Marchigiana, Swedish Red and White and Danish Red. Allele E1 was identified in Italian Brown, Rendena, Grigio Alpina, Piedmontese, Swedish Red and White and Danish Red. The recessive allele e, known to cause red coat colour, was fixed in Reggiana and almost fixed in Italian Simmental. This allele was observed also in Italian Holstein, Italian Brown, Rendena, Jersey and Modenese albeit with low frequency. Moreover, this allele was detected in Valdostana, Pezzata Rossa d\u2019Oropa, Piedmontese, Romagnola, Swedish Red and White, Danish Red, Charoleis and Salers. In the case of the Reggiana breed, which is fixed for allele e, the MC1R locus is highly informative with respect to breeds that carry other alleles or in which allele e is at very low frequency. In theory, using the MC1R locus it is possible to identify the presence of milk from some other breeds in Parmigiano Reggiano cheese labelled as exclusively from the Reggiana breed. This possibility was practically tested by setting up protocols to extract and analyse polymorphisms of the MC1R locus in several dairy products, including Parmigiano Reggiano cheese cured for 30 months. The lower detection limit was estimated to be 5% of non expected DNA. This test can represent a first deterrent against fraud and an important tool for the valorisation and authentication of Parmigiano Reggiano cheese obtained from only Reggiana milk

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Given the relevance of the pig proteome in different studies, including human complex maladies, a statistical validation of the annotation is required for a better understanding of the role of specific genes and proteins in the complex networks underlying biological processes in the animal. Presently, approximately 80% of the pig proteome is still poorly annotated, and the existence of protein sequences is routinely inferred automatically by sequence alignment towards preexisting sequences. In this article, we introduce SUS-BAR, a database that derives information mainly from UniProt Knowledgebase and that includes 26 206 pig protein sequences. In SUS-BAR, 16 675 of the pig protein sequences are endowed with statistically validated functional and structural annotation. Our statistical validation is determined by adopting a cluster-centric annotation procedure that allows transfer of different types of annotation, including structure and function. Each sequence in the database can be associated with a set of statistically validated Gene Ontologies (GOs) of the three main sub-ontologies (Molecular Function, Biological Process and Cellular Component), with Pfam functional domains, and when possible, with a cluster Hidden Markov Model that allows modelling the 3D structure of the protein. A database search allows some statistics demonstrating the enrichment in both GO and Pfam annotations of the pig proteins as compared with UniProt Knowledgebase annotation. Searching in SUS-BAR allows retrieval of the pig protein annotation for further analysis. The search is also possible on the basis of specific GO terms and this allows retrieval of all the pig sequences participating into a given biological process, after annotation with our system. Alternatively, the search is possible on the basis of structural information, allowing retrieval of all the pig sequences with the same structural characteristics

Investigation of SNPs in the ATP1A2, CA3 and DECR1 genes mapped to porcine chromosome 4: analysis in groups of pigs divergent for meat production and quality traits

