Response of the adenosine phosphate pool level to changes in the catabolic pattern of Saccharomyces cerevisiae

Changes in the catabolic pattern of Saccharomyces cerevisiae, growing in continuous culture, were effected by altering the glucose feed rate or the dissolved oxygen concentration. The cytochrome concentrations and the adenosine phosphate pool level of the yeast in a series of steady states and during three transitions were measured and compared with the glucose uptake rate (Q_G), the respiration rate (QO₂), and the rate of ethanolic fermentation (Q_E). Respiration was decreased at high glucose feed rates only if oxygen was low but cytochromes were glucose repressible at both high and low oxygen concentrations. In the main, Q_E and the levels of ATP, ADP, and AMP were decreased and cytochrome concentration were elevated at low Q_G values. No consistent relationship between any of the adenosine phosphate parameters and QO₂ was discernible. Evidence is presented for the concept that the Q_G directly controls the adenosine phosphate pool level and that a relationship between the concentration of adenosine phosphate anhydride bonds and the adenosine phosphate level is constantly maintained.     

Mutations of Loop 2 and Loop 3 Residues in Domain II of Bacillus thuringiensis Cry1C δ-Endotoxin Affect Insecticidal Specificity and Initial Binding to Spodoptera littoralis and Aedes aegypti Midgut Membranes

Site-directed mutagenesis was used to examine the role of predicted loops 2 (³⁷⁴QPWP³⁷⁷) and 3 (⁴³⁶QRSGTPF⁴⁴²) in domain II of the Bacillus thuringiensis Cry1C δ endotoxin for insecticidal specificity and receptor binding. Q³⁷⁴E, S⁴³⁸F, and G⁴³⁹A substitutions resulted in near or complete loss of toxicity toward both Spodoptera littoralis and Aedes aegypti. R⁴³⁷K, R⁴³⁷I, and G⁴³⁹V mutants exhibited significantly reduced toxicity to S. littoralis and A. aegypti, while mutations of T⁴⁴⁰, P⁴⁴¹, and F⁴⁴² showed only slight reductions in toxicity to both insects. Loop 2 mutations Q³⁷⁴N, P³⁷⁵A, W³⁷⁶Y, and P³⁷⁷A did not significantly affect S. littoralis toxicity but exhibited reduced activity to A. aegypti. In contrast, the loop 3 mutations Q⁴³⁶K, Q⁴³⁶E, and S⁴³⁸Y had no effect on A. aegypti toxicity, but showed significantly decreased S. littoralis activity. Heterologous competition binding assays with brush border membrane vesicles (BBMV) from both insects correlated well with the toxicity data with the exception of the R⁴³⁷ mutants, where steps other than initial receptor binding appear to be involved. Overall we conclude that, while loops 2 and 3 play an important role in binding and toxicity to both insects, loop 2 appears to play the greater role in A. aegypti activity, while loop 3 is more important for S. littoralis toxicity. Received: 5 March 1999 Accepted: 5 April 1999     

全球陆地生态系统光合作用与呼吸作用的温度敏感性

基于全球647套通量数据,定量分析了全球尺度下生态系统光合作用和呼吸作用的温度敏感性(Q10)随纬度、气候和植被的分布规律。结果表明:在全球尺度下,光合作用和呼吸过程的温度敏感性(Q10,G和Q10,R)都随纬度的升高而增加,其中Q10,G和Q10,R的均值分别为3.99±0.21和2.28±0.074。除热带多树草原、常绿落叶林外,Q10,G均大于Q10,R值。不同植被类型的温度敏感性存在显著性差异,表现为:针叶林阔叶林;落叶林常绿林,其中生态系统的季节性变异是造成差异的主要原因。当植被类型和纬度区域共同影响Q10值时,植被类型对Q10值的总变异贡献更大。气候类型对Q10,G和Q10,R都有显著影响。在气候带上,干旱带的Q10,G最小,而冷温带的Q10,G最高。不同气候类型下(除温带草原气候外)的Q10,G都大于Q10,R。在极端条件下,温度可能不在是主导因素,而水分对温度敏感性的影响不可忽略,今后的研究需要更多的关注生态系统温度敏感性对水分变化的响应。     

