Genetic analysis of pig survival in a crossbred population
Dufrasne, Marie ; ; et al
in Journal of Animal Science (2013), 91(E-Suppl.2), 193Detailed reference viewed: 27 (13 ULg)
Genetic analysis of pig survival up to commercial weight in a crossbred population
Dufrasne, Marie ; ; et al
in Livestock Science (2014), 167
Records from 99,384 crossbred pigs from Duroc sires and Large White x Landrace dams were used to estimate genetic parameters for survival traits at different stages of the fattening period, and their ... [more ▼]
Records from 99,384 crossbred pigs from Duroc sires and Large White x Landrace dams were used to estimate genetic parameters for survival traits at different stages of the fattening period, and their relations with final weight. Traits analyzed were preweaning mortality (PWM), culling between weaning and harvesting (Call), culling during the farrowing period (Cfar), in the nursery site (Cnur), during the finishing phase (Cfin), and hot carcass weight (HCW). Because of the binary nature of PWM and culling traits, threshold-linear models were used: Model 1, including PWM, Call, and HCW; Model 2, including PWM, Cfar, Cnur, Cfin, and HCW. Both models included sex and parity number as fixed effects for all traits. Contemporary groups were considered as fixed effect for HCW and as random effects for the binary traits. Random effects were sire additive genetic, common litter, and residual effects for all traits and models. Heritability estimates were 0.03 for PWM, and 0.15 for HCW with both models, 0.06 for Call with Model 1, and 0.06 for Cfar, 0.14 for Cnur, and 0.10 for Cfin with Model 2. Litter variance explained a large part of the total variance and its influence declined slightly with age. For Model 1, genetic correlations were -0.36 between PWM and Call, -0.02 between PWM and HCW, and -0.25 between Call and HCW; correlations for litter effect were -0.15 between PWM and Call, -0.19 between PWM and HCW, and -0.21 between Call and HCW. For Model 2, genetic correlations were all positive between PWM and culling traits, except between PWM and Cnur (-0.61). Genetic correlations between HCW and the other traits were moderate and negative to null. Correlations for common litter effect were all negative between traits, except between Cfar and Cfin, and between Cnur and Cfin. Heritability of PWM and culling traits increased with age period. Therefore, selection for survival after weaning may be more efficient. The low genetic correlations between PWM and culling traits suggest that different genes influence pre- and postweaning mortality. The HCW was not correlated with the other traits. However, relationships are not strongly unfavorable, therefore selection for survival and high final weight is possible. [less ▲]Detailed reference viewed: 17 (5 ULg)
Genetic analysis of polymorphisms in biologically relevant candidate genes in patients with abdominal aortic aneurysms
; ; et al
in Journal of Vascular Surgery (2005), 41(6), 1036-1042
Background: Abdominal aortic aneurysms (AAAs) are characterized by histologic signs of chronic inflammation, destructive remodeling of extracellular matrix, and depletion of vascular smooth muscle cells ... [more ▼]
Background: Abdominal aortic aneurysms (AAAs) are characterized by histologic signs of chronic inflammation, destructive remodeling of extracellular matrix, and depletion of vascular smooth muscle cells. We investigated the process of extracellular matrix remodeling by performing a genetic association study with polymorphisms in the genes for matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), and structural extracellular matrix molecules in AAA. Our hypothesis was that genetic variations in one or more of these genes contribute to greater or lesser activity of these gene products, and thereby contribute to susceptibility for developing AAAs. Methods: DNA samples from 812 unrelated white subject (AAA, n = 387; controls, n = 425) were genotyped for 14 polymorphisms in 13 different candidate genes: MMP1(nt-1607), MMP2(nt-955), MMP3(nt-1612), MMP9(nt-1562), MMP10(nt+180), MMP12(nt-82), MMP13(nt-77), TIMP1(nt+434), TIMP1(rs;2070584), TIMP2(rs2009196), TIMP3(nt-1296), TGFBI(nt-509), ELN(nt+422), and COL3A1(nt+581). Odds ratios and P values adjusted for gender and country of origin using logistic regression and stratified by family history of AAA were calculated to test for association between genotype and disease status. Haplotype analysis was carried out for the two TIMP1 polymorphisms; in