Computer aided identification of a Hevein-like antimicrobial peptide of bell pepper leaves for biotechnological use.

BACKGROUND: Antimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves ('Magali R') are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses. RESULTS: Aqueous extracts from leaves were enriched in peptide by salt fractionation and ultrafiltration. An antimicrobial peptide was isolated by tandem chromatographic procedures. Mass spectrometry, automated peptide sequencing and bioinformatics tools were used alternately for identification and partial characterization of the Hevein-like peptide, named HEV-CANN. The computational tools that assisted to the identification of the peptide included BlastP, PSI-Blast, ClustalOmega, PeptideCutter, and ProtParam; conventional protein databases (DB) as Mascot, Protein-DB, GenBank-DB, RefSeq, Swiss-Prot, and UniProtKB; specific for peptides DB as Amper, APD2, CAMP, LAMPs, and PhytAMP; other tools included in ExPASy for Proteomics; The Bioactive Peptide Databases, and The Pepper Genome Database. The HEV-CANN sequence presented 40 amino acid residues, 4258.8 Da, theoretical pI-value of 8.78, and four disulfide bonds. It was stable, and it has inhibited the growth of phytopathogenic bacteria and a fungus. HEV-CANN presented a chitin-binding domain in their sequence. There was a high identity and a positive alignment of HEV-CANN sequence in various databases, but there was not a complete identity, suggesting that HEV-CANN may be produced by ribosomal synthesis, which is in accordance with its constitutive nature. CONCLUSIONS: Computational tools for proteomics and databases are not adjusted for short sequences, which hampered HEV-CANN identification. The adjustment of statistical tests in large databases for proteins is an alternative to promote the significant identification of peptides. The development of specific DB for plant antimicrobial peptides, with information about peptide sequences, functional genomic data, structural motifs and domains of molecules, functional domains, and peptide-biomolecule interactions are valuable and necessary.

An innovative electronic health records system for rare and complex diseases.

BACKGROUND: There exists a large number of rare and complex diseases that are neglected due to the difficulty in diagnosis and treatment. Being rare, they normally do not justify the costs of developing an especialized Electronic Health Record (EHR) system to assist doctors and patients of these diseases. In this work we propose the use of Computer applications known as Laboratory Information Management Systems (LIMS) to address this issue. RESULTS: In this work we describe a fully customizable EHR system that uses a workflow based LIMS with an easy to adapt interface for data collection and retrieval. This system can easily be customized to manage different types of medical data. The customization for a new disease can be done in a few hours with the help of a specialist. CONCLUSION: We have used the proposed system to manage data from patients of three complex diseases: neuromyelitis optica, paracoccidioidomycosis and adrenoleukodistrofy. These diseases have very different symptoms, exams, diagnostics and treatments, but the FluxMED system is able to manage these data in a highly specialized manner without any modifications to its code.

FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data.

BACKGROUND: Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical. These assays may be used as an alternative to animal experimentation and are becoming increasingly important in modern laboratories. However, the execution of these assays in large scale and different laboratories requires, among other things, the management of protocols, reagents, cell lines used as well as the data produced, which can be a challenge. The management of all this information is greatly improved by the utilization of computational tools to save time and guarantee quality. However, a tool that performs this task designed specifically for cytotoxicity assays is not yet available. RESULTS: In this work, we have used a workflow based LIMS -- the Flux system -- and the Together Workflow Editor as a framework to develop FluxCTTX, a tool for management of data from cytotoxicity assays performed at different laboratories. The main work is the development of a workflow, which represents all stages of the assay and has been developed and uploaded in Flux. This workflow models the activities of cytotoxicity assays performed as described in the OECD 129 Guidance Document. CONCLUSIONS: FluxCTTX presents a solution for the management of the data produced by cytotoxicity assays performed at Interlaboratory comparisons. Its adoption will contribute to guarantee the quality of activities in the process of cytotoxicity tests and enforce the use of Good Laboratory Practices (GLP). Furthermore, the workflow developed is complete and can be adapted to other contexts and different tests for management of other types of data.

DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.