STUDIO DI TRE GENI (ATP1A2, CA3E DECR1) LOCALIZZATI SUL CROMOSOMA SUINO 4: ANALISIDELLE FREQUENZE ALLELICHE DI SNP IN SUINI ESTREMI PER ALCUNI CARATTERI PRODUTTIVITre geni (ATPase, Na+/K+transporting, \u3b12(+) polypeptide, ATP1A2; carbonic anhydrase III, CA3; 2,4-die-noyl CoA reductase 1, mitochondrial, DECR1), isolati da una libreria a cDNA ottenuta da muscolo scheletri-co di suino, sono stati scelti per questo studio sulla base del ruolo fisiologico della proteina codificata in pro-cessi cellulari e metabolici collegabili in modo diretto o indiretto con alcuni caratteri produttivi. La scelta dei tre geni \ue8 stata anche basata sulla loro localizzazione sul cromosoma 4 dove diversi QTL per caratteri pro-duttivi sono gi\ue0 stati identificati.Nella regione 3\u2019 non tradotta del gene CA3\ue8 stato identificato, mediante analisi SSCP, un polimorfismo bial-lelico. Il sequenziamento dei due alleli ha permesso di identificare una nuova mutazione puntiforme, che \ue8stata successivamente analizzata mediante PCR-RFLP. Per questo gene \ue8 stato effettuato il mappaggiogenetico sul cromosoma 4 mediante l\u2019analisi della mutazione nei campioni delle famiglie di riferimento delprogetto europeo di mappaggio del genoma suino (PiGMaP). Utilizzando il polimorfismo PCR-RFLP del geneATP1A2, gi\ue0 decritto in un precedente lavoro come SSCP, sono state tipizzate diverse famiglie di riferimen-to PiGMaP ed \ue8 stato confermato il mappaggio genetico di ATP1A2. Utilizzando queste informazioni e quel-le gi\ue0 disponibili per DECR1, per la prima volta, \ue8 stata ottenuta una mappa di linkage del cromosoma 4che comprende tutti e tre i geni analizzati. Il mappaggio genetico dei tre geni \ue8 stato anche confermatomediante tipizzazione di un pannello di ibridi di cellule irradiate (IMpRH 7000 rad).Le frequenze alleliche delle mutazioni identificate nei tre loci sono state studiate in 11 razze suine (LargeWhite Italiana, Landrace Italiana, Duroc Italiana, Landrace Belga, Hampshire, Pi\ue9train, Meishan, CintaSenese, Casertana, Calabrese and Nero Siciliano) per un totale di 272 animali. Inoltre, come approccio ini-ziale per poi scegliere i geni da analizzare in futuri studi di associazione, abbiamo confrontato le frequenzealleliche di mutazioni puntiformi per questi tre loci in gruppi di suini di razza Large White Italiana e DurocItaliana, analizzando animali con valori degli indici genetici estremi e divergenti per alcuni caratteri produt-tivi (accrescimento, spessore lardo dorsale, tagli magri e grasso intermuscolare visibile). Per il gene CA3 \ue8stata osservata una differenza nella distribuzione delle frequenze alleliche (P< 0,05) per i due caratteri taglimagri (nella razza Large White Italiana) e grasso intermusculare visibile (nella razza Duroc Italiana). Per ilgene DECR1, differenze significative sono state osservate per il carattere grasso intermuscolare visibile. Ilgene ATP1A2, che mappa vicino al locus FAT1, non ha presentato differenze statisticamente significativenelle frequenze tra i gruppi estremi per i caratteri oggetto di studio. Analizzando il livello di linkage disequi-librium(LD) tra i tre loci, \ue8 stato evidenziato un elevato livello di LD (D\u2019= 0,967; P< 0,0001) tra i geni CA3e DECR1, solo nella popolazione Duroc Italiana. Questi primi risultati pongono le basi per ulteriori studi perverificare se i geni CA3e DECR1sono associati con i caratteri oggetto di selezione nel suino pesante.Three genes (ATPase, Na+/K+ transporting, \u3b1 2(+) polypeptide, ATP1A2; carbonic anhydrase III, CA3; 2,4-dienoyl CoA reductase 1, mitochondrial, DECR1), isolated from a porcine skeletal muscle cDNA library and mapped on porcine chromosome 4 (SSC4), were investigated. A new single nucleotide polymorphism (SNP) was identified in the 3\u2019-untranslated region of the CA3 gene and used to genetically map this locus on SSC4 together with the ATP1A2 and DECR1 loci for which SNPs were already reported. Allele frequencies of the three loci were reported for 11 pig breeds (Italian Large White, Italian Landrace, Italian Duroc, Belgian Landrace, Hampshire, Pi\uf9train, Meishan, Cinta Senese, Casertana, Calabrese and Nero Siciliano). Radiation hybrid mapping of these genes confirmed the linkage mapping results as well as mapping information reported by other authors. Then, the SNPs identified in the ATP1A2, CA3 and DECR1 genes were genotyped in Italian Large White and Italian Duroc animal groups with extreme and divergent estimated breeding value for several production traits. For CA3 significant differences in allele frequencies (P< 0.05) were observed between the extreme groups of pigs for the lean cuts (Italian Large White) and visible intermuscular fat (Italian Duroc) traits. For DECR1, a significant difference in allele frequencies was observed only for the visible intermuscular fat trait. ATP1A2, which maps close to the FAT1 locus, did not show any significant difference. A very high linkage disequilibrium (D\u2019= 0.967; P< 0.0001) was identified between CA3 and DECR1 in the Italian Duroc population. Further investigations are needed to evaluate the effect of CA3 and DECR1 on the considered trait

Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds

Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources