Inequalities for estimative and predictive probabilities

Let μE be the estimative and μP the predictive measures for assessing Gaussian probabilities. It is shown for convex symmetric sets A that _μE(A) _μP(A) and that similar inequalities hold between members of a sequence of predictive measures. An application yields inequalities for generalized indices of atypicality associated with the two methods.     

Non-uniform stomatal closure and the apparent convexity of the photosynthetic photon flux density response curve

The photosynthetic response of leaves to photosynthetic photon flux density (PPFD) may be described by parameters for the rate of dark respiration (R), the initial slope (Ф), the PPFD-saturated rate of net photosynthesis (A_mQ) and the apparent convexity (θ_a). We tested the hypothesis that non-uniformity in stomatal aperture across a leaf results in a clearly lower θ_a because PPFD saturation will occur at different irradiances in different regions of the leaf. A computer model was constructed to simulate the effects of bell-shaped and other distributions of stomatal conductance for CO₂ (g_s) across a model leaf. In the model, Ф and A_mQ decreased by up to 50% whereas θ_a decreased by at most 8%, essentially negating the hypothesis. The relationship between photosynthetic rate and g_s determined the size of the responses of θ_a and Ф to non-uniform g_s. In support of the model, experiments on sunflower leaves showed that Ф and A_mQ decreased by 32 and 52%, respectively, while no measurable change in θ_a occurred, when abscisic acid was used to induce patchiness in g_s. Although not all possible patterns of non-uniform stomatal conductance have been tested, it appears that if large variations in θ_a occur in nature they do not result from non-uniform g_s.     

Biomass partitioning pattern of Rheum tanguticum on the Qinghai–Tibet Plateau was affected by water-related factors

To identify the patterns of aboveground biomass (M_A) and belowground biomass (M_B) partitioning of a tall perennial herbal plant, Rheum tanguticum Maxim. ex Balf. (R. tanguticum), we determined M_A, M_B, total biomass (M_T), and below- to aboveground biomass ratio (M_B/M_A) through three consecutive sampling campaigns during 2016–2018 on the Qinghai-Tibetan plateau. We then documented M_A, M_B, M_T, and M_B/M_A, and their log–log relationship with environmental factors using data from 47 sites. M_B/M_A showed a significant negative relationship with mean annual precipitation (MAP) and altitude but a positive relationship with mean annual temperature (MAT), soil total nitrogen content (TN), and soil humidity (SH). While M_T increased with altitude and decreased with MAT, TN, and SH, but the relationship between MAP and M_T was not significant. Reduced major axis analysis revealed a slope of the log–log relationship between M_A and M_B to be 1.16, supporting an allometric partitioning pattern of R. tanguticum. Furthermore, the scaling exponent revealed different changes to different environmental factors. Specifically, scaling exponent was sensitive to the gradient of MAP and SH, but not to the gradient of altitude, MAT, or TN. This indicated that the scaling exponent was affected by water availability.

     

The ontogeny of the locomotor wave in sevruga fish (Acipenser stellatus Pall.)

Continuous filming of the swimming movements of sevruga prelarvae (Acipenser stellatus Pall.) was performed over the first to the fifteenth post-hatching days. These data were used to determine three locomotor characteristics: {f(v, θ), A(v, θ), w(v, θ)} where f is the frequency of the transverse oscillations; A is the amplitude of the tail fin movements; w is the speed of the locomotor wave; v is the speed of the locomotion; and θ is the number of days during which the filming was carried out. In addition, the comparison of two characteristics was performed. These are the step length L(v, θ) and the wavelength λ(v, θ), where L ≡ vT is the distance that a fish covers in time T ≡ 1/f and λ is λ ≡ wT. The results led to the conclusion that the prelarva swimming movements achieve the carangiform mode by the end of the second week. This is characteristic of adults and coincides with the beginning of external feeding. The mode is represented by an equation that follows from the generalized Bainbridge’s law: f = f ₀ + f ₁ v/H. The equation includes one anatomical parameter H of total length and two kinematic parameters f ₀ and f ₁, which can be calculated by the linear approximation method. These are the kinematic parameters that are changed in the early ontogenesis when 1 ≤ θ ≤ 15. However, the parameters become stable when θ ≥ 15. This means that the parameter values are constant and similar to those of adult fish. The similar properties of stabilization and variability have the kinematic parameters of other locomotor characteristics.

