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A Scheduling Algorithm for Computational Grids that Minimizes Centralized Processing in Genome Assembly of Next-Generation Sequencing Data
Jakelyne Lima,Erick Bol,Vasco Azevedo
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00038
Abstract: Improvements in genome sequencing techniques have resulted in generation of huge volumes of data. As a consequence of this progress, the genome assembly stage demands even more computational power, since the incoming sequence files contain large amounts of data. To speed up the process, it is often necessary to distribute the workload among a group of machines. However, this requires hardware and software solutions specially configured for this purpose. Grid computing try to simplify this process of aggregate resources, but do not always offer the best performance possible due to heterogeneity and decentralized management of its resources. Thus, it is necessary to develop software that takes into account these peculiarities. In order to achieve this purpose, we developed an algorithm aimed to optimize the functionality of de novo assembly software ABySS in order to optimize its operation in grids. We run ABySS with and without the algorithm we developed in the grid simulator SimGrid. Tests showed that our algorithm is viable, flexible, and scalable even on a heterogeneous environment, which improved the genome assembly time in computational grids without changing its quality.
Brucella spp noncanonical LPS: structure, biosynthesis, and interaction with host immune system
Patrícia Cardoso, Gilson Macedo, Vasco Azevedo, Sergio Oliveira
Microbial Cell Factories , 2006, DOI: 10.1186/1475-2859-5-13
Abstract: Brucellae are Gram-negative cocccobacilli, facultative intracellular bacterial pathogens of both humans and animals. The bacteria penetrate the mucosa of the nasal, oral, or pharyngeal cavities and are phagocytized by host macrophages, where survival and replication occurs. Brucellosis is a zoonotic disease that is difficult to diagnose and treat that causes heavy economic losses and human suffering, characterized by undulant fever that, if untreated, can develop into a chronic infection with symptoms persisting for several months. Chronic infections may result in infection of secondary tissues, including heart and brain. Symptoms may also recur years after the original infection. The pathological manifestations of brucellosis are diverse and include arthritis, endocarditis, and meningitis in humans, while animal brucellosis is characterized by spontaneous abortion [1]. Six species are recognized within the genus Brucella: B. abortus, B. melitensis, B. suis, B. ovis, B. canis, and B. neotomae. This classification is mainly based on the difference in pathogenicity and in host preference [2]. The main pathogenic species worldwide are B. abortus, responsible for bovine brucellosis; B. melitensis, the main etiologic agent of ovine and caprine brucellosis, a disease that causes abortion in ewes and goats resulting in huge economic losses, particularly in Mediterranean countries and B. suis responsible for swine brucellosis. B. abortus infection is acquired by humans through contact with infected livestock and consumption of unpasteurized dairy products. B. ovis and B. canis are responsible for ram epididymitis and canine brucellosis, respectively [3]. For B. neotomae only strains isolated from desert rats have been reported. Brucella strains have also been isolated from a great variety of wildlife species such as bison, elk, feral swine, foxes, hares, African Buffalo, reindeer, and caribou [4]. Recently, two new species have been proposed to be added to this genus, Bruce
A novel strategy of epitope design in Neisseria gonorrhoeae
Debmalya Barh,Amarendra Narayan Misra,Anil Kumar,Vasco Azevedo
Bioinformation , 2010,
Abstract: In spite of genome sequences of both human and N. gonorrhoeae in hand, vaccine for gonorrhea is yet not available. Due to availability of several host and pathogen genomes and numerous tools for in silico prediction of effective B-cell and T-cell epitopes; recent trend of vaccine designing has been shifted to peptide or epitope based vaccines that are more specific, safe, and easy to produce. In order to design and develop such a peptide vaccine against the pathogen, we adopted a novel computational approach based on sequence, structure, QSAR, and simulation methods along with fold level analysis to predict potential antigenic B-cell epitope derived T-cell epitopes from four vaccine targets of N. gonorrhoeae previously identified by us [Barh and Kumar (2009) In Silico Biology 9, 0019]. Four epitopes, one from each protein, have been designed in such a way that each epitope is highly likely to bind maximum number of HLA molecules (comprising of both the MHC-I and -II) and interacts with most frequent HLA alleles (A*0201, A*0204, B*2705, DRB1*0101, and DRB1*0401) in human population. Therefore our selected epitopes are highly potential to induce both the B-cell and T-cell mediated immune responses. Of course, these selected epitopes require further experimental validation.
