Comparing real-time quantitative polymerase chain reaction analysis methods for precision,linearity, and accuracy of estimating amplification efficiency

New methods are used to compare seven qPCR analysis methods for their performance in estimating the quantification cycle (C_q) and amplification efficiency (E) for a large test data set (94 samples for each of 4 dilutions) from a recent study. Precision and linearity are assessed using chi-square (χ²), which is the minimized quantity in least-squares (LS) fitting, equivalent to the variance in unweighted LS, and commonly used to define statistical efficiency. All methods yield C_qs that vary strongly in precision with the starting concentration N₀, requiring weighted LS for proper calibration fitting of C_q vs log(N₀). Then χ² for cubic calibration fits compares the inherent precision of the C_qs, while increases in χ² for quadratic and linear fits show the significance of nonlinearity. Nonlinearity is further manifested in unphysical estimates of E from the same C_q data, results which also challenge a tenet of all qPCR analysis methods — that E is constant throughout the baseline region. Constant-threshold (C_t) methods underperform the other methods when the data vary considerably in scale, as these data do.     

Salt-Induced Conformation and Interaction Changes of Nucleosome Core Particles

Small angle x-ray scattering was used to follow changes in the conformation and interactions of nucleosome core particles (NCP) as a function of the monovalent salt concentration C_s. The maximal extension (D_max) of the NCP (145 ± 3-bp DNA) increases from 137 ± 5 Å to 165 ± 5 Å when C_s rises from 10 to 50 mM and remains constant with further increases of C_s up to 200 mM. In view of the very weak increase of the R_g value in the same C_s range, we attribute this D_max variation to tail extension, a proposal confirmed by simulations of the entire I(q) curves, considering an ideal solution of particles with tails either condensed or extended. This tail extension is observed at higher salt values when particles contain longer DNA fragments (165 ± 10 bp). The maximal extension of the tails always coincides with the screening of repulsive interactions between particles. The second virial coefficient becomes smaller than the hard sphere virial coefficient and eventually becomes negative (net attractive interactions) for NCP₁₄₅. Addition of salt simultaneously screens Coulombic repulsive interactions between NCP and Coulombic attractive interactions between tails and DNA inside the NCP. We discuss how the coupling of these two phenomena may be of biological relevance.     

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value

For real-time monitoring of PCR amplification of DNA, quantitative PCR (qPCR) assays use various fluorescent reporters. DNA binding molecules and hybridization reporters (primers and probes) only fluoresce when bound to DNA and result in the non-cumulative increase in observed fluorescence. Hydrolysis reporters (TaqMan® probes and QZyme? primers) become fluorescent during DNA elongation and the released fluorophore remains fluorescent during further cycles; this results in a cumulative increase in observed fluorescence. Although the quantification threshold is reached at a lower number of cycles when fluorescence accumulates, in qPCR analysis no distinction is made between the two types of data sets. Mathematical modeling shows that ignoring the cumulative nature of the data leaves the estimated PCR efficiency practically unaffected but will lead to at least one cycle underestimation of the quantification cycle (C_q value), corresponding to a 2-fold overestimation of target quantity. The effect on the target–reference ratio depends on the PCR efficiency of the target and reference amplicons. The leftward shift of the C_q value is dependent on the PCR efficiency and with sufficiently large C_q values, this shift is constant. This allows the C_q to be corrected and unbiased target quantities to be obtained.     

