Genome-wide variability and selection signatures in Italian island cattle breeds.

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo-Bruna and Sardo-Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within-breed genetic heterogeneity. The FST comparison revealing the largest number of significant SNPs was Sardo-Bruna vs. Sardo-Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo-Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo-Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi-dimensional scaling and the admixture analysis the Sardo-Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo-Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.

Genome wide association study on beef production traits in Marchigiana cattle breed.

A genomewide association study was carried out on a sample of Marchigiana breed cattle to detect markers significantly associated with carcass and meat traits. Four hundred and nine young bulls from 117 commercial herds were genotyped by Illumina 50K BeadChip assay. Eight growth and carcass traits (average daily gain, carcass weight, dressing percentage, body weight, skin weight, shank circumference, head weight and carcass conformation) and two meat quality traits (pH at slaughter and pH 24 h after slaughter) were measured. Data were analysed with a linear mixed model that included fixed effects of herd, slaughter date, fixed covariables of age at slaughter and SNP genotype, and random effects of herd and animal. A permutation test was performed to correct SNP genotype significance level for multiple testing. A total of 96 SNPs were significantly associated at genomewide level with one or more of the considered traits. Gene search was performed on genomic regions identified on the basis of significant SNP position and level of linkage disequilibrium. Interesting loci affecting lipid metabolism (SOAT1), bone (BMP4) and muscle (MYOF) biology were highlighted. These results may be useful to better understand the genetic architecture of growth and body composition in cattle.

Use of the canonical discriminant analysis to select SNP markers for bovine breed assignment and traceability purposes.

Several market research studies have shown that consumers are primarily concerned with the provenance of the food they eat. Among the available identification methods, only DNA-based techniques appear able to completely prevent frauds. In this study, a new method to discriminate among different bovine breeds and assign new individuals to groups was developed. Bulls of three cattle breeds farmed in Italy - Holstein, Brown, and Simmental - were genotyped using the 50K SNP Illumina BeadChip. Multivariate canonical discriminant analysis was used to discriminate among breeds, and discriminant analysis (DA) was used to assign new observations. This method was able to completely identify the three groups at chromosome level. Moreover, a genome-wide analysis developed using 340 linearly independent SNPs yielded a significant separation among groups. Using the reduced set of markers, the DA was able to assign 30 independent individuals to the proper breed. Finally, a set of 48 high discriminant SNPs was selected and used to develop a new run of the analysis. Again, the procedure was able to significantly identify the three breeds and to correctly assign new observations. These results suggest that an assay with the selected 48 SNP could be used to routinely track monobreed products.

Cisplatin-gemcitabine combination in advanced non-small-cell lung cancer: a phase II study.

PURPOSE: The nucleoside analog, gemcitabine, has shown activity as a single agent in the treatment of metastatic non-small-cell lung cancer (NSCLC). Its combination with cisplatin in preclinical models suggested synergy between the two drugs. The aim of the study was to evaluate the clinical efficacy and toxicity of the cisplatin-gemcitabine combination in advanced NSCLC. PATIENTS AND METHODS: Forty-eight consecutive previously untreated NSCLC patients entered the trial from January to June 1994. The median age was 60 years (range, 37 to 70) and performance status (PS) was 0 or 1; 22 patients had unresectable stage III disease (21 stage IIIB and one stage IIIA) and 26 had stage IV disease. Gemcitabine 1 g/m2 was administered weekly (days 1, 8, and 15) followed by a 1-week rest and cisplatin 100 mg/m2 on day 2 of each 28-day cycle. Survival and response were determined in accordance with the intention-to-treat principle in all enrolled patients. RESULTS: Of 48 assessable patients, one (stage IV) had a complete response (CR) and 25 achieved a partial response (PR). The overall response rate was 54% (95% confidence interval [CI], 40% to 68%). Thrombocytopenia was the main side effect, with 52% of patients experiencing grade III to IV toxicity, which was usually short-lived and responsible for the omission of gemcitabine administration on day 15 in 50% of chemotherapy courses. The median survival time was 61.5 weeks (95% CI, 40 to 71). CONCLUSION: The combination of gemcitabine and cisplatin induced a high response rate in both stage IIIB and IV NSCLC, with modest side effects. The regimen deserves further careful evaluation in a phase III prospective randomized trial.

Cloning and expression analysis of a Petunia hybrida flower specific mitotic-like cyclin.

A cyclin cDNA clone (Pethy;CycB1;1) was isolated from a Petunia hybrida ovary specific cDNA library. Sequence comparison revealed that Pethy;CYCB1;1 protein is highly homologous to mitotic B1 cyclins. Northern analysis and in situ hybridisation experiments showed that its expression is developmentally regulated and restricted to flower organs. We have attempted to define some of the cell division patterns which contribute to shaping each floral organ by analysing Pethy;CycB1;1 expression on Petunia flower sections. While in sepals, epidermis and parenchyma cell division patterns were comparable, there were two distinct cell division patterns in petals. In the epidermis, Pethy;CYCB1;1 expression was found both at the petal tip and along epidermis, whereas in the parenchyma only at the petal tips. In reproductive organs cell divisions were detected only in sporophytic tissues. No signals were detected inside meiotic cells.

Phase II study of high-dose paclitaxel and carboplatin in previously untreated, unresectable non-small cell lung cancer.

INTRODUCTION: This phase II study was designed to assess the activity and tolerability of the carboplatin-paclitaxel combination, given without routine growth factor support to previously untreated patients with stage IIIB and IV non-small cell lung cancer. PATIENTS AND METHODS: Sixty patients (15 stage IIIb and 45 stage IV) received paclitaxel 225 mg/ml on day 1, followed by carboplatin AUC 6 mg/ml per minute (Calvert formula) every 3 weeks. Paclitaxel was administered as a 3-h intravenous infusion followed by carboplatin over 30 min, on completion of paclitaxel administration. RESULTS: The combination showed a good safety profile with Grade 4 neutropenia occurring in 31% of patients without any serious infectious episodes requiring hospitalization. Moderate to severe anemia and thrombocytopenia seldom occurred. Sensorimotor peripheral neuropathy (Grade 2-3) and myalgia (Grade 3-4) were documented in 34 and 20% of the patients, respectively. Among 59 evaluable patients, there was one complete response and 26 partial responses for an overall response rate of 46% (95% C.I.: 34-59%). With a minimum follow-up duration of 16.5 months, the median overall survival time is 52 weeks and the 1-year survival rate is 50%. Median duration of response is 20 weeks (range: 4-52) and progression-free survival is 22 weeks (range: 5-77). CONCLUSION: In advanced NSCLC, the combination carboplatin-paclitaxel at doses of AUC 6 mg/ml per minute and 225 mg/ml every 3 weeks, is both active and relatively well-tolerated.