Publications by authors named "Valentina Riggio"

19 Publications

  • Page 1 of 1

4K ultra HD technology reduces operative time and intraoperative blood loss in colorectal laparoscopic surgery.

F1000Res 2020 11;9:106. Epub 2020 Feb 11.

General Surgery Department, Desio Hospital, ASST Monza, Desio, MB, Italy.

: HD systems are routinely used in laparoscopic surgery, 4K ultra HD monitors are mainly available within specialized, high-volume laparoscopic centers. The higher resolution of 4K ultra HD video could upgrade the surgical performance improving intraoperative and post-operative outcomes. : We performed a retrospective comparative analysis of intraoperative parameters and post-operative outcomes in a cohort of patients operated on for elective laparoscopic procedures for colo-rectal cancer during two different time frames: 2017 procedures performed using the Visera Elite full HD technology (® Olympus America, Medical) and the 2018 procedures performed the Visera 4K Ultra HD System (® Olympus America, Medical). : There was a statistically significant reduction in operative time in patients operated on with the 4K ultra HD technology compared to HD technology (p < 0.05). Intraoperative blood loss was significantly reduced in patients operated in 2018 (p < 0.05). There were no statistically significant differences in complication rate and postoperative outcomes between the two groups.
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http://dx.doi.org/10.12688/f1000research.21297.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400694PMC
February 2021

Symptomatic Uncomplicated Diverticular Disease and Incidence of Unexpected Abscess during Sigmoidectomy: A Multicenter Prospective Observational Study.

Dig Surg 2020 22;37(3):199-204. Epub 2019 May 22.

Department of Laparoscopic and Oncological General Surgery, ASST Monza, Desio Hospital, Desio, Italy.

Background: Symptomatic uncomplicated diverticular disease can affect patients' everyday routine. Considerable efforts have been made to identify clinical features that correlate to the severity of the disease. Unexpected intraoperative abscesses are reported in large retrospective series, showing how uncomplicated symptoms and presentations can underlie a complicated disease. The aim of this study was to investigate the incidence of pericolic or intramural abscess in patients undergoing elective sigmoidectomy for symptomatic uncomplicated diverticular disease and see if chronic symptoms correlate to the presence of an abscess.

Methods: Between January 2016 and June 2018, we prospectively collected data of patients who were given indication to elective sigmoidectomy for symptomatic uncomplicated diverticular disease. Patients were divided into 3 groups: acute resolving, smoldering, and atypical according to a previously described classification of uncomplicated diverticular disease.

Results: One hundred fifty-eight consecutive patients were enrolled in the study. The median age was 63 years (22- 88), and the mean body mass index was 26 (±7) kg/m2. There were 114 patients in the acute resolving group, 36 in the smoldering group, and 8 in the atypical group. An unexpected abscess was reported in 75 patients (47.5%) during surgery or pathological examination. The incidence of -abscess was greater for patient in the smoldering group (p = 0.0243).

Conclusion: Our series of patients affected by symptomatic uncomplicated diverticular disease showed an incidence of unexpected pericolic or intramural abscess of 47.5%. Patients affected by smoldering diverticular disease presented a greater abscess rate.
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http://dx.doi.org/10.1159/000500084DOI Listing
May 2019

Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs.

PLoS Genet 2019 01 30;15(1):e1007759. Epub 2019 Jan 30.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom.

