A mixed NCP pincer palladacycle as catalyst precursor for the coupling of aryl halides with aryl boronic acids

The reaction of phosphinite Me₂NCH₂CC(CH₂)₂OP(i-Pr)₂ (2) with Li₂PdCl₄ in methanol at room temperature affords the air and water stable mixed pincer palladacycle (Me₂NCH₂(Cl)CC(CH₂)₂OP(i-Pr)₂-κNκCκP)PdCl (3) whose structure has been ascertained by means of an X-ray diffraction study. This pincer palladacycle is a highly efficient catalyst precursor for the coupling of aryl boronic acids and aryl chlorides. Both electron-rich and -poor aryl chlorides are efficiently coupled in the presence of 3 to furnish the corresponding cross-coupled products in excellent yields, and a wide variety of functional groups are tolerated in both aryl chloride and aryl boronic acid. The experimental protocol has also been extended for the coupling of iodo and bromo arenes with aryl boronic acids for the generation of hindered biphenyls. The coupling process afforded very good yields of biphenyl products containing two ortho substituents. Steric hindrance is more sensitive for ortho substituents in the aryl boronic acid and is more pronounced when the coupling reaction involves three ortho substituents.     

Nonrandom Intragenic Variations in Patterns of Codon Bias Implicate a Sequential Interplay Between Transitional Genetic Drift and Functional Amino Acid Selection

Although most codon third bases appear to be functionless, the synonymous codons so defined exhibit a strikingly nonrandom distribution (codon bias) within human and other genes. To examine this phenomenon further, we generated a database of DNA sequences encoding human transmembrane cell-surface receptor proteins. Using this database we show here that the guanine and cytosine content of codon third bases (GC3) varies intragenically with the nature of the specified receptor domains (transmembrane > extracellular > intracellular domains; p < 0.001), the phenotype of the encoded amino acids (hydrophobic > hydrophilic > neutral amino acids; p < 0.001), and the receptor affiliation of the transmembrane domain superfamily (G-protein- coupled receptors > receptor tyrosine kinases; p < 0.001). Within gene regions specifying transmembrane domains, GC3 declines as domain functionality becomes redundant with increasing hydrophobicity (p < 0.001). Codons containing the second-base cytosine (XCZ, which encodes neutral amino acids) are selectively depleted of third-base adenine content (A3: XCA codons) when encoding transmembrane domain residues, consistent with positive selection for transitional mutation of XCG to XTG (which encodes hydrophobic amino acids) rather than to the synonymous XCA. Supporting this XCG XTG mechanism of codon bias, the G3:A3 ratio of codons specifying the transmembrane amino acid glycine (GGZ) is intermediate between that of its functional homolog alanine (GCZ) and that of hydrophobic valine (GTZ), even though the C3:T3 ratios are similar. Conversely, nearest-neighbor analysis of third bases 5 to codons specifying valine and leucine (CTZ) confirms a significant difference in C3:T3 but not G3:A3 ratios (i.e., C3/G1 T3/G1 > C3/A1; p < 0.001), consistent with the functionally advantageous retention of hydrophobic residues. These data raise the possibility that patterns of intragenic codon bias reflect a balance between negative and positive selection, suggesting in turn that analysis of codon third-base usage may help to predict the functional significance of encoded products. Supplementary information: Current address: (K. Lin) College of Life Sciences, Beijing Normal University, Beijing 100875, China     

The effect of cold-induced increased metabolic rate on the rate of <Superscript>13</Superscript>C and <Superscript>15</Superscript>N incorporation in house sparrows (<Emphasis Type="Italic">Passer domesticus</Emphasis>)

Animals with high metabolic rates are believed to have high rates of carbon and nitrogen isotopic incorporation. We hypothesized that (1) chronic exposure to cold, and hence an increase in metabolic rate, would increase the rate of isotopic incorporation of both ¹³C and ¹⁵N into red blood cells; and (2) that the rate of isotopic incorporation into red blood cells would be allometrically related to body mass. Two groups of sparrows were chronically exposed to either 5 or 22°C and switched from a ¹³C-depleted C₃-plant diet to a more ¹³C-enriched C₄-plant one. We used respirometry to estimate the resting metabolic rate of birds exposed chronically to our two experimental temperatures. The allometric relationship between the rate of ¹³C incorporation into blood and body mass was determined from published data. The of birds at 5°C was 1.9 times higher than that of birds at 22°C. Chronic exposure to a low temperature did not have an effect on the rate of isotopic incorporation of ¹⁵N save for a very small effect on the incorporation of ¹³C. The isotopic incorporation rate of ¹³C was 1.5 times faster than that of ¹⁵N. The fractional rate of ¹³C incorporation into avian blood was allometrically related to body mass with an exponent similar to −1/4. We conclude that the relationship between metabolic rate and the rate of isotopic incorporation into an animal’s tissues is indirect. It is probably mediated by protein turnover and thus more complex than previous studies have assumed.     

CELL CYCLE STUDY UP TO THE TIME OF HATCHING IN THE EMBRYOS OF THE SEA URCHIN,HEMICENTROTUS PULCHERRIMUS*

Cell cycles have been analyzed in 10 divisions up to the time of hatching in the embryos of the sea urchin, Hemicentrotus pulcherrimus. In the first 5 cleavages, division synchrony is very high. On the average, T_GC= 55.4 min, T_G1= 0 min, T_s= 12 min, T_G2=±0 min, T_M= 42 min. In the remaining 5 cleavages, T_GC becomes longer: 70 min for the 7th to 246 min for the 10th cleavage. G₁ and G₂ become definitely recognizable and become longer along with T_s. T_M stays more or less constant. Plots of the changing lengths of the four compartments (G₁, S, G₂, M) on the Y-axis against T_GC (X-axis) can be fitted to the following 4 regression equations; T_G1= 0.28T_GC - 19.7, T_s= 0.609T_GC - 15.2, T_G2= 0.104T_GC - 4.72 and T_M= 0.007T_GC+ 39.6.     

Glycine-U-14C Metabolism in Young Rats Fed the 10% Casein Diets Containing Excess Glycine

Nine hours after rats fed ad libitum for 14 days a 10% caein diet (10C), a 10% casein diet containing 7% glycine (10C7G) and a 10% casein diet containing 7% glycine with 1.4% l-arginine HCI and 0.9% l-methionine (10C7GArgMet) were force-fed 10 ml of each diet suspension containing 5 μCi of glycine-U-¹⁴C per 100 g of body weight, the radioactivity recoveries of ¹⁴C in expired CO₂, tissue components and urine were determined.

The radioactivity recovery of ¹⁴C in the expired C0₂ of the 10C7G group was generally higher than that of the 10C7GArgMet group, and those of both groups would have been much higher than that of the 10C group unless the isotope had been diluted. The amount of expiratory ¹⁴C of rats fed a 25 % casein diet containing 7% glycine was not different from that of the 10C7G group. The recovery of ¹⁴C in the trichloroacetic acid (TCA) soluble fraction of muscle of the 10C7G and the 10C7GArgMet groups were greater than that of the 10C group, but there was no difference between the 10C7G and the 10C7GArgMet groups. The recoveries of ¹⁴C in the TCA soluble fraction and protein of plasma and liver, and the muscle protein were negligible in all the groups. The amount of glycine-¹⁴C incorporated into the carcass lipids of the 10C7GArgMet group was larger than that of other groups. Those in the carcass lipids of the 10C7G and the 10C7GArgMet groups would have been much higher than that of the 10C group unless the dilution of the isotope had taken place. The recoveries of ¹⁴C in the liver and muscle glycogen, and liver lipids were remarkably small in all the groups. From the above results, it was suggested that the degradation of glycine-¹⁴C to expiratory CO₂ was not accelerated, but the rate of incorporation of the isotope into carcass lipids was increased by the supplementation of l-arginine and l-methionine to the 10C7G diet as compared with that of rats fed the 10C7G diet.     

