QTIPS: A novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments

Stable incorporation of labeled amino acids in cell culture is a simple approach to label proteins in vivo for mass spectrometric quantification. Full incorporation of isotopically heavy amino acids facilitates accurate quantification of proteins from different cultures, yet analysis methods for determination of incorporation are cumbersome and time-consuming. We present QTIPS, Quantification by Total Identified Peptides for SILAC, a straightforward, accurate method to determine the level of heavy amino acid incorporation throughout a population of peptides detected by mass spectrometry. Using QTIPS, we show that the incorporation of heavy amino acids in baker’s yeast is unaffected by the use of prototrophic strains, indicating that auxotrophy is not a requirement for SILAC experiments in this organism. This method has general utility for multiple applications where isotopic labeling is used for quantification in mass spectrometry.     

Incorporation of lithium into gallium phosphide electrodes from lithium salt electrolytes in the presence of crown ethers

Anodic stripping analysis of cathodically polarized n- and p-type Gap electrodes has revealed that incorporation of lithium into a surface region of the electrodes takes place in aqueous electrolytes containing lithium salts and crown ethers such as 15-crown-5. Changes in spectral response of p-type electrodes caused by cathodic polarization in such electrolytes give support to the lithium incorporation. The redox potential for the incorporation reaction was estimated to lie somewhere between −1.95 and −0.91 V vs. SCE. The roles of crown ethers in the incorporation reaction are discussed.     

Incorporation methods for cholic acid chitosan-g-mPEG self-assembly micellar system containing camptothecin

A water-insoluble anticancer agent, camptothecin (CPT) was incorporated to a polymeric micelle carrier system preparing from cholic acid chitosan-grafted poly (ethylene glycol) methyl ether (CS-mPEG-CA). CS-mPEG-CA formed a core–shell micellar structure with a critical micelle concentration (CMC) of 7.08 μg/ml. Incorporation efficiency was investigated by varying physical incorporation method and initial drug loading. Among three incorporation methods (dialysis, emulsion and evaporation methods), an emulsion method showed the highest CPT incorporation efficiency. Increasing the initial CPT loading from 5 to 40%, the incorporation efficiency decreased. In all examined CPT-loaded CS-mPEG-CA micelles, 5% initial drug loading showed the highest drug incorporation efficiency. Release of CPT from the micelles was sustained when increasing the initial CPT loading. This indicates the importance of incorporation method and the initial drug loading to obtain the optimum particle size with high drug loading and sustained drug release. When compared to the unprotected CPT, CPT-loaded CS-mPEG-CA micelles were able to prevent the hydrolysis of the lactone group of the drug. This novel CS-mPEG-CA polymer presents considerable potential interest in the further development of CPT carrier.     

PHOTOINDUCTION OF PHARBITIS FLOWERING: RELATIONSHIP TO RNA SYNTHESIS AND OTHER METABOLIC EVENTS

We have previously shown that a wave of enhanced uridine incorporation into RNA occurs in the more vegetative parts of the plumule at the end of the single dark period that evokes flowering in Pharbitis nil. We demonstrate here that a light break that suppresses flowering suppresses this wave as well. It does not shift the kinetics of the wave of uridine incorporation to a different time. The enhanced incorporation is into all RNA fractions. It had been concluded from excision experiments that the floral stimulus reaches the apex much after photoinduction. There is a metabolic shock caused by such excision of the cotyledons or surgical removal of the plumule that can suppress flowering if it is performed near the end of the inductive dark period. The terminal bud is more affected by this shock than lateral buds. Excision of the cotyledons enhances the rate of incorporation of exogenous uridine into the plumule. We propose that the “floral stimulus” stimulating incorporation into RNA reaches the plumule immediately after the end of the critical dark period.     

