Synthesis and physicochemical properties of 2'-deoxy-2',2'-difluoro-beta-D-ribofuranosyl and 2'-deoxy-2',2'-difluoro-alpha-D-ribofuranosyl oligonucleotides

We present procedures for nucleoside and oligonucleotide synthesis, binding affinity (Tm) and structural analysis (CD spectra) of 2'-deoxy-2',2'-difluoro-alpha-D-ribofuranosyl and 2'-deoxy-2',2'-difluoro-beta-D-ribofuranosyl oligothymidylates. Possible reasons for the thermal instability of duplexes formed between these compounds and RNA or DNA targets are discussed.     

The inhibitory activities of 2-acetamido-2,3-dideoxy-D-hex-2-enonolactones on 2-acetamido-2-deoxy-beta-D-glucosidase.

Treatment of 2-acetamido-2-deoxy-D-mannono-1,4-lactone with dicyclohexylamine in ethanolic solution afforded an unsaturated 1,4-lactone, 2-acetamido-2,3-dideoxy-D-erythro-hex-2-enono-1,4-lactone (1), in good yield. 2-Acetamido-2,3-dideoxy-D-threo-hex-2-enono-1,4-lactone (2) was similarly prepared from 2-acetamido-2-deoxy-D-galactono-1,4-lactone. An unsaturated 1,5-lactone, 2-acetamido-2,3-dideoxy-D-threo-hex-2-enono-1,5-lactone (4), was obtained through the oxidation of 2-acetamido-2-doexy-4,6-0-isopropylidene-D-galactopyranose with silver carbonate on Celite, followed by mild hydrolysis. The inhibitory activity of four isomeric 2-acetamido-2,3-dideoxy-D-hex-2-enonolactones [1, 2, 4, and 2-acetamido-2,3-dideoxy-D-erythro-hex-2-enono-1,5-lactone (3)] was assayed against 2-acetamido-2-deoxy-beta-D-glucosidase from bull epididymis. Only the erythro lactones 1 and 3 are weak competitive inhibitors, whereas the threo lactones 2 and 4 are practically inactive. The 1,4-lactone 1 inhibited 2-acetamido-2-deoxy-beta-D-glucosidase more strongly than the 1,5-lactone 3. The lactones 1-4 were found to be quite stable in aqueous solution or under inhibitory-assay conditions. In addition, two 2-acetamido-2-deoxy-D-glycals, 2-acetamido-1,5-anhydrohex-1-enitol (7) were tested; both are 10 times as active as 1.     

Trimeric architecture of homomeric P2X2 and heteromeric P2X1+2 receptor subtypes

Of the three major classes of ligand-gated ion channels, nicotinic receptors and ionotropic glutamate receptors are known to be organized as pentamers and tetramers, respectively. The architecture of the third class, P2X receptors, is under debate, although evidence for a trimeric assembly is accumulating. Here we provide biochemical evidence that in addition to the rapidly desensitising P2X1 and P2X3 receptors, the slowly desensitising subtypes P2X2, P2X4, and P2X5 are trimers of identical subunits. Similar (heteromeric) P2X subunits also formed trimers, as shown for co-expressed P2X1 and P2X2 subunits, which assembled efficiently to a P2X1+2 receptor that was exported to the plasma membrane. In contrast, P2X6 subunits, which are incapable of forming functional homomeric channels in Xenopus oocytes, were retained in the ER as apparent tetramers and high molecular mass aggregates. Altogether, we conclude from these data that a trimeric architecture is the structural hallmark of functional homomeric and heteromeric P2X receptors.     

BCL2-CISD2

CISD2, an ER BCL2-associated autophagy regulator also known as NAF-1, is responsible for the human degenerative disorder Wolfram Syndrome 2. In order to interrogate the physiological role of CISD2 we generated and characterized the Cisd2 gene deletion in mice. Cisd2 null mice manifest significant degeneration in skeletal muscle tissues, which is accompanied with augmented autophagy, dysregulated Ca²⁺ homeostasis and elongated mitochondria. Our findings describe a novel role for BCL2-CISD2 in the homeostatic maintenance of skeletal muscle. It remains to be elucidated how and if the antagonism of the BECN1 autophagy-initiating complex and modulation of ER Ca²⁺ homeostasis by BCL2-CISD2 are interconnected.     

Effect Sizes for 2×2 Contingency Tables

Sample size calculations are an important part of research to balance the use of resources and to avoid undue harm to participants. Effect sizes are an integral part of these calculations and meaningful values are often unknown to the researcher. General recommendations for effect sizes have been proposed for several commonly used statistical procedures. For the analysis of tables, recommendations have been given for the correlation coefficient for binary data; however, it is well known that suffers from poor statistical properties. The odds ratio is not problematic, although recommendations based on objective reasoning do not exist. This paper proposes odds ratio recommendations that are anchored to for fixed marginal probabilities. It will further be demonstrated that the marginal assumptions can be relaxed resulting in more general results.     

