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At least 19 recordsLinked to original sources

Immunoglobulin heavy chain and binding protein complexes are dissociated in vivo by light chain addition.

Immunoglobulin heavy chain binding protein (BiP, GRP78) associates stably with the free, nonsecreted Ig heavy chains synthesized by Abelson virus transformed pre-B cell lines. In cells synthesizing both Ig heavy and light chains, the Ig subunits assemble rapidly and are secreted. Only incompletely assembled Ig molecules can be found bound to BiP in these cells. In addition to Ig heavy chains, a number of mutant and incompletely glycosylated transport-defective proteins are stably complexed with BiP. When normal proteins are examined for combination with BiP, only a small fraction of the intracellular pool of nascent, unfolded, or unassembled proteins can be found associated. It has been difficult to determine whether these BiP-associated molecules represent assembly intermediates which will be displaced from BiP and transported from the cell, or whether these are aberrant proteins that are ultimately degraded. In order for BiP to monitor and aid in normal protein transport, its association with these proteins must be reversible and the released proteins should be transport competent. In the studies described here, transient heterokaryons were formed between a myeloma line producing BiP-associated heavy chains and a myeloma line synthesizing the complementary light chain. Introduction of light chain synthesis resulted in assembly of prelabeled heavy chains with light chains, displacement of BiP from heavy chains, and secretion of Ig into the culture supernatant. These data demonstrate that BiP association can be reversible, with concordant release of transportable proteins. Thus, BiP can be considered a component of the exocytic secretory pathway, regulating the transport of both normal and abnormal proteins.

Animals↗

Direction of elongation of poly(ADP-ribose) chains. Addition of residues at the polymerase-proximal terminus.

The mechanism of elongation of poly(ADP-ribose) on poly(ADP-ribose) polymerase was examined in two ways. The first technique involved a pulse-chase protocol. Poly(ADP-ribose) polymerase was labeled with radioactive NAD, excess precursor was removed by rapid gel filtration chromatography, and nonradioactive NAD was supplied for a second incubation. The products were released with alkali and digested with venom phosphodiesterase which generates AMP uniquely from the distal terminus. The distal residue that was labeled during the pulse remained at the distal terminus and was not converted to an internal residue during the chase. The second technique employed the NAD analog, 2'-deoxyNAD (dNAD), which can engage in mono-ADP-ribose addition reactions but lacks the 2'-OH that is required for polymer formation. dNAD inhibits ADP-ribose incorporation competitively but is not incorporated at the enzyme-distal chain terminus. These findings are inconsistent with a model of poly(ADP-ribose) synthesis in which new residues are added to the 2'-OH terminus of the growing chain, distal to the polymerase attachment. They are consistent with the alternative possibility that new residues are added at the 1" terminus, adjacent to the polymerase. Any such "proximal addition" model requires that there be at least two active center sites (akin to the ribosomal A and P sites), which at a certain stage of each elongation cycle will be occupied by ADP-ribose monomers and ADP-ribose polymers, respectively. Although dNAD does not enter poly(ADP-ribose), it does engage in a slow side reaction whereby a single dADP-ribose residue is added covalently to the polymerase itself, thereby inactivating the enzyme.

ADP Ribose Transferases↗

Covariate adjustment of event histories estimated from Markov chains: the additive approach.

Markov chain models are frequently used for studying event histories that include transitions between several states. An empirical transition matrix for nonhomogeneous Markov chains has previously been developed, including a detailed statistical theory based on counting processes and martingales. In this article, we show how to estimate transition probabilities dependent on covariates. This technique may, e.g., be used for making estimates of individual prognosis in epidemiological or clinical studies. The covariates are included through nonparametric additive models on the transition intensities of the Markov chain. The additive model allows for estimation of covariate-dependent transition intensities, and again a detailed theory exists based on counting processes. The martingale setting now allows for a very natural combination of the empirical transition matrix and the additive model, resulting in estimates that can be expressed as stochastic integrals, and hence their properties are easily evaluated. Two medical examples will be given. In the first example, we study how the lung cancer mortality of uranium miners depends on smoking and radon exposure. In the second example, we study how the probability of being in response depends on patient group and prophylactic treatment for leukemia patients who have had a bone marrow transplantation. A program in R and S-PLUS that can carry out the analyses described here has been developed and is freely available on the Internet.

