SDSE: A software package to simulate the evolution of a pair of DNA sequences

An algorithm to simulate DNA sequence evolution under a generalstochastic model, including as particular cases all the previouslyused schemes of nucleotide substitution, is described. The simulationis carried out on finite, variable length, DNA sequences througha strict stochastic process, according to the particular substitutionrates imposed by each scheme. Five FORTRAN programs, runningon an IBM PC and compatibles, carry out all the tasks neededfor the simulation. They are menu driven and interfaced to thesystem through a principal menu. All sequence data files usedand generated by the SDSE package conform to the standard GenBankdatabase format, thus allowing the use of any sequence retrievedfrom this databank, as well as the application of other packagesto analyse, manipulate or retrieve simulated sequences. Received on August 23, 1988; accepted on November 15, 1988     

Cessation of neutrophil influx in C5a-induced acute experimental arthritis is associated with loss of chemoattractant activity from the joint space

Neutrophil emigration is a critical component of the inflammatory process and is generally thought to play a role in host defense as well as in the tissue injury that often accompanies inflammation. Most inflammatory reactions exhibit a sequence of emigrating cell types, thus clearly demonstrating that the neutrophil influx eventually ceases and that the neutrophils are then removed from the lesion. It has been our premise that in order to understand the processes that lead to the progressive inflammatory reactions that underly so many disease processes, it is important to determine the mechanism by which the "normal" inflammatory response resolves. The purpose of this study was to identify the time of cessation of neutrophil influx in experimental arthritis induced by the injection of C5 fragments (C5f) and to investigate mechanisms underlying the cessation process. The migration of i.v. delivery pulses to inflamed joints was assessed by lavage of the joint space and by external scintigraphy. We found no evidence for the development of inhibitory systems against chemotactic factors or "desensitization" of the inflamed site, because a second injection of C5f into joints which had been injected previously with C5f resulted in enhancement rather than inhibition of migration. Neither was evidence found for altered tissue barriers to migration or for desensitization of neutrophils as possible explanations for cessation of influx. The major mechanism appeared to be a loss of chemoattractant activity in the joint space between 2 h and 6 h after C5f injection which was detected by transfer into a fresh joint. Radiolabeled C5a des-Arg had a t1/2 of disappearance from the joint of less than 1 h, which suggested that the transferred chemoattractant must, in part, have been due to the generation of new chemotaxins by C5f injection. These observations suggest that continued generation of chemoattractants or failure of their subsequent removal may be mechanisms leading to persistent neutrophil influx in chronic inflammation.     

The levels of ζ, γ, and δ chains in patients with Hb H disease

Summary Details are given of a study of blood samples from 24 patients with Hb H disease from different Mediterranean countries and from the Far East. Four different types of -thal-1 (--) were observed, namely-() ( 20.5-kb deletion);--MED-I ( 17.5-kb deletion);--MED-II (>26.5-kb deletion); and--SEA ( 18-kb deletion, in Orientals only). The -thal-2 was mainly of the deletion type (16 with the 3.7-kb deletion; 1 with the 4.2-kb deletion), while 4 of the 7 patients with a nondeletional type had the five-nucleotide deletion at the donor splice site of the first intron of the 2 gene. All patients had a mild-to-moderate hemolytic anemia; no significant differences in hematology were observed between the groups. Hb A₂ was decreased to about one-third of the normal level. The Hb H formation varied considerably and its quantitation was not always satisfactory. Patients with Hb H disease due to any -thal-1 combined with a nondeletional -thal-2 had the highest Hb H levels and a more marked anemia. The chain production was small and absent in patients with the MED-II type of -thal-1 because this deletion included the and genes. The highest chain levels were present in the four patients with the SEA type of -thal-1. The chain production was increased, particularly in patients with a mutation of C T at position-158 to the ^G globin gene. This chain was primarily present as Hb Bart's (or ₄) and only about 15% was recovered as Hb F or ₂₂. The evaluation of the rate of chains produced in these patients was greatly facilitated by data from one patient who had Hb H disease and a heterozygosity for the ^A-⁺. The low levels of Hb A₂ and of Hb F (relative to Hb Bart's) can be explained by a decreased affinity of chains for and chains as compared with chains in conditions of severe chain deficiency.     

Dopamine-1-mediated stimulation of phospholipase C activity in rat renal cortical membranes

