Constructing Confidence Intervals for Qtl Location

We describe a method for constructing the confidence interval of the QTL location parameter. This method is developed in the local asymptotic framework, leading to a linear model at each position of the putative QTL. The idea is to construct a likelihood ratio test, using statistics whose asymptotic distribution does not depend on the nuisance parameters and in particular on the effect of the QTL. We show theoretical properties of the confidence interval built with this test, and compare it with the classical confidence interval using simulations. We show in particular, that our confidence interval has the correct probability of containing the true map location of the QTL, for almost all QTLs, whereas the classical confidence interval can be very biased for QTLs having small effect.     

Compositional heterogeneity of the Escherichia coli genome: A role for VSP repair?

E. coli genes that contain a high frequency of the tetranucleotide CTAG are also rich in the tetramers CTTG, CCTA, CCAA, TTGG, TAGG, and CAAG (group-I tetramers). Conversely, E. coli genes lacking CTAG are rich in the tetranucleotides CCTG, CCAG, CTGG, and CAGG (group-II tetramers). These two gene samples differ also in codon usage, amino acid composition, frequency of Dcm sites, and contrast vocabularies. Group-I tetramers have in common that they are depleted by very-short-patch repair (VSP), while group-II tetramers are favored by VSP activity. The VSP system repairs G:T mismatches to G:C, thereby increasing the overall G+C content of the genome; for this reason the CTAG-rich sample has a lower G+C content than the CTAG-poor sample. This compositional heterogeneity can be tentatively explained by a low level of VSP activity on the CTAG-rich sample. A negative correlation is found between the frequency of group-I tetramers and the level of gene expression, as measured by the Codon Adaptation Index (CAI). A possible link between the rate of VSP activity and the level of gene expression is considered.Correspondence to: A. Marine     

再论假裸枝叠层石科*

内蒙古桌子山地区中奥陶统公乌素组遗迹化石十分丰富.本文共鉴定、描述14个遗迹属、17个遗迹种,其中1新遗迹属——Biscopulatichnus、4新遗种和6未定种.并根据不同遗迹属在不同层位中的相对丰度,建立了4个遗迹组合,自下而上的顺序是:1. Taenidium-Phycodes 组合;2. Volkichnium 组合;3. Helminthopsis 组合;4. Granularia-Circulichnus 组合,大致相当于 Seilacher (1967) 的 Zoophycos 遗迹相,反映出公乌素组沉积期,水体较深且宁静、缺氧、有机质含量高,推测应为大陆斜坡环境.     

Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations

In F₂ populations, gametic and zygotic selection may affect the analysis of linkage in different ways. Therefore, specific likelihood equations have to be developed for each case, including dominant and codominant markers. The asymptotic bias of the classical estimates are derived for each case, in order to compare them with the standard errors of the suggested estimates. We discuss the utility and the efficiency of a previous model developed for dominant markers. We show that dominant markers provide very poor information in the case of segregation distortion and, therefore, should be used with circumspection. On the other hand, the estimation of recombination fractions between codominant markers is less affected by selection than is that for dominant markers. We also discuss the analysis of linkage between dominant and codominant markers.     

Étude d'un extrait de Sporothrix schenckii (forme levure). Analyse électrophorétique et immunoélectrophorétique; caracterisation des activités enzymatiques

Résumé Un extrait de S. schenckii a été préparé à partir de levures vivantes provenant d'une culture agitée pendant 3 jours à 35° C et à l'obscurité dans du milieu BHI (brain heart infusion). Il a été obtenu par broyage au broyeur cellulaire MSK et amélioré par une congélation-décongélation. Ses constituants, séparés par électrophorèse, ont été révélés par leur activité enzymatique; 30 bandes ont ainsi pu être caractérisées. Ces activités enzymatiques ont été recherchées au niveau des fractions de l'extrait révélées par un hyperimmunsérum de lapin: 16 sur les 22 précipités sont identifiés par leur pouvoir catalytique. L'ordre d'apparition des premiers anticorps chez le lapin immunisé et leur identification complètent cette étude. Les conditions de culture et de préparation permettant d'améliorer la qualité de l'extrait sont également précisées.

