How Many Nucleotides Are Required to Resolve a Phylogenetic Problem? The Use of a New Statistical Method Applicable to Available Sequences

The evolution of bootstrap proportions (BP) with sequence length was studied using a 28S ribosomal RNA data set. For different sequence lengths, informative sites were jackknifed several times. Bootstrapping was subsequently performed on each of these subsamples. For each node, BPs so obtained were plotted against sequence length, showing the evolution of the robustness with increasing number of informative sites. For robust nodes (BP of 100%), the pattern of BPs is unvarying and is described by a simple function BP = 100(1− e^{−b(x − x′)}), where x is the number of informative sites and b and x′ are two parameters estimated using a nonlinear regression procedure. When a node has a BP <100% and the pattern of BPs fits this function, it is possible to estimate the number of informative sites required to obtain a given average BP. The method also identifies nonrobust nodes (nonascending clusters of BP dots), for which it seems to be more cost effective and fruitful to turn to other species and/or genes rather than to continue sequencing longer gene lengths from the same species to reach a BP of 95%.     

Secondary response of in vitro-primed human lymphocytes to allogeneic cells

In vitro-primed human lymphocytes proliferate in a secondary mixed lymphocyte reaction (MLR) under the control of MLR-S specificities. HL-A antigens are unable to induce a secondary Proliferation. In familial haploidentical combinations, the secondary proliferation is specific for the priming MLR-S specificity, i.e., as early as 24 to 48 hours after the re-stimulation, a clearcut response is observed toward the sensitizing MLR-S specificity. The secondary response is reflected in acceleration of the reaction rather than in the peak of (³H) TdR uptake. However, when either haploidentical familial primed responding cells or unrelated cells primed toward MLR-S homozygous cells were used, no early typing response was observed against unrelated cells. The level of (³H) TdR incorporation toward cells which possessed and those which did not possess the priming specificity was identical until day 3–4. Noneless, the peak response toward cells possessing the priming MLR-S specificity occurs regularly 24 to 48 hours prior to the peak response toward the cells negative for the priming specificity (day 3–4 as opposed to day 5). Technical improvements are therefore needed before such a technique will provide a clearcut MLR-S typing methodology.     

Effect of dietary fats on hepatic lipid metabolism in the growing turkey

The influence of dietary fatty acids on hepatic capacity of lipid synthesis and secretion was investigated in 7-week-old male turkeys. They were fed 10% of either lard (rich in saturated and monounsaturated fatty acids) or linseed oil (rich in polyunsaturated fatty acids, especially 18:3n-3). Fattening was identical with both diets (0.15-0.20% of abdominal adipose tissue), but the proportion of muscle Pectoralis major was lower with linseed oil (6.6 vs. 7.4%). Specific activities of lipogenic enzymes (ME, G6PDH, ACX, and Delta9-desaturase) were not influenced by the diet, however, FAS activity was lower with linseed oil (14.3 vs. 25.4 nM NADPH fixed/min). Fasting concentrations of lipoproteins synthesized and secreted by the liver, VLDL and HDL, were also lower with linseed oil, as well as plasma concentrations of phospholipids and cholesteryl esters. However, when VLDL catabolism was inhibited by injection of an antiserum against LPL, VLDL concentration was identical in both groups (100-120 mg/l), whereas that of phospholipids and cholesteryl esters, that are transported by HDL mainly, remained lower with linseed oil. Thus, in the growing turkeys, and contrary to mammals and the chicken, feeding n-3 polyunsaturated fatty acids did not decrease hepatic triglyceride synthesis and secretion, nor fattening. By contrast, in this species, n-3 polyunsaturated fatty acids appear to influence mostly HDL metabolism, with a negative impact on muscular growth.     

Ordering events of biochemical evolution

Metabolic pathways exhibit structures resulting from an evolutionary process. Pathways have been inherited through time with modification, from the earliest periods of life. It is possible to compare the structure of pathways as done in comparative anatomy, i.e. for inferring ancestral pathways or parts of it (ancestral enzymatic functions), using standard phylogenetic reconstruction. Thus a phylogenetic tree of pathways provides a relative ordering of the rise of enzymatic functions. It even becomes possible to order the birth of each complete pathway in time. This particular "DNA-free" conceptual approach to evolutionary biochemistry is reviewed, gathering all the justifications given for it. Then, the method of assigning a given pathway to a time span of biochemical development is revisited. The previous method used an implicit "clock" of metabolic development that is difficult to justify. We develop a new clock-free approach, using functional biochemical arguments. Results of the two methods are not significantly different; our method is just more precise. This suggests that the clock assumed in the first method does not provoke any important artefact in describing the development of biochemical evolution. It is just unnecessary to postulate it. As a result, most of the amino acid metabolic pathways develop forwards, confirming former models of amino acid catabolism evolution, but not those for amino acid anabolism. The order of appearance of sectors of universal cellular metabolism is: (1) amino acid catabolism, (2) amino acid anabolism and closure of the urea cycle, (3) glycolysis and glycogenesis, (4) closure of the pentose-phosphate cycle, (5) closure of the Krebs cycle and fatty acids metabolism, (6) closure of the Calvin cycle.     

The phylogeny of polar fishes and the structure,function and molecular evolution of hemoglobin

Fishes thriving in polar habitats offer many opportunities for comparative approaches to understanding protein thermal adaptations. Investigations on the remarkable evolutionary adaptations to these environments of basic proteins such as hemoglobin, the oxygen carrier, can provide new insights into the mechanisms studied in temperate organisms and can shed light on convergent processes evolved in response to thermal adaptations. At the molecular level, hemoglobins are one of the most intriguing systems for studying the relationships between environmental conditions and adaptations. This review summarizes the current knowledge on molecular structure, biological function and phylogeny of hemoglobins of fish species living in both polar habitats but having different evolutionary histories. In benthic, non-migratory, cold-adapted fishes, the stability of thermal conditions may have generated no or few variations in selective pressures on globin sequences through evolutionary time, so that sequences retain the species phylogenetic “signal”. In pelagic, migratory, cold-adapted or temperate fishes, variations in selective pressures on globin sequences caused by variations in temperature accompanying the dynamic life style may have disrupted the phylogenetic “signal” in phenetic trees.