Christian Bendixen

Aarhus University, Aarhus, Central Jutland, Denmark

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Publications (143)530.1 Total impact

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    ABSTRACT: The TOR1A (also named DYT1) gene encodes a protein, TorsinA, a member of the AAA+ superfamily of ATPases. The AAA+ proteins have diverse functions such as organelle biogenesis, proteosome function, chaperone function, membrane trafficking and microtubule regulation. However, the molecular function of TorsinA is still largely unknown. Mutations in the TOR1A gene, primarily a 3-bp (GAG) deletion are associated with early-onset autosomal dominant torsion dystonia. Animal models may help to provide information about the underlying cellular and molecular mechanism of early-onset generalized dystonia. The close anatomical, physiological, genetic and biochemical resemblance between man and pig suggest that this animal may constitute an excellent model for this disease. This work reports the cloning and analysis of the porcine (Sus scrofa) homologue of TOR1A. Two porcine TOR1A cDNAs were amplified by reverse transcriptase polymerase chain reaction (RT-PCR), using oligonucleotide primers derived from in silico sequences. The porcine TOR1A cDNAs both encode a protein of 333 amino acids which shows a very high similarity to human (92%) TorsinA. Protein structure comparison of human and porcine TorsinA sequences revealed that there were few differences in the amino acid sequences between the two species and these are not likely to alter TorsinA structure and function. Quantitative real-time RT-PCR detection exhibited TOR1A mRNA expression in all analyzed porcine tissues, although at different levels. The TOR1A gene was demonstrated to be localized on porcine chromosome 1. Single nucleotide polymorphism (SNP) analysis revealed several SNPs in the porcine TOR1A gene, both in the coding region and also in the 3' UTR region. Overexpression of mutant (DeltaE303-304) porcine TorsinA in neuroblastoma cells leads to a more perinuclear localization compared with a cytoplasmatic localization for wildtype TorsinA. Furthermore, inclusion-like structures were observed. In conclusion, the results obtained for porcine TOR1A suggest that the pig could be an ideal model for early-onset generalized dystonia.
    Gene 12/2008; 430(1-2):105-15. · 2.20 Impact Factor
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    ABSTRACT: The aim of this study was to 1) detect QTL across the cattle genome that influence the incidence of clinical mastitis and somatic cell score (SCS) in Danish Holsteins, and 2) characterize these QTL for pleiotropy versus multiple linked quantitative trait loci (QTL) when chromosomal regions affecting clinical mastitis were also affecting other traits in the Danish udder health index or milk production traits. The chromosomes were scanned using a granddaughter design where markers were typed for 19 to 34 grandsire families and 1,373 to 2,042 sons. A total of 356 microsatellites covering all 29 autosomes were used in the scan. Among the across-family regression analyses, 16 showed chromosome-wide significance for the primary traits incidence of clinical mastitis in first (CM1), second (CM2), and third (CM3) lactations, and SCS. Regions of chromosomes 5, 6, 9, 11, 15, and 26 were found to affect CM and regions of chromosomes 5, 6, 8, 13, 22, 23, 24, and 25 affected SCS. Markers on chromosomes 6, 11, 15, and 26 can be used to perform marker-assisted selection on CM without a direct negative selection on milk yield, because no effects were detected on the milk traits. Comparing multi-trait models assuming either a pleiotropic QTL affecting 2 traits or 2 QTL each affecting 1 trait gave some evidence to distinguish between these models. For Bos taurus autosome 5, the most likely models were a pleiotropic QTL affecting CM2, CM3, and SCS, and a linked QTL affecting fat yield index. For Bos taurus autosome 9, the most likely model is a pleiotropic QTL affecting CM1 and CM2 at approximately 8 cM.