Phospholipase C (PL-C) mediates transduction of neurotransmitter signals across membranes via hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP2), leading to generation of second messengers inositol-1,4,5-trisphosphate and diacylglycerol. In this study, dopamine-1 (DA-1) but not dopamine-2 (DA-2) agonists were shown to stimulate PL-C activity in renal cortical membranes. The DA-1 agonist, SKF 82526, stimulated the release of inositol phosphates from renal cortical membranes prelabeled with [3H]myoinositol. The majority of the label (75%) was found in phosphatidylinositol followed by PIP2 (15%) and phosphatidylinositol-4-phosphate (10%). A DA-1 specific effect on PL-C activity was also observed in an in vitro assay of PL-C activity in renal cortical membranes and basolateral and brush border membranes using [3H]PIP2 as the substrate. Dopamine and SKF 82526 stimulated the release of inositol phosphates from added [3H]PIP2 in a concentration-dependent manner. This release was blocked by the DA-1 antagonist SCH 23390 but not by the alpha-adrenergic antagonists phentolamine and prazosin. In contrast, the DA-2 agonist LY 171555 had no effect on inositol phosphate release. Guanosine 5'-(3-O-thio)triphosphate enhanced while guanyl-5'-yl thiophosphate attenuated the DA-1 agonist-stimulated PL-C activity. PL-C activity as measured by [3H]PIP2 hydrolysis had a pH optimum of 6.5, was inhibited by Mg2+ concentrations above 1 mM, was linear with time and protein concentration, and was sensitive to phosphatidylserine and calcium concentrations. We conclude that PL-C is activated by DA-1 but not DA-2 agonists in renal cortical membranes as well as both the basolateral and brush border renal tubular membranes. It is speculated that this action may mediate the natriuretic effects of dopamine in renal tubular epithelia.     

Muscle development in the tambaqui, an important Amazonian food fish

Eggs of the tambaqui Colossoma macropomum were incubated at 28 and 31) C. Somitogenesis started shortly after the formation of the neural plate and notochord. New somites were added at the rate of one every 13 min at 28) C and one every 11 min at 31) C. Myogenesis started in the most rostral myotomes at the 9-somite stage and proceeded in a caudal direction. Mononuclear myotubes with the morphological characteristic of muscle pioneer cells were observed lateral to the notochord. The majority of myotubes were formed from the fusion of 3–6 spindle-shaped myoblasts. Myofibril synthesis started soon after cell fusion at the periphery of myotubes. Close membrane contacts and 'gap'-type junctions were observed between myotubes, immature muscle fibres and at the inter-somite boundary, suggesting that the cells were electrically coupled. Embryos exhibited rhythmic movements at the 20-somite stage, and hatched at the 29–30-somite stage 15–18 h post-fertilisation (PFT) at 28° C and 11 h PFT at 31° C. Larvae hatched at a comparatively early stage of development prior to the completion of somitogenesis and the formation of eye pigment, pectoral fins and jaws. The myotomes comprised a single superficial layer of well-differentiated muscle fibres which contained abundant mitochondria, overlying an inner core of myotubes (presumptive white muscle layer). Differentiation and growth during the larval stages was extremely rapid, and the juvenile stage was reached after little more than 6 days at 28° C.     

The Roles of CRE, TRE, and TRE-Adjacent S1 Nuclease Sensitive Element in the Regulation of Tyrosine Hydroxylase Gene Promoter Activity by Angiotensin II

Abstract: The cis elements mediating activation of the tyrosine hydroxylase gene by angiotensin II were examined by transfecting tyrosine hydroxylase promoter-luciferase constructs into cultured bovine adrenal medullary cells. Angiotensin II-responsive elements are located within −54/+25-bp and −269/−55-bp promoter regions and were identified, respectively, as cyclic AMP (CRE)- and 12- O -tetradecanoylphorbol 13-acetate responsive element (TRE)-like sequences. Unlike CRE, TRE also supports basal promoter activity. Mutations of TRE or CRE that reduced angiotensin II stimulation abolished in vitro binding of nuclear proteins to those elements, suggesting that proteins forming CRE- and TRE-inducible complexes may mediate angiotensin II stimulation. The TRE is adjacent to a dyad symmetry element. Those two sites form a common regulatory unit in which the dyad symmetry element acts as a repressor of the TRE site. Isolated dyad symmetry element did not bind nuclear proteins in vitro. In supercoiled DNA it exhibited S1 nuclease sensitivity and was recognized by a DNA cruciform-specific antibody consistent with the extrusion of a cruciform structure that overlaps with the TRE. A mutation that abolished formation of the cruciform correlated with a loss of repressor activity. We propose a novel model of tyrosine hydroxylase gene regulation in which functions of the TRE are modulated via structural transition in the adjacent DNA.     

Molecular-size corrections to the strength of the hydrophobic effect: a critical review

Large increases in the strength of the hydrophobic effect and, consequently, in the estimates of the hydrophobic contribution to the thermodynamics of protein folding (and other biologically-relevant processes), have been recently advocated on the basis of the application, to model transfer thermodynamic data, of corrections for the solute/solvent size disparity. In this work we first examine the effect of molecular-size corrections on the values calculated from several types of model transfer data. For the transfer of a solute from an organic solvent to water, the above increase is exclusively associated with the application of a solute/water molecular-size correction. Secondly, we critically review and assess the several theoretical arguments that lead to these corrections. In particular, we show that, contrary to previous claims in the literature, the analysis of dissolution processes in terms of ideal-gas, intermediate states does not lead to the molecular-size correction term, but only to expressions equivalent (although not strictly identical) to those derived from the well-known Ben-Naim's statistical-mechanical approach. In general, the several analyses offered or discussed in this work disfavor the application of the solute/water molecular-size corrections.