Conjugation Pattern Research Articles

Mechanisms of Verbal Morphology Processing in Heritage Speakers of Russian

The goal of the study is to analyze the morphological processing of real and novel verb forms by heritage speakers of Russian in order to determine whether it differs from that of native (L1) speakers1 and second language (L2) learners; if so, how it is different; and which factors may guide the acquisition process. The experiment involved three groups of subjects: 28 adult native speakers, 14 adult heritage speakers, and 17 beginning American learners of Russian. The results demonstrate that (1) novel form production in heritage processing, as in native and L2 processing, is rule-based, and that rule application—i.e. the generalization rate of conjugational patterns—depends on the input-based mechanism of statistical probabilities (to be defined below), and (2) that heritage speakers' mental representations of morphological structures are unstable and their morphological processing is different from either adult native or L2 processing.

2,3-Diphenylbutadiene and Donor−Acceptor Functionalized Derivatives: Exploring the Competition between Conjugation Paths in Branched π-Systems

2,3-Diphenylbutadiene and its donor-acceptor functionalized derivatives represent branched pi systems consisting of three overlapping linearly conjugated units, namely a 1,3-butadiene and two phenylethene subsystems. The evaluation of pi conjugation using a scheme based on the natural bond orbital analysis shows that the details of the structure of these compounds is governed by electron delocalization. The potential energy surface of 2,3-diphenylbutadiene shows two minima, each one representing a distinct combination of conjugation patterns. These minima are shown to be connected by a low-energy path with transition structures that have one conjugation path fully activated, while conjugation is completely disrupted along the other path. We will show that, in response to donor-accptor functionalization, the 2,3-diphenylbutadiene backbone will switch to other conformations, which come along with substantial changes in the electronic structure.

Determination of isoflavones in nutritional supplements by HPLC with coulometric electrode array detection

In the present study eleven soy and/or red clover based supplements were analyzed after acid hydrolysis or direct extraction with 70% aqueous ethanol for their content of total isoflavone aglucones and free aglucones plus glucosides by high performance liquid chromatography in gradient elution mode coupled with coulometric electrode array detection. The ratio of the individual isoflavones and the conjugation pattern turned out to be highly variable in the investigated products. Whereas red clover based supplements contained isoflavones (mainly formononetin and biochanin A) exclusively in free form, soy containing preparations showed variable proportions of conjugated isoflavones. The total isoflavone aglucone content in products intended for direct consumption ranged from 12.0 to 45.6 mg per capsule or tablet, whereas the content of free aglucones and glucosides was between 12.2 and 51.6 mg per capsule or tablet. The experimentally determined isoflavone aglucone content was in agreement with or higher than the manufacturer’s claim in 6 of the 11 investigated products. Expression of the isoflavone content as a sum of free aglucones and glucosides raised the number of matched claims to 8.

Higher bioavailability of isoflavones after a single ingestion of a soya-based supplement than a soya-based food in young healthy males

Soya isoflavones, genistein and daidzein, are the focus of numerous studies investigating their potential effects on health and results remain controversial. Bioavailability is clearly a crucial factor influencing their bioefficacy and could explain these discrepancies. This study aimed at assessing: (1) the isoflavone content of sixty-nine European soya-derivative products sold on the French market; (2) the bioavailability of isoflavones comparing supplement with food. Twelve healthy volunteers were recruited in a randomized two-way crossover trial and received 35 mg isoflavones equivalent aglycone either through supplements or through cheese, both containing different patterns of isoflavone conjugates and different daidzein:genistein ratios. A specific ELISA method was used to assess the plasma and urinary concentrations of isoflavones and thus the pharmacokinetic parameters, which were then normalized to mg of each isoflavone ingested. Results showed that the normalized Cmax of daidzein (P = 0.002) and similarly the normalized AUC0 --> infinity and Cmax of genistein (P = 0.002) from soya-based capsules were higher than that from soya-based cheese. In conclusion, this work completes studies on isoflavone bioavailability and presents new data regarding isoflavone concentrations in soya-derivative products. Assuming that isoflavone conjugation patterns do not influence isoflavone bioavailability, this study shows that isoflavones contained in capsules are more bioavailable than those contained in soya-based cheese. Although the supplement is more bioavailable, the relative importance of this is difficult to interpret as there is little evidence that supplements are biologically active in human subjects to date and further studies will be necessary for this specific supplement to prove its efficacy.

