Oligomerization of adenosin‐5′‐O‐ylmethylphosphonate,an isopolar AMP analogue: Evaluation of the route to short oligoadenylates

In an attempt to prepare a library of short oligoadenylate analogues featuring both the enzyme‐stable internucleotide linkage and the 5′‐O‐methylphosphonate moiety and thus obtain a pool of potential RNase L agonists/antagonists, we studied the spontaneous polycondensation of the adenosin‐5′‐O‐ylmethylphosphonic acid (p_cA), an isopolar AMP analogue, and its imidazolide derivatives employing N,N′‐dicyclohexylcarbodiimide under nonaqueous conditions and uranyl ions under aqueous conditions, respectively. The RP LC–MS analyses of the reaction mixtures per se, and those obtained after the periodate treatment, along with analyses and separations by capillary zone electrophoresis, allowed us to characterize major linear and cyclic oligoadenylates obtained. The structure of selected compounds was supported, after their isolation, by NMR spectroscopy. Ab initio calculation of the model structures simulating the AMP‐imidazolide and p_cA‐imidazolide offered the explanation why the latter compound exerted, in contrast to AMP‐imidazolide, a very low stability in aqueous solutions. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 277–289, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

NMR‐based characterization of a refolding intermediate of β2‐microglobulin labeled using a wheat germ cell‐free system

In patients with dialysis‐related amyloidosis, β2‐microglobulin (β2‐m) is a major structural component of amyloid fibrils. It has been suggested that the partial unfolding of β2‐m is a prerequisite to the formation of amyloid fibrils, and that the folding intermediate trapped by the non‐native trans‐Pro32 isomer leads to the formation of amyloid fibrils. Although clarifying the structure of this refolding intermediate by high resolution NMR spectroscopy is important, this has been made difficult by the limited lifetime of the intermediate. Here, we studied the structure of the refolding intermediate using a combination of amino acid selective labeling with wheat germ cell‐free protein synthesis and NMR techniques. The HSQC spectra of β2‐ms labeled selectively at either phenylalanine, leucine, or valine enabled us to monitor the structures of the refolding intermediate. The results suggested that the refolding intermediate has an overall fold and cores similar to the native structure, but contains disordered structures around Pro32. The fluctuation of the β‐sheet regions especially the last half of the βB strand and the first half of the βE strand, both suggested to be important for amyloidogenicity, may transform β2‐m into an amyloidogenic structure.     

Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation

At present two alternative methods are available for analyzing the fluxes in a metabolic network: (1) combining measurements of net conversion rates with a set of metabolite balances including the cofactor balances, or (2) leaving out the cofactor balances and fitting the resulting free fluxes to measured (13)C-labeling data. In this study these two approaches are applied to the fluxes in the glycolysis and pentose phosphate pathway of Penicillium chrysogenum growing on either ammonia or nitrate as the nitrogen source, which is expected to give different pentose phosphate pathway fluxes. The presented flux analyses are based on extensive sets of 2D [(13)C, (1)H] COSY data. A new concept is applied for simulation of this type of (13)C-labeling data: cumulative bondomer modeling. The outcomes of the (13)C-labeling based flux analysis substantially differ from those of the pure metabolite balancing approach. The fluxes that are determined using (13)C-labeling data are shown to be highly dependent on the chosen metabolic network. Extending the traditional nonoxidative pentose phosphate pathway with additional transketolase and transaldolase reactions, extending the glycolysis with a fructose 6-phosphate aldolase/dihydroxyacetone kinase reaction sequence or adding a phosphoenolpyruvate carboxykinase reaction to the model considerably improves the fit of the measured and the simulated NMR data. The results obtained using the extended version of the nonoxidative pentose phosphate pathway model show that the transketolase and transaldolase reactions need not be assumed reversible to get a good fit of the (13)C-labeling data. Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model.     

Synthesis and odor of chiral partial structures of β‐vetivone,Part 2

Several stereoisomeric, monocyclic analogs of (−)‐β‐vetivone (1), one of the main constituents of vetiver oil, were studied to examine if the olfactory properties of (−)‐β‐vetivone (1) could be reproduced from these structurally simpler, synthetically accessible compounds. The effects of diastereomeric and enantiomeric structural differences on the odor of the partial vetivone structure were studied. A chiral phenyl sulfoximine was used for separation of the racemic mixtures. Detailed nuclear magnetic resonance (NMR)‐spectroscopic studies (¹H, ¹³C) were used to determine relative configurations whereas absolute configurations were determined by circular dichroism (CD) methods. Chirality 11:133–138, 1999. © 1999 Wiley‐Liss, Inc.     