Stereospecific 2'-amination and 2'-chlorination of adenosine by Actinomadura in the biosynthesis of 2'-amino-2'-deoxyadenosine and 2'-chloro-2'-deoxycoformycin

2'-Amino-2'-deoxyadenosine and 2'-chloro-2'-deoxycoformycin (2'-CldCF) are two nucleoside antibiotics produced by Actinomadura. The biosynthesis of these two nucleoside antibiotics has been studied by the addition of [U-14C]adenosine with or without unlabeled adenine to cultures of Actinomadura. By this experimental approach, it is possible to demonstrate that adenosine is the direct precursor for the biosynthesis of 2'-amino-2'-deoxyadenosine and 2'-CldCF. These conclusions are based on the observation that the percentage distribution of 14C in the aglyconic and pentofuranosyl moieties of 2'-amino-2'-deoxyadenosine and 2'-CldCF were similar to the distribution of 14C in the adenine and ribosyl moieties of the [U-14C]adenosine (i.e., 48:52) added to cultures of Actinomadura. Experimentally, the percentage distribution of 14C in the (i) adenine:2-amino-2-deoxy-beta-D-ribofuranose of 2'-amino-2'-deoxyadenosine is 51:49; (ii) 8-(R)-3,6,7,8-tetrahydroimidazo[4,5-d]-[1,3-diazepin-8-o1]:2 -chloro-2- beta-D-ribofuranose of 2'-CldCF is 45:55; and (iii) adenine:ribose of the adenosine isolated from the RNA of Actinomadura is 42:58. Further proof that adenosine is the direct precursor for the biosynthesis 2'-amino-2'-deoxyadenosine and 2'-CldCF was demonstrated by the addition of 75 mumol of unlabeled adenine together with [U-14C]adenosine to nucleoside-producing cultures of Actinomadura. The percentage distribution of 14C in the aglycon and the sugar moieties of 2'-amino-2'-deoxyadenosine and 2'-CldCF were 46:54 and 47:53, respectively; the percentage distribution of 14C in the adenine and ribose moieties of the adenosine isolated from the RNA of Actinomadura was 51:49. These data show that the hydroxyl on C-2' of the ribosyl moiety of adenosine undergoes a replacement by a 2'-amino or a 2'-chloro group to form 2'-amino-2'-deoxyadenosine or 2'-CldCF with retention of stereconfiguration at C-2'. Finally, Actinomadura can utilize inorganic chloride from the medium as demonstrated by the isolation of [36Cl]2'-CldCF following the addition of [36Cl]chloride to the culture medium. Mechanisms for the regioselective modification of the C-2' hydroxyl group and stereospecific insertion of the amino and chloro groups are discussed.     

E2A and E2-2 are subunits of B-cell-specific E2-box DNA-binding proteins.

A class of helix-loop-helix (HLH) proteins, including E2A (E12 and E47), E2-2, and HEB, that bind in vitro to DNA sequences present in the immunoglobulin (Ig) enhancers has recently been identified. E12, E47, E2-2, and HEB are each present in B cells. The presence of many different HLH proteins raises the question of which of the HLH proteins actually binds the Ig enhancer elements in B cells. Using monoclonal antibodies specific for both E2A and E2-2, we show that both E2-2 and E2A polypeptides are present in B-cell-specific Ig enhancer-binding complexes. E2-box-binding complexes in pre-B cells contain both E2-2 and E2A HLH subunits, whereas in mature B cells only E2A gene products are present. We show that the difference in E2-box-binding complexes in pre-B and mature B cells may be caused by differential expression of E2A and E2-2.     

The analysis of stratified 2 x 2 contingency tables

We consider the problem of testing for independence against the consistent superiority of one treatment over another when the response variable is binary and is compared across two treatments in each of several strata. Specifically, we consider the randomized clinical trial setting. A number of issues arise in this context. First, should tables be combined if there are small or zero margins? Second, should one assume a common odds ratio across strata? Third, if the odds ratios differ across strata, then how does the standard test (based on a common odds ratio) perform? Fourth, are there other analyzes that are more appropriate for handling a situation in which the odds ratios may differ across strata? In addressing these issues we find that the frequently used Cochran–Mantel–Haenszel test may have a poor power profile, despite being optimal when the odds ratios are common. We develop novel tests that are analogous to the Smirnov, modified Smirnov, convex hull, and adaptive tests that have been proposed for ordered categorical data. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

TXA2/PGI2与心血管疾病

血栓素(Thromboxane,TXA2)和前列环素(Prostacyclin,PGI2)均为花生四烯酸的代谢物,是前列腺素(Prostaglandins,PGs)中生物活性最强的一对。在正常情况下,二者在体内保持一定的平衡,相互拮抗、相互协调,共同维持血液循环畅通,与心血管疾病关系密切。本文即就其生物特性及与心血管病的关系等进行综述,对人们全面认识TXA2/PGI2具有一定的参考价值。     

