Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the species T. maritimum constitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoring Tenacibaculum infections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related to T. dicentrarchi, a recently described species.     

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.     

Aggressiveness and kinship in brown trout (Salmo trutta) parr

In a series of experiments, kin-biased behavior of young browntrout (Salmo trutta) was observed. The aggressiveness shownby groups of familiar siblings (siblings reared together sincefertilization) and groups of unfamiliar siblings (siblings rearedapart since fertilization) was significantly lower comparedto that of mixed groups of two unrelated sibling groups (offspringof two different pairs of parents). The evolution of kin-biasedbehavior, as shown by a reduction in aggressiveness, is assumedto have evolved through a kin-selective mechanism.[Behav Ecol7: 445-450 (1996)]     

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high‐quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype‐resolved genome resequencing at population scale, we investigated properties of linked‐read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high‐coverage data (46–68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25–4.6 Mb (N50) and 0.27–0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher‐quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase‐sized genomes like birds, linked‐read sequencing at moderate depth opens an affordable avenue towards haplotype‐resolved genome resequencing at population scale.     

Novel lipase-catalysed highly selective acetylation studies on D-arabino- and D-threo-polyhydroxyalkyltriazoles

Capabilities of lipases from Candida antarctica, Candida rugosa and porcine pancreas have been evaluated for regioselective acetylation of 2-phenyl-4-(D-arabino-tetrahydroxybutyl)-2H-1,2,3-triazole, 2-phenyl-4-(D-arabino-O-1',2'-isopropylidene-3',4'-dihydroxybutyl)-2H-1,2,3-triazole and 2-phenyl-4-(D-threo-trihydroxypropyl)-2H-1,2,3-triazole, precursors for the synthesis of triazolylacyclonucleosides. C. antarctica lipase and porcine pancreatic lipase exhibited exclusive selectivity for the acetylation of primary hydroxyl group over secondary hydroxyl group(s) in all the three cases.     

The mouse alpha 1(XII) and human alpha 1(XII)-like collagen genes are localized on mouse chromosome 9 and human chromosome 6.

Type XII collagen is a member of the FACIT (fibril-associated collagens with interrupted triple helices) group of extracellular matrix proteins. Like the other members of this group, collagen types IX and XIV, type XII has alternating triple-helical and non-triple-helical domains. Because of its structure, its association with collagen fibrils, and its distribution in dense connective tissues, type XII is thought possibly to act as a cross-bridge between fibrils and resist shear forces caused by tension. A portion of the ffuse gene was isolated by screening a genomic library with a chicken alpha 1 (XII) cDNA probe, followed by subcloning and sequence analysis. Comparison of exon sequences with the sequence of a mouse cDNA clone allowed the mouse gene to be identified as the alpha 1 (XII) collagen gene. In the mouse, Col12a1 is located on chromosome 9, as determined by linkage analysis using DNA from interspecific backcrosses with Mus spretus. Screening of a human genomic library also allowed the isolation of a human alpha 1(XII)-like gene (CoL12A1). This gene was mapped to chromosome 6 by blot hybridization to DNA from human/hamster hybrid cell lines. This information should prove useful in determining the role of type XII collagen genes as candidate genes in inheritable connective tissue diseases.     

Cloning and expression in Escherichia coli of the gene for extracellular phospholipase A1 from Serratia liquefaciens.

From a genomic library of Serratia liquefaciens, a cloned DNA fragment comprising a two-gene operon was isolated and expressed in Escherichia coli. One of the gene products was identified as a phospholipase A1, and the enzyme was found to be excreted to the outer environment from S. liquefaciens as well as from E. coli. Both genes were sequenced, and the relationship between open reading frames in the DNA sequence and in vitro-expressed polypeptides was established. The length of the phospholipase polypeptide was found to be 319 amino acids. In the amino-terminal end of the coding sequence was a stretch of about 20 hydrophobic amino acids, but, in contrast to consensus signal peptides, no basic residues were present. The length of the second polypeptide was 227 amino acids. It was found that expression of the phospholipase gene in both E. coli and S. liquefaciens was growth phase regulated (late expression).     

Short-term energy deficit causes net accumulation of linoleoyl-enriched triacylglycerols in rat liver

Energy depletion by reduced food intake over 4 days resulted in a 73% reduction in total rat liver triacylglycerols (TG). In liver TG of energy-depleted rats, dilinoleoyl oleoyl glycerol (OLL) and trilinoleoyl glycerol (LLL)) were quantitatively increased by 85% and 147%, respectively. The net increase in linoleoyl-enriched species could be quantitatively accounted for by the release of linoleate from monolinoleoyl species and its subsequent reacylation into dilinoleoyl species and trilinolein during energy depletion. Hence while palmitate, oleate and some linoleate are being hydrolyzed, presumably for oxidation some linoleate is retained and contributes to the remodelling of hepatic triacylglycerols during energy deficit.