male subjects. Results: Analyses with one polymorphism per test without interactions showed an association with the two TIMP1 gene polymorphisms (nt+434, P =.0047; rs2070584, P =.015) in male subjects without a family history of AAA. The association remained significant when analyzing TIMP1 haplotypes (x(2) p =.014 and empirical P =.009). In addition, we found a significant interaction between the polymorphism and gender for MMP10 (P=.037) in cases without a family history of AAA, as well as between the polymorphism and country of origin for ELN (P =.0169) and TIMP3 (P =.0023) in cases with a family history of AAA. Conclusions: These findings suggest that genetic variations in TIMP1, TIMP3, MMP10, and ELN genes may contribute to the pathogenesis of AAAs. Further work is needed to confirm the findings in an independent set of samples and to study the functional role of these variants in AAA. It is noteworthy that contrary to a previous study, we did not find an association between the MMP9 (nt-1562) polymorphism and AAA, suggesting genetic heterogeneity of the disease. Clinical Relevance: Abdominal aortic aneurysms (AAAs) are an important cardiovascular disease, but the genetic and environmental risk factors, which contribute to individual's risk to develop an aneurysm, are poorly understood. Histologically, AAAs are characterized by signs of chronic inflammation, destructive remodeling of the extracellular matrix, and depletion of vascular smooth muscle cells. We hypothesized that genes involved in these events could harbor changes that make individuals more susceptible to developing aneurysms. This study identified significant genetic associations between DNA sequence changes in tissue inhibitor of metalloproteinase I (TIMP1), TIMP3, matrix metalloproteinase 10 (MMP10) and elastin (ELN) genes, and AAA. The results will require confirmation using an independent set of samples. After replication it is possible that these sequence changes in combination with other risk factors could be used in the future to identify individuals who are at increased risk for developing an AAA. [less ▲]Detailed reference viewed: 9 (1 ULg)
Genetic Analysis of Rwandan Patients With Cystic Fibrosis-Like Symptoms: Identification of Novel Cystic Fibrosis Transmembrane Conductance Regulator and Epithelial Sodium Channel Gene Variants.
; ; Verhaeghe, Catherine et al
in CHEST (2009), 135(5), 1233-42
Background The defect in chloride and sodium transport in cystic fibrosis (CF) patients is a consequence of CFTR loss of function and of an abnormal interaction between CFTR and ENaC. A few patients were ... [more ▼]
Background The defect in chloride and sodium transport in cystic fibrosis (CF) patients is a consequence of CFTR loss of function and of an abnormal interaction between CFTR and ENaC. A few patients were described with CF-like symptoms, a single CFTR mutation and an ENaC mutation. Methods To study African patients with CF-like symptoms and to relate the disease to gene mutations of both CFTR and ENaC genes, we collected clinical data and DNA samples from 60 African patients with a CF phenotype. The CFTR gene was first analyzed in all patients by dHPLC followed by direct sequencing, whereas the SCNN1A, SCNN1B and SCNN1G subunits of ENaC gene were analyzed by sequencing in the five patients who carried only one CF mutation. The frequency of all identified ENaC variants was established in a control group of 200 healthy individuals and in the 55 CF-like patients without any CFTR mutation Results Three CFTR mutants, including one previously undescribed missense mutation (p.A204T), and a 5T/7T variant were identified in five patients. ENaC gene sequencing in these 5 patients detected 8 ENaC variants: c.72T>C and p.V573I in SCNN1A; p.V348M, p.G442V, c.1473 + 28C>T, and p.T577T in SCNN1B; and p.S212S, c.1176 + 30G>C in SCNN1G. In the 55 CF-like patients without any CFTR mutation, we identified five of these eight ENaC variants, including the frequent p.G442V polymorphism, but we did not detect the presence of the p.V348M, p.T577T, and c.1176 + 30G>C ENaC variants. Moreover, these last three ENaC variants, p.V348M, p.T577T, and c.1176 + 30G>C, were not found in the control group. Conclusion Our data suggest that CF-like syndrome in Africa could be associated with CFTR and ENaC mutations. [less ▲]Detailed reference viewed: 233 (12 ULg)
Genetic and biochemical characterization of cytoplasmic and mitochondrial ASN-tRNA synthetase fucntions in two mutant yeast strains.
