An expedient synthesis of flexible nucleosides via a regiocontrolled enzymatic glycosylation of functionalized imidazoles

A versatile two-step synthesis of C4- and C5-arylated 2′-deoxyribosylimidazoles was elaborated by enzymaticN-transglycosylation followed by microwave-assisted Pd-catalysed arylation reactions.

Effects of diesel exhaust particles on macrophage polarization

BACKGROUND

Exposure to diesel exhaust particles (DEP) has long been associated with increased cardiovascular morbidity and mortality. The development of DEP toxicity seems to be linked to inflammation in which macrophages play a critical role. Macrophages can be polarized into proinflammatory M1 or anti-inflammatory M2 macrophages. The aim of this study was to identify the role of inflammation in DEP-induced toxicity by assessing the effects of DEP on macrophage polarization.

METHODS

Monocyte-derived macrophages (Mϕ) were stimulated with interferon γ and lipopolysaccharide or interleukin (IL)-4 to obtain M1 and M2 subtypes, respectively. To test the polarization capacity of DEP, Mϕ cells were exposed to DEP and compared to Mϕ, M1, and M2. We also studied the effects of DEP on already-polarized M1 or M2. The M1 markers assessed were tumor necrosis factor α (TNF-α) and IL-1β, while the M2 markers were the mannose receptor C type 1 (MRC-1) and transglutaminase 2 (TGM2).

RESULTS

Western blots revealed a 31 kDa band corresponding to pro-IL-1β, but only in M1-polarized macrophages. In M1, we also observed an upregulation of TNF-α messenger RNA (mRNA) expression. MRC-1 and TGM2 mRNA expression were only significantly enhanced in M2. DEP had no effect on any of the M1/M2 markers assessed. Moreover, DEP were not able to modify the phenotype of already-polarized M1 or M2.

CONCLUSION

Mϕ incubation with DEP did not have any effect on macrophage polarization, at least on the markers assessed in this study, namely, TNF-α/IL-1β for M1, and MRC-1/TGM2 for M2. Hence, these data argue against an important role of inflammation in DEP-induced vascular toxicity.

Expedient and generic synthesis of imidazole nucleosides by enzymatic transglycosylation

A straightforward route to original imidazole-based nucleosides that makes use of an enzymatic N-transglycosylation step is reported in both the ribo- and deoxyribo-series. To illustrate the scope of this approach, a diverse set of 4-aryl and 4-heteroaryl-1H-imidazoles featuring variable sizes and hydrogen-bonding patterns was prepared using a microwave-assisted Suzuki-Miyaura cross-coupling reaction. These imidazole derivatives were examined as possible substrates for the nucleoside 2'-deoxyribosyltransferase from L. leichmannii and the purine nucleoside phosphorylase from E. coli. The optimum transglycosylation conditions, including the use of co-adjuvants to address solubility issues, were defined. Enzymatic conversion of 4-(hetero)arylimidazoles to 2'-deoxyribo- or ribo-nucleosides proceeded in good to high conversion yields, except bulky hydrophobic imidazole derivatives. Nucleoside deoxyribosyltransferase of class II was found to convert the widest range of functionalized imidazoles into 2'-deoxyribonucleosides and was even capable of bis-glycosylating certain heterocyclic substrates. Our findings should enable chemoenzymatic access to a large diversity of flexible nucleoside analogues as molecular probes, drug candidates and original building blocks for synthetic biology.

Development and assessment of a microwave void-fraction measurement system

The proof of concept of a non-invasive reflection-type void measurement system using microwaves is developed. Before constructing the instrument, governing equations are used to perform numerical simulations of different electrical components (reflectometer, antenna, etc.). Design and preliminary calibrations are performed based on these simulations. The results are then used to manufacture a setup that is installed on a Plexiglas vertical tube containing known volumetric fractions of gas in water at atmospheric conditions. The amount of injected gas and water are accurately controlled and the response of the system is compared with the simulations which confirm the suitability of such a system to study two-phase water-air mixtures.