Kinetic studies on partially liganded species of carboxyhemoglobin: alpha 2 CO beta 2 and alpha 2 beta 2CO

The valency hybrids of Hb A, alpha 2CO beta 2+, and alpha 2+ beta 2CO have been prepared by a new high pressure liquid chromatography method, and the kinetics of their CO-combination and dissociation reactions have been studied by double mixing and microperoxidase methods. Both reactions are biphasic. The slow phase in CO-combination and the fast phase in CO-dissociation are due to the reactions of alpha CO2 beta T2 or alpha 2 beta 2CO,T. The fast phase in CO-combination reaction has two components, one due to the dimers of the hybrid and the other due to the R-state tetramer. Immediately after the reduction of the valency hybrids, the overall system is represented by the equation: 2 alpha CO beta in equilibrium alpha 2CO beta 2R in equilibrium alpha 2CO beta 2T or (formula: see text) If the solutions are aged for 3-11 s, the R-state population is reduced gradually to a very small size, and the main species after 11 s of aging are dimers and T-state tetramers. Analysis of the kinetic data indicates slow R in equilibrium T equilibria in the absence of phosphates and significant dissociation of the T-state tetramer. It is concluded that the subunit contacts alpha 1-beta 2 (or alpha 2-beta 1) are impaired seriously in the hybrids. Very slow R in equilibrium T relaxation makes these hybrids unlikely intermediates in the sequential binding of CO to Hb tetramer.     

DNA polymerase recognition of 2'-deoxy-2'-fluoroarabinonucleoside 5'-triphosphates (2'F-araNTPs)

We examined the ability of 2'-deoxy-2'-fluroarabinonucleoside 5'-triphosphates (2'F-araNTPs) to serve as substrates of various DNA polymerases. In addition, we also examined the ability of these polymerases to accept DNA-FANA (2'-deoxy-2'-fluoroarabinonucleic acids) chimeras as template strands while synthesizing a DNA or FANA-DNA complementary strand. We provide preliminary data demonstrating that 2'F-araNTPs are indeed substrates of several DNA polymerases, and that FANA-DNA chimeric templates are generally well recognized by these polymerase enzymes.     

Exact sample size needed to detect dependence in 2 x 2 x 2 tables

In the Georgia Centenarian Study (Poon et al., Exceptional Longevity, 2006), centenarian cases and young controls are classified according to three categories (age, ethnic origin, and single nucleotide polymorphisms [SNPs] of candidate longevity genes), where each factor has two possible levels. Here we provide methodologies to determine the minimum sample size needed to detect dependence in 2 x 2 x 2 tables based on Fisher's exact test evaluated exactly or by Markov chain Monte Carlo (MCMC), assuming only the case total L and the control total N are known. While our MCMC method uses serial computing, parallel computing techniques are employed to solve the exact sample size problem. These tools will allow researchers to design efficient sampling strategies and to select informative SNPs. We apply our tools to 2 x 2 x 2 tables obtained from a pilot study of the Georgia Centenarians Study, and the sample size results provided important information for the subsequent major study. A comparison between the results of an exact method and those of a MCMC method showed that the MCMC method studied needed much less computation time on average (10.16 times faster on average for situations examined with S.E. = 2.60), but its sample size results were only valid as a rule for larger sample sizes (in the hundreds).     

2 x 2 kappa coefficients: measures of agreement or association

Two general but different contexts in which kappa might be used are defined: agreement and association. Two models, one for agreement and one for utility of association, are defined yielding different kappa coefficients and different sampling theory. Asymptotic results are derived for both models. Small-sample evaluations are presented for the model for agreement.     

Maximally selected chi2 statistics for k x 2 tables

It is common in epidemiologic analyses to summarize continuous outcomes as falling above or below a threshold. With such a dichotomized outcome, the usual chi2 statistics for association or trend can be used to test for equality of proportions across strata of the study population. However, if the threshold is chosen to maximize the test statistic, the nominal chi2 reference distributions are incorrect. In this paper, the asymptotic distributions of maximally selected chi2 statistics for association and for trend for the k x 2 table are derived. The methodology is illustrated with data from an AIDS clinical trial. The results of simulation experiments that assess the accuracy of the asymptotic distributions in moderate sample sizes are also reported.     

Rank Tests for the 2×2 Design with I Blocks

In this paper we suggest rank tests for main effects and for interaction when there are two factors and two levels within each factor and when, in addition, there are I blocks. The asymptotic distributions of the test statistics under H₀ are derived. The application of the tests is illustrated by an example and a simulation study investigates size and power of the tests.     

