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1.
J Anim Sci ; 89(6): 1661-8, 2011 Jun.
Article in English | MEDLINE | ID: mdl-21239666

ABSTRACT

In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (≥90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was ≥5, the number of mismatches was ≤1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.


Subject(s)
Genetic Markers , Polymorphism, Single Nucleotide/genetics , Swine/genetics , Animals , Female , Genotype , Male , Pedigree
2.
Anim Genet ; 41(2): 122-7, 2010 Apr.
Article in English | MEDLINE | ID: mdl-19821810

ABSTRACT

In this study, a proposal is presented for the allele nomenclature of 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) for equine genotyping (Equus caballus). The nomenclature is based on sequence data of the polymorphic region of the STR loci as recommended by the DNA commission of the International Society for Forensic Genetics for human DNA typing. For each STR locus, several alleles were selected and animals homozygous for those alleles were subjected to sequence analysis. The alleles of the 17 STR loci consisted either of simple (10), compound (6) or complex repeat patterns (1). Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats, including all variable regions within the amplified fragment.


Subject(s)
Horses/genetics , Microsatellite Repeats , Alleles , Animals , Forensic Sciences/standards
3.
Anim Genet ; 40(5): 630-6, 2009 Oct.
Article in English | MEDLINE | ID: mdl-19397508

ABSTRACT

In this study, a proposal is presented for the allele nomenclature of 16 polymorphic short tandem repeat (STR) loci (BM1824, BM2113, ETH10, ETH225, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH3, TGLA53, BM1818, CSRM60, CSSM66, HAUT27 and ILSTS006) for bovine genotyping (Bos taurus). The nomenclature is based on sequence data of the polymorphic region(s) of the STR loci as recommended by the DNA commission of the International Society of Forensic Genetics for human DNA typing. To cover commonly and rarely occurring alleles, a selection of animals homozygous for the alleles at these STR loci were analysed and subjected to sequence studies. The alleles of the STR loci consisted either of simple or compound dinucleotide repeat patterns. Only a limited number of alleles with the same fragment size showed different repeat structures. The allele designation described here was based on the number of repeats including all variable regions within the amplified fragment. The set of 16 STR markers should be propagated for the use in all bovine applications including forensic analysis.


Subject(s)
Alleles , Cattle/genetics , Forensic Genetics/standards , Microsatellite Repeats/genetics , Animals , Base Sequence , DNA Primers/genetics , Forensic Genetics/methods , Molecular Sequence Data , Sequence Analysis, DNA/veterinary , Terminology as Topic
4.
Mol Biotechnol ; 23(2): 117-25, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12632696

ABSTRACT

A novel DNA technology enables the detection of universal variable fragments (UVF), thus revealing genetic variation without a priori sequence information. The detection of UVF markers is based on two amplifications of genomic DNA with the polymerase chain reaction. In the first amplification, two short oligonucleotide primers produce a large number of fragments. One primer is based on a microsatellite sequence, whereas the second primer can have any sequence. In the second amplification, the length of the primers is increased in order to decrease the number of amplicons. This enables the selection of polymorphic fragments. Restriction digestion can be used to further increase the number of polymorphisms. Until now, we have demonstrated UVF in several different species. In addition, with the present study we have contributed to the linkage map of the rabbit by localizing 11 UVF markers on different linkage groups. Mendelian inheritance was shown in this linkage study through a backcross of two inbred rabbit strains. The power of the UVF technique is based on the selection for microsatellite variation in combination with the detection of single-nucleotide polymorphisms. UVF thus offers the possibility of increasing the clustering of markers and localizing genes in species for which sequence information is either not present or only scarcely present.