Stable forest–savanna mosaic in north‐western Tanzania: local‐scale evidence from δ13C signatures and 14C ages of soil fractions

Aim The spatio‐temporal dynamics of dry evergreen forest patches in the savanna biome of the Kagera region (north‐western Tanzania) are largely unknown owing to a lack of pollen and macrofossil evidence. Our aims were to reconstruct local‐scale shifts of the forest–savanna boundary in order to determine whether the forests have been expanding or retreating on a centennial and millennial time‐scale. Location The Kagera region of north‐western Tanzania, East Africa. Methods The vegetation reconstruction was based on analysing δ¹³C signatures in soils along a transect spanning both C₄ open savanna and C₃ forest vegetation. Furthermore, we fractionated soil organic matter (SOM) according to density and chemical stability to analyse δ¹³C values of soil fractions with distinct radiocarbon ages. Results We found sharp changes in δ¹³C signatures in bulk SOM from the forest to the savanna, within a few metres along the transect. The forest soil profiles carried a persistent C₃‐dominated signature. Radiocarbon dating of the oldest, most recalcitrant forest soil fraction yielded a mean age of 5500 cal. yr bp , demonstrating that the forest has existed since at least the mid‐Holocene. The savanna sites showed a typical C₄ isotopic signature in SOM of topsoils, but subsoils and more recalcitrant SOM fractions also contained signals of C₃ plants. The dense soil fraction (ρ > 1.6 g cm^?3) carrying a pure C₄ label had a mean age of c. 1200 cal. yr bp , indicating the minimum duration of the dominance of grass vegetation on the savanna site. At the forest edge, the older C₄ grass signature of SOM has steadily been replaced by the more negative δ¹³C fingerprint of the forest trees. As this replacement has occurred mainly in the 10‐m‐wide forest–savanna ecotone over the last c. 1200 years, the forest expansion must be very slow and is very likely less than 15 m century^?1. Main conclusions Our results suggest that forest patches in the Kagera savanna landscape are very stable vegetation formations which have persisted for millennia. During the last millennium, they have been expanding very slowly into the surrounding savanna at a rate of less than 15 m century^?1.     

Spectra,stability and labeling of 1‐(5‐carboxypentyl)‐4‐(2‐(N‐ethyl‐carbazole‐3‐yl) vinyl) pyridinium bromide with a large Stokes shift

Carbazole and its derivatives have been widely utilized as a functional building block in the fabrication of the organic medicine, pesticides, materials, etc., because of their excellent solubility, stability and biological activity. In this paper, 1‐(5‐carboxypentyl)‐4‐(2‐(N‐ethyl‐carbazole‐3‐yl) vinyl) pyridinium bromide with a large Stokes shift was synthesized and characterized by ¹H NMR and MS. The UV/vis absorption and fluorescence spectra in different solvents and at different pH values were investigated preliminarily. The photostability and thermostability were also studied and the results showed that the compound was stable. The compound was also used to label bovine serum albumin (BSA) and calf thymus (ct)DNA. The results showed that the fluorescence intensity is enhanced when labeling with BSA and the binding ability is stronger than ctDNA, making it may be used as a biological probe. Copyright © 2015 John Wiley & Sons, Ltd.     

Fast response of Scots pine to improved water availability reflected in tree‐ring width and δ13C

Drought‐induced forest decline, like the Scots pine mortality in inner‐Alpine valleys, will gain in importance as the frequency and severity of drought events are expected to increase. To understand how chronic drought affects tree growth and tree‐ring δ¹³C values, we studied mature Scots pine in an irrigation experiment in an inner‐Alpine valley. Tree growth and isotope analyses were carried out at the annual and seasonal scale. At the seasonal scale, maximum δ¹³C values were measured after the hottest and driest period of the year, and were associated with decreasing growth rates. Inter‐annual δ¹³C values in early‐ and latewood showed a strong correlation with annual climatic conditions and an immediate decrease as a response to irrigation. This indicates a tight coupling between wood formation and the freshly produced assimilates for trees exposed to chronic drought. This rapid appearance of the isotopic signal is a strong indication for an immediate and direct transfer of newly synthesized assimilates for biomass production. The fast appearance and the distinct isotopic signal suggest a low availability of old stored carbohydrates. If this was a sign for C‐storage depletion, an increasing mortality could be expected when stressors increase the need for carbohydrate for defence, repair or regeneration.     

