i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats

Using NMR methods, we have resolved the i-motif structures formed by d(AACCCC) and by d(CCCCAA), two versions of the DNA sequence repeated in the telomeric regions of the C-rich strand of tetrahymena chromosomes. Both oligonucleotides form fully symmetrical i-motif tetramers built by intercalation of two hemiprotonated duplexes containing four C•C⁺ pairs. The structures are extremely stable. In the tetramer of d(AACCCC), the outermost C•C⁺ pairs are formed by the cytidines of the 5′ ends of the cytidine tracts. A2 forms an A2•A2 (H6trans–N7) pair stacked to C3•C3⁺ and cross-strand stacked to A1. At 0°C, the lifetimes of the hemiprotonated pairs range from 1 ms for the outermost pair to ~1 h for the innermost pairs. The tetramer of d(CCCCAA) adopts two distinct intercalation topologies in slow conformational exchange. One, whose outermost C•C⁺ pairs are built by the cytidines of the 5′ end and the other by those of the 3′ end. In both topologies, the adenosine bases are fairly well stacked to the adjacent C•C⁺ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other.     

Forest-to-pasture conversion influences on soil organic carbon dynamics in a tropical deciduous forest

On a global basis, nearly 42% of tropical land area is classified as tropical deciduous forest (TDF) (Murphy and Lugo 1986). Currently, this ecosystem has very high deforestation rates; and its conversion to cattle pasture may result in losses of soil organic matter, decreases in soil fertility, and increases in CO₂ flux to the atmosphere. The soil organic matter turnover rate in a TDF after pasture conversion was estimated in Mexico by determining natural abundances of¹³C. Changes in these values would be induced by vegetation changes from the C₃ (forest) to the C₄ (pasture) photosynthetic pathway. The rate of loss of remnant forest-soil organic matter (fSOM) was 2.9 t ha^–1 year^–1 in 7-year-old pasture and decreased to 0.66 t ha^–1 year^–1 by year 11. For up to 3 years, net fSOM level increased in pastures; this increment can be attributed to decomposition of remnant forest roots. The sand-associated SOM fraction was the most and the silt-associated fraction the least depleted. TDF conversion to pasture results in extremely high rates of loss of remnant fSOM that are higher than any reported for any tropical forest.     

Relationship between C:N/C:O Stoichiometry and Ecosystem Services in Managed Production Systems

Land use and management intensity can influence provision of ecosystem services (ES). We argue that forest/agroforestry production systems are characterized by relatively higher C:O/C:N and ES value compared to arable production systems. Field investigations on C:N/C:O and 15 ES were determined in three diverse production systems: wheat monoculture (C_wheat), a combined food and energy system (CFE) and a beech forest in Denmark. The C:N/C:O ratios were 194.1/1.68, 94.1/1.57 and 59.5/1.45 for beech forest, CFE and C_wheat, respectively. The economic value of the non-marketed ES was also highest in beech forest (US$ 1089 ha^-1 yr^-1) followed by CFE (US$ 800 ha^-1 yr^-1) and C_wheat (US$ 339 ha^-1 yr^-1). The combined economic value was highest in the CFE (US$ 3143 ha^-1 yr^-1) as compared to the C_wheat (US$ 2767 ha^-1 yr^-1) and beech forest (US$ 2365 ha^-1 yr^-1). We argue that C:N/C:O can be used as a proxy of ES, particularly for the non-marketed ES, such as regulating, supporting and cultural services. These ES play a vital role in the sustainable production of food and energy. Therefore, they should be considered in decision making and developing appropriate policy responses for land use management.     

Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC)

At slightly acidic pH, the association of two d(5mCCTCACTCC) strands results in the formation of an i-motif dimer. Using NMR methods, we investigated the structure of [d(5mCCTCACTCC)]₂, the internal motion of the base pairs stacked in the i-motif core, the dimer formation and dissociation kinetics versus pH. The excellent resolution of the ¹H and ³¹P spectra provided the determination of dihedral angles, which together with a large set of distance restraints, improve substantially the definition of the sugar-phosphate backbone by comparison with previous NMR studies of i-motif structures. [d(5mCCTCACTCC)]₂ is built by intercalation of two symmetrical hairpins held together by six symmetrical C•C⁺ pairs and by pair T7•T7. The hairpin loops that are formed by a single residue, A5, cross the narrow grooves on the same side of the i-motif core. The base pair intercalation order is C9•C9⁺/5mC1•5mC1⁺/C8•C8⁺/C2•C2⁺/T7.T7/C6•C6⁺/C4•C4⁺. The T3 bases are flipped out in the wide grooves. The core of the structure includes four long-lived pairs whose lifetimes at 15°C range from 100 s (C8•C8⁺) to 0.18 s (T7•T7). The formation rate and the lifetime of [d(5mCCTCACTCC)]₂ were measured between pH 6.8 and 4.8. The dimer formation rate is three to four magnitude orders slower than that of a B-DNA duplex. It depends on pH, as it must occur for a bimolecular process involving non cooperative association of neutral and protonated residues. In the range of pH investigated, the dimer lifetime, 500 s at 0°C, pH 6.8, varies approximately as 10^−pH.     

Annual Carbon Emissions from Deforestation in the Amazon Basin between 2000 and 2010

Reducing emissions from deforestation and forest degradation (REDD+) is considered one of the most cost-effective strategies for mitigating climate change. However, historical deforestation and emission rates―critical inputs for setting reference emission levels for REDD+―are poorly understood. Here we use multi-source, time-series satellite data to quantify carbon emissions from deforestation in the Amazon basin on a year-to-year basis between 2000 and 2010. We first derive annual deforestation indicators by using the Moderate Resolution Imaging Spectroradiometer Vegetation Continuous Fields (MODIS VCF) product. MODIS indicators are calibrated by using a large sample of Landsat data to generate accurate deforestation rates, which are subsequently combined with a spatially explicit biomass dataset to calculate committed annual carbon emissions. Across the study area, the average deforestation and associated carbon emissions were estimated to be 1.59 ± 0.25 M ha•yr⁻¹ and 0.18 ± 0.07 Pg C•yr⁻¹ respectively, with substantially different trends and inter-annual variability in different regions. Deforestation in the Brazilian Amazon increased between 2001 and 2004 and declined substantially afterwards, whereas deforestation in the Bolivian Amazon, the Colombian Amazon, and the Peruvian Amazon increased over the study period. The average carbon density of lost forests after 2005 was 130 Mg C•ha⁻¹, ~11% lower than the average carbon density of remaining forests in year 2010 (144 Mg C•ha⁻¹). Moreover, the average carbon density of cleared forests increased at a rate of 7 Mg C•ha⁻¹•yr⁻¹ from 2005 to 2010, suggesting that deforestation has been progressively encroaching into high-biomass lands in the Amazon basin. Spatially explicit, annual deforestation and emission estimates like the ones derived in this study are useful for setting baselines for REDD+ and other emission mitigation programs, and for evaluating the performance of such efforts.     

Carbon isotope ratios demonstrate carbon flux from c(4) host to c(3) parasite

Carbon isotope ratios of mature leaves from the C₃ angiosperm root hemiparasites Striga hermonthica (Del.) Benth (−26.7‰) and S. asiatica (L.) Kuntze (−25.6‰) were more negative than their C₄ host, sorghum (Sorghum bicolor [L.] Moench cv CSH1), (−13.5‰). However, in young photosynthetically incompetent plants of S. hermonthica this difference was reduced to less than 1‰. Differences between the carbon isotope ratios of two C₃-C₃ associations, S. gesnerioides (Willd.) Vatke—Vigna unguiculata (L.) Walp. and Oryza sativa L.—Rhamphicarpa fistulosa (Hochst.) Benth differed by less than 1‰. Theoretical carbon isotope ratios for mature leaves of S. hermonthica and S. asiatica, calculated from foliar gas exchange measurements, were −31.8 and −32.0‰, respectively. This difference between the measured and theoretical δ¹³C-values of 5 to 6‰ suggests that even in mature, photosynthetically active plants, there is substantial input of carbon from the C₄ host. We estimate this to be approximately 28% of the total carbon in S. hermonthica and 35% in S. asiatica. This level of carbon transfer contributes to the host's growth reductions observed in Striga-infected sorghum.     