Characterization of second site mutations show that fast proton transfer to QB − is restored in bacterial reaction centers of Rhodobacter sphaeroides containing the Asp-L213 → Asn lesion

The structural basis for proton coupled electron transfer to Q_B in bacterial reaction centers (RCs) was studied by investigating RCs containing second site suppressor mutations (Asn M44 Asp, Arg M233 Cys, Arg H177 His) that complement the effects of the deleterious Asp L213 Asn mutation [DN(L213)]. The suppressor RCs all showed an increased proton coupled electron transfer rate k _AB ⁽²⁾(Q_A ^–Q_B ^– + H⁺ Q_AQ_BH^–) by at least 10³ (pH 7.5) and a recombination rate k _BD (D⁺Q_AQ_B ^– DQ_AQ_B) 15–40 times larger than the value found in DN(L213) RCs. Proton transfer was studied by measuring the dependence of k _AB ⁽²⁾ on the free energy for electron transfer (G_et). k _AB ⁽²⁾ was independent of G_et in DN(L213) RCs, but dependent on G_et in native and all suppressor RCs. This shows that proton transfer limits the k _AB ⁽²⁾ reaction with a rate of 0.1s^–1 in DN(L213) RCs but is not rate limiting and at least 10⁸-fold faster in native and 10⁵-fold faster in the suppressor RCs. The increased rate of proton transfer by the suppressor mutations are proposed to be due to: (i) a reduction in the barrier to proton transfer by providing a more negative electrostatic potential near Q_B ^–; and/or (ii) structural changes that permit fast proton transfer through the network of protonatable residues and water molecules near Q_B.     

Low-temperature modulation of the redox properties of the acceptor side of photosystem II: photoprotection through reaction centre quenching of excess energy

Although it has been well established that acclimation to low growth temperatures is strongly correlated with an increased proportion of reduced Q_A in all photosynthetic groups, the precise mechanism controlling the redox state of Q_A and its physiological significance in developing cold tolerance in photoautotrophs has not been fully elucidated. Our recent thermoluminescence (TL) measurements of the acceptor site of PSII have revealed that short‐term exposure of the cyanobacterium Synechococcus sp. PCC 7942 to cold stress, overwintering of Scots pine (Pinus sylvestris L.), and acclimation of Arabidopsis plants to low growth temperatures, all caused a substantial shift in the characteristic T_M of S₂Q_B^– recombination to lower temperatures. These changes were accompanied by much lower overall TL emission, restricted electron transfer between Q_A and Q_B, and in Arabidopsis by a shift of the S₂Q_A^–‐related peak to higher temperatures. The shifts in recombination temperatures are indicative of a lower activation energy for the S₂Q_B^– redox pair and a higher activation energy for the S₂Q_A^– redox pair. This results in an increase in the free‐energy gap between P680⁺Q_A^– and P680⁺Pheo^– and a narrowing of the free energy gap between Q_A and Q_B electron acceptors. We propose that these effects result in an increased population of reduced Q_A (Q_A^–), facilitating non‐radiative P680⁺Q_A^– radical pair recombination within the PSII reaction centre. The proposed reaction centre quenching could be an important protective mechanism in cyanobacteria in which antenna and zeaxanthin cycle‐dependent quenching are not present. In herbaceous plants, the enhanced capacity for dissipation of excess light energy via PSII reaction centre quenching following cold acclimation may complement their capacity for increased utilization of absorbed light through CO₂ assimilation and carbon metabolism. During overwintering of evergreens, when photosynthesis is inhibited, PSII reaction centre quenching may complement non‐photochemical quenching within the light‐harvesting antenna when zeaxanthin cycle‐dependent energy quenching is thermodynamically restricted by low temperatures. We suggest that PSII reaction centre quenching is a significant mechanism enabling cold‐acclimated organisms to acquire increased resistance to high light.     

