ABSTRACT
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.
Subject(s)
Genomics/methods , Computational Biology/methods , DNA/chemistry , Expressed Sequence Tags , Genome , Polymorphism, Single Nucleotide , Repetitive Sequences, Nucleic AcidABSTRACT
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.
Subject(s)
Epitopes, B-Lymphocyte/genetics , Macrophages/metabolism , Phosphoric Diester Hydrolases/genetics , Phosphoric Diester Hydrolases/metabolism , Pyrophosphatases/genetics , Pyrophosphatases/metabolism , Swine/genetics , Swine/metabolism , Amino Acid Sequence , Animals , Antibodies, Monoclonal , Base Sequence , Chromosome Mapping , Cloning, Molecular , Electrophoresis, Polyacrylamide Gel , Flow Cytometry , Humans , Immunohistochemistry , Immunoprecipitation , Liver/immunology , Liver/metabolism , Lung/immunology , Lung/metabolism , Macrophages/immunology , Mass Spectrometry , Molecular Sequence Data , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology, Amino Acid , Transcription, GeneticABSTRACT
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.
Subject(s)
Pulmonary Surfactant-Associated Protein C/genetics , Sus scrofa/genetics , Actinobacillus Infections/genetics , Actinobacillus Infections/metabolism , Actinobacillus pleuropneumoniae , Amino Acid Sequence , Animals , Animals, Newborn , Base Sequence , DNA, Complementary/genetics , Exons , Female , Fetus/metabolism , Gene Expression Regulation, Developmental , Genomics , Lung/embryology , Lung/growth & development , Lung/metabolism , Male , Molecular Sequence Data , Sequence Homology, Amino Acid , Sequence Homology, Nucleic AcidABSTRACT
A cross-sectional study of 661 9th grade pupils in Bergen municipality was conducted in November 1992. The pupils completed an anonymous questionnaire on their smoking habits. 25% of the girls and 16% of the boys reported smoking daily. Among the daily smokers, the average daily consumption of cigarettes was seven for both sexes. Most of the experimenting with cigarettes took place from the 6th to the 8th grade. Most youngsters tried their first cigarette when outdoors with friends. 27% of the regular smokers reported smoking at home, and 40% at school. In spite of legislation banning the sale of cigarettes to persons below the age of 16 years, 75% of the smokers bought the tobacco themselves.
