Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications

Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.      

Biological growth and spread modeled by systems of recursions. II. Biological theory

The mathematical theory developed in Part I is applied to a selection-migration model in population genetics with sex-linked locus and to the host-vector or venereal disease epidemic model. In both models, a constant c*(xi) is found for each unit vector xi. The mathematical results imply that under certain initial conditions, the frequency of the advantageous gene in the male and female gametic outputs or the epidemic will spread at a speed c*(xi) in the direction xi as time goes to infinity. Time is measured in discrete nonoverlapping generations. In most cases, we can find a formula for c*(xi).     

Identification of plasmin as the major contaminant in immunoglobulin preparations

A proteolytic enzyme could be isolated from rabbit serum by means of DEAE cellulose, Protein A-bound Sepharose and lysine-bound Sepharose chromatographies. This enzyme was found to be the major protease contaminating IgG preparations of rabbit serum. This enzyme was identified as plasmin because it displayed an apparent Mr of 90,000 on nonreduced SDS polyacrylamide gel electrophoresis, was able to directly lyse fibrin and the chromogenic substrate H-D-Val-Leu-Lys-p-nitroanilide, and was stable after heating at 56 degrees for 30 min but broke down at 80 degrees. Its Km toward the chromogenic substrate was 0.35 mM, which agreed well with the published value for plasmin.     

Analysis of gene expression in two human-derived cell lines exposed in vitro to a 1.9 GHz pulse-modulated radiofrequency field

There is considerable controversy surrounding the biological effects of radiofrequency (RF) fields, as emitted by mobile phones. Previous work from our laboratory has shown no effect related to the exposure of 1.9 GHz pulse-modulated RF fields on the expression of 22,000 genes in a human glioblastoma-derived cell-line (U87MG) at 6 h following a 4 h RF field exposure period. As a follow-up to this study, we have now examined the effect of RF field exposure on the possible expression of late onset genes in U87MG cells after a 24 h RF exposure period. In addition, a human monocyte-derived cell-line (Mono-Mac-6, MM6) was exposed to intermittent (5 min ON, 10 min OFF) RF fields for 6 h and then gene expression was assessed immediately after exposure and at 18 h postexposure. Both cell lines were exposed to 1.9 GHz pulse-modulated RF fields for 6 or 24 h at specific absorption rates (SARs) of 0.1-10.0 W/kg. In support of our previous results, we found no evidence that nonthermal RF field exposure could alter gene expression in either cultured U87MG or MM6 cells, relative to nonirradiated control groups. However, exposure of both cell-lines to heat-shock conditions (43 degrees C for 1 h) caused an alteration in the expression of a number of well-characterized heat-shock proteins.     

Is There an Optimal Level of Open-Endedness in Prebiotic Evolution?

In this paper we explore the question of whether there is an optimal set up for a putative prebiotic system leading to open-ended evolution (OEE) of the events unfolding within this system. We do so by proposing two key innovations. First, we introduce a new index that measures OEE as a function of the likelihood of events unfolding within a universe given its initial conditions. Next, we apply this index to a variant of the graded autocatalysis replication domain (GARD) model, Segre et al. (P Natl Acad Sci USA 97(8):4112-4117, 2000; Markovitch and Lancet Artif Life 18(3), 2012), and use it to study - under a unified and concise prebiotic evolutionary framework - both a variety of initial conditions of the universe and the OEE of species that evolve from them.     

Antioxidant effect of zinc and zinc-metallothionein in the acute cytotoxicity of hydrogen peroxide in Ehrlich ascites tumour cells