     

Immobilization of oxyreductases on inorganic supports based on alumina. Immobilization of lactate dehydrogenase on alumina by adsorption

Lactate dehydrogenase (LDH) was adsorbed on low-(γ, η) and high -(θ, α) temperature forms of alumina. θ-Al₂O₃ exhibited the greatest adsorption ability. The maximum adsorption value was 30 mg LDH/g of a carrier. The conditions for irreversible adsorption have been determined. An adsorption isotherm on θ-Al₂O₃ for pH 6.0 has been obtained; the LDH_ads surface area and the carrier surface portion accessible to the enzyme molecules have been calculated. The reaction kinetic parameter were determined by taking into account the reaction proceeding in the intradiffusional region. The specific catalytic activity (A_spec) of LDH_ads at small surface coverage of θ-Al₂O₃ is five times less than A_spec of the native enzyme and K_M^imm with respect to NADH exceeds K_M^nat by two orders or magnitude. The is evidence for a strong LDH–Al₂O₃ interaction and a considerable deformation of the enzyme globule. A_spec and K_M decrease as the amount of the enzyme attached to the carrier increases. Due to adsorption. LDH becomes thermostable and durable. The LDH_ads samples conserve 20–40% of their activity at room temperature during a year.     

Characterization of <Emphasis Type="Italic">methionine adenosyltransferase 2β</Emphasis> gene expression in skeletal muscle and subcutaneous adipose tissue from obese and lean pigs

Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S-adenosylmethionine. Two genes (MAT1A and MAT2A) encode for the catalytic subunit of MAT, while a third gene (MAT2β) encodes for a regulatory subunit (MAT II β) that regulates the activity of the MAT2A-encoded isoenzyme and intracellular S-adenosylmethionine levels. Our previous work identified MAT2β as a candidate gene for intramuscular fat (IMF) deposition in porcine skeletal muscle by microarray technology. Here, we cloned porcine MAT2β cDNA and compared its expression pattern in subcutaneous adipose tissue and skeletal muscle from obese (Rongchang Breed) and lean (Pig Improvement Company, PIC) pigs (n = 6). The porcine MAT2β cDNA was 1,800 bp long and encodes for 334 amino acids sharing high similarity with other species. MAT2β is expressed at a higher level in liver and duodenum, followed by the stomach, fat and longissinus dorsi muscle. As expected, both subcutaneous fat content and IMF content were higher in obese than in lean pigs (both P < 0.01). MAT2β mRNA abundance was lower in both subcutaneous adipose tissue and skeletal muscle in obese pigs compared with lean pigs (both P < 0.01). MAT II β protein content was lower in skeletal muscle in obese than in lean pigs (P < 0.05), whereas the opposite was observed in subcutaneous adipose tissue (P < 0.01). These data demonstrated an obesity-related expression variation of the MAT II β subunit in skeletal muscle and adipose tissue in pigs, and suggest a novel role for the MAT2β gene in regulation of IMF deposition in skeletal muscle.     

