LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces     

F Ytournel  S Teyssèdre  D Roldan  M Erbe  H Simianer  D Boichard  H Gilbert  T Druet  A Legarra 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2012,129(5):417-421

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.  相似文献   

Investigation of postpartum dairy cows' uterine microbial diversity using metagenomic pyrosequencing of the 16S rRNA gene     

Machado VS  Oikonomou G  Bicalho ML  Knauer WA  Gilbert R  Bicalho RC 《Veterinary microbiology》2012,159(3-4):460-469

The objective of this study was the use of metagenomic pyrosequencing of the 16S rRNA gene for the investigation of postpartum dairy cows' uterine bacterial diversity. The effect of subcutaneous supplementation of a trace mineral supplement containing Zn, Mn, Se, and Cu (Multimin North America, Inc., Fort Collins, CO) at 230 days of gestation and 260 days of gestation on dairy cows' uterine microbiota was also evaluated. Uterine lavage samples were collected at 35 DIM and were visually scored for the presence of purulent or mucopurulent secretion. The same samples were also used for the acquisition of bacterial DNA. The 16S rRNA genes were individually amplified from each sample. Pyrosequencing of the samples was carried at the Cornell University Life Sciences Core Laboratories Center using Roche 454 GS-FLX System Titanium Chemistry. The Ribosomal Database Project online tools were used for the analysis of the obtained sequences library. Bacteroides spp., Ureaplasma spp., Fusobacterium spp., Peptostreptococcus spp., Sneathia spp., Prevotella spp. and Arcanobacterium spp. prevalence was significantly (P<0.05) higher in samples derived from cows that had a higher uterine lavage sample score. Bacteroides spp., Ureaplasma spp., Fusobacterium spp., and Arcanobacterium spp. prevalence was significantly (P<0.05) higher in samples derived from cows that were not pregnant by 200 DIM. Anaerococcus spp., Peptostreptococcus spp., Parabacteroides spp., and Propionibacterium spp. prevalence was significantly (P<0.05) lower in samples derived from cows that were trace mineral supplemented.  相似文献   

Infiltration characteristics of volcanic sloping soils on Mt. Elgon,Eastern Uganda     

Yazidhi Bamutaze  Moses Makooma Tenywa  Mwanjalolo Jackson Gilbert Majaliwa  Veerle Vanacker  Festus Bagoora  Mathias Magunda  Joy Obando  John Ejiet Wasige 《CATENA》2010

Water infiltration is an important hydrological process that influences runoff and soil loss patterns in mountain ecosystems. In this paper, we present results on spatial variation in infiltration in croplands on the volcanic soils of Mt. Elgon, in Eastern Uganda. Twelve experimental sites with slope gradients ranging from 12 to 32% were established. Infiltration tests were carried out with a double ring infiltrometer and three measurements were taken at the upper, middle and lower sections of each experimental site to assess the local variability of infiltration. In addition soil information was collected on each experimental site. The soil infiltration data were then evaluated to fit to four commonly used water infiltration models: (1) Philip (1957), (2) Green–Ampt (1911), (3) Horton (1940) and (4) Kostiakov (1932). The twelve experimental sites cover two cropping systems: annual (6 sites) and perennial (6 sites) crops. Based on the results, we examine the spatial variability of infiltration, the relationship of infiltration to landscape position, and the influence of soil composition on infiltration rates on the slopes. The factors affecting spatial variability of soil infiltration were analysed using correlation and regression techniques. Steady state infiltration rates generally increased with the slope gradient and were crop type independent (P < 0.05). The performance of the four applied water infiltration models was generally good with mean R² values ranging from 0.79 to 0.87, although all the models tended to over-predict the steady state infiltration rates at most sites. Overall, the Philip's and Kostiakov gave better results than the Horton and Green–Ampt models in reproducing the infiltration process on Mt. Elgon.  相似文献   

Phenotype of macular corneal dystrophy in Labrador Retrievers: A multicenter study     

