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Biomedical subjects

J Miguel Ortega

Publications and source records attributed to J Miguel Ortega.

4 recordsLinked to original sources

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↗

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↗

Evaluation of alternative reporter genes for the yeast two-hybrid system.

The yeast two-hybrid system is a powerful tool for screening protein-protein interactions and has also been used for large-scale studies. We evaluated two protein-coding sequences as reporter genes for the yeast two-hybrid system, to determine if it was suitable as an alternative screening strategy. Aspergillus awamori glucoamylase activity results in clear haloes around colonies producing this enzyme after growth on starch plates and staining with iodine vapors. However, transcription activation by Gal4 on Gal-regulated promoters was insufficient for this type of phenotypic visualization. A modified gene of Aequoria victoria enhanced green fluorescent protein (EGFP) was tested to determine its suitability for interaction screenings with flow cytometry. When the EGFP reporter gene system was incorporated into the cells, Gal4 transcriptional activation produced sufficient fluorescence for detection with the flow cytometer, especially when there were strong interactions.

Base Sequence↗

Molecular basis for pacemaker cells in epithelia.

Intercellular signaling is highly coordinated in excitable tissues such as heart, but the organization of intercellular signaling in epithelia is less clear. We examined Ca(2+) signaling in hepatoma cells expressing the hepatocyte gap junction protein connexin32 (cx32) or the cardiac gap junction protein cx43, plus a fluorescently tagged V(1a) vasopressin receptor (V(1a)R). Release of inositol 1,4,5-trisphosphate (InsP(3)) in wild type cells increased Ca(2+) in the injected cell but not in neighboring cells, while the Ca(2+) signal spread to neighbors when gap junctions were expressed. Photorelease of caged Ca(2+) rather than InsP(3) resulted in a small increase in Ca(2+) that did not spread to neighbors with or without gap junctions. However, photorelease of Ca(2+) in cells stimulated with low concentrations of vasopressin resulted in a much larger increase in Ca(2+), which spread to neighbors via gap junctions. Cells expressing tagged V(1a)R similarly had increased sensitivity to vasopressin, and could signal to neighbors via gap junctions. Higher concentrations of vasopressin elicited Ca(2+) signals in all cells. In cx32 or cx43 but not in wild type cells, this signaling was synchronized and began in cells expressing the tagged V(1a)R. Thus, intercellular Ca(2+) signals in epithelia are organized by three factors: 1) InsP(3) must be generated in each cell to support a Ca(2+) signal in that cell; 2) gap junctions are necessary to synchronize Ca(2+) signals among cells; and 3) cells with relatively increased expression of hormone receptor will initiate Ca(2+) signals and thus serve as pacemakers for their neighbors. Together, these factors may allow epithelia to act in an integrated, organ-level fashion rather than as a collection of isolated cells.

Animals↗