Arrhenius and Gleason revisited: new hybrid models resolve an old controversy

Aim Studies have typically employed species–area relationships (SARs) from sample areas to fit either the power relationship or the logarithmic (exponential) relationship. However, the plots from empirical data often fall between these models. This article proposes two complementary and hybrid models as solutions to the controversy regarding which model best fits sample‐area SARs. Methods The two models are and , where S_A is number of species in an area, A, where z, b, c₁ and c₂ are predetermined parameters found by calculation, and where d and n are parameters to be fitted. The number of parameters is reduced from six to two by fixing the model at either end of the scale window of the data set, a step that is justified by the condition that the error or the bias, or both, in the first and the last data points is negligible. The new hybrid models as well as the power model and the logarithmic model are fitted to 10 data sets. Results The two proposed models fit well not only to Arrhenius’ and Gleason’s data sets, but also to the other six data sets. They also provide a good fit to data sets that follow a sigmoid (or triphasic) shape in log–log space and to data sets that do not fall between the power model and the logarithmic model. The log‐transformation of the dependent variable, S, does not affect the curve fit appreciably, although it enhances the performance of the new models somewhat. Main conclusions Sample‐area SARs have previously been shown to be convex upward, convex downward (concave), sigmoid and inverted sigmoid in log–log space. The new hybrid models describe successfully data sets with all these curve shapes, and should therefore produce good fits also to what are termed triphasic SARs.     

MAT2A Mutations Predispose Individuals to Thoracic Aortic Aneurysms

Up to 20% of individuals who have thoracic aortic aneurysms or acute aortic dissections but who do not have syndromic features have a family history of thoracic aortic disease. Significant genetic heterogeneity is established for this familial condition. Whole-genome linkage analysis and exome sequencing of distant relatives from a large family with autosomal-dominant inheritance of thoracic aortic aneurysms variably associated with the bicuspid aortic valve was used for identification of additional genes predisposing individuals to this condition. A rare variant, c.1031A>C (p.Glu344Ala), was identified in MAT2A, which encodes methionine adenosyltransferase II alpha (MAT IIα). This variant segregated with disease in the family, and Sanger sequencing of DNA from affected probands from unrelated families with thoracic aortic disease identified another MAT2A rare variant, c.1067G>A (p.Arg356His). Evidence that these variants predispose individuals to thoracic aortic aneurysms and dissections includes the following: there is a paucity of rare variants in MAT2A in the population; amino acids Glu344 and Arg356 are conserved from humans to zebrafish; and substitutions of these amino acids in MAT Iα are found in individuals with hypermethioninemia. Structural analysis suggested that p.Glu344Ala and p.Arg356His disrupt MAT IIα enzyme function. Knockdown of mat2aa in zebrafish via morpholino oligomers disrupted cardiovascular development. Co-transfected wild-type human MAT2A mRNA rescued defects of zebrafish cardiovascular development at significantly higher levels than mRNA edited to express either the Glu344 or Arg356 mutants, providing further evidence that the p.Glu344Ala and p.Arg356His substitutions impair MAT IIα function. The data presented here support the conclusion that rare genetic variants in MAT2A predispose individuals to thoracic aortic disease.     

The nonplanar peptide unit. III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data.

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles θ_N and Δω defining the nonplanarity of the amide unit are correlated approximately by the relation θ_N = ?2Δω, while θ_C is small and uncorrelated with Δω. The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (?,ψ), in working out polypeptide and protein structures.     

Distribution of Mating Types and Genetic Diversity of Ascochyta rabiei Populations in Tunisia Revealed by Mating-type-specific PCR and Random Amplified Polymorphic DNA Markers

The distribution of mating types of Ascochyta rabiei (teleomorph: Didymella rabiei) was determined in Tunisia using a MAT‐specific PCR assay. Among 123 isolates tested, 80% were MAT1‐1 and 20%MAT1‐2. Only MAT1‐1 isolates were present in the Beja and Bizerte regions of Tunisia, whereas both mating types were present in Nabeul, Kef and Jendouba. In the latter three regions, the hypothesis of random mating could not be rejected based on chi‐squared tests of mating‐type ratios (P > 0.05). The lower frequency of the MAT1‐2 coupled with the restricted distribution of this mating type in Tunisia may indicate a recent introduction of MAT1‐2 in Tunisia. This speculation is consistent with the recent (2001) observation of D. rabiei pseudothecia on chickpea debris in Tunisia. Forty isolates representative of the five regions were genetically analysed using 10 random amplified polymorphic DNA (RAPD) primers to provide a preliminary estimate of genetic diversity of the pathogen in Tunisia. Among 129 putative RAPD loci amplified, 81% were polymorphic and 32 unique RAPD fingerprints were detected. A high level of genetic differentiation was detected among subpopulations (G_ST = 0.33). Cluster analyses revealed that isolates from Bizerte, Beja and Jendouba were genetically similar and distinct from isolates sampled in Nabeul and Kef. MAT1‐1 isolates were clustered separately from MAT1‐2 isolates in Jendouba and Nabeul suggesting that recombination may not yet be occurring in these regions despite the occurrence of both mating types in equal frequency in these regions. This lack of recombination between MAT1‐1 and MAT1‐2 also supports the hypothesis of a recent introduction of MAT1‐2 into Tunisia.     

