Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny

Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly conserved regions of exons in order to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six species of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times < or = 40-50 Mya. We sequenced one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for comparison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be of limited use because they were paralogous with the gene in the outgroup. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA sequence divergence increased linearly with time < or = 40-50 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the allele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the consequences of a higher mutation rate rather than to a lower effective population size of mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences of individual scnDNA sequences, phylogenetically informative variation was insufficient to obtain robust phylogenies. However, the combined scnDNA sequences produced a well-supported phylogeny congruent with that derived from mtDNA. This analysis illustrates the high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining information from multiple short scnDNA sequences obtained using broadly applicable primers.      

Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence

In samples where the amount of DNA is limited, the polymerase chain reaction (PCR) can amplify specific regions of the DNA. A quantitative analysis of the PCR product would be desirable to ensure sufficient DNA is available for analysis. In this study, we examine the use of capillary electrophoresis (CE) with laser fluorescence detection for quantitation of PCR products. A coated open tubular capillary was used with a non-gel sieving buffer and a fluorescent intercalating dye to obtain results within 20 minutes. Using an internal standard, peak migration time was below 0.1% relative standard deviation (R.S.D.) with a peak area precision of 3% R.S.D. In comparison to quantitation by hybridization, (i.e., slot blot) and spectrophotometric analysis, capillary electrophoresis shows distinct advantages due to its ability to separate unincorporated primers and PCR byproducts from the targeted PCR product. The results demonstrate that CE can be used to monitor the quality and quantity of the PCR product.     

Incorporation of [35S]sulphate into glycosaminoglycans by mineralized tissues in vivo.

To investigate the metabolism of proteoglycans in young growing rats, calvaria, incisors, femoral diaphysis and metaphysis were labelled in vivo for 0.5-72 h with [35S]sulphate. At each time point the specific radioactivity, expressed as c.p.m. of [35S]sulphate/micrograms of uronic acid, of papain-resistant macromolecules in each tissue was determined. The identity of the glycosaminoglycans was established by the use of specific enzymic and chemical methods of degradation. Incorporation of the label into each tissue was maximal at 12 h; it then declined to 50-75% of that value by 72 h. Chondroitin sulphate was the predominant glycosaminoglycan in each tissue, representing 80-96% of the total; heparan sulphate comprised 2-14% of the total; in general, radioactive material sensitive to keratanase comprised less than 1% of the total. The relative amount of labelled chondroitin sulphate increased, whereas that of heparan sulphate decreased, with increasing time of incorporation. These data show that 25-50% of the newly synthesized glycosaminoglycans are lost from mineralizing tissues, during the time in which the newly secreted organic matrix becomes mineralized.     

A family of phosphohydrolases from bovine intestinal mucosa: 5'-nucleotidase

Bovine intestinal 5'-nucleotidase has been partially purified and characterized for comparison with two other phosphohydrolases from the same tissue, alkaline phosphatase and 5'-nucleotide phosphodiesterase, which are closely related structurally and mechanistically. Kinetic studies with a variety of nucleotides and phosphonate analogs show that, although 5'-nucleotidase is a monoesterase like alkaline phosphatase, it more closely resembles 5'-nucleotide phosphodiesterase in its high affinity and specificity for nucleotide binding. 5'-Nucleotidase is bound very strongly by an affinity column containing a bound phosphonate analog of ADP but is not bound by an affinity column containing a non nucleotide phosphonate which selectively binds alkaline phosphatase. 5'-Nucleotidase is strongly bound by immobilized antibodies prepared against 5'-nucleotide phosphodiesterase, and is less strongly bound by immobilized antibodies prepared against alkaline phosphatase. We conclude that 5'-nucleotidase is structurally more similar to 5'-nucleotide phosphodiesterase than to another monoesterase, alkaline phosphatase.     