Patterns of Biomass and Carbon Distribution across a Chronosequence of Chinese Pine (Pinus tabulaeformis) Forests

Patterns of biomass and carbon (C) storage distribution across Chinese pine (Pinus tabulaeformis) natural secondary forests are poorly documented. The objectives of this study were to examine the biomass and C pools of the major ecosystem components in a replicated age sequence of P. tabulaeformis secondary forest stands in Northern China. Within each stand, biomass of above- and belowground tree, understory (shrub and herb), and forest floor were determined from plot-level investigation and destructive sampling. Allometric equations using the diameter at breast height (DBH) were developed to quantify plant biomass. C stocks in the tree and understory biomass, forest floor, and mineral soil (0–100 cm) were estimated by analyzing the C concentration of each component. The results showed that the tree biomass of P. tabulaeformis stands was ranged from 123.8 Mg·ha^–1 for the young stand to 344.8 Mg·ha^–1 for the mature stand. The understory biomass ranged from 1.8 Mg·ha^–1 in the middle-aged stand to 3.5 Mg·ha^–1 in the young stand. Forest floor biomass increased steady with stand age, ranging from 14.9 to 23.0 Mg·ha^–1. The highest mean C concentration across the chronosequence was found in tree branch while the lowest mean C concentration was found in forest floor. The observed C stock of the aboveground tree, shrub, forest floor, and mineral soil increased with increasing stand age, whereas the herb C stock showed a decreasing trend with a sigmoid pattern. The C stock of forest ecosystem in young, middle-aged, immature, and mature stands were 178.1, 236.3, 297.7, and 359.8 Mg C ha^–1, respectively, greater than those under similar aged P. tabulaeformis forests in China. These results are likely to be integrated into further forest management plans and generalized in other contexts to evaluate C stocks at the regional scale.     

Evidence for the Involvement of Loosely Bound Plastosemiquinones in Superoxide Anion Radical Production in Photosystem II

Recent evidence has indicated the presence of novel plastoquinone-binding sites, Q_C and Q_D, in photosystem II (PSII). Here, we investigated the potential involvement of loosely bound plastosemiquinones in superoxide anion radical (O₂^•−) formation in spinach PSII membranes using electron paramagnetic resonance (EPR) spin-trapping spectroscopy. Illumination of PSII membranes in the presence of the spin trap EMPO (5-(ethoxycarbonyl)-5-methyl-1-pyrroline N-oxide) resulted in the formation of O₂^•−, which was monitored by the appearance of EMPO-OOH adduct EPR signal. Addition of exogenous short-chain plastoquinone to PSII membranes markedly enhanced the EMPO-OOH adduct EPR signal. Both in the unsupplemented and plastoquinone-supplemented PSII membranes, the EMPO-OOH adduct EPR signal was suppressed by 50% when the urea-type herbicide DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) was bound at the Q_B site. However, the EMPO-OOH adduct EPR signal was enhanced by binding of the phenolic-type herbicide dinoseb (2,4-dinitro-6-sec-butylphenol) at the Q_D site. Both in the unsupplemented and plastoquinone-supplemented PSII membranes, DCMU and dinoseb inhibited photoreduction of the high-potential form of cytochrome b₅₅₉ (cyt b₅₅₉). Based on these results, we propose that O₂^•− is formed via the reduction of molecular oxygen by plastosemiquinones formed through one-electron reduction of plastoquinone at the Q_B site and one-electron oxidation of plastoquinol by cyt b₅₅₉ at the Q_C site. On the contrary, the involvement of a plastosemiquinone formed via the one-electron oxidation of plastoquinol by cyt b₅₅₉ at the Q_D site seems to be ambiguous. In spite of the fact that the existence of Q_C and Q_D sites is not generally accepted yet, the present study provided more spectroscopic data on the potential functional role of these new plastoquinone-binding sites.     

