The effect of varying stimulus rate and duration on brain activity during reading

The effect of the presentation rate and exposure duration of visually presented words on brain activity was investigated using positron emission tomography. Subjects either read aloud or silently mouthed the names of words. In regions associated with early visual analysis, activity increased with both rate and duration; in regions associated with response generation, activity increased with increasing rate but was unaffected by duration; and in regions associated with word recognition, activity decreased with increasing duration. The variable responses of different brain regions illustrate the functional segregation of these regions. Of particular interest was the dissociation between activity in the posterior fusiform gyri and that in the medial lingual gyrus--in the former, activity increased with rate and duration but the latter was unaffected by either variable. This finding suggests that word processing in the lingual gyrus during reading is distinct from that in the posterior fusiform gyri. A further observation was that during reading aloud, when subjects can hear the sound of their own voice, the response in the primary auditory cortices increased with stimulus rate, demonstrating that subjects process the sound of their own voice in a qualitatively similar way to words spoken by another.     

Sequence database searches via de novo peptide sequencing by tandem mass spectrometry

A method is described for searching protein sequence databases using tandem mass spectra of tryptic peptides. The approach uses a de novo sequencing algorithm to derive a short list of possible sequence candidates which serve as query sequences in a subsequent homology-based database search routine. The sequencing algorithm employs a graph theory approach similar to previously described sequencing programs. In addition, amino acid composition, peptide sequence tags and incomplete or ambiguous Edman sequence data can be used to aid in the sequence determinations. Although sequencing of peptides from tandem mass spectra is possible, one of the frequently encountered difficulties is that several alternative sequences can be deduced from one spectrum. Most of the alternative sequences, however, are sufficiently similar for a homology-based sequence database search to be possible. Unfortunately, the available protein sequence database search algorithms (e.g. Blast or FASTA) require a single unambiguous sequence as input. Here we describe how the publicly available FASTA computer program was modified in order to search protein databases more effectively in spite of the ambiguities intrinsic in de novo peptide sequencing algorithms.