Qualitative effects of patchy stomatal conductance distribution features on gas-exchange calculations

The qualitative influence of patchy stomatal conductance distributions on the values of photosynthesis (A) and intercellular CO₂ concentration (c_i) as determined by gas-exchange measurements were investigated using computer modelling. Gas-exchange measurements were simulated for different conductance distributions by modelling photosynthesis explicitly for each patch, summing these rates, and inferring c_i from a diffusion equation. Qualitative relationships are presented between conductance distribution features and the difference between assimilation rates measured for patchy and homogeneous leaves at the same c_i (A_p and A_h, respectively). These data show that, although most conductance distributions have little effect on the value of A measured for a given c_i, some distribution features (which we have termed ‘bimodality’, ‘position’, ‘skewness’ and ‘range’) play a key role in controlling the magnitude of these effects. Distributions that are more nearly bimodal, span regions of lower conductance, are right-skewed, or have broader conductance ranges are associated with larger effects on the A(c_i) relationship. To clarify our mathematical analysis and illustrate some of the trends it predicts, we present conductance distributions and gas-exchange data from leaves of Malus dolgo var. Spring Snow Dial were treated with ABA. The results are discussed in the light of recent controversy over the effect of patchy stomatal conductance on gas-exchange data.     

不同光照条件下喜阴植物谢君魔芋对稳态和动态光源的响应特征

谢君魔芋(Amorphophallus xiei)是起源于云南西南地区热带雨林的典型喜阴植物,近年来得到了广泛种植和推广,在种植过程中,谢君魔芋需要采用遮荫栽培模式。为了揭示谢君魔芋对光照强度的适应策略,该研究探讨了生长在不同光照强度下(透光率为50%、29%、17%、7%)谢君魔芋叶片的光合作用特征、光合诱导特征、光合色素含量以及叶片氮素(N)含量和N分配。结果表明:随着生长环境光照强度的降低,单位叶面积和单位叶质量最大净光合速率、光合色素含量、最大羧化速率、最大电子传递速率及比叶面积均增大,而暗呼吸和光补偿点均减小。在光合诱导过程中,生长在透光率为17%光环境中的谢君魔芋完成50%光合诱导所需的时间最短,约为81.4 s;在光诱导进行10 min时,诱导状态最高,为87.3%。完成50%和90%光合诱导所需的时间与低光下初始气孔导度呈负相关关系。随着生长光照强度降低,叶片中的N分配到羧化组分和生物能转化组分中的比例先增大后减小,在透光率为17%的光环境下具有最大值;而叶片中的N分配到捕光色素组分中的比例随着生长环境光照强度降低而增加。该研究结果表明,喜阴植物谢君魔芋通过加强对低光和动态光源的利用能力及有效的N资源分配策略来适应低光照环境。     

Determination of DNA base compositions from melting profiles in dilute buffers

Equations were determined for the dependency of the melting temperature (T_m) of DNA upon the logarithm of the sodium ion concentration, for four DNA samples of widely different base compositions (θ_GC). The slopes of these T_m versus log M equations wore found to decrease with increasing θ_{G C}of the samples. An empirical equation relating T_m, log M (Na⁺) and θ_{G C} was derived, which also accounts for differences in T_m versus log M slopes. Data from the literature for some synthetic polynucleotides and for the crab(Cancer pagarus) satellite poly AT are discussed in relation to the above finding. The changes in T_m versus log M slopes with θ_{G C} are interpreted in terms of changes in the thermodynamic parameters ΔS and ΔH with base composition.     

