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PubMed1995

T cell receptor V beta repertoire in mice lacking endogenous mouse mammary tumor provirus.

When endogenous mouse mammary tumor virus (MMTV) superantigens (SAg) are expressed in the first weeks of life an efficient thymic deletion of T cells expressing MMTV SAg-reactive T cell receptor (TcR) V beta segments is observed. As most inbred mouse strains and wild mice contain integrated MMTV DNA, knowing the precise extent of MMTV influence on T cell development is required in order to study T cell immunobiology in the mouse. In this report, backcross breeding between BALB.D2 (Mtv-6, -7, -8 and -9) and 38CH (Mtv-) mice was carried out to obtain animals either lacking endogenous MMTV or containing a single MMTV locus, i.e. Mtv-6, -7, -8 or -9. The TcR V beta chain (TcR V beta) usage in these mice was analyzed using monoclonal antibodies specific for TcR V beta 2, V beta 3, V beta 4, V beta 5, V beta 6, V beta 7, V beta 8, V beta 11, V beta 12 and V beta 14 segments. Both Mtv-8+ mice and Mtv-9+ mice deleted TcR V beta 5+ and V beta 11+ T cells. Moreover, we also observed the deletion of TcR V beta 12+ cells by Mtv-8 and Mtv-9 products. Mtv-6+ and Mtv-7+ animals deleted TcR V beta 3+ and V beta 5+ cells, and TcR V beta 6+, V beta 7+ and V beta 8.1+ cells, respectively. Unexpectedly, TcR V beta 8.2+ cells were also deleted in some backcross mice expressing Mtv-7. TcR V beta 8.2 reactivity to Mtv-7 was shown to be brought by the 38CH strain and to result from an amino acid substitution (Asn-->Asp) in position 19 on the TcR V beta 8.2 fragment. Reactivities of BALB.D2 TcR V beta 8.2 and 38CH TcR V beta 8.2 to the exogenous infectious viruses, MMTV(SW) and MMTV(SHN), were compared. Finally, the observation of increased frequencies of TcR V beta 2+, V beta 4+ and V beta 8+ CD4+ T cell subsets in Mtv-8+ and Mtv-9+ mice, and TcR V beta 4+ CD4+ T cells in Mtv-6+ and Mtv-7+ mice, when compared with the T cell repertoire of Mtv- mice, is consistent with the possibility that MMTV products contribute to positive selection of T cells.

Alleles↗
PubMed2004

Association genetics of complex traits in conifers.

Association studies are becoming the experimental approach of choice to dissect complex traits in many organisms from humans to model plant systems. The candidate gene based-association approach has several important advantages for complex trait dissection in many coniferous forest tree species, including random mating and unstructured populations, adequate levels of nucleotide diversity, rapid decay of linkage disequilibrium, and precise evaluation of phenotype from clonal or progeny testing. Allele discovery using association approaches should lead to more-efficient methods of marker-assisted breeding and a deeper understanding of genetic adaptation in forest trees.

Chromosome Mapping↗
PubMedDate not supplied

Improved experimental procedures for achieving efficient germ line transmission of nonobese diabetic (NOD)-derived embryonic stem cells.

The manipulation of a specific gene in NOD mice, the best animal model for insulin-dependent diabetes mellitus (IDDM), must allow for the precise characterization of the functional involvement of its encoded molecule in the pathogenesis of the disease. Although this has been attempted by the cross-breeding of NOD mice with many gene knockout mice originally created on the 129 or C57BL/6 strain background, the interpretation of the resulting phenotype(s) has often been confusing due to the possibility of a known or unknown disease susceptibility locus (e.g., Idd locus) cosegregating with the targeted gene from the diabetes-resistant strain. Therefore, it is important to generate mutant mice on a pure NOD background by using NOD-derived embryonic stem (ES) cells. By using the NOD ES cell line established by Nagafuchi and colleagues in 1999 (FEBS Lett., 455, 101-104), the authors reexamined various conditions in the context of cell culture, DNA transfection, and blastocyst injection, and achieved a markedly improved transmission efficiency of these NOD ES cells into the mouse germ line. These modifications will enable gene targeting on a "pure" NOD background with high efficiency, and contribute to clarifying the physiological roles of a variety of genes in the disease course of IDDM.