Large-scale genomics initiatives such as the HapMap project and the 1000-genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from different sources, as well as to assist these scientists to perform their analyses efficiently. We developed such a bioinformatics platform, DIVERGENOME, to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups. The platform is composed of two integrated components, a relational database (DIVERGENOMEdb), and a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology (DIVERGENOMEtools). In DIVERGENOMEdb, information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in projects. These can be queried according to permissions. Here, we validated DIVERGENOME through a use case regarding the analysis of SLC2A4 genetic diversity in human populations. DIVERGENOME, with its intuitive Web interface and automatic data loading capability, facilitates its use by individuals without bioinformatics background, allowing complex queries to be easily interrogated and straightforward data format conversions (not available in similar platforms). DIVERGENOME is open source, freely available, and can be accessed online (pggenetica.icb.ufmg.br/divergenome) or hosted locally.

A System for Structuring, Storage and Georeferenciation of Dengue Vector Surveillance Data.

Dengue is a main public health issue around the world and is an epidemic in Brazil. As part of the Brazilian national program to fight the disease, every municipality has a Zoonosis Control Center responsible for health and case surveillance, among other actions. The fieldwork includes routine visiting of houses and strategic sites (e.g. industries and vacant lands), water sampling, container elimination, and larvicide administration. However, the field data are gathered and summarized by hand. In this work, our goal is to ease the collection and visualization of field data to support decision-making. We have developed a mobile system to collect and georeference field data which could then be used to build geospatial and geo-temporal visualizations of indices such as House, Container, and Breteau1 indices. This solution could enhance entomological surveillance and leverage action planning and evaluation.

Modeling and analysis of cell membrane systems with probabilistic model checking.

BACKGROUND: Recently there has been a growing interest in the application of Probabilistic Model Checking (PMC) for the formal specification of biological systems. PMC is able to exhaustively explore all states of a stochastic model and can provide valuable insight into its behavior which are more difficult to see using only traditional methods for system analysis such as deterministic and stochastic simulation. In this work we propose a stochastic modeling for the description and analysis of sodium-potassium exchange pump. The sodium-potassium pump is a membrane transport system presents in all animal cell and capable of moving sodium and potassium ions against their concentration gradient. RESULTS: We present a quantitative formal specification of the pump mechanism in the PRISM language, taking into consideration a discrete chemistry approach and the Law of Mass Action aspects. We also present an analysis of the system using quantitative properties in order to verify the pump reversibility and understand the pump behavior using trend labels for the transition rates of the pump reactions. CONCLUSIONS: Probabilistic model checking can be used along with other well established approaches such as simulation and differential equations to better understand pump behavior. Using PMC we can determine if specific events happen such as the potassium outside the cell ends in all model traces. We can also have a more detailed perspective on its behavior such as determining its reversibility and why its normal operation becomes slow over time. This knowledge can be used to direct experimental research and make it more efficient, leading to faster and more accurate scientific discoveries.

Can the vector space model be used to identify biological entity activities?

BACKGROUND: Biological systems are commonly described as networks of entity interactions. Some interactions are already known and integrate the current knowledge in life sciences. Others remain unknown for long periods of time and are frequently discovered by chance. In this work we present a model to predict these unknown interactions from a textual collection using the vector space model (VSM), a well known and established information retrieval model. We have extended the VSM ability to retrieve information using a transitive closure approach. Our objective is to use the VSM to identify the known interactions from the literature and construct a network. Based on interactions established in the network our model applies the transitive closure in order to predict and rank new interactions. RESULTS: We have tested and validated our model using a collection of patent claims issued from 1976 to 2005. From 266,528 possible interactions in our network, the model identified 1,027 known interactions and predicted 3,195 new interactions. Iterating the model according to patent issue dates, interactions found in a given past year were often confirmed by patent claims not in the collection and issued in more recent years. Most confirmation patent claims were found at the top 100 new interactions obtained from each subnetwork. We have also found papers on the Web which confirm new inferred interactions. For instance, the best new interaction inferred by our model relates the interaction between the adrenaline neurotransmitter and the androgen receptor gene. We have found a paper that reports the partial dependence of the antiapoptotic effect of adrenaline on androgen receptor. CONCLUSIONS: The VSM extended with a transitive closure approach provides a good way to identify biological interactions from textual collections. Specifically for the context of literature-based discovery, the extended VSM contributes to identify and rank relevant new interactions even if these interactions occur in only a few documents in the collection. Consequently, we have developed an efficient method for extracting and restricting the best potential results to consider as new advances in life sciences, even when indications of these results are not easily observed from a mass of documents.