Assessment of annual carbon exchange in a water-stressed Pinus radiata plantation: an analysis based on eddy covariance measurements and an integrated biophysical model

We used a combination of eddy flux, chamber and environmental measurements with an integrated suite of models to analyse the seasonality of net ecosystem carbon uptake (F_CO2) in an 8-year-old, closed canopy Pinus radiata D.Don plantation in New Zealand (42°52′ S, 172°45′ E). The analyses utilized a biochemically based, big-leaf model of tree canopy photosynthesis (A_c), coupled to multiplicative environmental-constraint functions of canopy stomatal conductance (G_c) via environmental measurements, a temperature-dependent model of ecosystem respiration (R_eco), and a soil water balance model. Available root zone water storage capacity at the measurement site is limited to about 50 mm for the very stony soil, and annual precipitation is only 660 mm, distributed evenly throughout the year. Accordingly the site is prone to soil moisture deficit throughout the summer. G _c and A_c obtained maximum rates early in the growing season when plentiful soil water supply was associated with sufficient quantum irradiance (Q_abs), and moderate air saturation deficit (D) and temperature (T). From late spring onwards, soil water deficit and D confined G_c and A_c congruously, which together with the solely temperature dependency of R_eco resulted in the pronounced seasonality in F_CO2. Reflecting a light-limitation of A_c in the closed canopy, modelled annual carbon (C) uptake was most sensitive to changes in Q_abs. However, Q_abs did not vary significantly between years, and changes in annual F_CO2 were mostly due to variability in summer rainfall and D. Annual C-uptake of the forest was 717 g C m^–2 in a near-average rainfall year, exceeding by one third the net uptake in a year with 20% less than average rainfall (515 g C m^–2).     

The IleL229 → Met mutation impairs the quinone binding to the QB-pocket in reaction centers of Rhodobacter sphaeroides

A spontaneous mutant (R/89) of photosynthetic purple bacterium Rhodobacter sphaeroides R-26 was selected for resistance to 200 M atrazin. It showed increased resistance to interquinone electron transfer inhibitors of o-phenanthroline (resistance factor, RF=20) in UQ_o reconstituted isolated reaction centers and terbutryne in reaction centers (RF=55) and in chromatophores (RF=85). The amino acid sequence of the Q_B binding protein of the photosynthetic reaction center (the L subunit) was determined by sequencing the corresponding pufL gene and a single mutation was found (Ile^L229 Met). The changed amino acid of the mutant strain is in van der Waals contact with the secondary quinone Q_B. The binding and redox properties of Q_B in the mutant were characterized by kinetic (charge recombination) and multiple turnover (cytochrome oxidation and semiquinone oscillation) assays of the reaction center. The free energy for stabilization of Q_AQ_B ^– with respect to Q_A ^–Q_B was G_AB=–60 meV and 0 meV in reaction centers and G_AB=–85 meV and –46 meV in chromatophores of R-26 and R/89 strains at pH 8, respectively. The dissociation constants of the quinone UQ_o and semiquinone UQ_o ^– in reaction centers from R-26 and R/89 showed significant and different pH dependence. The observed changes in binding and redox properties of quinones are interpreted in terms of differential effects (electrostatics and mesomerism) of mutation on the oxidized and reduced states of Q_B.Abbreviations BChl bacteriochlorophyll - Ile isoleucine - Met methionin - P primary donor - Q_A primary quinone acceptor - Q_B secondary quinone acceptor - RC reaction center protein - UQ_o 2,3-dimethoxy-5-methyl benzoquinone - UQ₁₀ ubiquinone 50 This work is dedicated to the memory of Randall Ross Stein (1954–1994) and is, in a small way, a testament to the impact which Randy's ideas have had on the development of the field of competitive herbicide binding.     