Substrate Modification with Lysine 63-linked Ubiquitin Chains through the UBC13-UEV1A Ubiquitin-conjugating Enzyme

Protein modification with lysine 63-linked ubiquitin chains has been implicated in the non-proteolytic regulation of signaling pathways. To understand the molecular mechanisms underlying this process, we have developed an in vitro system to examine the activity of the ubiquitin-conjugating enzyme UBC13-UEV1A with TRAF6 in which TRAF6 serves as both a ubiquitin ligase and substrate for modification. Although TRAF6 potently stimulates the activity of UBC13-UEV1A to synthesize ubiquitin chains, it is not appreciably ubiquitinated. We have determined that the presentation of Lys(63) of ubiquitin by UEV1A suppresses TRAF6 modification. Based on our observations, we propose that the modification of proteins with Lys(63)-linked ubiquitin chains occurs through a UEV1A-independent substrate modification and UEV1A-dependent Lys(63)-linked ubiquitin chain synthesis mechanism.

Allosteric Activation of Human Glucokinase by Free Polyubiquitin Chains and Its Ubiquitin-dependent Cotranslational Proteasomal Degradation

Human glucokinase (hGK) is a monomeric enzyme highly regulated in pancreatic beta-cells (isoform 1) and hepatocytes (isoforms 2 and 3). Although certain cellular proteins are known to either stimulate or inhibit its activity, little is known about post-translational modifications of this enzyme and their possible regulatory functions. In this study, we have identified isoforms 1 and 2 of hGK as novel substrates for the ubiquitin-conjugating enzyme system of the rabbit reticulocyte lysate. Both isoforms were polyubiquitinated on at least two lysine residues, and mutation analysis indicated that multiple lysine residues functioned as redundant acceptor sites. Deletion of its C-terminal alpha-helix, as part of a ubiquitin-interacting motif, affected the polyubiquitination at one of the sites and resulted in a completely inactive enzyme. Evidence is presented that poly/multiubiquitination of hGK in vitro serves as a signal for proteasomal degradation of the newly synthesized protein. Moreover, the recombinant hGK was found to interact with and to be allosterically activated up to approximately 1.4-fold by purified free pentaubiquitin chains at approximately 100 nm (with an apparent EC(50) of 93 nm), and possibly also by unidentified polyubiquitinated proteins assigned to their equilibrium binding to the ubiquitin-interacting motif site. The affinity of pentaubiquitin binding to hGK is regulated by the ligand (d-glucose)-dependent conformational state of the site. Both ubiquitination of hGK and its activation by polyubiquitin chains potentially represent physiological regulatory mechanisms for glucokinase-dependent insulin secretion in pancreatic beta-cells.

Noncovalent Binding of Small Ubiquitin-related Modifier (SUMO) Protease to SUMO Is Necessary for Enzymatic Activities and Cell Growth

SUMO proteases possess two enzymatic activities to hydrolyze the C-terminal region of SUMOs (hydrolase activity) and to remove SUMO from SUMO-conjugated substrates (isopeptidase activity). SUMO proteases bind to SUMOs noncovalently, but the physiological roles of the binding in the functions of SUMO proteases are not well understood. In this study we found that SUMO proteases (Axam, SENP1, and yeast Ulp1) show different preferences for noncovalent binding to various SUMOs (SUMO-1, -2, -3, and yeast Smt3) and that the hydrolase and isopeptidase activities of SUMO proteases are dependent on their binding to SUMOs through salt bridge. Expression of Smt3 suppressed the phenotype of yeast mutant lacking smt3, which exhibits growth arrest, and the binding of Ulp1 to Smt3 was essential for this rescue activity. Although expression of an Smt3 mutant (smt3R64E(GG)), which conjugates to substrate but loses the ability to bind to Ulp1, rescued the phenotype of yeast lacking smt3 partially, the mutant cells showed an increment in the doubling time and a delay of desumoylation of Smt3-conjugated Cdc3. These results indicate that the noncovalent binding of SUMO protease to SUMO through salt bridge is essential for the enzymatic activities and that the balance between sumoylation and desumoylation is important for cell growth control.