Catabolism of caffeine and related purine alkaloids in leaves ofCoffea arabica L.

In a study of purine alkaloid catabolism pathways in coffee,¹⁴C-labelled theobromine, caffeine, theophylline and xanthine were incubated with leaves ofCoffea arabica. Incorporation of label into¹⁴CO₂ was determined and methanol-soluble metabolites were analysed by high-performance liquid chromatography-radiocounting. The data obtained demonstrate catabolism of caffeine theophylline 3-methylxanthine xanthine. Xanthine is degraded further by the conventional purine catabolism pathway to CO₂ and NH₃ via uric acid, allantoin and allantoic acid. The conversion of caffeine to theophylline is the rate-limiting step in purine alkaloid catabolism and provides a ready explanation for the high concentration of endogenous caffeine found inC. arabica leaves. Although theobromine is converted primarily to caffeine, a small portion of the theobromine pool appears to be degraded to xanthine by a caffeine-independent pathway. In addition to being broken down to CO₂, via the purine catabolism pathway, xanthine is metabolised to 7-methylxanthine. Metabolism of [2-¹⁴C]xanthine byC. arabica leaves in the presence of 5 mM allopurinol results in very large increases in incorporation of radioactivity into 7-methylxanthine as degradation of the substrate via the purine catabolism pathway is blocked. The identity of 7-methylxanthine in these studies was confirmed by gas chromatography-mass spectrometry analysis.Abbreviations HPLC-RC high-performance liquid chromatography-radiocounting This work was supported by the British Council which provided H.A. with Japan-UK travel grants. F.M.G. was supported by a Biotechnology and Biological Sciences Research Council grant to A.C.     

<Emphasis Type="Italic">Gallaecimonas mangrovi</Emphasis> sp. nov., a novel bacterium isolated from mangrove sediment

A Gram-stain negative, rod-shaped, non-motile, strictly aerobic bacterium HK-28^T was isolated from a mangrove sediment sample in Haikou city, Hainan Province, China. Strain HK-28^T was able to grow at 10–45 °C (optimum 25–30 °C), pH 5.0–8.5 (optimum 6.0–7.0) and 0.5–12.0% (w/v) NaCl (optimum 1.0–3.0%, w/v). The major cellular fatty acids were C_16:0, Summed Feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), Summed Feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), C_17:0, C_12:0 3-OH and C_17:1ω8c. Ubiquinone-8 (Q-8) was the predominant respiratory quinone. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, four unidentified phospholipids, two unidentified glycolipid, an unidentified glycophospholipid, an unidentified aminolipid and an unidentified lipid. The DNA G+C content was 50.2 mol%. Accoroding to 16S rRNA gene sequence similarities, strain HK-28^T shared 97.1 and 96.7% sequence similarities to the validly named species Gallaecimonas xiamenensis MCCC 1A01354^T and Gallaecimonas pentaromativorans MCCC 1A06435^T, respectively, and shared lower sequence similarities (<?92.0%) to all other genera. Phylogenetic analysis showed strain HK-28^T was clustered with G. pentaromativorans MCCC 1A06435^T and G. xiamenensis MCCC 1A01354^T. Strain HK-28^T showed low DNA–DNA relatedness with G. xiamenensis MCCC 1A01354^T (28.3?±?1.5%) and G. pentaromativorans MCCC 1A06435^T (25.2?±?2.4%). On the basis of phenotypic, chemotaxonomic and genotypic characteristics, strain HK-28^T is considered to represent a novel species in the genus Gallaecimonas, for which the name Gallaecimonas mangrovi sp. nov. is proposed. The type strain is HK-28^T (=?KCTC 62177^T?=?MCCC 1K03441).     