Effects of Combinatorial Expression of selA,selB and selC Genes on the Efficiency of Selenocysteine Incorporation in Escherichia coli

In Escherichia coli, four gene products(selA, selB, selC and selD) and a selenocysteine(Sec) insertion sequence(SECIS) are required for the correct translation of UGA codons encoding Sec. Previous studies have shown that the stoichiometry of selenoproteine mRNA and elongation factor SelB affect the efficiency of Sec incorporation. Herein lies a detailed analysis of the effects of co-expressing selA, selB and selC genes under inducible promoters on the incorporation efficiency of Sec. Over-expression of either selA or selB reduced the efficiency of Sec incorporation by 61.1% or 11.6%, respectively, compared to the over-expression of the reporter vector alone did. Concomitant over-expression of selC with selA or selB completely reversed the reduce of the efficiency of Sec but still reduced the efficiency of the incorporation relative to that observed for expression of selC alone. Over-expression of selC gene alone under L-arabinose induction reduced the efficiency of the incorporation relative to that observed for co-expressing selC with selA and selB under the control of its endogenous promoter in the absence of L-arabinose. Co-expression of selA, selB and selC with selA or selB under the control of inducible promoters increased the efficiency of Sec incorporation by 69.7%. Moreover, inducing selenoprotein-related gene expression during the late exponential phase increased the efficiency of Sec incorporation by a factor of 5.4 relative to that observed for the reporter vector alone. These results suggest that the co-expression of selA, selB and selC in Escherichia coli under the control of inducible promoters is a viable and promising strategy for increasing the yields of selenoproteins.     

Anti-scratch and transparency properties of transparent conductive carbon nanotube films improved by incorporating polyethoxysiloxane

Transparent conductive films of single-walled carbon nanotubes (SWCNTs) were fabricated by a simple method to significantly enhance anti-scratch and transparency properties by the incorporation of polyethoxysiloxane (PES). The reasons for changes in the mechanical properties and transmittance were investigated through the reflection property and morphology of thin films. With the incorporation of PES, the sheet resistance of the SWCNT thin film remained unchanged after the anti-scratch test. It was found that the transmittance of the thin films suddenly increased when the thickness of the PES layer was ca 100 nm. Although the PES incorporation resulted in a slight increase in the sheet resistance, the experimental results revealed that the sheet resistance of the SWCNT thin films with PES was lower than that of films without PES for the same transmittance due to the increase of the transmittance caused by the PES incorporation. We have demonstrated that the sheet resistance was halved at a transmittance of ～86% due to PES incorporation. SWCNT thin films with PES showed better electrical properties than those without PES after a bend test.     

Should we use one‐, or multi‐compartment models to describe 13C incorporation into animal tissues?

Understanding rates of isotopic incorporation and discrimination factors between tissues and diet is an important focus of ecologists seeking to use stable isotopes to track temporal changes in diet. We used a diet-shift experiment to measure differences among tissues in (13)C incorporation rates in house sparrows (Passer domesticus). We predicted faster incorporation rates in splanchnic than in structural tissues. We also assessed whether isotopic incorporation data were better supported by the one-compartment models most commonly used by ecologists or by multi-compartment models. We found large differences in the residence time of (13)C among tissues and, as predicted, splanchnic tissues had faster rates of isotopic incorporation and thus shorter retention times than structural tissues. We found that one-compartment models supported isotopic incorporation data better in breath, excreta, red blood cells, bone collagen, and claw tissues. However, data in plasma, intestine, liver, pectoralis muscle, gizzard, and intestine tissues supported two-compartment models. More importantly, the inferences that we derived from the two types of models differed. Two-compartment models estimated longer (13)C residence times, and smaller tissue to diet differences in isotopic composition, than one-compartment models. Our study highlights the importance of considering both one- and multi-compartment models when interpreting laboratory and field isotopic incorporation studies. It also emphasizes the opportunities that measuring several tissues with contrasting isotopic residence times offer to elucidate animal diets at different time scales. Copyright (c) 2008 John Wiley & Sons, Ltd.     

A new incorporation mechanism for trivalent actinides into bioapatite: a TRLFS and EXAFS study

One of the most toxic byproducts of nuclear power and weapons production is the transuranics, which have a high radiotoxicity and long biological half-life due to their tendency to accumulate in the skeletal system. This accumulation is inhomogeneous and has been associated with the chemical properties and structure of the bone material rather than its location or function. This suggests a chemical driving force to incorporation and requires an atomic scale mechanistic understanding of the incorporation process. Here we propose a new incorporation mechanism for trivalent actinides and lanthanides into synthetic and biologically produced hydroxyapatite. Time-resolved laser fluorescence spectroscopy and extended X-ray absorption fine structure have been used to demonstrate that trivalent actinides and lanthanides incorporate into the amorphous grain boundaries of apatite. This incorporation site can be used to explain patterns in uptake and distribution of radionuclides in the mammalian skeletal system.     