α-Rhamnosidase and β-glucosidase expressed by naringinase immobilized on new ionic liquid sol-gel matrices: Activity and stability studies

Novel ionic liquid (IL) sol-gel materials development, for enzyme immobilization, was the goal of this work. The deglycosylation of natural glycosides were performed with α-l-rhamnosidase and β-d-glucosidase activities expressed by naringinase. To attain that goal ILs with different structures were incorporated in TMOS/Glycerol sol-gel matrices and used on naringinase immobilization.The most striking feature of ILs incorporation on TMOS/Glycerol matrices was the positive impact on the enzyme activity and stability, which were evaluated in fifty consecutive runs. The efficiency of α-rhamnosidase expressed by naringinase TMOS/Glycerol@ILs matrices increased with cation hydrophobicity as follows: [OMIM] > [BMIM] > [EMIM] > [C₂OHMIM] > [BIM] and [OMIM] ≈ [E₂-MPy] ? [E₃-MPy]. Regarding the imidazolium family, the hydrophobic nature of the cation resulted in higher α-rhamnosidase efficiencies: [BMIM]BF₄ ? [C₂OHMIM]BF₄ ? [BIM]BF₄. Small differences in the IL cation structure resulted in important differences in the enzyme activity and stability, namely [E₃-MPy] and [E₂-MPy] allowed an impressive difference in the α-rhamnosidase activity and stability of almost 150%. The hydrophobic nature of the anion influenced positively α-rhamnosidase activity and stability. In the BMIM series the more hydrophobic anions (PF₆⁻, BF₄⁻ and Tf₂N⁻) led to higher activities than TFA. SEM analysis showed that the matrices are shaped lens with a film structure which varies within the lens, depending on the presence and the nature of the IL.The kinetics parameters, using naringin and prunin as substrates, were evaluated with free and naringinase encapsulated, respectively on TMOS/Glycerol@[OMIM][Tf₂N] and TMOS/Glycerol@[C₂OHMIM][PF₆] and on TMOS/Glycerol. An improved stability and efficiency of α-l-rhamnosidase and β-glucosidase expressed by encapsulated naringinase on TMOS/Glycerol@[OMIM][Tf₂N] and TMOS/Glycerol@[C₂OHMIM][PF₆] were achieved. In addition to these advantageous, with ILs as sol-gel templates, environmental friendly processes can be implemented.     

Homogeneous oxidative coupling catalysts. Mechanism of conversion of 2,6-dimethylphenol [DMP] to 3,3′,5,5′-tetramethyl-4,4′-diphenoquinone [DPQ] by [(Pip)nCuX]4O2 (n = 1 or 2, Pip = piperidine, X = Cl, Br or I) in aprotic media

This paper represents the mechanism of the second half of the catalytic cycle, Scheme 1, which represents the conversion of 2,6-dimethylphenol [DMP] to 3,3′,5,5′-tetramethyl, 4,4′-diphenoquinone [DPQ] by homogenous oxidative coupling catalysts [(Pip)_nCuX]₄O₂ in aprotic media. The mechanism can be represented as a pre-equilibrium, K, between the catalyst and 2,6-dimethylphenol to form a complex intermediate which is converted into the activated complex through the rate determining step, k₂, to form the final products. The observed pseudo first-order rate constant is given by k_obs = K k₂[DMP]^y/(1 + K[DMP]^y). When the coordination number around copper(II) is equal to five as in [(Pip)CuX]₄O₂, the system suffers from kinetic saturation due to strong complex formation between catalyst and [DMP] and therefore K[DMP]^y > 10 and k_obs = k₂. Kinetic saturation has been avoided by using six coordinate copper(II) as in [(Pip)₂CuX]₄O₂. The influence of the coordination saturation of copper(II) in [(Pip)₂CuX]₄O₂ helps to evaluate both thermodynamic and kinetic parameters for the system as well as for the structure of the activated complex, (y = 2), which consists of one [(Pip)₂CuX]₄O₂ and two [DMP]. Reduction of copper(II) to copper(I) has been suggested as a rate determining step due to halogen, X, and solvent effects.     