Subject(s)
DNA Fingerprinting/methods , Gene Expression Profiling/methods , Genetic Markers/genetics , Polymerase Chain Reaction/methods , Animals , Animals, Inbred Strains , DNA Primers/genetics , Feasibility Studies , Genetic Linkage , Genetic Variation/genetics , Horses/genetics , Microsatellite Repeats/genetics , Polymorphism, Genetic/genetics , Rabbits/genetics , Random Amplified Polymorphic DNA Technique/methods , Reproducibility of Results , Sensitivity and Specificity
5.
FEMS Microbiol Lett ; 184(1): 35-40, 2000 Mar 01.
Article in English | MEDLINE | ID: mdl-10689162

ABSTRACT

Using a combination of dye adsorption and affinity elution we purified Aspergillus niger citrate synthase to homogeneity using a single column and characterised the enzyme. An A. niger citrate synthase cDNA was isolated by immunological screening and used to clone the corresponding citA gene. The deduced amino acid sequence showed high similarity to other fungal citrate synthases. After processing upon mitochondrial import, the calculated M(r) of A. niger citrate synthase is 48501, which agrees well with the estimated molecular mass of the purified protein (48 kDa). In addition to an N-terminal mitochondrial import signal, a peroxisomal target sequence (AKL) was found at the C-terminus of the protein. Whether both signals are functional in vivo is not clear. Strains overexpressing citA were made by transformation and cultured under citric acid-producing conditions. Up to 11-fold overproduction of citrate synthase did not increase the rate of citric acid production by the fungus, suggesting that citrate synthase contributes little to flux control in the pathway involved in citric acid biosynthesis by a non-commercial strain.


Subject(s)
Aspergillus niger/enzymology , Citrate (si)-Synthase/metabolism , Citric Acid/metabolism , Acetyl Coenzyme A/metabolism , Amino Acid Sequence , Aspergillus niger/genetics , Citrate (si)-Synthase/genetics , Citrate (si)-Synthase/isolation & purification , Cloning, Molecular , DNA, Complementary/chemistry , DNA, Complementary/genetics , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Fungal , Kinetics , Molecular Sequence Data , Oxaloacetates/metabolism , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Species Specificity , Transformation, Genetic
6.
Eur J Biochem ; 258(1): 223-32, 1998 Nov 15.
Article in English | MEDLINE | ID: mdl-9851713

ABSTRACT

The Aspergillus niger hexokinase gene hxkA has been cloned by heterologous hybridisation using the Aspergillus nidulans hexokinase gene as a probe. The DNA sequence of the gene was determined, and the deduced amino acid sequence showed significant similarity to other eukaryotic hexokinase and glucokinase proteins, in particular to those of the budding yeasts. The encoded protein was purified from a multicopy hxkA transformant, and extensively characterised. The hexokinase protein has a molecular mass of 54090, a pI of 4.9 and is a homodimer. D-Glucose, the glucose analogue 2-deoxy-D-glucose, D-fructose, D-mannose and D-glucosamine are phosphorylated by hexokinase, whereas the hexoses D-galactose, L-sorbose, methyl alpha-D-glucoside and the pentoses L-arabinose and D-xylose are not. The enzyme has high affinity for glucose (Km = 0.35 mM at pH 7.5) and for fructose (Km = 2.0 mM at pH 7.5) and is inhibited by ADP. The enzyme is strongly inhibited by physiological concentrations (0.1-0.2 mM) of trehalose 6-phosphate, which may be of importance for in vivo regulation of the enzyme. Inhibition of A. niger hexokinase by trehalose 6-phosphate is competitive towards the sugar substrate (Ki = 0.01 mM). Based on the kinetic constants of hexokinase and glucokinase their relative contribution to in vivo glucose phosphorylation was calculated and found to be strongly dependent on intracellular pH and glucose concentration. At pH 7.5 glucokinase is predominant, whereas at pH 6.5 hexokinase is predominant at glucose concentrations higher than 0.5 mM. Expression of the hexokinase and the glucokinase gene requires active carbon metabolism. Also on carbon sources which are not substrates for hexokinase or glucokinase, clear expression is observed. The hexokinase and glucokinase enzymes are quite stable in vivo. Even in the absence of transcription, active glucokinase and hexokinase remain present in the cells at almost the same level for at least 3-4 h after depletion of the carbon source.