Claudia Busse  Christiane Kafarnik  Rose Linn‐Pearl  Christelle Volmer  Kaspar Matiasek  Johana E. Premont  Thomas Dulaurent  Jean‐Yves Douet  Ida Gilbert  Sari Jalomäki  Katrin Trost  Pierre‐Francois Isard  Ryan Boyd  Isabelle Raymond 《Veterinary ophthalmology》2019,22(3):294-304

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Estimating direct genetic and maternal effects affecting rabbit growth and feed efficiency with a factorial design     

Herv Garreau  Julien Ruesche  Hlne Gilbert  Elodie Balmisse  Florence Benitez  Franois Richard  Ingrid David  Laurence Drouilhet  Olivier Zemb 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2019,136(3):168-173

The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross‐fostered with non‐selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 ± 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (?82.9 ± 9 g, p < 0.0001) and at 63 days (?161 ± 16 g, p < 0.0001). They also had a lower ADG (?2.36 ± 0.36 g/day, p < 0.0001), RFI (?521 ± 24 g/day, p < 0.0001) and a lower FI (?855 ± 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: ?0.35 ± 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): ?2.35 g/day versus 2.94 g/day for ADG, ?0.39 versus ?0.40 for FCR, ?577 g versus ?565 g for RFI and ?879 g versus ?859 g for FI, respectively). Thus, no genotype‐by‐environment (housing) interaction is expected at the commercial level, that is, no re‐ranking of the animals due to collective housing.  相似文献   

Oxytocin Secretion and Management of Parturition in the Pig     

CL Gilbert 《Reproduction in domestic animals》1999,34(3-4):193-200

This paper will examine the augmentation of oxytocin (OT) secretion in the final day before parturition in the pig, and review the key endocrine systems of influence. Recent experiments have shown that increases in plasma OT above baseline secretion were not seen until 7 hours prior to the birth of the first piglet. Progesterone release begins to decline some days before birth and is unlikely to provide such acute control of OT release immediately before birth. The involvement of relaxin is complex but it is possible that the prepartum relaxin surge, which ends close to the OT rise, attenuates OT secretion to prevent excessive myometrial activity until cervical softening has occurred. Increasing myometrial electromyographic activity appears to be seen as relaxin concentrations decline and OT increase. Endogenous opioid peptides within the hypothalamus exert a profound influence upon OT secretion during birth, and some effects are also seen prepartum. It has been proposed that this system may allow parturition to be interrupted or slowed in response to changes in environment. The therapeutic choice of exogenous injections of OT to control the onset time of parturition will be discussed in the light of current physiological knowledge.  相似文献   

Mass selection for small‐sized cysts in Artemia franciscana produced in Vinh Chau salt ponds,Vietnam     

Nguyen Thi Hong Van  Nguyen Van Hoa  Peter Bossier  Patrick Sorgeloos  Gilbert Van Stappen 《Aquaculture Research》2014,45(10):1591-1599

Unidirectional mass truncation selection for small‐sized cysts was carried out on brine shrimp (Artemia franciscana Kellogg 1906), Vinh Chau strain, Vietnam, through cyst sieving and then culturing the selected individuals (<5% of the population) under field and laboratory conditions over two successive generations (F₁ and F₂). The results showed that at both culture scales, the cyst size of the selected line was smaller (P < 0.05) compared with the control (non‐selected) line, illustrating that there was a response to selection. The cyst size decreased about 3% per generation and the accumulated gain on the target trait was in the range 5.82–6.07% at the end of the selection process compared with the base population. The realized heritability estimation (h²) for cyst size was 0.23 ± 0.06 and 0.74 ± 0.19 in the field trials and 0.34 and 0.51 in the laboratory test for the F₁ and F₂ generation respectively. The variations found between the respective trials may be explained as the result of environmental interaction with the selection process, but the results show that a selection program for small‐sized cysts in Artemia by mass selection is possible.  相似文献   

Staphylococcus pseudintermedius necrotizing fasciitis in a dog     

J. Scott Weese  Roberta Poma  Fiona James  Gilbert Buenviaje  Robert Foster  Durda Slavic 《The Canadian veterinary journal. La revue veterinaire canadienne》2009,50(6):655-656

