Sequence Analysis Of PCR-amplified DNA Research Articles

PR-1 gene family of grapevine: a uniquely duplicated PR-1 gene from a Vitis interspecific hybrid confers high level resistance to bacterial disease in transgenic tobacco

A functional contribution of pathogenesis-related 1 (PR-1) proteins to host defense has been established. However, systematic investigation of the PR-1 gene family in grapevine (Vitis spp.) has not been conducted previously. Through mining genomic databases, we identified 21 PR-1 genes from the Vitis vinifera genome. Polypeptides encoded by putative PR-1 genes had a signal sequence of about 25 residues and a mature protein of 10.9-29kDa in size. PR-1 mature proteins contained a highly conserved six-cysteine motif and pI values ranging from 4.6 to 9. A major cluster with 14 PR-1 genes was mapped to a 280-kb region on chromosome 3. One particular PR-1 gene within the cluster encoding a basic-type isoform (pI 7.77), herein named VvPR1b1, was isolated from various genotypes of grapevine (Vitis spp.) for functional studies. Sequence analysis of PCR-amplified DNA revealed that all genotypes contained a single VvPR1b1 gene except for a broad-spectrum bacterial and fungal disease resistant Florida bunch grape hybrid, 'BN5-4', from which seven different homologues were identified. Duplication of VvPR1b1-related genes encoding acidic-type PR-1 isoforms was also observed among several genotypes. However, transgenic expression analysis of grapevine PR-1 genes under strong constitutive promoters in transgenic tobacco revealed that only the basic-type VvPR1b1 gene duplicated in 'BN5-4' was capable of conferring high level resistance to bacterial disease caused by Pseudomonas syringae pv. tabaci.

Assessment of bioaerosols at a concentrated dairy operation

Increased bioaerosol loadings in downwind plumes from concentrated animal feeding operations (CAFOs) may increase the risk for allergy and infection in humans. In this study, we monitored airborne concentrations of culturable bacteria and fungi at upwind (background) and downwind sites at a 10,000 milking cow dairy over the course of a year. The average bacterial concentrations at the upwind site were 8.4 × 103 colony forming units (CFU) m−3 and increased to 9.9 × 105 CFU m−3 at the downwind edge of the cattle lots, decreasing to 6.3 × 104 CFU m−3 200 m farther downwind. At the same sites, the average fungal concentrations were 515, 945, and 1,010 CFU m−3, respectively. Significant correlations between the ambient weather conditions and airborne fungal and bacterial concentrations were identified. Sequence analysis of PCR-amplified DNA from bacterial clones and fungal isolates revealed genus and species level differences between upwind and downwind sites. Although we could not cultivate gram-negative bacteria, bacterial clones at downwind sites identified as being gram-negative matched with the following genera: Acinetobacter, Bradyrhizobium, Escherichia, Idiomarina, Methylobacterium, Ralstonia, and Novosphingobium. Fungal isolates from downwind matched with the following genera: Acremonium, Alternaria, Ascomycte, Aspergillus, Basidiomycete, Cladosporium, Davidiella, Doratomyces, Emericella, Lewia, Onygenales, Penicillium, Rhizopus, and Ulocladium. None of the bacterial and fungal sequence matches were affiliated with genera and species known to be pathogenic to humans. Overall, the data suggest that exposure to bioaerosols in the downwind environment decreases with increasing distance from the open-lot dairy.

Albumin Church Bay: 560 Lys→Glu a new mutation detected by electrospray ionisation mass spectrometry

Albumin Church Bay is a fast migrating genetic variant of human serum albumin which, in a heterozygous subject, formed about 50% of the circulating albumin. Reversed phase peptide mapping and electrospray ionisation mass spectrometry (ESI-MS) indicated that the C-terminal CNBr peptide had decreased polarity associated with a 1 Da increase in mass. Subdigestion of this peptide with trypsin and chymotrypsin revealed that the increased mass was associated with the chymotrypsin fragment VEKCCKADDKETCF (555–568) which had a mass of 1791.1 compared to 1790.2 for its normal counterpart. Sequence analysis of PCR-amplified DNA indicated an A→G mutation at position 98 of exon 13, which causes a point mutation of 560 Lys→Glu and results in a 1 Da mass increase.

Albumin Rugby Park: a truncated albumin variant caused by a G → C splice-site mutation in nitro 13

Three members of a family were found to be heterozygous for a fast albumin variant (Albumin Rugby Park) that made up only 8% of total serum albumin. Isoelectric focussing indicated an increased negative charge on the C-terminal CNBr peptide and C-terminal sequence analysis of the native protein showed an aberrant sequence of -Ser-Phe. Sequence analysis of PCR-amplified DNA indicated a G → C mutation at oposition 1 of the 13th intron and this was confirmed by restriction digestion. The replacement of the obligate GT sequence by CT at the exon/intron boundary prevents splicing of the 13th intron and translation continues for 21 nucleotides until a stop codon is reached. The new protein lacks the 14 amino acids coded for in the 14th exon (GKKLVAASQAALGH), but these are replaced by 7 new residues (LLQFSSF), giving a truncated albumin of 578 residues.

A dysfunctional Cl inhibitor protein with a new reactive center mutation (Arg-444→Leu)

A Pl mutation (Arg-444→Leu) was identified in a dysfunctional Cl inhibitor from a patient with type 2 hereditary angioneurotic edema. The mutation was defined at the level of the protein (by sequence analysis of the Pseudomonas aeruginosa elastase-derived reactive center peptide), and the mRNA (CGC→CTC) (by sequence analysis of PCR-amplified DNA).

Molecular defect in familial lecithin:Cholesterol acyltransferase (LCAT) deficiency: A single nucleotide insertion in LCAT gene causes a complete deficient type of the disease

Familial lecithin:cholesterol acyltransferase (LCAT) deficiency is a hereditary disorder with clinical manifestations including corneal opacity, premature atherosclerosis and renal failure. In this study, we analyzed the molecular base underlying a case of Japanese LCAT deficiency, in which both LCAT mass and activity of the proband were nearly absent. DNA blot hybridization analysis showed no gross rearrangement in the LCAT gene of the proband. The nucleotide sequence analysis of the cloned LCAT gene demonstrated only an extra nucleotide “C” insertion at the first exon, when compared to the sequence of wild type. This single base insertion caused a shift of the following reading frame, probably resulting in a truncated abnormal LCAT polypeptide that consist of only 16 amino acids. The direct sequence analysis of PCR-amplified DNA showed only the same insertion, indicating that the LCAT-deficient proband is a homozygote for the mutant allele. These results indicate that the clinical and biochemical feature of the patient is mainly caused by a complete deficiency of the enzyme based on a homozygous abnormality of LCAT gene.