Subject(s)
Aspergillus niger/enzymology , Hexokinase/metabolism , Sugar Phosphates/physiology , Trehalose/analogs & derivatives , Amino Acid Sequence , Base Sequence , Chromatography, Ion Exchange , Cloning, Molecular , DNA, Fungal , Glucokinase/metabolism , Glucose/metabolism , Hexokinase/antagonists & inhibitors , Hexokinase/genetics , Hydrogen-Ion Concentration , Kinetics , Molecular Sequence Data , Osmolar Concentration , Phosphorylation , Phylogeny , Substrate Specificity , Trehalose/physiology
7.
Biochim Biophys Acta ; 1334(2-3): 317-26, 1997 Mar 15.
Article in English | MEDLINE | ID: mdl-9101728

ABSTRACT

Phosphofructokinase and pyruvate kinase were overexpressed in the filamentous fungus Aspergillus niger. Moderate overexpression of these glycolytic enzymes in A. niger N400 (3-5-fold the wild-type level), either individually or simultaneously, did not increase citric acid production by the fungus significantly. Thus, phosphofructokinase and pyruvate kinase do not seem to contribute in a major way to flux control of the metabolism involved in the conversion of glucose to citric acid. Overexpression of phosphofructokinase and pyruvate kinase did not influence the activities of other enzymes in the pathway, nor did it change intermediary metabolite levels. However, in strains overexpressing phosphofructokinase, the level of fructose 2,6-bisphosphate, a positive allosteric effector of phosphofructokinase, was reduced almost 2-fold compared to the wild-type strain. Measurements with purified phosphofructokinase, using substrate, product and effector concentrations found intracellularly, showed that such a reduction in the fructose-2,6-bisphosphate level could decrease the specific activity of phosphofructokinase in the cell significantly. Thus, the fungus seems to adapt to overexpression of phosphofructokinase by decreasing the specific activity of the enzyme through a reduction in the level of fructose 2,6-bisphosphate.


Subject(s)
Aspergillus niger/enzymology , Citric Acid/metabolism , Phosphofructokinase-1/biosynthesis , Pyruvate Kinase/biosynthesis , Aspergillus niger/genetics , Cloning, Molecular , Fructosediphosphates/analysis , Molecular Sequence Data
8.
Eur J Biochem ; 240(3): 518-25, 1996 Sep 15.
Article in English | MEDLINE | ID: mdl-8856049

ABSTRACT

The Aspergillus niger glucokinase gene glkA has been cloned using a probe generated by polymerase chain reaction with degenerate oligonucleotides. The DNA sequence of the gene was determined, and the deduced amino acid sequence shows significant similarity to other eukaryotic hexokinase and glucokinase proteins, in particular to the Saccharomyces cerevisiae glucokinase protein. The encoded protein was purified from a multicopy glkA transformant, and extensively characterised. The protein has a molecular mass of 54536 Da and a pI of 5.2. The enzyme has high affinity for glucose (K(m) 0.063 mM at pH 7.5) and a relatively low affinity for fructose (K(m) 120 mM at pH 7.5), and in vivo fructose phosphorylation by glucokinase is consequently negligible. The configurations at C1 and C4 of the substrate appear to be essential for substrate specificity. The A. niger glucokinase shows non-competitive inhibition by ADP towards ATP and uncompetitive inhibition by ADP towards glucose. The kcal (turnover number) decreases rapidly below pH 7.5 (56% at pH 7.0 and 17% at pH 6.5) and this may have important implications for the in vivo regulation of activity. In addition, proof is provided for the presence of a second hexosephosphorylating enzyme in A. niger. This enzyme is probably a hexokinase, since unlike glucokinase, this activity is inhibited by trehalose 6-phosphate.


Subject(s)
Aspergillus niger/enzymology , Aspergillus niger/genetics , Glucokinase/chemistry , Glucokinase/genetics , Hexokinase/genetics , Adenosine Diphosphate/metabolism , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Base Sequence , Chemical Phenomena , Chemistry, Physical , Cloning, Molecular , DNA, Fungal/genetics , Genes, Fungal , Glucokinase/metabolism , Hexokinase/metabolism , Hexoses/metabolism , Isoelectric Point , Kinetics , Molecular Sequence Data , Molecular Weight , Phosphorylation , Phylogeny , Substrate Specificity
9.
FEMS Microbiol Lett ; 139(2-3): 223-28, 1996 Jun 01.
Article in English | MEDLINE | ID: mdl-8674991

ABSTRACT

Hexose phosphorylation was studied in Aspergillus nidulans wild-type and in a fructose non-utilising mutant (frA). The data indicate the presence of at least one hexokinase and one glucokinase in wild-type A. nidulans, while the frA1 mutant lacks hexokinase activity. The A. nidulans gene encoding hexokinase was isolated by complementation of the frA1 mutation. The absence of hexokinase activity in the frA1 mutant did not interfere with glucose repression of the enzymes involved in alcohol and L-arabinose catabolism. This suggest that, unlike the situation in yeast where mutation of hexokinase PII abolishes glucose repression, the A. nidulans hexokinase might not be involved in glucose repression.


