The phylogeny of the hominoid primates: a statistical analysis of the DNA-DNA hybridization data

Sibley and Ahlquist compared the single-copy nuclear DNA sequences of the hominoid primates using DNA-DNA hybridization. From this data set they estimated a phylogeny that clusters man and chimpanzees using a distance Wagner procedure. However, no assessment of statistical confidence in this estimated phylogeny was made, despite the fact that their data set contains internal inconsistencies concerning the correct branching order. This paper presents a modification of Pielou's Q- statistic that allows one to make nonparametric tests of phylogenetic relationship from distance data. The results of this analysis indicate that the estimated phylogeny of Sibley and Ahlquist is without statistical significance owing to the internal inconsistencies of the data set. A survey and additional analyses of other types of molecular data indicate that the phylogeny that clusters chimpanzees and gorillas and has the human lineage splitting off earlier is statistically consistent with all the molecular data (including the DNA-DNA hybridization data), whereas the phylogeny estimated by Sibley and Ahlquist can be rejected at the 5% level using the data on restriction- endonuclease sites in the mitochondrial genome.      

Regulation of citrate synthase in facultative methylotrophic bacteria

Commonly the TCA cycle fulfils an anabolic and a catabolic function in case of aerobic chemoorganoheterotrophic nutrition. In methylotrophic growth the TCA cycle is dispensable as a bioenergetic pathway. This is reflected by properties of citrate synthase in facultative methylotrophic bacteria. Two citrate synthases, a "chemoorganoheterotrophic" one, which is inhibited by NADH (or ATP in Acetobacter MB 58), and a "methylotrophic" one, which is not or less affected by energy indicators, were found in Pseudomonas oleovorans, Pseudomonas MS, Pseudomonas MA, and Acetobacter MB 58. The concentration of these citrate synthases depends on the manner of nutrition. Bacteria with ICL-negative-variant of the serine pathway and with ribulosebisphosphate pathway seem to possess only a "chemoorganoheterotrophic" citrate synthase. Possibly the anabolic function of this citrate synthase can be realized by metabolites.     

Measurement of Growth at Very Low Rates ((mu) >= 0), an Approach To Study the Energy Requirement for the Survival of Alcaligenes eutrophus JMP 134

Alcaligenes eutrophus JMP 134 was grown in a recycling-mode fermenter with 100% biomass retention on 2,4-dichlorophenoxyacetic acid (2,4-D), phenol, and fructose. The growth pattern obtained given a constant supply of substrates exhibited three phases of linear growth on all three substrates. The transition from phase 1 to phase 2, considered to correspond to the onset of stringent (growth) control as indicated by a significant increase in guanosine 5(prm1)-bisphosphate 3(prm1)-bisphosphate (ppGpp), took place at 0.016 h(sup-1) with 2,4-D and at about 0.02 h(sup-1) with phenol and fructose. In the final phase, phase 4, which was achieved after the growth rate on the respective substrates fell below 0.003 to 0.001 h(sup-1), a constant level of biomass was obtained irrespective of further feeding of substrate at the same rate. The yield coefficients decreased by 70 to 80% from phase 1 to phase 3 and were 0 in phase 4. The stationary substrate concentrations s(infmin) in phase 4, calculated from the kinetic constants of the strain, were 1.23, 0.34, and 0.23 (mu)M for 2,4-D, phenol, and fructose, respectively. These figures characterize the minimum stationary substrate concentrations required in a dynamic system to keep A. eutrophus alive. This is caused by a substrate flux which enables growth at a rate >=0 due to the provision of energy to an extent at least satisfying maintenance requirements. According to the constant feed rates of the substrates and the final and stable biomass concentrations, this maintenance energy amounts to 14.4, 4.0, and 2.4 (mu)mol of ATP (middot) mg of dry mass(sup-1) h(sup-1) for 2,4-D, phenol, and fructose, respectively, after correction for the fraction of living cells. The increased energy expenditure in the case of 2,4-D is discussed with respect to uncoupling.     