In vitro and in vivo characterization of DNA delivery using recombinant Lactococcus lactis expressing a mutated form of L. monocytogenes Internalin A
de Azevedo Marcela,Karczewski Jurgen,Lefévre Fran？ois,Azevedo Vasco
BMC Microbiology , 2012, DOI: 10.1186/1471-2180-12-299
Abstract: Background The use of food-grade Lactic Acid Bacteria (LAB) as DNA delivery vehicles represents an attractive strategy to deliver DNA vaccines at the mucosal surfaces as they are generally regarded as safe (GRAS). We previously showed that either native Lactococcus lactis (LL) or recombinant invasive LL expressing Fibronectin Binding Protein A of Staphylococcus aureus (LL-FnBPA+) or Internalin A of Listeria monocytogenes (LL-InlA+), were able to deliver and trigger DNA expression by epithelial cells, either in vitro or in vivo. InlA does not bind to its receptor, the murine E-cadherin, thus limiting the use of LL-InlA+ in in vivo murine models. Moreover, FnBPA binds to its receptors, integrins, via fibronectin introducing another limiting factor. In order to avoid the limitations of LL-InlA+ and LL-FnBPA+, a new L. lactis strain was engineered to produce a previously described mutated form of InlA (LL-mInlA+) allowing the binding of mInlA on murine E-cadherin. Results After showing the expression of mInLA at the surface of LL-mInlA+ strain, in vitro gentamycin survival assay in Caco-2 cells showed that LL-mInlA+ is 1000 times more invasive than LL. LL-mInlA+ invasivity was also validated by fluorescence microscopy. LL and LL-mInlA+ were transformed with pValacBLG, a plasmid containing the cDNA of bovine β-Lactoglobulin (BLG), resulting in strains LL-BLG and LL-mInlA+BLG. The plasmid transfer in vitro using LL-mInlA+BLG was increased 10 times compared to LL-BLG. Moreover, the number of mice producing BLG in isolated enterocytes after oral administration of LL-mInlA+BLG in vivo was slightly higher than after oral administration of LL-BLG. Conclusions We confirmed in this study that the production of mInlA at the surface of L. lactis is a promising strategy for plasmid transfer in vitro and in vivo.