New aspects of the interaction of the antibiotic coralyne with RNA: coralyne induces triple helix formation in poly(rA)?poly(rU)

The interaction of coralyne with poly(A)•poly(U), poly(A)•2poly(U), poly(A) and poly(A)•poly(A) is analysed using spectrophotometric, spectrofluorometric, circular dichroism (CD), viscometric, stopped-flow and temperature-jump techniques. It is shown for the first time that coralyne induces disproportionation of poly(A)•poly(U) to triplex poly(A)•2poly(U) and single-stranded poly(A) under suitable values of the [dye]/[polymer] ratio (C_D/C_P). Kinetic, CD and spectrofluorometric experiments reveal that this process requires that coralyne (D) binds to duplex. The resulting complex (AUD) reacts with free duplex giving triplex (UAUD) and free poly(A); moreover, ligand exchange between duplex and triplex occurs. A reaction mechanism is proposed and the reaction parameters are evaluated. For C_D/C_P> 0.8 poly(A)•poly(U) does not disproportionate at 25°C and dye intercalation into AU to give AUD is the only observed process. Melting experiments as well show that coralyne induces the duplex disproportionation. Effects of temperature, ionic strength and ethanol content are investigated. One concludes that triplex formation requires coralyne be only partially intercalated into AUD. Under suitable concentration conditions, this feature favours the interaction of free AU with AUD to give the AUDAU intermediate which evolves into triplex UAUD and single-stranded poly(A). Duplex poly(A)•poly(A) undergoes aggregation as well, but only at much higher polymer concentrations compared to poly(A)•poly(U).     

The formation pathway of i-motif tetramers

The i-motif is a four-stranded structure formed by two intercalated parallel duplexes containing hemiprotonated C•C⁺ pairs. In order to describe the sequence of reactions by which four C-rich strands associate, we measured the formation and dissociation rates of three [TC_n]₄ tetramers (n = 3, 4 and 5), their dissociation constant and the reaction order for tetramer formation by NMR. We find that TC_n association results in the formation of several tetramers differing by the number of intercalated C•C⁺ pairs. The formation rates of the fully and partially intercalated species are comparable but their lifetimes increase strongly with the number of intercalated C•C⁺ pairs, and for this reason the single tetramer detected at equilibrium is that with optimal intercalation. The tetramer half formation times vary as the power −2 of the oligonucleotide concentration indicating that the reaction order for i-motif formation is 3. This observation is inconsistent with a model supposing association of two preformed duplex and suggests that quadruplex formation proceeds via sequential strand association into duplex and triplex intermediate species and that triplex formation is rate limiting.     

NO? Binds Human Cystathionine β-Synthase Quickly and Tightly

The hexa-coordinate heme in the H₂S-generating human enzyme cystathionine β-synthase (CBS) acts as a redox-sensitive regulator that impairs CBS activity upon binding of NO^• or CO at the reduced iron. Despite the proposed physiological relevance of this inhibitory mechanism, unlike CO, NO^• was reported to bind at the CBS heme with very low affinity (K_d = 30–281 μm). This discrepancy was herein reconciled by investigating the NO^• reactivity of recombinant human CBS by static and stopped-flow UV-visible absorption spectroscopy. We found that NO^• binds tightly to the ferrous CBS heme, with an apparent K_d ≤0.23 μm. In line with this result, at 25 °C, NO^• binds quickly to CBS (k_on ∼ 8 × 10³ m⁻¹ s⁻¹) and dissociates slowly from the enzyme (k_off ∼ 0.003 s⁻¹). The observed rate constants for NO^• binding were found to be linearly dependent on [NO^•] up to ∼ 800 μm NO^•, and >100-fold higher than those measured for CO, indicating that the reaction is not limited by the slow dissociation of Cys-52 from the heme iron, as reported for CO. For the first time the heme of human CBS is reported to bind NO^• quickly and tightly, providing a mechanistic basis for the in vivo regulation of the enzyme by NO^•. The novel findings reported here shed new light on CBS regulation by NO^• and its possible (patho)physiological relevance, enforcing the growing evidence for an interplay among the gasotransmitters NO^•, CO, and H₂S in cell signaling.     

