Aldose reductase structures: implications for mechanism and inhibition

During chronic hyperglycaemia, elevated vascular glucose level causes increased flux through the polyol pathway, which induces functional and morphological changes associated with secondary diabetic complications. Inhibitors of aldose reductase (ARIs) have been widely investigated as potential therapeutic agents, but to date only epalrestat is successfully marketed for treatment of diabetic neuropathy, in Japan. Promising compounds during in vitro studies or in trials with animal models have failed to proceed beyond clinical trials and to everyday use, due to a lack of efficacy or adverse side effects attributed to lack of inhibitor specificity and likely inhibition of the related aldehyde reductase (ALR1). Knowledge of the catalytic mechanism and structures of the current inhibitors complexed with ALR2 are means by which more specific and tightly bound inhibitors can be discovered. This review will provide an overview of the proposed catalytic mechanism and the current state of structure-based drug design.     

Looking for structure in all the wrong places: Ramsey sentences, multiple realisability, and structure

‘Epistemic structural realism’ (ESR) insists that all that we know of the world is its structure, and that the ‘nature’ of the underlying elements remains hidden. With structure represented via Ramsey sentences, the question arises as to how ‘hidden natures’ might also be represented. If the Ramsey sentence describes a class of realisers for the relevant theory, one way of answering this question is through the notion of multiple realisability. We explore this answer in the context of the work of Carnap, Hintikka and Lewis. Both Carnap and Hintikka offer clear structuralist perspectives which, crucially, accommodate the openness inherent in theory change. Unfortunately there is little purchase for a viable form of realism in either case. Lewis’s approach, on the other hand, offers more scope for realism but, as we shall see, concerns arise as to whether a relevant form of structuralism can be maintained. In particular his thesis of Ramseyan humility undermines certain conceptions of scientific laws that the structural realist might naturally cleave to. Our overall conclusion is that the representational device of Ramsey sentence plus multiple realisability can accommodate either the structuralist or realist aspects of ESR but has difficulties capturing both.     

CSTX-9, a toxic peptide from the spider Cupiennius salei: amino acid sequence, disulphide bridge pattern and comparison with other spider toxins containing the cystine knot structure

CSTX-9 (68 residues, 7530.9 Da) is one of the most abundant toxic polypeptides in the venom of the wandering spider Cupiennius salei. The amino acid sequence was determined by Edman degradation using reduced and alkylated CSTX-9 and peptides generated by cleavages with endoproteinase Asp-N and trypsin, respectively. Sequence comparison with CSTX-1, the most abundant and the most toxic polypeptide in the crude spider venom, revealed a high degree of similarity (53% identity). By means of limited proteolysis with immobilised trypsin and RP-HPLC, the cystine-containing peptides of CSTX-9 were isolated and the disulphide bridges were assigned by amino acid analysis, Edman degradation and nanospray tandem mass spectrometry. The four disulphide bonds present in CSTX-9 are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7 (Cys₆-Cys₂₁, Cys₁₃-Cys₃₀, Cys₂₀-Cys₄₈, Cys₃₂-Cys₄₆). Sequence comparison of CSTX-1 with CSTX-9 clearly indicates the same disulphide bridge pattern, which is also found in other spider polypeptide toxins, e.g. agatoxins (ω-AGA-IVA, ω-AGA-IVB, μ-AGA-I and μ-AGA-VI) from Agelenopsis aperta, SNX-325 from Segestria florentina and curtatoxins (CT-I, CT-II and CT-III) from Hololena curta. CSTX-1/CSTX-9 belong to the family of ion channel toxins containing the inhibitor cystine knot structural motif. CSTX-9, lacking the lysine-rich C-terminal tail of CSTX-1, exhibits a ninefold lower toxicity to Drosophila melanogaster than CSTX-1. This is in accordance with previous observations of CSTX-2a and CSTX-2b, two truncated forms of CSTX-1 which, like CSTX-9, also lack the C-terminal lysine-rich tail. Received 23 July 2001; accepted 31 July 2001     

N-acetylmuramic acid 6-phosphate lyases (MurNAc etherases): role in cell wall metabolism, distribution, structure, and mechanism

