Rapid authentication of animal cell lines using pyrolysis mass spectrometry and auto-associative artificial neural networks

Summary Pyrolysis mass spectrometry (PyMS) was used to produce biochemical fingerprints from replicate frozen cell cultures of mouse macrophage hybridoma 2C11-12, human leukaemia K562, baby hamster kidney BHK 21/C13, and mouse tumour BW-O, and a fresh culture of Chinese hamster ovary CHO cells. The dimensionality of these data was reduced by the unsupervised feature extraction pattern recognition technique of auto-associative neural networks. The clusters observed were compared with the groups obtained from the more conventional statistical approaches of hierarchical cluster analysis. It was observed that frozen and fresh cell line cultures gave very different pyrolysis mass spectra. When only the frozen animal cells were analysed by PyMS, auto-associative artificial neural networks (ANNs) were employed to discriminate between them successfully. Furthermore, very similar classifications were observed when the same spectral data were analysed using hierarchical cluster analysis. We demonstrate that this approach can detect the contamination of cell lines with low numbers of bacteria and fungi; this approach could plausibly be extended for the rapid detection of mycoplasma infection in animal cell lines. The major advantages that PyMS offers over more conventional methods used to type cell lines and to screen for microbial infection, such as DNA fingerprinting, are its speed, sensitivity and the ability to analyse hundreds of samples per day. We conclude that the combination of PyMS and ANNs can provide a rapid and accurate discriminatory technique for the authentication of animal cell line cultures.     

Development ofgusA reporter gene constructs for cereal transformation: Availability of plant transformation vectors from the CAMBIA Molecular Genetic Resource Service

The use of reporter genes to characterise sequence elements that act to regulate gene expression in transgenic plants has been vital to the development of foreign gene expression strategies for use in cereal transformation. ThegusA locus ofEscherichia coli, which encodes the enzyme-glucuronidase (GUS), is by far the most popular reporter gene used in plant transformation. In this paper we extend the utility of the GUS reporter gene system in cereal transformation by describing and evaluating a number of novel constructs suitable for use in direct gene transfer experiments. These plasmids are all available from the Molecular Genetic Resource Service of the Center for the Application of Molecular Biology to International Agriculture.     

Inhibition of the mitochondrial Ca2+ uniporter by pure and impure ruthenium red

Commercial ruthenium red is often purified by a single recrystallization as described by Luft, J.H. (1971) Anat Rec 171, 347–368, which yields small amounts of material having an apparent molar extinction coefficient of 67,400 at 533 nm. A simple modification to the procedure dramatically improves the yield, allowing crystallization to be repeated. Three times recrystallized ruthenium red has an apparent extinction coefficient of 85,900, the highest value reported to date. Both crude and highly purified ruthenium red can be shown to inhibit reverse activity of the mitochondrial Ca²⁺ uniporter (uncoupled mitochondria), provided that care is taken to minimize and account for Ca²⁺ release through the permeability transition pore. Crude ruthenium red is 7–10 fold more potent than the highly purified material in this regard, on an actual ruthenium red concentration basis. The same relative potency is seen against forward uniport (coupled mitochondria), however, the I₅₀ values are 10 fold lower for both the crude and purified preparations. These data demonstrate unambiguously that the energy state of mitochondria affects the sensitivity of the Ca²⁺ uniporter to ruthenium red preparations, and that both the forward and reverse reactions are subject to complete inhibition. The data suggest, however, that the active inhibitor may not be ruthenium redper se, but one or more of the other ruthenium complexes which are present in ruthenium red preparations.Abbreviations CCP carbonyl cyanide p-chlorophenylhydrazone - CSA cyclosporin A - Hepes 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid     

A model and lexicon for pollen fate

As pollination biology undergoes unprecedented growth as a discipline, confusion in the use of terms has become increasingly common. The need for a flexible yet unambiguous terminology has become urgent. As an example we discuss how the term “pollination efficiency” is used differently by 18 studies, and “pollinator effectiveness” by seven others. Here we present flowcharts of two general models of pollination systems (biotic and abiotic) that trace all the events from pollen production to development of seed or fruit, and we develop a lexicon for the quantities of pollen, processes of transfers (to a vector, to a stigma), and ratios of quantities that are of interest in studies of pollination and mating systems. An appendix includes a glossary of the definitions we suggest.     