Balancing selection provides a plausible explanation for the maintenance of deleterious alleles at moderate frequency in livestock, including lethal recessives exhibiting heterozygous advantage in carriers. In the current study, a leg weakness syndrome causing mortality of piglets in a commercial line showed monogenic recessive inheritance, and a region on chromosome 15 associated with the syndrome was identified by homozygosity mapping. Whole genome resequencing of cases and controls identified a mutation causing a premature stop codon within exon 3 of the porcine Myostatin (MSTN) gene, similar to those causing a double-muscling phenotype observed in several mammalian species. The MSTN mutation was in Hardy-Weinberg equilibrium in the population at birth, but significantly distorted amongst animals still in the herd at 110 kg, due to an absence of homozygous mutant genotypes. In heterozygous form, the MSTN mutation was associated with a major increase in muscle depth and decrease in fat depth, suggesting that the deleterious allele was maintained at moderate frequency due to heterozygous advantage (allele frequency, q = 0.22). Knockout of the porcine MSTN by gene editing has previously been linked to problems of low piglet survival and lameness. This MSTN mutation is an example of putative balancing selection in livestock, providing a plausible explanation for the lack of disrupting MSTN mutations in pigs despite many generations of selection for lean growth.
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http://dx.doi.org/10.1371/journal.pgen.1007759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370237PMC
January 2019

Dissecting the Genomic Architecture of Resistance to Parasitism in the Chicken.

Front Genet 2018 26;9:528. Epub 2018 Nov 26.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom.

Coccidiosis in poultry, caused by protozoan parasites of the genus , is an intestinal disease with substantial economic impact. With the use of anticoccidial drugs under public and political pressure, and the comparatively higher cost of live-attenuated vaccines, an attractive complementary strategy for control is to breed chickens with increased resistance to parasitism. Prior infection with leads to complete immunity against challenge with homologous strains, but only partial resistance to challenge with antigenically diverse heterologous strains. We investigate the genetic architecture of avian resistance to primary infection and heterologous strain secondary challenge using White Leghorn populations of derived inbred lines, C.B12 and 15I, known to differ in susceptibility to the parasite. An intercross population was infected with Houghton (H) strain, followed 3 weeks later by Weybridge (W) strain challenge, while a backcross population received a single W infection. The phenotypes measured were parasite replication (counting fecal oocyst output or qPCR for parasite numbers in intestinal tissue), intestinal lesion score (gross pathology, scale 0-4), and for the backcross only, serum interleukin-10 (IL-10) levels. Birds were genotyped using a high density genome-wide DNA array (600K, Affymetrix). Genome-wide association study located associations on chromosomes 1, 2, 3, and 5 following primary infection in the backcross population, and a suggestive association on chromosome 1 following heterologous W challenge in the intercross population. This mapped several megabases away from the quantitative trait locus (QTL) linked to the backcross primary W strain infection, suggesting different underlying mechanisms for the primary- and heterologous secondary- responses. Underlying pathways for those genes located in the respective QTL for resistance to primary infection and protection against heterologous challenge were related mainly to immune response, with IL-10 signaling in the backcross primary infection being the most significant. Additionally, the identified markers associated with IL-10 levels exhibited significant additive genetic variance. We suggest this is a phenotype of interest to the outcome of challenge, being scalable in live birds and negating the requirement for single-bird cages, fecal oocyst counts, or slaughter for sampling (qPCR).
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http://dx.doi.org/10.3389/fgene.2018.00528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275401PMC
November 2018

Phenotypic and genetic variation in the response of chickens to Eimeria tenella induced coccidiosis.

Genet Sel Evol 2018 Nov 21;50(1):63. Epub 2018 Nov 21.

The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, UK.

Background: Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there are commercial incentives to breed chickens with greater resistance to this important production disease. To identify phenotypic biomarkers that are associated with the production impacts of coccidiosis, and to assess their covariance and heritability, 942 Cobb500 commercial broilers were subjected to a defined challenge with Eimeria tenella (Houghton). Three traits were measured: weight gain (WG) during the period of infection, caecal lesion score (CLS) post mortem, and the level of a serum biomarker of intestinal inflammation, i.e. circulating interleukin 10 (IL-10), measured at the height of the infection.