Cu(II) and Ni(II) complexes based on monofunctional and dendrimeric pyrrole-imine ligands: Applications in catalytic liquid phase hydroxylation of phenol

New bis(pyrrolide-imine) copper(II) and Ni(II) complexes C1 and C2 [{ (C₃H₇)-NCH (C₄H₃N)}₂Cu], [{(C₃H₇)-NCH-(C₄H₃N)}₂Ni] as well as the bimetallic dendrimeric (pyrrolide-imine) copper(II) and nickel(II) complexes C3 and C4, [DAB-{(NCH-C₄H₃N)₄}Cu₂], [DAB-{(NCH-C₄H₃N)₄}Ni₂] (DAB = G1-polypropyleneimine dendrimer with a diaminobutane core) were prepared in good yields. The structure and composition of the complexes were confirmed by a combination of analytical techniques. These complexes were investigated as catalysts in the hydroxylation of phenol in aqueous media in the pH range of 2-6 for the mononuclear complexes, C1 and C2 while the bimetallic systems, C3 and C4 were studied over the pH range 2-8. H₂O₂ was used as the oxidant under an oxygen atmosphere. The copper systems generally showed higher activity as compared to their nickel analogues. Catechol was the predominant product followed by hydroquinone with small amounts of para-benzoquinone. The nickel complexes showed better selectivity for catechol. The pH of the reaction medium also plays a role in both activity and selectivity with pH 3 being optimal for activity and pH 6 for selectivity to catechol.     

Inorganic carbon assimilation in the Isoetids,Isoetes lacustris L. and Lobelia dortmanna L.

Summary The inorganic carbon fixation patterns of Isoetes lacustris and Lobelia dortmanna from an oligotrophic Scottish loch have been examined by following titratable acidity changes in plant sap and light/dark ¹⁴CO₂ incorporation by roots and shoots. The diurnal pattern of titratable acidity changes in I. lacustris suggests crassulacean acid metabolism (CAM) while the lack of any change in titratable acidity in L. dortmanna suggests C₃ metabolism. Of the carbon fixed by L. dortmanna, 99.9% was taken up through the roots and fixation occurred primarily during the day. In Isoetes, CO₂ was taken up by both roots and shoots and during both day and night. Regardless of the site of CO₂ uptake, fixation occurred only in the shoots of both plants. Analysis of carbon isotope ratios of plant organic material was used to further investigate the photosynthetic mechanisms of these Isoetids. Considering the absence of a nighttime peak in titratable acidity in L. dortmanna, the ¹³C (=¹³C plant-¹³C source) value of the shoots of L. dortmanna (-14.2) is indicative of C₃ photosynthesis limited by the rate of CO₂ diffusion. The less negative of I. lacustris (-6.0) is consistent with both dark acidification of CAM and CO₂ limited C₃ photosynthesis. This is in contrast to the terrestrial Isoetes durieui which is shown to have a value which is similar to a terrestrial C₃ plant. The carbon fixation patterns of these Isoetids suggest that the CO₂ concentration in the loch may be growth limiting, and that root uptake and/or dark acidification are means of optimising CO₂ supply. However, in view of the relatively high levels of CO₂ in sediment and bulk water, it is suggested that low levels of nutrients may also limit growth in these plants.     

Unambiguous through-bond sugar-to-base correlations for purines in 13C, 15N-labeled nucleic acids: The HsCsNb,HsCs(N)bCb,and HbNbCb experiments

Summary A set of three 3D (¹H, ¹³C, ¹⁵N) triple-resonance correlation experiments has been designed to provide H1-H8 intraresidue sugar-to-base correlations in purines in an unambiguous and efficient manner. Together, the H_sC_sN_b, H_sC_s(N)_bC_b, and H_bN_bC_b experiments correlate the H1 sugar proton to the H8 proton of the attached base by means of the {H1, C1, N9, C8, H8} heteronuclear scalar coupling network. The assignment strategy presented here allows for unambiguous H1-H8 intraresidue correlations, provided that no two purines have both the same H1 and C1 chemical shifts and the same C8 and N9 chemical shifts. These experiments have yielded H1-H8 intraresidue sugar-to-base correlations for all five guanosines in the [¹³C, ¹⁵N] isotopically labeled RNA duplex r(GGCGCUUGCGUC)₂.     

