Statistical models of the overdispersed molecular clock

The most commonly used statistical model to describe the rate constancy of molecular evolution (molecular clock) is a simple Poisson process in which the variance of the number of amino acid or nucleotide substitutions in a particular gene should be equal to the mean and henceforth the dispersion index, the ratio of the variance to the mean, should be equal to one. Recent sequence data, however, have shown that the substitutional process in molecular evolution is often considerably overdispersed and have called into question the generality of using a simple Poisson process. Several efforts have been made to develop more realistic models of molecular evolution. In this paper, I will show that the spatial (site-specific) variation in the rate of molecular evolution is an improbable cause of the overdispersion and then review various statistical models which take the temporal variation into account. Although these models do not immediately specify what the mechanisms of molecular evolution might be, they do make qualitatively different predictions and give some insight into their inference. One way to distinguish them is suggested. In addition, effects of selected substitutions that presumably occur after a major change in a molecule are quasi-quantitatively examined. It is most likely that the overdispersion of molecular clock is due either to a major molecular reconfiguration (fluctuating neutral space) led by a series of subliminal neutral changes or to selected substitutions fine-tuning a molecule after a major molecular change. Although the latter possibility, of course, violates the simplest neutrality assumption, it would not impair the neutral theory as a whole.     

A repeating unit of the DYZ1 family on the human Y chromosome consists of segments with partial male-specificity

An average-sized human Y chromosome contains about 3,000 copies of the repeating DNA family DYZ1. A major repeating unit of the family, pHY10, has been cloned and an entire 3,564-bp sequence has already been determined by Nakahori et al. (1986). In the present study, pHY10 was divided into six consecutive segments, A to F, which were independently amplified by the PCR technique to see if they were strictly male-specific. pHY10 appears to consist of segments of various male-specificity. The B segment was apparently male-specific; however, the use of additional techniques (Southern-blot analysis or second PCR amplification in combination with the standard PCR) revealed homologous sequences in some females. None of the six segments of pHY10 may be male-specific in a strict sense. Different segments appear to be conserved during evolution to different extents. The 323-bp E segment appears to be the least conserved and to be responsible for the generation of most variations within the DYZ1 family.     

The superoxide-generating respiratory burst oxidase of human neutrophil plasma membrane. Phosphatidylserine as an effector of the activated enzyme

The superoxide-generating respiratory burst oxidase is an integral membrane enzyme found in the plasma membrane of polymorphonuclear leukocytes (neutrophils). NADPH-dependent superoxide generation is seen in isolated plasma membranes and in their detergent extracts following activation of the intact cells with phorbol myristate acetate. We have herein examined the effects of phospholipids on the activity of the solubilized oxidase. Solubilization of plasma membranes with 0.5% each of Tween 20 plus deoxycholate resulted in an approximately 2-fold enhancement of activity. Inclusion of phospholipids in the extraction medium resulted in further activation. At 1.0 mg/ml the order of effectiveness was phosphatidylserine (PS) greater than cardiolipin greater than phosphatidylethanolamine greater than phosphatidylinositol; phosphatidylcholine and phosphorylated inositol lipids were not effective. The concentrations required for half-maximal activation by PS and phosphatidylethanolamine were 85 and 200 micrograms/ml, respectively. When PS was used at a maximally activating concentration (0.5 mg/ml), the activity was enhanced 3-5-fold. Detergent solubilization alone elevated the Km of the oxidase for NADPH from 68 microM in intact plasma membranes to 123 microM, but inclusion of PS with detergent restored the Km to near or below that seen in intact membranes. PS also increased the Vmax by a factor of 2-3, but had no effect on the pH optimum. A plot of the activity versus enzyme concentration was linear when membranes were used, but activity showed a quadratic dependence on concentration in solubilized membrane, with lower than expected activity at lower enzyme concentration. PS restored linearity of the concentration-activity plot. The activation by PS was not influenced by the addition of Ca2+, EGTA, or dioctanoylglycerol, indicating that activation was not dependent on protein kinase C. These results implicate phosphatidylserine as a direct effector of the NADPH-oxidase.     

The adenine nucleotide binding site on yeast hexokinase PII. Affinity labeling of Lys-111 by pyridoxal 5'-diphospho-5'-adenosine

The adenine nucleotide analog, [3H]pyridoxal 5'-diphospho-5'-adenosine (PLP-AMP), is shown to be a potent and specific inhibitor of yeast hexokinase PII. Evidence that the analog binds specifically at the ATP binding site includes the demonstration that glucose binding enhances PLP-AMP binding and that PLP-AMP and ATP bind competitively with an apparent Ki(PLP-AMP) = 23 microM. In addition, from the relationship between the degree of inhibition and extent of modification, it is estimated that the incorporation of 1 mol of PLP-AMP/mol of subunit is required for complete inhibition. Borohydride reduction of the Schiff's base complex formed between hexokinase and [3H]PLP-AMP gives a stable product. The reduced derivative was digested with trypsin and a single radioactive peptide was isolated by reversed-phase high-pressure liquid chromatography. Amino acid sequence analysis identified Lys-111 as the modified residue. Taking into account the known structures of the binary complexes (Shoham, M., and Steitz, T. A. (1980) J. Mol. Biol. 140, 1-14), the results suggest that Lys-111, located in the smaller of the two lobes of hexokinase, moves into the active site upon formation of the ternary complex.     