    Journal of Dairy Science 11/2008; 91(10):4028-36. · 2.57 Impact Factor
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    ABSTRACT: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs that is primarily caused by high levels of androstenone and skatole in adipose tissue. Androstenone is a steroid and its levels are mainly genetically determined. Studies on androstenone metabolism have, however, focused on a limited number of genes. Identification of additional genes influencing levels of androstenone may facilitate implementation of marker assisted breeding practices. In this study, microarrays were used to identify differentially expressed genes and pathways related to androstenone metabolism in the liver from boars with extreme levels of androstenone in adipose tissue. Liver tissue samples from 58 boars of the two breeds Duroc and Norwegian Landrace, 29 with extreme high and 29 with extreme low levels of androstenone, were selected from more than 2500 individuals. The samples were hybridised to porcine cDNA microarrays and the 1% most significant differentially expressed genes were considered significant. Among the differentially expressed genes were metabolic phase I related genes belonging to the cytochrome P450 family and the flavin-containing monooxygenase FMO1. Additionally, phase II conjugation genes including UDP-glucuronosyltransferases UGT1A5, UGT2A1 and UGT2B15, sulfotransferase STE, N-acetyltransferase NAT12 and glutathione S-transferase were identified. Phase I and phase II metabolic reactions increase the water solubility of steroids and play a key role in their elimination. Differential expression was also found for genes encoding 17beta-hydroxysteroid dehydrogenases (HSD17B2, HSD17B4, HSD17B11 and HSD17B13) and plasma proteins alpha-1-acid glycoprotein (AGP) and orosomucoid (ORM1). 17beta-hydroxysteroid dehydrogenases and plasma proteins regulate the availability of steroids by controlling the amount of active steroids accessible to receptors and available for metabolism. Differences in the expression of FMO1, NAT12, HSD17B2 and HSD17B13 were verified by quantitative real competitive PCR. A number of genes and pathways related to metabolism of androstenone in liver were identified, including new candidate genes involved in phase I oxidation metabolism, phase II conjugation metabolism, and regulation of steroid availability. The study is a first step towards a deeper understanding of enzymes and regulators involved in pathways of androstenone metabolism and may ultimately lead to the discovery of markers to reduce boar taint.
    BMC Veterinary Research 09/2008; 4:29. · 1.86 Impact Factor
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    ABSTRACT: The Paleo-Eskimo Saqqaq and Independence I cultures, documented from archaeological remains in Northern Canada and Greenland, represent the earliest human expansion into the New World's northern extremes. However, their origin and genetic relationship to later cultures are unknown. We sequenced a mitochondrial genome from a Paleo-Eskimo human by using 3400-to 4500-year-old frozen hair excavated from an early Greenlandic Saqqaq settlement. The sample is distinct from modern Native Americans and Neo-Eskimos, falling within haplogroup D2a1, a group previously observed among modern Aleuts and Siberian Sireniki Yuit. This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-Eskimos that replaced them.
    Science 07/2008; 320(5884):1787-9. · 31.20 Impact Factor
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    ABSTRACT: The gamma-synuclein protein is involved in breast carcinogenesis and has also been implicated in other forms of cancer and in ocular diseases. Furthermore, gamma-synuclein is believed to have a role in certain neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease. This work reports the cloning and characterization of the porcine (Sus scrofa) gamma-synuclein cDNA (SNCG). The SNCG cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine SNCG cDNA codes for a protein of 126 amino acids which shows a high similarity to bovine (90%), human (87%) and mouse (83%) gamma-synuclein. A genomic clone containing the entire porcine SNCG gene was isolated and its genomic organization determined. The gene is composed of five exons, the general structure being observed to be very similar to that of the human SNCG gene. Expression analysis by quantitative real-time RT-PCR revealed the presence of SNCG transcripts in all examined organs and tissues. Differential expression was observed, with very high levels of SNCG mRNA in fat tissue and high expression levels in spleen, cerebellum, frontal cortex and pituitary gland. Expression analysis also showed that porcine SNCG transcripts could be detected in different brain regions during early stages of embryo development. The porcine SNCG orthologue was mapped to chromosome 14q25-q29. The distribution of recombinant porcine gamma-synuclein was studied in three different transfected cell lines and the protein was found to be predominantly localized in the cytoplasm.