Base-promoted synthesis of monometallic and bimetallic platinum complexes containing chelating O,O- or S,S-donor ligands

Dichloroplatinum complexes [PtCl₂L₂] (L₂ = cod, dppp) react with 1,2-C₆H₄E₂ (E = O, S) in the presence of a base to produce mononuclear complexes. The diene was not readily displaced from [Pt(E₂C₆H₄-EE)(cod)]. A second approach to complexes containing dianionic chelating ligands involved [Pt(acac)₂] as precursor. Reaction with dppp and oxalic acid gave [Pt(C₂O₄)(dppp)], whereas the analogous reaction with Ph₂PCCPPh₂ produced the bimetallic complex [Pt(C₂O₄-OO)(μ-Ph₂PCCPPh₂)]₂. Similar reactions with 1,2-C₆H₄E₂ (E = O, S) also gave bimetallic products. The structures of [Pt(C₂O₄)(dppp)] and [Pt(C₂O₄-OO)(μ-Ph₂PCCPPh₂)]₂ have been determined by X-ray crystallography.     

The treatment of cheese whey wastewater by sequential anaerobic and aerobic steps in a single digester at pilot scale

The treatment of reconstituted whey wastewater was performed in a 400 L digester at 20 °C, with an anaerobic digestion step, followed by a step of aerobic treatment at low oxygen concentration in the same digester. In a first set of 48 cycles, total cycle time (T_C) of 2, 3 and 4 days were tested at varying organic loading rates (OLR). The COD removal reached 89 ± 4, 97 ± 3 and 98 ± 2% at T_C of 2, 3 and 4 days and OLR of 0.56, 1.04 and 0.78 gCOD L⁻¹ d⁻¹, respectively. The activity of the biomass decreased for the methanogenic population, while increasing by 400% for the acidogens, demonstrating a displacement in the predominant trophic group in the biomass bed. A second set of 16 cycles was performed with higher soluble oxygen concentration in the bulk liquid (0.5 mg L⁻¹) during the aerobic treatment at a T_C of 2 days and an OLR of 1.55 gCOD L⁻¹ d⁻¹, with a soluble COD removal of 88 ± 3%. The biomass specific activities showed a compartmentalization of the trophic group with methanogenic activity maintained in the biomass bed and a high acidogenic activity in the suspended flocs.     

Haptotropic shifts in mononuclear complexes of substituted pentalenes: A DFT investigation of the [CpFe(C8H4R2)] (R = H, Me, NH2, CF3, CN ; q = −1, 0, +1) series

The haptotropic migration of Fe from the unsubstituted ring to the substituted one in the pentalenic complexes [CpFe(η⁵-1,3 C₈H₄R₂)]^q (q = +1, 0, −1) has been investigated by the means of DFT calculations in the case of R = H, CH₃, NH₂, CF₃ and CN. The low energy pathway is a least-motion one-step process in the cationic case. In the anionic series, it is a two-step process involving an intermediate in which the metal moiety is η³-bonded in an exocyclic way to the pentalene ligand. The activation barriers and the preference for the Fe coordination on one ring rather on the other one is investigated with respect to the donor or acceptor abilities of R. The effect of changing q on the haptotropic situation is analyzed in terms of redox molecular switching.     

