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  • 2010-2014  (99)
  • 1995-1999  (42)
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  • 1
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  • 3
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 500 (2013): 453–457, doi:10.1038/nature12326.
    Description: Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
    Description: This work was supported by Genoscope-CES (where most of the sequencing was performed), by US National Science Foundation grants MCB-0821956 and MCB-1121334 to I.A., by German Research Foundation grant HA 5163/2-1 to O.H., by grant 11.G34.31.0008 fromthe Ministry of Education and Science of the Russian Federation to A.S.K., by grant NSF CAREER number 0644282 to M.K., by US National Science Foundation grant MCB-0923676 to D.B.M.W., by FRFC grant 2.4.655.09.F from the Belgian Fonds National de la Recherche Scientifique (FNRS) and a start-up grant from the University of Namur to K.V.D.; J.F.F. and K.V.D. thank also J.-P. Descy (University of Namur) for funding support.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 4
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The homopentameric B subunit of verotoxin 1 (VT1) binds to the glycosphingolipid receptor globotriaosylceramide (Gb3). We produced mutants with alanine substitutions for residues found near the cleft between adjacent subunits. Substitution of alanine for phenylalanine 30 (Phe-30) resulted in a fourfold reduction in B subunit binding affinity for Gb3 and a 10-fold reduction in receptor density in a solid-phase binding assay. The interaction of wild-type and mutant B subunits with Pk trisaccharide in solution was examined by titration microcalorimetry. The carbohydrate binding of the mutant was markedly impaired compared with that of the wild type and was too weak to allow calculation of a binding constant. These results demonstrate that the mutation significantly impaired the carbohydrate-binding function of the B subunit. To ensure that the mutation had not caused a significant change in structure, the mutant B subunit was crystallized and its structure was determined by X-ray diffraction. Difference Fourier analysis showed that its structure was identical to that of the wild type, except for the substitution of alanine for Phe-30. The mutation was also produced in the VT1 operon, and mutant holotoxin was purified to homogeneity. The cytotoxicity of the mutant holotoxin was reduced by a factor of 105 compared to that of the wild type in the Vero cell cytotoxicity assay. The results suggest that the aromatic ring of Phe-30 plays a major role in binding of the B subunit to the Galα1-4Galβ1-4Glc trisaccharide portion of Gb3. Examination of the VT1 B crystal structure suggests two potential carbohydrate-binding sites which lie on either side of Phe-30.
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  • 5
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The Verotoxin 1 (VT1) B subunit binds to the glycosphingolipid receptor globotriaosylceramide (Gb3). Receptor-binding specificity is associated with the terminally linked Galα(1–4) Galβ disaccharide sequence of the receptor. Recently, three globotriose (Galα[1–4] Galβ [1–4] Glcβ) binding sites per B-subunit monomer were identified by crystallography. Two of these sites (sites I and II) are located adjacent to phenylalanine-30. Site I was originally predicted as a potential Gb3 binding site on the basis of sequence conservation, and site II was additionally predicted based on computer modelling and receptor docking. The third (site III) was also identified by crystallography and is located at the N-terminal end of the α-helix. To determine the biological significance of sites II and III, and to support our previous findings of the significance of site I, we examined the binding properties and cytotoxicity of VT1 mutants designed to block Gb3 binding at each site selectively. The Scatchard analysis of saturation-binding data for each mutant revealed that only the amino acid substitutions predicted to affect site I (D-17E) or site II (G-62T) caused reductions in the binding affinity and capacity of VT1 for Gb3. Similarly, those mutations at sites I and II also caused significant reductions in both Vero and MRC-5 cell cytotoxicity (by seven and five logs, respectively, for G-62T and by four and two logs, respectively, for D-17E). In contrast, the substitution of alanine for W-34 at site III did not reduce the high-affinity binding of the B subunit, despite causing a fourfold reduction in the receptor-binding capacity. The corresponding mutant W-34A holotoxin had a two-log reduction in cytotoxicity on Vero cells and no statistically significant reduction on MRC-5 cells. We conclude that the high-affinity receptor binding most relevant for cell cytotoxicity occurs at sites I and II. In contrast, site III appears to mediate the recognition of additional Gb3 receptor epitopes but with lower affinity. Our results support the significance of the indole ring of W-34 for binding at this site.