; Vandenbol, Micheline ; Portetelle, Daniel et al
in Yeast (Chichester, England) (1995), 11Detailed reference viewed: 3 (0 ULg)
Genetic and biochemical characterization of cytoplasmic and mitochondrial ASN-tRNA synthetase functions in two mutans yeast strains.
; Vandenbol, Micheline ; Portetelle, Daniel et al
Poster (1995)Detailed reference viewed: 8 (0 ULg)
Genetic and environmental interactions on the development of rheumatoid arthritis
MALAISE, Olivier ; VON FRENCKELL, Christian ; Malaise, Michel
in Revue Médicale de Liège (2012), 67(5-6), 305-13Detailed reference viewed: 11 (0 ULg)
Genetic and environmental relationships between body condition score and milk production traits in Canadian Holsteins.
; Bastin, Catherine ; et al
in Journal of Dairy Science (2012), 95(1), 410-9
The objective of this research was to estimate genetic parameters of first-lactation body condition score (BCS), milk yield, fat percentage (Fat%), protein percentage (Prot%), somatic cell score (SCS ... [more ▼]
The objective of this research was to estimate genetic parameters of first-lactation body condition score (BCS), milk yield, fat percentage (Fat%), protein percentage (Prot%), somatic cell score (SCS), milk urea nitrogen (MUN), lactose percentage (Lact%), and fat to protein ratio (F:P) using multiple-trait random regression animal models. Changes in covariances between BCS and milk production traits on a daily basis have not been investigated before and could be useful for determining which BCS estimated breeding values (EBV) might be practical for selection in the future. Field staff from Valacta milk recording agency (Sainte-Anne-de-Bellevue, QC, Canada) collected BCS from Quebec herds several times per cow throughout the lactation. Average daily heritabilities and genetic correlations among the various traits were similar to literature values. On an average daily basis, BCS was genetically unfavorably correlated with milk yield (i.e., increased milk yield was associated with lower body condition). The unfavorable genetic correlation between BCS and milk yield became stronger as lactation progressed, but was equivalent to zero for the first month of lactation. Favorable genetic correlations were found between BCS with Prot%, SCS, and Lact% (i.e., greater BCS was associated with greater Prot%, lower SCS, and greater Lact%). These correlations were strongest in early lactation. On an average daily basis, BCS was not genetically correlated with Fat% or MUN, but was negatively correlated with F:P. Furthermore, BCS at 5 and 50 d in milk (DIM) had the most favorable genetic correlations with milk production traits over the lactation (at 5, 50, 150, and 250 DIM). Thus, early lactation BCS EBV shows potential for selection. Regardless, this study showed that the level of association BCS has with milk production traits is not constant over the lactation. Simultaneous selection for both BCS and milk production traits should be considered, mainly due to the unfavorable genetic correlation between BCS with milk yield. [less ▲]Detailed reference viewed: 33 (8 ULg)
Genetic and evolutionary perspectives on genogroup III, genotype 2 bovine noroviruses
Mauroy, Axel ; ; et al
in Archives of Virology (2013)Detailed reference viewed: 10 (3 ULg)
Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition
; Farnir, Frédéric ; Karim, Latifa et al
in Proceedings of the National Academy of Sciences of the United States of America (2004), 101(8), 2398-2403
We recently used a positional cloning approach to identify a nonconservative lysine to alanine substitution (K232A) in the bovine DGAT1 gene that was proposed to be the causative quantitative trait ... [more ▼]
We recently used a positional cloning approach to identify a nonconservative lysine to alanine substitution (K232A) in the bovine DGAT1 gene that was proposed to be the causative quantitative trait nucleotide underlying a quantitative trait locus (QTL) affecting milk fat composition, previously mapped to the centromeric end of bovine chromosome 14. We herein generate genetic and functional data that confirm the causality of the DGAT1 K232A mutation. We have constructed a high-density single-nucleotide polymorphism map of the 3.8-centimorgan BULGE30-BULGE9 interval containing the QTL and show that the association with milk fat percentage maximizes at the DGAT1 gene. We provide evidence that the K allele has undergone a selective sweep. By using a baculovirus expression system, we have expressed both DGAT1 alleles in Sf9 cells and show that the K allele, causing an increase in milk fat percentage in the live animal, is characterized by a higher V-max in producing triglycerides than the A allele. [less ▲]Detailed reference viewed: 12 (2 ULg)
Genetic and functional evidence for a role of CYLD in Crohn’s Disease: results from a European consortium
; ; et al
in Journal of Crohn’s and Colitis [=JCC] (2012)Detailed reference viewed: 21 (5 ULg)
Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water.