PRODIS: a proteomics data management system with support to experiment tracking.

BACKGROUND: A research area that has greatly benefited from the development of new and improved analysis technologies is Proteomics and large amounts of data have been generated by proteomic analysis as a consequence. Previously, the storage, management and analysis of these data have been done manually. This is, however, incompatible with the volume of data generated by modern proteomic analysis. Several attempts have been made to automate the tasks of data analysis and management. In this work we propose PRODIS (Proteomics Database Integrated System), a system for proteomic experimental data management. The proposed system enables an efficient management of the proteomic experimentation workflow, simplifies controlling experiments and associated data and establishes links between similar experiments through the experiment tracking function. RESULTS: PRODIS is fully web based which simplifies data upload and gives the system the flexibility necessary for use in complex projects. Data from Liquid Chromatography, 2D-PAGE and Mass Spectrometry experiments can be stored in the system. Moreover, it is simple to use, researchers can insert experimental data directly as experiments are performed, without the need to configure the system or change their experiment routine. PRODIS has a number of important features, including a password protected system in which each screen for data upload and retrieval is validated; users have different levels of clearance, which allow the execution of tasks according to the user clearance level. The system allows the upload, parsing of files, storage and display of experiment results and images in the main formats used in proteomics laboratories: for chromatographies the chromatograms and lists of peaks resulting from separation are stored; For 2D-PAGE images of gels and the files resulting from the analysis are stored, containing information on positions of spots as well as its values of intensity, volume, etc; For Mass Spectrometry, PRODIS presents a function for completion of the mapping plate that allows the user to correlate the positions in plates to the samples separated by 2D-PAGE. Furthermore PRODIS allows the tracking of experiments from the first stage until the final step of identification, enabling an efficient management of the complete experimental process. CONCLUSIONS: The construction of data management systems for Proteomics data importing and storing is a relevant subject. PRODIS is a system complementary to other proteomics tools that combines a powerful storage engine (the relational database) and a friendly access interface, aiming to assist Proteomics research directly at data handling and storage.

SIGLa: an adaptable LIMS for multiple laboratories.

BACKGROUND: The need to manage large amounts of data is a clear demand for laboratories nowadays. The use of Laboratory Information Management Systems (LIMS) to achieve this is growing each day. A LIMS is a complex computational system used to manage laboratory data with emphasis in quality assurance. Several LIMS are available currently. However, most of them have proprietary code and are commercialized with a high cost. Moreover, due to its complexity, LIMS are usually designed to comply with the needs of one kind of laboratory, making it very difficult to reuse a LIMS. In this work we describe the Sistema Integrado de Gerência de Laboratórios (SIGLa), an open source LIMS with a new approach designed to allow it to adapt its activities and processes to various types of laboratories. RESULTS: SIGLa incorporates a workflow management system, making it possible to create and manage customized workflows. For each new laboratory a workflow is defined with its activities, rules and procedures. During the execution, for each workflow created, the values of attributes defined in a XPDL file (which describe the workflow) are stored in SIGLa's database, allowing then to be managed and retrieved upon request. These characteristics increase system's flexibility and extend its usability to include the needs of multiple types of laboratories. To construct the main functionalities of SIGLa a workflow of a proteomic laboratory was first defined. To validate the SIGLa capability of adapting to multiples laboratories, on this paper we study the process and the needs of a microarray laboratory and define its workflow. This workflow has been defined in a period of about two weeks, showing the efficiency and flexibility of the tool. CONCLUSIONS: Using SIGLa it has been possible to construct a microarray LIMS in a few days illustrating the flexibility and power of the method proposed. With SIGLa's development we hope to contribute positively to the area of management of complex data in laboratory by managing its large amounts of data, guaranteeing the consistency of the data and increasing the laboratory productivity. We also hope to make possible to laboratories with little resources to afford a high level system for complex data management.

Differential abundances of four forms of Binder of SPerm 1 in the seminal plasma of Bos taurus indicus bulls with different patterns of semen freezability.

