Mitochondrial D-loop sequence variation among Italian horse breeds

The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano) was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences

A high-resolution CNV map across Brown Swiss cattle populations.

Genomic studies and their use in selection programs are having a strong impact in dairy cattle selection (E. Liu et al., 2010). The first aim was to create a high resolution map of CNV regions (CNVRs) in Brown Swiss cattle and the characterization of identified CNVs as markers for quantitative and population genetic studies. CNVs were called in a set of 164 sires with PennCNV and genoCN. PennCNV identified 2,377 CNVRs comprising 1,162 and 1,131 gain and loss events, respectively, and 84 regions of complex nature. GenoCN detected 41,519 CNVRs comprising 3,475 and 34,485 gain and loss events, respectively, and 3,559 regions of complex ones. Consensus calls between algorithms were summarized to CNVRs at the population level. GenoCN was also used to identify total allelic content in consensus CNVRs. Moreover, population haplotype frequencies were calculated. Linkage disequilibrium (LD) was established between CNVs and SNPs in and around CNVRs. In this study the potential contribution of CNVs as genetic markers for genome wide association studies (GWAS) has been assessed thanks to PIC and LD values. The next aim is to investigate genomic structural variation in cattle using dense SNP information in more than 1000 samples of the Italian and Swiss Brown Swiss breed genotyped on HD Bovine BeadChips. Today there is still no CNV map available across Brown Swiss populations belonging to different countries. This study therefore expands the catalogue of CNVRs in the bovine genome, delivers an international based high-resolution map of CNVRs specific to Brown Swiss dairy cattle and will lastly provide information for GEBV estimation with CNVs

Paraoxonase 1 L55M, Q192R and paraoxonase 2 S311C alleles in atherothrombosis

Increased oxidative stress is known to play a role in the pathogenesis of atherosclerosis, and polymorphisms in genes encoding for enzymes involved in modulation of oxidant stress, such as paraoxonases (PONs), provide a potentially powerful approach to study the risk of disease susceptibility. Aim of our study is to investigate the possible association among PONs polymorphisms, clinical and metabolic factors, and atherothrombotic events in an Italian population. We evaluated in 105 subjects, with or without atherosclerotic risk factors, the presence of PON1 L55M, PON1 Q192R, and PON2 S311C genetic variants, as well as lipid profile, the concentration of aminothiols (blood reduced glutathione, plasma total glutathione, homocysteine, cysteine, cysteinyl glycine), and malondialdehyde as markers of lipid peroxidation

Mitochondrial DNA control region variation in Sanfratellano horse and two other Sicilian autochthonous breeds

Mitochondrial D-loop hypervariable region was analysed in 20 Sanfratellano and two other Sicilian autochthonous horse breeds (20 Sicilian Oriental Purebred and 20 Sicilian Indigenous) in order to investigate matrilineal genetic diversity. A total of 20 different haplotypes were identified sequencing a fragment of 397 bp; overall, haplotypes showed 31 polymorphic sites (7.8%). High diversity was detected in Sanfratellano (11 haplotypes) and Sicilian Indigenous (13 haplotypes), whereas only one haplotype was found in Sicilian Oriental Purebred. Sanfratellano sequences were compared with those belonging to the other Sicilian autochthonous horses and 118 sequences selected from the GenBank database in order to calculate the statistics of molecular diversity. Six haplotypes were exclusive of Sanfratellano which shares haplotype C, D, H, and O with the Sicilian Indigenous and haplotype U with the Sicilian Oriental Purebred; not significant differentiation was found between Sanfratellano and Sicilian Indigenous. BLAST search showed Sicilian haplotypes overlap with the database sequences but for three. Phylogenetic analysis did not show monophyletic group for Sanfratellano samples or the other breeds included in this analysis

Advantages of intraoperative implant for interstitial brachytherapy for accelerated partial breast irradiation either frail patients with early-stage disease or in locally recurrent breast cancer

Purpose: to describe the intraoperative multicatheter implantation technique for accelerated partial breast irradiation (APBI) delivered with high-dose-rate brachytherapy (HDR-BT). Secondarily, to evaluate outcomes and toxicity in a series of 83 patients treated with this technique at our institution. Material and methods: retrospective analysis of a series of patients treated with HDR-BT APBI after intraoperative multicatheter interstitial implant between November 2006 and June 2017 at our institution. We assessed cosmesis, toxicity, overall survival (OS), and disease-free survival (DFS). Results: eighty-three patients were included: 59 patients (71.1%) with primary early-stage breast cancer and 24 (28.9%) with locally recurrent breast cancer. Tumorectomy was performed in all cases, with intraoperative tumor margin assessment and sentinel node biopsy. Median age was 82 years (range, 44-92). The total prescribed dose was 32 Gy (8 treatment fractions) in 60 patients (72.3%), and 34 Gy (10 fractions) in 23 patients (27.7%). Median follow-up was 40 months (range, 1-136 months). Three-year OS and DFS in the recurrent and primary cancer groups were 87% vs. 89%, and 96 % vs. 97.8%, respectively. Five patients died from non-cancer related causes. No local relapses were observed. Rates of acute and late toxicity were low in both groups. The cosmesis was good or excellent in most of patients treated for primary disease; in patients who underwent salvage brachytherapy for local recurrence, cosmesis was good in 49 patients and fair in 6. Conclusions: this technique, although time-consuming, achieves good local disease control with a satisfactory toxicity profile in both early-stage and local recurrent breast cancer patients. It may be especially suitable for frail patients