Diferrocenes containing thiadiazole connectivities

2,5-Diferrocenyl-1,3,4-thiadiazole, 2,5-Fc₂-^cC₂N₂S, (3) has been synthesized by a two-fold Negishi ferrocenylation of dibromothiadiazole (1) with FcZnCl (2) (Fc = Fe(η⁵-C₅H₄)(η⁵-C₅H₅)) in presence of [Pd(Ph₃P)₄] as catalyst. Additional spacer units between the ferrocenyls and the ^cC₂N₂S core could be introduced by using the Sonogashira C,C cross-coupling protocol. Reaction of 2,5-Br₂-^cC₂N₂S (1) or 2,5-(C₆H₄-4′-I)₂-^cC₂N₂S (6) with FcCCH (4) using [PdCl₂(Ph₃P)₂] and [CuI] as catalyst produced the appropriate organometallics 2,5-(FcCC)₂-^cC₂N₂S (5) or 2,5-(C₆H₄-4′-CCFc)₂-^cC₂N₂S (7). The electronic and structural properties of 3, 5, and 7 were investigated with UV-Vis spectroscopy and single crystal X-ray diffraction (3). Complex 3 adopts a solid state structure with none of the ferrocenyl substituents being coplanar with the thiadiazole ring. Cyclic, square wave, linear sweep voltammetry and in-situ NIR spectro-electrochemistry highlight the electrochemical properties of 3. In dichloromethane (0.1 mol L⁻¹ [N(ⁿBu)₄][B(C₆F₅)₄]), compound 3 displays two well resolved electrochemical reversible one-electron events with formal reduction potentials of 0.192 and 0.338 V versus FcH/FcH⁺. In contrast, in presence of [N(ⁿBu)₄][PF₆], the thiadiazoles 3 (E⁰ = 0.22 V), 5 (E⁰ = 0.18 V) and 7 (E⁰ = 0.09 V) show simultaneously oxidation of the two ferrocenyl termini versus FcH/FcH⁺. Spectro-electrochemical studies, performed in a dichloromethane solution of 0.2 mol L⁻¹ [N(ⁿBu)₄][B(C₆F₅)₄], also show that 3 can successively be oxidized via 3⁺ to 3²⁺. A weak IVCT absorption (ε ca. 300 L mol⁻¹ cm⁻¹) at 1560 nm was found and is consistent with appreciable interactions between neutral ferrocenyl and positively charged ferrocenium mixed valent intermediates. Mixed-valent compound 3⁺ corresponds to a class II molecule according to Robin and Day.     

Probing the steric barrier of nonionic surfactant vesicles with melittin

The role of the surface polymer brush of nonionic surfactant vesicles (NSV) in inhibiting interactions with small membrane-perturbing molecules was investigated using the bee venom peptide melittin as a probe. The interaction between melittin and NSV was compared with that of distearoylphosphatidylcholine (DSPC) vesicles and sterically stabilised liposomes (SSL) containing 5 mol% pegylated distearoylphosphatidylethanolamine (DSPE.E₄₄). The degree of melittin interaction with the various vesicles was determined by measuring peptide binding and folding, using intrinsic tryptophan fluorescence and circular dichroism respectively, in addition to monitoring the release of encapsulated carboxyfluorescein dye. NSV composed of 1,2-di-O-octadecyl-rac-glyceryl-3-(ω-dodecaethylene glycol) (2C₁₈E₁₂) showed a strong affinity for melittin, whilst exhibiting ~ 50% less bound peptide than SSL. 2C₁₈E₁₂:Chol vesicles showed reduced melittin interaction, in a manner consistent with Chol incorporation into DSPC vesicles. These results are discussed with respect to the effect of Chol on the in-plane order of 2C₁₈E₁₂ bilayers and consequent attenuation of hydrophobic interactions with the peptide. NSV formed from equimolar mixtures of polyoxyethylene-n-stearoyl ethers C₁₈E₂ and C₁₈E₂₀ showed a greater interaction with melittin than 2C₁₈E₁₂. However, replacing C₁₈E₂₀ with C₁₈E₁₀ was sufficient to achieve an attenuation of melittin interaction similar to that observed in 2C₁₈E₁₂:Chol vesicles. This indicates that the presence of surface polymer brush alone may confer resistance to melittin, provided hydrophobic interactions between the peptide and the vesicles can be minimised, through improved in-plane bilayer order.     

Chemical implantation of Group 4 cations on silica via cyclopentadienyl- and N,N-dialkylcarbamato derivatives

Chemical implantation of Group 4 cations [Ti(III), Ti(IV), Zr(IV), Hf(IV)] has been carried out under mild conditions by the reaction of polycyclopentadienyl- (MCp_n; M = Ti, n = 3, 4; M = Zr, Hf, n = 4), mixed cyclopentadienyl/N,N-dialkylcarbamato (ML_x(O₂CNEt₂)_y; M = Ti, L = Cp, C₅Me₅ (Cp*), x = 2, y = 1; M = Hf, L = Cp, x = 1, y = 3), and N,N-dialkylcarbamato (M(O₂CNR₂)_n, M = Ti, n = 3, R = ⁱPr; M = Ti, Hf, n = 4, R = Et; M = Zr, n = 4, R = ⁱPr) derivatives, with the silanol groups of amorphous silica. Cyclopentadiene/pentamethylcyclopentadiene and/or carbon dioxide and the secondary amine are released in the process. The amount of implanted cations depends on the metal and on the ligands, the pentamethylcyclopentadienyl complex being less reactive than the unsubstituted congener. The starting complexes and the final products have been characterized by EPR or by ¹³C CP-MAS NMR spectroscopy.     

