Fine-mapping, mutation analyses, and structural mapping of cerebrotendinous xanthomatosis in U.S. pedigrees

Cerebrotendinous xanthomatosis (CTX) is a rare autosomal recessive disorder of bile acid biosynthesis. Clinically, CTX patients present with tendon xanthomas, juvenile cataracts, and progressive neurological dysfunction and can be diagnosed by the detection of elevated plasma cholestanol levels. CTX is caused by mutations affecting the sterol 27-hydroxylase gene (CYP27 ). CTX has been identified in a number of populations, but seems to have a higher prevalence in the Japanese, Sephardic Jewish, and Italian populations. We have assembled 12 previously unreported pedigrees from the United States. The CYP27 locus had been previously mapped to chromosome 2q33-qter. We performed linkage analyses and found no evidence of genetic heterogeneity. All CTX patients showed segregation with the CYP27 locus, and haplotype analysis and recombinant events allowed us to precisely map CYP27 to chromosome 2q35, between markers D2S1371 and D2S424. Twenty-three mutations were identified from 13 probands analyzed thus far; 11 were compound heterozygotes and 2 had homozygous mutations. Of these, five are novel mutations [Trp100Stop, Pro408Ser, Gln428Stop, a 10-base pair (bp) deletion in exon 1, and a 2-bp deletion in exon 6 of the CYP27 gene]. Three-dimensional structural modeling of sterol 27-hydroxylase showed that, while the majority of the missense mutations disrupt the heme-binding and adrenodoxin-binding domains critical for enzyme activity, two missense mutations (Arg94Trp/Gln and Lys226Arg) are clearly located outside these sites and may identify a potential substrate-binding or other protein contact site.     

Nuclease S1 mapping of 16S ribosomal RNA in ribosomes

Escherichia coli 16S rRNA and 16S-like rRNAs from other species have several universally conserved sequences which are believed to be single-stranded in ribosomes. The quantitative disposition of these sequences within ribosomes is not known. Here we describe experiments designed to explore the availability of universal 16S rRNA sequences for hybridization with DNA probes in 30S particles and 70S ribosomes. Unlike previous investigations, quantitative data on the accessibility of DNA probes to the conserved portions of 16S rRNA within ribosomes was acquired. Uniquely, the experimental design also permitted investigation of cooperative interactions involving portions of conserved 16S rRNA. The basic strategy employed ribosomes, 30S subunits, and 16S rRNAs, which were quantitatively analyzed for hybridization efficiency with synthetic DNA in combination with nuclease S1. In deproteinated E. coli 16S rRNA and 30S subunits, the regions 520-530, 1396-1404, 1493-1504, and 1533-1542 are all single-stranded and unrestricted for hybridization to short synthetic DNAs. However, the quantitative disposition of the sequences in 70S ribosomes varies with each position. In 30S subunits there appear to be no cooperative interactions between the 16S rRNA universal sequences investigated.     

Evaluation of transgenic Bacillus thuringiensis corn hybrids against Cry1Ab-susceptible and -resistant sugarcane borer (Lepidoptera: Crambidae)

A Louisiana strain of the sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), was selected for resistance to the CrylAb protein of Bacillus thuringiensis (Bt) by using an F2 screening procedure. Survival of Bt-resistant, -susceptible, and -heterozygous genotypes of sugarcane borer was evaluated on vegetative and reproductive stages of five non-Bt and seven Bt field corn, Zea mays L., hybrids in a greenhouse study. Larval survival was recorded 21 d after infestation of neonates on potted plants. Larval survival across the three sugarcane borer genotypes and five non-Bt corn hybrids after 21 d ranged from 23.6 +/- 5.2% (mean +/- SEM) to 57.5 +/- 5.2%. Mean survival of Cry1Ab-resistant larvae on vegetative and reproductive plant stages was 12 and 21%, respectively. During the vegetative stages, all seven Bt corn hybrids were highly efficacious against Cry1Ab-susceptible and -heterozygous genotypes of sugarcane borer, with a larval survival rate of <2% for the Bt-susceptible genotype and < or =5% for the heterozygotes. However, 8-18% of the heterozygous genotype survived on reproductive stage plants for four of the seven Bt corn hybrids tested. The variation in performance of Bt corn cultivars at vegetative and reproductive growth stages against Cry1Ab resistant sugarcane borer suggests differential seasonal expression that may hasten resistance in the field. Bt corn hybrids expressing a "high dose" for European corn borer, Ostrinia nubilalis (Hübner), may not produce a sufficient high dose for the sugarcane borer.     

Cytological studies on F1 hybrids of Solanum integrifolium with S. melongena and S. melongena var. insanum

S. integrifolium (2n = 24) can easily be crossed as the pistillate parent with S. melongena (2n = 24) and S. melongena var. insanum (2n = 24). However, crosses in the other direction do not succeed. Both hybrids are vigorous. Chromosome association at diakinesis and metaphase I was studied. Chromosome associations higher than bivalents were observed in the hybrids indicating structural repatterning of chromosomes. The modal chromosome association in hybrids was twelve bivalents per PMC. This is suggestive of the retention of ancestral chromosome homeologies by the taxa concerned. Despite regular meiosis both hybrids were highly pollen-sterile (about 95%), which was attributed to segregational events of the recombined chromosomes.     

Regional mapping of the human No. 1 and X chromosome in interspecific cell hybrids using an X/1 translocation.

Fibroblasts from a carrier of an X/1 translocation, 46,XY,t(X;1)(q28;q31), were fused with Chinese hamster cells. The resulting hybrids were analyzed for human No. 1 and X-chromosome markers. The data indicate that the loci for PGM1, PGD, PPH, and GuK1 are situated either in the long arm proximal to a break point in band 1q31 or in the short arm. The loci for Pep-C, FH, and GuK1 are located distal to the break point. HPRT and G6PD are probably situated distal to a break point in band q28 of the X chromosome; alpha-Gal A is situated proximal to the break point, either on the long or short arm of the chromosome.     

Phenolic glycosides and condensed tannins in Salix sericea, S. eriocephala and their F1 hybrids: not all hybrids are created equal

The performance of hybrids depends upon the inheritance and expression of resistance traits. Secondary chemicals are one such resistance trait. In this study, we measured the concentrations of phenolic glycosides and condensed tannins in parental and F1 hybrid willows to examine the sources of chemical variation among hybrids. S. sericea produces phenolic glycosides, salicortin and 2'-cinnamoylsalicortin, and low concentrations of condensed tannin in its leaves. In contrast, S. eriocephala produces no phenolic glycosides but high concentrations of condensed tannins in its leaves. These traits are inherited quantitatively in hybrids. On average, F1 hybrids are intermediate for condensed tannins, suggesting predominantly additive inheritance or balanced ambidirectional dominance of this defensive chemical from the parental species. In contrast, the concentration of phenolic glycosides is lower than the parental midpoint, indicating directional dominance. However, there is extensive variation among F1 hybrids. The concentration of tannin and phenolic glycosides in F1 hybrid families is either (1) lower than the midpoint, (2) higher than the midpoint, or (3) indistinguishable from the midpoint of the two parental taxa. It appears that the production of the phenolic glycosides, especially 2'-cinnamoylsalicortin, is controlled by one or more recessive alleles. We also observed a two-fold or greater difference in concentration between some hybrid families. We discuss how chemical variation may effect the relative susceptibility of hybrid willows to herbivores.     

High-resolution mapping of S1- and DNase I-hypersensitive sites in chromatin.

A new and easy technique for accurately mapping DNase I- and S1 nuclease-hypersensitive sites is described. The technique is a modification of primer extension and S1 nuclease methods conventionally used to map RNA ends.     

Complementation mapping in microcell hybrids: localization of Fpgs and Ak-1 on Mus musculus chromosome 2

The gene encoding folylpolyglutamyl synthetase (FPGS) was assigned to mouse chromosome 2 by complementation mapping. Chinese hamster ovary cells (AuxBl) deficient in FPGS, and consequently auxotrophic for glycine, adenosine, and thymidine (gat-), were employed as recipients in microcell-mediated chromosome transfer experiments. Mouse chromosomes derived from diploid embryo fibroblasts were introduced into hamster AuxBl cells, and gat+ microcell hybrids were selected in medium lacking adenosine and thymidine. Mouse chromosome 2 was the only donor chromosome whose presence correlated with expression of FPGS activity. Furthermore, every gat+ hybrid clone expressed murine AK-1, a marker previously assigned to chromosome 2. Eight of 20 clones analyzed retained deletion chromosomes derived from mouse chromosome 2. These clones were used to localize murine Fpgs and Ak-1 to a region of this chromosome, namely 2 (cen leads to Cl).     

gyrB mutations in coumermycin A1-resistant Borrelia burgdorferi.

We have isolated and characterized mutants of Borrelia burgdorferi that are resistant to the antibiotic coumermycin A1, which targets the B subunit of DNA gyrase. Mutants had either 100- or 300-fold higher resistance to coumermycin A1 than wild-type B. burgdorferi. In each case, a single point mutation in the gyrB gene converted Arg-133 to Gly or Ile. Mutations in the homologous Arg residue of Escherichia coli DNA gyrase are also associated with resistance to coumarin antimicrobial agents.     

Mechanistic analyses of site-specific degradation in DNA-RNA hybrids by prototypic DNA cleavers.