Animals↗
PubMed2006

The mutational consequences of plant transformation.

Plant transformation is a genetic engineering tool for introducing transgenes into plant genomes. It is now being used for the breeding of commercial crops. A central feature of transformation is insertion of the transgene into plant chromosomal DNA. Transgene insertion is infrequently, if ever, a precise event. Mutations found at transgene insertion sites include deletions and rearrangements of host chromosomal DNA and introduction of superfluous DNA. Insertion sites introduced using Agrobacterium tumefaciens tend to have simpler structures but can be associated with extensive chromosomal rearrangements, while those of particle bombardment appear invariably to be associated with deletion and extensive scrambling of inserted and chromosomal DNA. Ancillary procedures associated with plant transformation, including tissue culture and infection with A tumefaciens, can also introduce mutations. These genome-wide mutations can number from hundreds to many thousands per diploid genome. Despite the fact that confidence in the safety and dependability of crop species rests significantly on their genetic integrity, the frequency of transformation-induced mutations and their importance as potential biosafety hazards are poorly understood.

Journal Article↗
PubMed1978

[Farmer's lung disease in the Aveyron department (a retrospective study of 82 cases)].

The authors present a retrospective study of 82 cases of farmer's lung disease in the Aveyron department. Observations were selected on precise diagnostic criteria classified on acute (8 cases), progressive (69 cases) and chronic alveolitis (5 cases). They observe an almost exclusive repartition in the bovine breeding areas, which are regions of large hay culture and of high humidity. They show the annual repartition of cases is strongly linked to the pluviometry of the previous hay-making. They underline the fact that the modernising of agricultural work reduces some factors favourable to the disease but can promote new ones.

Acute Disease↗
PubMed2024

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats.

INTRODUCTION: Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations. OBJECTIVES: The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly. METHODS: In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants. RESULTS: AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified. CONCLUSION: AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://cat.annotation.jp/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine.

Animals↗
PubMed1999

Ferret nutrition.

The unusually short intestinal tract of ferrets and closely related mustelids lacks a cecum and ileocolic valve. As a result, the transit time of ingesta in these carnivores is very rapid compared with other animals, and their food is inefficiently digested. Although the precise nutritional requirements of ferrets have not been determined by feeding defined diets, information has been compiled from experience feeding commercial and analyzed homemade diets to breeding ferrets, fitch, and mink at all stages of their lives. The requirements of spayed or neutered pet ferrets are met by allowing them constant access to drinking water and a palatable, pelleted, or extruded, 90% dry matter, premium cat or ferret food that, as fed, contains at least 15% fat and 30% high quality, meat source protein, less than 30% carbohydrates, and approximately 4 Kcal of metabolizable energy per gram. Lower density diets with more carbohydrate and less protein are associated with poor reproductive performance and growth and greater susceptibility to infectious and metabolic diseases.

Animal Nutritional Physiological Phenomena↗
PubMed2006

Genetic relatedness analysis: modern data and new challenges.

Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.

Animals↗
PubMed2004

Mitochondrial encephalomyopathies: diagnostic approach.

Mitochondrial diseases have extremely heterogeneous clinical presentations due to the ubiquitous nature of mitochondria and the dual genetic control of the respiratory chain. Thus, mitochondrial disorders can be multisystemic (mitochondrial encephalomyopathies) or confined to a single tissue, and they can be sporadic or transmitted by mendelian or maternal inheritance. Mendelian disorders are usually inherited as autosomal recessive traits, tend to present earlier in life, and usually "breed true" in each family. By contrast, mitochondrial DNA-related diseases usually start later and vary in their presentation within members of the same family. Precise diagnosis is often a challenge; we go through the traditional steps of the diagnostic process, trying to highlight clues to mitochondrial dysfunction in the family history, physical and neurological examinations, routine and special laboratory tests, and histo-chemical and biochemical results of the muscle biopsy. The ultimate goal is to reach, whenever possible, a definitive molecular diagnosis, which permits rational genetic counseling and a prenatal diagnosis.