Conversion of the g = 4.1 EPR signal to the multiline conformation during the S2 to S3 transition of the oxygen evolving complex of Photosystem II

The oxygen evolving complex of Photosystem II undergoes four light-induced oxidation transitions, S₀-S₁,…,S₃-(S₄)S₀ during its catalytic cycle. The oxidizing equivalents are stored at a (Mn)₄Ca cluster, the site of water oxidation. EPR spectroscopy has yielded valuable information on the S states. S₂ shows a notable heterogeneity with two spectral forms; a g = 2 (S = 1/2) multiline, and a g = 4.1 (S = 5/2) signal. These oscillate in parallel during the period-four cycle. Cyanobacteria show only the multiline signal, but upon advancement to S₃ they exhibit the same characteristic g = 10 (S = 3) absorption with plant preparations, implying that this latter signal results from the multiline configuration. The fate of the g = 4.1 conformation during advancement to S₃ is accordingly unknown. We searched for light-induced transient changes in the EPR spectra at temperatures below and above the half-inhibition temperature for the S₂ to S₃ transition (ca 230 K). We observed that, above about 220 K the g = 4.1 signal converts to a multiline form prior to advancement to S₃. We cannot exclude that the conversion results from visible-light excitation of the Mn cluster itself. The fact however, that the conversion coincides with the onset of the S₂ to S₃ transition, suggests that it is triggered by the charge-separation process, possibly the oxidation of tyr Z and the accompanying proton relocations. It therefore appears that a configuration of (Mn)₄Ca with a low-spin ground state advances to S₃.     

The role of phase separation and feed cycle length in leach beds coupled to methanogenic reactors for digestion of a solid substrate (Part 1): Optimisation of reactors' performance

A two-phase system composed by a leach bed and a methanogenic reactor was modified for the first time to improve volumetric substrate degradation and methane yields from a complex substrate (maize; Zeamays). The system, which was operated for consecutive feed cycles of different durations for 120 days, was highly flexible and its performance improved by altering operational conditions. Daily substrate degradation was higher the shorter the feed cycle, reaching 8.5 g TS_destroyed d⁻¹ (7-day feed cycle) but the overall substrate degradation was higher by up to 55% when longer feed cycles (14 and 28 days) were applied. The same occurred with volumetric methane yields, reaching 0.839 m³ (m³)⁻¹ d⁻¹. The system performed better than others on specific methane yields, reaching 0.434 m³ kg⁻¹ TS_added, in the 14-day and 28-day systems. The UASB and AF designs performed similarly as second stage reactors on methane yields, SCOD and VFA removal efficiencies.     

Disinfection and toxicological assessments of pulsed UV and pulsed-plasma gas-discharge treated-water containing the waterborne protozoan enteroparasite Cryptosporidium parvum