Combined effects of conjugation pattern and alkoxy side chains on the photovoltaic properties of thiophene‐containing PPE‐PPVs

AbstractThis contribution presents the synthesis and properties of four thiophene‐containing poly(‐p‐arylene‐ethynylene)/poly(‐p‐arylene‐vinylene)s, PIa‐b and PIIa‐b, whose repeating units (RU) consist either of 1:2 or 2:2 triple bond/double bond ratio, and which bear linear alkoxy side chains not longer than octyloxy and branched 2‐ethylhexyloxy. PIa‐b and PIIa‐b exhibit similar absorption and emission behaviour in dilute solution (λa = 483–486 nm, λe = 540 nm) as well as in solid state (λa = 500, 530 nm, λe = 560 nm), whereby slightly higher fluorescence quantum yields (Φf) were obtained for PI than for PII systems, as a result of higher number of thiophene units within the RU of PII. An enhancement of the Φf‐value from 0% to 3% is obtained after replacing linear octadecyloxy in PIIc‐e by bulky branched 2‐ethylhexyloxy in PIIa‐b. Nonoptimized solar cells of configuration ITO/PEDOT:PSS/polymer: PCBM (1:3 weight ratio)/LiF/Al show open circuit voltages as high as 900 mV for PIa‐b and 800 mV for PIIa‐b. Reducing the size of the side chain from R = 2‐ethylhexyl in PIa to R = methyl in PIb leads to a significant increase of the short circuit current, ISC, from ca. 2.5 mA to ca. 3.7 mA and consequently to an enhancement of the energy conversion efficiency, ηAM1.5, from ca. 1.2% to ca. 1.7%. This is due to an extended donor‐acceptor interfacial area, as evidenced by AFM topology pictures showing smaller nanoscale clusters size in PIb than in PIa active layer. The same change led to minimal effect in PII systems. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1619–1631, 2007

Interaction of Native Bile Acids with Human Apical Sodium-Dependent Bile Acid Transporter (hASBT): Influence of Steroidal Hydroxylation Pattern and C-24 Conjugation

The human apical sodium-dependent bile acid transporter (hASBT) is a potential target for drug delivery, but an understanding of hASBT substrate requirements is lacking. The objective of this study was to characterize hASBT interaction with its native substrates, bile acids, and to evaluate C-24 conjugation and steroidal hydroxylation on transport affinity and inhibition potency. Transport and inhibition kinetics of 15 bile acids were evaluated (cholate, chenodeoxycholate, deoxycholate, ursodeoxycholate, and lithocholate, including their glycine and taurine conjugates) with an hASBT-Madin-Darby canine kidney (MDCK) monolayer assay. Samples were analyzed via liquid chromatography-mass spectrometry (LC-MS) or chromatography-mass spectrometry-mass spectrometry (LC-MS-MS). C-24 conjugation improved the inhibitory potency of all native bile acids. There was an inverse association between number of steroidal hydroxyl groups and inhibitory potency. Glycolithocholate and taurolithocholate were the most potent inhibitors. Results from transport studies followed trends from inhibition studies. Conjugated dihydroxy and monohydroxy bile acids exhibited the highest hASBT-mediated transport (i.e., lower Kt and higher Jmax). Across the 15 bile acids, Kt generally followed Ki. Additionally, Jmax correlated with Ki, where greater inhibition potency was associated with higher transport capacity. C-24 conjugation and steroidal hydroxylation pattern modulated native bile acid interaction with hASBT, with C-24 effect dominating steroidal hydroxylation effect. Results indicate that bile acid binding to hASBT may be the rate-limiting step in the apical transport of bile acids.

Higher-order spectral analysis of complex signals

Even though higher-order spectral analysis is by now a mature field, complex signals are still not routinely used, as they are in second-order analysis. The reason is the complexity of the complex case: nth order moment functions of a complex signal can be defined in 2 n different ways, depending on the placement of complex conjugate operators. It is demonstrated that only a few of these different moments are required for a complete nth order description. Properties of nth order moments and spectra with different conjugation patterns are investigated. For the special case of analytic signals, it is shown how spectra with different conjugation patterns provide different information about the signal. Both energy and power signals and deterministic and stochastic signals are discussed. A major focus lies on extending results from continuous-time signals to their sampled versions. Such an extension is not straightforward due to a phenomenon called higher-order or dimension-reduction aliasing. It is demonstrated why spectra of sampled nonstationary signals may suffer from dimension-reduction aliasing unless they are sufficiently oversampled.