Staphylococcus pseudintermedius was implicated as the cause of rapidly progressive and fatal necrotizing fasciitis in a dog. The isolate was methicillin-susceptible and did not contain genes encoding the Panton-Valentine leukocidin. While Streptococcus canis is typically considered to be the main cause of necrotizing fasciitis in dogs, staphylococci should also be considered.  相似文献   

Platelet aggregation responses in clinically healthy adult llamas     

Rosanne M. Gilbert  Karyn E. Bird  Michelle A. Kutzler 《Veterinary clinical pathology / American Society for Veterinary Clinical Pathology》2009,38(1):42-45

Background: Limited information exists regarding hemostasis in camelids despite the importance of platelet function testing in the accurate identification of platelet disorders. As further importation of llamas to North America is restricted, variability in breeding stock will continue to decrease, potentially leading to an increase in heritable bleeding disorders. Objective: The objective of this study was to measure platelet aggregation responses in clinically healthy llamas and provide baseline data to which abnormal platelet function may be compared in the future. Methods: Blood samples were collected from 39 healthy adult llamas, citrated, and centrifuged to produce platelet‐rich plasma (PRP). Within 4 hours of the blood draw, 20 μL of each agonist reagent were added to 180 μL of PRP. Final concentrations of agonists were 2 × 10^?5 M ADP, 0.19 mg collagen/mL PRP, 1 × 10^?4 M epinephrine, and 500 μg arachidonic acid/mL PRP. Results: Llama platelets were most responsive to ADP and collagen, with a maximum percent aggregation (mean±SD) of 71.3±18.6% and 55.8±19% and aggregation rates of 9.5±3.9 and 6.7±3.7 cm/min, respectively. Llama platelet aggregation in response to epinephrine and arachidonic acid was minimal to absent. Conclusions: This study is the first of its kind to establish baseline values for platelet aggregation in healthy adult llamas.  相似文献   

Interrelationship of growth hormone AluI polymorphism and hyperketonemia with plasma hormones and metabolites in the beginning of lactation in dairy cows     

O. Balogh  K. Kovcs  M. Kulcsr  A. Gsprdy  H. Fbel  A. Zsolnai  L. Fsüs  C. Delavaud  Y. Chilliard  R.O. Gilbert  Gy. Huszenicza 《Livestock Science》2009,123(2-3):180-186

A polymorphic site of the growth hormone gene (AluI polymorphism) that results in an amino acid change at position 127 of the protein chain (leucine, L to valine, V) has been linked to differences in circulating metabolites and metabolic hormones of calves and bulls and to milk yield traits of lactating cows. Our objective was to investigate the interrelationship of this polymorphism with plasma concentrations of β-hydroxybutyrate, insulin, IGF-I and leptin in postpartum dairy cows. Blood samples were taken from clinically healthy, spring-calving, group-fed Holstein-Friesian cows (n = 257; 7 large-scale farms) 4–13 days after calving. Of all herds, 100 cows had plasma β-hydroxybutyrate levels above 1.2 mmol/l and 157 cows were normoketonemic. The proportion of valine carriers and LL cows was not different within groups of normo- and hyperketonemic animals. Genotype was not associated with plasma β-hydroxybutyrate, insulin, IGF-I and leptin levels either in all of the herds or in the two with the highest proportion of the valine allele carriers (n = 28, 72%). We found significantly lower insulin, IGF-I and leptin concentrations in the presence of hyperketonemia compared to normoketonemic cows. There were strong negative correlations between BHB and the other blood parameters, while insulin, IGF-I and leptin were positively related to each other. In conclusion, in the first two weeks after calving we could not demonstrate any effect of AluI polymorphism on plasma concentrations of β-hydroxybutyrate and metabolic hormones studied. Hyperketonemia was associated with a significant decrease in insulin, IGF-I and leptin blood levels. We infer that cows homozygous for the leucine allele or carrying the valine allele may have a similar endocrine and metabolic response to the challenge of increased nutrient demand early postpartum and that the presence of hyperketonemia is mainly linked to the hormonal and metabolic changes occurring at the onset of lactation.  相似文献