Crystal structure of the Y52F/Y73F double mutant of phospholipase A2: increased hydrophobic interactions of the phenyl groups compensate for the disrupted hydrogen bonds of the tyrosines.

The enzyme phospholipase A2 (PLA2) catalyzes the hydrolysis of the sn-2 ester bond of membrane phospholipids. The highly conserved Tyr residues 52 and 73 in the enzyme form hydrogen bonds to the carboxylate group of the catalytic Asp-99. These hydrogen bonds were initially regarded as essential for the interfacial recognition and the stability of the overall catalytic network. The elimination of the hydrogen bonds involving the phenolic hydroxyl groups of the Tyr-52 and -73 by changing them to Phe lowered the stability but did not significantly affect the catalytic activity of the enzyme. The X-ray crystal structure of the double mutant Y52F/Y73F has been determined at 1.93 A resolution to study the effect of the mutation on the structure. The crystals are trigonal, space group P3(1)21, with cell parameters a = b = 46.3 A and c = 102.95 A. Intensity data were collected on a Siemens area detector, 8,024 reflections were unique with an R(sym) of 4.5% out of a total of 27,203. The structure was refined using all the unique reflections by XPLOR to a final R-factor of 18.6% for 955 protein atoms, 91 water molecules, and 1 calcium ion. The root mean square deviation for the alpha-carbon atoms between the double mutant and wild type was 0.56 A. The crystal structure revealed that four hydrogen bonds were lost in the catalytic network; three involving the tyrosines and one involving Pro-68. However, the hydrogen bonds of the catalytic triad, His-48, Asp-99, and the catalytic water, are retained. There is no additional solvent molecule at the active site to replace the missing hydroxyl groups; instead, the replacement of the phenolic OH groups by H atoms draws the Phe residues closer to the neighboring residues compared to wild type; Phe-52 moves toward His-48 and Asp-99 of the catalytic diad, and Phe-73 moves toward Met-8, both by about 0.5 A. The closing of the voids left by the OH groups increases the hydrophobic interactions compensating for the lost hydrogen bonds. The conservation of the triad hydrogen bonds and the stabilization of the active site by the increased hydrophobic interactions could explain why the double mutant has activity similar to wild type. The results indicate that the aspartyl carboxylate group of the catalytic triad can function alone without additional support from the hydrogen bonds of the two Tyr residues.     

A Combined Invariant Test for a Null Variance Ratio

This paper investigates the properties of a test that combines the Wald and LMPI (locally most powerful invariant) tests of variance components in unbalanced mixed models. The combined test statistic is easily computed and its null distribution may be approximated by a central F distribution with the degrees of freedom of the numerator adjusted in accordance with the degree of imbalance of the design. Numerical methods are used to show that the approximation is accurate over a wide range of conditions and that the efficiency of the combined test, relative to the power envelope, is satisfactorily high overall.     

Diet overlap among three sympatric African annual killifish species Nothobranchius spp. from Mozambique

The diet patterns of three Nothobranchius species (N. furzeri, N. orthonotus and N. rachovii), small, short‐lived annual killifish from temporary pools in African savannah were investigated. Four sites with contrasting fish density and water surface area were sampled in 2008 and 2009 in southern Mozambique. Stomach content analysis showed that all the species examined were generalists, with diets largely based on aquatic invertebrates. The same invertebrate prey categories were consumed by all three species, but their relative proportions varied across species. The largest species, N. orthonotus, showed the most distinct diet and consumed vertebrates (juvenile lungfish Protopterus annectens and larval Amphibia) and a relatively high proportion of Odonata, Coleoptera and Ephemeroptera larvae. The diet of the other two species (N. furzeri and N. rachovii) showed a stronger overlap, did not include vertebrates, but was rich in small crustaceans (Cladocera, Copepoda, Ostracoda and Conchostraca). Mosquito (Diptera) larvae formed only a negligible part of the diet of all the three species.     