Analysis of Variance↗

Microarray glass slides coated with block copolymer brushes obtained by reversible addition chain-transfer polymerization.

The reversible addition-fragmentation chain-transfer polymerization was used to prepare microarray slides grafted with polymer brushes for DNA-based applications. Block copolymer brushes of N,N-dimethylacrylamide (DMA) and glycidyl methacrylate (GMA), poly(DMA-b-GMA) were prepared by extending living poly(dimethylacrylamide) chains. The functional surface was used as a substrate for oligonucleotide hybridization experiments. The results were compared to those provided by glass slides coated by a self-assembled monolayer made of (3-glycidyloxypropyl)trimethoxysilane. Surfaces coated with block polymer brushes bearing oxirane groups are more efficient as substrates for oligonucleotide hybridization than surfaces coated with nonpolymeric self-assembled monolayers containing the same functional group. The high probe grafting density and hybridization efficiency achieved with this polymeric coating reveal the importance of the block architecture to ensure good accessibility of the immobilized probe. The new surface was characterized by static angle measurements and diffuse reflectance FT-IR spectroscopy on a silica model system.

Acrylic Resins↗

Prostaglandin analogues possessing antinidatory effects. 2. Modification of the alpha chain.

Additional double bonds were introduced into the alpha chain in 16-phenoxy-, 16-(3-chlorophenoxy)-, 16-[3-(tri-fluoromethyl)phenoxy]-, and 16-(4-chlorophenoxy)-17,18,19,20-tetranorprostaglandins which have antinidatory effects. Of these analogues, the delta 3-cis-delta 5 analogues 23b is 1200 times more potent than prostaglandin F2 alpha in antinidatory effect in the rat and more potent than any other known prostaglandin analogues.

Abortifacient Agents, Nonsteroidal↗

Polyploidy Arithmetic.

Polyploidy occurs in plants and animals, and is an important force in speciation and genome evolution. The main focus of this paper is the following fundamental question that was recently posed by Huber and Maher: Given the ploidy numbers of a collection of extant species, or their ploidy profile, what is the smallest number of hybridizations needed in any evolutionary history for these species to completely represent these numbers? In this paper, we shall show that this question can be rephrased in terms of addition chains and the closely related addition sequences, which have been studied for over a century in mathematics and computer science. These are sequences of natural numbers that start with 1, so that each number in the sequence larger than 1 is the sum of two other numbers arising earlier in the sequence. In our first main result, we show that finding the smallest number of hybridization events to explain a ploidy profile, or the hybrid number, is equivalent to solving the so-called addition sequence problem. This immediately implies that computing the hybridization number is computationally intractable. Even so, it also leads to new connections to representing polyploid evolution using networks. More specifically, in our second main result we show that ploidy profiles representable by tree-child networks are exactly the addition chains, implying a polynomial-time algorithm for identifying these profiles. We then consider beaded tree-child networks, which permit the representation of autopolyploidy events, and in our third main result we provide a greedy polynomial-time algorithm to decide whether a given profile can be realized by such a network. We expect that our results can be leveraged in future work through, for example, making use of known algorithms for computing short addition sequences to give bounds for the hybrid number, and in guiding network reconstruction for polyploid species.

Polyploidy↗

NH4+-induced down-regulation of the Saccharomyces cerevisiae Gap1p permease involves its ubiquitination with lysine-63-linked chains.

Addition of ammonium ions to yeast cells growing on proline as the sole nitrogen source induces internalization of the general amino acid permease Gap1p and its subsequent degradation in the vacuole. An essential step in this down-regulation is Gap1p ubiquitination through a process requiring the Npi1p/Rsp5p ubiquitin ligase. We show in this report that NPI2, a second gene required for NH4+-induced down-regulation of Gap1p, codes for the ubiquitin hydrolase Doa4p/Ubp4p/Ssv7p and that NH4+-induced Gap1p ubiquitination is strongly reduced in npi2 cells. The npi2 mutation results in substitution of an aromatic amino acid located in a 33-residue sequence shared by some ubiquitin hydrolases of the Ubp family. In this mutant, as in doa4(delta) cells, the amount of free monomeric ubiquitin is at least four times lower than in wild-type cells. Both ubiquitination and down-regulation of the permease can be restored in npi2 cells by over-expression of ubiquitin. In proline-grown wild-type and npi2/doa4 cells overproducing ubiquitin, Gap1p appears to be mono-ubiquitinated at two lysine acceptor sites. Addition of NH4+ triggers rapid poly-ubiquitination of Gap1p, the poly-ubiquitin chains being specifically formed by linkage through the lysine 63 residue of ubiquitin. Gap1p is thus ubiquitinated differently from the proteins targeted by ubiquitination for proteolysis by the proteasome, but in the same manner as the uracil permease, also subject to ubiquitin-dependent endocytosis. When poly-ubiquitination through Lys63 is blocked, the Gap1p permease still undergoes NH4+-induced down-regulation, but to a lesser extent.

