NITPICK: peak identification for mass spectrometry data

Background  

The reliable extraction of features from mass spectra is a fundamental step in the automated analysis of proteomic mass spectrometry (MS) experiments.     

Cancer therapy

In recent years a growing recognition that molecularly-targeted therapies face formidable obstacles has revived interest in more generic tumor cell phenotypes that could be exploited for therapy. Two recent reports demonstrate that cancer cell survival is critically dependent on the activity of MTH1, a nucleotide pyrophosphatase that converts the oxidized nucleotides 8-oxo-dGTP and 2-OH-dATP to the corresponding monophosphates, thus preventing their incorporation into genomic DNA. Tumor cells frequently overexpress MTH1, probably because malignant transformation creates oxidative stress that renders the nucleotide pool highly vulnerable to oxidation. As a result, MTH1 inhibition in cancer cells results in accumulation and incorporation of 8-oxo-dGTP and 2-OH-dATP into DNA, leading to DNA damage and cell death. This toxic effect is highly cancer cell-specific, as MTH1 is generally dispensable for the survival of normal, untransformed cells. Importantly, MTH1 proves to be a “druggable” enzyme that can be inhibited both by an existing protein kinase inhibitor drug, crizotinib, and by novel compounds identified through screening. Inhibition of MTH1 leading to toxic accumulation of oxidized nucleotides specifically in tumor cells therefore represents an example of a “non-personalised” approach to cancer therapy.     

Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, reduction of NAD(+) to NADH occurs in dissimilatory as well as in assimilatory reactions. This review discusses mechanisms for reoxidation of NADH in this yeast, with special emphasis on the metabolic compartmentation that occurs as a consequence of the impermeability of the mitochondrial inner membrane for NADH and NAD(+). At least five mechanisms of NADH reoxidation exist in S. cerevisiae. These are: (1) alcoholic fermentation; (2) glycerol production; (3) respiration of cytosolic NADH via external mitochondrial NADH dehydrogenases; (4) respiration of cytosolic NADH via the glycerol-3-phosphate shuttle; and (5) oxidation of intramitochondrial NADH via a mitochondrial 'internal' NADH dehydrogenase. Furthermore, in vivo evidence indicates that NADH redox equivalents can be shuttled across the mitochondrial inner membrane by an ethanol-acetaldehyde shuttle. Several other redox-shuttle mechanisms might occur in S. cerevisiae, including a malate-oxaloacetate shuttle, a malate-aspartate shuttle and a malate-pyruvate shuttle. Although key enzymes and transporters for these shuttles are present, there is as yet no consistent evidence for their in vivo activity. Activity of several other shuttles, including the malate-citrate and fatty acid shuttles, can be ruled out based on the absence of key enzymes or transporters. Quantitative physiological analysis of defined mutants has been important in identifying several parallel pathways for reoxidation of cytosolic and intramitochondrial NADH. The major challenge that lies ahead is to elucidate the physiological function of parallel pathways for NADH oxidation in wild-type cells, both under steady-state and transient-state conditions. This requires the development of techniques for accurate measurement of intracellular metabolite concentrations in separate metabolic compartments.     

The formation of the mesoderm in urodelean amphibians

Summary Xenoplastic recombinations of animal and vegetative parts ofAmbystoma mexicanum and Triturus alpestris blastulae, and similar recombinations of parts of³H-thymidinelabelled and unlabelledAmbystoma mexicanum blastulae demonstrate convincingly that the vegetative part (zone IV, see Nieuwkoop, 1969a) of such a recombinate does not contribute to mesoderm formation, but exclusively forms endodermal derivatives. In contrast, the animal cap of the blastula (zones I.II)—which only gives rise to atypical ectoderm if isolated—not only furnishesall the ecto-neurodermal derivatives, butall the mesodermal structures of the developing recombinate as well, and finally to a varying extent forms additional endodermal structures in the recombinate.In the recombinates endodermization of the ectodermal cap occurred at the anterior end of the invaginated archenteron—corresponding to the presumptive pharyngeal endoderm —, and along the dorsal side of the endodermal tube, while an endoderm-like epithelium is formed at the boundary between the caudal endoderm and the ectoderm (proctodaeum formation). These results suggest that in normal development also endodermization occurs in the ectodermal half of the egg. This occurs particularly on the dorsal side, leading to the formation of the presumptive pharyngeal endoderm situated above the dorsal blastoporal groove.These experiments show that the vegetative half of the amphibian blastula is firmly determined as the future endoderm, whereas the animal half is still virtually undetermined and pluripotent.     

