study of fatty acid synthase and adiponectin snps in the italian duroc breed

AbstractFatty acid synthase (FASN) is a multifunctional enzyme that plays a central role in fatty acid biosynthesis catalysing the conversion of acetyl-CoA and malonyl-CoA into long-chain saturated fatty acids and has an important role in energy homeostasis. Pig FASN gene has been assigned to chromosome 12p1.5 and a T>C polymorphism in the fourth exon was found. Adiponectin (ADN) is a fat-derived hormone involved in insulin sensitivity, in lipid and glucose metabolism. In literature is reported that the gene was mapped on chromosome 13 at 53.6 cM, in a region containing QTL for intramuscolar fat (IMF). In this gene several SNPs were identified and one of these polymorphisms (a G>A missense mutation within the 60th codon) determining the Val-Ile substitution in the protein, has been previously reported.The aim of this work is to analyse the variability of polymorphisms of fatty acid synthase described by Munoz et al., 2003 (Anim. Genet. 34:234) and adiponectin genes, candidates for meat and carcass quality..

VCF2Networks: applying genotype networks to single-nucleotide variants data

Summary: A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a representation of the set of genotypes associated with a single phenotype, and they allow one to estimate properties such as the robustness of the phenotype to mutations, and the ability of its associated genotypes to evolve new adaptations. So far, though, genotype networks analysis has rarely been applied to population genetics data. To help fill this gap, here we present VCF2Networks, a tool to determine and study genotype network structure from single-nucleotide variant data. Availability and implementation: VCF2Networks is available at https://bitbucket.org/dalloliogm/vcf2networks. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

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

Ocorrência de helmintos e protozoários em cães capturados da cidade de São João da Boa Vista-SP

O artigo não apresenta resumo

L1cam as an e-selectin ligand in colon cancer

Metastasis is the main cause of death among colorectal cancer (CRC) patients. E-selectin and its carbohydrate ligands, including sialyl Lewis X (sLeX) antigen, are key players in the binding of circulating tumor cells to the endothelium, which is one of the major events leading to organ invasion. Nevertheless, the identity of the glycoprotein scaffolds presenting these glycans in CRC remains unclear. In this study, we firstly have characterized the glycoengineered cell line SW620 transfected with the fucosyltransferase 6 (FUT6) coding for the \u3b11,3-fucosyltransferase 6 (FUT6), which is the main enzyme responsible for the synthesis of sLeX in CRC. The SW620FUT6 cell line expressed high levels of sLeX antigen and E-selectin ligands. Moreover, it displayed increased migration ability. E-selectin ligand glycoproteins were isolated from the SW620FUT6 cell line, identified by mass spectrometry, and validated by flow cytometry and Western blot (WB). The most prominent E-selectin ligand we identified was the neural cell adhesion molecule L1 (L1CAM). Previous studies have shown association of L1CAM with metastasis in cancer, thus the novel role as E-selectin counter-receptor contributes to understand the molecular mechanism involving L1CAM in metastasis formation

A first comparative map of copy number variations in the sheep genome

We carried out a cross species cattle–sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (Pb0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds

Follow-Up Assessment of Intracranial Aneurysms Treated with Endovascular Coiling: Comparison of Compressed Sensing and Parallel Imaging Time-of-Flight Magnetic Resonance Angiography

