Use of a DNA probe for mapping by electron microscopy the ribosomal sequences in ribosomal RNA precursors from duck cells

This report describes the use of purified ribosomal DNA to map by electron microscopy the relative positions of the 18 S and 28 S RNA regions within the duck rRNA precursor and their relationship to the non-conserved portions of the precursor molecule. By repeated fractionation of the total DNA, based on the relative reassociation rates of the DNA sequences with different degrees of repetition, a fraction of the rapidly renaturing DNA was obtained which comprised only 6% of the total DNA, but contained 71% of the rRNA cistrons. Further purification of the rDNA was achieved by saturation hybridization with rRNA and separation of the rRNA-rDNA hybrids by banding in CsCl. In this manner, an rDNA-rRNA fraction was obtained which had a buoyant density of 1.805 g/cm³, an RNA to DNA ratio of 1.01, and a base composition for the RNA present in the hybrid identical to that of an equimolar mixture of 18 S and 28 S rRNA. The final yield of rDNA isolated by this procedure is 32%. When the purified rDNA was annealed with a mixture of 18 S and 28 S rRNA and the hybrids spread for electron microscopy, they appeared as two distinct populations with a number-average length of 0.62 ± 0.13 μm and 1.37 ± 0.18 μm, respectively. Likewise, hybrids between the rRNA precursor, isolated from duck embryo fibroblasts, and the rDNA appeared as structures containing two duplex regions of lengths 0.60 ± 0.11 μm and 1.38 ± 0.15 μm, separated from each other by a single-stranded region appearing as a large bush: this represents a portion of the precursor molecule not conserved during processing of the parent molecule. From these observations a model of the structure of the duck rRNA precursor is proposed.     

A new type of EcoRI polymorphism of the human ribosomal DNA repeating unit revealed by analysis of cloned DNA fragments

Several clones of rDNA have been isolated from an adult human liver DNA Charon 4A library by using cDNA probes synthesized from human 18S and 28S rRNA. The insert of one recombinant Charon 4A clone contained, besides the already known 5.7-kb EcoRI fragment of rDNA, comprising the major portion of the 18S rRNA gene and all the external transcribed spacer (ETS), a previously unidentified EcoRI fragment of rDNA of 8.5 kb in size. DNA transfer hybridization experiments utilizing EcoRI digests of the human DNA used to construct the library and of another human DNA showed the presence of the 8.5-kb EcoRI fragment in a minority of the rDNA repeats on the 5'-end side of the 5.7-kb fragment, thus defining a hitherto unidentified type of EcoRI polymorphism of these repeats.     

Amino acid specificity of the transfer RNA species coded for by HeLa cell mitochondrial DNA

The amino acid specificity of the tRNA species coded for by HeLa cell mitochondrial DNA has been investigated by carrying out hybridizations between amino acid-tRNA complexes labeled in the amino acid and separated mitochondrial DNA strands.The results indicate that there are in HeLa cell mitochondria at least 17 distinct tRNA species hybridizable with mitochondrial DNA, which are specific for 16 amino acids. For 14 of the 16 amino acids, amino-acyl-tRNA synthetase activities distinct from the cytoplasmic ones have been detected in mitochondria. The remaining four amino acids (asparagine, glutamine, histidine and proline) have consistently failed to charge to any detectable extent mitochondrial tRNA species hybridizable with mitochondrial DNA.No obvious relationship appears to exist between the amino acids incorporated into tRNAs hybridizable to mitochondrial DNA and the previously observed pattern of chloramphenicol-sensitive amino acid incorporation by HeLa cell mitochondria.     

JADE: An approach for interconnecting bioinformatics databases

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.     

Design of a bovine low-density SNP array optimized for imputation

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.