The Binder of SPerm 1 (BSP1) protein is involved in the fertilization and semen cryopreservation processes and is described to be both beneficial and detrimental to sperm. Previously, the relationship of BSP1 with freezability events has not been completely understood. The objective of this work was to determine the differential abundance of the forms of the BSP1 protein in cryopreserved seminal plasma of Bos taurus indicus bulls with different patterns of semen freezability using proteomics. A wide cohort of adult bulls with high genetic value from an artificial insemination center was used as donors of high quality, fresh semen. Nine bulls presenting different patterns of semen freezability were selected. Two-dimensional gel electrophoresis showed differential abundance in a group of seven protein spots in the frozen/thawed seminal plasma from the bulls, ranging from 15 to 17 kDa, with pI values from 4.6 to 5.8. Four of these spots were confirmed to be BSP1 using mass spectrometry, proteomics, biochemical, and computational analysis (Tukey's test at P < 0.05). The protein spot weighing 15.52 ± 0.53 kDa with a pI value of 5.78 ± 0.12 is highlighted by its high abundance in bulls with low semen freezability and its absence in bulls presenting high semen freezability. This is the first report showing that more than two forms of BSP1 are found in the seminal plasma of Nelore adult bulls and not all animals have a similar abundance of each BSP1 form. Different BSP1 forms may be involved in different events of fertilization and the cryopreservation process.

Mining microorganism EST databases in the quest for new proteins.

Microorganisms with large genomes are commonly the subjects of single-round partial sequencing of cDNA, generating expressed sequence tags (ESTs). Usually there is a great distance between gene discovery by EST projects and submission of amino acid sequences to public databases. We analyzed the relationship between available ESTs and protein sequences and used the sequences available in the secondary database, clusters of orthologous groups (COG), to investigate ESTs from eight microorganisms of medical and/or economic relevance, selecting for candidate ESTs that may be further pursued for protein characterization. The organisms chosen were Paracoccidioides brasiliensis, Dictyostelium discoideum, Fusarium graminearum, Plasmodium yoelii, Magnaporthe grisea, Emericella nidulans, Chlamydomonas reinhardtii and Eimeria tenella, which have more than 10,000 ESTs available in dbEST. A total of 77,114 protein sequences from COG were used, corresponding to 3,201 distinct genes. At least 212 of these were capable of identifying candidate ESTs for further studies (E. tenella). This number was extended to over 700 candidate ESTs (C. reinhardtii, F. graminearum). Remarkably, even the organism that presents the highest number of ESTs corresponding to known proteins, P. yoelii, showed a considerable number of candidate ESTs for protein characterization (477). For some organisms, such as P. brasiliensis, M. grisea and F. graminearum, bioinformatics has allowed for automatic annotation of up to about 20% of the ESTs that did not correspond to proteins already characterized in the organism. In conclusion, 4093 ESTs from these eight organisms that are homologous to COG genes were selected as candidates for protein characterization.

Probabilistic model checking analysis of palytoxin effects on cell energy reactions of the Na+/K+-ATPase.

Probabilistic model checking (PMC) is a technique used for the specification and analysis of complex systems. It can be applied directly to biological systems which present these characteristics, including cell transport systems. These systems are structures responsible for exchanging ions through the plasma membrane. Their correct behavior is essential for animal cells, since changes on those are responsible for diseases. In this work, PMC is used to model and analyze the effects of the palytoxin toxin (PTX) interactions with one of these systems. Our model suggests that ATP could inhibit PTX action. Therefore, individuals with ATP deficiencies, such as in brain disorders, may be more susceptible to the toxin. We have also used heat maps to enhance the kinetic model, which is used to describe the system reactions. The map reveals unexpected situations, such as a frequent reaction between unlikely pump states, and hot spots such as likely states and reactions. This type of analysis provides a better understanding on how transmembrane ionic transport systems behave and may lead to the discovery and development of new drugs to treat diseases associated to their incorrect behavior.

Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies.

BACKGROUND: Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases. Despite the advent of next-generation sequencing technologies, Sanger sequencing is still the most popular approach in population genetics studies because of the widespread availability of automatic sequencers based on capillary electrophoresis and because it is still less prone to sequencing errors, which is critical in population genetics studies. Two popular software applications for re-sequencing studies are Phred-Phrap-Consed-Polyphred, which performs base calling, alignment, graphical edition and genotype calling and DNAsp, which performs a set of population genetics analyses. These independent tools are the start and end points of basic analyses. In between the use of these tools, there is a set of basic but error-prone tasks to be performed with re-sequencing data. RESULTS: In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp. CONCLUSION: We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses.

