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Biomedical subjects

M Fredholm

Publications and source records attributed to M Fredholm.

At least 19 recordsLinked to original sources
PubMed2006

Porcine ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1/CD203a): cloning, transcription, expression, mapping, and identification of an NPP1/CD203a epitope for swine workshop cluster 9 (SWC9) monoclonal antibodies.

Swine workshop cluster 9 (SWC9) antibody identifying a porcine epitope on macrophages and thymocytes was used to precipitate and characterize the molecule from biotinylated macrophages and to obtain peptide sequence by mass spectrometry. The protein was identified as ecto-nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1/CD203a). The porcine NPP1/CD203a encoding gene was mapped to chromosome 1 using a radiation hybrid panel, and transcription was investigated by RT-PCR analysis of several tissues. The cDNA was cloned and introduced into COS7 cells resulting in expression of functionally active enzyme and verification of the specificity of an SWC9 reacting monoclonal antibody. The antibody was used for immunohistochemical examination of various porcine tissues. Most prominent expression of NPP1/CD203a was found in lung macrophages and liver sinusoids.

Amino Acid Sequence↗
PubMed2006

MicroRNA sequence motifs reveal asymmetry between the stem arms.

The processing of micro RNAs (miRNAs) from their stemloop precursor have revealed asymmetry in the processing of the mature and its star sequence. Furthermore, the miRNA processing system between organism differ. To assess this at the sequence level we have investigated mature miRNAs in their genomic contexts. We have compared profiles of mature miRNAs within their genomic context of the 5' and 3' stemloop precursor arms and we find asymmetry between mature sequences of the 5' and 3' stemloop precursor arms. The main observation is that vertebrate organisms have a characteristic motif on the 5' arm which is in contrast to the 3' arm motif which mainly show the conserved U at the position of the mature start. Also the vertebrate 5' arm motif show a semi-conserved G 13 nucleotides upstream from the first position. We compared the 5' and 3' arm profiles using the average log likelihood ratio (ALLR) score, as defined by Wang and Stormo (2003) [Wang T., Stormo, G.D., 2003. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2369-2380.] and computing a p-value we find that the two profiles differs significantly in their 3' end where the 5' arm motif (in contrast to the 3' arm motif) has a semi-conserved GU rich region. Similar findings are also obtained for other organisms, such as fly, worm and plants. The observed similarities and differences between closely and distantly related organisms are discussed and related to current knowledge of miRNA processing.

Animals↗
PubMed2006

Molecular characterization of the porcine surfactant, pulmonary-associated protein C gene.

The surfactant, pulmonary-associated protein C (SFTPC) is a peptide secreted by the alveolar type II pneumocytes of the lung. We have characterized the porcine SFTPC gene at genomic, transcriptional, and protein levels. The porcine SFTPC is a single-copy gene on pig chromosome 14. Two transcripts were found in a newborn pig lung cDNA library: a full-length clone and a clone missing exon 5. cDNA sequence comparison revealed four synonymous and two nonsynonymous substitutions and in-frame insertions at the beginning of exon 5. Comparison of the SFTPC coding region between several mammals showed high levels of conservation. Northern blot studies showed lung-specific expression of the full-length SFTPC transcript, appearing in 50-day-old fetus and increasing during lung development. Both SFTPC transcripts were detected mainly in lung by real-time RT-PCR and they were significantly down-regulated in necrotic lungs of pigs infected with Actinobacillus pleuropneumoniae. Additionally, the protein levels were also decreased or absent in the necrotic tissue.

Actinobacillus Infections↗
PubMed2006

Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I: carcass traits.

We report the identification of quantitative trait loci (QTL) affecting carcass composition, carcass length, fat deposition and lean meat content using a genome scan across 462 animals from a combined intercross and backcross between Hampshire and Landrace pigs. Data were analysed using multiple linear regression fitting additive and dominance effects. This model was compared with a model including a parent-of-origin effect to spot evidence of imprinting. Several precisely defined muscle phenotypes were measured in order to dissect body composition in more detail. Three significant QTL were detected in the study at the 1% genome-wide level, and twelve significant QTL were detected at the 5% genome-wide level. These QTL comprise loci affecting fat deposition and lean meat content on SSC1, 4, 9, 10, 13 and 16, a locus on SSC2 affecting the ratio between weight of meat and bone in back and weight of meat and bone in ham and two loci affecting carcass length on SSC12 and 17. The well-defined phenotypes in this study enabled us to detect QTL for sizes of individual muscles and to obtain information of relevance for the description of the complexity underlying other carcass traits.

Animal Husbandry↗
PubMed2006

Linkage mapping of gene-associated SNPs to pig chromosome 11.