Genomic variability in Mexican chicken population using Copy Number Variation

Copy number variants (CNVs) are polymorphisms which influence phenotypic variation and are an important source of genetic variability [1]. In Mexico the backyard poultry population is a unique widespread Creole chicken (Gallus gallus domesticus) population, an undefined cross among different breeds brought to Mexico from Europe and under natural selection for almost 500 years [2-3]. The aim of this study was to investigate genomic variation in the Mexican chicken population using CNVs.A total of 256 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array were used in the analyses. The individual CNV calling, based on log-R ratio and B-allele frequency values, was performed using the Hidden Markov Model (HMM) of PennCNV software on the autosomes [4-5]. CNVs were summarized to CNV regions (CNVRs) at a population level (i.e. overlapping CNVs), using BEDTools.The HMM detected a total of 1924 CNVs in the genome of 256 samples resulting, at population level, in 1216 CNV regions, of which 959 gains, 226 losses and 31 complex CNVRs (i.e. containing both losses and gains), covering a total of 47 Mb of sequence length corresponding to 5,12 % of the chicken galGal4 assembly autosome. A comparison among this study and 7 previous reports about CNVs in chicken was performed, finding that the 1,216 CNVRs detected in this study overlap with 617 regions (51%) mapped by others studies. This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been never genetically characterized with SNP markers. Based on a cluster analysis (pvclust – R package) on CNV markers the population, even if presenting extreme morphological variation, does not resulted divided in differentiated genetic subpopulations. Finally this study provides a CNV map based on the 600K SNP chip array jointly with a genome-wide gene copy number estimates in Mexican chicken population.

Second breast-conserving therapy with interstitial brachytherapy (APBI) as a salvage treatment in ipsilateral breast tumor recurrence: a retrospective study of 40 patients

Purpose: breast-conserving treatment (BCT) have emerged as an alternative to mastectomy in patients with ipsilateral breast tumor recurrence (IBTR). We evaluated survival outcomes and treatment-related toxicity in a series of 40 patients with IBTR, who underwent tumorectomy plus interstitial brachytherapy (APBI) as a salvage treatment. Material and methods: retrospective analysis included 40 patients diagnosed with IBTR and treated with intraoperative (26 patients) or post-operative (14 patients) multicatheter brachytherapy for APBI at our institution between June 2002 and October 2017. We assessed cosmesis, toxicity, overall survival (OS), and cancer-specific survival (CSS). Results: tumorectomy was performed in all cases, including intraoperative tumor margin assessment and sentinel node biopsy. Median age was 65 years (range, 41-92). The total prescribed dose was 32 Gy (8 fractions) in 19 patients and 34 Gy (10 fractions) in 20 patients. One elderly patient (age 92) received a single fraction of 16 Gy. Median follow-up was 61.5 months (range, 6-153). A median of 14 tubes were inserted. Mean treated V100 was 115 cc. Two patients developed a second relapse at 3 and 5 years after salvage treatment: one patient underwent salvage mastectomy and remains alive 10 years after brachytherapy, and the second one developed both local relapse and bone metastasis. The disease is stable at present. Five-year OS and CSS rates were 85.3% and 97.5%, respectively. Two patients died from cancer-related causes. Acute and late toxicity rates were low; seven patients developed acute infectious mastitis. Late fibrosis > grade 3 and late mastitis were observed in 14 and 6 cases, respectively. Conclusions: second BCT with APBI as a salvage treatment in ipsilateral breast recurrence achieves good local disease control, with a satisfactory toxicity profile compared to mastectomy. This approach seems to be safe and effective, although more data from randomized trials are needed

Association Between BoLA-DRB3.2 Polymorphism and Bovine Papillomavirus Infection for Bladder Tumor Risk in Podolica Cattle

Blood samples from 260 unrelated cattle (132 animals affected by papillomavirus-associated bladder tumors and 128 healthy) were genotyped using the classic polymerase chain reaction/restriction fragment length polymorphism method to screen MHC class II bovine leukocyte antigen-DRB3. 2 polymorphism. The DRB3*22 allele was significantly (p ≤ 0.01) detected in healthy cattle, thus appearing to have a negative association (protective effect) with virus infection of the urinary bladder known to represent a bladder tumor risk for cattle living free at pasture. Considering the two sequence alleles identified in animals carrying DRB3*22, DRB3*011:01 allele from samples of animals harboring the unexpressed bovine papillomaviruses (BPV)-2 E5 gene was characterized by amino acid residues believed to have a protective effect against BPV infection such as arginine at position 71 (R71) in pocket 4, histidine at position 11 (H11) in pocket 6, and both glutamine at position 9 (Q9) and serine at position 57 (S57) in pocket 9 of the antigen-binding groove. The DRB3*011:02v allele from affected animals was characterized by amino acids believed to be susceptibility residues such as lysine (K71), tyrosine (Y11), glutamic acid (E9), and aspartic acid (D57) in these pockets. These results suggest that animals harboring the DRB3*011:01 allele may have a lower risk of BPV infection and, consequently, a reduced risk of bladder tumors

Luces en una crisis global

El segundo semestre de 2008 fue especialmente difícil, en donde destacaron diversos puntos que se recogen en este número de Análisis Plural, como: los secuestros y el “ya basta”; los efectos de la crisis en México; el narcotráfico, terrorismo y corrupción; la “inacabada” reforma energética; el “avionazo” de Mouriño; la crisis en el Partido de la Revolución Democrática; el estallido bursátil estadounidense, de resonancia mundial, y los problemas energéticos agudizados por la globalización