Behavior of Escherichia coli O26:H11 in the presence of Hafnia alvei in a model cheese ecosystem

This study was designed to evaluate the capacity of three Hafnia strains to inhibit the growth of an E. coli strain O26:H11 in an uncooked pressed model cheese, in the presence or absence of a microbial consortium added to mimic a cheese microbial community. Inoculated at 2 log CFU/ml into pasteurized milk without Hafnia, the E. coli O26:H11 strain reached 5 log CFU/g during cheese-making and survived at levels of 4 to 5 log CFU/g beyond 40 days. Inoculated into milk at 6 log CFU/ml, all three tested Hafnia strains (H. alvei B16 and HA, H. paralvei 920) reached values close to 8 log CFU/g and reduced E. coli O26:H11 counts in cheese on day 1 by 0.8 to 1.4 log CFU/g compared to cheeses inoculated with E. coli O26:H11 and the microbial consortium only. The Hafnia strains slightly reduced counts of Enterococcus faecalis (~-0.5 log from day 1) and promoted Lactobacillus plantarum growth (+0.2 to 0.5 log from day 8) in cheese. They produced small amounts of putrescine (~1.3 mmol/kg) and cadaverine (~0.9 mmol/kg) in cheese after 28 days, and did not affect levels of volatile aroma compounds. Further work on H. alvei strain B16 showed that E. coli O26:H11, inoculated at 2 log CFU/ml, was inhibited by H. alvei B16 inoculated at 6 log CFU/ml and not at 4.5 log CFU/ml. The inhibition was associated neither with lower pH values in cheese after 6 or 24h, nor with higher concentrations of lactic acid. Enhanced concentrations of acetic acid on day 1 in cheese inoculated with H. alvei B16 (4 to 11 mmol/kg) could not fully explain the reduction in E. coli O26:H11 growth. A synergistic interaction between H. alvei B16 and the microbial consortium, resulting in an additional 0.7-log reduction in E. coli O26:H11 counts, was observed from day 8 in model cheeses made from pasteurized milk. However, E. coli O26:H11 survived better during ripening in model cheeses made from raw milk than in those made from pasteurized milk, but this was not associated with an increase in pH values. In vitro approaches are required to investigate the mechanisms and causative agents of this interaction. H. alvei B16 appears to be a promising strain for reducing E. coli O26:H11 growth in cheese, as part of a multi-hurdle approach.

Distinct regulation by lipopolysaccharides of the expression of interleukin-1β by murine macrophages and salivary glands

The regulation of interleukin (IL)-1 expression and secretion by salivary glands and macrophages in response to lipopolysaccharides (LPS) was compared. In wild-type mice, injection of LPS significantly decreased the volume of saliva stimulated by pilocarpine and increased its protein and amylase concentration. It did not modify the salivary concentration of IL-1β. The cytokine was expressed by submandibular acini and ducts. Macrophages also expressed IL-1β but at lower concentration than salivary glands. The pre-incubation of macrophages with LPS increased the phosphorylation of IκB and the expression of IL-1β. Adenosine triphosphate also promoted the secretion of the cytokine by these cells. These responses were absent in submandibular gland cells. These glands expressed CD14, TLR4 and MyD88. P2X(7)-KO mice secreted a lower volume of saliva which contained less proteins and amylase. In conclusion, IL-1β is constitutively expressed by submandibular glands and its secretion is not regulated by a P2X(7) agonist. In these cells, LPS do not activate the nuclear factor-κB-pro-IL-1β axis in spite of the expression of the proteins involved in their recognition.

Role of sodium in mitochondrial membrane depolarization induced by P2X7 receptor activation in submandibular glands

The effect of ATP on mitochondrial membrane depolarization in rat submandibular glands was investigated. Exposure of the cell suspension to high concentrations of ATP induced a sustained depolarization of mitochondrial membrane. This effect was blocked in the presence of magnesium and reproduced by low concentrations of 2',3'-O-(4-benzoylbenzoyl)adenosine 5'-triphosphate (BzATP), suggesting the implication of the P2X(7) purinergic receptor. This point was confirmed by comparison of the response to ATP by wild-type and P2X(7) knock-out (P2X(7)R(-/-)) mice. Mitochondria took up calcium after ATP stimulation but the depolarization of the mitochondrial membrane by ATP was not affected by the removal of calcium from the extracellular medium. It was nearly fully suppressed in the absence of sodium and partially blocked by the mitochondrial Na/Ca exchanger inhibitor 7-chloro-5-(2-chlorophenyl)-1,5-dihydro-4,1-benzothiazepin-2(3H)-one (CGP-37157). Both ATP and monensin increased the uptake of extracellular sodium (as shown by the depolarization of the plasma membrane) but the sodium ionophore did not affect the mitochondrial membrane potential. It is concluded that the activation of P2X(7) receptors depolarizes the mitochondrial membrane. The uptake of extracellular sodium is necessary but not sufficient to induce this response.