Reaction centers from three herbicide resistant mutants of Rhodobacter sphaeroides 2.4.1: Kinetics of electron transfer reactions

Electron transfer rates were measured in RCs from three herbicide-resistant mutants with known amino acid changes to elucidate the structural requirements for last electron transfer. The three herbicide resistant mutants were IM(L229) (Ile-L229 Met), SP(L223) (Ser-L223 Pro) and YG(L222) (Tyr-L222 Gly). The electron transfer rate D⁺Q_A ^-Q_BD⁺Q_AQ_B (k _AB) is slowed 3 fold in the IM(L229) and YG(L222) RCs (pH 8). The stabilization of D⁺Q_AQ_B ^- with respect to D⁺Q_AQ_B ^- (pH 8) was found to be eliminated in the IM(L229) mutant RCs (G⁰ 0 meV), was partially reduced in the SP(L223) mutant RCs (G⁰=–30 meV), and was unaltered in the YG(L222) mutant RCs (G⁰=–60 meV), compared to that observed in the native RCs (G⁰=–60 meV). The pH dependences of the charge recombination rate D⁺Q_AQ_B ^-DQ_AQ_B (k _BD) and the electron transfer from Q_A ^- (k _QA ^-Q_A) suggest that the mutations do not affect the protonation state of Glu-L212 nor the electrostatic interactions of Q_B and Q_B ^- with Glu-L212. The binding affinities of UQ₁₀ for the Q_B site were found in order of decreasing values to be native IM(L229) > YG(L222) SP(L223). The altered properties of the mutant RCs are used to deduce possible structural changes caused by the mutations and are dicscussed in terms of photosynthetic efficiency of the herbicide resistant strains.Abbreviations Bchl bacteriochlorophyll - Bphe bacteriopheophytin - cholate 3,7,12-trihydroxycholanic acid - D donor (bacteriochlorophyll dimer) - EDTA ethylenediamine tetraacetic acid - Fe²⁺ non-heme iron atom - LDAO lauryl dimethylamine oxide - PS II photosystem II - Q_A and Q_B primary and secondary quinone acceptors - RC bacterial reaction center - Tris tris(hydroxymethyl)aminomethane - UQ₀ 2,3-dimethoxy-5-methyl benzoquinone - UQ₁₀ ubiquinone 50     

Canopy gradients in leaf intercellular CO2 mole fractions revisited: interactions between leaf irradiance and water stress need consideration

Intercellular CO₂ mole fractions (C_i) are lower in the upper canopy relative to the lower canopy leaves. This canopy gradient in C_i has been associated with enhanced rates of carbon assimilation at high light, and concomitant greater draw‐downs in C_i. However, increases in irradiance in the canopy are generally also associated with decreases in leaf water availability. Thus, stress effects on photosynthesis rates (A) and stomatal conductance (G), may provide a further explanation for the observed C_i gradients. To test the hypotheses of the sources of canopy variation in C_i, and quantitatively assess the influence of within‐canopy differences in stomatal regulation on A, the seasonal and diurnal variation in G was studied in relation to seasonal average daily integrated quantum flux density (Q_int) in tall shade‐intolerant Populus tremula L. trees. Daily time‐courses of A were simulated using the photosynthesis model of Farquhar et al. (Planta 149, 78–90, 1980). Stable carbon isotope composition of a leaf carbon fraction with rapid turnover rate was used to estimate canopy gradient in C_i during the simulations. Daily maximum G (G_max) consistently increased with increasing Q_int. However, canopy differences in G_max decreased as soil water availability became limiting during the season. In water‐stressed leaves, there were strong mid‐day decreases in G that were poorly associated with vapour pressure deficits between the leaf and atmosphere, and the magnitude of the mid‐day decreases in G occasionally interacted with long‐term leaf light environment. Simulations indicated that the percentage of carbon lost due to mid‐day stomatal closure was of the order of 5–10%, and seasonal water stress increased this percentage up to 20%. The percentage of carbon lost due to stomatal closure increased with increasing Q_int. Canopy differences in light environment resulted in a gradient of daily average C_i of approximately 20 µmol mol^?1. The canopy variation in seasonal and diurnal reductions in G led to a C_i gradient of approximately 100 µmol mol^?1, and the actual canopy C_i gradient was of the same magnitude according to leaf carbon isotope composition. This study demonstrates that stress effects influence C_i more strongly than within‐canopy light gradients, and also that leaves acclimated to different irradiance and water stress conditions may regulate water use largely independent of foliar photosynthetic potentials.     