The aim of our study was to compare compressed sensing (CS) time-of-flight (TOF) magnetic resonance angiography (MRA) with parallel imaging (PI) TOF MRA in the evaluation of patients with intracranial aneurysms treated with coil embolization or stent-assisted coiling. We enrolled 22 patients who underwent follow-up imaging after intracranial aneurysm coil embolization. All patients underwent both PI TOF and CS TOF MRA during the same examination. Image evaluation aimed to compare the performance of CS to PI TOF MRA in determining the degree of aneurysm occlusion, as well as the depiction of parent vessel and vessels adjacent to the aneurysm dome. The reference standard for the evaluation of aneurysm occlusion was PI TOF MRA. The inter-modality agreement between CS and PI TOF MRA in the evaluation of aneurysm occlusion was almost perfect (κ = 0.98, p < 0.001) and the overall inter-rater agreement was substantial (κ = 0.70, p < 0.001). The visualization of aneurysm parent vessel in CS TOF images compared with PI TOF images was evaluated to be better in 11.4%, equal in 86.4%, and worse in 2.3%. CS TOF MRA, with almost 70% scan time reduction with respect to PI TOF MRA, yields comparable results for assessing the occlusion status of coiled intracranial aneurysms. Short scan times increase patient comfort, reduce the risk of motion artifacts, and increase patient throughput, with a resulting reduction in costs. CS TOF MRA may therefore be a potential replacement for PI TOF MRA as a first-line follow-up examination in patients with intracranial aneurysms treated with coil embolization

Transient asymptomatic pulmonary opacities and interstitial lung disease in EGFR-mutated non-small cell lung cancer treated with osimertinib

Introduction: Osimertinib is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) approved as first-line therapy for advanced EGFR-mutated non-small cell lung cancer (NSCLC). Some osimertinib-related interstitial lung diseases (ILDs) were shown to be transient, called transient asymptomatic pulmonary opacities (TAPO)—clinically benign pulmonary opacities that resolve despite continued osimertinib treatment—and are not associated with the clinical manifestations of typical TKI-associated ILDs. Methods: In this multicentric study, we retrospectively analyzed 92 patients with EGFR-mutated NSCLC treated with osimertinib. Computed tomography (CT) examinations were reviewed by two radiologists and TAPO were classified according to radiologic pattern. We also analyzed associations between TAPO and patients’ clinical variables and compared clinical outcomes (time to treatment failure and overall survival) for TAPO-positive and TAPO-negative groups. Results: TAPO were found in 18/92 patients (19.6%), with a median follow-up of 114 weeks. Median onset time was 16 weeks (range 6–80) and median duration time 14 weeks (range 8–37). The most common radiologic pattern was focal ground-glass opacity (54.5%). We did not find any individual clinical variable significantly associated with the onset of TAPO or significant difference in clinical outcomes between TAPO-positive and TAPO-negative groups. Conclusions: TAPO are benign pulmonary findings observed in patients treated with osimertinib. TAPO variability in terms of CT features can hinder the differential diagnosis with either osimertinib-related mild ILD or tumor progression. However, because TAPO are asymptomatic, it could be reasonable to continue therapy and verify the resolution of the CT findings at follow-up in selected cases

Electrocardiogram Monitoring Wearable Devices and Artificial-Intelligence-Enabled Diagnostic Capabilities: A Review

Worldwide, population aging and unhealthy lifestyles have increased the incidence of high-risk health conditions such as cardiovascular diseases, sleep apnea, and other conditions. Recently, to facilitate early identification and diagnosis, efforts have been made in the research and development of new wearable devices to make them smaller, more comfortable, more accurate, and increasingly compatible with artificial intelligence technologies. These efforts can pave the way to the longer and continuous health monitoring of different biosignals, including the real-time detection of diseases, thus providing more timely and accurate predictions of health events that can drastically improve the healthcare management of patients. Most recent reviews focus on a specific category of disease, the use of artificial intelligence in 12-lead electrocardiograms, or on wearable technology. However, we present recent advances in the use of electrocardiogram signals acquired with wearable devices or from publicly available databases and the analysis of such signals with artificial intelligence methods to detect and predict diseases. As expected, most of the available research focuses on heart diseases, sleep apnea, and other emerging areas, such as mental stress. From a methodological point of view, although traditional statistical methods and machine learning are still widely used, we observe an increasing use of more advanced deep learning methods, specifically architectures that can handle the complexity of biosignal data. These deep learning methods typically include convolutional and recurrent neural networks. Moreover, when proposing new artificial intelligence methods, we observe that the prevalent choice is to use publicly available databases rather than collecting new data