Stereospecific formation of alpha-hydroxycarboxylato oxo peroxo complexes of vanadium(V). Crystal structure of (NBu4)2[V2O2(O2)2(L-lact)2] x 2H2O and (NBu4)2[V2O2(O2)2(D-lact)(L-lact)] x 2H2O

An overview of structurally characterized alpha-hydroxycarboxylatodioxo- and alpha-hydroxycarboxylatooxoperoxovanadates(V) is presented and the geometric parameters of the V2O2 bridging core are discussed. The first case of a stereospecific formation of oxoperoxovanadates(V) is reported: The crystal structures of the isomeric compounds (NBu4)2[V2O2(O2)2(L-lact)2] x 2H2O and (NBu4)2[V2O2(O2)2(D-lact)(L-lact)] x 2H2O (lact = C3H4O3(2-), the anion of the lactic acid) differ mainly in the arrangement of the V2O2 core and in mutual orientation of the V=O bonds. The complexes with achiral ligands adopt the same structural type as the complexes formed from a racemic mixture of a chiral ligand, while the structure obtained using an enantiopure L,L-hydroxycarboxylate is different.     

Crystal structures of O-acetylated 2-acylamino-2-deoxy-D-galactose derivatives

The X-ray structures of 1,3,4,6-tetra-O-acetyl-2-deoxy-alpha-D-galactopyranoside derivatives with four different 2-(acylamino) substituents have been determined with Mo K(alpha) radiation at 123 K. The structure of the 2-acetylamino derivative and of its acyl-homologs with a 2-(propanoylamino)-, 2-(butanoylamino)-, and 2-(2-methyl-propanoylamino)-group crystallized in the monoclinic space group C2. The pyranose unit of all compounds has the usual 4C(1) shape. The different orientations of the 6-O-acetyl-groups are discussed. Conformations of the acylamino-group are compared to those found in the crystal structure of N-acetyl-alpha-D-galactosamine.     

TIN2 mediates functions of TRF2 at human telomeres

Telomeres are protective structures at chromosome ends and are crucial for genomic stability. Mammalian TRF1 and TRF2 bind the double-stranded telomeric repeat sequence and in turn are bound by TIN2, TANK1, TANK2, and hRAP1. TRF1 is a negative regulator of telomere length in telomerase-positive cells, whereas TRF2 is important for telomere capping. TIN2 was identified as a TRF1-interacting protein that mediates TRF1 function. We show here that TIN2 also interacts with TRF2 in vitro and in yeast and mammalian cells. TIN2 mutants defective in binding of TRF1 or TRF2 induce a DNA damage response and destabilize TRF1 and TRF2 at telomeres in human cells. Our findings suggest that the functions of TRF1 and TRF2 are linked by TIN2.     

Biogeneration of 2-phenylethanol and 2-phenylethylacetate important aroma components

Summary 2-Phenylethanol and 2-phenylethylacetate important aroma components are obtained in substantial amounts whenHansenula anomala CBS 110 andKloeckera saturnus CBS 5761 are grown with L-phenylalanine as sole nitrogen source. Up to 2 g/L of mixtures of alcohol and ester are obtained. While in the first microorganism the alcohol predominates, in the second the acetate is formed almost exclusively. Experiments with 1-¹³C-d-Glucose show complete incorporation of the label into the methyl group of the acetate.     

Decrease of H2O2 plasma membrane permeability during adaptation to H2O2 in Saccharomyces cerevisiae

Contrary to what is widely believed, recent published results show that H2O2 does not freely diffuse across biomembranes. The fast removal of H2O2 by antioxidant enzymes is able to generate a gradient if H2O2 is produced in a different compartment from that containing the enzymes (Antunes, F., and Cadenas, E. (2000) FEBS Lett. 475, 121-126). In this work, we extended these studies and tested whether an active regulation of biomembranes permeability characteristics is part of the cell response to oxidative stress. Using Saccharomyces cerevisiae as a model, we showed that: (a) H2O2 gradients across the plasma membrane are formed upon exposure to external H2O2; (b) there is a correlation between the magnitude of the gradients and the resistance to H2O2; (c) there is not a correlation between the intracellular capacity to remove H2O2 and the resistance to H2O2; (d) the plasma membrane permeability to H2O2 decreases by a factor of two upon acquisition of resistance to this agent by pre-exposing cells either to nonlethal doses of H2O2 or to cycloheximide, an inhibitor of protein synthesis; and (e) erg3Delta and erg6Delta mutants, which have impaired ergosterol biosynthesis pathways, show higher plasma membrane permeability to H2O2 and are more sensitive to H2O2. Altogether, the regulation of the plasma membrane permeability to H2O2 emerged as a new mechanism by which cells respond and adapt to H2O2. The consequences of the results to cellular redox compartmentalization and to the origin and evolution of the eukaryotic cell are discussed.