MurNAc etherases cleave the uniqued-lactyl ether bond of the bacterial cell wall sugar N-acetylmuramic acid (MurNAc). Members of this newly discovered family of enzymes are widely distributed among bacteria and are required to utilize peptidoglycan fragments obtained either from the environment or from the endogenous cell wall (i.e., recycling). MurNAc etherases are strictly dependent on the substrate MurNAc possessing a free reducing end and a phosphoryl group at C6. They carry a single conserved sugar phosphate isomerase/sugar phosphate- binding (SIS) domain to which MurNAc 6-phosphate is bound. Two subunits form an enzymatically active homodimer that structurally resembles the isomerase module of the double-SIS domain protein GlmS, the glucosamine 6-phosphate synthase. Structural comparison provides insights into the two-step lyase-type reaction mechanism of MurNAc etherases: β-elimination of the D-lactic acid substituent proceeds through a 2,3-unsaturated sugar intermediate to which water is subsequently added. Received 31 August 2007; received after revision 12 October 2007; accepted 1 November 2007     

Genetic variation in the New World: Ancient teeth,bone, and tissue as sources of DNA

Examination of ancient and contemporary Native American mtDNA variation via diagnostic restriction sites and the 9-pb Region V deletion suggests a single wave of migration into the New World. This is in contrast to data from Torroni et al.³⁴ which suggested two waves of migration into the New World (the NaDene and Amerind). All four founding lineage types are present in populations in North, Central, and South America suggesting that all four lineages came over together and spead throughout the New World. Ancient Native American DNA shows that all four lineages were present before European contact in North America, and at least two were present in South America. The presence of all four lineages in the NaDene and the Amerinds argues against separate migrations founding these two groups, although admixture between the groups is still a viable explanation for the presence of all four types in the NaDene.     

The neuroligin and neurexin families: from structure to function at the synapse

Proper brain connectivity and neuronal transmission rely on the accurate assembly of neurotransmitter receptors, cell adhesion molecules and several other scaffolding and signaling proteins at synapses. Several new exciting findings point to an important role for the neuroligin family of adhesion molecules in synapse development and function. In this review, we summarize current knowledge of the structure of neuroligins and neurexins, their potential binding partners at the synapse. We also discuss their potential involvement in several aspects of synapse development, including induction, specificity and stabilization. The implication of neuroligins in cognitive disorders such as autism and mental retardation is also discussed. Received 6 February 2006; received after revision 17 March 2006; accepted 26 April 2006     

Surface receptors and functional interactions of human natural killer cells: from bench to the clinic

The past 10years have witnessed dramatic progress in our understanding of how natural killer (NK) cells function and their role in innate immunity. Thanks to an array of inhibitory receptors specific for different HLA class I molecules, human NK cells can sense the decrease or loss of even single alleles at the cell surface. This represents a typical condition of a potential danger, i.e. the presence of tumor or virally infected cells. NK cell triggering and lysis of these cells is mediated by several activating receptors and coreceptors that have recently been identified and cloned. While normal cells are usually resistant to NK-mediated attack, a remarkable exception is represented by dendritic cells (DCs). In their immature form they are susceptible to NK-mediated lysis because of the expression of low levels of surface HLA class I molecules. The process of DC maturation (mDCs) is characterized by the surface expression of high levels of HLA class I molecules. Accordingly, mDCs become resistant to NK cells. A recent major breakthrough highlighted the role played by donor NK cells in allogenic bone marrow transplantation to cure acute myeloid leukemias. Alloreactive NK cells derived from donor hematopoietic precursors not only prevented leukemic relapses, but also prevented graft rejection and graft-versus-host disease.Received 12 March 2003; received after revision 18 April 2003; accepted 30 April 2003     

Term premia and the maturity composition of the Federal debt: new evidence from the term structure of interest rates

This paper models bond term premia empirically in terms of the maturity composition of the federal debt and other observable economic variables in a time‐varying framework with potential regime shifts. We present regression and out‐of sample forecasting results demonstrating that information on the age composition of the Federal debt is useful for forecasting term premia. We show that the multiprocess mixture model, a multi‐state time‐varying parameter model, outperforms the commonly used GARCH model in out‐of‐sample forecasts of term premia. The results underscore the importance of modelling term premia, as a function of economic variables rather than just as a function of asset covariances as in the conditional heteroscedasticity models. Copyright © 2001 John Wiley & Sons, Ltd.     

Signs, toy models, and the a priori: from Helmholtz to Wittgenstein

The Marburg neo-Kantians argue that Hermann von Helmholtz’s empiricist account of the a priori does not account for certain knowledge, since it is based on a psychological phenomenon, trust in the regularities of nature. They argue that Helmholtz’s account raises the ‘problem of validity’ (Gültigkeitsproblem): how to establish a warranted claim that observed regularities are based on actual relations. I reconstruct Heinrich Hertz’s and Ludwig Wittgenstein’s Bild theoretic answer to the problem of validity: that scientists and philosophers can depict the necessary a priori constraints on states of affairs in a given system, and can establish whether these relations are actual relations in nature. The analysis of necessity within a system is a lasting contribution of the Bild theory. However, Hertz and Wittgenstein argue that the logical and mathematical sentences of a Bild are rules, tools for constructing relations, and the rules themselves are meaningless outside the theory. Carnap revises the argument for validity by attempting to give semantic rules for translation between frameworks. Russell and Quine object that pragmatics better accounts for the role of a priori reasoning in translating between frameworks. The conclusion of the tale, then, is a partial vindication of Helmholtz’s original account.     