Interrelations between C4 Ketogenesis, C5 Ketogenesis, and Anaplerosis in the Perfused Rat Liver

We investigated the interrelations between C₄ ketogenesis (production of β-hydroxybutyrate + acetoacetate), C₅ ketogenesis (production of β-hydroxypentanoate + β-ketopentanoate), and anaplerosis in isolated rat livers perfused with ¹³C-labeled octanoate, heptanoate, or propionate. Mass isotopomer analysis of C₄ and C₅ ketone bodies and of related acyl-CoA esters reveal that C₄ and C₅ ketogenesis share the same pool of acetyl-CoA. Although the uptake of octanoate and heptanoate by the liver are similar, the rate of C₅ ketogenesis from heptanoate is much lower than the rate of C₄ ketogenesis from octanoate. This results from the channeling of the propionyl moiety of heptanoate into anaplerosis of the citric acid cycle. C₅ ketogenesis from propionate is virtually nil because acetoacyl-CoA thiolase does not favor the formation of β-ketopentanoyl-CoA from propionyl-CoA and acetyl-CoA. Anaplerosis and gluconeogenesis from heptanoate are inhibited by octanoate. The data have implications for the design of diets for the treatment of long chain fatty acid oxidation disorders, such as the triheptanoin-based diet.The regulation of the metabolism of C₄ ketone bodies, i.e. β-hydroxybutyrate (BHB)² and acetoacetate (AcAc) has been extensively investigated in vivo in isolated livers, hepatocytes, and subcellular preparations (for reviews, see Refs. 1–4). In contrast, very little information is available on the metabolism of C₅ ketone bodies, i.e. β-hydroxypentanoate (BHP) and β-ketopentanoate (BKP), which are known in the clinical literature as 3-hydroxyvalerate and 3-ketovalerate (5, 6). The C₅ ketone bodies are formed in liver from the partial oxidation of odd-chain fatty acids (see Fig. 1, center column). C₅ ketogenesis uses the same enzymes of the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) cycle as C₄ ketogenesis. The counterpart of HMG-CoA in C₅ ketogenesis is 3-hydroxy-3-ethylglutaryl-CoA (HEG-CoA). We only found one report on the formation of [¹⁴C]HEG-CoA in liver extract incubated with propionyl-CoA and [1-¹⁴C]acetyl-CoA (7).Open in a separate windowFIGURE 1.Scheme of C₄ ketogenesis and C₅ ketogenesis in the liver. Numbers refer to the following enzymes: 3-ketoacyl-CoA thiolase (1), HMG-CoA synthase (2), HMG-CoA lyase (3), and β-hydroxybutyrate dehydrogenase (4). The figure also shows the link between propionyl-CoA and the CAC via anaplerosis.Because odd-chain fatty acids are absent from the diet of non-ruminant mammals, body fluids contain only traces of C₅ ketone bodies. However, C₅ ketone bodies and hydroxyethylglutarate are found in body fluids of patients with disorders of the anaplerotic pathway, propionyl-CoA → methylmalonyl- CoA → succinyl-CoA, such as deficiency in propionyl-CoA carboxylase and methylmalonyl-CoA mutase as well as biotin or vitamin B12 deficiency (5, 6, 8). The formation of C₅ ketone bodies in these pathological states involves either the conversion of propionyl-CoA to BKP-CoA via 3-ketoacyl-CoA thiolase (Fig. 1, reaction 1) or the β-oxidation of odd-chain fatty acids synthesized in these patients (9) using propionyl-CoA as a primer (10).Like their C₄ counterparts, the C₅ ketone bodies are interconverted by mitochondrial BHB dehydrogenase (11). In peripheral tissues, C₅ ketone bodies are converted to propionyl-CoA (which is anaplerotic) + acetyl-CoA via 3-oxoacid-CoA transferase (12) and 3-ketoacyl-CoA thiolase. Peripheral tissues have a high capacity to utilize exogenous C₅ ketone bodies (13), especially heart, kidney, and brain, which have high activities of 3-oxoacid-CoA transferase (14, 15).Our interest in C₅ ketone body metabolism arose from an ongoing clinical trial where patients with long chain fatty acid oxidation disorders are treated with a diet containing triheptanoin (16, 17) instead of the classical treatment with the even-chain triglyceride trioctanoin. These patients suffer from muscle weakness and rhabdomyolysis, manifested by the release of creatine kinase in plasma. It was hypothesized that the accumulation of long chain acyl-CoAs and long chain acylcarnitines results in membrane damage with release of large and small molecules from cells. The leakage of small molecules would deplete intermediates of the citric acid cycle (CAC) which carry acetyl groups as they are oxidized. It was further hypothesized that boosting anaplerosis with a suitable substrate would compensate for the chronic cataplerosis and improve heart and muscle function. The catabolism of heptanoate yields propionyl-CoA, which can be used for anaplerosis in most tissues, and C₅ ketone bodies in liver. C₅ ketone bodies are converted to propionyl-CoA, which can be used for anaplerosis in peripheral tissues. The marked improvement of the patients'' conditions after switching from a trioctanoin- to a triheptanoin-based diet supported the hypothesis.After ingestion of meals containing triheptanoin as the only lipid component, both C₅ ketone bodies and C₄ ketone bodies accumulated in the plasma of patients that have been diagnosed with disorders of long chain fatty acid oxidation (16). This suggested that acetyl groups derived from heptanoate can be used for the synthesis of C₄ and C₅ ketone bodies. Alternatively, the accumulation of C₄ ketone bodies after triheptanoin ingestion might result from the inhibition of the utilization of C₄ ketone bodies in peripheral tissues by C₅ ketone bodies.The aim of the present study was to investigate the interaction between C₄ and C₅ ketogenesis in rat livers perfused with octanoate and/or heptanoate. To gain insight on the fates of the acetyl groups of both fatty acids and on the fate of the propionyl-CoA moiety of heptanoate, we conducted the experiments with a series of labeled substrates: [1-¹³C]octanoate, [8-¹³C]octanoate, [5,6,7-¹³C₃]heptanoate, [1-¹³C]heptanoate, and [¹³C₃]propionate. The outcome of the propionyl-CoA moiety of [5,6,7-¹³C₃]heptanoate and [¹³C₃]propionate was traced by measurements of anaplerosis and glucose labeling by mass isotopomer³ analysis (18). In previous studies on the metabolism of odd-chain fatty acids in liver or hepatocytes (19, 20), ketone bodies were assayed with BHB dehydrogenase. This assay does not differentiate C₄ from C₅ ketone bodies. In the present study we used gas chromatography-mass spectrometry to specifically assay C₄ and C₅ ketone bodies (13).     