Results: Phenotypic analysis of the challenged chicken cohort revealed a significant positive correlation between CLS and IL-10, with significant negative correlations of both these traits with WG. Eigenanalysis of phenotypic covariances between measured traits revealed three distinct eigenvectors. Trait weightings of the first eigenvector, (EV1, eigenvalue = 59%), were biologically interpreted as representing a response of birds that were susceptible to infection, with low WG, high CLS and high IL-10. Similarly, the second eigenvector represented infection resilience/resistance (EV2, 22%; high WG, low CLS and high IL-10), and the third eigenvector tolerance (EV3, 19%; high WG, high CLS and low IL-10), respectively. Genome-wide association studies (GWAS) identified two SNPs that were associated with WG at the suggestive level.

Conclusions: Eigenanalysis separated the phenotypic impact of a defined challenge with E. tenella on WG, caecal inflammation/pathology, and production of IL-10 into three major eigenvectors, indicating that the susceptibility-resistance axis is not a single continuous quantitative trait. The SNPs identified by the GWAS for body weight were located in close proximity to two genes that are involved in innate immunity (FAM96B and RRAD).
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http://dx.doi.org/10.1186/s12711-018-0433-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249784PMC
November 2018

Amyand Hernia in an elderly patient.

Ann Ital Chir 2018 May 30;7. Epub 2018 May 30.

Introduction: Inguinal hernia is one of the most common surgical entities and often poses technical dilemmas, even for the experienced surgeon. Amyand's hernia is an inguinal hernia; a protrusion of abdominal cavity content through the inguinal canal, with a vermiform appendix.

Case Report: A 77 years old Caucasian male was referred to our institution for the evaluation of a recurrent right inguinal hernia. During the surgery, we discovered a rare type I Amyand hernia. Following the guidelines we performed, a prosthetic tension-free inguinal ernioplasty without appendectomy.The patient was discharged on the first post-operative day. The follow-up at 7 days was uneventful.

Discussion: First described by Claudius Amyand (1660-1740), a French born English surgeon, who successfully performed the first reported appendectomy for inflamed appendix encountered during herniotomy on an 11 year-old boy in 1735 at St George's hospital.The incidence of Amyand's hernia is between 1%. The association of appendicitis is even rarer and reported to be around of 0.1%. Losanoff and Basson proposed a classification scheme to determine the surgical management of Amyand's hernia, depending on the status of the appendix KEY WORD: Amyand Hernia, Appendix, Elderly.
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May 2018

Association of subclinical mastitis prevalence with sheep breeds in Greece.

J Dairy Res 2018 Aug 21;85(3):317-320. Epub 2018 Jun 21.

Veterinary Faculty,University of Thessaly,Karditsa,Greece.

The objective of the research described in this Research Communication was to describe potential associations of subclinical mastitis with sheep breeds in Greece. A countrywide survey (2198 ewes in 111 farms) was performed. Prevalence of subclinical mastitis was 0·260. Results did not indicate any difference in the prevalence of subclinical mastitis between farms with pure-bred and farms with cross-bred animals, nor any difference in prevalence between farms with Greek pure-bred animals and farms with imported pure-bred animals. Results indicated that prevalence of subclinical mastitis was smaller in farms with Assaf-breed (0·100) and higher in farms with Frisarta-breed (0·625) (P < 0·02). Prevalence of mastitis was smaller in farms with Greek traditional indigenous breeds (0·221) (P = 0·007). In a model that included sheep breed and management system in farm, breed emerged as a significant factor for prevalence of subclinical mastitis (P = 0·003).
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http://dx.doi.org/10.1017/S0022029918000407DOI Listing
August 2018

Age-related gene expression changes, and transcriptome wide association study of physical and cognitive aging traits, in the Lothian Birth Cohort 1936.

Aging (Albany NY) 2017 12;9(12):2489-2503

Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK.

Gene expression is influenced by both genetic variants and the environment. As individuals age, changes in gene expression may be associated with decline in physical and cognitive abilities. We measured transcriptome-wide expression levels in lymphoblastoid cell lines derived from members of the Lothian Birth Cohort 1936 at mean ages 70 and 76 years. Changes in gene expression levels were identified for 1,741 transcripts in 434 individuals. Gene Ontology enrichment analysis indicated an enrichment of biological processes involved in the immune system. Transcriptome-wide association analysis was performed for eleven cognitive, fitness, and biomedical aging-related traits at age 70 years (N=665 to 781) and with mortality. Transcripts for genes ( and ) previously identified as being differentially methylated or expressed in smoking or smoking-related cancers were overexpressed in smokers compared to non-smokers and the expression of transcripts for genes ( and ) previously associated with stress response, autoimmune disease and cancer were associated with telomere length. No associations between expression levels and other traits, or mortality were identified.
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http://dx.doi.org/10.18632/aging.101333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764388PMC
December 2017

A candidate gene approach to study nematode resistance traits in naturally infected sheep.

Vet Parasitol 2017 Aug 10;243:71-74. Epub 2017 Jun 10.

The Roslin Institute & R(D)SVS, University of Edinburgh, UK.

Sheep naturally acquire a degree of resistant immunity to parasitic worm infection through repeated exposure. However, the immune response and clinical outcome vary greatly between animals. Genetic polymorphisms in genes integral to differential T helper cell polarization may contribute to variation in host response and disease outcome. A total of twelve single nucleotide polymorphisms (SNPs) were sequenced in IL23R, RORC2 and TBX21 from genomic DNA of Scottish Blackface lambs. Of the twelve SNPs, six were non-synonymous (missense), four were within the 3' UTRs and two were intronic. The association between nine of these SNPs and the traits of body weight, faecal egg count (FEC) and relative T. circumcincta L3-specific IgA antibody levels was assessed in a population of domestic Scottish Blackface ewe lambs and a population of free-living Soay ewe lambs both naturally infected with a mixture of nematodes. There were no significant associations identified between any of the SNPs and phenotypes recorded in either of the populations after adjustment for multiple testing (Bonferroni corrected P value≤0.002). In the Blackface lambs, there was a nominally significant association (P=0.007) between IL23R p.V324M and weight at 20 weeks. This association may be worthy of further investigation in a larger sample of sheep.
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http://dx.doi.org/10.1016/j.vetpar.2017.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567408PMC
August 2017

Tumor regression grades, K-RAS mutational profile and c-MET in colorectal liver metastases.

Pathol Res Pract 2017 Aug 21;213(8):1002-1009. Epub 2017 Apr 21.

Surgical and Medical Department of Traslational Medicine, University of Rome "La Sapienza", Sant'Andrea Hospital of Rome, Italy.

Introduction: Recently TRG, necrosis grade and the rate of viable cancer cells of colorectal liver metastases were correlated with the response to chemotherapy treatments, whereas K-RAS mutations and c-MET over-expression were correlated with the prognosis.

Methods: 58 resection specimens were assessed for regression grades. Patients undergone neo-adjuvant treatments were compared to patients who underwent therapy exclusively adjuvantly. We investigated the K-RAS mutational profile, the c-MET over-expression along with patients' survivals curves.

Results: Patients undergone neo-adjuvant treatment presented significant higher fibrosis rates and lower rates of viable cells. 36.7% of the patients had a K-RAS mutation and the 26.7% presented c-MET over-expression, but these features did not correlate with patients' clinical/pathological data. Survival analysis documented that K-RAS WT patients presenting c-MET over-expression had worse outcomes.

Conclusion: Fibrosis and the rate of viable cells significantly correlate with the response to chemotherapy treatments. c-MET is a promising marker in K-RAS WT patients.
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http://dx.doi.org/10.1016/j.prp.2017.04.013DOI Listing
August 2017

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle.

BMC Genet 2017 03 23;18(1):27. Epub 2017 Mar 23.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.

Background: The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics.

Methods: The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control.

Results: The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB.

