Computational complexity of inferring phylogenies from dissimilarity matrices

Molecular biologists strive to infer evolutionary relationships from quantitative macromolecular comparisons obtained by immunological, DNA hybridization, electrophoretic or amino acid sequencing techniques. The problem is to find unrooted phylogenies that best approximate a given dissimilarity matrix according to a goodness-of-fit measure, for example the least-squares-fit criterion or Farris'sf statistic. Computational costs of known algorithms guaranteeing optimal solutions to these problems increase exponentially with problem size; practical computational considerations limit the algorithms to analyzing small problems. It is established here that problems of phylogenetic inference based on the least-squares-fit criterion and thef statistic are NP-complete and thus are so difficult computationally that efficient optimal algorithms are unlikely to exist for them. The Natural Sciences and Engineering Research Council of Canada partially supported this research through an individual operating grant (A4142) to W.H.E. Day.     

Polymorphisms of DQ β genes in HLA-DR4 haplotypes from healthy and diabetic individuals

The restriction fragment length polymorphism (RFLP) of DQ was assessed in a panel of control and insulin-dependent diabetes (IDD) patients who were serologically typed as HLA-DR4 homozygotes or HLA-DR3, DR4 heterozygotes. Digestions of genomic DNA with Barn HI, Bg1 II, Pst I, Xba I, and Hind III revealed a total of 15 RFLPs in the panel of 71 HLA-DR4 chromosomes. These RFLPs were organized into six allelic groups on the basis of segregation analysis in families. Complete RFLP haplotypes for the 5 restriction enzymes could be constructed for 42 of the HLA-DR4 chromosomes. This analysis revealed 18 RFLP haplotypes of DQ associated with the DR4 chromosomes tested. Two of these haplotypes, designated DQ3.DR4.a and DQ3.DR4.b, accounted for over 50 % of the DR4 chromosomes analyzed. These two haplotypes were antithetical for the RFLPs detected by all five enzymes, indicating that they represent very distinct forms of DQ . The remaining 16 haplotypes were infrequent or unique and were closely related to either a DQ3.DR4.a or DQ3.DR4.b. Two of the RFLPs detected, a 5.8 kb Bg1 II fragment and a 10.5 kb Barn HI fragment, had increased frequencies in disease-associated chromosomes. However, none of the RFLPs we detected exhibited a statistically significant increase in IDD or control populations. In contrast, the DQ3.DR4.b DQ haplotype was significantly decreased in IDD-associated DR4 chromosomes. (P=0.04). These results suggest that the DQ3.DR4.b DQ allele may be protective for the development of IDD.     

Neutral mutations and repetitive DNA

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.     

Photoproduction of amino acids by mutant strains of N2-fixing cyanobacteria

Summary Mutant strains of the N₂-fixing cyanobacterium bacterium Anabaena variabilis resistant to 6-fluorotryptophan or to ethionine were isolated. Many of these strains liberated amino acids into their media in the absence of 6-fluorotryptophan and ethionine. Nitrogenase activity was higher in mutant strains than in the parent strain. Mutant strains were immobilised in calcium alginate and sustained photoproduction of amino acids has been demonstrated.Abbreviations ETH ethionine - FT 6-fluorotryptophan - Hepes 4-(2-hydroxyethyl)-1, piperazine ethanesulphonic acid - PEP phosphoenolpyruvate - DAHP 3-deoxy-d-arabinoheptulosonate 7-phosphate - chl a chlorophyll a     

Tyrosine Hydroxylase Is Activated and Phosphorylated on Different Sites in Rat Pheochromocytoma PC12 Cells Treated with Phorbol Ester and Forskolin

Abstract: Incubation of rat pheochromocytoma PC12 cells with 4β-phorbol-12β-myristate-13α-acetate (PMA), an activator of Ca²⁺/phospholipid-dependent protein kinase (protein kinase C), or forskolin, an activator of adenylate cyclase, is associated with increased activity and enhanced phosphorylation of tyrosine hydroxylase. Neither the activation nor increased phosphorylation of tyrosine hydroxylase produced by PMA is dependent on extracellular Ca²⁺. Both activation and phosphorylation of the enzyme by PMA are inhibited by pretreatment of the cells with trifluo-perazine (TFP). Treatment of PC 12 cells with l-oleoyl-2-acetylglycerol also leads to increases in the phosphorylation and enzymatic activity of tyrosine hydroxylase; 1, 2-diolein and 1, 3-diolein are ineffective. The effects of forskolin on the activation and phosphorylation of the enzyme are independent of Ca²⁺ and are not inhibited by TIT⁵. Forskolin elicits an increase in cyclic AMP levels in PC 12 cells. The increases in both cyclic AMP content and the enzymatic activity and phosphorylation of tyrosine hydroxylase following exposure of PC 12 cells to different concentrations of forskolin are closely correlated. In contrast, cyclic AMP levels do not increase in cells treated with PMA. Tryptic digestion of the phosphorylated enzyme isolated from untreated cells yields four phosphopeptides separable by HPLC. Incubation of the cells in the presence of the Ca²⁺ ionophore ionomycin increases the phosphorylation of three of these tryptic peptides. However, in cells treated with either PMA or forskolin, there is an increase in the phosphorylation of only one of these peptides derived from tyrosine hydroxylase. The peptide phosphorylated in PMA-treated cells is different from that phosphorylated in forskolin-treated cells. The latter peptide is identical to the peptide phosphorylated in dibutyryl cyclic AMP-treated cells. These results indicate that tyrosine hydroxylase is activated and phosphorylated on different sites in PC 12 cells exposed to PMA and forskolin and that phosphorylation of either of these sites is associated with activation of tyrosine hydroxylase. The results further suggest that cyclic AMP-dependent and Ca²⁺/ phospholipid-dependent protein kinases may play a role in the regulation of tyrosine hydroxylase in PC 12 cells.     