Studies on bacteriophage T7 DNA synthesis in vitro. II. Reconstitution of the T7 replication system using purified proteins.

Summary DNA synthesis in vitro using intact duplex T7 DNA as template is dependent on a novel group of three phage T7-induced proteins: DNA-priming protein (activity which complements a cell extract lacking the T7 gene 4-protein), T7 DNA polymerase (gene 5-protein plus host factor), and T7 DNA-binding protein. The reaction requires, in addition to the four deoxyribonucleoside triphosphates, all four ribonucleoside triphosphates and is inhibited by low concentrations of actinomycin D. Evidence is presented that the priming protein serves as a novel RNA polymerase to form a priming segment which is subsequently extended by T7 DNA polymerase. T7 RNA polymerase (gene 1-protein) can only partially substitute for the DNA-priming protein. At 30°C, deoxyribonucleotide incorporation proceeds for more than 2 hours and the amount of newly synthesized DNA can exceed the amount of template DNA by 10-fold. The products of synthesis are not covalently attached to the template and sediment as short (12S) DNA chains in alkaline sucrose gradients. Sealing of these fragments into DNA of higher molecular weight requires the presence of E. coli DNA polymerase I and T7 ligase. Examination of the products in the electron microscope reveals many large, forked molecules and a few eye-shaped structures resembling the early replicative intermediates normally observed in vivo.     