Subject(s)
Aspergillus nidulans/genetics , Hexokinase/metabolism , Hexoses/metabolism , Amino Acid Sequence , Aspergillus nidulans/enzymology , Fructose/metabolism , Genetic Complementation Test , Glucose/metabolism , Molecular Sequence Data , Mutation/genetics , Phosphorylation , Trehalose/metabolism
10.
Appl Microbiol Biotechnol ; 40(2-3): 318-26, 1993 Nov.
Article in English | MEDLINE | ID: mdl-7764386

ABSTRACT

Secretion of endo-1,5-alpha-L-arabinase A (ABN A) by an Aspergillus niger xylulose kinase mutant upon mycelium transfer to medium containing L-arabitol was immunochemically followed with time to monitor its induction profile. A cDNA expression library was made from polyA+ RNA isolated from the induced mycelium. This library was immunochemically screened and one ABN A specific clone emerged. The corresponding abnA gene was isolated from an A. niger genomic library. Upon Southern blot analysis, a 3.1-kb HindIII fragment was identified and subcloned to result in plasmid pIM950. By means of co-transformation using the A. niger pyrA gene as selection marker, the gene was introduced in both A. niger and A. nidulans uridine auxotrophic mutants. Prototrophic A. niger and A. nidulans transformants overproduced A. niger ABN A upon growth in medium containing sugar beet pulp as the sole carbon source, thereby establishing the identity and functionality of the cloned gene. The DNA sequence of the complete HindIII fragment was determined and the structure of the abnA gene as well as of its deduced gene product were analysed. Gene abnA contains three introns within its structural region and codes for a protein of 321 amino acids. Signal peptide processing results in a mature protein of 302 amino acids with a deduced molecular mass of 32.5 kDa. A. niger abnA is the first gene encoding an ABN to be isolated and characterized.


Subject(s)
Aspergillus niger/enzymology , Genes, Fungal/genetics , Glycoside Hydrolases/genetics , Amino Acid Sequence , Aspergillus niger/genetics , Base Sequence , Cloning, Molecular , Gene Expression , Glycoside Hydrolases/isolation & purification , Molecular Sequence Data
11.
Mol Gen Genet ; 234(2): 217-27, 1992 Aug.
Article in English | MEDLINE | ID: mdl-1508148

ABSTRACT

Cells of the mouse T-lymphoma line GRSL13 were treated with 8-methoxy-psoralen plus longwave ultraviolet light (PUVA) under conditions where the biological effects are mainly due to non-persistent DNA cross-links (PUVA-CL treatment). Fluctuation analysis showed that PUVA-CL treatment resulted in an enhancement of the mutation rate in the progeny of treated cells, which persisted until the eleventh generation after treatment. Since only 5 cross-links are available to account for 52 mutational events observed in the coding region, about 90% of the induced mutational events must have been untargeted. This was confirmed by molecular analysis of these mutations, which showed that 53% of the point mutations arose at sites which are not a target for psoralens. This supports the hypothesis that stress responses may give rise to untargeted mutagenesis. Further support for this hypothesis is provided by the observation that 8-methoxy-psoralen (8-MOP) or UVA alone (both of which are known to induce many pleiotropic effects) each acted as indirect mutagen by enhancing the mutation rate 2-4 fold in the progeny of treated cells.


Subject(s)
DNA Damage/genetics , Hypoxanthine Phosphoribosyltransferase/genetics , Mutagenesis/genetics , Animals , Base Sequence , DNA/drug effects , DNA/radiation effects , Dose-Response Relationship, Radiation , Flow Cytometry , Male , Methoxsalen/toxicity , Mice , Molecular Sequence Data , Mutagenicity Tests , Mutation/genetics , Tumor Cells, Cultured , Ultraviolet Rays
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