Amino Acid Sequence↗

First report of reversible addition-fragmentation chain transfer (RAFT) polymerisation in room temperature ionic liquids.

The Reversible Addition-Fragmentation chain Transfer (RAFT) polymerisation of acrylates, methacrylates and styrene is reported for the first time in room temperature ionic liquids; the acrylate and methacrylate polymerisations show a living character and lead to well-characterised polymers, with narrow polydispersity (< 1.3); in the case of styrene, the insolubility of the polymer in the ionic liquids stops the polymerisation at an early stage.

Journal Article↗

Well-controlled reversible addition-fragmentation chain transfer radical polymerisation under ultraviolet radiation at ambient temperature.

Controlled reversible addition-fragmentation chain transfer radical polymerisation of methyl acrylate was carried out under long-wave (lambda > or = 365 nm) ultraviolet radiation using an acylphosphine oxide as a photoinitiator at ambient temperature; the polymerisation shows a "living" character at high conversions of polymerisation and leads to well-defined polymers with narrow polydispersities (Mw/Mn < 1.1).

Journal Article↗

Bacteriophage receptor development and synthesis of O-specific side chains after addition of D-galactose to the uridine diphosphate-galactose-4-epimeraseless mutant Salmonella typhimurium LT2-M1.

The formation of complete cell wall core lipopolysaccharide (LPS) and O-antigenic side chains after addition of d-galactose to the uridine diphosphate-galactose-4-epimeraseless mutant, Salmonella typhimurium LT2-M1, has been studied by (i) determination of adsorption rates of smooth and rough specific bacteriophages, (ii) passive hemagglutination inhibition, and (iii) qualitative and quantitative determination of the polysaccharide composition and structure. A rapid synthesis of the complete core LPS and O side chains occurred in bacteria in the log phase and the early stationary phase. Phage C21, which attaches to unsubstituted Rc structures, was adsorbed by the bacteria for only 10 min after the addition of d-galactose. Unsubstituted Rc structures, however, could still be detected after 160 min by immunological and chemical assays. Attachment of the P22 phage, which requires O-specific side chains with more than one repeating unit for adsorption, was demonstrated 10 min after the addition of d-galactose. Attachment of the Felix O-1 phage, which requires a complete core, was observed between 20 and 80 min after the addition of d-galactose. The rough specific phages 6SR and Br2 did not adsorb to the bacteria at any time after the addition of d-galactose. By passive hemagglutination inhibition, the presence of O-specific structures could be demonstrated after 10 min. No antigenic activity of the Ra and Rb structures was observed in the LPS preparations isolated at any time after the addition of d-galactose. Methylation analysis of LPS preparations isolated at 10 and 160 min after the addition of d-galactose showed that the O-specific side chains contained an average of 11 and 15 repeating units, respectively. In the 10-min sample, every 25th "Rc structure" carried a side chain, compared to every 3rd residue in the 160-min sample.

Adsorption↗

The kinetics of addition and fragmentation in reversible addition fragmentation chain transfer polymerization: An ab initio study.