Fontaine, Michaël C. ; ; Michaux, Johan et al
in Proceedings of the Royal Society B : Biological Sciences (2010), 277(1695), 2829-37
Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing ... [more ▼]
Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing the repercussions on apex marine predators remains a challenging issue, especially for pelagic species. In this study, we use Bayesian coalescent modelling of microsatellite variation to track the population demographic history of one of the smallest temperate cetaceans, the harbour porpoise (Phocoena phocoena) in European waters. Combining genetic inferences with palaeo-oceanographic and historical records provides strong evidence that populations of harbour porpoises have responded markedly to the recent climate-driven reorganization in the eastern North Atlantic food web. This response includes the isolation of porpoises in Iberian waters from those further north only approximately 300 years ago with a predominant northward migration, contemporaneous with the warming trend underway since the 'Little Ice Age' period and with the ongoing retreat of cold-water fishes from the Bay of Biscay. The extinction or exodus of harbour porpoises from the Mediterranean Sea (leaving an isolated relict population in the Black Sea) has lacked a coherent explanation. The present results suggest that the fragmentation of harbour distribution range in the Mediterranean Sea was triggered during the warm 'Mid-Holocene Optimum' period (approx. 5000 years ago), by the end of the post-glacial nutrient-rich 'Sapropel' conditions that prevailed before that time. [less ▲]Detailed reference viewed: 50 (16 ULg)
Genetic and kinetic characterization of the novel AmpC beta-lactamases DHA-6 and DHA-7.
; ; Kerff, Frédéric et al
in Antimicrobial agents and chemotherapy (2014)
During a Spanish surveillance study, two natural variants of DHA beta-lactamases, DHA-6 and DHA-7 were found, with the replacements Ala226Thr and Phe322Ser respect to DHA-1, respectively. The enzymes were ... [more ▼]
During a Spanish surveillance study, two natural variants of DHA beta-lactamases, DHA-6 and DHA-7 were found, with the replacements Ala226Thr and Phe322Ser respect to DHA-1, respectively. The enzymes were isolated from Escherichia coli and Enterobacter cloacae clinical isolates, respectively. The aim of the study was the genetic, microbiological and biochemical characterization of the DHA-6 and DHA-7 beta-lactamases. The blaDHA-6 andblaDHA-7 genes were located in I1 and HI2 incompatibility group plasmids of 87.3 and 310.4 kb, respectively. The gene context of both blaDHA-6 andblaDHA-7 was similar to that already described for blaDHA-1 gene and included the qnrB4 and aadA genes. The MICs for cephalothin, aztreonam, cefotaxime and ceftazidime were 8 to 30 fold lower for the DHA-6 than for DHA-1 and DHA-7 expressed in the same isogenic E.coli TG1 strain. Interestingly the MIC for cefoxitin was higher in DHA-6 expressing transformant compared to DHA-1 and DHA-7. Biochemical studies with pure beta-lactamases revealed a slightly lower catalytic efficiency of DHA-6 against cephalothin, ceftazidime and cefotaxime compared to DHA-1 and DHA-7. To understand this behavior, stability experiments were carried out and showed that the DHA-6 protein displayed a significantly higher stability than DHA-1 and DHA-7 enzymes. The proximity of Thr226 to the N-terminal in the tertiary protein structure in DHA-6 may promote this stabilization and consequently could induce a slight reduction of the dynamic of this enzyme primarily affecting the hydrolysis of some of the bulkiest antibiotics. [less ▲]Detailed reference viewed: 15 (1 ULg)
Genetic and microbial factors modulating the ubiquitin proteasome system in inflammatory bowel disease.