Analysis of quality raw data of second generation sequencers with Quality Assessment Software
Rommel TJ Ramos, Adriana R Carneiro, Jan Baumbach, Vasco Azevedo, Maria PC Schneider, Artur Silva
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-130
Abstract: We developed Quality Assessment Software, with which one can review graphs showing the distribution of quality values from the sequencing reads. This software allow us to adopt more stringent quality standards for sequence data, based on quality-graph analysis and estimated coverage after applying the quality filter, providing acceptable sequence coverage for genome construction from short reads.Quality filtering is a fundamental step in the process of constructing genomes, as it reduces the frequency of incorrect alignments that are caused by measuring errors, which can occur during the construction process due to the size of the reads, provoking misassemblies. Application of quality filters to sequence data, using the software Quality Assessment, along with graphing analyses, provided greater precision in the definition of cutoff parameters, which increased the accuracy of genome construction.The introduction of second-generation genome sequencing has reduced the cost and time required for genome construction; this method generates large amounts of data and increased sequencing coverage when compared to the dideoxy terminal Sanger method [1]. However, this new methodology reduces the size of the readings and has brought challenges to the genome assembly process, such as a need to develop efficient algorithms to reconstruct the genome [2]. Several examples of programs suitable for genome assembly from short reads are Velvet [3], Edena [4], SHARCGS [5], VCAKE [6], ALLPATHS [7], Euler-SR [8], and Quality-value guided Short Read Assembler (QSRA) [9]. All of them involve a process of connecting overlapping DNA sequences; however, only QRSA considers the quality of the reads during the assembly process.Regardless of the assembly method used, data preparation is necessary. One step in this preparation is the quality filter, whenever readings are taken with a lower phred quality [10]. Independent of the genome construction system, it is necessary to prepare the data. One
Efficient production and secretion of bovine β-lactoglobulin by Lactobacillus casei
Stéphane Hazebrouck, Laetitia Pothelune, Vasco Azevedo, Gérard Corthier, Jean-Michel Wal, Philippe Langella
Microbial Cell Factories , 2007, DOI: 10.1186/1475-2859-6-12
Abstract: Using a nisin-inducible plasmid system, we first showed that L. casei BL23 strain could efficiently secrete a reporter protein, the staphylococcal nuclease (Nuc), with the lactococcal signal peptide SPUsp45 fused to its N-terminus. The fusion of SPUsp45 failed to drive BLG secretion but led to a 10-fold increase of intracellular BLG production. Secretion was significantly improved when the synthetic propeptide LEISSTCDA (hereafter called LEISS) was added to the N-terminus of the mature moiety of BLG. Secretion rate of LEISS-BLG was 6-fold higher than that of BLG alone while intracellular production reached then about 1 mg/L of culture. The highest yield of secretion was obtained by using Nuc as carrier protein. Insertion of Nuc between LEISS and BLG resulted in a 20-fold increase in BLG secretion, up to 27 μg/L of culture. Furthermore, the lactococcal nisRK regulatory genes were integrated into the BL23 chromosome. The nisRK insertion allowed a decrease of BLG synthesis in uninduced cultures while BLG production increased by 50% after nisin induction. Moreover, modification of the induction protocol led to increase the proportion of soluble BLG to around 74% of the total BLG production.BLG production and secretion in L. casei were significantly improved by fusions to a propeptide enhancer and a carrier protein. The resulting recombinant strains will be further tested for their ability to modulate the immune response against BLG via mucosal delivery in a cow's milk allergy model in mice.Lactic acid bacteria are non-invasive and non-pathogenic Gram-positive bacteria with GRAS (generally regarded as safe) status that are widely used for food-processing and preservation. In addition, some strains were reported to exert probiotic effects [1-5]. Using the Nisin-Controlled Expression (NICE) system, β-lactoglobulin (BLG), a major cow's milk allergen, was successfully produced in Lactococcus lactis [6-8]. Administrations of BLG-producing lactococci to mice has been shown to
Molecular characterization and T and B cell epitopes prediction of Mycoplasma synoviae 53 strain VlhA hemagglutinin
Camargo, Ilana Lopes;Fonseca, Cristina Toscano;Teixeira, Santuza Ribeiro;Azevedo, Vasco;Myioshi, Anderson;Oliveira, Sergio Costa;
Genetics and Molecular Biology , 2007, DOI: 10.1590/S1415-47572007000200013
Abstract: mycoplasma sinoviae is a major pathogen of poultry causing synovitis and respiratory infection. m. synoviae hemagglutinin (vlha) is a lipoprotein encoded by related multigene families that appear to have arisen by horizontal gene transfer. it is an abundant immunodominant surface protein involved in host-parasite interaction mediating binding to host erythrocytes. herein, we have performed in silico analysis of the vlha gene product from the mycoplasma synoviae 53 strain and compared it to the vlha protein of m. synoviae wuv1853 strain. the vlha of the m. synoviae 53 strain possesses 569 amino acids and showed 85% identity with the vlha protein of the m. synoviae wuv1853 strain. further, a signal peptide was identified from amino acid m1 to d28 and a cleavage site between d28 and q29, both located in the n-terminal domain of the molecule. additionally, an insertion of papt amino acids was observed between t30-p35 and a deletion of the amino acids gtpgnp within the prr region of the vlha from the m. synoviae 53 strain, which may be related to its reduced virulence. finally, we have identified 17 b cell epitopes and 22 t cells epitopes within the vlha from the m. synoviae 53 strain. the b cell epitope s263-d277 and the t cell epitopes n45-n54 and g58-n67 showed 100% and 87-100% identity, respectively, with regions of vlha protein of tested mycoplasma synoviae and mycoplasma galisepticum strains. thus, these peptides represent new candidate molecules for the development of efficient diagnostic assays and new subunit vaccines.