Conclusion: Genomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle susceptibility to bTB and enhance genetic improvement programmes aiming at controlling and eradicating the disease.
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http://dx.doi.org/10.1186/s12863-017-0493-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364629PMC
March 2017

Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs.

Genet Sel Evol 2016 Feb 8;48:11. Epub 2016 Feb 8.

The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.

Background: Improving meat quality including taste and tenderness is critical to the protection and development of markets for sheep meat. Phenotypic selection for such measures of meat quality is constrained by the fact that these parameters can only be measured post-slaughter. Carcass composition has an impact on meat quality and can be measured on live animals using advanced imaging technologies such as X-ray computed tomography (CT). Since carcass composition traits are heritable, they are potentially amenable to improvement through marker-assisted and genomic selection. We conducted a genome-wide association study (GWAS) on about 600 Scottish Blackface lambs for which detailed carcass composition phenotypes, including bone, fat and muscle components, had been captured using CT and which were genotyped for ~40,000 single nucleotide polymorphisms (SNPs) using the Illumina OvineSNP50 chip.

Results: We confirmed that the carcass composition traits were heritable with moderate to high (0.19-0.78) heritabilities. The GWAS analyses revealed multiple SNPs and quantitative trait loci (QTL) that were associated with effects on carcass composition traits and were significant at the genome-wide level. In particular, we identified a region on ovine chromosome 6 (OAR6) associated with bone weight and bone area that harboured SNPs with p values of 5.55 × 10(-8) and 2.63 × 10(-9), respectively. The same region had effects on fat area, fat density, fat weight and muscle density. We identified plausible positional candidate genes for these OAR6 QTL. We also detected a SNP that reached the genome-wide significance threshold with a p value of 7.28 × 10(-7) and was associated with muscle density on OAR1. Using a regional heritability mapping approach, we also detected regions on OAR3 and 24 that reached genome-wide significance for bone density.

Conclusions: We identified QTL on OAR1, 3, 24 and particularly on OAR6 that are associated with effects on muscle, fat and bone traits. Based on available evidence that indicates that these traits are genetically correlated with meat quality traits, these associated SNPs have potential applications in selective breeding for improved meat quality. Further research is required to determine whether the effects associated with the OAR6 QTL are caused by a single gene or several closely-linked genes.
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http://dx.doi.org/10.1186/s12711-016-0191-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4745175PMC
February 2016

Regional Heritability Mapping to identify loci underlying genetic variation of complex traits.

BMC Proc 2014 7;8(Suppl 5):S3. Epub 2014 Oct 7.

The Roslin Institute and the R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.

Background: Genome-wide association studies can have limited power to identify QTL, partly due to the stringent correction for multiple testing and low linkage-disequilibrium between SNPs and QTL. Regional Heritability Mapping (RHM) has been advanced as an alternative approach to capture underlying genetic effects. In this study, RHM was used to identify loci underlying variation in the 16(th) QTLMAS workshop simulated traits.

Methods: The method was implemented by fitting a mixed model where a genomic region and the overall genetic background were added as random effects. Heritabilities for the genetic regional effects were estimated, and the presence of a QTL in the region was tested using a likelihood ratio test (LRT). Several region sizes were considered (100, 50 and 20 adjacent SNPs). Bonferroni correction was used to calculate the LRT thresholds for genome-wide (p < 0.05) and suggestive (i.e., one false positive per genome scan) significance.

Results: Genomic heritabilities (0.31, 0.32 and 0.48, respectively) and genetic correlations (0.80, -0.42 and 0.19, between trait-pairs 1&2, 1&3 and 2&3) were similar to the simulated ones. RHM identified 7 QTL (4 at genome-wide and 3 at suggestive level) for Trait1; 4 (2 genome-wide and 2 suggestive) for Trait2; and 7 (6 genome-wide and 1 suggestive) for Trait3. Only one of the identified suggestive QTL was a false-positive. The position of these QTL tended to coincide with the position where the largest QTL (or several of them) were simulated. Several signals were detected for the simulated QTL with smaller effect. A combined analysis including all significant regions showed that they explain more than half of the total genetic variance of the traits. However, this might be overestimated, due to Beavis effect. All QTL affecting traits 1&2 and 2&3 had positive correlations, following the trend of the overall correlation of both trait-pairs. All but one QTL affecting traits 1&3 were negatively correlated, in agreement with the simulated situation. Moreover, RHM identified extra loci that were not found by association and linkage analysis, highlighting the improved power of this approach.