Cholesterol depletion perturbs calcium handling by rat submandibular glands

The sensitivity to cholesterol depletion of calcium handling by rat submandibular glands was investigated. The glands were digested with collagenase. After homogenization, the lysate was extracted at 4 degrees C with 0.5% Triton X-100 and the extract was submitted to an ultracentrifugation in a sucrose discontinuous gradient. A population of detergent-resistant membranes (DRM) was collected at the 5%-35% interface. The DRM had a higher content of cholesterol, saturated and long-chain fatty acids. Caveolin-1 and alpha(q/11) were located in these membranes. They were more ordered than vesicles from total cellular lysate as determined by anisotropy measurement. They disappeared after cholesterol extraction with methyl-beta-cyclodextrin (MCD). Exposure of the cellular suspension with MCD nearly abolished the response to carbachol, epinephrine, and substance P and inhibited the activation of phospholipase C (PLC) by these agonists and by sodium fluoride. MCD did not affect the mobilization of intracellular pools of calcium by thapsigargin. It increased the uptake of extracellular calcium or barium and did not inhibit the uptake of calcium after depletion of the intracellular stores of this ion. From these results, it is concluded that Triton X-100 can extract a fraction of membrane resistant to detergents. Treatment of the cells with MCD disrupts these membranes. The coupling between the heterotrimeric GTP-binding protein G(q/11) and poly-phosphoinositide-specific PLC is affected by disruption of these membrane fractions. At the opposite, the store-operated calcium channel (SOCC) is not affected by DRM-disruption.

Synthesis and recognition by DNA polymerases of a reactive nucleoside for DNA diversification

The synthesis of 1-(2-deoxy-beta-D-erythro-pentofuranosyl)imidazole-4-hydrazide having the features of an ambigous base is reported. The recognition of the analogue by DNA polymerases as an incoming triphosphate as well as a template base was investigated. The mutagenic properties was evaluated by PCR. The potential of this new monomer for DNA diversification is illustrated by the reactivity of the nucleobase towards various aldehydes.

Regulation by clozapine of calcium handling by rat submandibular acinar cells

The effect of clozapine on the intracellular concentration of calcium ([Ca2+](i)) in rat submandibular acinar cells was tested. By itself clozapine had no effect on the mobilization of intracellular pools of calcium or on the uptake of extracellular calcium. It inhibited the increase of the [Ca2+](i) in response to carbachol (half-maximal inhibitory concentrations, IC(50)=100nM) and to norepinephrine and epinephrine (IC(50)=10nM) without affecting the response to substance P, extracellular ATP or thapsigargin. Clozapine inhibited the uptake of extracellular calcium in response to epinephrine but not to substance P, ATP or thapsigargin. It also decreased the production of inositol phosphates elicited by epinephrine but not by substance P or fluoride. It is concluded that, by itself, clozapine has no effect on the [Ca2+](i) in rat salivary acinar cells. It selectively inhibits muscarinic and adrenergic receptors in the acinar plasma membrane.

Amperometric determination of choline released from rat submandibular gland acinar cells using a choline oxidase biosensor

A choline (CHO) biosensor based on the determination of H(2)O(2) generated at the electrode surface by the enzyme choline oxidase (CHOx) was developed. The biosensor consisted of CHOx retained onto a horseradish peroxidase (HRP) immobilized solid carbon paste electrode (sCPE). The HRPsCPE contained the molecule phenothiazine as redox mediator and CHOx was physically retained on the electrode surface using a dialysis membrane. Several parameters have been studied such as, mediator amount, influence of applied potential, etc. The CHO measurements were performed in 0.1 M phosphate buffer, pH 7.4. Amperometric detection of CHO was realized at an applied potential of 0.0 mV vs Ag/AgCl. The response is linear over the concentration range 5.0x10(-7)-7.0x10(-5) M, with a detection limit of 1.0x10(-7) M. This biosensor was used to detect choline released from phosphatidylcholine (PC) by phospholipase D (PLD) in isolated rat salivary gland cells stimulated by a purinergic agonist (ATP).