Higher-order spectral analysis of complex signals

Even though higher-order spectral analysis is by now a mature field, complex signals are still not routinely used, as they are in second-order analysis. The reason is the complexity of the complex case: nth order moment functions of a complex signal can be defined in 2n different ways, depending on the placement of complex conjugate operators. It is demonstrated that only a few of these different moments are required for a complete nth order description. Properties of nth order moments and spectra with different conjugation patterns are investigated. For the special case of analytic signals, it is shown how spectra with different conjugation patterns provide different information about the signal. Both energy and power signals and deterministic and stochastic signals are discussed. A major focus lies on extending results from continuous-time signals to their sampled versions. Such an extension is not straightforward due to a phenomenon called higher-order or dimension-reduction aliasing. It is demonstrated why spectra of sampled nonstationary signals may suffer from dimension-reduction aliasing unless they are sufficiently oversampled.

Evolution of fracture and fault-controlled fluid pathways in carbonates of the Albanides fold-thrust belt

The process of fracture and fault formation in carbonates of the Albanides fold-thrust belt has been systematically documented using hierarchical development of structural elements from hand sample, outcrop, and geologic-map scales. The function of fractures and faults in fluid migration was elucidated using calcite cement and bitumen in these structures as a paleoflow indicator. Two prefolding pressure-solution and vein assemblages were identified: an overburden assemblage and a remote tectonic stress assemblage. Sheared layer-parallel pressure-solution surfaces of the overburden assemblage define mechanical layers. Shearing of mechanical layers associated with folding resulted in the formation of a series of folding assemblage fractures at different orientations, depending on the slip direction of individual mechanical layers. Prefolding- and folding-related fracture assemblages together formed fragmentation zones in mechanical layers and are the sites of incipient fault localization. Further deformation along these sites was accommodated by rotation and translation of fragmented rock, which formed breccia and facilitated fault offset across multiple mechanical layers. Strike-slip faults formed by this process are organized in two sets in an apparent conjugate pattern. Calcite cement and bitumen that accumulated along fractures and faults are evidence of localized fluid flow along fault zones. By systematic identification of fractures and faults, their evolution, and their fluid and bitumen contents, along with subsurface core and well-log data, we identify northeast-southwest–trending strike-slip faults and the associated structures as dominant fluid pathways in the Albanides fold-thrust belt.

Diyne-Containing PPVs: Solid-State Properties and Comparison of Their Photophysical and Electrochemical Properties with Those of Their Yne-Containing Counterparts

Diyne-containing poly(p-phenylene−vinylene)s, 4a − d, of general chemical structure −(Ph−C⋮C−C⋮C−Ph−CH═CH−Ph−CH═CH−) n , obtained through polycondensation reactions of 1,4-bis(4-formyl-2,5-dioctyloxyphenyl)-buta-1,3-diyne (2) with various 2,5-dialkoxy-p-xylylenebis(diethylphosphonates), 3a − d, are the subject of this report. The polymers exhibit great disparity in their degree of polymerization, n, which might be ascribed to side-chain-related differences in reactivity of the reactive species during the polycondensation process and which led to n-dependent absorption (solution and solid state) and emission (solution) behaviors of the polymers. Polarizing optical microscopy and differential scanning calorimetry are employed to probe their thermal behavior. The structure is investigated by means of wide-angle X-ray diffraction for both isotropic and macroscopically oriented samples. Comparison of photophysical (experimental and theoretical) and electrochemical properties of the polymers with those of their yne-containing counterparts 6a − d [−(Ph−C⋮C−Ph−CH═CH−Ph−CH═CH−) n ] has been carried out. Similar photophysical behavior was observed for both types of polymers despite the difference in backbone conjugation pattern. The introduction of a second yne unit in 4 lowers the HOMO and LUMO levels, thereby enhancing the electron affinity of polymers 4 compared to polymers 6. The “wider opening” introduced by the second yne unit facilitates moreover the movement of charges during the electrochemical processes leading to minimal discrepancy, ΔE g, between the optical and electrochemical band gap energies. Polymers 6, in contrast, show significant side-chain-dependent ΔE g values. Low turn-on voltages between 2 and 3 V and maximal luminous efficiencies between 0.32 and 1.25 cd/A were obtained from LED devices of configuration ITO/PEDOT:PSS/polymer 4/Ca/Al.

