Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.

BACKGROUND: Upstream open reading frames (uORFs) in the 5'-untranslated regions (5'-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups. RESULTS: To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides. CONCLUSIONS: This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.

Enhanced stability of nitrogen-sealed carbon nanotube saturable absorbers under high-intensity irradiation.

Due to their broadband saturable absorption and fast response, carbon nanotubes have proven to be an excellent material for the modelocking of fiber lasers and have become a promising device for the implementation of novel laser configurations. However, it is imperative to address the issue of their long-term reliability under intense optical pulses before they can be exploited in widespread commercial applications. In this work, we study how carbon nanotubes degrade due to oxidation when exposed to high-intensity continuous-wave light and we demonstrate that by sealing the carbon nanotubes in a nitrogen gas, the damage threshold can be increased by over one order of magnitude. We then monitor over 24 hours the performance of the carbon nanotube saturable absorbers as the passive modelocking device of an erbium-doped fiber laser with intracavity powers ranging from 5 mW to 316 mW. We observe that when the carbon nanotubes are sealed in nitrogen environment, oxidation can be efficiently prevented and the laser can operate without any deterioration at intracavity powers higher than 300 mW. However, in the case where carbon nanotubes are unprotected (i.e. those directly exposed to the air in the environment), the nanotubes start to deteriorate at intracavity powers lower than 50 mW.

Optical deposition of graphene and carbon nanotubes in a fiber ferrule for passive mode-locked lasing.

Mode-locked fiber lasers are currently undergoing a significant evolution towards higher pulse energies and shorter pulse durations. A key enabler in this progress has been the discovery of novel saturable absorbers (SA) such as carbon nanotubes (CNT) and graphene. The exceptional properties of CNTs as SA have been extensively studied in recent years. Graphene, a one atom thick planar sheet of carbon atoms arranged into a hexagonal lattice, has been recently proposed as an alternative to CNTs in several photonics applications. Here, we propose a method for the integration of graphene into a fiber ferrule using an optical deposition technique, which has been also employed for the deposition of CNT directly on the core of a fiber edge and in tapered fibers. We investigate and compare the optical properties of CNT-SA and graphene-SA fabricated by this optical deposition technique. Soliton-like, mode-locked lasing is confirmed using an erbium doped optical fiber in an all-fiber ring cavity laser configuration.