Predicting functional upstream open reading frames in Saccharomyces cerevisiae

Background  

Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive.     

Identification of Leishmania spp. by Radiorespirometry

SYNOPSIS Preliminary investigation of the application of radiorespirometric technic to protozoan parasites of man indicates a potential for rapid identification. This technic, developed for identification of bacteria, was modified for use with culture forms of Leishmania. Five strains of Leishmania were compared: 2 of L. donovani , 2S and K; L. brasiliensis , 2936 and B; and 1 of L. tropica , A. Consistent and rapid (2 hr) identification was obtained by the radiorespirometric procedure. A computer-type analysis of the radiorespirometric profiles of the 5 strains permitted correct identification of each isolate at the strain level 100% of the time. This technic offers several advantages over many current procedures for identification of protozoan parasites: (A) It is simple, rapid and highly reproducible. (B) Since it does not rely on visual or spectrophoto-metric determination, it may be conducted in the presence of optically complex substances. (C) It requires relatively low numbers of organisms (2 × 10⁵/¹⁴C-labeled substrate). (D) It is based on differential enzymic activity between species and strains of organisms and therefore, ultimately, on inherent genetic determinates of the parasites. (E) Further development of the procedure and accumulation of a data reference "bank" would allow automation of most of the identification process.     

Combining protein evolution and secondary structure

An evolutionary model that combines protein secondary structure and amino acid replacement is introduced. It allows likelihood analysis of aligned protein sequences and does not require the underlying secondary (or tertiary) structures of these sequences to be known. One component of the model describes the organization of secondary structure along a protein sequence and another specifies the evolutionary process for each category of secondary structure. A database of proteins with known secondary structures is used to estimate model parameters representing these two components. Phylogeny, the third component of the model, can be estimated from the data set of interest. As an example, we employ our model to analyze a set of sucrose synthase sequences. For the evolution of sucrose synthase, a parametric bootstrap approach indicates that our model is statistically preferable to one that ignores secondary structure.      

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

Background  

The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis.