Influence of HAART on Alternative Reading Frame Immune Responses over the Course of HIV-1 Infection

Background: Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8(+) T cells on the virus has already been observed in vitro. HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo. Methodology/Principal findings: In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance: These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.

The use of Open Reading frame ESTs (ORESTES) for analysis of the honey bee transcriptome

Abstract Background The ongoing efforts to sequence the honey bee genome require additional initiatives to define its transcriptome. Towards this end, we employed the Open Reading frame ESTs (ORESTES) strategy to generate profiles for the life cycle of Apis mellifera workers. Results Of the 5,021 ORESTES, 35.2% matched with previously deposited Apis ESTs. The analysis of the remaining sequences defined a set of putative orthologs whose majority had their best-match hits with Anopheles and Drosophila genes. CAP3 assembly of the Apis ORESTES with the already existing 15,500 Apis ESTs generated 3,408 contigs. BLASTX comparison of these contigs with protein sets of organisms representing distinct phylogenetic clades revealed a total of 1,629 contigs that Apis mellifera shares with different taxa. Most (41%) represent genes that are in common to all taxa, another 21% are shared between metazoans (Bilateria), and 16% are shared only within the Insecta clade. A set of 23 putative genes presented a best match with human genes, many of which encode factors related to cell signaling/signal transduction. 1,779 contigs (52%) did not match any known sequence. Applying a correction factor deduced from a parallel analysis performed with Drosophila melanogaster ORESTES, we estimate that approximately half of these no-match ESTs contigs (22%) should represent Apis-specific genes. Conclusions The versatile and cost-efficient ORESTES approach produced minilibraries for honey bee life cycle stages. Such information on central gene regions contributes to genome annotation and also lends itself to cross-transcriptome comparisons to reveal evolutionary trends in insect genomes.

Research and theory driven insights: ten suggestions for L2 reading instruction

[EN]Research and theory on second language reading has reached heightened dimensions in recent years. It is through reading that learners access much information concerning the target language and culture, and consequently reading is an important part of almost all language programs across stages of acquisition. The purpose of this article is to offer informed suggestions for the foreign language instructor of reading. The ideas given in this paper constitute a collaborative project that developed as part of a graduate seminar on L2 Reading and Writing taught at Washington University in St. Louis.

Reading strategies in Stargardt's disease with foveal sparing

ABSTRACT: BACKGROUND: Subjects with a ring scotoma can use two retinal loci, a foveal and a peripheral, for reading. Our aim was to investigate the relative use of both retinal loci as a function of the spared foveal area size and the spatial resolution at both retinal loci. FINDINGS: Two patients with Stargardt's disease and ring scotomas read through a scanning laser ophthalmoscope a series of letters and words at various character sizes. The number of fixations made using each retinal locus was quantified. The relative use of each retinal locus depended on character size of the stimulus. Both patients used exclusively the eccentric retinal locus to read words of large character sizes. At small character sizes, the central retinal locus was predominantly used. For reading letters or words, once foveal fixation was used, patients did not shift back to the eccentric retinal locus. When spatial resolution allowed deciphering at both the eccentric and the central areas, patients consistently fixated with the eccentric retinal locus. CONCLUSIONS: Spatial resolution at the eccentric locus appears as a determinant factor to select the retinal area for reading. Reading strategies in patients with Stargardt's disease and a ring scotoma demonstrate a pattern of coordination of both eccentric and central retinal loci, reflecting a high degree of adaptation.