Conclusions: RHM identified the largest QTL among the simulated ones, with some signals for the ones with small effect. Moreover, RHM performed better than association and linkage analysis, in terms of both power and resolution.
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http://dx.doi.org/10.1186/1753-6561-8-S5-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195407PMC
December 2014

Receiver-operating characteristic curves for somatic cell scores and California mastitis test in Valle del Belice dairy sheep.

Vet J 2013 Jun 12;196(3):528-32. Epub 2013 Jan 12.

DEMETRA Department, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy.

Using receiver-operating characteristic (ROC) curve methodology this study was designed to assess the diagnostic effectiveness of somatic cell count (SCC) and the California mastitis test (CMT) in Valle del Belice sheep, and to propose and evaluate threshold values for those tests that would optimally discriminate between healthy and infected udders. Milk samples (n=1357) were collected from 684 sheep in four flocks. The prevalence of infection, as determined by positive bacterial culture was 0.36, 87.7% of which were minor and 12.3% major pathogens. Of the culture negative samples, 83.7% had an SCC<500,000/mL and 97.4% had <1,000,000cells/mL. When the associations between SC score (SCS) and whole sample status (culture negative vs. infected), minor pathogen status (culture negative vs. infected with minor pathogens), major pathogen status (culture negative vs. infected with major pathogens), and CMT results were evaluated, the estimated area under the ROC curve was greater for glands infected with major compared to minor pathogens (0.88 vs. 0.73), whereas the area under the curve considering all pathogens was similar to the one for minor pathogens (0.75). The estimated optimal thresholds were 3.00 (CMT), 2.81 (SCS for the whole sample), 2.81 (SCS for minor pathogens), and 3.33 (SCS for major pathogens). These correctly classified, respectively, 69.0%, 73.5%, 72.6% and 91.0% of infected udders in the samples. The CMT appeared only to discriminate udders infected with major pathogens. In this population, SCS appeared to be the best indirect test of the bacteriological status of the udder.
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http://dx.doi.org/10.1016/j.tvjl.2012.11.010DOI Listing
June 2013

Effect of the prior distribution of SNP effects on the estimation of total breeding value.

BMC Proc 2012 May 21;6 Suppl 2:S6. Epub 2012 May 21.

DNA Landmarks Inc, St-Jean-Sur-Richelieu, J3B 6X3 Quebec, Canada.

Background: Five main methods, commonly applied in genomic selection, were used to estimate the GEBV on the 15th QTLMAS workshop dataset: GBLUP, LASSO, Bayes A and two Bayes B type of methods (BBn and BBt). GBLUP is a mixed model approach where GEBV are obtained using a relationship matrix calculated from the SNP genotypes. The remaining methods are regression-based approaches where the SNP effects are first estimated and, then GEBV are calculated given the individuals' genotypes.

Methods: The differences between the regression-based methods are in their prior distributions for the SNP effects. The prior distribution for LASSO is a Laplace distribution, for Bayes A is a scaled Student-t distribution, and the Bayes B type methods have a Spike and Slab prior where only a proportion (π) of SNP has an effect, following a given distribution. In this study, two different distributions were considered for the Bayes B type methods: (i) normal and (ii) scaled Student-t. They are referred here as the BBn and BBt methods, respectively. These prior distributions are defined by one or more parameters controlling their scale/rate (λ), shape (df) or proportion of SNP with effect (π). LASSO requires one (λ); two for Bayes A (λ, df) and Bayes Bn (λ, π); and three for Bayes Bt (λ, df, π). In this study, all parameters were estimated from the data. An extra scenario for Bayes A and BBt was included where df was not estimated but fixed to 4 (suffixed _4df). The implementation of GBLUP was done using ASREML, the heritability was also estimated from the data. All other methods were implemented using a MCMC approach.