The opsins of the vertebrate retina: insights from structural,biochemical, and evolutionary studies

The vertebrate retina contains several classes of visual pigments responsible for such diverse functions as image- and nonimage-forming vision, the entrainment of circadian cycles, and the pupilary light response. With vision being vital to the survival of many species, the elucidation of the structural and biochemical properties of visual pigments has been the focus of a large body of research that has led to rapid advances in the field of photoreception. In this review, the current understanding of the structure, function, biochemistry, and evolution of the opsins that make up the photopigments in the vertebrate retina will be reviewed. These include the rod and cone opsins, melanopsin, RGR, peropsin, and VA-opsin. The goal is to highlight important questions that have been answered and to define some of the remaining questions in the field that will provide future directions for research.     

Molecular parasitology: Progress towards the development of vaccines for malaria,filariasis, and schistosomiasis

Summary Advances in molecular biology have allowed for the identification of potential vaccine candidates against several parasitic diseases. Antigens from various life stages ofPlasmodium andSchistosoma species and filarial worms have been cloned, sequenced and tested as vaccines. Results to date in animal models have been promising. Modest levels of protection against experimental human malaria have been obtained using both sporozoite and blood-stage antigens. However, a greater understanding of the mechanisms which lead to immunity against parasites is required before effective vaccines can be developed.     

Copernicus and Fracastoro: the dedicatory letters to Pope Paul III, the history of astronomy, and the quest for patronage

Copernicus’s De revolutionibus (1543) and Girolamo Fracastoro’s Homocentrica (1538) were both addressed to Pope Paul III (1534-1549). Their dedicatory letters represent a rhetorical exercise in advocating an astronomical reform and an attempt to obtain the papal favour. Following on from studies carried out by Westman (1990) and Barker & Goldstein (2003), this paper deals with cultural, intellectual and scientific motives of both texts, and aims at underlining possible relations between them, such as that Copernicus knew of Fracastoro’s Homocentrica, and that at least part of the rhetorical strategy laid out in De revolutionibus’s dedicatory letter can be read as a sophisticated response to Fracastoro’s arguments.     

Marine antitumor agents: 14-deoxycrassin and pseudoplexaurol,new cembranoid diterpenes from the Caribbean gorgonianPseudoplexaura porosa

Two new cytotoxic antitumor diterpenoids of the cembrane class, named 14-deoxycrassin (3) and pseudoplexaurol (4), have been isolated from the Caribbean gorgonian octocoralPseudoplexaura porosa. The structure of lactone3, possessing the infrequently encountered -methylene--lactone ring, has been established from spectral and chemical data and that of alcohol4 has been established from spectral data.     

Chromatin assembly during S phase: contributions from histone deposition, DNA replication and the cell division cycle

During S phase of the eukaryotic cell division cycle, newly replicated DNA is rapidly assembled into chromatin. Newly synthesised histones form complexes with chromatin assembly factors, mediating their deposition onto nascent DNA and their assembly into nucleosomes. Chromatin assembly factor 1, CAF-1, is a specialised assembly factor that targets these histones to replicating DNA by association with the replication fork associated protein, proliferating cell nuclear antigen, PCNA. Nucleosomes are further organised into ordered arrays along the DNA by the activity of ATP-dependent chromatin assembly and spacing factors such as ATP-utilising chromatin assembly and remodelling factor ACF. An additional level of controlling chromatin assembly pathways has become apparent by the observation of functional requirements for cyclin-dependent protein kinases, casein kinase II and protein phosphatases. In this review, we will discuss replication-associated histone deposition and nucleosome assembly pathways, and we will focus in particular on how nucleosome assembly is linked to DNA replication and how it may be regulated by the cell cycle control machinery.     

Serotonin is localized in endothelial cells of coronary arteries and released during hypoxia: A possible new mechanism for hypoxia-induced vasodilatation of the rat heart

Summary In this report we demonstrate the immunocytochemical localization of serotonin in endothelial cells of rat coronary vessels and a significant increase in the release of serotonin into the perfusate of Langendorff rat heart preparations during hypoxia. It is suggested that serotonin, localized in endothelial cells, is released during hypoxia and could provide part of a pathophysiological mechanism for vasodilatation to protect the heart from damage due to hypoxia.This research was supported by the British Heart Foundation and the excellent technical assistance of Jon Bokor is gratefully acknowledged.     