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An extract from living yeast forms of S. schenckii was prepared. The yeasts originated from a shake culture in B.H.I. broth (Difco) incubated for 3 days at 35°C in darkness; they were harvested, washed and disrupted with glass beads in a model MSK Braun mechanical cell homogenizer; a freezing-thawing was added to improve the extract.After electrophoretic separation in agarose gel, the extract's components were characterized by their enzymic activity; with this technique, 30 bands were revealed. These enzymic activities were also investigated on the antigenic fractions of the extract revealed by a rabbit hyperimmunserum: 16 among 22 immunoprecipitates are identified by their catalytic properties. Study of the earliest precipitating antibodies (appearing-order and enzymic caracterization) in rabbits just immunized completes this work. How to ameliorate the quality of the extract by culture and extraction conditions is also specified.

     

Inverted pyramidal neurons and their axons in the neocortex of reeler mutant mice

Summary Inverted pyramidal neurons are very abundant in the cerebral cortex of the adult reeler mutant mouse. Two types of inverted pyramid are found in rapid Golgi impregnations. In the first type the axon starts from the base of the cell body and bends towards the white matter. In the second type, which is more common, the axon emerges from the apical dendritic tree and descends directly towards the white matter.Despite its abnormal topography, the site of origin of the axon in pyramids of the second type displays a normal differentiation, when analysed with the electron microscopic Golgi technique, suggesting that the ectopic initial axon segment is able to fulfil its normal functions.     

XYLARY UNION BETWEEN THE NEW SHOOT AND OLD STEM DURING TERMINAL BUD BREAK IN POPULUS DELTOIDES

Bursting terminal buds and subtending stems of Populus deltoides Bartr. ex Marsh. plants were examined at several stages to determine the pattern of xylary union between the 1st- and 2nd-yr growth increments. Metaxylem vessels differentiated first in traces serving the basalmost leaf in the bud. As successively younger leaves began growth, metaxylem vessels differentiated in their traces. The site of metaxylem reactivation was in the second or third internode beneath the bud (i.e., in the 1st-yr stem), and subsequent differentiation progressed bidirectionally in each set of traces as the leaves they served expanded. Traces leading either to abscised leaf positions on the 1st-yr stem or to bud-scale leaf positions were reactivated by the tangential “spread” of activity from adjacent traces serving expanding leaves. The new elements were all secondary xylem vessels, as were those of the basipetal trace components, although they were functionally continuous with the metaxylem vessels that differentiated acropetally. Xylem fibers were initiated in the same position and differentiated in the same sequence as vessels. However, fiber differentiation lagged behind that of vessels. Whereas vessel differentiation was associated with leaf expansion, fiber differentiation was associated with leaf maturation. As each leaf matured in sequence, the primary-secondary transition zone advanced acropetally to the bud base and then in the new shoot until it attained a positional relation with leaf maturation comparable to that of 1st-yr plants.     

Initial stages of tunic morphogenesis in the ascidian Halocynthia: a fine structural study

Tunic morphogenesis in embryos of the ascidian Halocynthia roretzi was examined by scanning and transmission electron microscopy. For this purpose it was necessary to modify the classical embedding procedure. Soon after reaching the initial tail-bud stage, tunic deposition is initiated on the dorsal side of the embryo. As soon as the embryo is completely covered by the tunic, larval fins are formed. The test cells settle onto the embryo. At this stage only the outer cuticle and the outer tunic compartment have appeared. Tunic morphogenesis is accompanied by ultrastructural modifications of the epidermis characteristic of secreting cells. Cytochemical investigations reveal polysaccharide glycogen-like material in the lumen of epidermal lacunae and in the outer compartment of the tunic. Our observations strongly suggest that this material is stored in the lacunae and discharged into the outer compartment. The significance of fluffy osmiophilic material that appears at the early tail-bud stage and enlaces the whole embryo is discussed.     

Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.