Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.     

Modeling the Role of Negative Cooperativity in Metabolic Regulation and Homeostasis

A significant proportion of enzymes display cooperativity in binding ligand molecules, and such effects have an important impact on metabolic regulation. This is easiest to understand in the case of positive cooperativity. Sharp responses to changes in metabolite concentrations can allow organisms to better respond to environmental changes and maintain metabolic homeostasis. However, despite the fact that negative cooperativity is almost as common as positive, it has been harder to imagine what advantages it provides. Here we use computational models to explore the utility of negative cooperativity in one particular context: that of an inhibitor binding to an enzyme. We identify several factors which may contribute, and show that acting together they can make negative cooperativity advantageous.     

Neopterin Retards Loss of Serotonin N-Acetyltransferase Activity from Cultured Chick Pineal Glands

Abstract: d -Neopterin at 10 μ M delayed start of the decline of serotonin N -acetyltransferase (NAT) activity from the peak level in the cycle exhibited by chick pineal glands cultured under standard conditions in the dark. A less marked retardation of decline of NAT activity was found with glands cultured under diurnal illumination or those exposed prematurely to light. There were no significant effects of neopterin on the increases of NAT activity or peak levels of activity developed. The pteridine also retarded loss of NAT activity from the peak level developed in the dark when the time of explanting into culture was later in the (solar) day, but not when it was earlier. Neopterin had no effect on the cycle in cyclic GMP content of cultured chick pineal glands.     

Copper deficiency in rats increases pancreatic enkephalin-containing peptides and insulin

Free enkephalins (enk) and higher molecular weight enkephalin-containing peptides (enk-c-p) are present in the endocrine pancreas of rats, presumably in B cells. To determine whether these opioid peptides show dynamic alterations as insulin content of pancreas changes, we utilized a copper deficient rat model, in which the exocrine pancreas atrophies and the endocrine pancreas is “intact” and insulin (IRI) content increases. Dietary copper deficiency (−C) was produced in weanling male rats for 4 and 7 weeks. The deficient and copper supplemented (+C) groups were further subdivided to receive all dietary carbohydrate as either 62% fructose (F) or 62% starch (S). −CF rats showed the most severe deficiency. After 7 weeks, total units of pancreatic IRI in −CF were 7.5, +CF 2.1, −CS 7.9 and in +CS 2.8 (p<0.001). Pancreatic content of Met⁵- and Leu⁵-enk was measured in extracts which were purified on C-18 Seppaks with and without prior treatment with trypsin and carboxypeptidase B. −C animals showed progressive, significant increases in pancreatic content of Leu-enk-c-p, with a decrease in free Leu- and Met-enk (p<0.02-0.01). The pancreatic findings are compatible with a co-localization of enkephalins and insulin in the endocrine pancreas and are suggestive of co-regulation.     

Metabolism of 20-hydroxyeicosatetraenoic acid by cyclooxygenase. Formation and identification of novel endothelium-dependent vasoconstrictor metabolites

We recently demonstrated that 20-hydroxyeicosatetraenoic acid (20-HETE) constricts rat aortic rings. The contractile response was partially dependent on the presence of endothelium and was abolished by pretreatment of the rings with either indomethacin or the endoperoxide/thromboxane receptor antagonist, SQ29548. Addition of GSH or SnCl2 to the organ bath diminished the contractile response of 20-HETE, whereas preincubation of the rings with a thromboxane synthase inhibitor did not affect the 20-HETE induced contractions. Short time incubation (2 min) of 20-HETE with ram seminal vesicle microsomes in the presence of p-hydroxymercurybenzoate yielded metabolites which migrated similarly on thin layer chromatography to the known arachidonate endoperoxides prostaglandin (PG) G2 and PGH2 and possess vasoconstrictory properties. The vasoconstriction was dose-dependent with a half-life of approximately 6.3 +/- 0.6 min. Addition of SQ29548 to the aortic ring bath 1 min after metabolite elicited vasoconstriction produced immediate relaxation. Furthermore, pretreatment of the rings with SQ29548 totally abolished the contraction. SnCl2 reduction of the metabolites produced in incubation of rat seminal vesicles with 20-HETE and p-hydroxymercurybenzoate resulted in a single radioactive peak which was further identified by gas chromatography/mass spectrometry as 20-hydroxy-PGF2 alpha. The inhibitory effect of SQ29548, the appearance of labile metabolites with a half-life of approximately 6 min and the production of 20-hydroxy-PGF2 alpha by SnCl2 reduction clearly indicate that the vasoconstrictor metabolites of 20-HETE are the labile endoperoxides of 20-HETE, 20-hydroxy-PGG2, and 20-hydroxy-PGH2.     

Cytogenetic characteristics of a population of Chironomus riparius Meigen 1804 (Diptera, Chironomidae) from a polluted Po river station

A population of Chironomus riparius from a Po river station near Moncalieri (a trace-metal polluted station) was studied. In this population was established a great variability of band structure of polytene chromosomes as well as paracentric heterozygous inversions, deletions, deficiencies, partial breaks, diploid chromosome fragments, and changes in functional activity and appearance of heterochromatin. In arms A through F, some bands had an increased size compared to the standard chromosomic map. Some bands appeared in a heterozygous or normal homozygous state or were amplified. In all arms, many condensed stable bands appeared in the decondensed state when compared to the standard map. Asynaptic zones in arms E and G as well as heterozygous Balbiani rings and NORs were established. Very often the 4th chromosome was almost completely heteropycnotic and looded like a pompon chromosome. For the first time in this species, a high frequency of ectopic pairings of different arms was observed. Telomeric regions involved in ectopic pairings had a granular appearance, as did some centromeres. The hypothesis is advanced that such a high frequency of structural rearrangements could be correlated with genomic distribution of specific mobile elements.