This study was concerned with the role of zinc (Zn) and zinc-metallothionein (Zn-MT) in oxidative stress. Hydrogen peroxide-induced oxidative injury was examined in Ehrlich ascites tumour cells isolated from control host mice, mice pretreated with 10 mg/kg ZnSO4 (i.p.) to increase cellular Zn/Zn-MT levels, and mice exposed to Zn-deficient diet to reduce the cellular Zn/Zn-MT levels. The results of the present study showed that Ehrlich cells with seven-fold differences in Zn-MT concentrations could be obtained by manipulating the Zn status of host mice and that high Zn and Zn-MT levels can make Ehrlich cells more resistant to H2O2-induced oxidative injury (cell viability, lipid peroxidation, [Ca2+]i) while cells with reduced Zn/Zn-MT levels were more susceptible to this treatment. H2O2 treatment resulted in oxidation of MT thiolate groups and loss of its metal binding capacity with translocation of Zn released from oxidized MT to other cellular sites. Preincubation of Ehrlich cells with ZnSO4 in vitro also conferred some degree of resistance to H2O2 toxicity, suggesting the inherent antioxidative property of Zn ions. These data suggested that Zn-MT can be considered as an antioxidant by virtue of its thiolate groups and its Zn ions that are released in the presence of oxidative stress.     

A Monte Carlo evaluation of five interval estimators for the relative risk in sparse data

The relative risk (RR) is one of the most frequently used indices to measure the strength of association between a disease and a risk factor in etiological studies or the efficacy of an experimental treatment in clinical trials. In this paper, we concentrate attention on interval estimation of RR for sparse data, in which we have only a few patients per stratum, but a moderate or large number of strata. We consider five asymptotic interval estimators for RR, including a weighted least-squares (WLS) interval estimator with an ad hoc adjustment procedure for sparse data, an interval estimator proposed elsewhere for rare events, an interval estimator based on the Mantel-Haenszel (MH) estimator with a logarithmic transformation, an interval estimator calculated from a quadratic equation, and an interval estimator derived from the ratio estimator with a logarithmic transformation. On the basis of Monte Carlo simulations, we evaluate and compare the performance of these five interval estimators in a variety of situations. We note that, except for the cases in which the underlying common RR across strata is around 1, using the WLS interval estimator with the adjustment procedure for sparse data can be misleading. We note further that using the interval estimator suggested elsewhere for rare events tends to be conservative and hence leads to loss of efficiency. We find that the other three interval estimators can consistently perform well even when the mean number of patients for a given treatment is approximately 3 patients per stratum and the number of strata is as small as 20. Finally, we use a mortality data set comparing two chemotherapy treatments in patients with multiple myeloma to illustrate the use of the estimators discussed in this paper.     

Metabolic fingerprinting to discriminate diseases of stored carrots

Volatile metabolites from headspace gas of carrot cv. Vita‐treat inoculated with water or four different pathogens Botrytis cinerea, Erwinia carotovora subsp. carotovora, Aspergillus niger and Fusarium avenaceum were profiled using gas chromatography and mass spectrometry to develop a technology to discriminate diseases. The inoculation of carrot roots with water or different pathogens released a total of 137 different volatile metabolites. Among them, 39 compounds were relatively consistent and 11 were specific to one or more diseases/inoculations. E. carotovora subsp. carotovora produced seven disease‐specific metabolites: 1‐butanol, 3‐methyl; 1‐pentanol; 1‐propanol, 2‐methyl; 2,3‐butanedione; boronic acid, ethyl; butane, 1‐methoxy‐3‐methyl; and ethane, ethoxy. Some metabolites were disease/inoculation discriminatory and were not detected in all treatments: 1,2‐dimethoxy‐ethene was common in carrots inoculated with E. carotovora subsp. carotovora and B. cinerea, while 2‐butanone, 3‐chloro‐4‐hydroxy‐1,4‐diphenyl was common in carrots inoculated with E. carotovora subsp. carotovora, F. avenaceum and water‐inoculated control. The significant mass ions, based on univariate analysis, from a total of 150 (46–195 m/z) and compounds from a total of 32 were further subjected to stepwise discriminant analysis and discriminant analysis. The models for 3 days after inoculation (DAI) were better than those for 6 DAI and 3 + 6 DAI, where up to 90% of the observations were correctly classified into respective inoculations. The disease‐discriminatory compounds from different diseases/inoculations and discriminant analysis models developed here have the potential for the early detection and discrimination of postharvest diseases of carrot cv. Vita‐treat, after validation under commercial conditions.