Metabonomics with 1H-NMR spectroscopy and liquid chromatography-mass spectrometry applied to the investigation of metabolic changes caused by gentamicin-induced nephrotoxicity in the rat

The model nephrotoxin gentamicin was administered to male Wistar-derived rats daily, for 7 days, at 60 mg kg−1 day−1, subcutaneously, twice daily. Conventional clinical chemistry urinalysis showed a significant increase in N-acetyl-β-D-glucosaminidase (NAG) activity from day 3. At necropsy on day 9, clear histological damage to the kidney was noted with all animals showing a generally severe nephropathy primarily focused on the proximal convoluted tubules. The urinary excretion pattern of endogenous metabolites over the time course of the study was studied using a combination of 1H-NMR spectroscopy and HPLC-TOF-MS/MS using electrospray ionization (ESI). Changes in the pattern of endogenous metabolites as a result of daily administration of gentamicin were readily detected by both techniques with significant perturbations of the urinary profile observed from day 7 onwards. The findings by 1H-NMR included raised glucose and reduced trimethylamine N-oxide (TMAO). Changes in metabonomic profiles were observed by HPLC-MS in both positive and negative ESI. The MS data showed reduced xanthurenic acid and kynurenic acid, whilst neutral loss experiments also revealed a changed pattern of sulphate conjugation on gentamicin administration.

Patterns of peripheral steroid metabolism vary with sex, season, and tissue type in blotched blue-tongued lizards ( Tiliqua nigrolutea)

We examined sexual and seasonal variation in the ability of reproductively relevant tissues (liver, skin, adrenal gland, cloaca, kidney, renal sexual segment, epididymis, oviduct, muscle, testis, and ovary) to metabolise a primary steroid [testosterone (T) or estradiol (E2)] in the scincid lizard, Tiliqua nigrolutea. We observed considerable variation between sexes and across seasons in the patterns of conjugation and derivatisation of the primary steroids by these tissues. All tissues demonstrated the ability to conjugate the relevant primary steroid. Other general trends included increased conjugation by all tissues of gestating females, reduced metabolism of E2 by female tissues during late vitellogenesis, and reduced metabolism of T by males during early spermatogenesis. 5α-Dihydrotestosterone was the most commonly detected derivative in males, and production varied with season and tissue type. We suggest that seasonal variation in the ability of reproductively relevant tissues may be important in the physiological regulation of reproduction in this species.

Mlp-dependent anchorage and stabilization of a desumoylating enzyme is required to prevent clonal lethality

Myosin-like proteins 1 and 2 (Mlp1 and Mlp2) form filaments attached to the nucleoplasmic side of the nuclear pore complexes via interaction with the nucleoporin Nup60. Here, we show that Mlps and Nup60, but not several other nucleoporins, are required to localize and stabilize a desumoylating enzyme Ulp1. Moreover, like Mlps, Ulp1 exhibits a unique asymmetric distribution on the nuclear envelope. Consistent with a role in regulating Ulp1, removal of either or both MLPs affects the SUMO conjugate pattern. We also show that deleting MLPs or the localization domains of Ulp1 results in DNA damage sensitivity and clonal lethality, the latter of which is caused by increased levels of 2-micron circle DNA. Epistatic and dosage suppression analyses further demonstrate that Mlps function upstream of Ulp1 in 2-micron circle maintenance and the damage response. Together, our results reveal that Mlps play important roles in regulating Ulp1 and subsequently affect sumoylation stasis, growth, and DNA repair.

Related to ubiquitin 1 and 2 are redundant and essential and regulate vegetative growth, auxin signaling, and ethylene production in Arabidopsis.