Results: All Bayes A and B methods showed accuracy (correlation between True and Estimated BV) as high as 0.94 except for BA_4df (r = 0.91). Compared to the traditional BLUP using pedigree information, these methods improved the accuracy between 50 and 55%. GBLUP and LASSO were less accurate (0.81 and 0.85 respectively) and the improvements were 34 and 40% compared to BLUP.

Conclusions: Results of all methods were consistent and the accuracies for GEBV ranged between 0.81 and 0.94. When all parameters were estimated the results were similar for the Bayes A and Bayes B methods. Results showed that Bayes A was more sensitive to the changes in the shape parameter, and the parameter changes led to change in the accuracy of GEBV. However BBt was more robust to the change in this parameter. This may be explained by the fact that BBt estimates one extra parameter and it can buffer against a non-proper shape parameter.
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http://dx.doi.org/10.1186/1753-6561-6-S2-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3363160PMC
May 2012

Polymorphisms of β-defensin genes in Valle del Belice dairy sheep.

Mol Biol Rep 2011 Nov 10;38(8):5405-12. Epub 2011 Mar 10.

Dipartimento DEMETRA-Sezione Produzioni Animali, Università di Palermo, Viale delle Scienze Parco d'Orleans, 90128 Palermo, Italy.

The aim of this work was to study β-defensin 1 (SBD1) and β-defensin 2 (SBD2) genes in Valle del Belice dairy sheep in order to identify polymorphisms that can be utilized as markers of the analyzed genes, and search for the functional effects and roles of the identified polymorphisms (variation of the amino acid sequence of the protein and stability of mRNA molecule). The study was conducted on 300 randomly selected animals belonging to four flocks. A total of seven SNPs were identified, two in SBD1 and five in SBD2. The two SNPs identified in SBD2 coding region, at position 1659 and position 1667, were non-synonymous, leading to amino acid changes in the protein product. Nevertheless, the functional effects predicted by the two SNPs demonstrated that amino acid substitutions may not have effect on β-defensin 2 protein function. Moreover, we demonstrated that SBD2 mutant sequence shows changes in mRNA secondary structure. These results suggest that identified SNPs could play a role in the modulation of the immune response.
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http://dx.doi.org/10.1007/s11033-011-0694-5DOI Listing
November 2011

An initial comparative map of copy number variations in the goat (Capra hircus) genome.

BMC Genomics 2010 Nov 17;11:639. Epub 2010 Nov 17.

DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, Via F.lli Rosselli 107, 42123 Reggio Emilia, Italy.

Background: The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.

Results: We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P < 0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals.

Conclusions: We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.
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http://dx.doi.org/10.1186/1471-2164-11-639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3011854PMC
November 2010

Genetic parameters for somatic cell score according to udder infection status in Valle del Belice dairy sheep and impact of imperfect diagnosis of infection.

Genet Sel Evol 2010 Jul 26;42:30. Epub 2010 Jul 26.

Dipartimento S.En.Fi.Mi.Zo.-Sezione Produzioni Animali, Università degli Studi di Palermo, Palermo, Italy.

Background: Somatic cell score (SCS) has been promoted as a selection criterion to improve mastitis resistance. However, SCS from healthy and infected animals may be considered as separate traits. Moreover, imperfect sensitivity and specificity could influence animals' classification and impact on estimated variance components. This study was aimed at: (1) estimating the heritability of bacteria negative SCS, bacteria positive SCS, and infection status, (2) estimating phenotypic and genetic correlations between bacteria negative and bacteria positive SCS, and the genetic correlation between bacteria negative SCS and infection status, and (3) evaluating the impact of imperfect diagnosis of infection on variance component estimates.