Multiple effects of trichloroethanol on calcium handling in rat submandibular acinar cells

The effect of trichloroethanol (TCEt), the active metabolite of chloral hydrate, on the intracellular concentration of calcium ([Ca(2+)](i)) was investigated in rat submandibular glands (RSMG) acini loaded with fura-2. TCEt (1 - 10 mM) increased the [Ca(2+)](i) independently of the presence of calcium in the extracellular medium. Dichloroethanol (DCEt) and monochloroethanol (MCEt) reproduced the stimulatory effect of TCEt but at much higher concentrations (about 6 fold higher for DCEt and 20 fold higher for MCEt). TCEt mobilized an intracellular pool of calcium, which was depleted by a pretreatment with thapsigargin, an inhibitor of the sarcoplasmic and endoplasmic reticulum calcium-dependent ATPases, but not with FCCP, an uncoupler of mitochondria. TCEt 10 mM inhibited by 50% the thapsigargin-sensitive microsomal Ca(2+)-ATPase. DCEt 10 mM and MCEt 10 mM inhibited the ATPase by 20 and 10%, respectively. TCEt inhibited the increase of the [Ca(2+)](i) and the production of inositol phosphates in response to carbachol, epinephrine and substance P. TCEt inhibited the uptake of calcium mediated by the store-operated calcium channel (SOCC). ATP and Bz-ATP increased the [Ca(2+)](i) in RSMG acini and this effect was blocked by extracellular magnesium, by Coomassie blue and by oxydized ATP (oATP). TCEt potentiated the increase of the [Ca(2+)](i) and of the uptake of extracellular calcium in response to ATP and Bz-ATP. TCEt had no effect on the uptake of barium and of ethidium bromide in response to purinergic agonists. These results suggest that TCEt, at sedative concentrations, exerts various effects on the calcium regulation: (1) it mobilizes a thapsigargin-sensitive intracellular pool of calcium in RSMG acini; (2) it inhibits the uptake of calcium via the SOCC; (3) it inhibits the activation by G protein-coupled receptors of a polyphosphoinositide-specific phospholipase C. It does not interfere with the activation of the ionotropic P2X receptors. The use of chloral hydrate should be avoided in studies exploring the in vivo responses to sialagogues.

Effect of genetic potential and level of feeding on milk protein composition

Two groups of 15 multiparous cows in mid-lactation were used in a Latin square design experiment with 4-week experimental periods. The genetic milk protein concentration level was high in the first group and low in the second. Each group of cows was given in a random order three feeding levels that covered 85, 100 and 115% of energy requirements and 90, 110 and 125% of nitrogen requirements, respeetively. In both groups, increasing level of feeding induced a significant increase in milk yield (+ 2.4 kg/d between lowest and highest levels) and in protein concentration (+ 1.7 g/kg). The proportion of paracasein in total proteins was not altered by either genetics or nutrition. The proportion of casein in total proteins was slightly increased by 0.5 percentage points (P < 0.05) with the intermediate level of feeding. Plasmin and plasminogen activities were not significantly modified by the genetic milk concentration level. Plasmin activity significantly increased with nutrient supplementation, but only in animals of low genetic potential (+ 21% between low and high levels, P < 0.01). Casein composition was not significantly altered by the genetics or level of nutrition. Over the whole range of individual measurements taken (n = 90), the relationships between casein or paracasein and total protein concentrations were linear and very narrow (R2 = 0.92 and 0.95, respectively). The proportion of casein or paracasein in total proteins significantly decreased as plasmin activity increased.

Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes

We have overexpressed in Escherichia coli the thymidylate kinase of Mycobacterium tuberculosis (TMPKmt). Biochemical and physico-chemical characterization of TMPKmt revealed distinct structural and catalytic features when compared to its counterpart from yeast (TMPKy) or E. coli (TMPKec). Denaturation of the dimeric TMPKmt by urea under equilibrium conditions was studied by intrinsic fluorescence and circular dichroism (CD) spectroscopy. It suggested a three-state unfolding mechanism with a monomeric intermediate. On the other hand, 3'-azido-3'-deoxythymidine monophosphate (AZT-MP), which is substrate for TMPKy and TMPKec acts as a potent competitive inhibitor for TMPKMT: We propose a structural model of TMPKmt in which the overall fold described in TMPKy and TMPKec is conserved and slight differences at the level of primary and 3D-structure explain strong variations in the phosphorylation rate of substrate analogs. According to the model, we synthesized dTMP analogs acting either as substrates or specific inhibitors of TMPKMT: This approach based on slight structural differences among similar proteins could be applied to other essential enzymes for the design of new species-specific antimicrobials.

Potentiation by propofol of the response of rat submandibular acinar cells to purinergic agonists

The effect of propofol (2,6-diisopropylphenol) on the intracellular concentration of calcium ([Ca(2+)](i)) and on the response of rat submandibular acini to purinergic agonists was studied. By itself, propofol (60 to 200 microM) slowly increased the [Ca(2+)](i) without affecting the production of inositol phosphates. The increase of the [Ca(2+)](i) involved for about 50% the mobilization of thapsigargin-sensitive intracellular calcium pools. The rest of the calcium originated from a pool distinct from mitochondria. Propofol also increased the uptake of extracellular calcium but not manganese by a mechanism inhibited by nickel. The variation of the [Ca(2+)](i) by propofol provoked a decrease of cell volume measured by light scattering. Propofol increased the effect of a maximal concentration of extracellular ATP on the [Ca(2+)](i). This interaction could be observed when propofol and ATP were added simultaneously to the medium but not when propofol had been removed from the medium before adding ATP. Among ATP analogs, propofol only increased the response to benzoyl-ATP (Bz-ATP). The blockade of P2X(7) receptors with oxidized ATP or Coomassie blue did not prevent the interaction between propofol and ATP. The effect of propofol could also be observed even when the concentration of ATP(4-) was decreased by extracellular magnesium to such a level that only P2X(4) receptors could possibly be activated by the nucleotide. Propofol had no effect on the uptake of manganese, the formation of pores and the activation of phospholipase D in response to a P2X(7) agonist. These results exclude an interaction with this receptor. It is concluded that, in rat submandibular acini, propofol can increase the [Ca(2+)](i) and decrease the cell volume. Propofol can also modulate the activation of P2X(4) receptors by extracellular nucleotides. These effects are observed at concentrations of propofol reached during the induction of anesthesia and might explain why hypersalivation has been reported as one of the side-effects of propofol.

Reverse transcriptase incorporation of 1,5-anhydrohexitol nucleotides

Several reverse transcriptases were studied for their ability to accept anhydrohexitol triphosphates, having a conformationally restricted six-membered ring, as substrate for template-directed synthesis of HNA. It was found that AMV, M-MLV, M-MLV (H(-)), RAV2 and HIV-1 reverse transcriptases were able to recognise the anhydrohexitol triphosphate as substrate and to efficiently catalyse the incorporation of one non-natural anhydrohexitol nucleotide opposite a natural complementary nucleotide. However, only the dimeric enzymes, the RAV2 and HIV-1 reverse transcriptases, seemed to be able to further extend the primer with another anhydrohexitol building block. Subsequently, several HIV-1 mutants (4xAZT, 4xAZT/L100I, L74V, M184V and K65A) were likewise analysed, resulting in selection of K65A and, in particular, M184V as the most succesful mutant HIV-1 reverse transcriptases capable of elongating a DNA primer with several 1,5-anhydrohexitol adenines in an efficient way. Results of kinetic experiments in the presence of this enzyme revealed that incorporation of one anhydrohexitol nucleotide of adenine or thymine gave an increased (for 1,5-anhydrohexitol-ATP) and a slightly decreased (for 1,5-anhydrohexitol-TTP) K(m) value in comparison to that of their natural counterparts. However, no more than four analogues could be inserted under the experimental conditions required for selective incorporation. Investigation of incorporation of the altritol anhydrohexitol nucleotide of adenine in the presence of M184V and Vent (exo(-)) DNA polymerase proved that an adjacent hydroxyl group on C3 of 1,5-anhydrohexitol-ATP has a detrimental effect on the substrate activity of the six-ring analogue. These results could be rationalised based on the X-ray structure of HIV-1 reverse transcriptase.