We report for the first time on the comparative use of pulsed-plasma gas-discharge (PPGD) and pulsed UV light (PUV) for the novel destruction of the waterborne enteroparasite Cryptosporidium parvum. It also describes the first cyto-, geno- and ecotoxicological assays undertaken to assess the safety of water decontaminated using PPGD and PUV. During PPGD treatments, the application of high voltage pulses (16 kV, 10 pps) to gas-injected water (N₂ or O₂, flow rate 2.5 L/min) resulted in the formation of a plasma that generated free radicals, ultraviolet light, acoustic shock waves and electric fields that killed ca. 4 log C. parvum oocysts in 32 min exposure. Findings showed that PPGD-treated water produced significant cytotoxic properties (as determined by MTT and neutral red assays), genotoxic properties (as determined by comet and Ames assays), and ecotoxic properties (as determined by Microtox™, Thamnotox™ and Daphnotox™ assays) that are representative of different trophic levels in aquatic environment (p < 0.05). Depending in part on the type of injected gas used, PPGD-treated water became either alkaline (pH ≤ 8.58, using O₂) or acidic (pH ≥ 3.21, using N₂) and contained varying levels of reactive free radicals such as ozone (0.8 mg/L) and/or dissociated nitric and nitrous acid that contributed to the observed disinfection and toxicity. Chemical analysis of PPGD-treated water revealed increasing levels of electrode metals that were present at ≤ 30 times the tolerated respective values for EU drinking water. PUV-treated water did not exhibit any toxicity and was shown to be far superior to that of PPGD for killing C. parvum oocysts taking only 90 s of pulsing [UV dose of 6.29 μJ/cm²] to produce a 4-log reduction compared to a similar reduction level achieved after 32 min PPGD treatment as determined by combined in vitro CaCo-2 cell culture-qPCR.     

Antioxidant,metal-binding and DNA-damaging properties of flavonolignans: A joint experimental and computational highlight based on 7-O-galloylsilybin

Besides the well-known chemoprotective effects of polyphenols, their prooxidant activities via interactions with biomacromolecules as DNA and proteins are of the utmost importance. Current research focuses not only on natural polyphenols but also on synthetically prepared analogs with promising biological activities. In the present study, the antioxidant and prooxidant properties of a semi-synthetic flavonolignan 7-O-galloylsilybin (7-GSB) are described. The presence of the galloyl moiety significantly enhances the antioxidant capacity of 7-GSB compared to that of silybin (SB). These findings were supported by electrochemistry, DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging activity, total antioxidant capacity (CL-TAC) and DFT (density functional theory) calculations. A three-step oxidation mechanism of 7-GSB is proposed at pH 7.4, in which the galloyl moiety is first oxidized at E_p,1 = +0.20 V (vs. Ag/AgCl_{3M KCl}) followed by oxidation of the 20-OH (E_p,2 = +0.55 V) and most probably 5-OH (E_p,3 = +0.95 V) group of SB moiety. The molecular orbital analysis and the calculation of O–H bond dissociation enthalpies (BDE) fully rationalize the electrooxidation processes. The metal (Cu²⁺) complexation of 7-GSB was studied, which appeared to involve both the galloyl moiety and the 5-OH group. The prooxidant effects of the metal-complexes were then studied according to their capacity to oxidatively induce DNA modification and cleavage. These results paved the way towards the conclusion that 7-O-galloyl substitution to SB concomitantly (i) enhances antioxidant (ROS scavenging) capacity and (ii) decreases prooxidant effect/DNA damage after Cu complexation. This multidisciplinary approach provides a comprehensive mechanistic picture of the antioxidant vs. metal-induced prooxidant effects of flavonolignans at the molecular level, under ex vivo conditions.     

The rate of allelism of lethal genes in a geographically structured population

The expected rate of allelism, E[I(x)], of lethal genes between two colonies with distance x in a structured population is studied by using one- and two-dimensional stepping-stone models. It is shown that E[I(x)] depends on the magnitude of selection in heterozygous condition (h), the rate of migration among adjacent colonies (m), the number of loci which produce lethal mutations (n) and the effective population size of each colony (N).——E[I(x)] always decreases with distance x. The rate of decrease is affected strongly by the magnitude of m. The rate of decrease is faster when m is small. E[I(x)] also decreases with increasing N and n. The effect of h on E[I(x)] is somewhat complicated. However, E[I(0)] is always smaller when h is small than when it is large.——For large x, the following approximate formulae may be obtained: (see PDF) where q and Var (q) are the mean and the variance of gene frequencies in each colony, t is approximated as t=h, (see PDF), -h for the partially recessive, completely recessive, and overdominant lethals, respectively, and C₀ is a function of m and t. It is clear that E[I(x)] declines exponentially with x in a one-dimensional habitat. The decrease E[I(x)] is faster in a two-dimensional habitat than in a one-dimensional habitat. The present result is applied to some of the existing data and the estimation of population parameters is also discussed.     