    Molecular Biology Reports 06/2008; 36(5):971-9. · 2.51 Impact Factor
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    ABSTRACT: After parenchymal loss, the liver regenerates restoring normal mass and metabolic function. Prevailing theories on triggering events leading to regeneration include humoral, metabolic, and flow-mediated mechanisms, the latter emphasizing the importance of shear stress mediated nitric oxide regulation. We aimed to investigate whether the grade of resection and hence the portal venous pressure and sinusoidal shear stress increase would be reflected in the gene expression profiles in the liver remnant by using a global porcine cDNA microarray chip with approximately 23,000 genes represented. Six pig livers were resected with 62% (low portal pressure resection) and 75% (high portal pressure resection), resulting in a portal venous pressure increase from a baseline of 6.1-8.2 and 12 mmHg, respectively. By sampling consecutive biopsies from the liver remnants, we found differentially expressed genes in the high portal pressure resection group to have functions related primarily to apoptosis, nitric oxide metabolism and oxidative stress, whereas differentially expressed genes in the low portal pressure resection group potentially regulate the cell cycle. Common to both groups was the upregulation of genes regulating inflammation, transport, cell proliferation, development, and protein metabolism. Also common to both groups was both up- and downregulation of genes regulating cell-cell signaling, signal transduction, cell adhesion, and translation. Genes regulating the metabolism of lipids, hormones, amines, and alcohol were downregulated in both groups. In conclusion, the genetic regenerative response in the liver remnant to varies according to the level of resection.
    AJP Gastrointestinal and Liver Physiology 04/2008; 294(3):G819-30. · 3.65 Impact Factor
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    ABSTRACT: Recent studies of mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report a first account of CNVs in the pig genome covering part of the chromosomes 4, 7, 14, and 17 already sequenced and assembled. A custom tiling oligonucleotide array was used with a median probe spacing of 409 bp for screening 12 unrelated Duroc boars that are founders of a large family material. After a strict CNV calling pipeline, 37 copy number variable regions (CNVRs) across all four chromosomes were identified, with five CNVRs overlapping segmental duplications, three overlapping pig unigenes and one overlapping a RefSeq pig mRNA. This CNV snapshot analysis is the first of its kind in the porcine genome and constitutes the basis for a better understanding of porcine phenotypes and genotypes with the prospect of identifying important economic traits.
    PLoS ONE 02/2008; 3(12):e3916. · 3.53 Impact Factor
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    ABSTRACT: Recent developments in sequencing technology have allowed the generation of millions of short read sequences in a fast and inexpensive way. This enables the cost effective large scale identification of hundreds of thousands of SNPs needed for the development of high density SNP arrays. Currently, a high density swine SNP chip is being developed as part of an integrated effort of several European and American institutions involved in swine genomics research. The future pig SNP chip will include already validated SNPs as well as SNPs identified de novo using second generation sequencing on the Illumina 1 G analyzer (Solexa) and the Roche 454 sequencer. Towards this end, a total of 15 DNA libraries were prepared using pooled DNA samples from five breeds (Duroc, Landrace, Large White, Pietrain and Wild Boar) digested with three restriction enzymes (AluI, HaeIII, MspI). Fragments in the size range of 150-200 bp were selected for sequencing. The ends of these fragments (35 bp) will be sequenced at 30X coverage complemented with 2X sequencing of the complete fragment using 454 sequence technology. The Solexa short sequence reads will be filtered using several quality criteria to produce the dataset used for SNP discovery. Additional criteria for the selection of the 60K SNPs include the estimated minor allele frequency and genome position of the SNPs. The high density 60K SNP chip will be an extremely valuable tool for the pig genomics community for a variety of applications including QTL and LD mapping, association studies and genomic selection.
    01/2008;
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    ABSTRACT: Innate immune system abnormalities, e.g., mannan-binding lectin (MBL) genotype variants, have been demonstrated to modify the disease course of rheumatoid arthritis (RA). Surfactant protein D (SP-D) shares important structural and functional properties with MBL suggesting that SP-D may be an additional RA disease modifier. The Met11Thr polymorphism in the N-terminal part of SP-D is an important determinant for the SP-D serum level, but this polymorphism is also essential to the function and assembly into oligomers. We aimed to compare the serum levels of SP-D in a cohort of newly diagnosed untreated RA patients with healthy matched controls, and to investigate if there was an association to core measures of disease activity within the first year after disease onset. Secondly, we aimed to investigate whether the Met11Thr polymorphism was associated with RA. Serum SP-D was significantly lower in DMARD naive RA patients compared with healthy controls (P = 0.016). Median SP-D concentration at inclusion was 878 ng/ml (95% CI: 730-1033) and 1164 ng/ml (95% CI: 1093-1366) in RA patients and matched controls, respectively. SP-D increased during Methotrexate treatment (P < 0.0001), and at 1-year follow-up median SP-D was 1032 ng/ml (95% CI: 777-1255). SP-D levels did not correlate with traditional disease activity measures. The Thr11/Thr11 genotype and the Thr11 allele tended to be more frequent in RA patients. In conclusion, the low serum level of SP-D and the lack of correlation with traditional disease activity measures indicate that SP-D reflects a distinctive aspect in the RA pathogenesis.
    Scandinavian Journal of Immunology 01/2008; 67(1):71-6. · 2.20 Impact Factor
  • Anu Sironen, Johanna Vilkki, Christian Bendixen, Bo Thomsen
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    ABSTRACT: The KPL2 gene is expressed predominantly in cells with cilia or flagella. We have previously demonstrated that a large intronic insertion in KPL2 is associated with immotile sperm cells and infertility in the domesticated pig (Sus scrofa). To fully characterize the structure of the mutation, we have now cloned and sequenced the insertion. The data identified the presence of a long interspersed nuclear element-1 (LINE-1) encoding all activities required for retrotransposition, including a 5'-untranslated region (UTR) with an internal RNA polymerase II promoter, two open reading frames (ORF1 and ORF2) separated by an intergenic region and a 3' UTR containing a polyadenylation signal. Characterization of the junctions between the LINE-1 and the genomic target revealed the presence of direct repeats of 14 bp at both ends, showing that integration occurred by target-primed reverse transcription. Furthermore, sequence analysis suggested that the aberrant splicing pattern of KPL2 transcripts induced by the LINE-1 element is caused by interference with putative intronic splice signals and activation of a cryptic splice site. These data demonstrate that integration of a transposition-competent L1 element into KPL2 is responsible for the defective spermatozoa, which accentuates the role of mobile DNA elements as insertional mutagens in mammalian genomes.
    Molecular and General Genetics 11/2007; 278(4):385-91. · 2.88 Impact Factor
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    ABSTRACT: Expansion in the repeat number of intragenic trinucleotide repeats (TNRs) is associated with a variety of inherited human neurodegenerative diseases. To study the composition of TNRs in a mammalian species representing an evolutionary intermediate between humans and rodents, we describe in this paper the identification of porcine noncoding and polyglutamine-encoding TNR regions and the comparison to the homologous TNRs from human, chimpanzee, dog, opossum, rat, and mouse. Several of the porcine TNR regions are highly polymorphic both within and between different breeds. The TNR regions are more conserved in terms of repeat length between humans and pigs than between humans and rodents suggesting that TNR lengths could be implicated in mammalian evolution. The TNRs in the FMR2, SCA6, SCA12, and Huntingtin genes are comparable in length to alleles naturally occurring in humans, and also in FMR1, a long uninterrupted CGG TNR was identified. Most strikingly, we identified a Huntingtin allele with 21 uninterrupted CAG repeats encoding a stretch of 24 polyglutamines. Examination of this particular Huntingtin TNR in 349 porcine offspring showed stable transmission. The presence in the porcine genome of TNRs within genes that, in humans, can undergo pathogenic expansions support the usage of the pig as an alternative animal model for studies of TNR evolution, stability, and functional properties.
    Neurogenetics 09/2007; 8(3):207-18. · 3.58 Impact Factor
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    ABSTRACT: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct manual annotation, which is immediately accessible and can be easily shared with external collaborators. Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs was selected for experimental validation by resequencing and genotyping. This study provides a web-based DNA chromatogram and contig browser that facilitates the evaluation and selection of candidate SNPs, which can be applied as genetic markers for genome wide genetic studies. The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant. Supplementary data are available at Bioinformatics online.
    Bioinformatics 08/2007; 23(13):i387-91. · 5.47 Impact Factor
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    ABSTRACT: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis. We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.
    PLoS ONE 02/2007; 2(2):e197. · 3.53 Impact Factor
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    ABSTRACT: Gene expression microarrays have been intensively applied to screen for genes involved in specific biological processes of interest such as diseases or responses to environmental stimuli. For mammalian species, cataloging of the global gene expression profiles in large tissue collections under normal conditions have been focusing on human and mouse genomes but is lacking for the pig genome. Here we present the results from a large-scale porcine study establishing microarray cDNA expression profiles of approximately 20.000 genes across 23 healthy tissues. As expected, a large portion of the genes show tissue specific expression in agreement with mappings to gene descriptions, Gene Ontology terms and KEGG pathways. Two-way hierarchical clustering identified expected tissue clusters in accordance with tissue type and a number of cDNA clusters having similar gene expression patterns across tissues. For one of these cDNA clusters, we demonstrate that possible tissue associated gene function can be inferred for previously uncharacterized genes based on their shared expression patterns with functionally annotated genes. We show that gene expression in common porcine tissues is similar to the expression in homologous tissues of human. The results from this study constitute a valuable and publicly available resource of basic gene expression profiles in normal porcine tissues and will contribute to the identification and functional annotation of porcine genes.