Phenol coupling initiated by one-electron oxidation of tyrosine units in peptides and histone

Phenoxyl radicals generated pulse radiolytically by the reaction of N.3 with Gly-Tyr decay biomolecularly (2k = 4.7 X 10(8)M-1 s-1) with efficient formation of 2,2'-dimers, which enolize rapidly (k = 2.7 X 10(4) s-1) to produce the 2,2'-biphenolic product. The build-up of the characteristic 2,2'-biphenol fluorescence (400 nm) and absorption also indicated a delayed (k = 80 s-1) process, probably involving the phenoxyl <-> phenoxy-quinol equilibrium. About 60 per cent of the Gly-Tyr phenoxyls were found to dimerize to the 2,2'-biphenol, and a similarly efficient 2,2'-coupling seems to occur with other tyrosyls, such as Lys-Tyr-Lys and histone. gamma-Radiolysis was applied to estimate relative yields of formation of 2,2'-biphenols under various conditions. Dimerization is almost completely inhibited by cysteine or oxygen, consistent with phenoxyl 'repair' by cysteine or O-.2; disproportionation of O-.2 with SOD prevents repair. The phenol 2,2'-coupling is less efficient for .OH- and inefficient for e-aq-initiation.     

Effect of waterfowl (Anas platyrhynchos) on indicator bacteria populations in a recreational lake Madison, Wisconsin.

A public swimming beach in Madison, wis., experienced intermittent high fecal coliform counts during the late summer and early fall of 1978. Public health officials closed the beach on a number of occasions. A public health survey identified a combination of waterfowl wastes and meteorological events as the explanation for the high bacteria counts. Fecal coliform bacteria were deposited by mallard ducks and multiplied in the beach sands. The bacteria were subsequently transported into the lake and resulted in high fecal coliform counts in the swimming area.     

Synchronization of the desmidStaurastrum gracile

Summary Cultures ofStaurastrum gracile maintained in a liquid medium in a 168 hours light: dark regime were asynchronous. Alteration of the regime to 1410 or 186 failed to induce synchrony, as did variation of the light and dark temperatures. The cultures were synchronized by eliminating a light period to give a total dark period of 32 hours. One such cycle gave 54% synchrony, the cells entering division at the onset of the second light period after treatment. The omission of a second light period 72 hours after the first produced no increase in the level of synchrony. The level was improved by omitting a further light period 48 hours after the first to give a 321632 induction treatment which resulted in 64% synchrony. In no instance did the cells divide between the dark treatment and the synchronized wave of cytokinesis. The mechanism of this synchrony may be explained by the existence of an essential, dark-labile division precursor.This work forms part of a thesis submitted byRoy Rowley to the University of Manchester for the degree of M.Sc.     

Binding of chloramphenicol and a fragment of aminoacyl-transfer ribonucleic acid to ribosomes and a ribosome precursor from a mutant of Escherichia coli.

During exponential growth, the mutatn strain Escherichia coli 15-28 accumulates 47S particles, which are unusual precursors to 50S ribosomal subunits. The 47S particles have little ability to bind chloramphenicol, but binding of a fragment of aminoacyl-tRNA is about half that by completed subunits. The 70S (and 50S) ribosomes of strain 15-28 and its parent (strain 15TP) do not differ in chloramphenicol binding. Although ribosomes from the mutant are less able than those from the parent to bind the fragment, this difference is not as marked as was found previously [Sims & Wild (1976) Biochem. J. 160, 721-726] for the binding of an analogue of peptidyl-tRNA and for peptidyltransferase activity. The altered activities may arise because strain 15-28 misassembles 50S subunits of altered conformation and because the few proteins that 47S patricles lack have vital functions in some of the partial reactions of protein synthesis.     

Studies on the ferrochelatase activity of mitochondria and submitochondrial particles with special reference to the regulatory function of the mitochondrial inner membrane

The question addressed in the title was examined by measuring fluorescence emission spectra and light-induced fluorescence-yield changes of chloroplasts which had been frozen to ?196 °C rapidly, as very thin samples adsorbed into substrates which were plunged directly into liquid nitrogen, or slowly by the cooling action of liquid nitrogen through the wall of the cuvette. Contrary to previous reports, we found that the rate of cooling had no influence on the shape of the emission spectrum, the extent of the variable fluorescence or the fraction of the absorbed quanta which are delivered initially to Photosystem I.