ALBERT

Description: Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better performance compared with earlier developed algorithms such as TopHat and MapSplice. To improve detection of splice junctions, TrueSight uses information on statistical patterns of nucleotide ordering in intronic and exonic DNA. This line of research led to yet another new algorithm, UnSplicer, designed for eukaryotic species with compact genomes where functional alternative splicing is likely to be dominated by splicing noise. Genome-specific parameters of the new algorithm are generated by GeneMark-ES, an ab initio gene prediction algorithm based on unsupervised training. UnSplicer shares several components with TrueSight; the difference lies in the training strategy and the classification algorithm. We tested UnSplicer on RNA-Seq data sets of Arabidopsis thaliana , Caenorhabditis elegans , Cryptococcus neoformans and Drosophila melanogaster . We have shown that splice junctions inferred by UnSplicer are in better agreement with knowledge accumulated on these well-studied genomes than predictions made by earlier developed tools.

Description: Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit.

Description: Aims Clear-cutting is a common forest management practice, especially in subtropical China. However, the potential ecological consequences of clear-cutting remain unclear. In particular, the effect of clear-cutting on soil processes, such as the carbon cycle, has not been quantified in subtropical forests. Here, we investigated the response of soil respiration (Rs) to clear-cutting during a 12-month period in a subtropical forest in eastern China. Methods We randomly selected four clear-cut (CC) plots and four corresponding undisturbed forest (UF) plots. Measurements of Rs were made at monthly time points and were combined with continuous climatic measurements in both CC and UF. Daily Rs was estimated by interpolating data with an exponential model dependent on soil temperature. Daily Rs was cumulated to annual Rs estimates. Important Findings In the first year after clear-cutting, annual estimates of Rs in CC (508±23g C m –2 yr –1 ) showed no significant difference to UF plots (480±12g C m –2 yr –1 ). During the summer, soil temperatures were usually higher, whereas the soil volumetric water content was lower in CC than in UF plots. The long-term effects of clear-cutting on Rs are not significant, although there might be effects during the first several months after clear-cutting. Compared with previous work, this pattern was more pronounced in our subtropical forest than in the temperate and boreal forests that have been studied by others. With aboveground residuals off-site after clear-cutting, our results indicate that the stimulation of increasing root debris, as well as environmental changes, will not lead to a significant increase in Rs. In addition, long-term Rs will not show a significant decrease from the termination of root respiration, and this observation might be because of the influence of fast-growing vegetation after clear-cutting in situ .

Description: Anthropogenic nitrogen (N) emissions to atmosphere have increased dramatically in China since 1980s, and this increase has aroused great concerns on its ecological impacts on terrestrial ecosystems. Previous studies have showed that terrestrial ecosystems in China are acting as a large carbon (C) sink, but its potential in the future remains largely uncertain. So far little work on the impacts of the N deposition on C sequestration in China’s terrestrial ecosystems has been assessed at a national scale. Aiming to assess and predict how ecological processes especially the C cycling respond to the increasing N deposition in China’s forests, recently researchers from Peking University and their partners have established a manipulation experimental network on the ecological effects of the N deposition: Nutrient Enrichment Experiments in China’s Forests Project (NEECF). The NEECF comprises 10 experiments at 7 sites located from north to south China, covering major zonal forest vegetation in eastern China from boreal forest in Greater Khingan Mountains to tropical forests in Hainan Island. This paper introduces the framework of the NEECF project and its potential policy implications.

Description: Aims Nitrogen (N) addition could affect the rate of forest litter and soil organic matter decomposition by regulating extracellular enzyme activity (EEA). The impact of N addition on EEA may differ across different age stands with different organic matter quality. We were interested in whether the impact of N addition on EEA in litter and mineral soil during the growing season was dependent on stand age of a larch plantation in North China. Methods We added three levels of N (0, 20 and 50kg N ha –1 year –1 ) in three age stands (11, 20 and 45 years old) of Larix principis-rupprechtii plantation in North China. We measured potential activities of β-1,4-glucosidase (BG), cellobiohydrolase (CB), β-1,4-N-acetyl-glucosaminidase (NAG) and phenol oxidase (PO) in litter (organic horizon) and mineral soil (0–10cm) during the second growing season after N amendment. We also measured C and N concentrations, microbial biomass C and N, and KCl-extractable ammonium and nitrate in both litter and mineral soil. Important Findings We observed unimodal patterns of EEA during the growing season in all three stands, consistent with the seasonal variations of soil temperature. Stand age had a strong effect on EEA in both litter and mineral soil, and this effect differed between litter and mineral soil as well as between different enzymes. N addition did not significantly affect the activities of BG or CB but significantly suppressed the activity of NAG in litter. We also found stand age-specific responses of PO activity to N addition in both litter and mineral soil. N addition suppressed PO activity of the high C:N ratio litters in 20- and 45-year-old stands but had no significant effect on PO activity of the low C:N ratio litter in 11-year-old stand. Moreover, N addition inhibited PO activity of the high C:N ratio soil in 20-year-old stand but had no significant impact on PO activity of the low C:N ratio soils in 11- and 45-year-old stands. Overall, stand age had a greater effect on EEA in litter and mineral soil compared to 2 years of N addition. Moreover, the effect of N addition on PO activity is stand age dependent, which may affect the long-term soil carbon storage in this forest.

Description: miRNAs play important roles in many biological processes, including erythropoiesis. Although several miRNAs regulate erythroid differentiation, how the key erythroid regulator, GATA-1, directly orchestrates differentiation through miRNA pathways remains unclear. In this study, we identified miR-23a as a key regulator of erythropoiesis, which was upregulated both during erythroid differentiation and in GATA-1 gain-of-function experiments, as determined by miRNA expression profile analysis. In primary human CD34+ hematopoietic progenitor cells, miR-23a increased in a GATA-1-dependent manner during erythroid differentiation. Gain- or loss-of-function analysis of miR-23a in mice or zebrafish demonstrated that it was essential for normal morphology in terminally differentiated erythroid cells. Furthermore, a protein tyrosine phosphatase, SHP2, was identified as a downstream target of miR-23a that mediated its regulation of erythropoiesis. Taken together, our data identify a key GATA-1–miRNA axis in erythroid differentiation.