NMO-DBr: the Brazilian Neuromyelitis Optica Database System.

OBJECTIVE: To present the Brazilian Neuromyelitis Optica Database System (NMO-DBr), a database system which collects, stores, retrieves, and analyzes information from patients with NMO and NMO-related disorders. METHOD: NMO-DBr uses Flux, a LIMS (Laboratory Information Management Systems) for data management. We used information from medical records of patients with NMO spectrum disorders, and NMO variants, the latter defined by the presence of neurological symptoms associated with typical lesions on brain magnetic resonance imaging (MRI) or aquaporin-4 antibody seropositivity. RESULTS: NMO-DBr contains data related to patient's identification, symptoms, associated conditions, index events, recurrences, family history, visual and spinal cord evaluation, disability, cerebrospinal fluid and blood tests, MRI, optic coherence tomography, diagnosis and treatment. It guarantees confidentiality, performs cross-checking and statistical analysis. CONCLUSION: NMO-DBr is a tool which guides professionals to take the history, record and analyze information making medical practice more consistent and improving research in the area.

Efficient secondary database driven annotation using model organism sequences.

The use of sequences from specific organisms for annotation requires that it does not represent great loss of information and that the sequences available suffice for annotation. In order to investigate whether or not sequences from model organisms may suffice for annotation of sequences from the trematode Schistosoma mansoni, we performed local BLAST searches of S. mansoni sequences against other organisms sequences present in the NCBI database nr. Results have been inserted into a relational database and hits to sequences from three model organisms, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens have been computed and compared to hits to sequences from other organisms present in nr; score values of each alignment have also been registered. Our observations have shown that a large fraction of orthologous proteins exists in the set of sequences from the three model organisms selected, and therefore a similar fraction of transcripts can be annotated when using either nr or model organism datasets. Moreover, hits to model organisms' sequences are largely as informative as nr. Results suggest that model organisms provide a reliable set of sequences to use as a reference database for S. mansoni sequence annotation, showing the clear possibility of using a restricted dataset of expected better quality for functional annotation and therefore supporting secondary database driven annotation approaches.

Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni.

The number of sequences generated by genome projects has increased exponentially, but gene characterization has not followed at the same rate. Sequencing and analysis of full-length cDNAs is an important step in gene characterization that has been used nowadays by several research groups. In this work, we have selected Schistosoma mansoni clones for full-length sequencing, using an algorithm that investigates the presence of the initial methionine in the parasite sequence based on the positions of alignment start between two sequences. BLAST searches to produce such alignments have been performed using parasite expressed sequence tags produced by Minas Gerais Genome Network against sequences from the database Eukaryotic Cluster of Orthologous Groups (KOG). This procedure has allowed the selection of clones representing 398 proteins which have not been deposited as S. mansoni complete CDS in any public database. Dedicated sequencing of 96 of such clones with reads from both 5' and 3' ends has been performed. These reads have been assembled using PHRAP, resulting in the production of 33 full-length sequences that represent novel S. mansoni proteins. These results shall contribute to construct a more complete view of the biology of this important parasite.

NMO-DBr: the Brazilian Neuromyelitis Optica Database System / NMO-DBr: o banco de dados brasileiro em neuromielite óptica

OBJECTIVE: To present the Brazilian Neuromyelitis Optica Database System (NMO-DBr), a database system which collects, stores, retrieves, and analyzes information from patients with NMO and NMO-related disorders. METHOD: NMO-DBr uses Flux, a LIMS (Laboratory Information Management Systems) for data management. We used information from medical records of patients with NMO spectrum disorders, and NMO variants, the latter defined by the presence of neurological symptoms associated with typical lesions on brain magnetic resonance imaging (MRI) or aquaporin-4 antibody seropositivity. RESULTS: NMO-DBr contains data related to patient's identification, symptoms, associated conditions, index events, recurrences, family history, visual and spinal cord evaluation, disability, cerebrospinal fluid and blood tests, MRI, optic coherence tomography, diagnosis and treatment. It guarantees confidentiality, performs cross-checking and statistical analysis. CONCLUSION: NMO-DBr is a tool which guides professionals to take the history, record and analyze information making medical practice more consistent and improving research in the area.