东北地区部分大型藓类植物遗传多样性的RAPD研究

采用RAPD标记构建了东北地区20种大型藓类植物的系统关系。从200个随机引物中筛选出清晰且多态性高的7个引物,共产生了82条DNA片段,其中79条谱带具有遗传多态性,约占96.34%,平均每个引物扩增的DNA片段数为11.71条。采用NTSYS-pc数据分析软件,计算Nei氏相似性系数,建立了UPGMA聚类图。结果表明：以遗传相似性系数0.27为界限划分,可将20种苔藓植物分为二大类,即泥炭藓类和真藓类。以遗传相似性系数0.42为界限划分,可将20种苔藓植物划分为四大类群,即泥炭藓类、顶蒴单齿亚类、顶蒴双齿亚类和侧蒴双齿类。从整个聚类图可以看出,泥炭藓类是较原始的类群,而金发藓类是较进化的类群,这一结果和大多数苔藓植物经典分类系统相同。     

On Some Nuisance Parameter Free Uniformly Most Powerful Tests

TAKEUCHI (1969) provides a uniformly most powerful (UMP) one side test for testing the location parameter of the two parameters exponential model when the scale parameter is unknown. The power of his similar size α test depends, however, on the unknown scale parameter. In this case and in more general situations when there exists a sufficient statistic for the nuisance parameter, the theory of generalized THOMPSON's distributions, more specifically, the Thompsonization of a test statistic, LAURENT (1959, 1972) provides a UMP test whose power does not depend on the nuisance parameter. Examples of application of the general nuisance parameter free test procedure include here the truncated exponential, the inverse Gaussian, and the geometric distributions.     

Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study

We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla , Lasius and Tetramorium . The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable.     

Simple sequence repeat genetic linkage maps of A-genome diploid cotton (Gossypium arboreum)

This study introduces the construction of the first intraspacific genetic linkage map of the A-genome diploid cotton with newly developed simple sequence repeat (SSR) markers using 189 F2 plants derived from the cross of two Asiatic parents were detected using 6 092 pairs of SSR primers. Two-hundred and sixty-eight pairs of SSR pdmers with better polymorphisms were picked out to analyze the F2 population. In total, 320 polymorphic bands were generated and used to construct a linkage map with JoinMap3.0. Two-hundred and sixty-seven loci, Including three phenotypic traits were mapped at a logarithms of odds ratio (LOD) ≥ 3.0 on 13 linkage groups. The total length of the map was 2 508.71 cM, and the average distance between adjacent markers was 9.40 cM. Chromosome assignments were according to the association of linkages with our backbone tetraploid specific map using the 89 similar SSR loci. Comparisons among the 13 suites of orthologous linkage groups revealed that the A-genome chromosomes are largely collinear with the At and Dt sub-genome chromosomes. Chromosomes associated with inversions suggested that allopolyploidization was accompanied by homologous chromosomal rearrangement. The inter-chromosomal duplicated loci supply molecular evidence that the A-genome diploid Asiatic cotton is paleopolyploid.     

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.     

Proton pumping in the bc1 complex: A new gating mechanism that prevents short circuits

The Q-cycle mechanism of the bc₁ complex explains how the electron transfer from ubihydroquinone (quinol, QH₂) to cytochrome (cyt) c (or c₂ in bacteria) is coupled to the pumping of protons across the membrane. The efficiency of proton pumping depends on the effectiveness of the bifurcated reaction at the Q_o-site of the complex. This directs the two electrons from QH₂ down two different pathways, one to the high potential chain for delivery to an electron acceptor, and the other across the membrane through a chain containing heme b_L and b_H to the Q_i-site, to provide the vectorial charge transfer contributing to the proton gradient. In this review, we discuss problems associated with the turnover of the bc₁ complex that center around rates calculated for the normal forward and reverse reactions, and for bypass (or short-circuit) reactions. Based on rate constants given by distances between redox centers in known structures, these appeared to preclude conventional electron transfer mechanisms involving an intermediate semiquinone (SQ) in the Q_o-site reaction. However, previous research has strongly suggested that SQ is the reductant for O₂ in generation of superoxide at the Q_o-site, introducing an apparent paradox. A simple gating mechanism, in which an intermediate SQ mobile in the volume of the Q_o-site is a necessary component, can readily account for the observed data through a coulombic interaction that prevents SQ anion from close approach to heme b_L when the latter is reduced. This allows rapid and reversible QH₂ oxidation, but prevents rapid bypass reactions. The mechanism is quite natural, and is well supported by experiments in which the role of a key residue, Glu-295, which facilitates proton transfer from the site through a rotational displacement, has been tested by mutation.