Bleomycin (BLM) binding and chemistry are apparently sensitive to differences in nucleic acid conformation and could conceivably be developed as a probe for sequence-dependent elements of conformation. We report on the development of a new methodology to synthesize heterogeneous DNA-RNA hybrids of defined sequence and present the results of our comparative studies on the cleavage of DNA and DNA-RNA hybrids by four drugs: BLM, neocarzinostatin and esperamicins A1 and C. In the case of BLM with duplex DNA, purine-pyrimidine steps such as GT and GC, are consistently hit, as previously observed. However, in heterogeneous sequence hybrids, not all GC sites are recognized by the drug, although all GT sites are. Suppressed GC sites are consistently flanked by pyrimidines on both the 3' and 5' sides, suggesting that the BLM binding site in hybrids spans at least four bases. Kinetic isotope studies with specifically deuterated substrates (kH/kD = 1.2-4.0) and the effect of oxygen on the product profile are presented in support of a mechanism consistent with 4'-hydrogen abstraction in hybrids. The powerful double-labeled probe technique was extended to study the mechanism of action of other DNA degrading drugs on DNA-RNA hybrids. For neocarzinostatin, the sequence specificity lies in the AT-rich region for hybrids and is similar to that of DNA, however, the overall cleavage pattern for the hybrid is significantly different from that for the same sequence of DNA. In the hybrid, a stretch of AT residues is essential and the A sites are damaged to a greater extent than they are in DNA. However, no kinetic isotope effects are observed and, based on the product profile, the mechanism of degradation of the DNA strand of hybrids seems to be limited to abstraction of the 5'-hydrogen. For esperamicin A1, damage on the DNA strand of hybrids occurs exclusively via 5'-hydrogen abstraction in a non-rate determining step and primarily at A and T sites. Esperamicin C behaves similarly, exhibiting no isotope effects at 1', 4' and 5' positions. Overall, the differences observed in site-specific cleavage between the two substrates is proposed to be a result of conformational differences between the DNA strand of duplex DNA and DNA-RNA hybrids.     

introgress: a software package for mapping components of isolation in hybrids

A new software package (introgress) provides functions for analysing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. The software works with co-dominant, dominant and haploid marker data, and does not require fixed allelic differences between parental populations for the sampled genetic markers. Permutation and parametric procedures generate neutral expectations for introgression and provide a basis for significance tests of observed genomic clines. The software also implements maximum likelihood estimates of hybrid index from genotypic data and a number of graphical analyses. The package is an extension of the R statistical software, is written in the R language and is freely available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). In this study, we describe introgress and demonstrate its use with a sample data set.     

Elimination of Solanum phureja nucleolar chromosomes in S. tuberosum + S. phureja somatic hybrids

Summary The karyotype of the dihaploid SVP1 line of S. tuberosum (2n=2x=24) showed two nucleolar chromosomes with differently sized satellites. The diploid SVP5 line (2n=2x=24) and tetraploid regenerants of S. phureja had larger but similar satellites. Somatic hybrids between the diploid lines of these potato species with genome combinations 4 tub + 2 ph (plants 1–3), 2 tub + 4 ph (plants 4–7) and 4 tub + 4 ph (plant 8) had lost 2 phureja nucleolar chromosomes if 4 phureja genomes were present. One phureja nucleolar chromosome of plants 1–3 and both of plants 5 and 7 had rearranged satellites. Elimination of the two nucleolar chromosomes occurred preferentially, was under genetic control, and probably took place during early callus development. NOR activity resulting in rear-rangements between NORs may have caused the elimination.     

Assay of DNA-RNA hybrids by S1 nuclease digestion and adsorption to DEAE-cellulose filters.

A fast and accurate assay procedure for DNA-RNA hybrids is described in which exhaustive digestion of unhybridized DNA with S1 nuclease is followed by binding of hybrids to filter discs of DEAE-cellulose. The digested DNA can be efficiently washed from the filters so that background levels of 0.1-0.2% of input tracer DNA can be achieved, in contrast to the much higher (approximately 1-5%) backgrounds obtained using TCA precipitation procedures. Short duplexes, as small as 36 nucleotides in length, which are inefficiently bound to hydroxyapatite, are quantitatively bound to the DEAE-cellulose filters.     

Chromosomal and embryological analyses in sexual x apomictic hybrids ofPanicum maximum Jacq.

Summary Cytological analyses in series of crosses between 7 sexual pistillate and 8 apomictic staminate parents of speciesPanicum maximum (Gramineae) are reported. Although these 15 progenitors were tetraploid (2n = 32), 2 dihaploids (2n = 16), 45 hexaploids (2n = 48) and 5 octoploids (2n = 64) were observed among 333 progeny plants. The role of unreduced gametes as the originators of polyploidy is discussed in relation to the so-called elements of apomixis. The 2 dihaploids appeared to be sexual while the hexaploids and octoploids were all apomictic. At the tetraploid level sexual and apomictic hybrids segregated in a ratio close to 11. These results were then compared to those already obtained from studies on other tropical grasses and indicate a simple genetic determinism for gametophytic apomixis.