Modulation by propranolol of the uptake of ethidium bromide by rat submandibular acinar cells exposed to a P2X(7) agonist or to maitotoxin

We have compared the formation of pores in rat submandibular acinar cells in response to 2',3'-O-(4-benzoylbenzoyl) adenosine 5'-triphosphate (Bz-ATP) and maitotoxin. Bz-ATP (100 microM) permeabilized the cells to ethidium bromide. The uptake of ethidium increased to 29+/-1% of maximal uptake in 10 min. DL-Propranolol (300 microM) inhibited the Bz-ATP-induced uptake of ethidium bromide by 40% without affecting the P2X(7)-gated cation channel. The inhibitory effect of DL-propranolol on the formation of pores by Bz-ATP was reproduced by D-propranolol, an optical isomer with very poor beta-blocking activity. Tenidap, an antiinflammatory drug, enhanced the permeabilization in response to Bz-ATP. Propanolol inhibited the response to tenidap plus Bz-ATP. The effect of propranolol was reproduced by labetolol, a beta-adrenergic antagonist with membrane-stabilizing properties, but not by atenolol, which blocks beta-adrenergic receptors but has no effect on the stability of the membrane. In the presence of extracellular calcium, maitotoxin also increased the uptake of ethidium bromide. Tenidap had no effect on this response, which was delayed by propranolol. In conclusion, we have shown that propranolol, in a range of 10-300 microM, inhibits the pore-forming activity of the P2X(7) receptor without affecting the opening of the cation channel coupled to this receptor. This inhibition is not related to its beta-adrenergic blocking activity but rather to its membrane-stabilizing properties. Propranolol also delays the uptake of ethidium bromide in response to maitotoxin. This is in agreement with the current view that P2X(7) agonists and maitotoxin share a common pore.

Enzymatic incorporation in DNA of 1,5-anhydrohexitol nucleotides

The ability of several DNA polymerases to catalyze the template-directed synthesis of duplex oligonucleotides containing a base pair between a nucleotide with anhydrohexitol ring and its natural complement has been investigated. All DNA polymerases were able to accept the chemically synthesized anhydrohexitol triphosphate as substrate and to catalyze the incorporation of one anhydrohexitol nucleotide. However, only family B DNA polymerases succeeded in elongating the primer after the incorporation of an anhydrohexitol nucleotide. In this family, Vent (exo(-)) DNA polymerase is the most successful one and was therefore selected for further investigation. Results revealed that at high enzyme concentrations six hATPs could be incorporated; however, a selective incorporation proved only feasible under experimental conditions where no more than two analogues could be inserted. Also the synthesis of a mixed HNA-DNA sequence was examined. Kinetic parameters for incorporation of one anhydrohexitol adenine nucleoside were similar to those of its natural analogue.

Bromoenol lactone enhances the permeabilization of rat submandibular acinar cells by P2X7 agonists

The permeabilizing effect of P2X(7) agonists was tested in rat submandibular acinar cells using the uptake of ethidium bromide as an index. The uptake of ethidium bromide by acini incubated at 37 degrees C in the presence of 1 mM ATP increased with time and reached after 5 min about 10% of maximal uptake measured in the presence of digitonin. The response to ATP was dose-dependent (half-maximal concentration around 40 microM) and it was decreased when the temperature was lowered to 25 degrees C. Benzoyl-ATP reproduced the response to ATP (half-maximal concentration around 10 microM). UTP or 2-methylthioATP had no effect. The permeabilization in response to ATP was blocked by oxidized ATP and by magnesium and inhibited by Coomassie blue. ATP increased the activity of a calcium-insensitive phospholipase A(2) (iPLA(2)). Bromoenol lactone (BEL) inhibited the iPLA(2) stimulated by ATP but potentiated the uptake of ethidium bromide in response to the purinergic agonist. From these results it is concluded that the activation of P2X(7) receptors permeabilizes rat submandibular acinar cells. The pore-forming activity of the receptor might be negatively regulated by the concomitant activation of the iPLA(2) by the receptor.