Irradiation induces G2/M cell cycle arrest and apoptosis in p53-deficient lymphoblastic leukemia cells without affecting Bcl-2 and Bax expression

The tumor suppressor p53 has been implicated in gamma irradiation-induced apoptosis. To investigate possible consequences of wild-type p53 loss in leukemia, we studied the effect of a single dose of gamma irradiation upon p53-deficient human T-ALL (acute lymphoblastic leukemia) CCRF - CEM cells. Exposure to 3 - 96 Gy caused p53-independent cell death in a dose and time-dependent fashion. By electron microscopic and other criteria, this cell death was classified as apoptosis. At low to intermediate levels of irradiation, apoptosis was preceded by accumulation of cells in the G2/M phase of the cell division cycle. Expression of Bcl-2 and Bax were not detectably altered after irradiation. Expression of the temperature sensitive mouse p53 V135 mutant induced apoptosis on its own but only slightly increased the sensitivity of CCRF - CEM cells to gamma irradiation. Thus, in these, and perhaps other leukemia cells, a p53- and Bcl-2/Bax-independent mechanism is operative that efficiently senses irradiation effects and translates this signal into arrest in the G2/M phase of the cell cycle and subsequent apoptosis.     

The formation of the mesoderm in urodelean amphibians

Summary Dorsal (D), lateral (L and R), and ventral (V) portions of the endoderm of blastulae ofAmbystoma mexicanum of different age (stages 8⁺ to 10^–) were combined with ectodermal caps of stage 8⁺ blastulae. All V and most L and R portions induced only ventrocaudal mesodermal structures — ventral type of mesoderm induction. Almost all D portions induced much more voluminous structures of predominantly axial character — dorsal type of mesoderm induction. The difference in mesoderm-inducing capacity of the dorsal as against the lateral and ventral endoderm is probably purely quantitative in character. The dorsal endoderm exhibits a pronounced dominance in mesoderm-inducing capacity. During the early symmetrization of the amphibian egg it is apparently especially the presumptive dorsal endoderm that becomes endowed with strong mesoderm-inducing properties.A comparison of the results obtained with endodermal portions of blastulae of different age showed that the mesoderm-inducing capacity first begins to decline in the dorsal endoderm (around stage 9), subsequently in the lateral, and finally in the ventral endoderm (at stage 10^–). At stage 10^– the dorsal endoderm no longer has mesoderm-inducing capacities.In the recombinates there is a striking correspondence between the regional differentiation of the mesoderm and that of the endoderm. The latter differs markedly from the presumptive significance of the various endodermal regions in the normal embryo.Primordial germ cells, which constitute a characteristic component of the ventral type of mesoderm induction, can be induced not only by ventral, but also by lateral and to some extent even by dorsal endoderm. The development of primordial germ cells from the ectodermal component of the various recombinates indicates that in the urodeles the origin of the primordial germ cells differs markedly from that in the anurans.The authors want to thank Miss A. de wit for expert technical assistance, Miss E. Bartová for making the drawings, and Dr. J. Faber for editorial help.     

Regulation of nod gene expression in Bradyrhizobium japonicum

Summary The best inducers of nod:: lacZ translational fusions in Bradyrhizobium japonicum are isoflavones, primarily genistein and daidzein. Upstream of the nodABC genes in B. japonicum is a novel gene, nodY, which is coregulated with nodABC. Measurements of the activity of lacZ fusions to the nodD gene of B. japonicum show that this gene is inducible by soybean seed extract and selected flavonoid chemicals. The induction of the nodY ABC and nodD operons appears to require a functional nodD gene, indicating that the nodD gene product controls its own synthesis as well as other nod genes.     

Origins of asexuality in <Emphasis Type="Italic">Bryobia</Emphasis>mites (Acari: Tetranychidae)

Background  

Obligate asexual reproduction is rare in the animal kingdom. Generally, asexuals are considered evolutionary dead ends that are unable to radiate. The phytophagous mite genus Bryobia contains a large number of asexual species. In this study, we investigate the origin and evolution of asexuality using samples from 111 populations in Europe, South Africa and the United States, belonging to eleven Bryobia species. We also examine intraspecific clonal diversity for one species, B. kissophila, by genotyping individuals from 61 different populations. Knowledge on the origin of asexuality and on clonal diversity can contribute to our understanding of the paradox of sex.