Tracing sources of carbon and hydrogen to stored lipids in the migratory moth,Mythimna unipuncta using stable isotopes (δ2H, δ13C)

Stable isotope measurements of insect tissues can be used to determine origin and migratory patterns. The isotopic links between diet and stored lipids in laboratory reared true armyworm moths (Mythimna unipuncta, Haw.) were investigated using δ¹³C and δ²H measurements. Newly emerged moths were fed synthetic nectars, consisting of different carbohydrate and water sources that were isotopically distinct from those in the larval diet. After 4 days of feeding, insects were sacrificed, and fat‐body lipids were extracted for isotopic analysis. When held on a constant nectar source, adult diet contributed ～87% of the C and 44% H of lipids. For H, 27% and ～ 17% of lipid was derived from carbohydrates and water, respectively, with the remainder presumably from the larval stage. When the isotopic composition of the nectar source was switched there was rapid and exponential temporal change in lipid isotopic profiles. The relevance of our findings to tracing origins of stored lipids in migrant Lepidoptera is discussed.     

Changing gull diet in a changing world: A 150‐year stable isotope (δ13C, δ15N) record from feathers collected in the Pacific Northwest of North America

The world's oceans have undergone significant ecological changes following European colonial expansion and associated industrialization. Seabirds are useful indicators of marine food web structure and can be used to track multidecadal environmental change, potentially reflecting long‐term human impacts. We used stable isotope (δ¹³C, δ¹⁵N) analysis of feathers from glaucous‐winged gulls (Larus glaucescens) in a heavily disturbed region of the northeast Pacific to ask whether diets of this generalist forager changed in response to shifts in food availability over 150 years, and whether any detected change might explain long‐term trends in gull abundance. Sampled feathers came from birds collected between 1860 and 2009 at nesting colonies in the Salish Sea, a transboundary marine system adjacent to Washington, USA and British Columbia, Canada. To determine whether temporal trends in stable isotope ratios might simply reflect changes to baseline environmental values, we also analysed muscle tissue from forage fishes collected in the same region over a multidecadal timeframe. Values of δ¹³C and δ¹⁵N declined since 1860 in both subadult and adult gulls (δ¹³C, ~ 2–6‰; δ¹⁵N, ~4–5‰), indicating that their diet has become less marine over time, and that birds now feed at a lower trophic level than previously. Conversely, forage fish δ¹³C and δ¹⁵N values showed no trends, supporting our conclusion that gull feather values were indicative of declines in marine food availability rather than of baseline environmental change. Gradual declines in feather isotope values are consistent with trends predicted had gulls consumed less fish over time, but were equivocal with respect to whether gulls had switched to a more garbage‐based diet, or one comprising marine invertebrates. Nevertheless, our results suggest a long‐term decrease in diet quality linked to declining fish abundance or other anthropogenic influences, and may help to explain regional population declines in this species and other piscivores.     

Neonatal Persistent Exposure to 6‐Propyl‐2‐thiouracil,a Thyroid‐Disrupting Chemical,Differentially Modulates Expression of Hepatic Catalase and C/EBP‐β in Adult Rats

Persistent exposure of rats to 6‐propyl‐2‐thiouracil (PTU) from birth resulted in decreases in plasma thyroid hormone (TH) levels and hepatic expression of catalase and CCAAT enhancer binding protein β (C/EBP‐β). Catalase promoter region (–185 to +52) that contains binding sites for C/EBP‐β showed an augmentation in the methylation level along with a change in methylation pattern of CpG islands in response to PTU treatment. PTU withdrawal on 30 days of birth restored TH levels and C/EBP‐β to control rats in adulthood. Although catalase expression was restored to some extent in adult rats in response to PTU withdrawal, a permanent change in its promoter CpG methylation pattern was recorded. The results suggest that downregulation of adult hepatic catalase gene in response to persistent neonatal PTU exposure may not solely be attributed to thyroid‐disrupting properties of PTU. It is possible that besides thyroid‐disrupting behavior, PTU may impair expression of hepatic catalase by altering methylation pattern of its promoter.     