Pressure Stabilization of Proteins from Extreme Thermophiles

We describe the stabilization by pressure of enzymes, including a hydrogenase from Methanococcus jannaschii, an extremely thermophilic deep-sea methanogen. This is the first published report of proteins from thermophiles being stabilized by pressure. Inactivation studies of partially purified hydrogenases from an extreme thermophile (Methanococcus igneus), a moderate thermophile (Methanococcus thermolithotrophicus), and a mesophile (Methanococcus maripaludis), all from shallow marine sites, show that pressure stabilization is not unique to enzymes isolated from high-pressure environments. These studies suggest that pressure stabilization of an enzyme may be related to its thermophilicity. Further experiments comparing the effects of increased pressure on the stability of α-glucosidases from the hyperthermophile Pyrococcus furiosus and Saccharomyces cerevisiae support this possibility. We have also examined pressure effects on several highly homologous glyceraldehyde-3-phosphate dehydrogenases from mesophilic and thermophilic sources and a rubredoxin from P. furiosus. The results suggest that hydrophobic interactions, which have been implicated in the stabilization of many thermophilic proteins, contribute to the pressure stabilization of enzymes from thermophiles.     

Phylogeny of Drosophila and related genera inferred from the nucleotide sequence of the Cu,Zn Sod gene

The phylogeny and taxonomy of the drosophilids have been the subject of extensive investigations. Recently, Grimaldi (1990) has challenged some common conceptions, and several sets of molecular data have provided information not always compatible with other taxonomic knowledge or consistent with each other. We present the coding nucleotide sequence of the Cu,Zn superoxide dismutase gene (Sod) for 15 species, which include the medfly Ceratitis capitata (family Tephritidae), the genera Chymomyza and Zaprionus, and representatives of the subgenera Dorsilopha, Drosophila, Hirtodrosophila, Scaptodrosophila, and Sophophora. Phylogenetic analysis of the Sod sequences indicates that Scaptodrosophila and Chymomyza branched off the main lineage before the major Drosophila radiations. The presence of a second intron in Chymomyza and Scaptodrosophila (as well as in the medfly) confirms the early divergence of these two taxa. This second intron became deleted from the main lineage before the major Drosophila radiations. According to the Sod sequences, Sophophora (including the melanogaster, obscura, saltans, and willistoni species groups) is older than the subgenus Drosophila; a deep branch splits the willistoni and saltans groups from the melanogaster and obscura groups. The genus Zaprionus and the subgenera Dorsilopha and Hirtodrosophila appear as branches of a prolific “bush” that also embraces the numerous species of the subgenus Drosophila. The Sod results corroborate in many, but not all, respects Throckmorton's (King, R.C. (ed) Handbook of Genetics. Plenum Press, New York, pp. 421–469, 1975) phylogeny; are inconsistent in some important ways with Grimaldi's (Bull. Am. Museum Nat. Hist. 197:1–139, 1990) cladistic analysis; and also are inconsistent with some inferences based on mitochondrial DNA data. The Sod results manifest how, in addition to the information derived from nucleotide sequences, structural features (i.e., the deletion of an intron) can help resolve phylogenetic issues. Correspondence requests to: F. J. Ayala     

H-2T24 and Pema T24: orthologous expressed MHC class Ib genes from mouse and Peromyscus maniculatus

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers U03104 and L22338.     

The biogeochemistry of a north-temperate grassland with native ungulates: Nitrogen dynamics in Yellowstone National Park

Nutrient dynamics of large grassland ecosystems possessing abundant migratory grazers are poorly understood. We examined N cycling on the northern winter range of Yellowstone National Park, home for large herds of free-roaming elk (Cervus elaphus) and bison (Bison bison). Plant and soil N, net N mineralization, and the deposition of ungulate fecal-N were measured at five sites, a ridgetop, mid-slope bench, steep slope, valley-bottom bench, and riparian area, within a watershed from May, 1991 to April, 1992.Results indicated similarities between biogeochemical properties of Yellowstone grassland and other grassland ecosystems: (1) landscape position and soil water affected nutrient dynamics, (2) annual mineralization was positively related to soil N content, and (3) the proportion of soil N mineralized during the year was negatively related to soil C/N.Grazers were a particularly important component of the N budget of this grassland. Estimated rates of N flow from ungulates to the soil ranged from 8.1 to 45.6 kg/ha/yr at the sites (average = 27.0 kg/ha/yr), approximately 4.5 times the amount of N in senescent plants. Rates of nitrogen mineralization for Yellowstone northern range grassland were higher than those measured in other temperate grassland ecosystems, possibly due to grazers promoting N cycling in Yellowstone.