<Emphasis Type="Italic">Aestuariibaculum marinum</Emphasis> sp. nov., a marine bacterium isolated from seawater in South Korea

A Gram-negative, non-motile, aerobic bacterium, designated strain IP7^T, was isolated from seawater at the shore of the Incheon Eulwang-ri beach, South Korea. Cells of strain IP7^T are straight or slightly rod-shaped and colonies are round, convex and orange-yellow. Strain IP7^T is flexirubin-negative, mild halophile, catalase-and oxidase-positive, and produces a yellow-orange carotenoid pigment. Growth is optimal at 30°C, pH 7–9, and 2.0–4.0% NaCl (w/v). On the basis of 16S rRNA gene sequence similarity, strain IP7^T is affiliated with genus Aestuariibaculum in the family Flavobacteriaceae, the closest relative being Aestuariibaculum suncheonense SC17^T (98.3% sequence similarity). The DNA G + C content of the novel strain is 37.4 mol%. The only quinone is MK-6 menaquinone. Iso-branched C_15:0, iso-branched C_15:1 G, and iso-branched C_17:0 3-OH are major fatty acids. The major polar lipids are phosphatidylethanolamine, an unidentified aminoglycolipid and two unidentified glycolipids. The DNA-DNA hybridization value of strain IP7^T with Aestuariibaculum suncheonense SC17^T is 28.87%. Based on the collective DNA-DNA hybridization, biochemical, phylogenetic and physiological data, we report a novel species of the genus Aestuariibaculum for which the name Aestuariibaculum marinum sp. nov. is proposed. The type strain is IP7^T (= KCTC 52521^T = JCM 31725^T).     

[C7GC4]4 Association into supra molecular i-motif structures

The self-associative properties of cytidine-rich oligonucleotides into symmetrical i-motif tetramers give to these oligonucleotides the capacity of forming supramolecular structures (sms) that have potential applications in the nanotechnology domain. In order to facilitate sms formation, oligonucleotides containing two cytidine stretches of unequal length (C_nXC_m) separated by a non-cytidine spacer were synthesized. They were designed to associate into a tetramer including an i-motif core built by intercalation of the C·C⁺ pairs of the longer C stretch with the two dangling non-intercalated strands of the shorter C stretch at each end. Gel filtration chromatography shows that the non-intercalated C-rich ends give to this structure the capacity of forming extremely stable sms. Using C₇GC₄ as a model, we find that the sms formation rate varies as the oligonucleotide concentration and increases at high temperature. Competitively with the tetramer involved in sms elongation, C_nXC_m oligonucleotides form i-motif dimers that compete with sms elongation. The dimer stability is strongly reduced when the pH is moved away from the cytidine pK. This results in an equilibrium shift towards the tetramer and in the acceleration of the sms formation rate. The chromatograms of the sms formed by C₇GC₄ indicate a broad distribution. In a 1.5 mM solution incubated at 37°C, the equilibrium distribution is centered on a molecular weight corresponding to the assembly of nine tetramers and the upper limit corresponds to 80 tetramers. The lifetime of this structure is about 4 days at 40°C, pH 4.6.     

<Emphasis Type="Italic">Dankookia rubra</Emphasis> gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream

WS-10^T–a Gram-negative, non-motile, and aerobic bacterial strain–was isolated from the sediment of a shallow stream in Korea. The optimum ranges of temperature and pH for growth were 20–40°C (optimum 28°C) and pH 6.0–8.0 (optimum pH 7.0), respectively. The DNA G+C content of strain WS-10^T was 72.7 mol%. The major fatty acids (>5%) were summed feature 8 (C_18:1ω7c), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), C_16:0, and C_18:1 2-OH. The major polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminolipids. Q-10 was the predominant respiratory quinone. The highest similarities in the 16S rRNA gene sequence were shown with Paracraurococcus ruber (95.3%), Belnapia soli (95.3%), B. moabensis (95.1%), and B. rosea (95.0%). A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain WS-10T formed a distinct line within a clade containing the genera Paracraurococcus, Craurococcus, and Belnapia in the family Acetobacteraceae. On the basis of polyphasic evidence, strain WS-10^T represents a novel species of a new genus in the family Acetobacteraceae, for which the name Dankookia rubra gen. nov., sp. nov. is proposed. The type strain of the type species is WS-10^T (= KACC 18533^T = JCM 30602^T).     