Adenosine A2B receptor antagonist suppresses differentiation to regulatory T cells without suppressing activation of T cells

Extracellular adenosine activates P1 receptors (A₁, A_2A, A_2B, A₃) on cellular membranes. Here, we investigated the involvement of P1 receptor-mediated signaling in differentiation to regulatory T cells (Treg). Treg were induced in vitro by incubating isolated CD4⁺CD62L⁺ naïve murine T cells under Treg-skewing conditions. Antagonists of A₁ and A_2B receptors suppressed the expression of Foxp3, a specific marker of Treg, and the production of IL-10, suggesting the involvement of A₁ and A_2B receptors in differentiation to Treg. We also investigated the effect of these antagonists on T cell activation, which is essential for differentiation to Treg, and found that A₁ antagonist, but not A_2B antagonist, suppressed T cell activation. We conclude that A₁ and A_2B receptors are both involved in differentiation to Treg, but through different mechanisms. Since A_2B antagonist blocked differentiation to Treg without suppressing T cell activation, it is possible that blockade of A_2B receptor would facilitate tumor immunity.     

Two criteria for the comparison of multiple arrangements of experiments and their use to answer the question: Is it better to compare p treatment groups with p controls or with a single control

In experimental situations examining the effectiveness of p(p>1) treatments by comparing treated groups and untreated controls the following question arose: Which experimental arrangement is more appropriate, an arrangement A₁ using for the p comparisons only one single control, or an arrangement A₂ using for every comparison another control. To answer this question two criteria are formulated. The first criterion takes into consideration the expected numbers of type I and type II errors, and the second criterion the probabilities of type I and of type II errors. According to the first criterion A₁ and A₂ do not differ, generally. According to the second criterion A₁ with the comparison of means of normal distributed variables is better than A₂. Pooling of all p controls is better than A₂ according to both criteria. A₁ is better also according to the often used experimentwise type I error rate. The formulated criteria have some analogy to those of MILLER (1966). It may be possible to use them not only for comparing experimental arrangements but also tests.     

Unconditional Non-Asymptotic One-Sided Tests for Independent Binomial Proportions When the Interest Lies in Showing Non-Inferiority and/or Superiority

For two independent binomial proportions Barnard (1947) has introduced a method to construct a non-asymptotic unconditional test by maximisation of the probabilities over the ‘classical’ null hypothesis H₀= {(θ₁, θ₂) ∈ [0, 1]²: θ₁ = θ₂}. It is shown that this method is also useful when studying test problems for different null hypotheses such as, for example, shifted null hypotheses of the form H₀ = {(θ₁, θ₂) ∈ [0, 1]²: θ₂ ≤ θ₁ ± Δ } for non-inferiority and 1-sided superiority problems (including the classical null hypothesis with a 1-sided alternative hypothesis). We will derive some results for the more general ‘shifted’ null hypotheses of the form H₀ = {(θ₁, θ₂) ∈ [0, 1]²: θ₂ ≤ g(θ₁ )} where g is a non decreasing curvilinear function of θ₁. Two examples for such null hypotheses in the regulatory setting are given. It is shown that the usual asymptotic approximations by the normal distribution may be quite unreliable. Non-asymptotic unconditional tests (and the corresponding p-values) may, therefore, be an alternative, particularly because the effort to compute non-asymptotic unconditional p-values for such more complex situations does not increase as compared to the classical situation. For ‘classical’ null hypotheses it is known that the number of possible p-values derived by the unconditional method is very large, albeit finite, and the same is true for the null hypotheses studied in this paper. In most of the situations investigated it becomes obvious that Barnard's CSM test (1947) when adapted to the respective null space is again a very powerful test. A theorem is provided which in addition to allowing fast algorithms to compute unconditional non-asymptotical p-values fills a methodological gap in the calculation of exact unconditional p-values as it is implemented, for example, in Stat Xact 3 for Windows (1995).     