Related to Ubiquitin (RUB)/Nedd8 is a ubiquitin-like protein that covalently attaches to cullins, a subunit of the SCF (for Skp, Cdc53p/Cul1, and F-box protein) complex, an E3 ubiquitin ligase, and has been shown to be required for robust function of the complex. The effects of reducing protein levels for two Rub proteins, RUB1 and RUB2, were characterized in Arabidopsis thaliana. T-DNA insertional null lines homozygous at a single RUB-encoding locus were analyzed and found to have a wild-type phenotype. A double mutant was never recovered. More than one-quarter of the progeny from the self-fertilization of plants with a single functional RUB-encoding gene died as embryos at the two-cell stage. Outcrosses demonstrated reduced inheritance of the null allele from both the male and female parent. Hemigglutinin-tagged forms of RUB1 and RUB2 conjugate to the same cullin protein, CUL1, and produce the same conjugation pattern. To further understand the function of the RUB proteins, a construct designed to produce a double-stranded RUB1 mRNA was introduced into plants, and three lines with reduced levels of RUB1- and RUB2-encoding mRNA and RUB1/2 protein content were analyzed in detail. Mature plants were severely dwarfed, seedlings were insensitive to auxin in root assays, and dark-grown seedlings had a partial triple-response phenotype that was suppressed when seedlings were grown on ethylene perception or synthesis inhibitors. The dsrub lines produced threefold to fivefold more ethylene than the wild type. This study illustrates that RUB1 and RUB2 are genetically and biochemically redundant and demonstrates that RUB1/2 proteins are essential for early embryonic cell divisions and that they regulate diverse processes.

Third-order nonlinear optical behaviour of hybrid phenylene–ethynylene/phenylene–vinylene polymers

The |n2|-values of novel hybrid phenylene?ethynylene/phenylene?vinylene polymers 1, 2, 3, 4, together with those of corresponding phenyleneethynylene 5 and phenylenevinylene 6 and 7 'homopolymers', have been studied by time-resolved degenerate four-wave mixing (DFWM). The measurements were performed on thin films at 800?nm with femtosecond time resolution using a folded boxcars setup. No clear relationship between |n2|-values and the backbone conjugation pattern of the compounds could be established. In contrast, a quasi-exponential relationship between film thickness and the |n2|-value was observed, irrespective of the chemical structure of the samples.

Hepatocyte Nuclear Factor 4α Is a Central Regulator of Bile Acid Conjugation

Hepatocyte nuclear factor 4alpha (HNF4alpha) has an important role in regulating the expression of liver-specific genes. Because bile acids are produced from cholesterol in liver and many enzymes involved in their biosynthesis are preferentially expressed in liver, the role of HNF4alpha in the regulation of bile acid production was examined. In mice, unconjugated bile acids are conjugated with taurine by the liver-specific enzymes, bile acid-CoA ligase and bile acid-CoA:amino acid N-acyltransferase (BAT). Mice lacking hepatic HNF4alpha expression exhibited markedly decreased expression of the very long chain acyl-CoA synthase-related gene (VLACSR), a mouse candidate for bile acid-CoA ligase, and BAT. This was associated with markedly elevated levels of unconjugated and glycine-conjugated bile acids in gallbladder. HNF4alpha was found to bind directly to the mouse VLACSR and BAT gene promoters, and the promoter activities were dependent on HNF4alpha-binding sites and HNF4alpha expression. In conclusion, HNF4alpha plays a central role in bile acid conjugation by direct regulation of VLACSR and BAT in vivo.

Influence of the Conjugation Pattern on the Photophysical Properties of Alkoxy-Substituted PE/PV Hybrid Polymers

Alkoxy-substituted phenylene−ethynylene (PE)/phenylene−vinylene (PV) hybrid polymers of general constitutional structure (−Ar−C⋮C−Ar−CHCH−)n (2), (−Ar−C⋮C−Ar−CHCH−Ar−C⋮C−)n (3), and (−Ar−C⋮C−Ar−C⋮C−Ar−CHCH−Ar−CHCH−)n (4) have been synthesized and characterized. Comparisons of their photophysical properties in solution as well as in solid state (photoconductivity, absorption, emission, and electroluminescence) with those of their corresponding alkoxy-substituted poly(phenylene−ethynylene) (1) and poly(phenylene−vinylene) (5) have been carried out. Large octadecyloxy groups were selected as side chains in order to reduce the effect of π−π stacking interaction on the properties of the polymers in the solid state. This resulted in easy detection of photoconductivity and higher fluorescence quantum yields in solid state. The hybrid conjugation pattern in 4 is more favorable for photoconductivity than that in 2. A red shift of the absorption and emission spectra in solution is observed from 1 over 2b, 3, and 4 ...