Modification of the B-ring during flavonoid synthesis in Petunia hybrida: Introduction of the 3′-hydroxyl group regulated by the gene Ht1

The flower-color mutants of Petunia hybrida W37 and W18, which are homozygous recessive for the anthocyanin gene An3, accumulate flavanone glycosides in the flowers. It is concluded that the gene An3 is not directly involved in the synthesis of the C₁₅ skeleton, but that it probably takes part in modifying the skeleton. Complementation experiments with the mutants W18 and M5 show that the hydroxylating gene Ht1, which is reponsible for the introduction of the second hydroxyl group in the B-ring at position 3, is expressed after gene An3. In P. hybrida introduction of the 3-hydroxyl group is therefore not achieved by specific incorporation of caffeic acid during synthesis of the C₁₅ skeleton, but by hydroxylation of a C₁₅ skeleton. When anthocyanin synthesis is blocked by homozygous recessive hydroxylating genes Ht1 and Hf1, as in the mutant M5, dihydrokaempferol-7-glucoside is accumulated. This intermediate is discussed as a possible substrate for B-ring hydroxylation.     

Synthesis and structure of an unusual di-rhodium diarylbutadiyne π-complex featuring a μ-(1,2-η2):(3,4-η2)-p-CF3C6H4–CC–CC–C6H4-p-CF3 moiety

Reaction of the salt [Rh(PMe₃)₄]Cl (1) with p-F₃C–C₆H₄–CC–CC–C₆H₄-p-CF₃ (2) in THF gives a mixture of two related neutral π-bound diyne complexes of [Rh(PMe₃)₃Cl], each having two distinct CF₃ resonances of equal intensity in the in situ ¹⁹F{¹H} NMR spectrum. The ratio of the two products can be varied by varying the stoichiometry of the reagents. On the basis of the spectroscopic data and literature precedent, we propose Rh(PMe₃)₃(Cl)((1,2-η²)-p-F₃C–C₆H₄–CC–CC–C₆H₄-p-CF₃) (3a) and [Rh(PMe₃)₃(Cl)]₂(μ-(1,2-η²):(1,2-η²)-p-F₃C–C₆H₄–CC–CC–C₆H₄-p-CF₃) (3b) as the most likely structures of the species in solution. However, upon standing overnight, single crystals of the unusual, dinuclear complex [Rh(PMe₃)₃(Cl)]₂(μ-(1,2-η²):(3,4-η²)-p-F₃C–C₆H₄–CC–CC–C₆H₄-p-CF₃) (4), an isomer of 3b, form reproducibly and in good yield as two different solvates from THF/C₆D₆ solution. The centrosymmetric structure of 4, obtained from single-crystal X-ray diffraction data, displays a transoid orientation of the bridging diarylbutadiyne ligand.     

Template-directed synthesis with 2-aminoadenosine

Summary A random copolymer, poly(CA), containing approximately equal amounts of cytidine (C) and adenosine (A), when incubated with a mixture of guanosine-5-phosphoro-(2-methylimidazole) (2-MeImpG) and uridine-5-phosphoro-(2-methylimidazole) (2-MeImpU), facilitates the incorporation of uridine (U) into oligomeric products with low efficiency. If 2-aminoadenosine (aA) is substituted for adenosine in the template, U is incorporated into the products with much higher efficiency. Random copolymers of C and U act as templates for the efficient synthesis of oligomers from 2-MeImpG and 2-MeImpA only if the concentration of substrates is relatively high (0.1 M). The substitution of 2-MeImpaA permits the reaction to occur with much lower substrate concentrations. This effect is most prominent for template containing large amounts of U.