Extensive deletions in the Q region of the mouse major histocompatibility complex

By use of Southern blot analyses and low copy number probes, the fine structure of the Q region of the mouse major histocompatibility complex was studied in more detail. With a probe recognizing the even-numbered genes Q4, Q6, and Q8, it was evident that Q4 and/or the regions flanking Q4 are polymorphic, whereas Q6 and Q8, and their flanking regions are nonpolymorphic. Perhaps the most noteworthy finding is that at least two strain haplotypes, H-2 ^k and H-2 ^f, possessed extensive deletions in the Q region. The most striking deletion was found in the H-2 ^f haplotype, where the QI through Q9 genes appear to be missing. Because of these extensive deletions the functional importance of the Q region is questioned.     

METHYLATED AMINO ACID RESIDUES OF PROTEINS OF BRAIN AND OTHER ORGANS

—Methods for the determination of methyl-lysine, methyllarginine and methylhistidine residues of tissue proteins are described. They consist of preliminary purification of basic amino acids, enzymic removal of lysine, arginine and histidine followed by amino acid analysis. Recovery rates and specificities of the method were satisfactory. The contents of methylamino acids in proteins of mammalian organs were determined. The distribution of proteins containing the methylamino acids in human brain showed that the concentrations of methyl-lysine and N^G,N′^G-dimethylarginine were highest in the gray matter of the cerebellar cortex and relatively high in regions rich in gray matter, while those of N^G-mono- and N^G,N′^G-dimethylarginine were highest in the white matter. The following findings suggest that most of the N^G-mono- and N^G,N′^G-dimethylarginine was associated with the myelin basic protein. The distribution of the methylarginine residues of acid-soluble proteins in bovine brains coincided with the cerebroside pattern. The concentrations of the amino acids in acid-soluble proteins of rat brain increased concomitantly with the increase of cerebroside. The methylamino acid content in proteins increased during the purification of the myelin basic protein from the white matter of human and bovine brains. Proteins containing N^G,N^G-dimethyiarginine and di- and trimethyl-lysine are concentrated in cell nuclei. The first amino acid was found mainly in nucleoplasmic proteins and the other two were found in histones. The concentration of 3-methylhistidine residue, highest in muscular proteins, is low in cerebral proteins and is probably derived from proteins of walls of blood vessels in the brain.     

A test of the hydraulic limitation hypothesis in fast-growing Eucalyptus saligna

The hydraulic limitation hypothesis proposes that (1) reduced growth in taller trees is caused by decreased photosynthesis resulting from a decrease in hydraulic conductance promoted by a longer root‐to‐leaf flow path, and (2) this mechanism reduces stand productivity after canopy closure. This hypothesis was tested by comparing the physiology of 7 m (1 year) and 26 m (5 year) Eucalyptus saligna plantations where above‐ground productivity for the 26 m trees was approximately 69% of that for the 7 m trees, and water and nutrients were not limiting. The study compared whole tree physiology [water flux (Q_l), average crown conductance (G_T), crown hydraulic conductance per unit leaf area (K_L), carbon isotope discrimination (δ¹³C)] and leaf physiology under light saturation (leaf water potential at the canopy top (Ψ_LEAF), photosynthetic capacity (A_max), and photosynthesis (A) and stomatal conductance (g_s). K_L was 50% lower in the taller trees, but whole tree Q_l and G_T were the same for the 7 m and 26 m trees. Photosynthetic capacity was the same for leaves at the canopy top, but δ¹³C was ?1.8‰ lower for the 26 m trees. A and g_s were either lower in the taller trees or equal, depending on sampling date. The taller trees maintained 0.8 MPa lower Ψ_LEAF during the day and had 2.6‐times higher sapwood area per unit leaf area; these factors compensated for the effects of increased height and gravitational potential in the taller trees to maintain higher G_T. The hydraulic limitation hypothesis (as originally stated) failed to explain the sharp decline in net primary productivity after canopy closure in this study. The effects of increased height appear to be a universal hydraulic problem for trees, but compensation mitigated these effects and maintained Q_l and G_T in the present study. Compensation may induce other problems (such as lower Ψ_LEAF or higher respiratory costs) that could reduce carbon gain or shift carbon allocation, and future studies of hydraulic limitation should consider compensation and associated carbon costs. In this study, the combination of similar G_T and lower δ¹³C for the 26 m trees suggests that total crown photosynthesis was lower for the 26 m trees, perhaps a result of the lower Ψ_LEAF.     