Effect of stratospheric ozone depletion and enhanced ultraviolet radiation on marine bacteria at Palmer Station, Antarctica in the early austral spring

We investigated the interactions between ozone-depleted air masses and subsequent changes in UVB on marine bacterial abundance and production at Palmer Station, Antarctica from September to November 1999. During periods of low total column ozone (TCO), bacterial cell concentrations declined by 57%. Photoinhibition of bacterial [(3)H]-leucine (Leu) and [(3)H]-thymidine (TdR) incorporation due to UVB was greatest during periods of low TCO in September and early October. During diel ( approximately 28 h) exposure experiments, light treatment samples exhibited >75-100% inhibition of TdR incorporation by mid-afternoon. Leu incorporation exhibited maximum inhibition (50-100%) at sunset and early evening hours. Leu and TdR incorporation in light treatment samples did not exhibit recovery during subsequent periods of darkness. Bacterial Leu and TdR incorporation rates were inversely related to Setlow Dose during a period of recovery from low TCO. These data further suggested a threshold exposure below which bacterial Leu and TdR incorporation recovered rapidly. Recovery of bacterial production after acute Setlow Dose exposures lagged recovery of TCO and was linearly related to TCO measured 2 days previously. This lag in recovery may have resulted from the energetically expensive repair of UVR-induced DNA damage acquired during periods of low TCO.     

Biosynthetic origins of C-P bond containing tripeptide K-26

[reaction: see text] Primary metabolic precursors for K-26, a naturally occurring tripeptide phosphonic acid from Actinomyces sp. K-26, are investigated by heavy-atom isotope labeled substrate incorporation experiments. A highly sensitive selected reaction monitoring (SRM)-based method for isotopic incorporation estimation in natural products is reported. The incorporation of heavy-atom isotope labeled tyrosine compounds into the (R)-1-amino-2-(4-hydroxyphenyl)-ethylphosphonic acid moiety of compound K-26 suggests a new mechanism of biosynthesis of phosphonate functionality in natural products.     

Discrimination Between 8‐Oxo‐2′‐Deoxyguanosine and 2′‐Deoxyguanosine in DNA by the Single Nucleotide Primer Extension Reaction with Adap Triphosphate

The adenosine derivative of 2‐oxo‐1,3‐diazaphenoxazine (Adap) exhibits a superb ability to recognize and form base pairs with 8‐oxo‐2′‐deoxyguanosine (8‐oxo‐dG) in duplex DNA. In this study, the triphosphate of Adap (dAdapTP) was synthesized and tested for single nucleotide incorporation into primer strands using the Klenow Fragment. The efficiency of dAdapTP incorporation into 8‐oxo‐dG‐containing templates was more than 36‐fold higher than with dG‐containing templates, and provides better discrimination than does the incorporation of natural 2′‐deoxyadenosine triphosphate (dATP). The selective incorporation of dAdapTP into 8‐oxo‐dG templates was therefore applied to the detection of 8‐oxo‐dG in human telomeric DNA sequences extracted from H₂O₂‐treated HeLa cells. The enzymatic incorporation of dAdapTP into 8‐oxo‐dG‐containing templates may provide a novel basis for sequencing oxidative DNA damage in the genome.     

