Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

February 2005: ARTstor Adds to Panoply of Databases

http://digitalcommons.winthrop.edu/dacusfocus/1027/thumbnail.jpg

Transparent access to relational, autonomous and distributed databases using semantic web and service oriented technologies

With the constant grow of enterprises and the need to share information across departments and business areas becomes more critical, companies are turning to integration to provide a method for interconnecting heterogeneous, distributed and autonomous systems. Whether the sales application needs to interface with the inventory application, the procurement application connect to an auction site, it seems that any application can be made better by integrating it with other applications. Integration between applications can face several troublesome due the fact that applications may not have been designed and implemented having integration in mind. Regarding to integration issues, two tier software systems, composed by the database tier and by the “front-end” tier (interface), have shown some limitations. As a solution to overcome the two tier limitations, three tier systems were proposed in the literature. Thus, by adding a middle-tier (referred as middleware) between the database tier and the “front-end” tier (or simply referred application), three main benefits emerge. The first benefit is related with the fact that the division of software systems in three tiers enables increased integration capabilities with other systems. The second benefit is related with the fact that any modifications to the individual tiers may be carried out without necessarily affecting the other tiers and integrated systems and the third benefit, consequence of the others, is related with less maintenance tasks in software system and in all integrated systems. Concerning software development in three tiers, this dissertation focus on two emerging technologies, Semantic Web and Service Oriented Architecture, combined with middleware. These two technologies blended with middleware, which resulted in the development of Swoat framework (Service and Semantic Web Oriented ArchiTecture), lead to the following four synergic advantages: (1) allow the creation of loosely-coupled systems, decoupling the database from “front-end” tiers, therefore reducing maintenance; (2) the database schema is transparent to “front-end” tiers which are aware of the information model (or domain model) that describes what data is accessible; (3) integration with other heterogeneous systems is allowed by providing services provided by the middleware; (4) the service request by the “frontend” tier focus on ‘what’ data and not on ‘where’ and ‘how’ related issues, reducing this way the application development time by developers.

Haematologic and immunologic parameters of bullfrogs, Lithobates catesbeianus, fed probiotics

The effects of two probiotics (P(1) - Lactobacillus acidophilus, Bifidobacterium bifidum and Enterococcus faecium and P(2) - Bacillus subtilis) supplemented to commercial feed (40% crude protein) on the haematological and immunological parameters of the bullfrog Lithobates catesbeianus were studied. Two doses of each probiotic (5 and 10 g kg-1 of food) were added to the diets and fed to frogs, totalling five treatments over 112 days. Haematological analyses consisted of total and differential leucocyte counts, erythrocyte and thrombocyte counts, haematocrit, haemoglobin levels and RBC indices (mean corpuscular volume, mean corpuscular haemoglobin - and mean corpuscular haemoglobin concentration) and the immunological parameters included phagocytic capacity and phagocytic index of peritoneal phagocytes. The results showed that the probiotics did not significantly influence any of the haematological parameters measured. However, immunological assays showed that the probiotics had an immunostimulating effect. The greatest effects were seen with probiotic P(1) fed at a dose of 10 g kg-1 of diet and probiotic P(2) fed at 5 g kg-1 of diet.

Pediatric Antiphospholipid Syndrome: Clinical and Immunologic Features of 121 Patients in an International Registry

OBJECTIVES. The purpose of this study was to obtain data on the association of antiphospholipid antibodies with clinical manifestations in childhood and to enable future studies to determine the impact of treatment and long-term outcome of pediatric antiphospholipid syndrome.PATIENTS and METHODS. A European registry extended internationally of pediatric patients with antiphospholipid syndrome was established as a collaborative project of the European Antiphospholipid Antibodies Forum and Lupus Working Group of the Pediatric Rheumatology European Society. To be eligible for enrollment the patient must meet the preliminary criteria for the classification of pediatric antiphospholipid syndrome and the onset of antiphospholipid syndrome must have occurred before the patient's 18th birthday.RESULTS. As of December 1, 2007, there were 121 confirmed antiphospholipid syndrome cases registered from 14 countries. Fifty-six patients were male, and 65 were female, with a mean age at the onset of antiphospholipid syndrome of 10.7 years. Sixty (49.5%) patients had underlying autoimmune disease. Venous thrombosis occurred in 72 (60%), arterial thrombosis in 39 (32%), small-vessel thrombosis in 7 (6%), and mixed arterial and venous thrombosis in 3 (2%). Associated nonthrombotic clinical manifestations included hematologic manifestations (38%), skin disorders (18%), and nonthrombotic neurologic manifestations (16%). Laboratory investigations revealed positive anticardiolipin antibodies in 81% of the patients, anti-beta(2)-glycoprotein I antibodies in 67%, and lupus anticoagulant in 72%. Comparisons between different subgroups revealed that patients with primary antiphospholipid syndrome were younger and had a higher frequency of arterial thrombotic events, whereas patients with antiphospholipid syndrome associated with underlying autoimmune disease were older and had a higher frequency of venous thrombotic events associated with hematologic and skin manifestations.CONCLUSIONS. Clinical and laboratory characterization of patients with pediatric antiphospholipid syndrome implies some important differences between antiphospholipid syndrome in pediatric and adult populations. Comparisons between children with primary antiphospholipid syndrome and antiphospholipid syndrome associated with autoimmune disease have revealed certain differences that suggest 2 distinct subgroups. Pediatrics 2008; 122: e1100-e1107

Short-term clinical and immunologic effects of scaling and root planing with Er : YAG laser in chronic periodontitis

Background: Recently, the erbium-doped:yttrium, aluminum, and garnet (Er:YAG) laser has been used for periodontal therapy. This study compared Er:YAG laser irradiation (100 mJ/pulse, 10 Hz, 12.9 J/cm(2)) with or without conventional scaling and root planing (SRP) to SRP only for the treatment of periodontal pockets affected with chronic periodontitis.Methods: Twenty-one subjects with pockets from 5 to 9 mm in non-adjacent sites were studied. In a split-mouth design, each site was randomly allocated to a treatment group: SRP and laser (SRPL), laser only (L), SRP only (SRP), or no treatment (C). The plaque index (PI), gingival index (GI), bleeding on probing (BOP), and interleukin (IL)-1 beta levels in crevicular fluid were evaluated at baseline and at 12 and 30 days postoperatively, whereas probing depth (PD), gingival recession (GR), and clinical attachment level (CAL) were evaluated at baseline and 30 days after treatment. A statistical analysis was conducted (P<0.05).Results: Twelve days postoperatively, the PI decreased for SRPL and SRP groups (P<0.05); the GI increased for L, SRP, and C groups but decreased for the SRPL group (P<0.05); and BOP decreased for SRPL, L, and SRP groups (P<0.01). Thirty days postoperatively, BOP decreased for treated groups and was lower than the C group (P<0.05). PD decreased in treated groups (P<0.001), and differences were found between SRPL and C groups (P<0.05). CAL gain was significant only for the SRP group (P<0.01). GR increased for SRPL and L groups (P<0.05). No difference in IL-1 beta was detected among groups and periods.Conclusion: Er:YAG laser irradiation may be used as an adjunctive aid for the treatment of periodontal pockets, although a significant CAL gain was observed with SRP alone and not with laser treatment.