Fractionation of charge-modified low density lipoproteins by fast protein liquid chromatography.

We describe a methodology developed to separate different forms of charge-modified low density lipoproteins (LDL) using the fast protein liquid chromatography (FPLC) system from Pharmacia. Lipoproteins were isolated by sequential ultracentrifugation and introduced onto an anion-exchange column (Mono Q HR 5/5). The multistep NaCl gradient elution was optimized and the analytical variables were determined on copper-oxidized LDL. After oxidation by copper for various times (up to 48 h), five forms were obtained (fractions A, B, C, D, and E). Within-run and day-to-day reproducibility were better than 8.6% and 10%, respectively. Protein and cholesterol recovery after the chromatographic separation was good (greater than 82%) and the detection limit was about 1 microgram. The more negative forms of collected LDL were mainly characterized by an increase in the lipid peroxidation product content, a depletion of vitamin E, an alteration of apoB and increased degradation by macrophages. The proposed methodology was applied to the study of LDL modifications generated by human umbilical endothelial cells and the protective effect of antioxidants (vitamin E and probucol).     

Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.).

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms are useful as DNA markers for genetic analysis or positional cloning with segregating populations of crosses. Pairwise comparison between cultivars and a neighbor-joining tree calculated from SNPs agreed very well with relationships between rice strains predicted from pedigree data or calculated with other DNA markers such as p-SINE1 and simple sequence repeats (SSRs), suggesting that whole-genome SNP information can be used for analysis of evolutionary relationships. Using multiple SNPs to identify alleles, we drew a map to illustrate the alleles shared among the eight cultivars and the accession. The map revealed that most of the genome is mono- or di-allelic among japonica cultivars, whereas alleles well conserved among modern japonica paddy rice cultivars were often shared with indica cultivars or wild rice, suggesting that the genome structure of modern cultivars is composed of chromosomal segments from various genetic backgrounds. Use of allele-sharing analysis and association analysis were also tested and are discussed.     

Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags

We have constructed a rice function map by collating the results on quantitative trait loci (QTLs) for 23 important physiological and agronomic characters (including 13 newly measured traits) obtained using backcross inbred lines of japonica Nipponbare×indica Kasalath. Using these materials, The Rice Genome project (RGP) has developed a high-density genetic map. QTLs controlling yield did not overlap with those controlling the morphological and physiological traits supposed to relate to yield, such as photosynthetic ability. This result suggests that these traits do not influence yield, at least in this genetic background and environment. QTLs controlling yield also did not overlap with the structural genes controlling carbon metabolism (rbcS, cytosolic or plastidic fructose-1,6-bisphosphate, R-enzyme, and sucrose synthase).The combination of a function map and results from the RGP can be advantageous. The utility of this map is discussed. Received: 1 October 1999 / Accepted: 28 July 2000     

Saturation mapping with subclones of YACs: DNA marker production targeting the rice blast disease resistance gene, Pi-b

Saturation mapping of a very small genomic region is indispensable for map-based cloning. We applied a method based on sub-cloning and the Southern-hybridization technique for generating RFLP markers directly from yeast artificial chromosomes (YACs). Two YACs overlapping each other and covering the locus of the rice blast resistance gene, Pi-b, were used to construct a plasmid sub-library. Rice-specific and single-copy clones suitable as probes for RFLP analysis were selected from this sub-library by hybridization to the blots of digested DNAs of rice, YACs, and yeast. As a result, 22 markers were produced within a small chromosomal region including Pi-b. This case study shows that overlapping YACs known to cover the gene of interest are very useful in fine-scale physical mapping leading to map-based cloning of the target gene. Received: 2 May 1996 / Accepted: 2 August 1996     

Combining many multiple alignments in one improved alignment

MOTIVATION: The fact that the multiple sequence alignment problem is of high complexity has led to many different heuristic algorithms attempting to find a solution in what would be considered a reasonable amount of computation time and space. Very few of these heuristics produce results that are guaranteed always to lie within a certain distance of an optimal solution (given a measure of quality, e.g. parsimony). Most practical heuristics cannot guarantee this, but nevertheless perform well for certain cases. An alignment, obtained with one of these heuristics and with a bad overall score, is not unusable though, it might contain important information on how substrings should be aligned. This paper presents a method that extracts qualitatively good sub-alignments from a set of multiple alignments and combines these into a new, often improved alignment. The algorithm is implemented as a variant of the traditional dynamic programming technique. RESULTS: An implementation of ComAlign (the algorithm that combines multiple alignments) has been run on several sets of artificially generated sequences and a set of 5S RNA sequences. To assess the quality of the alignments obtained, the results have been compared with the output of MSA 2.1 (Gupta et al., Proceedings of the Sixth Annual Symposium on Combinatorial Pattern Matching, 1995; Kececioglu et al., http://www.techfak.uni-bielefeld. de/bcd/Lectures/kececioglu.html, 1995). In all cases, ComAlign was able to produce a solution with a score comparable to the solution obtained by MSA. The results also show that ComAlign actually does combine parts from different alignments and not just select the best of them. AVAILABILITY: The C source code (a Smalltalk version is being worked on) of ComAlign and the other programs that have been implemented in this context are free and available on WWW (http://www.daimi.au.dk/ ?caprani). CONTACT: klaus@bucka-lassen.dk; jotun@pop.bio.au.dk;ocaprani@daimi.au.dk     

Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63.

Staphylococcus auriculans DBF63, which can grow on dibenzofuran (DBF) or fluorene (FN) as the sole source of carbon and energy, was isolated. Salicylic acid and gentisic acid accumulated in the culture broth of this strain when DBF was supplied as a growth substrate. Also, the formation of 9-fluorenol, 9-fluorenone, 4-hydroxy-9-fluorenone, and 1-hydroxy-9-fluorenone was demonstrated, and accumulation of 1,1a-dihydroxy-1-hydro-9-fluorenone was observed when this strain grew on FN. On the basis of these results, the degradation pathways of DBF and FN were proposed. The analogous oxidation products of dibenzo-p-dioxin were obtained by incubation with DBF-grown S. auriculans DBF63 cells.     

Breakpoints in Robertsonian translocations are localized to satellite III DNA by fluorescence in situ hybridization.

We characterized 21 t(13;14) and 3 t(14;21) Robertsonian translocations for the presence of DNA derived from the short arms of the translocated acrocentric chromosomes and identified their centromeres. Nineteen of these 24 translocation carriers were unrelated. Using centromeric alpha-repeat DNA as chromosome-specific probe, we found by in situ hybridization that all 24 translocation chromosomes were dicentric. The chromatin between the two centomeres did not stain with silver, and no hybridization signal was detected with probes for rDNA or beta-satellite DNA that flank the distal and proximal ends of the rDNA region on the short arm of the acrocentrics. By contrast, all 24 translocation chromosomes gave a distinct hybridization signal when satellite III DNA was used as probe. This result strongly suggests that the chromosomal rearrangements leading to Robertsonian translocations occur preferentially in satellite III DNA. We hypothesize that guanine-rich satellite III repeats may promote chromosomal recombination by formation of tetraplex structures. The findings localize satellite III DNA to the short arm of the acrocentric chromosomes distal to centromeric alpha-repeat DNA and proximal to beta-satellite DNA.     

Experimental evidence of a potentially increased thrombo-embolic disease risk by domestic electromagnetic field exposure

We have used the EaHy926 endothelial cell line, able to secrete both pro and anti-aggregant platelet agents, as a model for thrombo-embolic diseases. We experimentally established, by comparing these two secretions with or without a Faraday cage, that the environmental electromagnetic field significantly increases the thrombo-embolic risks in this endothelial cell line.     

A comparison of the effects of equine luteinizing hormone (eLH), equine growth hormone (eGH) and human recombinant insulin-like growth factor (hrIGF-I) on steroid production in cultured equine Leydig cells during sexual maturation

There are several hormones and local testicular factors involved in the initiation and control of steroidogenesis and spermatogenesis during puberty. GH and its mediator, IGF-I, increase substantially during puberty, and in addition to LH, these growth-promoting hormones can have direct effects upon testicular function. The objective of this work was to investigate the effects of eLH, eGH and hrIGF-I upon Leydig cells derived from testes of colts and stallions representing different stages of development. Testes were obtained from 48 light horse colts and stallions at the time of routine castration, horses were categorized according to age group (prepubertal, pubertal and postpubertal) and a Leydig cell enriched preparation was utilized for cell culture. Cells derived from all 48 horses were treated with doses of eLH, and a subset of 21 horses received doses of eGH and hrIGF-I. Cells were plated at a concentration of 1 x 10(6) cells/ml and incubated for 24 h at 32 degrees C. Production of testosterone and estradiol was measured by validated RIA. Leydig cells from prepubertal colts secreted greater basal amounts of testosterone but lesser basal amounts of estradiol compared with the other age groups (p < 0.001). Pubertal stallions exhibited the greatest relative response to eLH (p < 0.05). Neither eGH nor hrIGF-I elicited a steroidogenic response over baseline concentrations in any of the three age groups.