Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both?

Many members of the nudix hydrolase family exhibit considerable substrate multispecificity and ambiguity, which raises significant issues when assessing their functions in vivo and gives rise to errors in database annotation. Several display low antimutator activity when expressed in bacterial tester strains as well as some degree of activity in vitro towards mutagenic, oxidized nucleotides such as 8-oxo-dGTP. However, many of these show greater activity towards other nucleotides such as ADP-ribose or diadenosine tetraphosphate (Ap₄A). The antimutator activities have tended to gain prominence in the literature, whereas they may in fact represent the residual activity of an ancestral antimutator enzyme that has become secondary to the more recently evolved major activity after gene duplication. Whether any meaningful antimutagenic function has also been retained in vivo requires very careful assessment. Then again, other examples of substrate ambiguity may indicate as yet unexplored regulatory systems. For example, bacterial Ap₄A hydrolases also efficiently remove pyrophosphate from the 5′ termini of mRNAs, suggesting a potential role for Ap₄A in the control of bacterial mRNA turnover, while the ability of some eukaryotic mRNA decapping enzymes to degrade IDP and dIDP or diphosphoinositol polyphosphates (DIPs) may also be indicative of new regulatory networks in RNA metabolism. DIP phosphohydrolases also degrade diadenosine polyphosphates and inorganic polyphosphates, suggesting further avenues for investigation. This article uses these and other examples to highlight the need for a greater awareness of the possible significance of substrate ambiguity among the nudix hydrolases as well as the need to exert caution when interpreting incomplete analyses.     

Synthesis of dinucleoside tetraphosphates in transfected cells by a firefly luciferase reporter gene

The firefly luciferase gene is widely used as a reporter gene and its expression is generally considered to be non-toxic. In addition to its light-producing reaction, luciferase can synthesise dinucleoside polyphosphates, intracellular signalling molecules, in vitro. Here we show that COS-7 cells transfected with a luciferase expression vector accumulate up to 0.5 mM adenine-containing dinucleoside tetraphosphates (Ap₄N) during the 24 h following luciferin addition. The optimal external concentration of luciferin was 0.4–0.6 mM. In agreement with its poor ability to synthesise adenine-containing dinucleoside triphosphates in vitro, the level of these compounds did not increase after transfection. Consequently, the results of experiments involving luciferase-mediated light production by live cells should now be viewed in the light of the possible effects of an increased intracellular Ap₄N concentration on the properties of the system under investigation. This observation also points to a useful non-invasive procedure for the specific enhancement of intracellular Ap₄N for studies directed at understanding the functions of these compounds.Received 12 November 2003; received after revision 10 December 2003; accepted 12 December 2003     

La FAM fatale: USP9X in development and disease

Deubiquitylating enzymes (DUBs), act downstream of ubiquitylation. As such, these post-post-translational modifiers function as the final arbitrators of a protein substrate’s ubiquitylation status, thus regulating its fate. In most instances, DUBs moderate the absolute level of a substrate, its locality or activity, rather than being an “all-or-none” phenomenon. Yet, disruption of this quantitative regulation can produce dramatic qualitative differences. The ubiquitin-specific protease 9X (USP9X/FAM) is a substrate-specific DUB, which displays an extraordinarily high level of sequence conservation from Drosophila to mammals. It is primarily the recent revelations of USP9X’s pivotal role in human cancers, both as oncogene or tumour suppressor, in developmental disorders including intellectual disability, epilepsy, autism and developmental delay that has led to a subsequent re-examination of its molecular and cellular functions. Results from experimental animal models have implicated USP9X in neurodegeneration, including Parkinson’s and Alzheimer’s disease, as well as autoimmune diseases. In this review, we describe the current and accumulated knowledge on the molecular, cellular and developmental aspects of USP9X function within the context of the biological consequences during normal development and disease.     

Über die Wirkung von Cobalt-II-nitrat auf Kern und Cytoplasma vonAcetabularia mediterranea

Summary The effect of Cobalt-II-nitrate was tested on the marine green algaAcetabularia. Application of Co immediately stopped regeneration as well as synthesis of cytoplasmic proteins. Later on a decrease of the protein contents was observed. Without affecting the size of the nucleus, Co caused a reduction of the nucleolar size and shape within 4 days. By histochemical methods, Co was found to be stored in the nucleus and nucleolus. However, it is not clear whether the Co was already boundin vivo. Size and distribution of the polyphosphate bodies were not changed within 6 days. No storage of Coin vivo could be observed within the polyphosphates.

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Mit Unterstützung durch die Deutsche Forschungsgemeinschaft.     

