Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program. we identified 50 potential microRNAs (miRNAs) in Giardia lamblia. one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs.

Present status and changes of the phytoplankton community after invasion of Neosalanx taihuensis since 1982 in a deep oligotrophic plateau lake, Lake Fuxian in the subtropical China

Phytoplankton assemblages in the subtrophical oligotrophic Lake Fuxian, the second deepest lake in China, were investigated monthly from September 2002 to August 2003. A total of 113 species belonging to seven phyla were identified, among them, a filamentous green alga, Mougeotia sp., dominated almost throughout the study period and comprised most of the total phytoplankton biomass. Mougeotia sp. has made a substantial development during the past decades: it was absent in 1957, only occasionally present in 1983, increased substantially in 1993, and became predominant in 2002-2003. It is likely that natural invasion of the Taihu Lake noodlefish (Neosalanx taihuensis) has led to a change of dominant herbivorous zooplankton from small to large calanoid, which has increased grazing pressure on small edible algae, and thus has indirectly favored the development of the inedible filamentous Mougeotia sp.

Annihilation of deep level defects in InP through high temperature annealing

Deep level transient spectroscopy (DLTS) and thermally stimulated current spectroscopy (TSC) have been used to investigate defects in semi-conducting and semi-insulating (SI) InP after high temperature annealing, respectively. The results indicate that the annealing in iron phosphide ambient has an obvious suppression effect of deep defects, when compared with the annealing in phosphorus ambient. A defect annihilation phenomenon has also been observed in Fe-doped SI-InP materials after annealing. Mechanism of defect formation and annihilation related to in-diffusion of iron and phosphorus is discussed. Nature of the thermally induced defects has been discussed based on the results. (c) 2007 Elsevier Ltd. All rights reserved.

Deep levels in high resistivity GaN detected by thermally stimulated luminescence and first-principles calculations

Thermally stimulated luminescence spectroscopy has been applied to study the deep centres in unintentionally doped high resistivity GaN epilayers grown by the metal organic chemical vapour deposition method on c-sapphire substrates. Two trap states with activation energies of 0.12 and 0.62 eV are evaluated from two luminescence peaks at 141.9 and 294.7 K in the luminescence curve. Our spectroscopy measurement, in combination with more accurate first-principles studies, provided insights into the microscopic origin of these levels. Our investigations suggest that the lower level at 0.12 eV might originate from C-N, which behaves as a hole trap state; the deeper level at 0.62 eV can be correlated with V-Ga that corresponds to the yellow luminescence band observed in low-temperature photoluminescence spectra.

Annealing ambient controlled deep defect formation in InP

Deep defects in annealed InP have been investigated by deep level transient capacitance spectroscopy (DLTS), photo induced current transient spectroscopy (PICTS) and thermally stimulated current spectroscopy (TSC). Both DLTS results of annealed semiconducting InP and PICTS and TSC results of annealed semi-insulating InP indicate that InP annealed in phosphorus ambient has five defects, while lid? annealed in iron phospbide ambient has two defects. Such a defect formation phenomenon is explained in terms of defect suppression by the iron atom diffusion process. The correlation of the defects and the nature of the defects in annealed InP are discussed based on the results.

Deep level defects in high temperature annealed InP

Deep level defects in high temperature annealed semi-conducting InP have been studied by deep level transient spectroscopy (DLTS). There is obvious difference in the deep defects between as-grown InP, InP annealed in phosphorus ambient and iron phosphide ambient, as far as their quantity and concentration are concerned. Only two defects at 0.24 and 0.64 eV can be detected in InP annealed in iron phosphide ambient, while defects at 0.24, 0.42, 0.54 and 0.64 eV have been detected in InP annealed in phosphorus ambient, in contrast to two defects at 0.49 and 0.64 eV or one defect at 0.13 eV in as-grown InP. A defect suppression phenomenon related to iron diffusion process has been observed. The formation mechanism and the nature of the defects have been discussed.

An n-type SiGe/Ge QC structure utilizing the deep Ge quantum well for electron at the Gamma point

In this paper, an n-type Si1-xGex/Ge (x >= 0.85) quantum cascade (QC) structure utilizing a deep Ge quantum well for electrons at the Gamma point is proposed. Based on linear interpolation, a conduction band offset at the Gamma point in a Si1-xGex/Ge ( x >= 0.85) heterostructure is presented, which is suitable for designing a QC laser. This approach has the advantages of a large conduction band offset at the Gamma point, a low lattice mismatch between the Si1-xGex/Ge ( x >= 0.85) active layers and the Si1-yGey ( y > x) virtual substrate, a small electron effective mass in the Gamma band, simple conduction energy band structures and a simple phonon scattering mechanism in the Ge quantum well. The theory predicts that if high-energy electrons are continuously injected into the Gamma band, a quasi-equilibrium distribution of electrons between the Gamma and L bands can be reached and held, i.e., electrons with a certain density will be kept in the Gamma band. This result is supported by the intervalley scattering experiments. In n-type Si1-xGex/Ge ( x >= 0.85) QC structures, population inversion between the laser's upper and lower levels is demonstrated.

Generation and suppression of deep level defects in InP

Deep level defects in as-grown and annealed n-type and semi-insulating InP have been studied. After annealing in phosphorus ambient, a large quantity of deep level defects were generated in both n-type and semi-insulating InP materials. In contrast, few deep level defects exist in InP after annealing in iron phosphide ambient. The generation of deep level defects has direct relation with in-diffusion of iron and phosphorus in the annealing process. The in-diffused phosphorus and iron atoms occupy indium sites in the lattice, resulting in the formation of P anti-site defects and iron deep acceptors, respectively. T e results indicate that iron atoms fully occupy indium sites and suppress the formation of indium vacancy and P anti-site, etc., whereas indium vacancies and P anti-site defects. are formed after annealing in phosphor-us ambient. The nature of the deep level defects in InP has been studied based on the results.

Influence of deep level defects on electrical compensation in semi-insulating InP materials

In this paper, we analyze and compare electrical compensation and deep level defects in semi-insulating ( SI) materials prepared by Fe-doping and high temperature annealing of undoped InP. Influence of deep level defects in the SI-InP materials on the electrical compensation has been studied thermally stimulated current spectroscopy (TSC). Electrical property of the Fe-doped SI-InP is deteriorated due to involvement of a high concentration of deep level defects in the compensation. In contrast, the concentration of deep defects is very low in high temperature annealed undoped SI-InP in which Fe acceptors formed by diffusion act as the only compensation centre to pin the Fermi level, resulting in excellent electrical performance. A more comprehensive electrical compensation model of SI-InP has been given based on the research results.