Effects of light regime and oxygen profile on transformation of oxolinic acid in pond sediment

This study investigated the effects of light (visible light - 5800 lux, 24 h) or dark regime and aerobic or anaerobic condition on the decay of added oxolinic acid (OA) at 5, 10 and 20 mg L⁻¹ in eel pond sediment. An asymptotic decaying exponential model C_t = C_min + C_o × exp (−k × t) was used to facilitate quantitative approach to OA transformation, where C_t is the concentration of OA after t days, C_min the estimated level-off concentration of OA residue, C_o the concentration of added OA and k the decaying coefficient. OA decayed faster under light (C_min = 4.6 mg L⁻¹) than under dark (C_min = 7.8 mg L⁻¹) and also decayed faster under aerobic (C_min = 4.0 mg L⁻¹) than under anaerobic condition (C_min = 8.5 mg L⁻¹). C_min increased with C_o. Sundrying and tilling eel pond bottom should be able to reduce OA residue significantly.     

Relationship of rapid light curves of variable fluorescence to photoacclimation and non-photochemical quenching in a benthic diatom

The response of rapid light–response curves (RLCs) of variable fluorescence to changes in short- and long-term photoacclimation status was studied in an estuarine benthic diatom. The diatom Nitzschia palea was grown under low- (LL, 20 μmol m⁻² s⁻¹) and high-light (HL, 400 μmol m⁻² s⁻¹) conditions, with the purpose of characterising the effects of long-term photoacclimation on (i) steady-state light–response curves (LC) of relative electron transport rate, rETR, (ii) the response of RLCs to changes in ambient irradiance (E, the irradiance to which the sample is acclimated to immediately before the RLCs), (iii) the relationship of RLCs to LC parameters and non-photochemical quenching (NPQ). Photoacclimation to LL and HL conditions induced distinct light–response patterns of rETR and NPQ. Higher growth light resulted in rETR vs. E curves with lower initial slopes (α, 0.591 μmol⁻¹ m² s vs. 0.661 μmol⁻¹ m² s, for HL and LL, respectively) and markedly higher maximum rates (rETR_m, 95.9 vs. 29.3), reached under higher E levels (higher light-saturation coefficient, E_k: 162.4 μmol m⁻² s⁻¹ vs. 44.3 μmol m⁻² s⁻¹). Acclimation to HL induced bi-phasic NPQ vs. E curves, with minimum values reached under low E levels (15–25 μmol m⁻² s⁻¹) and not on dark-acclimated samples. The response of RLCs to changes in ambient irradiance varied with the long-term photoacclimation status of the samples. The initial slope, α_RLC, decreased monotonically with E in LL cultures, from 0.68 to 0.25 μmol⁻¹ m² s, while varied bi-phasically in HL-acclimated samples. Typically, α_RLC of HL cultures increased under low E, reaching a maximum of 0.61 μmol⁻¹ m² s under 25–55 μmol m⁻² s⁻¹, and decreased gradually under higher E levels to 0.25 μmol⁻¹ m² s. RLC maximum rETR, rETR_m,RLC, and saturation coefficient E_k,RLC, increased with E following a saturation-like pattern, with the HL cultures presenting markedly higher values for all the E range (maximum rETR_m,RLC values were 108.6 and 33.4 for HL and LL cultures, respectively). An inverse relationship was consistently found between α_RLC and NPQ, both on LL and HL cultures, causing strong correlations (P < 0.001 in all cases) between NPQ and the high light-induced decrease of α_RLC, Δα_RLC. RLCs were confirmed to also provide information on the long-term photoacclimation status, as significant correlations (P < 0.001 both for HL and LL cultures) were verified between E_k and an index based on RLC parameters, Ê_k, both for LL and HL cultures. These results reinforce the usefulness of RLCs as a tool for inferring on the short- and long-term photoacclimation status of samples with different long-term light histories, through the estimation of LC parameters and the monitoring of NPQ levels.     