Enzymatic fractionation of carbon isotopes by phosphoenolpyruvate carboxylase from c(4) plants

The carbon atoms of glucose and malate in C₄ plants are 2 to 3‰ enriched in ¹²C with respect to atmospheric CO₂; whereas these intermediates in C₃ plants are 15 to 18‰ enriched with ¹²C with respect to atmospheric CO₂. The enzymatic synthesis of malate from phosphoenolpyruvate and bicarbonate in preparations of leaves of Sorghum bicolor, Haygrazer result in a carbon isotope fractionation of about 3‰. The enzymatic synthesis of phosphoglyceric acid from ribulose 1,5-diP and CO₂ in these preparations (contaminated with carbonic anhydrase) at 24 C and 37 C result in a carbon isotope fractionation of 33.7‰ and 18.3‰, respectively. These data are consistent with the conclusion that the small enrichment of ¹²C in the carbon atoms of malate and glucose (with respect to atmospheric CO₂) in leaves of Sorghum bicolor, Haygrazer occurs at the phosphoenolpyruvate carboxylase step.     

Formation of 8-oxo-7,8-dihydroguanine-radicals in gamma-irradiated DNA by multiple one-electron oxidations

Electron spin resonance (ESR) studies of radicals formed by radiation-induced multiple one-electron oxidations of guanine moieties in DNA are reported in this work. Annealing of gamma-irradiated DNA from 77 to 235 K results in the hydration of one electron oxidized guanine (G^•+) to form the 8-hydroxy-7,8-dihydroguanin-7-yl-radical (•GOH) having one β-proton coupling of 17–28 G and an anisotropic nitrogen coupling, A_‖, of ~20 G, A = 0 with g_‖ = 2.0026 and g = 2.0037. Further annealing to 258 K results in the formation of a sharp singlet at g = 2.0048 with line-width of 5.3 G that is identified as the 8-oxo-7,8-dihydroguanine one-electron-oxidized radical (8-oxo-G^•+). This species is formed via two one-electron oxidations of •GOH. These two one-electron oxidation steps leading to the formation of 8-oxo-G^•+ from •GOH in DNA, are in accordance with the expected ease of oxidation of •GOH and 8-oxo-G. The incorporation of oxygen from water in G^•+ leading to •GOH and to 8-oxo-G^•+ is verified by ESR studies employing ¹⁷O isotopically enriched water, which provide unambiguous evidence for the formation of both radicals. ESR analysis of irradiated-DNA in the presence of the electron scavenger, Tl³⁺, demonstrates that the cationic pathway leads to the formation of the 8-oxo-G^•+. In irradiated DNA–Tl³⁺ samples, Tl³⁺ captures electrons. Tl²⁺ thus produced is a strong oxidant (2.2 V), which is metastable at 77 K and is observed to increase the formation of G^•+ and subsequently of 8-oxo-G^•+ upon annealing. We find that in the absence of the electron scavenger the yield of 8-oxo-G^•+ is substantially reduced as a result of electron recombinations with G^•+ and possible reaction with •GOH.     

Production of Superoxide Anions by Keratinocytes Initiates P. acnes-Induced Inflammation of the Skin

Acne vulgaris is a chronic inflammatory disorder of the sebaceous follicles. Propionibacterium acnes (P. acnes), a gram-positive anareobic bacterium, plays a critical role in the development of these inflammatory lesions. This study aimed at determining whether reactive oxygen species (ROS) are produced by keratinocytes upon P. acnes infection, dissecting the mechanism of this production, and investigating how this phenomenon integrates in the general inflammatory response induced by P. acnes. In our hands, ROS, and especially superoxide anions (O₂ ^•−), were rapidly produced by keratinocytes upon stimulation by P. acnes surface proteins. In P. acnes-stimulated keratinocytes, O₂ ^•− was produced by NAD(P)H oxidase through activation of the scavenger receptor CD36. O₂ ^•− was dismuted by superoxide dismutase to form hydrogen peroxide which was further detoxified into water by the GSH/GPx system. In addition, P. acnes-induced O₂ ^•− abrogated P. acnes growth and was involved in keratinocyte lysis through the combination of O₂ ^•− with nitric oxide to form peroxynitrites. Finally, retinoic acid derivates, the most efficient anti-acneic drugs, prevent O₂ ^•− production, IL-8 release and keratinocyte apoptosis, suggesting the relevance of this pathway in humans.     