    PLoS ONE 02/2007; 2(11):e1203. · 3.53 Impact Factor
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    ABSTRACT: The transmembrane presenilin (PSEN) proteins, PSEN1 and PSEN2, have been proposed to be the catalytic components of the gamma-secretase protein complex, which is an intramembranous multimeric protease involved in development, cell regulatory processes, and neurodegeneration in Alzheimer's disease. Here we describe the sequencing, chromosomal mapping, and polymorphism analysis of PSEN1 and PSEN2 in the domestic pig (Sus scrofa domesticus). The porcine presenilin proteins showed a high degree of homology over their entire sequences to the PSENs from mouse, bovine, and human. PSEN1 and PSEN2 transcription was examined during prenatal development of the brain stem, hippocampus, cortex, basal ganglia, and cerebellum at embryonic days 60, 80, 100, and 114, which revealed distinct temporal- and tissue-specific expression profiles. Furthermore, immunohistochemical analysis of PSEN1 and PSEN2 showed similar localization of the proteins predominantly in neuronal cells in all examined brain areas. The data provide evidence for structural and functional conservation of PSENs in mammalian lineages, and may suggest that the high sequence similarity and colocalization of PSEN1 and PSEN2 in brain tissue reflect a certain degree of functional redundancy. The data show that pigs may provide a new animal model for detailed analysis of the developmental functions of the PSENs.
    BMC Neuroscience 02/2007; 8:72. · 3.00 Impact Factor
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    ABSTRACT: The bacterium Actinobacillus pleuropneumoniae is responsible for porcine pleuropneumonia, a widespread, highly contagious and often fatal respiratory disease of pigs. The general porcine innate immune response after A. pleuropneumoniae infection is still not clarified. The objective of this study was hence to characterise the transcriptional response, measured by using cDNA microarrays, in pigs 24 hours after experimental inoculation with A. pleuropneumoniae. Microarray analyses were conducted to reveal genes being differentially expressed in inflamed versus non-inflamed lung tissue sampled from inoculated animals as well as in liver and tracheobronchial lymph node tissue sampled from three inoculated animals versus two non-inoculated animals. The lung samples were studied using a porcine cDNA microarray with 5375 unique PCR products while liver tissue and tracheobronchial lymph node tissue were hybridised to an expanded version of the porcine microarray with 26879 unique PCR products. A total of 357 genes differed significantly in expression between infected and non-infected lung tissue, 713 genes differed in expression in liver tissue from infected versus non-infected animals and 130 genes differed in expression in tracheobronchial lymph node tissue from infected versus non-infected animals. Among these genes, several have previously been described to be part of a general host response to infections encoding immune response related proteins. In inflamed lung tissue, genes encoding immune activating proteins and other pro-inflammatory mediators of the innate immune response were found to be up-regulated. Genes encoding different acute phase reactants were found to be differentially expressed in the liver. The obtained results are largely in accordance with previous studies of the mammalian immune response. Furthermore, a number of differentially expressed genes have not previously been associated with infection or are presently unidentified. Determination of their specific roles during infection may lead to a better understanding of innate immunity in pigs. Although additional work including more animals is clearly needed to elucidate host response to porcine pleuropneumonia, the results presented in this study demonstrate three subsets of genes consistently expressed at different levels depending upon infection status.
    Acta Veterinaria Scandinavica 02/2007; 49:11. · 1.00 Impact Factor
  • K Larsen, L B Madsen, A Høj, C Bendixen
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    ABSTRACT: The PARK7 gene encodes a protein, DJ-1, with several functions such as protection of cells from oxidative stress, sperm maturation and fertilization and chaperone activity. Mutations in the PARK7 gene are associated with autosomal recessive early-onset Parkinson's disease (Parkinsonism). This work reports the cloning and analysis of the porcine (Sus scrofa) homologue of DJ-1. The porcine PARK7 cDNA was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using oligonucleotide primers derived from in silico sequences. The porcine PARK7 cDNA (SsPARK7) encodes a protein of 189 amino acids which shows a very high similarity to bovine (97%), to human (96%) and to canine (95%) DJ-1. Protein structure comparison of human and porcine DJ-1 sequences revealed that amino acid changes were few between the two species and not likely to alter DJ-1 structure and function. Quantitative real-time RT-PCR detection exhibited SsPARK7 mRNA expression in all analyzed porcine tissues, although at different levels. Furthermore, expression analysis showed that SsPARK7 transcripts could be detected early in embryo development in different brain regions. The PARK7 gene was demonstrated to be located on porcine chromosome 6. Single-nucleotide polymorphism (SNP) analysis revealed one SNP in the porcine PARK7 gene, giving rise to a silent mutation in exon 6.