The Nudix hydrolase superfamily

Nudix hydrolases are found in all classes of organism and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, dinucleoside and diphosphoinositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity. Some superfamily members, such as Escherichia coli MutT, have the ability to degrade potentially mutagenic, oxidised nucleotides while others control the levels of metabolic intermediates and signalling compounds. In prokaryotes and simple eukaryo tes, the number of Nudix genes varies from 0 to over 30, reflecting the metabolic complexity and adaptability of the organism. Mammals have around 24 Nudix genes, several of which encode more than one variant. This review integrates the sizeable recent literature on these proteins with information from global functional genomic studies to provide some insights into the possible roles of different superfamily members in cellular metabolism and homeostasis and to stimulate discussion and further research into this ubiquitous protein family. Received 16 August 2005; received after revision 3 October 2005; accepted 13 October 2005     

Nerve-growth promoting action of isaxonine in rat.

After sciatic nerve lesion by freezing, the length of the most rapidly regenerating fibres was significantly increased by i.p. injection of isaxonine (N-isopropyl-amino-2-pyrimidine orthophosphate) in the rat. A dose-effect relationship was demonstrated. Both sensory and motor function returned earlier in treated animals.     

Nerve-growth promoting action of isaxonine in rat

Summary After sciatic nerve lesion by freezing, the length of the most rapidly regenerating fibres was significantly increased by i.p. injection of isaxonine (N-isopropyl-amino-2-pyrimidine orthophosphate) in the rat. A dose-effect relationship was demonstrated. Both sensory and motor function returned earlier in treated animals.     

Acceleration of the speed of neuronal growth by a new neurotropic substance: N-isopropyl-amino-2-pyrimidine]

16 hrs. after per os administration of 14C N-isopropyl-amino-2-pyrimidine (IAP) in the Rat, radioactivity of the sciatic nerve is significantly higher than in plasma and other organs. In vitro IAP (base, orthophosphate or dichloracetate) accelerates neurite outgrowth of explained spinal ganglion after 48 hrs. of incubation in nutritive medium. Results suggest that IAP incorporated in nerve cell acts on cellular mechanisms controlling nerve growth.     

Semiparametric forecast intervals

Consider forecasting the economic variable Y_t+h with predictors X _t, where h is the forecast horizon. This paper introduces a semiparametric method that generates forecast intervals of Y_t+h| X _t from point forecast models. First, the point forecast model is estimated, thereby taking advantage of its predictive power. Then, nonparametric estimation of the conditional distribution function (CDF) of the forecast error conditional on X _t builds the rest of the forecast distribution around the point forecast, from which symmetric and minimum‐length forecast intervals for Y_t+h| X _t can be constructed. Under mild regularity conditions, asymptotic analysis shows that (1) regardless of the quality of the point forecast model (i.e., it may be misspecified), forecast quantiles are consistent and asymptotically normal; (2) minimum length forecast intervals are consistent. Proposals for bandwidth selection and dimension reduction are made. Three sets of simulations show that for reasonable point forecast models the method has significant advantages over two existing approaches to interval forecasting: one that requires the point forecast model to be correctly specified, and one that is based on fully nonparametric CDF estimate of Y_t+h| X _t. An application to exchange rate forecasting is presented. Copyright © 2010 John Wiley & Sons, Ltd.     

Effect of phosphorylated constituents on the growth of Pseudomonas fluorescens in media containing potassium oxalatoberyllate]

Differences in the extent of beryllium inhibition on the growth of Pseudomonas fluorescens cultivated in various media are related to the concentration and nature of phosphorus-containing constituents of the substrate. Quantitative studies are carried out for interaction processes leading to reduction in beryllium toxicity. These include sequestration of beryllium in soluble form by beta-glycerophosphate and formation of sparingly soluble derivatives with inorganic orthophosphate ions.     

Annexin V interactions with collagen

Annexin V was originally identified as a collagen-binding protein called anchorin CII and was isolated from chondrocyte membranes by affinity chromatography on native type II collagen. The binding of annexin V to native collagen type II is stable at physiological ionic strength when annexin V is reconstituted in liposomes. The binding to native collagen types II and X, and to some extent to type I as well, was confirmed using recombinant annexin V. A physiological role for annexin V interactions with extracellular collagen is consistent with the localization of annexin V on the outer cell surface of chondrocytes, microvilli of hypertrophic chondrocytes, fibroblasts and osteoblasts. A breakthrough in our understanding of the function of annexin V was made with the discovery of its calcium channel activity. At least one of several putative functions of annexin V became obvious from studies on matrix vesicles derived from calcifying cartilage. It was found that calcium uptake by matrix vesicles depend on collagen type II and type X binding to annexin V in the vesicles and was lost when collagens were digested with collagenase; calcium influx was reconstituted after adding back native collagen II or V. These findings indicate that annexin V plays a major role in matrix vesicle-initiated cartilage calcification as a collagen-regulated calcium channel.     

Differences in chromosome A arrangement betweenDrosophila madeirensis andDrosophila subobscura

Summary The proximal half of the A (=X) chromosome ofD. madeirensis has a gene arrangement very similar to the A1 or A6 inversions found inD. subobscura. Polytene chromosome analysis of hybrids betweenD. madeirensis and strains ofD. subobscura homozygous for such inversions shows, however thatD. madeirensis has a gene arrangement different from any known forD. subobscura. These results provide evidence for a greater differentiation of the X chromosome in these species than has previously been described; it seems that the X chromosome is the only one that has undergone structural variation during the speciation process.     