Altered Mitochondrial Respiration in Selectively Vulnerable Brain Subregions Following Transient Forebrain Ischemia in the Rat

Mitochondrial respiratory function, assessed from the rate of oxygen uptake by homogenates of rat brain subregions, was examined after 30 min of forebrain ischemia and at recirculation periods of up to 48 h. Ischemia-sensitive regions which develop extensive neuronal loss during the recirculation period (dorsal-lateral striatum, CA1 hippocampus) were compared with ischemia-resistant areas (paramedian neocortex, CA3 plus CA4 hippocampus). All areas showed reductions (to 53-69% of control) during ischemia for oxygen uptake rates determined in the presence of ADP or an uncoupling agent, which then recovered within 1 h of cerebral recirculation. In the ischemia-resistant regions, oxygen uptake rates remained similar to control values for at least 48 h of recirculation. After 3 h of recirculation, a significant decrease in respiratory activity (measured in the presence of ADP or uncoupling agent) was observed in the dorsal-lateral striatum which progressed to reductions of greater than 65% of the initial activity by 24 h. In the CA1 hippocampus, oxygen uptake rates were unchanged for 24 h, but were significantly reduced (by 30% in the presence of uncoupling agent) at 48 h. These alterations parallel the development of histological evidence of ischemic cell change determined previously and apparently precede the appearance of differential changes between sensitive and resistant regions in the content of high-energy phosphate compounds. These results suggest that alterations of mitochondrial activity are a relatively early change in the development of ischemic cell death and provide a sensitive biochemical marker for this process.     

Chloroplast photooxidation inhibits the expression of a set of nuclear genes

Summary Mutations or herbicides which inhibit the accumulation of carotenoid pigments in higher plants also result in the arrest of chloroplast development at a very early stage. The cause is extensive photooxidative damage within the chloroplast in the absence of protective carotenoids. Because the extent of photooxidation is dependent upon light intensity, normal chloroplast development can occur when carotenoid-deficient seedlings are grown in very dim light. Normal accumulation of chloroplastic and cytosolic mRNAs encoding chloroplast proteins proceeds only under permissive dim light conditions. Illumination with higher intensity light causes rapid chlorophyll photooxidation and the loss of two cytosolic mRNAs coding for proteins destined for the chloroplast, but does not affect another light-regulated cytosolic mRNA encoding a cytosolic protein. This experimental system may have uncovered a mechanism which coordinates the expression of genes in different cellular compartments.Abbreviations LHCP light-harvesting chlorophyll a/b protein - SSu small subunit - RuBP fibulose 1,5-bisphoshate - PEP phosphoenolpyruvate     

Genetic research with nonhuman primates: serving the needs of mankind Symposium summary and future prospects

The wide array of papers delivered at this symposium, ranging from population genetics to molecular genetics, is convincing evidence that genetic research with nonhuman primates is in full bloom. In fact, progress has been quite remarkable considering that a significant number of pedigreed colonies of nonhuman primates have been available for less than 25 years, which is hardly enough time to raise 3 generations of chimpanzees, 5 generations of baboons or 6 generations of rhesus monkeys. Were it not for these pedigreed colonies, we would not have been privileged to have this assemblage of papers on behavior, social structure, predisposition to disease and management of breeding colonies. It is indeed exciting that preliminary evidence has been obtained for major genes that play a role in susceptibility to dyslipoproteinemias in baboons, and that monoclonal antibodies and DNA markers are helping us to understand cholesterol metabolism. And thanks to computers, we can now rank animals in a colony in terms of their useful genotypes as well as their productivity. One can not help but be impressed with the commonality of humans and nonhuman primates at the structural and functional levels. For example, the major histocompatibility systems and the maternal-fetal relationships are very similar. We heard that this similarity is even more striking at the chromosomal, biochemical and DNA levels. A provocative question yet to be answered is, “what accounts for the obvious differences between humans and nonhuman primates in view of these incredible similarities?” In light of these advances, this symposium was at the cutting edge of primate genetics and the papers published in this issue of Genetica are certain to be hallmarks in the literature.     

Genetic Hitchhiking and the Evolution of Reduced Genetic Activity of the Y Sex Chromosome

We report experiments designed to test homology dependence for gene conversion between duplicated chromosomal sequences in cultured mammalian cells. The experimental system is such that gene conversion events not associated with reciprocal exchange are recoverable. For this study four plasmids were constructed. Each contains a different duplication of the herpes simplex virus thymidine kinase (HSV tk) gene sequence. In particular, the interacting sequences share different lengths of homology. Our results indicate that for shared homologies between 295 base pairs (bp) and 1.8 kilobase pairs (kbp) in length, conversion is efficient with the rate being directly proportional to the extent of homology. In contrast, conversion with either 200 bp or 95 bp of homology is inefficient, and the rate is reduced at least seven- or 100-fold, respectively, relative to that observed with 295 bp of homology. These results are consistent with the notion that greater than 200 bp of homology are required for efficient gene conversion between repeated chromosomal sequences in mammalian cells.