Analysis of CYP2C9*2, CYP2C9*3 and VKORC1 ‐1639 G>A polymorphisms in a population from South‐Eastern Europe

The CYP2C9 enzyme metabolizes a wide range of relevant drugs, among which are oral anticoagulants. VKORC1 is the pharmacodynamic target of the oral anticoagulants. The genetic polymorphisms CYP2C9*2, CYP2C9*3 and VKORC1 ‐1639 G>A are the major determinants of the inter‐individual variability in the dosage requirements of oral anticoagulants. This study provides a first evaluation of these 3 polymorphisms in a Romanian population. A total of 332 Romanian individuals were genotyped for the CYP2C9*2, CYP2C9*3 and VKORC1 ‐1639 G>A polymorphisms using the PCR‐RFLP technique. Sixty‐two individuals (18.7%) were heterozygous for CYP2C9*2, whereas 47 individuals (14.1%) were heterozygous for CYP2C9*3. Fourteen individuals (4.2%) had a CYP2C9*2 homozygous, CYP2C9*3 homozygous or CYP2C9*2/CYP2C9*3 compound heterozygous genotype. These individuals are predicted to have the lowest CYP2C9 enzymatic activity. The allele frequencies of the CYP2C9*2 and CYP2C9*3 polymorphisms were 11.3% and 9.3% respectively. For the VKORC1 ‐1639 G>A polymorphism, there were 170 heterozygotes (51.2%) and 55 (16.6%) homozygotes for the A allele. The frequency of the A allele was 42.2%. Overall, the distribution of the CYP2C9*2, CYP2C9*3 and VKORC1 ‐1639 G>A polymorphisms observed in our cohort is in accordance with other Caucasian populations. A large number of Romanians are expected to harbour at least one CYP2C9 variant allele and/or one VKORC1 ‐1639 G>A allele. This frequency has major implications in the pharmacogenomics of oral anticoagulants in Romanians.     

The effects of Paraloid B‐72 and Butvar B‐98 treatment and organic solvent removal on δ13C, δ15N,and δ18O values of collagen and hydroxyapatite in a modern bone

Stable isotopes in bones are a powerful tool for diet, provenance, climate, and physiological reconstructions, but necessarily require well‐preserved specimens unaltered by postmortem diagenesis or conservation practices. This study examines the effects of Paraloid B‐72 and Butvar B‐98, two common consolidants used in field and museum conservation, on δ¹³C, δ¹⁵N, and δ¹⁸O values from bone collagen and hydroxyapatite. The effects of solvent removal (100% acetone, 100% ethanol, 9:1 acetone:xylenes, 9:1 ethanol:xylenes) and drying methods (ambient air, vacuum, oven drying at 80°C) were also examined to determine if bones treated with these consolidants can successfully be cleaned and used for stable isotope analyses. Results show that introduction of Paraloid B‐72 or Butvar B‐98 in 100% acetone or 100% ethanol, respectively, with subsequent removal by the same solvents and drying at 80°C facilitates the most successful removal of consolidants and solvents. The δ¹³C values in collagen, δ¹⁵N in collagen, δ¹⁸O in hydroxyapatite phosphate, and δ¹³C in hydroxyapatite structural carbonate were unaltered by treatments with Paraloid or Butvar and subsequent solvent removal. The δ¹⁸O in hydroxyapatite structural carbonate showed nonsystematic variability when bones were treated with Paraloid and Butvar, which is hypothesized to be a result of hydroxyl exchange when bones are exposed to consolidants in solution. It is therefore recommended that δ¹⁸O in hydroxyapatite structural carbonate should not be used in stable isotope studies if bones have been treated with Paraloid or Butvar. Am J Phys Anthropol 157:330–338, 2015. © 2015 Wiley Periodicals, Inc.     