Interaction and interrelation of P2X7 and P2X4 receptor complexes in mouse lung epithelial cells

P2X4 and P2X7 receptors are ATP-gated ion channels that are co-expressed in alveolar epithelial type I cells. Both receptors are localized to the plasma membrane and partly associated with lipid rafts. Here we report on our study in an alveolar epithelial cell line of the molecular organization of P2X7R and P2X4R receptors and the effect of their knockdown. Native gel electrophoresis reveals three P2X7R complexes of ~430, ~580 and ~760 kDa. The latter two correspond exactly in size to signals of Cav-1, the structural protein of caveolae. Interestingly knockdown of P2rx7 affects protein levels, the intracellular distribution and the supramolecular organization of Cav-1 as well as of P2X4R, which is mainly detected in a complex of ~430 kDa. Our data suggest upregulation of P2X4R as a compensatory mechanism of P2X7R depletion.     

Action du rayonnement X sur la croissance des cellules internodales de l'algueChara vulgaris L

Summary We have irradiated internodal cells ofChara vulgaris L. at different doses of X rays from 50 to 600 kr. These internodal cells never show mitotic activity and are of plasmodial constitution. When elongations are measured 7, 14 and 21 days after irradiation, we observe increased clongations from 0 to 150 kr. Then, elongations diminish when doses increase from 150 to 600 kr. This absence of proportionality between doses and biological effect is believed to be in relation to the increased amount of certain enzymes liberated by X rays.     

Differences in chromosome A arrangement between Drosophila madeirensis and Drosophila subobscura

The proximal half of the A (= X) chromosome of D. madeirensis has a gene arrangement very similar to the A1 or A6 inversions found in D. subobscura. Polytene chromosome analysis of hybrids between D. madeirensis and strains of D. subobscura homozygous for such inversions shows, however, that D. madeirensis has a gene arrangement different from any known for D. subobscura. These results provide evidence for a greater differentiation of the X chromosome in these species than has previously been described; it seems that the X chromosome is the only one that has undergone structural variation during the speciation process.     

Deflationary representation,inference, and practice

This paper defends the deflationary character of two recent views regarding scientific representation, namely RIG Hughes' DDI model and the inferential conception. It is first argued that these views' deflationism is akin to the homonymous position in discussions regarding the nature of truth. There, we are invited to consider the platitudes that the predicate “true” obeys at the level of practice, disregarding any deeper, or more substantive, account of its nature. More generally, for any concept X, a deflationary approach is then defined in opposition to a substantive approach, where a substantive approach to X is an analysis of X in terms of some property P, or relation R, accounting for and explaining the standard use of X. It then becomes possible to characterize a deflationary view of scientific representation in three distinct senses, namely: a “no-theory” view, a “minimalist” view, and a “use-based” view—in line with three standard deflationary responses in the philosophical literature on truth. It is then argued that both the DDI model and the inferential conception may be suitably understood in any of these three different senses. The application of these deflationary ‘hermeneutics’ moreover yields significant improvements on the DDI model, which bring it closer to the inferential conception. It is finally argued that what these approaches have in common—the key to any deflationary account of scientific representation—is the denial that scientific representation may be ultimately reduced to any substantive explanatory property of sources, or targets, or their relations.     

Glischropus tylopus,the first known old-world bat with an X-autosome translocation

Summary Glischropus tylopus shows an X-autosome translocation in which a small acrocentric chromosome has been transferred to the X. The diploid number is 30 for the females and 31 for the males. RBG banding shows that in the late replicating X of the female only the original X replicates late, the autosomal part replicates early, showing the same pattern as the corresponding autosomal Y₂ of the male. In the X chromosome, a heterochromatic band separates the autosomal from the gonosomal sequences.23 January 1987I am very grateful to Prof. R.A. Pfeiffer for giving me the opportunity to work at the Department of Human Genetics.My stay in Malaysia was supported by a grant of the DAAD.     

Selection of the relevant information set for predictive relationships analysis between time series

In time series analysis, a vector Y is often called causal for another vector X if the former helps to improve the k‐step‐ahead forecast of the latter. If this holds for k=1, vector Y is commonly called Granger‐causal for X . It has been shown in several studies that the finding of causality between two (vectors of) variables is not robust to changes of the information set. In this paper, using the concept of Hilbert spaces, we derive a condition under which the predictive relationships between two vectors are invariant to the selection of a bivariate or trivariate framework. In more detail, we provide a condition under which the finding of causality (improved predictability at forecast horizon 1) respectively non‐causality of Y for X is unaffected if the information set is either enlarged or reduced by the information in a third vector Z . This result has a practical usefulness since it provides a guidance to validate the choice of the bivariate system { X , Y } in place of { X , Y , Z }. In fact, to test the ‘goodness’ of { X , Y } we should test whether Z Granger cause X not requiring the joint analysis of all variables in { X , Y , Z }. Copyright © 2002 John Wiley & Sons, Ltd.