Single nucleotide polymorphisms (SNPs) were discovered in porcine expressed sequence tags (ESTs) orthologous to genes from human chromosome 13 (HSA13) and predicted to be located on pig chromosome 11 (SSC11). The SNPs were identified as sequence variants in clusters of EST sequences from pig cDNA libraries constructed in the Sino-Danish pig genome project. In total, 312 human gene sequences from HSA13 were used for similarity searches in our pig EST database. Pig ESTs showing significant similarity with HSA13 genes were clustered and candidate SNPs were identified. Allele frequencies for 26 SNPs were estimated in a group of 80 unrelated pigs from Danish commercial pig breeds: Duroc, Hampshire, Landrace and Large White. Eighteen of the 26 SNPs genotyped in the PiGMaP Reference Families were mapped by linkage analysis to SSC11. The EST-based SNPs published here are new genetic markers useful for linkage and association studies in commercial and experimental pig populations. This study represents the first gene-associated SNP linkage map of pig chromosome 11 and adds new comparative mapping information between SSC11 and HSA13. Furthermore, our data facilitate future studies aimed at the identification of interesting regions on pig chromosome 11, positional cloning and fine mapping of quantitative trait loci in pig.

Animals↗
PubMed2006

Evaluation of the porcine melanocortin 4 receptor (MC4R) gene as a positional candidate for a fatness QTL in a cross between Landrace and Hampshire.

Melanocortin 4 receptor (MC4R) is expressed in the appetite-regulating areas of the brain where it is central in the regulation of feed intake and energy balance. A mutation in MC4R causing an Asp298Asn substitution has been associated with fatness, high daily gain and feed intake in the pig. In a previously performed genome scan based on a Hampshire x Landrace cross, we detected one quantitative trait loci (QTL) affecting carcass fat/meat ratio and one QTL affecting the biceps femoris muscle, both close to the position of MC4R on porcine chromosome 1. In this study, the two lines were found to be close to fixation for alternative alleles of the Asp298Asn polymorphism. Additional QTL analyses supported our hypothesis of MC4R as a positional candidate gene but only for the fat/meat QTL. The Asp298Asn polymorphism was also evaluated as a selection target for daily gain in a Danish pig breeding population that included four breeds (Hampshire, Duroc, Landrace and Yorkshire). Over a 12-year period (1990-2002), a significant increase in the allele frequency of 298Asn was found in Landrace and Duroc, whereas a non-significant decrease in the 298Asn allele frequency was observed in Yorkshire. The Hampshire breed was fixed for the 298Asn allele in 1990. The high 298Asn allele frequencies in Hampshire, Landrace and Duroc are most likely due to selection for daily gain, whereas selection for daily gain in the Yorkshire breed apparently focuses on other loci.

Alleles↗
PubMed2004

FISH mapping and sequence analysis of 87 porcine BAC clones.

Ninety-one bacterial artificial chromosomes (BAC) clones, selected effectively at random from our library, were used as probes for fluorescence in situ hybridization. Of these, 87 clones gave a specific signal in one, two or three different pair(s) of swine metaphase chromosomes. The ends of 35 BAC clones were sequenced in order to obtain information for comparative mapping. Fifteen of them gave useful comparative mapping information.

Animals↗
PubMed2003

Evaluation of the present breeding programme against copper toxicosis in Danish Bedlington terriers.

A breeding programme to eradicate copper toxicosis in Danish Bedlington terriers has been established based on a DNA marker test. Genotyping of both parents is compulsory and after 1 January 2000, only homozygous non-carriers are used for breeding. In this study, two groups of Bedlington terriers were genotyped at 18 microsatellite loci. One group represented the original population of Bedlington terriers before introducing the breeding programme (n = 23); the other represented a group of homozygous non-carriers (n = 24) available for breeding after year 2000. Allele numbers, allele frequencies, observed heterozygosities (Ho), expected heterozygosities (He), locus-specific coefficients of inbreeding (Fl) and Nei's genetic distance (D) was calculated. Individual coefficients of inbreeding (Fi) were calculated from the pedigrees and an assignment test was performed. Four rare alleles were lost in the group of homozygous non-carriers. No significant differences were observed between the mean values of allele numbers, Ho, He, Fl and Fi of the two populations of dogs. Nei's genetic distance between the two populations was 0.06 and 88% of the homozygous non-carriers were assigned correctly in the assignment test. The overall diversity of the breed was low (Ho = 0.41) and the breeders were advised to include the heterozygous carriers again.

Alleles↗
PubMed2003

Linkage and comparative mapping of the locus controlling susceptibility towards E. COLI F4ab/ac diarrhoea in pigs.