Assessing the Macroeconomic Forecasting Performance of Boosting: Evidence for the United States,the Euro Area and Germany

The use of large datasets for macroeconomic forecasting has received a great deal of interest recently. Boosting is one possible method of using high‐dimensional data for this purpose. It is a stage‐wise additive modelling procedure, which, in a linear specification, becomes a variable selection device that iteratively adds the predictors with the largest contribution to the fit. Using data for the United States, the euro area and Germany, we assess the performance of boosting when forecasting a wide range of macroeconomic variables. Moreover, we analyse to what extent its forecasting accuracy depends on the method used for determining its key regularization parameter: the number of iterations. We find that boosting mostly outperforms the autoregressive benchmark, and that K‐fold cross‐validation works much better as stopping criterion than the commonly used information criteria. Copyright © 2014 John Wiley & Sons, Ltd.     

The mutator phenotype theory of carcinogenesis and the complex histopathology of tumours: support for the theory from the independent occurrence of nuclear abnormality,loss of specialisation and invasiveness among occasional neoplastic lesions

The mutator phenotype theory of carcinogenesis suggests that genetic instability is an early and essential part of tumour development. This instability provides for substantially random cell-to-cell genomic variation (genomic heterogeneity) to arise among cells of individual tumours. Genetically unstable cells then produce 'successful' clones of cells with the necessary mutations for malignant behaviour. In a previous paper (Bignold L. P., Cell. Mol. Life Sci. 2002; 59: 950-958), it was pointed out that a population of cells which is heterogeneous for behaviour-related genes may well also be heterogeneous for morphology-related genes. This would result in cellular pleomorphism among cells of individual tumours, and so explain this almost universal characteristic of solid malignancies. paragraph sign If the concept of random genomic variability applies fully to the histopathology of tumours, then most tumours should show a mixture of neoplastic features, especially nuclear atypia, loss of specialised function (such as loss of production of mucus by glandular cells) and invasiveness. However, occasional lesions might be expected to occur which show these characteristics independently. That is, lesions should exist which exhibit one or two of the three characteristics of neoplasms without the other(s). paragraph sign This paper identifies, among human tumours, lesions which show independence of these characteristics. Two of the examples discussed are a Bowenoid solar keratosis that shows severe nuclear atypia, but no apparent loss of specialisation and no invasiveness. On the other hand, anaplastic small cell carcinoma of the lung often exhibits marked loss of differentiation, very aggressive invasion and metastasis, but little nuclear pleomorphism. paragraph sign These examples are considered to provide further support for the importance of the mutator phenotype to the pathogenesis of neoplasia.     

Arresting the mitotic oscillator and the control of cell proliferation: insights from a cascade model for cdc2 kinase activation

We consider a minimal cascade model previously proposed¹¹ for the mitotic oscillator driving the embryonic cell division cycle. The model is based on a bicyclic phosphorylation-dephosphorylation cascade involving cyclin and cdc2 kinase. By constructing stability diagrams showing domains of periodic behavior as a function of the maximum rates of the kinases and phosphatases involved in the two cycles of the cascade, we investigate the role of these converter enzymes in the oscillatory mechanism. Oscillations occur when the balance of kinase and phosphatase rates in each cycle is in a range bounded by two critical values. The results suggest ways to arrest the mitotic oscillator by altering the maximum rates of the converter enzymes. These results bear on the control of cell proliferation.     

Changes in calpastatin localization and expression during calpain activation: a new mechanism for the regulation of intracellular Ca<Superscript>2+</Superscript>-dependent proteolysis

The amount of calpastatin directly available in cytosol is under the control of [Ca²⁺] and [cyclic AMP]. Prolonged calpain activation also promotes degradation of calpastatin. The fluctuation of calpastatin concentration in cell soluble fraction is accompanied by an initial decrease in calpastatin gene expression, followed by a fivefold increase in its expression when the inhibitor protein is degraded. This process can be conceptualized as a mechanism to regulate calpastatin availability in the cell. This conclusion is supported by the fact that calpain, the other component of this proteolytic system, undergoes changes in its levels of expression in a much more limited manner. Furthermore, this process can be observed both in cells exposed to different natural stimuli, or in other cell lines. Modification of calpastatin gene expression might represent a new tool for the in vivo control of the regulatory machinery required for the modulation of Ca²⁺-dependent proteolysis.Received 18 July 2003; received after revision 3 September 2003; accepted 23 September 2003