Phosphane- and phosphite-silver(I) phenolates: Synthesis, characterization and their use as CVD precursors

The silver(I) salts [AgOR] (3a, R = C₉H₆N; 3b, R = C₆H₄-2-CHO, 3c, R = C₆H₄-2-Cl; 3d, R = C₆H₄-2-CN; 3e, R = C₆H₄-2-NO₂) are accessible by the stoichiometric reaction of [AgNO₃] (1) with HOR (2a, R = C₉H₆N; 2b, R = C₆H₄-2-CHO; 2c, R = C₆H₄-2-Cl; 2d, R = C₆H₄-2-CN; 2e, R = C₆H₄-2-NO₂) in presence of NEt₃. Treatment of 3a-3e with PⁿBu₃ (4), P(OMe)₃ (5a) or P(OCH₂CF₃)₃ (5b) in the ratios of 1:1 and 1:2, respectively, produced complexes [L_mAgOR] (L = PⁿBu₃, m = 1: 6a, R = C₉H₆N; 6b, R = C₆H₄-2-CHO; 6c, R = C₆H₄-2-Cl; 6d, R = C₆H₄-2-CN; 6e, R = C₆H₄-2-NO₂. m = 2: 7a, R = C₉H₄; 7b, R = C₆H₄-2-CHO; 7c, R = C₆H₄-2-Cl; 7d, R = C₆H₄-2-CN; 7e, R = C₆H₄-2-NO₂. L = P(OMe)₃, m = 1: 8a, R = C₆H₄-2-CHO; 8b, R = C₆H₄-2-NO₂. m = 2: 9, R = C₆H₄-2-NO₂. L = P(OCH₂CF₃)₃, m = 1: 10, R = C₆H₄-2-NO₂). Based on TGA, temperature-programmed and in situ molecular beam mass spectrometry metal-organic 7e was applied as CVD precursor in the deposition of silver onto glass substrates. The resulting silver films were characterized by XRD. The SEM image of a film grown from 7e at 350 °C showed a homogeneous surface with grain sizes of 40 nm. The molecular structures of 8b and 10 in the solid state were determined. They are isostructural and are cubane-like structured. Low-temperature ³¹P{¹H} NMR studies showed that the title complexes are dynamic in solution and exchange at room temperature their ligands.     

Using fractal self‐similarity to increase precision of shrub biomass estimates

We show that aerial tips are self‐similar fractals of whole shrubs and present a field method that applies this fact to improves accuracy and precision of biomass estimates of tall‐shrubs, defined here as those with diameter at root collar (DRC) ≥ 2.5 cm. Power function allometry of biomass to stem diameter generates a disproportionate prediction error that increases rapidly with diameter. Thus, biomass should be modeled as a single measure of stem diameter only if stem diameter is less than a threshold D_max. When stem diameter exceeds D_max, then the stem internode should be treated as a conic frustrum requiring two additional measures: a second, node‐adjacent diameter and a length. If the second diameter is less than D_max, then the power function allometry can be applied to the aerial tip; otherwise an additional internode is measured. This “two‐component” allometry—internodes as frustra and aerial tips as shrubs—can reduce estimated biomass error propagated to the plot‐level by as much as 50% or more where very large shrubs are present D_max is any diameter such that the ratio of single‐component to two‐component uncertainty exceeds the ratio of two‐component to single‐component measurement time. Guidelines for estimating D_max based on pilot field data are provided. Tall shrubs are increasing in abundance and distribution across Arctic, alpine, boreal, and dryland ecosystems. Estimating their biomass is important for both ecological studies and carbon accounting. Reducing field‐sample prediction error increases precision in multi‐stage modeling because additional measures efficiently improve plot‐level biomass precision, reducing uncertainty for shrub biomass estimates.