Interactions ofCandida albicans with bacteria and salivary molecules in oral biofilms

The yeastCandida albicans coaggregates with a variety of streptococcal species, an interaction that may promote oral colonization by yeast cells.C. albicans andCandida tropicalis are the yeasts most frequently isolated from the human oral cavity and our data demonstrate that both these species bind toStreptococcus gordonii NCTC 7869 while two otherCandida species (Candida krusei andCandida kefyr) do not. Adherence ofC. albicans was greatest when the yeast had been grown at 30° C to mid-exponential growth phase. For 21 strains ofC. albicans there was a positive correlation between the ability to adhere toS. gordonii and adherence to experimental salivary pellicle. Whole saliva either stimulated or slightly inhibited adherence ofC. albicans toS. gordonii depending on the streptococcal growth conditions. The results suggest that the major salivary adhesins and coaggregation adhesins ofC. albicans are co-expressed.     

Construction of broad-host-range plasmids for the expression of heterologous genes in Acetobacter methanolicus B58

The construction of different plasmids reported here on the basis of a broad-host-range RSF1010 replicon allows an efficient expression of heterologous genes in the acidophilic methanol-assimilating bacterium Acetobacter methanolicus B58. The promoter-probe vector pRS201 was used for the identification and isolation of the promoter containing sequences derived from the DNA of the Acetobacter phage Acm1. Further, this plasmid was coupled with the Escherichia coli promoters tac and p_r creating the expression vectors pRS201tac and pRS201p_r, respectively. After the insertion of the chloramphenicol acetyltransferase (cat) gene of the cloned promoters downstream, the chloramphenicol acetyltransferase (CAT) was determined in a cell-free extract of both E. coli and A. methanolicus. Using E. coli promoters as well as promoters of the Acetobacter phage Acm1 arranged in tandem with the promoters of the heterologous genes to be expressed, the pectat lyase gene (ptlB) of Erwinia carotovora and the threonine A gene (thrA) of E. coli were successfully expressed in A. methanolicus. The stability of recombinant plasmids under various conditions in A. methanolicus strains was tested using antibiotic-free media.     

Determination of substrate utilization patterns of soil microbial communities: An approach to assess population changes after hydrocarbon pollution

Abstract: Changes in hydrocarbon content in soils resulted in characteristic shifts of the substrate utilization patterns as tested with the Biolog system. The altered patterns of substrate utilization corresponded to similar changes in abundance of hydrocarbon-utilizing bacteria and the occurrence of specific bacterial groups in the soils. Substrate utilization patterns as recorded with the Biolog system are suitable for rapidly assessing dynamics of autochthonous soil communities and evaluating their biodegradative potential.     

Glucose as an auxiliary substrate

Summary A theoretical consideration is presented of the comparative efficiency of carbon conversion of glucose by the Embden-Meyerhof-Parnas (EMP) and the oxidative hexosemonophosphate (HMP) pathways. As a result it is shown that maximum carbon conversion, that is 89%, is possible when glucose is assimilated via the EMP pathway. This value is diminished in proportion to the participation of the HMP pathway in carbon assimilation and is halved when glucose is incorporated entirely via this pathway. If NADPH is included as a source of energy, glucose may behave both as an excess carbon and an excess energy substrate, the latter being the case when greater portions of the HMP pathway operate, and the extent of this is in turn dependent on the P/O quotient. If NADPH cannot be used for ATP synthesis, glucose remains an excess carbon substrate throughout, although when the HMP pathway accounts for more than 26% of glucose assimilation an increasing excess of reduction equivalents is produced. These results are interpreted in terms of mixed-substrate utilization for improving growth yield when glucose is to be used as the excess carbon component.     

Calculating affinity constants of substrate mixtures in a chemostat

An “oversimplified” method for calculating affinity constants in substrate mixtures is evaluated concerning its validity. It is shown that the real affinity to the mixture as determined by using the correct method is always higher, i.e., leads to a lower affinity constant, as compared to the wrong method frequently used.     

Monoclonal antibodies to rabbit liver cytochrome P-448

Cytochrome P-448 (mol wt 55,000 Daltons) from rabbit liver was purified to a specific content of 16.6 nmol/mg. Mice were immunised with this preparation, their spleens removed and dissociated lymphocytes hybridised with myeloma cells. Four monoclonal antibodies against cytochrome P-448 were raised and partially characterised. All four antibodies interacted with cytochrome P-448 in intact microsomal fractions and selectively immunoadsorbed cytochrome P-448 from solubilised microsomal preparations. One of the antibodies inhibited benzo[a] pyrene hydroxylase activity in a reconstituted system, one had no effect on activity and two increased activity. The possible applications of such antibodies are discussed.