Methods: Data on SCS and udder infection status for 1,120 ewes were collected from four Valle del Belice flocks. The pedigree file included 1,603 animals. The SCS dataset was split according to whether animals were infected or not at the time of sampling. A repeatability test-day animal model was used to estimate genetic parameters for SCS traits and the heritability of infection status. The genetic correlation between bacteria negative SCS and infection status was estimated using an MCMC threshold model, implemented by Gibbs Sampling.

Results: The heritability was 0.10 for bacteria negative SCS, 0.03 for bacteria positive SCS, and 0.09 for infection status, on the liability scale. The genetic correlation between bacteria negative and bacteria positive SCS was 0.62, suggesting that they may be genetically different traits. The genetic correlation between bacteria negative SCS and infection status was 0.51. We demonstrate that imperfect diagnosis of infection leads to underestimation of differences between bacteria negative and bacteria positive SCS, and we derive formulae to predict impacts on estimated genetic parameters.

Conclusions: The results suggest that bacteria negative and bacteria positive SCS are genetically different traits. A positive genetic correlation between bacteria negative SCS and liability to infection was found, suggesting that the approach of selecting animals for decreased SCS should help to reduce mastitis prevalence. However, the results show that imperfect diagnosis of infection has an impact on estimated genetic parameters, which may reduce the efficiency of selection strategies aiming at distinguishing between bacteria negative and bacteria positive SCS.
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http://dx.doi.org/10.1186/1297-9686-42-30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915952PMC
July 2010

Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: association with red and black coat colour phenotypes but with unexpected evidences.

BMC Genet 2009 Aug 25;10:47. Epub 2009 Aug 25.

DIPROVAL, Sezione di Allevamenti Zootecnici, University of Bologna, 42100 Reggio Emilia, Italy.

Background: Agouti and Extension loci control the relative amount of eumelanin and pheomelanin production in melanocytes that, in turn, affects pigmentation of skin and hair. The Extension locus encodes the melanocortin 1 receptor (MC1R) whose permanent activation, caused by functional mutations, results in black coat colour, whereas other inactivating mutations cause red coat colour in different mammals.

Results: The whole coding region of the MC1R gene was sequenced in goats of six different breeds showing different coat colours (Girgentana, white cream with usually small red spots in the face; Maltese, white with black cheeks and ears; Derivata di Siria, solid red; Murciano-Granadina, solid black or solid brown; Camosciata delle Alpi, brown with black stripes; Saanen, white; F1 goats and the parental animals). Five single nucleotide polymorphisms (SNPs) were identified: one nonsense mutation (p.Q225X), three missense mutations (p.A81V, p.F250V, and p.C267W), and one silent mutation. The stop codon at position 225 should cause the production of a shorter MC1R protein whose functionality may be altered. These SNPs were investigated in a larger sample of animals belonging to the six breeds. The Girgentana breed was almost fixed for the p.225X allele. However, there was not complete association between the presence of red spots in the face and the presence of this allele in homozygous condition. The same allele was identified in the Derivata di Siria breed. However, its frequency was only 33%, despite the fact that these animals are completely red. The p.267W allele was present in all Murciano-Granadina black goats, whereas it was never identified in the brown ones. Moreover, the same substitution was present in almost all Maltese goats providing evidence of association between this mutation and black coat colour.

Conclusion: According to the results obtained in the investigated goat breeds, MC1R mutations may determine eumelanic and pheomelanic phenotypes. However, they are probably not the only factors. In particular, the surprising not complete association of the nonsense mutation (p.Q225X) with red coat colour raises a few hypotheses on the determination of pheomelanic phenotypes in goats that should be further investigated.
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http://dx.doi.org/10.1186/1471-2156-10-47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748843PMC
August 2009