On single and multiple models of protein families for the detection of remote sequence relationships

Background  

The detection of relationships between a protein sequence of unknown function and a sequence whose function has been characterised enables the transfer of functional annotation. However in many cases these relationships can not be identified easily from direct comparison of the two sequences. Methods which compare sequence profiles have been shown to improve the detection of these remote sequence relationships. However, the best method for building a profile of a known set of sequences has not been established. Here we examine how the type of profile built affects its performance, both in detecting remote homologs and in the resulting alignment accuracy. In particular, we consider whether it is better to model a protein superfamily using a single structure-based alignment that is representative of all known cases of the superfamily, or to use multiple sequence-based profiles each representing an individual member of the superfamily.     

Cellular localization of a Hsp90 homologue in Porphyromonas gingivalis

We previously reported an association between elevated serum antibody titers to the 90-kDa human heat shock protein (Hsp90), periodontal health and colonization by Porphyromonas gingivalis. In this study, we examined the cellular localization of the Hsp90 homologue of P. gingivalis. Cultures of P. gingivalis were heat-stressed (45 degrees C) and examined for localization of the Hsp90 homologue. Heat stress induced a 4-5-fold increase in anti-Hsp90 antibody reactivity over that of the unstressed controls. Western blot analysis revealed two bands (44 and 68 kDa) that reacted with anti-Hsp90 antibodies. The 68-kDa band was heat-inducible, while the 44-kDa band was not. Immunogold staining revealed that the Hsp90 homologue localized principally to the membrane and extracellular vesicles. Subcellular fractionation confirmed that the Hsp90 homologue was primarily membrane-associated.     

Conductive hearing loss caused by eustachian tube dysfunction according to the data of functional computed tomography

The paper deals with computed tomography (CT) diagnosis of Eustachian tube dysfunction. A functional multislice spiral (MS) CT protocol has been first elaborated for the Eustachian tube. Twenty-three patients with unilateral conductive hearing loss and Eustachian tube dysfunction were examined. The normal functional anatomy of the Eustachian tube was evaluated on the side without evidence of pathology in 23 patients. Functional MSCT showed that the cartilaginous portion of the Eustachian tube opened partially and closed completely in 9 patients. Ten patients were found to have steady changes in the cartilaginous portion of the Eustachian tube. The developed method could confirm the cause of conductive hearing loss and optimally define a treatment policy.     

On the identity of Festuca jubata Lowe (Poaceae) and the description of a new Festuca species in the Azores Islands

The majority of authors consider Festuca jubata Lowe as an endemic species common to Madeira and the Azores. Saint-Yves proposed that F. jubata was an Azorean endemic and described a geovicarious taxon in Madeira: F. filiformis C. Sm. ex Link in Buch ssp. mandonii St.-Yves. We undertook a complete bibliographical revision of the taxonomy, nomenclature, and chorology of F. jubata s.l. , and contrasted it with morphological and anatomical studies performed on samples from the Azores and Madeira. Azorean plants usually identified as F. jubata had a character combination distinct from that of those with a Madeiran provenance. Saint-Yves' proposal of two independent taxa was correct, but he erroneously considered F. jubata as an Azorean endemic because the name F. jubata was based on Madeiran plants. Consequently, F. jubata auct. pl. from the Azores belongs to a new species.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 493–499.     

The Effect of Mineral Particulate Matter on the Productive Characteristics of Bacterioplankton and the Degradation of Labile Organic Material

The effect of mineral particulate matter on the population of bacterioplankton, its aggregation, and productive characteristics was studied in model experiments with different concentrations of particulate kaolin and the same concentration of organic substance (sodium humate). It was found that the presence of mineral particulate matter stimulated the aggregation of bacterioplankton, improved bacterial production, and extended the productive period of bacterioplankton. The integral specific production of aggregated bacterioplankton was higher than that of free-swimming bacterioplankton. The energy metabolic coefficient K ₂ of bacterioplankton in the presence of mineral particulate matter was higher than in its absence.     