Phosphorylation of the pheromone-responsive Gβ protein of Saccharomyces cerevisiae does not affect its mating-specific signaling function

The pheromone-responsive G_β subunit of Saccharomyces cerevisiae (encoded by STE4) is rapidly phosphorylated at multiple sites when yeast cells are exposed to mating pheromone. It has been shown that a mutant form of Ste4 lacking residues 310–346, ste4Δ310–346, cannot be phosphorylated, and that its expression leads to defects in recovery from pheromone stimulation. Based on these observations, it was proposed that phosphorylation of Ste4 is associated with an adaptive response to mating pheromone. In this study we used site-directed mutagenesis to create two phosphorylation null (Pho⁻) alleles of STE4: ste4-T320 A/S335A and ste4-T322 A/S335A and ste4-T322A/S335A. When expressed in yeast, these mutant forms of Ste4 remained unphosphorylated upon pheromone stimulation. The elimination of Ste4 phosphorylation has no discernible effect on either signaling or adaptation. In addition, disruption of the FUS3 gene, which encodes a pheromone-specific MAP kinase, leads to partial loss of pheromone-induced Ste4 phosphorylation. Two-hybrid analysis suggests that the ste4Δ310–346 deletion mutant is impaired in its interaction with Gpa1, the pheromone-responsive G_α of yeast, whereas the Ste4-T320A/S335A mutant has normal affinity for Gpa1. Taken together, these results indicate that pheromone-induced phosphorylation of Ste4 is not an adaptive mechanism, and that the adaptive defect exhibited by the 310–346 deletion mutant is likely to be due to disruption of the interaction between Ste4 and Gpa1. Received: 14 February 1998 / Accepted: 28 February 1998     

Gibberellins in developing fruits of Pisum sativum cv. Alaska: Studies on their role in pod growth and seed development

Gibberellins A₁, A₈, A₂₀ and A₂₉ were identified by capillary gas chromatography-mass spectrometry in the pods and seeds from 5-d-old pollinated ovaries of pea (Pisum sativum cv. Alaska). These gibberellins were also identified in 4-d-old non-developing, parthenocarpic and pollinated ovaries. The level of gibberellin A₁ within these ovary types was correlated with pod size. Gibberellin A₁, applied to emasculated ovaries cultured in vitro, was three to five times more active than gibberellin A₂₀. Using pollinated ovary explants cultured in vitro, the effects of inhibitors of gibberellin biosynthesis on pod growth and seed development were examined. The inhibitors retarded pod growth during the first 7 d after anthesis, and this inhibition was reversed by simultaneous application of gibberellin A₃. In contrast, the inhibitors, when supplied to 4-d-old pollinated ovaries for 16 d, had little effect on seed fresh weight although they reduced the levels of endogenous gibberellins A₂₀ and A₂₉ in the enlarging seeds to almost zero. Paclobutrazol, which was one of the inhibitors used, is xylem-mobile and it efficiently reduced the level of seed gibberellins without being taken up into the seed. In intact fruits the pod may therefore be a source of precursors for gibberellin biosynthesis in the seed. Overall, the results indicate that gibberellin A₁, present in parthenocarpic and pollinated fruits early in development, regulates pod growth. In contrast the high levels of gibberellins A₂₀ and A₂₉, which accumulate during seed enlargement, appear to be unnecessary for normal seed development or for subsequent germination.Abbreviations GA_(a) gibberellin A_n - GC-MS combined gas chromatography-mass spectrometry - HPLC high-performance liquid chromatography - PFK perfluorokerosene - PVP polyvinylpyrrolidone     

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (V_A) and trait differentiation (Q_ST) from small to large population size. Alternatively, small populations might exhibit larger variation in V_A and Q_ST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating V_A and Q_ST using nine fragmented populations of brook trout varying 50‐fold in census size N (179–8416) and 10‐fold in effective number of breeders, N_b (18–135). Across 15 traits, no evidence was found for consistent differences in V_A and Q_ST with population size and almost no evidence for increased variability of V_A or Q_ST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.