Incorporation of nonionic emulsifiers inside particles in emulsion polymerization: mechanism and methods of suppression

Emulsion polymerizations of styrene were carried out using two kinds of polyoxyethylene lauryl ether nonionic emulsifiers having different hydrophilic-lipophilic balances (HLB): Emulgen 109P (HLB 13.6); and Emulgen 150 (HLB 18.3). In both cases, incorporation of emulsifier inside polystyrene (PS) particles was clearly observed, as previously reported for the emulsion polymerization of styrene and methacrylic acid using polyoxyethylene nonyl phenyl ether (Emulgen 911, HLB 13.7) nonionic emulsifier. The generality of the incorporation phenomenon of nonionic emulsifier inside polymer particles in emulsion polymerization was clarified. In the case of Emulgen 109P, which is more hydrophobic than Emulgen 150, about 30% of the total amount was incorporated inside the PS particles, higher than for Emulgen 150 (15%). The difference seemed to be ascribed to the difference in the affinities between the nonionic emulsifiers and styrene, which cause the incorporation of emulsifier. On the basis of this idea, suppression of the incorporation was achieved by decreasing the polymerization temperature and the monomer-feed rate. This strongly supports the proposed incorporation mechanism.     

Gas-phase ion/ion reactions of transition metal complex cations with multiply charged oligodeoxynucleotide anions

Multiply deprotonated hexadeoxyadenylate anions, (A6-nH)(n-), where n = 3-5, have been subjected to reaction with a range of divalent transition-metal complex cations in the gas phase. The cations studied included the bis- and tris-1,10-phenanthroline complexes of CuII, FeII, and CoII, as well as the tris-1,10-phenanthroline complex of RuII. In addition, the hexadeoxyadenylate anions were subjected to reaction with the singly charged FeIII and CoIIIN,N'-ethylenebis(salicylideneiminato) complexes. The major competing reaction channels are electron-transfer from the oligodeoxynucleotide anion to the cation, the formation of a complex between the anion and cation, and the incorporation of the transition-metal into the oligodeoxynucleotide. The latter process proceeds via the anion/cation complex and involves displacement of the ligand(s) in the transition-metal complex by the oligodeoxynucleotide. Competition between the various reaction channels is governed by the identity of the transition-metal cation, the coordination environment of the metal complex, and the oligodeoxynucleotide charge state. In the case of the divalent metal phenanthroline complexes, competition between electron-transfer and metal ion incorporation is particularly sensitive to the coordination number of the reagent metal complexes. Both electron-transfer and metal ion incorporation occur to significant extents with the bis-phenanthroline ions, whereas the tris-phenanthroline ions react predominantly by metal ion incorporation. To our knowledge this work reports the first observations of the gas-phase incorporation of multivalent transition-metal cations into oligodeoxynucleotide anions and represents a means for the selective incorporation of transition-metal counter-ions into gaseous oligodeoxynucleotides.     

Concomitant increase in putrescine incorporation with transferrin uptake into rat reticulocytes.

Concomitant increase in putrescine incorporation with transferrin uptake into rat reticulocytes was found. [14C]Putrescine incorporation occurred in the presence of transferrin at 37 degrees C. The subcellular distribution of incorporated [14C]putrescine showed that the incorporation in the plasma membrane time dependently increased. Both 125I-labeled transferrin uptake and [14C]putrescine incorporation decreased when ethylene glycol bis(2-aminoethyl ether)-N,N,N',N'-tetraacetic acid was added, while it increased with the addition of A23187.     

Incorporation of a lipophilic series,as coenzyme Q Homologs,din phospholipid vesicles

The incorporation of Coenzyme Q† homologs into phospholipid vesicles to achieve a concentration close to the quinone content of mitochondria has been studied with different methods. The results obtained can be summarized as follows: (a) stirring does not lead to comparable incorporation of the various CoQs tested; (b) ultrasonic irradiation results in a homogeneous incorporation both of the naturally occurring homologs of Coenzyme Q (polyisoprenoid chainlength ranging from ten to six units) and of the nonphysiological shorter chain homologs; (c) ethanol injection, which is a simple, rapid, and inexpensive technique, gives results comparable to those obtained by ultrasonication.     

Metal Ion Incorporated VPO Phases as Novel Catalysts

Vanadium phosphates function as catalysts for the selective oxidation of hydrocarbons with their activity being strongly dependent on their structure. Consequently, attempts have been made to synthesise novel phases in the VPO system through metal ion incorporation and evaluate the catalytic activity of these phases. It is shown that the incorporation of palladium or platinum leads to novel phases which vary according to the method of syntheses. The incorporated metal ions are catalytically active both for oxidation and reduction reactions with the activity varying according to the mode of incorporation. These phases constitute a novel class of compounds in which oxidation centres are substituted or dispersed within a VPO oxidation catalyst.     