Ambiguous base pairing of the purine analogue 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide during PCR

In principle the hydrogen bonding capacities of 1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide (dY), and its N-propyl derivative (dYPr), allow them to pair to all four deoxynucleosides. Their triphosphate derivatives (dYTP and dYPrTP) are preferentially incorporated as dATP analogues in a PCR reaction. However, once incorporated into a DNA template their ambiguous hydrogen bonding potential gave rise to misincorporation at frequencies of approximately 3 x 10(-2) per base per amplification. Most of the substitutions were transitions resulting from rotation about the carboxamide bond when part of the template. Between 11-15% of transversions were noted implying rotation of purine or imidazole moieties about the glycosidic bond. As part of a DNA template, dYPr behaved in the same way as dY, despite its propyl moiety. These deoxyimidazole derivatives are among the most radical departures from the canonical bases used so far as substrates in PCR and could be used to generate mutant gene libraries.

Determination of fat, protein, and lactose in raw milk by Fourier transform infrared spectroscopy and by analysis with a conventional filter-based milk analyzer

The accuracy of fat, crude protein (CP), true protein (TP), and lactose determinations of raw milk by Fourier transform infrared (FTIR) spectroscopy and by analysis with a conventional filter-based milk analyzer was assessed in 6 trials performed over a 10-month period. At each trial, 30 bulk milk samples collected from 15 European countries and 11 reconstituted milks made from raw milk components were analyzed. When calibrations were performed with reconstituted milks at each trial, accuracy standard deviations for fat, CP, TP, and lactose were, respectively, 0.050, 0.048, 0.035, and 0.076 g/100 g for the filter instrument and 0.047, 0.046, 0.042, and 0.065 g/100 g for the FTIR instrument. When a single calibration was made instead of calibrations at each trial, accuracy standard deviations increased for the filter instrument to 0.130, 0.119, 0.121, and 0.083 for fat, CP, TP, and lactose, respectively, and for the FTIR instrument to 0.082, 0.053, 0.044, and 0.084 g/100 g. Because the FTIR instrument provides more spectral information related to milk composition than does the filter instrument, single-calibration FTIR analysis of milk samples collected in different seasons is more accurate. Using reconstituted milks, prepared such that there is no correlation between fat, CP, and lactose, provides a more robust calibration than using genuine bulk milk, especially when milks with unusual composition are analyzed.

Construction of a self-complementary nucleoside from deoxyguanosine

The 8-hydroxyguanine:adenine mispairing scheme that spontaneously occurs in vivo through oxidative metabolism of DNA was edited to obtain a pair closely fitting the Watson-Crick geometry in which 2 purine bases of identical structure but oppositely rotated in the syn and anti configurations are hydrogen-bonded. The structure thus designed, 2-amino-8-hydroxypurine, was synthesized as a DNA precursor from deoxyguanosine in 8 steps by oxidation at carbon 8 of guanine followed by reduction at carbon 6. Polydeoxynucleotides embodying this self-complementary base are expected to undergo direct copying processes through polymerase catalysis.

Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation

Deformylase performs an essential step in the maturation of proteins in eubacteria, by removing the formyl group from the N-terminal methionine residue of ribosome-synthesized polypeptides. In spite of this important role in translation, the enzyme had so far eluded characterization because of its instability. We report the isolation of the deformylase gene of Escherichia coli, def, by overexpression of a genomic library from a high-copy-number plasmid and selection for utilization of the substrate analogue formyl-leucyl-methionine as a source of methionine. The def gene encodes a 169 amino acid polypeptide that bears no obvious resemblance to other known proteins. It forms an operon with the fmt gene, that encodes the initiator methionyl-tRNA(i) transformylase, which was recently characterized (Guillon et al., J. Bacteriol., 174, 4294-4301, 1992). This operon was mapped at min 72 of the E. coli chromosome. The def gene could be inactivated if the fmt gene was also inactivated, or if biosynthesis of N10-formyl-tetrahydrofolate, the formyl donor in methionyl-tRNA(i) transformylation, was blocked by trimethoprim. These findings designate deformylase as a target for antibacterial chemotherapy.