Further crystallographic evidence of NH· · ·π (system) and CO· · ·π (system) interactions: The structures of bis(diarylhydrazonecarbonyl)methylene derivatives [{ArPhCNNH—C(O)}2CH2] (Ar = Ph, 2‐C5H4N, 2‐C4H3S)

In this study are reported the syntheses of three bis(diarylhydrazonecarbonyl)methylene derivatives [{ArPhCNNH C(O)}₂CH₂] [Ar = 2 C₅H₄N (5), C₆H₅ (6), and 2‐C₄H₃S (7)], obtained by condensation of corresponding hydrazones with carbon suboxide, C₃O₂. The solid‐state self‐assembly of these carbonyl derivatives, giving rise to polymeric and dimeric networks, is described. In the formation of these structural features, in addition to N—H· · ·OC intermolecular hydrogen bonds, stabilizing intramolecular NH· · · π (systems) and intermolecular CO· · ·π (systems) interactions also seem to play an important role. Solution ¹H‐nmr data of compounds 5–7 indicate that the polymeric and dimeric structures are not maintained in solution and show the occurrence of keto‐enolic equilibria. © 1999 John Wiley & Sons, Inc. Biopoly 49: 541–549, 1999     

Foliar δ13C response patterns along a moisture gradient arising from genetic variation and phenotypic plasticity in grassland species of Inner Mongolia

Plants depend upon both genetic differences and phenotypic plasticity to cope with environmental variation over different timescales. The spatial variation in foliar δ¹³C levels along a moisture gradient represents an overlay of genetic and plastic responses. We hypothesized that such a spatial variation would be more obvious than the variation arising purely from a plastic response to moisture change. Leymus chinensis and Stipa spp. were sampled from Inner Mongolia along a dry‐wet transect, and some of these species were transplanted to an area with a moisture gradient. For Stipa spp., the slope of foliar δ¹³C and mean annual precipitation along the transect was significantly steeper than that of foliar δ¹³C and mean annual precipitation after the watering treatment. For L. chinensis, there was a general decreasing trend in foliar δ¹³C under the different (increasing) watering levels; however, its populations showed an irregular relationship between foliar δ¹³C and moisture origin. Therefore, support for our hypothesis was obtained from Stipa spp., but not from L. chinensis.     

In Vitro and In Vivo Evaluation of N‐{2‐[4‐(3‐Cyanopyridin‐2‐yl)piperazin‐1‐yl]ethyl}‐3‐[11C]methoxybenz­amide,a Positron Emission Tomography (PET) Radioligand for Dopamine D4 Receptors,in Rodents

The D₄ dopamine receptor belongs to the D₂‐like family of dopamine receptors, and its exact regional distribution in the central nervous system is still a matter of considerable debate. The availability of a selective radioligand for the D₄ receptor with suitable properties for positron emission tomography (PET) would help resolve issues of D₄ receptor localization in the brain, and the presumed diurnal change of expressed protein in the eye and pineal gland. We report here on in vitro and in vivo characteristics of the high‐affinity D₄ receptor‐selective ligand N‐{2‐[4‐(3‐cyanopyridin‐2‐yl)piperazin‐1‐yl]ethyl}‐3‐[¹¹C]methoxybenzamide ([¹¹C] 2 ) in rat. The results provide new insights on the in vitro properties that a brain PET dopamine D₄ radioligand should possess in order to have improved in vivo utility in rodents.     

Carbon isotope compositions (δ13C) of leaf,wood and holocellulose differ among genotypes of poplar and between previous land uses in a short‐rotation biomass plantation

The efficiency of water use to produce biomass is a key trait in designing sustainable bioenergy‐devoted systems. We characterized variations in the carbon isotope composition (δ¹³C) of leaves, current year wood and holocellulose (as proxies for water use efficiency, WUE) among six poplar genotypes in a short‐rotation plantation. Values of δ¹³C_wood and δ¹³C_{holocellulose} were tightly and positively correlated, but the offset varied significantly among genotypes (0.79–1.01‰). Leaf phenology was strongly correlated with δ¹³C, and genotypes with a longer growing season showed a higher WUE. In contrast, traits related to growth and carbon uptake were poorly linked to δ¹³C. Trees growing on former pasture with higher N‐availability displayed higher δ¹³C as compared with trees growing on former cropland. The positive relationships between δ¹³C_leaf and leaf N suggested that spatial variations in WUE over the plantation were mainly driven by an N‐related effect on photosynthetic capacities. The very coherent genotype ranking obtained with δ¹³C in the different tree compartments has some practical outreach. Because WUE remains largely uncoupled from growth in poplar plantations, there is potential to identify genotypes with satisfactory growth and higher WUE.