Biomedical subjects

Francisco Prosdocimi

Publications and source records attributed to Francisco Prosdocimi.

5 recordsLinked to original sources

PubMed2006

A set of amino acids found to occur more frequently in human and fly than in plant and yeast proteomes consists of non-essential amino acids.

We investigated the hypothesis that essential amino acids are being replaced in proteins by non-essential amino acids. We compared the amino acid composition in human, worm and fly proteomes, organisms that cannot synthesize all amino acids, with the amino acids of the proteomes of plant, bakers yeast and budding yeast, which are capable of synthesizing them. The analysis covered 460,737 proteins (212,197,907 amino acids). The data suggest a bias towards the usage of non-essential amino acids (mostly the set GAPQC) by metazoan organisms, except for the worm, a Pseudocoelomata. Our results support the hypothesis that non-essential amino acids have been substituting essential ones in the Coelomata.

Amino Acids↗

PubMed2005

Genetic algorithm for analysis of mutations in Parkinson's disease.

OBJECTIVE: Mitochondrial genetics has unique features that impede analysis of the biological significance of mitochondrial mutations. Simple searches for differences in total mutational load between normal and pathological samples have been frequently unrewarding, raising the possibility that more complex patterns of mutations may be responsible for some conditions. We explore this possibility in the context of Parkinson's disease (PD). METHODS AND MATERIALS: We report the development of a modified genetic algorithm suited for detection of biologically meaningful patterns of mitochondrial mutations. The algorithm is applied to a database of mutations derived from biological samples, and verified by the use of shuffled data, and repeated leave-one-out testing. RESULTS: It is possible to derive, from a very small sample, multiple accurate classifier functions that correlate with biological features. The methodology is validated statistically through experiments with fabricated data. CONCLUSION: This algorithm might be generally applicable to conditions where interactions among multiple mitochondrial DNA mutations are important. The patterns embodied in the classifier functions obtained should be the subject of further experimental study.

Algorithms↗

PubMed2005

Accessing optimal primer distance from insert.

When building either DNA or cDNA libraries, a researcher looks at the vector multiple cloning site and chooses which restriction enzyme(s) will be used to clone the inserts. Although this procedure does not seem to be important, the accurate choosing of primer to insert distance can save time and money from genome and transcriptome projects. Here, 846 single-pool pUC18 sequences were produced and compared with the pUC18 consensus using local alignment tools. Data show that reads often contain 0-20 miscalled bases at the beginning of read and noise to signal transition is frequently found at 46-54 bases from the first 3' base downstream the sequencing primer. For SWAT-based approaches, 60 bases was the distance where over 90% of the sequences provided reliable information, presenting 13 vector bases on average. Looking at the data, it is possible to choose the most appropriate primer to insert distance for many applications.

Algorithms↗

PubMed2004

Evaluation of window cohabitation of DNA sequencing errors and lowest PHRED quality values.

When analyzing sequencing reads, it is important to distinguish between putative correct and wrong bases. An open question is how a PHRED quality value is capable of identifying the miscalled bases and if there is a quality cutoff that allows mapping of most errors. Considering the fact that a low quality value does not necessarily indicate a miscalled position, we decided to investigate if window-based analyses of quality values might better predict errors. There are many reasons to look for a perfect window in DNA sequences, such as when using SAGE technique, looking for BLAST seeding and clustering sequences. Thus, we set out to find a quality cutoff value that would distinguish non-perfect windows from perfect ones. We produced and compared 846 reads of pUC18 with the published pUC consensus, by local alignment. We then generated a database containing all mismatches, insertions and gaps in order to map real perfect windows. An investigation was made to find the potential to predict perfect windows when all bases in the window show quality values over a given cutoff. We conclude that, in window-based applications, a PHRED quality value cutoff of 7 masks most of the errors without masking real correct windows. We suggest that the putative wrong bases be indicated in lower case, increasing the information on the sequence databases without increasing the size the files.

Algorithms↗

PubMed2002

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.

Amino Acid Sequence↗