    Cytogenetic and Genome Research 02/2007; 116(1-2):93-9. · 1.84 Impact Factor
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    ABSTRACT: Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages. Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
    Genome biology 02/2007; 8(4):R45. · 10.30 Impact Factor
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    ABSTRACT: Lameness is an important factor for culling animals. Strong legs and feet improve herd life of dairy cows. Therefore, many countries include leg and feet conformation traits in their breeding programs, often as early predictors of longevity. However, few countries directly measure lameness related traits to include these in a breeding program. Lameness indices in 3 different lactations and 5 leg conformation traits (rear legs side view, rear legs rear view, hock quality, bone quality, and foot angle) were measured on granddaughters of 19 Danish Holstein grandsires with 33 to 105 sons. A genome scan was performed to detect quantitative trait loci (QTL) based on the 29 autosomes using microsatellite markers. Data were analyzed across and within families for QTL affecting lameness and leg conformation traits. A regression method and a variance component method were used for QTL detection. Two QTL each for lameness in the first [Bos taurus autosome (BTA); BTA5, BTA26] and second (BTA19, BTA22) lactations were detected. For the 5 different leg conformation traits, 7 chromosome-wise significant QTL were detected across families for rear legs side view, 5 for rear legs rear view, 4 for hock quality, 4 for bone quality, and 1 for foot angle. For those chromosomes where a QTL associated with 2 different traits was detected (BTA1, BTA11, BTA15, BTA26, and BTA27), a multitrait-1-QTL model and a multitrait-2-QTL model were performed to characterize these QTL as single QTL with pleiotropic effects or distinct QTL.
    Journal of Dairy Science 02/2007; 90(1):472-81. · 2.57 Impact Factor
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    ABSTRACT: Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels, which is essential for recognising potential molecular markers for breeding purposes. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26,877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting the possibility of both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint.
    BMC Genomics 01/2007; 8:405. · 4.40 Impact Factor

Publication Stats

3k Citations
530.10 Total Impact Points

Institutions

  • 1990–2014
    • Aarhus University
      • • Department of Molecular Biology and Genetics
      • • Department of Genetics and Biotechnology
      Aarhus, Central Jutland, Denmark
  • 2012
    • Lund University
      • Department of Clinical Sciences
      Lund, Skane, Sweden
  • 2010
    • Technical University of Denmark
      • Center for Biological Sequence Analysis
      København, Capital Region, Denmark
    • University of Copenhagen
      • Centre for GeoGenetics
      Copenhagen, Capital Region, Denmark
  • 2009
    • Uppsala University
      Uppsala, Uppsala, Sweden
  • 2007–2009
    • Norwegian University of Life Sciences (UMB)
      • Department of Animal and Aquacultural Sciences (IHA)
      Ås, Akershus Fylke, Norway
  • 2002–2009
    • University of Southern Denmark
      • Department of Biology
      Copenhagen, Capital Region, Denmark
    • Huazhong Agricultural University
      Wu-han-shih, Hubei, China
  • 2008
    • University Hospital of North Norway
      Tromsø, Troms, Norway
  • 2006
    • University of South Bohemia in České Budějovice
      Budejovice, Jihočeský, Czech Republic
  • 2003
    • Aarhus University Hospital
      Aarhus, Central Jutland, Denmark
  • 2001
    • Virginia Polytechnic Institute and State University
      • Department of Biomedical Sciences and Pathobiology
      Blacksburg, VA, United States
    • Masaryk University
      Brünn, South Moravian, Czech Republic
  • 1996
    • The University of York
      • Department of Biology
      York, England, United Kingdom
  • 1994–1996
    • Columbia University
      • Department of Genetics and Development
      New York City, NY, United States