Clinical Laboratory Techniques↗
PubMed2005

Genetic variance and breeding values for resistance to a wind-borne disease [Sphaerotheca macularis (Wallr. ex Fr.)] in strawberry (Fragaria x ananassa Duch.) estimated by exploring mixed and spatial models and pedigree information.

A mixed model approach was used to estimate variance components and heritabilities for resistance to powdery mildew, a wind-borne disease in strawberry. In order to improve precision in the statistical computations, spatial error control effects were included to account for systematic environmental variations in the large field trials. Pedigree information was included where feasible. Seedling families obtained from an incomplete 63-by-63 diallel cross were grown at six locations and scored subjectively for mildew attack three times during the growing season. The 63 parents included both European and American cultivars as well as advanced selections from various breeding programmes. A total of 298 full-sib families were realized, including 26 reciprocal families. No reciprocal differences were found. On a plot-mean basis, the broad-sense heritability was found to be intermediate, H(2) = 0.44-0.50, depending on whether the pedigree information was included in the model or not. The increase was mainly due to a substantial increase in the additive variance component. Likewise, the narrow-sense heritability increased from h(2) = 0.39 to h(2) = 0.45 when the pedigree information was included, while the ratio of the specific combining ability variance to the general combining ability variance fell from 13% to 10%. The predicted breeding values of the 63 parents demonstrate that important cultivars such as Elsanta and Korona are unlikely to produce progenies with a high degree of resistance. On the other hand, the Norwegian cultivar Solprins, the Canadian cultivar Kent and the Italian cultivar Patty appeared to give highly resistant progeny. At the full-sib level, the estimated disease scores ranged from 1.15 (Kent x Induka) to 4.19 (Cavendish x Avanta), revealing a huge range of variation for powdery mildew resistance available for selection.

Analysis of Variance↗
PubMed2006

Finding the genes underlying adaptation to hypoxia using genomic scans for genetic adaptation and admixture mapping.

The complete sequencing the human genome and recent analytical advances have provided the opportunity to perform genome-wide studies of human variation. There is substantial potential for such population-genomic approaches to assist efforts to uncover the historical and demographic histories of human populations. Additionally, these genome-wide datasets allow for investigations of variability among genomic regions. Although all genomic regions in a population have experienced the same demographic events, they have not been affected by these events in precisely the same way. Much of the variability among genomic regions is simply the result of genetic drift (i.e., gene frequency changes resulting from the effects of small breeding-population size), but some is also the result of genetic adaptation, which will only affect the gene under selection and nearby regions. We have used a new DNA typing assay that allows for the genotyping of thousands of SNPs on hundreds of samples to identify regions most likely to have been affected by genetic adaptation. Populations that have inhabited different niches (e.g., high-altitude regions) can be used to identify genes underlying the physiological differences. We have used two methods (admixture mapping and genome scans for genetic adaptation) founded on the population-genomic paradigms to search for genes underlying population differences in response to chronic hypoxia. There is great promise that together these methods will facilitate the discovery of genes influencing hypoxic response.

Alleles↗
PubMedDate not supplied

Genes preserved in relatives.

The genes of an individual are said to be preserved in his relatives if they possess, collectively, all copies of his genes. We present a method for computing the probability that an individual's genes are preserved in his relatives. Using this method, we compute gene preservation probabilities (up to three linked loci) for a variety of relationships for humans and for haplodiploid species. The results suggest that some widely held notions in ethology and sociobiology seem to be questionable. From the gene preservation viewpoint, two brothers are far from enough to justify the sacrifice of one's own life, because the probability that an individual's genes are preserved in his two siblings is dismally small. The precise probability that an individual's genes are all preserved in a group of his relatives depends on the precise specification of the pedigree structure. We also demonstrate that, for a hymenopteran female, there is no practical difference, in terms of gene preservation probability, between helping her sisters to breed and breeding her own offspring. In fact, since the genes of her sister will be either lost or preserved in her nieces/nephews, it is more appropriate to compare the probability of preserving her genes through her own offspring with that through her nieces/nephews. We show that her chance of preserving all her genes is much higher if she chooses to breed her own offspring instead of helping her sister.