RANDOM DISTRIBUTION OF HIGHLY REPETITIVE AND INTERMEDIATE FREQUENCY MOUSE L-929 CELL DNA SEQUENCES SYNTHESIZED AFTER UV LIGHT EXPOSURE

Abstract— The DNA precursor ³H-thymidine incorporation rate (dpm/pg DNA) in mouse L-929 cells decreases immediately after exposure to UV light. This decrease is initially dose dependent, but at exposures greater than 22.5 J/m² appears to be radio-resistant. This was not explained by measurements of uptake of ³H-thymidine into the acid soluble pool (dpm/pg DNA). The radio-resistant incorporation amounted to approximately 35% of the control rate. DNA reassociation ("C₀T") studies were performed with DNA labeled with ³H-thymidine immediately after exposure of L-929 cells with a dose of UV resulting in radio-resistant incorporation to determine whether this radio-resistant incorporation was occurring in sequences of a particular repetitious frequency. These studies, performed in the highly repetitive to intermediate range, showed that the radio-resistant incorporation was occurring in DNA of all classes of repetitious frequency. DNA synthesized at different times after UV exposure, during the period when post-replication repair can occur, was similarly labeled for short intervals and isolated. The DNA reassociation studies showed that this DNA synthesis was also of all classes of repetitious frequency.     

Carotenoid incorporation into microsomes: yields, stability and membrane dynamics

The carotenoids beta-carotene (BC), lycopene (LYC), lutein (LUT), zeaxanthin (ZEA), canthaxanthin (CTX) and astaxanthin (ASTA) have been incorporated into pig liver microsomes. Effective incorporation concentrations in the range of about 1-6 nmol/mg microsomal protein were obtained. A stability test at room temperature revealed that after 3 h BC and LYC had decayed totally whereas, gradually, CTX (46%), LUT (21%), ASTA (17%) and ZEA (5%) decayed. Biophysical parameters of the microsomal membrane were changed hardly by the incorporation of carotenoids. A small rigidification may occur. Membrane anisotropy seems to offer only a small tolerance for incorporation of carotenoids and seems to limit the achievable incorporation concentrations of the carotenoids into microsomes. Microsomes instead of liposomes should be preferred as a membrane model to study mutual effects of carotenoids and membrane dynamics.     

Phenanthriporphyrin: An Antiaromatic Aceneporphyrinoid as a Ligand for a Hypervalent Organophosphorus(V) Moiety

The incorporation of a phenanthrene moiety into a porphyrin framework results in the formation of a hybrid macrocycle—phenanthriporphyrin—merging the structural features of polycyclic aromatic hydrocarbons and porphyrins. An antiaromatic aceneporphyrinoid, adopting the trianionic {CCNN} core, is suitable for the incorporation of a phosphorus(V) center to form a hypervalent organophosphorus(V) derivative.     

Effect of promoters on the structures and properties of the RuB/γ-Al2O3 catalyst

Effect of promoters (Co, Fe, Sn, Zn) on structures, properties and catalytic performance of RuB/γ-Al₂O₃ catalyst was studied using in situ XRD, TEM, H₂-TPD, XPS and liquid-phase hydrogenation of ethyl lactate to 1,2-propanediol (PDO). It was found that incorporation of Sn or Fe improved the dispersion and thermal stability of RuB. The electron density of Ru and the strength and capacity of H₂ adsorption on the RuB catalyst were also enhanced by the incorporation of Sn or Fe. The incorporation of Co or Zn led to a significant decrease in H₂ adsorption capacity of the RuB catalyst. Both ethyl lactate conversion and selectivity to 1,2-PDO increased with the incorporation of Sn or Fe. The ethyl lactate conversion decreased sharply with the incorporation of Zn or Co accompanied by an increase in selectivity to 1,2-PDO and lactic acid. The effect of promoters on reaction behavior was discussed on the basis of the characterizations.