Stable isotope canopy effects for sympatric monkeys at Ta? Forest,C?te d'Ivoire

This study tests the hypothesis that vertical habitat preferences of different monkey species inhabiting closed canopy rainforest are reflected in oxygen isotopes. We sampled bone from seven sympatric cercopithecid species in the Taï forest, Côte d''Ivoire, where long-term study has established taxon-specific patterns of habitat use and diet. Modern rib samples (n = 34) were examined for oxygen (δ¹⁸O_ap) and carbon (δ¹³C_ap) from bone apatite (‘bioapatite’), and carbon (δ¹³C_co) and nitrogen (δ¹⁵N_co) from bone collagen. Results are consistent for C₃ feeders in a closed canopy habitat. Low irradiance and evapotranspiration, coupled with high relative humidity and recycled CO₂ in forest understory, contribute to observed isotopic variability. Both δ¹³C_co and δ¹³C_ap results reflect diet; however, δ¹³C values are not correlated with species preference for canopy height. By contrast, δ¹⁸O_ap results are correlated with mean observed height and show significant vertical partitioning between taxa feeding at ground, lower and upper canopy levels. This oxygen isotope canopy effect has important palaeobiological implications for reconstructing vertical partitioning among sympatric primates and other species in tropical forests.     

Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase–pyrophosphatases that act via a covalent aspartyl–phosphate intermediate

Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast—Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PP_i. Crystal structures of metal-free Duf89 and Co²⁺-bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 Å movement of Duf8901 Asp195, vis-à-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl₂ and NaF in the presence of divalent cations Co²⁺, Ni²⁺, or Zn²⁺ generated covalent Duf8901-(Asp248)–beryllium trifluoride (BeF₃)•Co²⁺, Duf8901-(Asp248)–BeF₃•Ni²⁺, or Duf8901-(Asp248)–BeF₃•Zn²⁺ adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)–phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF₃•Co²⁺ squelched p-nitrophenylphosphatase activity. A 1.8 Å structure of a Duf8901-(Asp248)–AlF₄–OH₂•Co²⁺ transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.     

Integrated Analysis of COX-2 and iNOS Derived Inflammatory Mediators in LPS-Stimulated RAW Macrophages Pre-Exposed to Echium plantagineum L. Bee Pollen Extract

Oxidative stress and inflammation play important roles in disease development. This study intended to evaluate the anti-inflammatory and antioxidant potential of Echium plantagineum L. bee pollen to support its claimed health beneficial effects. The hydromethanol extract efficiently scavenged nitric oxide (^•NO) although against superoxide (O₂ ^•−) it behaved as antioxidant at lower concentrations and as pro-oxidant at higher concentrations. The anti-inflammatory potential was evaluated in LPS-stimulated macrophages. The levels of ^•NO and L-citrulline decreased for all extract concentrations tested, while the levels of prostaglandins, their metabolites and isoprostanes, evaluated by UPLC-MS, decreased with low extract concentrations. So, E. plantagineum bee pollen extract can exert anti-inflammatory activity by reducing ^•NO and prostaglandins. The extract is able to scavenge the reactive species ^•NO and O₂ ^•− and reduce markers of oxidative stress in cells at low concentrations.     

Genetic Characterization and Role in Virulence of the Ribonucleotide Reductases of Streptococcus sanguinis

Streptococcus sanguinis is a cause of infective endocarditis and has been shown to require a manganese transporter called SsaB for virulence and O₂ tolerance. Like certain other pathogens, S. sanguinis possesses aerobic class Ib (NrdEF) and anaerobic class III (NrdDG) ribonucleotide reductases (RNRs) that perform the essential function of reducing ribonucleotides to deoxyribonucleotides. The accompanying paper (Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., and Stubbe, J. (2014) J. Biol. Chem. 289, 6259–6272) indicates that in the presence of O₂, the S. sanguinis class Ib RNR self-assembles an essential diferric-tyrosyl radical (Fe^III₂-Y^•) in vitro, whereas assembly of a dimanganese-tyrosyl radical (Mn^III₂-Y^•) cofactor requires NrdI, and Mn^III₂-Y^• is more active than Fe^III₂-Y^• with the endogenous reducing system of NrdH and thioredoxin reductase (TrxR1). In this study, we have shown that deletion of either nrdHEKF or nrdI completely abolishes virulence in an animal model of endocarditis, whereas nrdD mutation has no effect. The nrdHEKF, nrdI, and trxR1 mutants fail to grow aerobically, whereas anaerobic growth requires nrdD. The nrdJ gene encoding an O₂-independent adenosylcobalamin-cofactored RNR was introduced into the nrdHEKF, nrdI, and trxR1 mutants. Growth of the nrdHEKF and nrdI mutants in the presence of O₂ was partially restored. The combined results suggest that Mn^III₂-Y^•-cofactored NrdF is required for growth under aerobic conditions and in animals. This could explain in part why manganese is necessary for virulence and O₂ tolerance in many bacterial pathogens possessing a class Ib RNR and suggests NrdF and NrdI may serve as promising new antimicrobial targets.     

