Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management.

Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre 'Alameda del Obispo' (Córdoba, Spain), one of the world's largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross 'Picual' × 'Arbequina' cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.

Refining borders of genome-rearrangements including repetitions.

BACKGROUND: DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR), the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP) is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. METHODS AND RESULTS: We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB) and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. CONCLUSION: The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements.

Web service catalogue for Biomedical Grid infrastructure.

A great variety of services have been developed to address problems in the field of biomedicine. The EU project Advancing Clinico-Genomics Trials on Cancer (ACGT - http://www.eu-acgt.org) provides a Grid-based platform for improved medical knowledge discovery and integration of biomedical data in clinical trials on cancer. Metadata describing biomedical services needs to be shared to enable discovery and service composition (as workflows). This paper reports a catalogue for knowledge-based discovery of service metadata and a software module to wrap existing command line programs as a secure Grid service able to handle sensitive information.

Assessment of the efficacy of nonablative long-pulsed 1064-nm Nd:YAG laser treatment of wrinkles compared at 2, 4, and 6 months.

Rhytides represent an aesthetic problem for a large percentage of the population. Many methods, both noninvasive and invasive, have been used for the treatment of wrinkles. Recently, the long-pulsed 1064-nm Nd:YAG laser has been shown to enhance dermal collagen synthesis without damaging the epidermis. The purpose of this preliminary study is to evaluate the use of the long-pulsed Nd:YAG laser in the nonablative treatment of periocular and perioral wrinkles. Ten patients with facial wrinkles were treated with the long-pulsed 1064-nm Nd:YAG laser, at a spot size of 5 mm in diameter, energy density of 13 J/cm2, exposure time per pulse of 300 microseconds, and a repetition rate of 7 Hz. All patients had a total of three treatments, once every 2 weeks. Subjective (patient satisfaction index [SI]) and objective (both physician- and computer program-based clinical index [CI]) assessments were performed before the first and third treatment sessions, and at 2, 4, and 6 months after the last treatment. At 6 months after the final treatment session, the patients' subjective SI was maintained at 40%, and had peaked at 50% 2 months after the final session. Physician assessment showed a CI of 40% at the 6-month assessment point and the computer program showed a 50% CI. The greatest level of effect with long-pulsed Nd:YAG laser nonablative skin rejuvenation for facial wrinkles was seen 2 months after the final treatment. Effects were still visible at the 6-month period, but showed a tendency to decrease. Maintenance treatments are required to achieve good patient satisfaction.

An 810 nm diode laser in the treatment of small (< or = 1.0 mm) leg veins: a preliminary assessment.

A consistently effective treatment for small leg veins (< or = 1.0 mm) is still being sought. The efficacy of an 810 nm diode laser in vein removal was assessed in a preliminary study. Fifteen females, skin types I to III, vein diameters 0.5-1 mm, aged from 25 to 42 years, participated in the study. An 810 nm diode laser (90 W, 20 ms/pulse, 10 Hz rep rate, 4.0 mm hand piece) was applied along the target veins. Biopsies were taken from two patients before and after the first treatment session. No compression was applied post-treatment. Four weeks later, a second treatment was given. Results were assessed subjectively from the patients' satisfaction index (SI) and objectively from clinical photography done by an independent clinician, who also judged the venous morphology before and 4 weeks after the second session. All patients completed the trial. Pain was moderate to severe at the time of treatment and erythema which was mild, which was seen in all 15 patients; oedema occurred in 12 patients and blistering in only one. No scarring was noticed. The overall satisfaction indices at the 4- and 8-week assessments were 20.7% and 55.1%, respectively. No patient got worse. The objective evaluations at the 4- and 8-week assessments showed increasing improvement in all aspects examined. Pain at the time of treatment was a problem for all patients, so epidermal cooling should be added. Despite this, the 810 laser diode was an interesting and promising device for treatment of small leg veins, warranting further study in larger patient cohorts with a longer-term follow up.

Long pulse Nd:YAG laser for treatment of leg veins in 40 patients with assessments at 6 and 12 months.

BACKGROUND AND OBJECTIVES: This study assessed subjectively and objectively the efficacy of a long-pulsed Nd:YAG laser system in clearing dermal leg veins, successful treatment of which remains problematic. STUDY DESIGN/PATIENTS AND METHODS: Forty female patients (24-58 years old, skin types II-IV) with leg veins were treated with synchronized micropulses from a long-pulsed 1,064 nm Nd:YAG laser, 6 mm diameter spot size, 130 and 140 J/cm2. One to three treatments were given at 6-week intervals, with post-treatment assessments at 6 and 12 months. Patients assessed improvement subjectively with a satisfaction index (SI). Objective assessment was based on the clinical photography, and in addition on computer-generated data from a Canny operator-based edge-detection program. RESULTS: The overall patient satisfaction rates and objective assessments at the 6 and 12 month assessments were 42.5 and 57.5%, and 75 and 82.5%, respectively. CONCLUSIONS: The long-pulsed Nd:YAG laser offered efficient treatment of leg veins. Side effects were minimal and transient. The edge-detection program may help patients appreciate better the actual results of the treatment.

AnaGram: protein function assignment.

SUMMARY: AnaGram is a web service for protein function assignment based on identity detection of small significant fragments (protomotifs) that can act as modular pieces in peptide construction. The system is able to assign function by finding correlations between protomotifs and functional annotations contained in SWISS-PROT and Medline databases. In addition, function ontologies are used for hierarchical organization of the predicted functions. Extensive tests have been carried out to evaluate the accuracy and performance of the system. AVAILABILITY: http://jaguar.genetica.uma.es/anagram.htm

A metadata classification schema for semantic content analysis of videos.