High-level ab initio calculations of the forward and reverse rate coefficients have been performed for a series of prototypical reversible addition fragmentation chain transfer (RAFT) reactions: R* + S=C(Z)SCH3 --> R-SC*(Z)SCH3, for R = CH3, with Z = CH3, Ph, and CH2Ph; and Z = CH3, with R = (CH3), CH2COOCH3, CH2Ph, and C(CH3)2CN. The addition reactions are fast (ca. 10(6)-10(8) L mol(-1) s(-1)), typically around three orders of magnitude faster than addition to the C=C bonds of alkenes. The fragmentation rate coefficients are much more sensitive to the nature of the substituents and vary from 10(-4) to 10(7) s(-1). In both directions, the qualitative effects of substituents on the rate coefficients largely follow those on the equilibrium constants of the reactions, with fragmentation being favored by bulky and radical-stabilizing R-groups and addition being favored by bulky and radical-stabilizing Z-groups. However, there is evidence for additional polar and hydrogen-bonding interactions in the transition structures of some of the reactions. Ab initio calculations were performed at the G3(MP2)-RAD//B3-LYP/6-31G(d) level of theory, and rates were obtained via variational transition state theory in conjunction with a hindered-rotor treatment of the low-frequency torsional modes. Various simplifications to this methodology were investigated with a view to identifying reliable procedures for the study of larger polymer-related systems. It appears that reasonable results may be achievable using standard transition state theory, in conjunction with ab initio calculations at the RMP2/6-311+G(3df,2p) level, provided the results for delocalized systems are corrected to the G3(MP2)-RAD level using an ONIOM-based procedure. The harmonic oscillator (HO) model may be suitable for qualitative "order-of-magnitude" studies of the kinetics of the individual reactions, but the hindered-rotor (HR) model is advisable for quantitative studies.

Journal Article↗

Facile preparation of transition metal nanoparticles stabilized by well-defined (co)polymers synthesized via aqueous reversible addition-fragmentation chain transfer polymerization.

Herein we disclose a facile method for the preparation of (co)polymer-stabilized transition metal colloids, via the "grafting-to" approach. The method takes advantage of the fact that (co)polymers synthesized in aqueous media, in a controlled fashion, via reversible addition-fragmentation chain transfer bear thiocarbonylthio end groups. These are readily reduced to yield (co)polymers with thiol end groups. When the reduction is performed, with NaBH(4), for example, in aqueous media in the presence of an appropriate transition metal species, (co)polymer-stabilized metal nanoparticles are formed in which the size and size distribution are dependent upon the individual transition metals. Colloid formation is confirmed by transmission electron microscopy and UV-vis spectroscopy.

Journal Article↗

Blood-ocular barrier permeability and electroretinogram after intravitreal silicone oils of varying composition.

Silicone oils, used as long-term retinal tamponades, cause retinal toxicity that may be related to certain ingredients. Specific additives, proven to increase corneal endothelial permeability, were added to a purified oil, and placed into the vitreous of rabbits to assess their effects on the retina. Oils were exchanged for vitreous at constant intraocular pressure to 1 ml oil volume. Blood-ocular barrier permeability was measured with fluorophotometry after intravenous dye, and retinal function was measured using dark-adapted electroretinography (ERG). Each parameter was determined at eight week intervals: this periodicity was chosen to allow any toxicity to develop based upon prior data in the literature. The fluorescein concentration in different ocular compartments indicated an increased aqueous humor fluorescein concentration after pure oil (a non-statistically significant 50% increase) or oil plus long chain additive (a significant 240% increase). After oil plus a linear series of compounds both aqueous humor (2000%) and anterior vitreous fluorescence (8000%) was statistically significantly increased, indicating a breakdown of the blood-aqueous barrier. The height of the b-wave of the ERG was unaffected by any oil in the presence or absence of additive. Overt changes were minimal with oil alone, increased with oil containing linear chain additive, and were extensive with oil with long chain additive.

Animals↗

Human variant sex hormone-binding globulin (SHBG) with an additional carbohydrate chain has a reduced clearance rate in rabbit.

