Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

Five hundred and six EST-derived markers, 313 SSR markers and 26 BAC end-derived or SCAR markers were anchored by PCR on a subset of a Cabernet Sauvignon BAC library representing six genome equivalents pooled in three dimensions. In parallel, the 12,351 EST clusters of the grapevine UniGene set (build #11) from NCBI were used to design 12,125 primers pairs and perform electronic PCR on 67,543 nonredundant BAC-end sequences. This in silico experiment yielded 1,140 positive results concerning 638 different markers, among which 602 had not been already anchored by PCR. The data obtained will provide an easier access to the regulatory sequences surrounding important genes (represented by ESTs). In total, 1,731 islands of BAC clones (set of overlapping BAC clones containing at least one common marker) were obtained and 226 of them contained at least one genetically mapped anchor. These assigned islands are very useful because they will link the genetic map and the future fingerprint-based physical map and because they allowed us to indirectly place 93 ESTs on the genetic map. The islands containing two or more mapped SSR markers were also used to assess the quality of the integrated genetic map of the grapevine genome.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .Didier Lamoureux and Anne Bernole contributed equally to this work.     

Seasonal and microhabitat influences on diatom assemblages and their representation in sediment traps and surface sediments from adjacent High Arctic lakes: Cape Bounty,Melville Island,Nunavut

The spatial (i.e. microhabitat) and temporal (i.e. seasonal) characteristics of diatom assemblages in adjacent High Arctic lakes were studied intensively June–August 2004. These baseline data are used to improve understanding of modern diatom community dynamics, as well to inform paleoenvironmental reconstructions. Diatoms were collected approximately weekly through the melt season from each principal benthic substrate (moss/macrophyte, rock scrapes, littoral sediment), plankton, and sediment traps, and were compared to the uppermost 0.5 cm of a surface core obtained from the deepest part of the lake where sediment cores are routinely collected. Water samples were collected concurrently with diatom samples to investigate species–environment relationships. The lakes share approximately half of their common taxa, the most abundant overall in both lakes being small Cyclotella species. Results of detrended correspondence analysis (DCA) indicate that the largest gradient in species turnover existed between benthic and planktonic communities in both lakes, and that sediment trap and the surface core top samples most closely resemble the planktonic assemblage, with an additional contribution from the lotic environment. Our results indicate clear micro-spatial controls on species assemblages and a degree of disconnection between the benthos and deep lake sediments that manifests as an under-representation of benthic taxa in deep lake surface sediments. These findings are particularly relevant in the context of interpreting the paleoenvironmental record and assessing ecosystem sensitivity to continued climate change.     

Tooth histology,attachment, and replacement in the Ichthyopterygia reviewed in an evolutionary context

Ichthyosaurs, an extinct group of Mesozoic marine diapsids, show a relatively small range of tooth crown morphologies. With few exceptions, members of the group bear a large number of conical teeth and show only minor heterodonty within a jaw. This uniformity in gross morphology masks a high degree of variation in both the quantity and arrangement of the mineralized tooth tissues. Here, we describe tooth tissue structure and distribution in derived ichthyosaurs. We synthesize these new observations with the historical literature, to map changes in the quantity and arrangement of tooth tissues. These changes affected tooth attachment, tooth replacement, plicidentine morphology, and the amount and distribution of cellular cementum. The amount of variation detected in features relating to ichthyosaurian dentition is not surprising given the geological longevity and morphological disparity of the group, but does emphasize the importance of extensive taxon sampling in studies of tooth histology and evolution. This study is important in that it incorporates morphological and histological information in a phylogenetic and developmental context, something that is rarely done for marine reptile dentitions.     

Cytomechanics of axonal development

Mechanical tension is a robust regulator of axonal development of cultured neurons. We review work from our laboratory, using calibrated glass needles to measure or apply tension to chick sensory neurons, chick forebrain neurons, and rat PC12 cells. We survey direct evidence for two different regimes of tension effects on neurons, a fluid-like growth regime, and a nongrowth, elastic regime. Above a minimum tension threshold, we observe growth effects of tension regulating four phases of axonal development:

1. Initiation of process outgrowth from the cell body;
2. Growth cone-mediated elongation of the axon;
3. Elongation of the axon after synaptogenesis, which normally accommodates the skeletal growth of vertebrates; and
4. Axonal elimination by retraction.