Simple ancillary metadata, such as those encompassed by the 15 elements of the Dublin Core, may be sufficient and entirely appropriate for basic coarse-granularity cross-domain resource discovery. However, they are insufficient and inappropriate for content description of complex data types such as videos, which require more detailed relational models. We propose a metadata classification schema for the characterization of items and events in videos that permits subsequent query by content. Following MPEG-7 nomenclature, metadata intrinsic to the information content of the video are defined as either structural or semantic, where structural metadata are numerical feature primitives produced by analysing the colour, shape, texture, structure and motion within the video frames, whereas semantic metadata describe the locations and timings of individual items and particular actions or events in the video, and are thus of higher information value. In this paper, the semantic metadata required to describe the visual information content of videos are defined and classified into four distinct classes: Media Entities; Content Items; Events; and Supplementary Items, and three types of property tables are defined: Identity Tables; Spatio-Temporal Position Tables; and Event Tables, in which these metadata may be stored in a relational database.

A computational strategy for protein function assignment which addresses the multidomain problem.

A method for assigning functions to unknown sequences based on finding correlations between short signals and functional annotations in a protein database is presented. This approach is based on keyword (KW) and feature (FT) information stored in the SWISS-PROT database. The former refers to particular protein characteristics and the latter locates these characteristics at a specific sequence position. In this way, a certain keyword is only assigned to a sequence if sequence similarity is found in the position described by the FT field. Exhaustive tests performed over sequences with homologues (cluster set) and without homologues (singleton set) in the database show that assigning functions is much 'cleaner' when information about domains (FT field) is used, than when only the keywords are used.

On the parallelisation of bioinformatics applications.

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.

Clinical and histologic effects of facial skin rejuvenation with pulsed- and continuous-wave flash-scanned CO(2) lasers.

LEARNING OBJECTIVES: The reader is presumed to have some understanding of the use of lasers in skin resurfacing. After studying the article, the participant should be able to: Physicians may earn 1 hour of Category 1 CME credit by successfully completing the examination based on material covered in this article. The examination begins on page 409. BACKGROUND: The selection of the ideal laser for facial resurfacing is debatable. OBJECTIVE: The purpose of the study was to determine whether any clinical and histologic differences existed in short- and long-term results after treatment with the Coherent UltraPulse 5000G laser (a pulsed laser; PL) and the Sharplan Silk Touch laser (a continuous-wave laser [CWL] with a flash scanner). METHODS: Eight patients underwent facial resurfacing treatment on different areas. In each case, one side was treated with the PL and the other with the CWL. The condition of the patients and the treated tissue were monitored periodically after treatment. Histologic assessment of punch biopsies was performed 3 months and 1 year after treatment with hematoxylin-eosin, Masson trichromic, and Verhoeff's stains. RESULTS: The areas treated with the PL achieved earlier epithelialization with a good appearance. Longer-lasting erythema was observed on the side treated with the CWL. On a histologic level, although the PL-treated tissue epithelialized more quickly, at 3 months and 1 year the collagen was better compacted and better aligned in the CWL-treated tissue, and the macroscopic appearance of the CWL-treated areas was more enhanced. CONCLUSIONS: The more active vascularization seen in the CWL-treated tissue, associated with the longer-lasting erythema and possibly greater collateral thermal injury, is possibly the reason for the better collagenization and remodeling of collagen and elastin fibers as compared with the results with the PL-treated tissue. This may explain the longer effect associated with CWL treatment. The clinician would do well to bear in mind the histologic findings as well as the macroscopic clinical results when assessing the long-term effects of laser skin resurfacing. (Aesthetic Surg J 2001;21:399-411.).

New phylogenetic venues opened by a novel implementation of the DNAml algorithm.

SUMMARY: This note describes the parallelization of a key biological application, such as the construction of phylogenetic trees, using the DNAml program. A careful run-time analysis allowed us to propose an efficient parallelization that scaled very well to large problem sizes. AVAILABILITY: By anonymous ftp at ftp.ac.uma. es (/pub/ots/pDNAml) or from our web site http://www.cnb.uam. es/www/software/software_index.html CONTACT: ots@ac.uma.es

Computational space reduction and parallelization of a new clustering approach for large groups of sequences.

MOTIVATION: The explosive growth of the biological sequences databases stimulated by genome projects has modified the framework of several applications in the biological sequence analysis area. In most cases, this new scenario is characterized by studies on large sets of sequences, suggesting the need for effective and automatic methods for their clustering. A more effective clustering of the database could be followed by the application of common family analysis schemes to the groups so formed. RESULTS: In this work, we present a new strategy to reduce the computational cost associated with the clustering of large sets of sequences which are expected to contain several families. The strategy is based on the grouping of the sequences into families by using a dynamic threshold on a pairwise sequence similarity criterion. Routine clustering of large data sets can now be done very efficiently. The method developed here achieves a computational space reduction of about an order of magnitude over more traditional ones of all-versus-all comparisons. The outcome of this approach produces family groupings that reproduce closely already accepted biological results. Our work includes a parallel implementation for distributed memory multiprocessors with a dynamic scheduling strategy for performance optimization. AVAILABILITY: By anonymous ftp at ftp.ac.uma.es (/pub/ots/pCluster directory), or from our Web site http://www.cnb. uam.es/www/software/software_index.html CONTACT: ots@ac.uma.es