Substitution rates of organelle and nuclear genes in sharks: implicating metabolic rate (again)

Rates of nucleotide substitution for nuclear genes are thought to be governed primarily by the number of germ line replication events (the so-called "generation time" hypothesis). In contrast, rates of mitochondrial DNA evolution appear to be set primarily by DNA damage pathways of mutation mediated by mutagenic by-products of oxidative phosphorylation (the so-called "metabolic-rate" hypothesis). Comparison of synonymous substitution rates estimated for the mitochondrial cytochrome b gene and nuclear-encoded dlx, hsp70, and RAG-1 genes in mammals and sharks shows that rates of molecular evolution for sharks are approximately an order of magnitude slower than those for mammals for both nuclear and mitochondrial genes. In addition, there is significant positive covariation of substitution rate for mitochondrial and nuclear genes within sharks. These results, interpreted in light of the pervasiveness of DNA damage by mutagenic by-products of oxygen metabolism to both nuclear and mitochondrial genes and coupled with increasing evidence for cross-genome activity of DNA repair enzymes, suggest that molecular clocks for mitochondrial and nuclear genes may be set primarily by common mutational mechanisms.      

Metabolic rate and directional nucleotide substitution in animal mitochondrial DNA

There is marked heterogeneity of nucleotide composition in mitochondrial DNA across divergent animals. Differences in nucleotide composition presumably reflect differences in directional nucleotide substitution for A+T or G+C nucleotides. In mitochondrial DNA, there is A+T directional nucleotide substitution in most (if not all) animals surveyed, and the magnitude of directional A+T nucleotide substitution differs greatly within and among groups. Differences in directional nucleotide substitution among lineages of mammals can be explained by changes in metabolic physiology. This relationship is thought to be mediated by the effect of oxygen radicals because these toxic compounds are by-products of aerobic metabolism and are known mutagens. Association between metabolism and nucleotide composition provides additional evidence in favor of the hypothesis that rates and patterns of nucleotide substitution in mitochondrial DNA can be influenced by factors that impinge on rates of endogenous DNA damage.      

Mitochondrial DNA sequence evolution in sharks: rates, patterns, and phylogenetic inferences

Abundant representation of sharks in the fossil record makes this group a superb system in which to investigate rates and patterns of molecular evolution and to explore the strengths and weaknesses of phylogenetic inferences from molecular data. In this report, the molecular evolution of the cytochrome b gene in sharks is described and the information related to results from phylogenetic analysis of the data evaluated in the light of a phylogeny derived independently of the molecular data. Across divergent lineages of sharks there is evidence for significant substitution rate variation, departure from compositional equilibrium, and substantial homoplasy; nevertheless, the signal of evolutionary history is evident in patterns of shared transversions and amino acid replacements.      

Phenotypic conversion of cultured mouse embryo cells by aza pyrimidine nucleosides.

Cells of the $\text{C3H}\text{10}\text{T}\text{1}\text{2}\text{CL8}$ line, which are nonmyoblastic in nature, form functional myotubes when treated with low concentrations of 5-azacytidine. Further characterization of the myotubes revealed that they arise from the fusion of mononucleated precursors and not as a result of endoreplication. They accumulate histochemically detectable myosin ATPase activity as well as acetylcholine receptors capable of binding radioactively labeled α-bungarotoxin. The deoxy analog, 5-aza-2′-deoxycytidine, induced myogenic conversion at one-tenth of the maximally effective concentration of 5-azacytidine. The ability of both analogs to induce myotube formation and to cause cytotoxicity was strongly influenced by cotreatment with certain pyrimidine nucleosides. These effects were consistent with a requirement for metabolism of both aza compounds to phosphorylated derivatives and with a mechanism of action based on their incorporation into DNA. Concentrations of the analogs causing myogenic conversion did not substantially alter rates of DNA, RNA, or protein synthesis as measured by precursor incorporation into intact cells. The induction of myotubes by 5-azacytidine in cells synchronized by two different methods required that treatment with the analog was carried out at a critical phase early in S phase. Thus the mechanism of drug action appears to be linked to specific DNA synthesis.     

Immobilization of Brevibacterium flavum cells on collagen for the production of glutamic acid in a recycle reactor

In this study, live cells of Brevibacterium flavum were immobilized for the production of glutamic acid. The reason for such a choice was that glutamic acid fermentation is an extensively studied fermentation and one which requires the viability of entire cellular faculties for the acid production. Brevibacterium flavum was chosen because it is an industrially used bacterium, and is very potent via a vis glutamic acid production. Studies were performed to find aeration and agitation conditions for optimal growth and glutamic acid productivity. Experiments were also done to find the optimum harvesting time. The cell activity peaks during the run of fermentation, and the time at which the peak occurs, was found. Conventional methods for immobilizing the cells on collagen were found to be lacking. The pH and drying were the two main reasons for loss of viability of the cells; the latter being more important. A modified immobilization procedure has been devised, which can immobilize live cells at any given pH and ionic strength, in contrast to the conventional method which requires the pH to be above 11 or below 3. This new method involves dialysis of collagen in suitable dialysis bags against water at pH7 (or buffer at any desired pH). The dialysed collagen blended at 20,000 rpm, resulted in a very smooth dispersion, unnoticeably different from collagen dispersion prepared at pH 11. The dispersed collagen was then cast and dried at an elevated temperature, and high air flow rate over the cast membrane, decreasing the time of drying from 6–8 hr ( in the conventional method) to 1.5–2 hr. The membrane has been tested for glutamic acid producing capabilities in a column reactor with the membrane spirally wound. The reactor has been operated under continuous conditions for 5–10 days with stable activities.     

Comparison of the Respiratory Metabolism of Plantago lanceolata L. and Plantago major L.

Bryce, J. H. and ap Rees, T. 1985. Comparison of the respiratorymetabolism of Plantago lanceolata L. and Plantago major L.—J.exp. Bot. 36 1559–1565. The aim of this work was to discover if the respiratory metabolismof the roots of Plantago lanceolata L. differed from that ofthe roots of Plantago major L. Measurements of oxygen uptakeand dry weight of excised root systems during growth of seedlingsprovided evidence that the two species differed in the amountof respiration needed to support a given increase in dry weight.Excised root systems were given a 6-h pulse in [U-¹⁴C]sucrosefollowed by a 16.5-h chase in sucrose. The detailed distributionof ¹⁴C amongst the major components of the roots at the endof the pulse and the chase revealed no significant differencebetween the two species. Patterns of ¹⁴CO₂ production from [1-¹⁴C],[2-¹⁴C], [3,4-¹⁴C], and [6-¹⁴C]glucose of excised root systemsfrom plants of three ages were similar for the two species.It is suggested that there is no conclusive evidence for anysignificant inherent difference in the respiratory metabolismof the roots of the two species. Key words: ¹⁴C sugar metabolism, respiration, roots, Plantago