Animals↗
PubMed2001

Use of the preconditioned conjugate gradient algorithm as a generic solver for mixed-model equations in animal breeding applications.

Utility of the preconditioned conjugate gradient algorithm with a diagonal preconditioner for solving mixed-model equations in animal breeding applications was evaluated with 16 test problems. The problems included single- and multiple-trait analyses, with data on beef, dairy, and swine ranging from small examples to national data sets. Multiple-trait models considered low and high genetic correlations. Convergence was based on relative differences between left- and right-hand sides. The ordering of equations was fixed effects followed by random effects, with no special ordering within random effects. The preconditioned conjugate gradient program implemented with double precision converged for all models. However, when implemented in single precision, the preconditioned conjugate gradient algorithm did not converge for seven large models. The preconditioned conjugate gradient and successive overrelaxation algorithms were subsequently compared for 13 of the test problems. The preconditioned conjugate gradient algorithm was easy to implement with the iteration on data for general models. However, successive overrelaxation requires specific programming for each set of models. On average, the preconditioned conjugate gradient algorithm converged in three times fewer rounds of iteration than successive overrelaxation. With straightforward implementations, programs using the preconditioned conjugate gradient algorithm may be two or more times faster than those using successive overrelaxation. However, programs using the preconditioned conjugate gradient algorithm would use more memory than would comparable implementations using successive overrelaxation. Extensive optimization of either algorithm can influence rankings. The preconditioned conjugate gradient implemented with iteration on data, a diagonal preconditioner, and in double precision may be the algorithm of choice for solving mixed-model equations when sufficient memory is available and ease of implementation is essential.

Algorithms↗
PubMed1984

Variability in isolate recovery rates from multiple and single breeds of outbred pigmented rabbits in an experimental model of Candida keratitis.

We evaluated variability of isolate recovery rates in an experimental model of Candida keratitis for both heterogeneous, pigmented, outbred rabbits and homogeneous Dutch-belted rabbits. Our purpose was to achieve more precise evaluation of topical antifungal agents in our model by substantially reducing the component of variance due to inter-rabbit differences. For the homogeneous Dutch-belted rabbits, the overall variance was reduced by a factor of 2.34 (p = 0.18) vis a vis the heterogenous outbred rabbits. The greatest reduction, a factor of 3.5, was achieved for the inter-rabbit component of variance. The upper bound for the hereditability measure was reduced from 29% to 18%. These data suggest that (1) researchers using animal models should perform a components of variance analysis to identify the factors influencing experimental precision, and (2) for our model, additional reduction in variability must come from refinement of experimental technique.

Analysis of Variance↗
PubMed1990

The replication of bluetongue virus in Culicoides vectors.

BTV is maintained in nature by an endless series of alternating cycles of replication in Culicoides midges and various mammalian ruminant species. Experimentation has shown that the ability of the virus to infect Culicoides persistently and be transmitted by them is restricted to a relatively small number of species. In essence, therefore, the world distribution map of BTV is little more than a distribution map of competent insect vectors. Once ingested by a competent vector, BTV attaches to the luminal surface of the mid-gut cells, infects these cells and replicates in them. Progeny virus is then released through the basement lamina into the haemocoel from where the secondary target organs including the salivary glands are infected. Subsequent to virus replication in the salivary glands transmission can taken place. The whole cycle from infection to transmission takes between 10-15 days at 25 degrees C and individual vectors once infected usually remain so for life. Not all female midges within a vector species are susceptible to infection with BTV, or if infected, are competent to transmit the virus. A series of barriers or constraints exists within certain individuals of a vector species which either prevents virus infection or else restricts it in such a way as to stop transmission. Each population of a vector species of Culicoides has a variable proportion of these so-called refractory midges. The refractory and susceptible traits for BTV within a vector species are under genetic control, and by selective breeding, highly susceptible or completely insusceptible populations can be obtained. However, the mechanisms by which these traits are expressed are poorly understood. Further studies are therefore urgently required to determine the precise biochemical nature of these mechanisms and their mode of operation.