Significantly, the quantitative relationship between the force and the growth response is suprisingly similar to the simple relationship characteristic of Newtonian fluid mechanical elements: elongation rate is directly proportional to tension (above the threshold), and this robust linear relationship extends from physiological growth rates to far-above-physiological rates. Thus, tension apparently integrates the complex biochemistry of axonal elongation, including cytoskeletal and membrane dynamics, to produce a simple “force input/growth output” relationship. In addition to this fluid-like growth response, peripheral neurons show elastic behaviors at low tensions (below the threshold tension for growth), as do most cell types. Thus, neurites could exert small static forces without diminution for long periods. In addition, axons of peripheral neurons can actively generate modest tensions, presumably similar to muscle contraction, at tensions near zero. The elastic and force-generating capability of neural axons has recently been proposed to play a major role in the morphogenesis of the brain.     

Growth and elongation within and along the axon

Mechanical tension is a particularly effective stimulus for axonal elongation, but little is known about how it leads to the formation of new axon. To better understand this process, we examined the movement of axonal branch points, beads bound to the axon, and docked mitochondria while monitoring axonal width. We found these markers moved in a pattern that suggests elongation occurs by viscoelastic stretching and volume addition along the axon. To test the coupling between “lengthening” and “growth,” we measured axonal width while forcing axons to grow and then pause by controlling the tension applied to the growth cone or to the cell body. We found axons thinned during high rates of elongation and thickened when the growth cones were stationary. These findings suggest that forces cause lengthening because they stretch the axon and that growth occurs, in a loosely coupled step, by volume addition along the axon. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2010     

Validation of Catquest-9SF Questionnaire in a Chinese Cataract Population

Purpose

To develop and validate a Chinese version of the Catquest-9SF questionnaire in a cataract population.

Methods

The Catquest-9SF Questionnaire was translated and back translated into Chinese. Preoperative patients were recruited at a tertiary eye hospital and their demographic information and visual acuity were documented. Psychometric properties of the Catquest-9SF, including ordered thresholds, the ability to distinguish between different strata of person ability, absence of misfitting items, unidimentionality, differential item functioning (DIF) and construct validity were tested, using Rasch analysis.

Results

A total of 102 patients (100% response rate) were enrolled. The participants''mean age was 70.2 year (SD = 12.1) and 46.9% were female. Rasch analysis showed that this version of the questionnaire had ordered response thresholds and was free of DIF. The items fit a single overall construct and unidimensional by principal components analysis of the residuals. Patients with visual impairment had significantly poorer Rasch scores on the Catquest-9SF (mean change, -2.5, p = 0.035, compared with non-visually impaired patients).

Conclusion

The Chinese version of Catquest-9SF is a valid and reliable questionnaire for assessing the visual disability outcomes of Chinese patients with cataract, and it may be recommended for routine clinical use.     

Regulation of osteoprotegerin pro- or anti-tumoral activity by bone tumor microenvironment

Tumor development in bone is often associated with fractures, bone loss and bone pain, and improvement is still needed in therapeutic approaches. Bone tumors are related to the existence of a vicious cycle between bone resorption and tumor proliferation in which the molecular triad osteoprotegerin (OPG)/receptor activator of NF-kappaB (RANK)/RANK ligand (RANKL) plays a pivotal role. RANKL, a member of the TNF superfamily, is one of the main inducers of bone resorption. Its soluble receptor OPG represents a promising therapeutic candidate as it prevents bone lesions and inhibits associated tumor growth. However, its therapeutic use in bone tumors remains controversial due to its ability to bind and inhibit another member of the TNF superfamily, TNF related apoptosis inducing ligand (TRAIL), which is a potent inducer of tumor cell apoptosis. Through its heparin binding domain, OPG is also able to bind proteoglycans present in the bone matrix. This paper is an overview of the involvement of the micro-environment, as represented by the balance of RANKL/TRAIL and the presence of proteoglycans in the regulation of OPG biological activity in bone tumors.