CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43050/1/10858_2005_Article_4079.pd

A new case of late-acting self-incompatibility in Capparis L. (Brassicaceae): C. jacobinae Moric. ex Eichler, an endemic andromonoecious species of the Caatinga, Pernambuco State, Brazil

We studied the reproductive system of Capparis jacobinae Moric ex Eichler (Brassicaceae), based on controlled hand-pollination and observation of pollen tube growth made in a fluorescence microscope. Of 105 self-pollinated flowers only one produced fruits (success = 0.95%), all the other flowers abscised at the same time, between the eighth and tenth day after anthesis. Nevertheless, self- and cross-pollinated pollen tubes reached the micropyle. The rate of penetrated ovules in self-pollinated flowers was lower during the first 24 h after pollination; thereafter this rate was similar between self- and cross-pollinated flowers for treatments of 48 h, 72 h and 96 h after pollination. In addition, we carried out two indirect estimates of the reproductive system, based on pollen/ovule and seed/ovule ratios, which resulted in typical features of xenogamous species. We concluded that C. jacobinae has a late-acting self-incompatibility system. This is the third record of this mechanism for the genus and the first for a species of Capparis endemic to the Caatinga. We suggest that this self-incompatibility system may occur in other species of the same genus and family

Mating system of Calluna vulgaris (L.) Hull : self-sterility and outcrossing estimations

The evolutionary significance of a mixed mating system is currently under debate. Calluna vulgaris (L). Hull, a widespread European shrub, is likely to undergo mixed mating because of geitonogamy. Mating system was investigated in three populations of C. vulgaris is by means of greenhouse controlled crosses, pollen tube observations, and outcrossing rate estimations from allozyme markers. The species is highly self-sterile, most probably as a result of early inbreeding depression. Mean fruit set and mean seed number per fruit following hand self-pollination were 48 and 13%, respectively, of those following cross-pollination, Pollen tubes produced by self pollen penetrated the ovary with the same success as those from cross-pollination. Multilocus estimates of the outcrossing rates ranged from 0.71 to 0.90, and two estimates were significantly different from 1.00. Calluna vulgaris could thus be classified as being mixed mating with predominant allogamy. Single-locus estimates did not differ significantly from multilocus estimates suggesting that biparental inbreeding did not contribute to the apparent selfing rate. The maintenance of high early inbreeding depression despite an intermediate level of selfing is discussed with respect to recent theories on mating system evolution

Sistema reprodutivo do Ipê-Branco: Tabebuia roseo-alba (Ridley) Sandwith (Bignoniaceae) Breeding system of the White Trumpet Tree: Tabebuia roseo-alba (Ridley) Sandwith (Bignoniaceae)

Estudos sobre sistemas reprodutivos têm indicado o predomínio da autoincompatibilidade de ação tardia (AIT) em Bignoniaceae, embora poucas espécies tenham sido investigadas e ocorram outros tipos de sistemas reprodutivos na família. O presente estudo objetivou determinar o sistema reprodutivo de T. roseo-alba através de experimentos de polinizações controladas, análise histológica dos eventos posteriores à polinização, verificação do desenvolvimento in situ dos tubos polínicos e testes de germinação de sementes. Apesar de os tubos polínicos penetrarem e fecundarem a maioria dos óvulos em pistilos autopolinizados, o aborto de 100% dos mesmos foi verificado e, embora sua abscisão tenha ocorrido entre o quarto e o sexto dia após o início da antese, observou-se um ligeiro crescimento dos óvulos e do ovário precedendo a abscisão, porém inferior ao crescimento nos pistilos submetidos à polinização cruzada. A endospermogênese inicial e a formação do tubo proembriônico também foram mais lentas nos pistilos autopolinizados. A longevidade dos pistilos autopolinizados foi maior que a de pistilos não polinizados, e a taxa de germinação de sementes foi de 93%, sendo todas as sementes monoembriônicas. Os resultados demonstram que T. roseo-alba é espécie auto-estéril, destituída de poliembrionia e que apresenta AIT pós-zigótica.<br>Breeding system studies have indicated the predominance of late-acting self-incompatibility (LSI) in Bignoniaceae, despite the relatively few species investigated, and the occurrence of other kinds of breeding systems in this family. This study aimed to determine the breeding system in T. roseo-alba by means of controlled experimental pollination, histological analysis of post-pollination events, and studies of pistil longevity, in situ pollen tube growth and seed germination. Despite pollen tube penetration and fertilization of most ovules of selfed pistils, 100% of these pistils aborted uniformly between the fourth and sixth day after anthesis onset. Ovary and ovule growth, as well as initial endospermogenesis and proembryonal tube formation were verified in selfed pistils before abscission, but the progress of post-pollination development in these pistils was slower than in crossed pistils. The longevity of self-pollinated pistils was greater than in non-pollinated pistils. Seed germinability was 93%, and all seeds were monoembryonic. These results show that T. roseo-alba is a species with post-zygotic LSI, and with no polyembryony