Sequential principal components analysis,a tool for cluster detection in large bacteriophage-typing data samples

Using, as an example, the susceptibility of 437 bacterial strains (belonging to nomenspecies of the genera,Pseudomonas andXanthomonas) to 86 bacteriophage preparations, this study describes how sequential removal of the more distinctive emerging clusters (or selected groups of elements with prior knowledge of their taxonomic relationships) in a principal components analysis can be employed to analyze, the affinities among the remaining original numerical units. The initial, well-defined clusters had a constraining impact on other elements. This constraint was eased upon successive removal from the data matrix of initially distinctive clusters, thereby enabling clearer views of the relationships among the remaining elements. This procedure (sequential principal components analysis) might be used to evaluate the impacts of individual taxa in a numerical classification.     

Southeast Asian Mitochondrial DNA Analysis Reveals Genetic Continuity of Ancient Mongoloid Migrations

Human mitochondrial DNAs (mtDNAs) from 153 independent samples encompassing seven Asian populations were surveyed for sequence variation using the polymerase chain reaction (PCR), restriction endonuclease analysis and oligonucleotide hybridization. All Asian populations were found to share two ancient AluI/DdeI polymorphisms at nps 10394 and 10397 and to be genetically similar indicating that they share a common ancestry. The greatest mtDNA diversity and the highest frequency of mtDNAs with HpaI/HincII morph 1 were observed in the Vietnamese suggesting a Southern Mongoloid origin of Asians. Remnants of the founding populations of Papua New Guinea (PNG) were found in Malaysia, and a marked frequency cline for the COII/tRNA(Lys) intergenic deletion was observed along coastal Asia. Phylogenetic analysis indicates that both insertion and deletion mutations in the COII/tRNA(Lys) region have occurred more than once.     

PATMAT: a searching and extraction program for sequence, pattern and block queries and databases

A program has been developed that provides molecular biologistswith multiple tools for searching databases, yet uses a verysimple interface. PATMATcan use protein or (translated) DNAsequences, patterns or blocks of aligned proteins as queriesof databases consisting of amino acid or nucleotide sequences,patterns or blocks. The ability to search databases of blocksby ‘on-the-fly’ conversion to scoring matrices providesa new tool for detection and evaluation of distant relationships.PATMAT uses a pull-down, menu-driven interface to carry outits multiple searching, extraction and viewing functions. Eachquery or database type is recognized, reported, and the appropriatesearch carried out, with matches and alignments reported inwindows as they occur. Any of the high scoring matches can beexported to a file, viewed and recalled as a query using onlya few keystrokes or mouse selections. Searches of multiple databasefiles are carried out by user selection within a window. PATMATruns under DOS; the searching engine also runs under UNIX.     

Analysis of pipecolic acid in biological fluids using capillary gas chromatography with electron-capture detection and [H11]pipecolic acid as internal standard

A sensitive and accurate stable isotope dilution assay was developed for the measurement of pipecolic acid in body fluids using capillary gas chromatography with electron-capture detection. The method utilizes [²H₁₁]pipecolic acid as the internal standard. Sample preparation consisted of derivatization in aqueous solution (pH 11.5) of the amine moiety with methyl chloroformate to the N-methylcarbamate, followed by acidic ethyl acetate extraction at pH ≤ 2 and further derivatization of the carboxyl moiety with pentafluorobenzyl bromide, the excess of which was removed by solid-phase extraction. Control values have been determined in the plasma of at-term infants, age > 1 week (n = 21, mean = 1.36 μM, range = 0.47–3.27 μM). The utility of the method was demonstrated by quantitating pipecolic acid in biological fluids derived from patients with peroxisomal disorders. The method was validated against an established electron-capture negative ion mass fragmentographic technique.     

Complete moles have paternal chromosomes but maternal mitochondrial DNA

Summary Complete hydatidiform moles contain only paternal chromosomes. To learn more of their origin, we used restriction endonuclease site polymorphisms found in the parental mitochondrial DNAs to demonstrate that moles contain exclusively maternal mitochondrial DNA. Thus, moles must arise from the fusion of one or two sperm with a mature but anucleate ovum.     

Correlation between adult transformation and aldehyde oxidase staining pattern in wing discs ofApterous genotypes inDrosophila melanogaster

Summary The aldehyde oxidase staining pattern in wing discs ofDrosophila melanogaster bearing the genotypesap ^blt /ap ^blt andap ^blt andap ^blt /ap ⁷³ⁿ showns changes from the wild-type pattern. Extensive areas of the presumptive dorsal posterior wing blade, which are normally unstained, have enzyme activity in these mutants. In wings of these genotypes, dorsal posterior structures are replaced by dorsal anterior wing structures. A strong correlation has been found between the frequencies of various staining patterns in the discs and the extent of transformation in the cuticular structures of the wing, which is consistent with the idea that aldehyde oxidase activity can be used as an indicator in the wing disc of this transformation. Unlike the homoeotic mutationengrailed, apterous has not been interpreted as a selector gene yet the work reported here shows thatapterous alleles can cause changes resembling those of theengrailed phenotype both in aldehyde oxidase staining behaviour and in the cuticular transformation.     

Stream detritus dynamics: Regulation by invertebrate consumers

Summary Insecticide treatment of a small, Appalachian forest stream caused massive downstream insect drift and reduced aquatic insect densities to <10% of an adjacent untreated reference stream. Reduction in breakdown rates of leaf detritus was accompanied by differences in quantity and composition of benthic organic matter between the two streams. Following treatment, transport of particulate organic matter was significantly lower in the treated stream than in the reference stream whereas no significant differences existed prior to treatment. Our results indicate that macroinvertebrate consumers, primarily insects, are important in regulating rates of detritus processing and availability to downstream communities.     

The Receptor-Mediated Activation of Tyrosine Hydroxylation in the Superior Cervical Ganglion of the Rat

The addition of carbachol to superior cervical ganglia causes a rapid increase in tyrosine hydroxylation in situ. The increase occurs in ganglia from both newborn and adult animals, and in ganglia from animals pretreated with reserpine. The increase is not due to increased transport of the substrate. The increase is dependent upon the presence of calcium, and is additive to the stimulation produced by dibutyryl cyclic AMP. The stimulation seems specific for tyrosine hydroxylation; dopamine beta-hydroxylation is not increased. Preincubation experiments suggest that the carbachol-induced stimulation is due to a change in the availability of, or the affinity of the enzyme for, reduced pterin cofactor. The stimulation is inhibited by atropine and also by low concentrations of phenoxybenzamine or haloperidol, which suggests that it is caused by an action of carbachol on the interneurons in the ganglia.