In 1995, Edfors-Lilja and coworkers mapped the locus for the E. COLI K88ab (F4ab) and K88ac (F4ac) intestinal receptor to pig chromosome 13 (SSC13). Using the same family material we have refined the map position to a region between the microsatellite markers Sw207 and Sw225. Primers from these markers were used to screen a pig BAC library and the positive clones were used for fluorescent in situ hybridization (FISH) analysis. The results of the FISH analysis helped to propose a candidate gene region in the SSC13q41-->q44 interval. Shotgun sequencing of the FISH-mapped BAC clones revealed that the candidate region contains an evolutionary breakpoint between human and pig. In order to further characterise the rearrangements between SSC13 and human chromosome 3 (HSA3), detailed gene mapping of SSC13 was carried out. Based on this mapping data we have constructed a detailed comparative map between SSC13 and HSA3. Two candidate regions on human chromosome 3 have been identified that are likely to harbour the human homologue of the gene responsible for susceptibility towards E. COLI F4ab/ac diarrhoea in pigs.

Animals↗
PubMed2000

Why do we still find anonymous ESTs?

During recent years, there has been an exponential rise in the number of sequences accessible in the public databases. Despite this, a high percentage of partial sequences of cDNA (ESTs) submitted to the databases remain unrecognized (anonymous ESTs). This lack of similarities could be explained by several hypotheses: i) a different part of the transcript is present in the GenBank; ii) the transcript represents a novel gene not yet isolated in other species; iii) alternative splicing of the same gene in different species; iv) inaccurate sequence data; and/or v) the sequence of the transcript has diverged to the extent that it is not recognized as an ortholog. In the present study we selected a sample of 20 ESTs from a pool of 656 anonymous pig small intestine ESTs in order to investigate the possible cause for the lack of similarities with database entries. To test the significant hypotheses we carried out total sequencing of each insert along with zoo-blot and Northern-blot analysis. Extended analyses of the 20 ESTs showed significant matches to seven existing database entries, whereas 13 still did not show significant hits. The results are discussed in the context of the hypothesis listed above.

Animals↗
PubMed2000

Microsatellite marker C04107 as a diagnostic marker for copper toxicosis in the Danish population of Bedlington terriers.

The linkage phase of marker C04107 was evaluated before implementation of the marker in a diagnostic test. Blood samples from 68 dogs were collected and genotyped by PCR. Two alleles were detected with sizes of 160 bp and 164 bp and allele frequencies of 0.45 and 0.55 respectively. Genotyping revealed that 35 dogs were heterozygous (51.5%), 22 dogs were homozygous for the normal allele (32.3%) and 11 dogs were homozygous for the disease allele (16.2%). Liver biopsies were taken from 14 selected dogs and the copper content was evaluated histologically. Biopsies from 8 dogs homozygous for the disease allele showed many copper granules along with single cell necrosis, haemosiderosis and cellular infiltration. In liver biopsies from 6 dogs genotyped to be heterozygous or homozygous for the normal allele, copper granules were absent or moderate in number and no lesions were present. The survey demonstrates that the linkage phase of marker C04107 in the Danish population of Bedlington terriers is similar to the linkage phase detected in other countries. Thus, the marker can be used in a diagnostic test for copper toxicosis in Denmark.

Animals↗
PubMed1998

Improvement of the porcine transcription map: localization of 33 genes, of which 24 are orthologous.

From a resource of porcine ESTs, 52 transcripts were selected for regional chromosomal assignments in a somatic cell hybrid panel. Except for six ESTs, the chosen transcripts represented genes where the BLASTX database searches showed high similarity scores (>90%) with a part of the single pass 5' sequence to human, bovine, mouse, or pig entries. PCR primers for hybrid cell analysis of the ESTs were positioned in the 3'UTR of the sequences. Confident regional assignments to pig chromosomes were obtained for 33 of the 52 porcine ESTs. Comparative human mapping data were available for 27 of these. Twenty-four proved to be orthologous genes now placed on the porcine transcription map. The data presented provide further comparative data for 13 autosomes and the X chromosome.

Animals↗
PubMed1998

Mapping of porcine genes belonging to two different cytochrome P450 subfamilies.

Three cDNA clones from a porcine small intestine cDNA library, tentatively identified as transcripts of two different cytochrome P450 (CYP) gene subfamilies, were sequenced and mapped. One of the clones was found to comprise an open reading frame of 503 amino acids and showed up to an 80% similarity to genes from the CYP3A subfamily. Translation of the other two cDNA clones revealed high similarity to genes from the CYP2C subfamily. One of these clones was truncated, lacking a part of the 5' end of the coding region, whereas the other encodes a putative pseudogene. The CYP3A gene was mapped cytogenetically by means of a pig/rodent somatic hybrid cell panel to pig chromosome 3, in the region p16-p17 or p11. The CYP2C pseudogene was mapped genetically to pig chromosome 14, using the PiGMaP shared reference pedigrees. The localisations provide information for the human/pig comparative map.

Amino Acid Sequence↗