Directed evolution of biosynthetic pathways. Recruitment of cysteine thioethers for constructing the cell wall of Escherichia coli

We report that expansion of thioether biosynthesis in Escherichia coli generates sulfur-containing amino acids that can replace meso-diaminopimelate, the essential amino acid used for cross-linking the cell wall. This was accomplished by jointly overexpressing the metB gene coding for L-cystathionine gamma-synthase and disrupting the metC gene, whose product, L-cystathionine beta-lyase, is responsible for the destruction of L-cystathionine and other L-cysteine thioethers. As a result, meso-lanthionine and L-allo-cystathionine were produced endogenously and incorporated in the peptidoglycan, thereby enabling E. coli strains auxotrophic for diaminopimelate to grow in its absence. Thus, current techniques of metabolic engineering can be applied to evolving the chemical constitution of living cells beyond its present state.

Synthesis and enzymatic polymerisation of 5-amino-1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide-5'- triphosphate

The chemical synthesis of 5-amino-1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide, referred to as dZ, and of its 5'-triphosphate derivative (dZTP), from 2'-deoxyinosine is described. The polymerisation of dZTP using terminal deoxynucleotidyltransferase to give a homopolymer is also presented.

Preparation and use of a universal primed Sepharose for the purification of DNA-binding proteins

We have devised a novel method for the construction of a DNA affinity matrix and tested its use in the purification of a sequence-specific DNA-binding protein from the yeast Saccharomyces cerevisiae. The matrix was prepared in two steps: first, a palindromic oligonucleotide containing an XhoI cohesive end was covalently linked via its loop to a Sepharose matrix; second, directly to this 'universal' primed Sepharose was ligated a 37-bp oligonucleotide, with XhoI cohesive ends, containing the sequence of the upstream activation sequence 1 (UAS1) site of the yeast iso-1-cytochrome c (CYC1) gene. After fractionating a yeast crude extract through DEAE-cellulose, heparin ultrogel and Mono Q columns, a single pass through the affinity matrix allowed the purification to apparent homogeneity of the 120-kDa protein factor P, which is responsible for the binding to the UAS1 site.

IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations

Tridecamers containing a central no-base residue (X) have been synthesized and hybridized to their complementary strands, so as to constitute duplexes consisting of two hexamers separated by central mismatched X-A or X-T pairs. The effect of the introduction of this deoxyribose derivative on duplex stability was investigated by measuring UV absorbance as a function of salt concentration and temperature. As expected, the duplexes containing the abnormal base pairs (X-T and X-A) are less stable when compared to the totally complementary duplexes (A-T and T-A). The X-T mismatched duplex shows the most unstable thermodynamical behaviour. The conformational changes of these duplexes were studied by IR spectroscopy in condensed phase as a function of water content. At high relative humidity, the IR spectra show that these tridecamers form B-type double stranded duplex structures. If the water content is decreased, only the duplexes m5CGm5CGCTXAGCTTC GCGCGAATCGAAG and, to a lesser degree, m5CGm5CGCTXAGCTTC GCGGCATTCGAAG undergo a partial B---Z transition involving the methylated hexamer, the conformation of the second segment remaining of the B type. These results show that only one apurinic residue leads to a flexible junction between B and Z forms in a short duplex containing 5-methyl-2'-deoxycytidines.

NMR, CD and IR spectroscopies of a tridecanucleotide containing a no-base residue: coexistence of B and Z conformations

The synthesis of the tridecadeoxynucleotide d(CGm5CGCGxACATGT), where x is the 1-cyano-2-deoxy-beta-D-erythropentofuranose, is described. The NMR, IR, CD studies at various salt concentrations and temperatures of this oligomer show that the B and Z conformations are simultaneously present in the same short DNA fragment. A single apurinic residue is sufficient for the coexistence of the B and Z helices on this oligomer.