Variation in karyotypes of Dugesia japonica japonica (Turbellaria) from Ôsaka Prefecture,Central Japan

An analysis of the karyotypes of Dugesia japonica japonica Ichikawa et Kawakatsu, 1964, from 30 localities of seven river systems in Ôsaka Prefecture, Central Japan, revealed a total of 26 karyotypes of which 12 are new-found varieties. More than two karyotypes were found in many localities. The mixoaneuploidic triploid karyotype showed the widest distribution (21 localities), orthoploidic diploid karyotype and orthoploidic mixoploid of diploid and triploid karyotype were next (13 localities, respectively), and other karyotypes (triploidic aneuploid, orthoploidic triploid and mixoploid of triploid & tetraploid) were also found. Some correlation of karyotype with elevation was also detected.     

An outbreak of staphylococcal dermatitis in laboratory mice

An epizootic of dermatitis with erosion, ulcer and crust broke out in an experimental colony of JCL-ICR mouse over a period from December 1975 to June 1976. The disease was detected in 592 of a total of 1831 mice of 3-24 months old, especially in males of 7-24 months old (517/821). At the beginning of December 1975, only a few males of 12 months old were found to have the lesion on the back skin, and thereafter the dermatitis prevailed gradually among the mice. Histopathologic examinations showed the loss of the epidermis, necrosis and/or collapse of the corium, accumulation of serous exudate with neutrophilic cell infiltration and a few cocci scattered on the surface. In chronic cases, fibrous granulation tissues with neutrophilic cell infiltration were formed in the corium. Staphylococcus aureus was isolated in pure culture from the skin lesions in all of the mice examined. Skin disease similar to that of the field case was reproduced in mice inoculated subcutaneously with 10(7) viable organisms of the fresh isolate. By giving chlortetracycline in drinking water for 7 days, treatment of the affected mice was efficacious in mild cases, but not in severe cases.     

Biological properties, phage typing and antimicrobial susceptibility of Staphylococcus aureus isolated from dermatitis in laboratory mice

The characteristics of 167 isolates of S. aureus from 106 mice suffering dermatitis were examined. All 167 isolates coagulated both rabbit and human plasmas and 161 of them also coagulated bovine plasma. All the isolates produced heat-stable and heat-labile DNase, phosphatase and yellow pigment, reduced nitrate, hydrolysed egg yolk, Tween 80, and hippurate, and grew on crystal violet agar in colonies of the negative type C and on medium with 10% NaCl. The majority of them produced fibrinolysin, protease and acetoin. Fifty-three percent were gelatinase positive. In hemolysis tests, 25, 57 and 45 isolates showed alpha-, beta-, alpha beta-hemolysis, respectively. Forty isolates did not produce hemolysins in the rabbit and sheep blood agar. All of 75 isolates tested produced acid from fructose, galactose, glucose, glycerol and mannose, but did not from arabinose, dextrin, inulin, raffinose, salicin, sorbitol and xylose. Most of these isolates produced acid from lactose, mannitol, sucrose and trehalose. All of the 75 isolates were highly sensitive to penicillin, methylphenylisoxazolyl penicillin, erythromycin, spiramycin, lincomycin, chloramphenicol, tetracycline, kanamycin, gentamicin and cephaloridine, but were resistant to sulfisoxazole. With phages of human set, all 167 isolates were typable at 100 X RTD. All but one of the typable isolates belonged to mixed lytic groups. These were I + III (35 isolates), I + M (1), I + III + M (124) and I + II + III + M (6), with long phage patterns. When the 167 isolates were biotyped as described by Hájek and Marsálek [7, 8], 5 belonged to biotype A, 1 to biotype B and 60 to biotype C.(ABSTRACT TRUNCATED AT 250 WORDS)     

Effects of 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (platelet activating factor) on cardiac function in perfused guinea-pig heart

The direct cardiac action of 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF) was studied in isolated perfused guinea-pig heart preparations. PAF produced a fall in left ventricular pressure, decreases in the rate of rise of the left ventricular pressure (dp/dt) and coronary flow, but had no effect on heart rate. These results indicate that PAF is a cardiodepressant with inotropic selectivity and this effect on heart is blocked by CV-3988, a specific PAF antagonist.     

Gene Genealogy and Variance of Interpopulational Nucleotide Differences

A mathematical theory is developed for computing the probability that m genes sampled from one population (species) and n genes sampled from another are derived from l genes that existed at the time of population splitting. The expected time of divergence between the two most closely related genes sampled from two different populations and the time of divergence (coalescence) of all genes sampled are studied by using this theory. It is shown that the time of divergence between the two most closely related genes can be used as an approximate estimate of the time of population splitting (T) only when T identical to t/(2N) is small, where t and N are the number of generations and the effective population size, respectively. The variance of Nei and Li's estimate (d) of the number of net nucleotide differences between two populations is also studied. It is shown that the standard error (Sd) of d is larger than the mean when T is small (T much less than 1). In this case, Sd is reduced considerably by increasing sample size. When T is large (T greater than 1), however, a large proportion of the variance of d is caused by stochastic factors, and increase in the sample size does not help to reduce Sd. To reduce the stochastic variance of d, one must use data from many independent unlinked gene loci.