[show abstract][hide abstract] ABSTRACT: To identify the mechanisms controlling chronic myeloid leukemia (CML) and acute myeloid leukemia (AML) in humans, we analyzed genome-wide transcription dynamics in three myeloid leukemia cell lines (K562, HL-60, and THP1) using high-throughput sequencing technology. Using KEGG analysis, we found that the ERK/MAPK, JAK-STAT and ErbB pathways promoted proliferation and metabolism in CML. However, in AML, differentiation and apoptosis blocking resulted in the accumulation of blast cells in marrow. In addition, each cell type had unique characteristics. K562 cells are an ideal model for studying erythroid differentiation and globin gene expression. The chemokine signaling pathway and Fc gamma R-mediated phagocytosis were markedly upregulated in HL-60 cells. In THP1 cells, highly expressed genes ensured strong phagocytosis by monocytes. Further, we provide a new insight into myeloid development. The abundant data sets and well-defined analysis methods will provide a resource and strategy for further investigation of myeloid leukemia.
[show abstract][hide abstract] ABSTRACT: In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species
was determined to be Enteromorpha prolifera (Ulva prolifera O. F. Müller), a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating
U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the
thalli of U. prolifera and acquired 10 072 high-quality expressed sequence tags (ESTs). These ESTs were assembled into 3 519 nonredundant gene groups,
including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to
be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis
and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive
carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed
that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of
cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum (Ulvophyceae).
Chinese Journal of Oceanology and Limnology 04/2012; 28(1):26-36. · 0.58 Impact Factor
[show abstract][hide abstract] ABSTRACT: We acquired more than 4 million useful sequences using a high-throughput method from a library for miRNA identification, which is constructed from a mixture of 14 RNA samples from different developmental stages. We mapped 247,410 reads to known silkworm miRNAs in miRBase (13.0), 701,913 reads to other RNA molecules based on sequence homology, and 3,219,395 reads to the silkworm genome. Our analysis identified 54 silkworm known miRNAs. A striking strand bias between miRNAs and their corresponding miRNA*s was found, and was speculated to reflect that transcripts from the passenger strand of pre-miRNAs may have important biological roles. Using an elaborate screening protocol, we predicted 287 candidate novel miRNAs (represent 116,494 short reads), and 59 of them have both miRNA and miRNA* sequences. Most of the previously identified silkworm miRNAs are cross-species conserved with a high abundance, while those predicted candidates tend to be species-specific miRNAs. Our discovery of SNPs among miRNAs implied within-species functional diversity. Target prediction uncovers that considerable silkworm miRNAs may aim at modulating more than one hormone signaling pathway components and/or hormone biosynthesis-related proteins implying their important roles in silkworm development.