; ; et al
in Gut (2013)
OBJECTIVE: Altered microbiota composition, changes in immune responses and impaired intestinal barrier functions are observed in IBD. Most of these features are controlled by proteases and their ... [more ▼]
OBJECTIVE: Altered microbiota composition, changes in immune responses and impaired intestinal barrier functions are observed in IBD. Most of these features are controlled by proteases and their inhibitors to maintain gut homeostasis. Unrestrained or excessive proteolysis can lead to pathological gastrointestinal conditions. The aim was to validate the identified protease IBD candidates from a previously performed systematic review through a genetic association study and functional follow-up. DESIGN: We performed a genetic association study in a large multicentre cohort of patients with Crohn's disease (CD) and UC from five European IBD referral centres in a total of 2320 CD patients, 2112 UC patients and 1796 healthy controls. Subsequently, we did an extensive functional assessment of the candidate genes to explore their causality in IBD pathogenesis. RESULTS: Ten single nucleotide polymorphisms (SNPs) in four genes were significantly associated with CD: CYLD, USP40, APEH and USP3. CYLD was the most significant gene with the intronically located rs12324931 the strongest associated SNP (pFDR=1.74e-17, OR=2.24 (1.83 to 2.74)). Five SNPs in four genes were significantly associated with UC: USP40, APEH, DAG1 and USP3. CYLD, as well as some of the other associated genes, is part of the ubiquitin proteasome system (UPS). We therefore determined if the IBD-associated adherent-invasive Escherichia coli (AIEC) can modulate the UPS functioning. Infection of intestinal epithelial cells with the AIEC LF82 reference strain modulated the UPS turnover by reducing poly-ubiquitin conjugate accumulation, increasing 26S proteasome activities and decreasing protein levels of the NF-kappaB regulator CYLD. This resulted in IkappaB-alpha degradation and NF-kappaB activation. This activity was very important for the pathogenicity of AIEC since decreased CYLD resulted in increased ability of AIEC LF82 to replicate intracellularly. CONCLUSIONS: Our results reveal the UPS, and CYLD specifically, as an important contributor to IBD pathogenesis, which is favoured by both genetic and microbial factors. [less ▲]Detailed reference viewed: 26 (1 ULg)
Genetic and molecular characterisation of Pichia anomala (strain K), antagonistic yeast against postharvest diseases on apples
; Jijakli, Haissam ; Vandenbol, Micheline
Poster (2002)Detailed reference viewed: 9 (0 ULg)
Genetic and non genetic effects on growth traits of West African Dwarf sheep in Benin (West Africa)
; ; et al
in Livestock Production Science (2008)Detailed reference viewed: 75 (25 ULg)
Genetic and splice variations of Bos taurus CD46 shift cell permissivity to BVDV, the bovine pestivirus.
Zezafoun, Hussein ; ; Desmecht, Daniel
in Veterinary Microbiology (2011), 152(3-4), 315-27
The pestivirus bovine viral diarrhea virus (BVDV) is known to bind to the CD46 molecule, which subsequently promotes entry of the virus. Mapping of the BVD-virion-binding site has shown that two peptides ... [more ▼]
The pestivirus bovine viral diarrhea virus (BVDV) is known to bind to the CD46 molecule, which subsequently promotes entry of the virus. Mapping of the BVD-virion-binding site has shown that two peptides, 66EQIV69 and 82GQVLAL87, located on antiparallel beta sheets in the most distal complement control protein module (CCP1), provide the attachment platform. In the present study, we reveal the existence of ten distinct allelic versions of the CCP1 module, varying significantly in frequency among taurine and indicine races. A complex mRNA splicing pattern was also evidenced for bovine CD46, generating three different serine-threonine-proline segments and five different cytoplasmic domains. The four most frequent allelic variants and the six splice variants were then expressed in BVDV-nonpermissive porcine cells and the quantity of progeny virions generated by each cell preparation was measured 48 h post-infection. As expected, ectopic expression of the 10 bovine CD46 isoforms rendered the PK15 cells permissive to BVDV, as attested by the 100,000-fold greater recovery of virions from these cells than from non-transfected cells. This permissivity increase was significantly lower (-33%, P<0.001) when the canonical CCP1 was replaced with the variant most frequent in zebus, suggesting positive or negative selection of this allele in the latter and in the former, respectively. The predicted secondary structure of this variant suggests that the measured loss of function is due to the disappearance of one of the two beta sheets constituting the BVDV attachment platform. On the other hand we showed that for a given CCP1, the titer recovered at 48 hpi also depended on the nature of the CD46 cytoplasmic domain (P<0.001). This result implies that virus binding generates a cytoplasmic-tail-dependent outside-in signal that determines permissivity to BVDV. [less ▲]Detailed reference viewed: 38 (4 ULg)
Genetic association and functional role of Crohn disease risk alleles involved in microbial sensing, autophagy, and endoplasmic reticulum (ER) stress.