DESCRIPTION OF THE SENSORY CHARACTERISTICS OF SPANISH UNIFLORAL HONEYS BY FREE CHOICE PROFILING

Different Spanish unifloral honeys (eucalyptus, sunflower, rosemary, thyme, lavender, citrus, anise, quercus, and lemon blossom) and one multifloral honey were studied by Free-Choice Profiling (FCP) analysis. Generalized Procrustes Analysis (GPA) applied to the FCP data allowed discrimination between samples and provided information on the attributes responsible for the differences observed. The honeys had significantly different sensory characteristics. Textural attributes were the predominant factor in discriminating between samples, and appearance (color included) was also correlated with GPA dimensions to a lesser extent.     

Reproductive ecology of Rhododendron ponticum (Ericaceae) in relict Mediterranean populations

In the southern Iberian Peninsula, Rhododendron ponticum occurs in restricted and vulnerable populations as a Tertiary relict. Population structure and the main phases of the reproductive process were examined in order to shed light on recruitment patterns and limitations. Rhododendron ponticum flowers are self-compatible and attract a diverse array of insects, which are responsible for a considerable number of seeds set in the populations. Nevertheless, only adults form populations, whilst seedlings are scarce and saplings virtually absent (only two juveniles out of 2489 adults sampled). Non-specialized vegetative multiplication by layering was observed. Recruitment failure seems to depend on the scarcity of safe microsites, which are free from drought, for seedling establishment. The observations contrast with R. ponticum 's reputation as an aggressive invader in temperate Atlantic areas. It is proposed that the species shows a variable balance between sexual reproduction and vegetative multiplication depending on environmental conditions. At present, only the latter seems to be prevailing in relict populations in the Iberian Peninsula. This flexible reproductive strategy is also discussed as a mechanism allowing persistence during geological climatic oscillations.  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 297–311.     

New species of Leaf-beetles (Coleoptera,Chrysomelidae) from China: XI

New species of the subfamilies Megalopodinae (Temnaspis humerosa sp. n.), Chrysomelinae [Chrysolina furialis sp. n., Ch. oxanae sp. n., Ch. pingchuana sp. n., Oreomelina (Oreomelina) obtusa sp. n., O. (Oreomelina) splendens sp. n. from Sichuan], and Galerucinae (Liroëtis obliquevirgata sp. n. from Sichuan, Hyphaenia lutescens sp. n. from Chongqing, H. potanini sp. n. from Sichuan, and H. kabaki sp. n. from Shaangxi) are described.     

Diffusional and Electrical Properties of T-Tubules Are Governed by Their Constrictions and Dilations

Cardiac t-tubules (TTs) form a network of complex surface membrane invaginations that is essential for proper excitation-contraction coupling. Although electron and optical microscopy studies provided a wealth of important information about the structure of TTs, assessing their functional properties remains a challenge. In this study, we investigated the diffusional accessibility of TTs in intact isolated adult mouse ventricular myocytes using, to our knowledge, a novel fluorescence-based assay. In this approach, a small part of TTs is first locally filled with fluorescent dextran and then its diffusion out of TTs is monitored after rapid removal of extracellular dextran. In normal cells, diffusion of 3 kDa dextran is characterized by an average time constant of 3.9 ± 1.2 s with the data ranging from 1.8 to 10.5 s. The data are consistent with essentially free diffusion of dextran in TTs although measurable contribution of binding is also evident. TT fluorescence is abolished in cells treated with high concentration of formamide or after hyposmotic stress. Importantly, the assay we use allows for quantitative, repetitive measurements of subtle dynamic changes in TT structure of the same cell that are not possible to observe with other approaches. In particular, dextran diffusion rate decreases two-to-threefold during cell swelling, suggesting significant structural remodeling of TTs. Computer modeling shows that diffusional accessibility and electrical properties of TTs are primarily determined by the constrictions and dilations of individual TTs and that, from a functional perspective, TTs cannot be considered as a network of cylinders of the same average diameter. Constriction/dilation model of cardiac TTs is in a quantitative agreement with previous high-resolution microscopy studies of TT structure and alternative measurements of diffusional and electrical time constants of TTs. The data also show that the apparent electrical length constant of cardiac TTs is likely several-fold smaller than that estimated in earlier studies.