Genetic diversity of b-glucuronidase activity among 14 strains of the dominant human gut anaerobe Ruminococcus gnavus
Beaud, Diane;Ladiré, Monique;Azevedo, Vasco;Bridonneau, Chantal;Anba-Mondoloni, Jamila;
Genetics and Molecular Biology , 2006, DOI: 10.1590/S1415-47572006000200026
Abstract: bacterial b-glucuronidase activity in the gut increases the enterohepatic circulation of toxic compounds and plays a major role in the etiology of colon cancer. previously, we had found that the gus gene, which codes for b-glucuronidase in a dominant anaerobic species of the gut microbiota, ruminococcus gnavus strain e1, is transcribed as part of an operon that includes three orfs that code for b-glucoside permeases of the phosphotransferase systems. this genetic organization had never been described. we have now compared b-glucuronidase activity and the genetic environment of the gus gene in 14 strains of ruminococcus gnavus.we found that five out of the seven glucuronidase-positive r. gnavus strains possessed another glucuronidase gene different from the gusa operon of r. gnavus e1. this dominant commensal intestinal species appears to have a high degree of genetic diversity in the genes that control b-glucuronidase activity.
Biomphalaria tenagophila: dominant character of the resistance to Schistosoma mansoni in descendants of crossbreedings between resistant (Taim, RS) and susceptible (Joinville, SC) strains
Rosa, Florence Mara;Godard, Ana Lúcia Brunialti;Azevedo, Vasco;Coelho, Paulo Marcos Zech;
Memórias do Instituto Oswaldo Cruz , 2005, DOI: 10.1590/S0074-02762005000100004
Abstract: the aim of the present work was to study parasitological, molecular, and genetic aspects in descendants of crossbreedings between a totally resistant biomphalaria tenagophila strain (taim, rs) and another one highly susceptible (joinville, sc) to schistosoma mansoni. descendants f1 and f2 were submitted to s. mansoni infection (le strain). the susceptibility rates for individuals from group f1 were 0 to 0.6%, and from group f2 was 7.2%. the susceptible individuals from group f2 discharged a lower number of cercariae, when compared with the susceptible parental group, and in 2 out of 9 positive snails the cercarial elimination was discontinued. in order to identify genetic markers associated with resistance the genotype of parental snails and their offspring f1 and f2 were analyzed by means of the randomly amplified polymorphic dna method. nevertheless, it was not possible to detect any marker associated to resistance, but the results showed that in the mentioned species the resistance character is determined by two dominant genes.
Update of the Gene Discovery Program in Schistosoma mansoni with the Expressed Sequence Tag Approach
Rabelo élida ML,Franco Glória R,Azevedo Vasco AC,Pena Heloisa B
Memórias do Instituto Oswaldo Cruz , 1997,
Abstract: Continuing the Schistosoma mansoni Genome Project 363 new templates were sequenced generating 205 more ESTs corresponding to 91 genes. Seventy four of these genes (81%) had not previously been described in S. mansoni. Among the newly discovered genes there are several of significant biological interest such as synaptophysin, NIFs-like and rho-GDP dissociation inhibitor
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