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  • 6
    ISSN: 0948-5023
    Keywords: Gibbs-Ensemble MD ; Monte Carlo ; Particle exchange ; Adsorption
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We discuss a novel simulation method suitable for simulating phenomena involving particle exchange. The method is a molecular dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been developed some years ago for the direct simulation of phase equilibria in fluid systems. The idea is to have two separate simulation boxes, which can exchange particles or molecules in a thermodynamically consistent fashion. We discuss the general idea of the Gibbs-Ensemble Molecular Dynamics technique and present examples for different simple atomic and molecular fluids. Specifically we will discuss Gibbs-Ensemble Molecular Dynamics simulations of gas-liquid and liquid-solid equilibria in Lennard-Jones systems and in hexane as well as an application of the method to adsorption.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Journal of molecular modeling 2 (1996), S. 330-340 
    ISSN: 0948-5023
    Keywords: MD simulation ; Micellar system ; Force field ; Water models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We present the results of an atomistic molecular dynamics simulation based on the AMBER/OPLS force field applied to segments of isolated one-dimensional micelles, 2,3,6,7,10,11-Hexa-(1,4,7-Trioxaoctyl)-Triphenylene, in aqueous solution using the SPC/E water model. The quantities which we study include the intra-micellar monomer structure, e.g., the equilibrium monomer-monomer separation along the micelle, the micelle-water interface, which yields the effective micellar diameter, and the flexibility of the micelle in terms of its persistence length as a function of temperature. In addition, we determine the micelle size distribution at low concentration via the free enthalpy gain per monomer-monomer contact using a hydration shell model in combination with thermodynamic integration. Finally, we locate the isotropic-to-nematic transition by using our results as input for an analytical model.
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  • 8
    ISSN: 1573-739X
    Keywords: Nitric oxide radical ; •NO, scavenging ; Thiol ; S–nitrosothiol (electrochemical) ; NO sensing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A new method for the quantification of the nitric oxide (•NO) scavenging activity of compounds in aqueous solutions is described using an amperometric •NO sensor. After correction for the spontaneous degradation of •NO, second–order rate kinetics of the scavenging reaction are observe. The rate constant for hemoglobin found with this method is comparable with that found with an established spectrophotometric method. To demonstrate the capability of the method, several sulfur–containing compounds were tested (GSH, GSSG, S–methyl glutathione, N–acetyl cysteine, lipoic acid and dihydrolipoic acid). Of these compounds, only those that contained a thiol group displayed a considerable •NO scavenging activity.
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  • 9
    ISSN: 0899-0042
    Keywords: lipoic acid ; reduction ; dihydrolipoamide dehydrogenase ; antioxidant ; enantiomers ; Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: For the antioxidant effect of lipoic acid, reduction to dihydrolipoic acid is considered to be important. Dihydrolipoamide dehydrogenase (LipHD) preferentially reduces R-lipoic acid and in a subsequent reaction, the R-dihydrolipoic acid formed may non-enzymatically reduce S-lipoic acid. Using circular dichroism (CD) spectroscopy, the second order rate constant of the latter reaction was determined (k2 = 15 M-1 sec-1). In vitro, it was found that S-lipoic acid is reduced by LipDH using R-lipoic acid as a catalyst. The non-enzymatic dithiol-disulfide reaction leads to synergistic reduction of the enantiomers which can explain the higher antioxidant activity of racemic lipoic acid found in vivo (Maitra et al. Biochem. Biophys. Res. Commun. 221:422-429, 1996) in comparison to the enantiomers. Lipoic acid is therapeutically active in several diseases via antioxidant activity. These findings suggest that racemic lipoic acid can be therapeutically more active than the separate enantiomers. Chirality 9:362-366, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, N.Y. : Wiley-Blackwell
    Journal of Cellular Biochemistry 59 (1995), S. 219-222 
    ISSN: 0730-2312
    Keywords: Detection molecular markers ; ovarian cancer ; prevention ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: More than 90% of epithelial ovarian cancers arise from single cells. Malignant transformation can be associated with a number of molecular alterations including upregulation of tyrosine kinases and phosphatases, physiologic activation of ras, mutation of p53, amplification of myc, and increased activity of matrix metalloproteinases 2 and 9. Proliferation of transformed epithelial cells can be enhanced through the persistence of autocrine growth stimulation by TGF-α, loss of autocrine growth inhibition by TGF-β, as well as paracrine growth stimulation by macrophage derived cytokines and OCAF, a novel lyso-phospholipid. Ascites tumor cells retain responsiveness to growth inhibition by TGF-β which induces apoptosis in malignant ovarian epithelial cells, but not in normal ovarian surface epithelium.Proliferation of surface epithelial cells following ovulation my contribute to the pathogenesis of ovarian cancer. Use of oral contraceptives that suppress evulation has been associated with reduced risk of ovarian cancer in later life. Retinoids also deserve further evaluation for chemoprevention. Treatement with fenretinide was associated with decreased incidence of ovarian cancer. Additive or synergistic inhibition of ovarian tumor cell proliferation has been observed with TGF-β in combination with all-trans-retinoic acid.Early detection of ovarian cancer could improve survival. Transvaginal sonography (TVS) and serum markers such as CA-125 have been evaluated in multiple clinical trials. The former lacks adequate specificity, whereas the latter is not sufficiently sensitive. Use of multiple serum markers can improve sensitivity. A combination of CA-125, M-CSF and OVX-1 has detected 〉 95% of Stage I ovarian cancers. If similar results are obtained with different data sets, multiple serum markers could be used to trigger the performance of TVS, providing a potentially cost effective screening strategy. Prospective trials will be required to demonstrate that screening for early stage ovarian actually impacts on survival.
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