OBJETIVO: Apresentar o Brazilian Neuromyelitis Optica Database System (NMO-DBr), um sistema de banco de dados que coleta, arquiva, recupera e analisa informações de pacientes com neuromielite óptica (NMO) e doenças relacionadas. MÉTODO: NMO-DBr usa o sistema Flux, um LIMS (Laboratory Information Management Systems) para gerenciamento de informações. As informações foram colhidas dos prontuários de pacientes com espectro de NMO e variantes de NMO, estas últimas definidas por quadro neurológico associado a lesões encefálicas típicas à imagem pela ressonância magnética (IRM) ou à soropositividade do anticorpo anti-aquaporina-4. RESULTADOS: NMO-DBr contém dados relativos a identificação, sintomas, condições associadas, eventos índices, recorrências, história familiar, avaliação visual e da medula, incapacidade, exames do líquor e de sangue, IRM, tomografia de coerência óptica (OCT), diagnóstico e tratamento. O sistema assegura confidencialidade, cruza dados e faz análises estatísticas. CONCLUSÃO: NMO-DBr é uma ferramenta que possibilita a prática médica mais consistente e promove a pesquisa na área.

Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages.

The study of the Schistosoma mansoni genome, one of the etiologic agents of human schistosomiasis, is essential for a better understanding of the biology and development of this parasite. In order to get an overview of all S. mansoni catalogued gene sequences, we performed a clustering analysis of the parasite mRNA sequences available in public databases. This was made using softwares PHRAP and CAP3. The consensus sequences, generated after the alignment of cluster constituent sequences, allowed the identification by database homology searches of the most expressed genes in the worm. We analyzed these genes and looked for a correlation between their high expression and parasite metabolism and biology. We observed that the majority of these genes is related to the maintenance of basic cell functions, encoding genes whose products are related to the cytoskeleton, intracellular transport and energy metabolism. Evidences are presented here that genes for aerobic energy metabolism are expressed in all the developmental stages analyzed. Some of the most expressed genes could not be identified by homology searches and may have some specific functions in the parasite.

Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni

The number of sequences generated by genome projects has increased exponentially, but gene characterization has not followed at the same rate. Sequencing and analysis of full-length cDNAs is an important step in gene characterization that has been used nowadays by several research groups. In this work, we have selected Schistosoma mansoni clones for full-length sequencing, using an algorithm that investigates the presence of the initial methionine in the parasite sequence based on the positions of alignment start between two sequences. BLAST searches to produce such alignments have been performed using parasite expressed sequence tags produced by Minas Gerais Genome Network against sequences from the database Eukaryotic Cluster of Orthologous Groups (KOG). This procedure has allowed the selection of clones representing 398 proteins which have not been deposited as S. mansoni complete CDS in any public database. Dedicated sequencing of 96 of such clones with reads from both 5' and 3' ends has been performed. These reads have been assembled using PHRAP, resulting in the production of 33 full-length sequences that represent novel S. mansoni proteins. These results shall contribute to construct a more complete view of the biology of this important parasite.

Clustering of Schistosoma mansoni mRNA sequences and analysis of the most transcribed genes: implications in metabolism and biology of different developmental stages

The study of the Schistosoma mansoni genome, one of the etiologic agents of human schistosomiasis, is essential for a better understanding of the biology and development of this parasite. In order to get an overview of all S. mansoni catalogued gene sequences, we performed a clustering analysis of the parasite mRNA sequences available in public databases. This was made using softwares PHRAP and CAP3. The consensus sequences, generated after the alignment of cluster constituent sequences, allowed the identification by database homology searches of the most expressed genes in the worm. We analyzed these genes and looked for a correlation between their high expression and parasite metabolism and biology. We observed that the majority of these genes is related to the maintenance of basic cell functions, encoding genes whose products are related to the cytoskeleton, intracellular transport and energy metabolism. Evidences are presented here that genes for aerobic energy metabolism are expressed in all the developmental stages analyzed. Some of the most expressed genes could not be identified by homology searches and may have some specific functions in the parasite