; ; et al
in Autophagy (2013), 9(12), 2046-55
Genome-wide association studies have identified several genes implicated in autophagy (ATG16L1, IRGM, ULK1, LRRK2, and MTMR3), intracellular bacterial sensing (NOD2), and endoplasmic reticulum (ER) stress ... [more ▼]
Genome-wide association studies have identified several genes implicated in autophagy (ATG16L1, IRGM, ULK1, LRRK2, and MTMR3), intracellular bacterial sensing (NOD2), and endoplasmic reticulum (ER) stress (XBP1 and ORMDL3) to be associated with Crohn disease (CD). We studied the known CD-associated variants in these genes in a large cohort of 3451 individuals (1744 CD patients, 793 ulcerative colitis (UC) patients and 914 healthy controls). We also investigated the functional phenotype linked to these genetic variants. Association with CD was confirmed for NOD2, ATG16L1, IRGM, MTMR3, and ORMDL3. The risk for developing CD increased with an increasing number of risk alleles for these genes (P<0.001, OR 1.26 [1.20 to 1.32]). Three times as many (34.8%) CD patients carried a risk allele in all three pathways, in contrast to 13.3% of the controls (P<0.0001, OR = 3.46 [2.77 to 4.32]). For UC, no significant association for one single nucleotide polymorphism (SNP) was found, but the risk for development of UC increased with an increasing total number of risk alleles (P = 0.001, OR = 1.10 [1.04 to 1.17]). We found a genetic interaction between reference SNP (rs)2241880 (ATG16L1) and rs10065172 (IRGM) in CD. Functional experiments hinted toward an association between an increased genetic risk and an augmented inflammatory status, highlighting the relevance of the genetic findings. [less ▲]Detailed reference viewed: 23 (1 ULg)
Genetic basis of congenital erythrocytosis: mutation update and online databases.
; ; et al
in Human mutation (2014), 35(1), 15-26
Congenital erythrocytosis (CE), or congenital polycythemia, represents a rare and heterogeneous clinical entity. It is caused by deregulated red blood cell production where erythrocyte overproduction ... [more ▼]
Congenital erythrocytosis (CE), or congenital polycythemia, represents a rare and heterogeneous clinical entity. It is caused by deregulated red blood cell production where erythrocyte overproduction results in elevated hemoglobin and hematocrit levels. Primary congenital familial erythrocytosis is associated with low erythropoietin (Epo) levels and results from mutations in the Epo receptor gene (EPOR). Secondary CE arises from conditions causing tissue hypoxia and results in increased Epo production. These include hemoglobin variants with increased affinity for oxygen (HBB, HBA mutations), decreased production of 2,3-bisphosphoglycerate due to BPGM mutations, or mutations in the genes involved in the hypoxia sensing pathway (VHL, EPAS1, and EGLN1). Depending on the affected gene, CE can be inherited either in an autosomal dominant or recessive mode, with sporadic cases arising de novo. Despite recent important discoveries in the molecular pathogenesis of CE, the molecular causes remain to be identified in about 70% of the patients. With the objective of collecting all the published and unpublished cases of CE the COST action MPN&MPNr-Euronet developed a comprehensive Internet-based database focusing on the registration of clinical history, hematological, biochemical, and molecular data (http://www.erythrocytosis.org/). In addition, unreported mutations are also curated in the corresponding Leiden Open Variation Database. [less ▲]Detailed reference viewed: 17 (2 ULg)