The plant growth regulator activity of the fungicide,epoxiconazole, on Galium aparine L. (cleavers)

The plant growth regulator activity of epoxiconazole, a new triazole fungicide, was investigated by time-course, dose-response and histology experiments with Galium aparine L. (cleavers). Seven days after treatment with 125g ai ha^–1 epoxiconazole (field rate), plant height was reduced by 43%. After seventeen days, leaflet area was reduced by 27% but leaflet fresh weight was not significantly influenced. This was partly because leaflet thickness had increased by 20% following epoxiconazole application. Chlorophyll concentrations were also increased on a unit area basis. Examination of leaflet anatomy showed that epoxiconazole elongated palisade, spongy mesophyll and upper epidermal cells. For example, 125g ai ha^–1 caused a 35% increase in the length of spongy mesophyll cells. Epoxiconazole also prevented cell separation as there were significantly more palisade and spongy mesophyll cells per unit area than in leaflets sprayed with water. Stem development was reduced and 125g ai ha^–1 inhibited the elongation of pith cells in stem tissue by 53%. However, the simultaneous application of gibberellin A₃ (GA₃) with epoxiconazole resulted in stem elongation similar to that of control plants. These observations are consistent with the expected effects following the inhibition of cytochrome P-450 dependent enzyme activity.Abbreviations GA₃ gibberellin A₃ - g ai ha^–1 grams of active ingredient per hectare - L ha^–1 litres per hectare - PPFD photosynthetic photon flux density - RH relative humidity - SE standard error     

Stable Isotope Labeled n-Alkanes to Assess Digesta Passage Kinetics through the Digestive Tract of Ruminants

We describe the use of carbon stable isotope (¹³C) labeled n-alkanes as a potential internal tracer to assess passage kinetics of ingested nutrients in ruminants. Plant cuticular n-alkanes originating from intrinsically ¹³C labeled ryegrass plants were pulse dosed intraruminally in four rumen-cannulated lactating dairy cows receiving four contrasting ryegrass silage treatments that differed in nitrogen fertilization level (45 or 90 kg nitrogen ha⁻¹) and maturity (early or late). Passage kinetics through the gastrointestinal tract were derived from the δ¹³C (i.e. the ratio ¹³C:¹²C) in apparently undigested fecal material. Isotopic enrichment was observed in a wide range of long-chain n-alkanes (C₂₇–C₃₆) and passage kinetics were determined for the most abundant C₂₉, C₃₁ and C₃₃ n-alkanes, for which a sufficiently high response signal was detected by combustion isotope ratio mass spectrometry. Basal diet treatment and carbon chain length of n-alkanes did not affect fractional passage rates from the rumen (K ₁) among individual n-alkanes (3.71–3.95%/h). Peak concentration time and transit time showed a quantitatively small, significant (p≤0.002) increase with carbon chain length. K ₁ estimates were comparable to those of the ¹³C labeled digestible dry matter fraction (3.38%/h; r = 0.61 to 0.71; p≤0.012). A literature review has shown that n-alkanes are not fermented by microorganisms in the rumen and affirms no preferential depletion of ¹³C versus ¹²C. Our results suggest that ¹³C labeled n-alkanes can be used as nutrient passage tracers and support the reliability of the δ¹³C signature of digestible feed nutrients as a tool to measure nutrient-specific passage kinetics.