Animals↗
PubMed1991

The repeatability and effect of season on seminal characteristics and computer-aided sperm analysis in the stallion.

The within-stallion repeatability and effect of season on sperm movement characteristics, determined by computer-aided sperm analysis (CASA), were compared with those of other seminal characteristics. The computer-aided determinations of sperm movement were more repeatable than the seminal characteristics of gel-free volume and sperm cell concentration based on coefficients of variation obtained from the analysis of multiple ejaculates from the same stallions. A significant (P<0.05) seasonal effect on the computer-aided movement characteristic of mean sperm linearity was observed, with a reduction in sperm linearity in the winter months. The percentage of motile and progressively motile cells and mean sperm velocity determined by CASA also tended to be lower in the winter months. These changes in sperm movement characteristics paralleled changes in other seminal characteristics. The use of CASA may have value in the potential fertility evaluation of a stallion in that it can provide relatively precise quantification of sperm movement characteristics from the evaluation of only a few ejaculates. Some CASA derived sperm movement characteristics may be lower during the physiological nonbreeding season than during the breeding season.

Journal Article↗
PubMed1991

DNA fingerprinting in cattle using oligonucleotide probes.

Oligonucleotide probes specific for simple tandem repeat sequences produce individual specific DNA fingerprints in man and all animal species tested so far. Here 11 different synthetic probes were hybridized to bovine genomic DNAs which had been digested with the restriction endonucleases HinfI, AluI and HaeIII. Two of these probes gave DNA fingerprint patterns which were analysed for three German breeds. Different parameters were calculated, such as the average number of bands per individual or the probability of finding identical fingerprints in two unrelated individuals. The number of polymorphic bands varies from 11 to 23 in the different breeds and the probability of finding the same banding pattern in two unrelated individuals ranges from 1.5 x 10(-7) to 2.4 x 10(-7). Hence this DNA fingerprinting procedure allows precise identification of individuals. It is also a useful additional method for paternity testing in cattle.

Animals↗
PubMed2006

Major advances in determining appropriate selection goals.

Substantial increases of 3,500 kg of milk, 130 kg of fat, and 100 kg of protein per cow per lactation have resulted from improvements in genetics, nutrition, and management during the past 20 yr. At the same time, the interval from calving to conception increased (unfavorable) by 24 d. Genetics has accounted for about 55% of gains in the yield traits and about one-third of the change in interval to conception. Genetic gains in the yield traits and productive life have accumulated to around 1.7 and 1.2 genetic standard deviations since 1980. Unfavorable genetic changes in conception interval since 1980 and somatic cell score since 1990 have accumulated to 1.0 and 0.12 genetic standard deviations. The most important advance in selection indexes has been the introduction of nonyield traits. Advances in selection indexes have gone hand in hand with advances in data collection and genetic evaluation. As new traits were recorded in dairy management databases and as genetic evaluations were developed for these traits, they were incorporated into selection indexes. Until 1994, when somatic cell score and productive life were introduced, selection indexes provided by USDA included only yield traits. In 2000, composite type indexes for udder, feet and legs, and body size were added. Daughter pregnancy rate and service sire- and daughter-calving ease were included in 2003. The lifetime merit indexes introduced in 2003 have, for the first time, resulted in theoretical selection responses in the desired direction for all traits. During this time, the percentage relative economic weights in selection indexes increased from 0 to 45% for the nonyield traits. Selection emphasis on nonyield traits should continue to increase as additional traits (e.g., calf survival, metabolic disease, and male fertility) are introduced in the future. Wide variation exists among countries in traits included in selection indexes and in relative economic weights. Molecular genetic studies have identified many chromosome regions with potentially important major genes for economic traits. Use of DNA markers for genetic improvement is currently limited by lack of precision in marker location. Discovery of major genes will be accelerated by the availability of the bovine genome sequence, comparative genome maps and genome sequences across species, and increased use of breed crosses in molecular studies. As major genes are identified, their effects will be incorporated into genetic evaluations and selection indexes.

Animals↗