Sex hormone-binding globulin (SHBG) is the specific plasma transport protein for sex steroid hormones in humans. Considerable variation in SHBG plasma concentration exists between individuals, irrespective of gender, body weight, or thyroid status. In the present work, the influence of carbohydrate chains on the half-life of human SHBG (hSHBG) was investigated using a rabbit model. A variant hSHBG, with a point mutation in exon 8 (GAC --> AAC) encoding an amino acid substitution (Asp327Asn), which introduces an additional consensus site for N-glycosylation, has recently been identified. This mutation suppresses a recognition site for the restriction enzyme Bbs-I, allowing the development of a simple restriction-fragments length polymorphism (RFLP) screening procedure. In a population of patients (272 female and 49 male) consulting in our Endocrinology Clinic, 48 patients (41 female and 7 male) were heterozygous for the variant hSHBG allele and 3 (2 female and 1 male) were homozygous. In this population, the total variant allele frequency was 0.083. The hSHBG genotype, as determined by RFLP, corresponded in all cases to the phenotype as determined by the migration profile of hSHBG by Western blot analysis. The influence of such an additional glycosylation site on the biological half-life of variant hSHBG was investigated. SHBG from serum of patients carrying one of the three hSHBG genotypes was purified and labeled with biotin, then injected into rabbits, as we have recently described for rabbit SHBG. Biotinylated hSHBG was captured from rabbit serum samples on tubes coated with an anti-hSHBG antibody and detected by luminometry with the streptavidine-alkaline phosphatase-dioxetane (AMPPD) system. The results showed that the half-life value was significantly higher (P < 0.05) for SHBG purified from homozygous variant serum (t1/2 beta = 51.43 +/- 1.15 and 63.63 +/- 3.92 h, for male and a female subjects SHBG respectively) than for SHBG purified from heterozygous variant serum (t1/2 beta = 40.19 +/- 0.12 h) or wild-type (t1/2 beta = 38.18 +/- 7.22 h). This study demonstrated that an additional carbohydrate chain on hSHBG decreases the clearance rate of this protein. The low frequency of this variant allele means that further study will be required to determine whether it is associated with higher serum SHBG concentration.

Adrenal Hyperplasia, Congenital↗

An additional carbohydrate chain in the variant thyroxine-binding globulin-Gary (TBGAsn-96) impairs its secretion.

The T4-binding globulin-Gary (TBG-G) variant has severely impaired T4 binding, is unstable at 37 C, and presents an apparent anodal shift of all isoforms when submitted to isoelectric focusing. Inheritance of this abnormal TBG produces a profound decrease in the serum levels of native TBG with reciprocal changes in its denatured form, causing thyroid hormone concentrations to be as low as those found in complete TBG deficiency. The TBG-G gene possesses a single nucleotide substitution replacing the normal IIe96 (ATC) with Asn (AAC), thus creating a new site for N-linked glycosylation. In order to determine whether TBG-G contains an additional carbohydrate chain as indirectly suggested by the isoelectric focusing results, cDNAs containing the normal TBG (TBG-N), and TBG-G were inserted in the appropriate vectors to allow their expression in mammalian cells (COS-1) and in amphibian (Xenopus) oocytes. In both systems, expression of TBG-G yielded a larger molecule than TBG-N when analyzed by polyacrylamide gel electrophoresis under denaturing conditions. However, both were identical in size when synthesized in COS-1 cells in the presence of tunicamycin or when deglycosylated after their synthesis in Xenopus oocytes. Pulse chase experiments revealed impaired secretion and excessive overall intracellular degradation of TBG-G relative to TBG-N. As expected from studies on serum from affected subjects, in vitro expressed TBG-G had a 10-fold lower affinity for T4. These studies prove that the new site for potential glycosylation created by the point mutation in TBG-G is indeed glycosylated.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Multiple hemoglobin alpha-chains in the sika deer (Cervus nippon).

Investigation of the hemoglobin alpha-chains of an Asiatic deer, the sika (Cervus nippon), was prompted by the heterogenity of alpha-chain gene loci in the Virginia white-tailed deer (Odocoileus virginianus). Although electrophoresis of hemoglobin chains from 10 sika revealed only a single alpha-chain band, peptide mapping demonstrated variations in the alpha-TPIII and alpha-TPIV peptides. Substitutions at positions 15, 20, and 22 produced a minimum of five alpha-chains; two possible additional chains could noy be proven because of inseparability of the whole alpha-chains. The most common chain contains Asp-15, Lys-20 and Pro-22 but in other chains glycine is present at position 15, Asx at position 20, and either serine or Asx at position 22. The probable explanation for the large number of alpha-chains is gene duplication which may have been produced by breedings between subspecies from different geographical areas. Comparison with the alpha-chain structure of the white-tailed deer suggests that the sika may have evolved from the lineage which produced the white tailed-deer after the alpha-chain genes of the latter species had duplicated. In addition, these data provide further examples of the unusual variability of this portion of the alpha-chain.

Amino Acid Sequence↗