Thermoluminescence and Delayed Luminescence Investigation of the Green Alga,Chlamydobotrys stellata

Thermoluminescence and delayed luminescence investigations of the autotrophically and photoheterotrophically cultivated green alga, Chlamydobotrys stellata, demonstrated that both the thermoluminescence and delayed luminescence yields are much lower in the photoheterotophic algae than in the autotrophic ones due to an efficient luminescence quenching of unknown mechanism. The relative contributions of the so called Q (S₂Q^?_A charge recombination) and B (S₂Q^?_B and S₃Q^?_B charge recombinations) thermoluminescence bands to the glow curve as well as the Q_A(S₂Q^?_B charge recombination) and Q_B (S₂Q^?_B and S₃Q^?_B charge recombinations) delayed luminescence components to the delayed luminescence decay of autotrophically and photoheterotrophically cultivated Chl. stellata were compared using a computer assisted curve resolution method. It was found that, while in the autotrophic cells the area of the B band was considerably larger than of the Q band, in photoheterotrophic cells the Q band was more effectively charged than the B band. In the delayed luminescence decay curves measured in the seconds to minutes time region the amplitude of the Q_A component relative to that of the Q_B component was larger in the photoheterotrophic cells than in the autotrophic ones. These observations demonstrate that, after light-induced charge separation in the photosystem II reaction centers of autotrophic cells, electrons are “quasipermanently” stored mainly in the secondary quinone acceptor pool, Q_B but in the nonquenched photosystem II reaction centers of photoheterotrophic cells the main reservoir of electrons is the primary quinone acceptor, Q_A. This behaviour indicates an inhibition of electron transport in the photoheterotrophic alga at the level of the secondary quinone acceptor, Q_B.     

Relationships within the Melanogaster subgroup species of the genus Drosophila (Sophophora)

Five members of the melanogaster species subgroup of the subgenus Sophophora have been studied cytologically, their mitotic chromosomes analysed after Giemsa, C-banding and quinacrine staining. In all five species (D. yakuba, D. teissieri, D. erecta, D. orena and D. mauritiana) n=4 and all of the species except D. orena have a typical melanogaster like mitotic karyotype though there are clear differences between species in the distribution of both C⁺ and Q⁺ material. D. orena has large metacentric X and Y chromosomes due to the accumulation of intensively fluorescing material on these elements with respect to their homologues in melanogaster. This extra heterochromatin of D. orena correlates with a very high proportion of satellite DNA in its nuclear genome (S. Barnes, unpublished). The polytene chromosomes of these species were studied after quinacrine staining and Q⁺ material found to be restricted to the polytene fourth chromosomes, with the exception of D. orena which possesses considerable Q⁺ material in its chromocentre. These findings are discussed in the light of other studies of karyotype evolution in the genus Drosophila.     

Comparisons of Some Chi-Squared Goodness-of-Fit Test Statistics in Sparse One-Way Multinomials

The behavior of Pearson's X² test, the likelihood ratio test Y² and the two of its derivatives, G² and G_k², the Freeman-Tukey test (FT) and the Cressie and Read test Statistic I(2/3) are examined in this study. Estimated attained α levels based on 1000 simulated samples when the approximating distribution is χ_k-1², are computed for these tests for the various values of k, n and seven null hypotheses. Results from estimated power computations indicate that none of the test statistics has a clear advantage over any others, and that the choice of which test to use must therefore rest mainly on the performances with regards to the attained α levels when the χ² approximation is invoked. In this respect, the log-normal approximation proposed by Lawal and Upton (1980) is strongly recommended. This is closely followed by the I(2/3).     

Pivotal surfaces in inverse hexagonal and cubic phases of phospholipids and glycolipids

Data on the location and dimensions of the pivotal surfaces in inverse hexagonal (H_II) and inverse cubic (Q_II) phases of phospholipids and glycolipids are reviewed. This includes the H_II phases of dioleoyl phosphatidylethanolamine, 2:1 mol/mol mixtures of saturated fatty acids with the corresponding diacyl phosphatidylcholine, and glucosyl didodecylglycerol, and also the Q_II^230/G gyroid inverse cubic phases of monooleoylglycerol and glucosyl didodecylglycerol. Data from the inverse cubic phases are largely compatible with those from inverse hexagonal H_II-phases. The pivotal plane is located in the hydrophobic region, relatively close to the polar–apolar interface. The area per lipid at the pivotal plane is similar in size to lipid cross-sectional areas found in the fluid lamellar phase (L_α) of lipid bilayers.     

Kinetics of ubiquinone reduction by the resolved succinate: Ubiquinone reductase

A significant lag in the thenoyltrifluoroacetone (TTFA)-sensitive succinate: ubiquinone reductase activity was observed when a ubiquinone-deficient resolved preparation of the enzyme was assayed in the presence of exogenous ubiquinone-2 (Q2) and 2,6-dichlorophenolindophenol. No such lag was seen when the free radical of N,N,N′,N′-tetramethyl-p-phenylenediamine (Wurster's Blue) was used as the terminal electron acceptor, or when the reduction of Q2 was directly measured. The apparent Km value for exogenous Q2 was determined in the Q2-mediated TTFA-sensitive succinate: Wurster's Blue reductase reaction. When the enzyme activity was measured directly by monitoring Q2 reduction without terminal acceptors, the time course of the reaction deviated from zero-order kinetics at Q2 concentrations which were much higher than those expected from the KQ2m value determined in the presence of Wurster's Blue. The time course of Q2 reduction fits a curve describing a competitive interrelationship between oxidized and reduced Q2 at the specific binding site. The data obtained are in agreement with the Q-pool behavior of ubiquinone in mitochondrial membranes and suggest that the rate of ubiquinone reduction by succinate is dependent on the ratio.     

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q ² and Discriminant Q ² (DQ ²) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q ² and Discriminant Q ² (DQ ²). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ ² and Q ² (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies.

     

Organization and function of cytochromeb and ubiquinone in the cristae membrane of beef heart mitochondria

The arrangement and function of the redox centers of the mammalianbc ₁ complex is described on the basis of structural data derived from amino acid sequence studies and secondary structure predictions and on the basis of functional studies (i.e., EPR data, inhibitor studies, and kinetic experiments). Two ubiquinone reaction centers do exist—a QH₂ oxidation center situated at the outer, cytosolic surface of the cristae membrane (Q₀ center), and a Q reduction center (Q _i center) situated more to the inner surface of the cristae membrane. The Q₀ center is formed by theb-566 domain of cytochromeb, the FeS protein, and maybe an additional small subunit, whereas the Q _i center is formed by theb-562 domain of cytochromeb and presumably the 13.4kDa protein (QP-C). The Q binding proteins are proposed to be protein subunits of the Q reaction centers of various multiprotein complexes. The path of electron flow branches at the Q₀ center, half of the electrons flowing via the high-potential cytochrome chain to oxygen and half of the electrons cycling back into the Q pool via the cytochromeb path connecting the two Q reaction centers. During oxidation of QH₂, 2H⁺ are released to the cytosolic space and during reduction of Q, 2H⁺ are taken up from the matrix side, resulting in a net transport across the membrane of 2H⁺ per e^– flown from QH₂ to cytochromec, the H⁺ being transported across the membrane as H (H⁺ + e^–) by the mobile carrier Q. The authors correct their earlier view of cytochromeb functioning as a H⁺ pump, proposing that the redox-linkedpK changes of the acidic groups of cytochromeb are involved in the protonation/deprotonation processes taking place during the reduction and oxidation of Q. The reviewers stress that cytochromeb is in equilibrium with the Q pool via the Q _i center, but not via the Q₀ center. Their view of the mechanisms taking place at the reductase is a Q cycle linked to a Q-pool where cytochromeb is acting as an electron pump.