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Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF

Background Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies. Results The 2,739,625 base pair chromosome of OG1RF was found to contain approximately 232 kilobases unique to this strain compared to V583, the only publicly available...

Evaluation of safety and efficacy of gefitinib ('iressa', zd1839) as monotherapy in a series of Chinese patients with advanced non-small-cell lung cancer: experience from a compassionate-use programme

Background The gefitinib compassionate-use programme has enabled >39,000 patients worldwide to receive gefitinib ('Iressa', ZD1839) treatment. This paper reports the outcome of gefitinib treatment in Chinese patients who enrolled into the 'Iressa' Expanded Access Programme (EAP) at the Peking Union Medical College Hospital. Methods Thirty-one patients with advanced or metastatic...

Protein Kinase Cδ Stimulates Proteasome-Dependent Degradation of C/EBPα during Apoptosis Induction of Leukemic Cells

Background The precise regulation and maintenance of balance between cell proliferation, differentiation and death in metazoan are critical for tissue homeostasis. CCAAT/enhancer-binding protein alpha (C/EBPα) has been implicated as a key regulator of differentiation and proliferation in various cell types. Here we investigated the potential dynamic change and role of C/EBP...

The central role of EED in the orchestration of polycomb group complexes

journals • PubMed • Google ScholarSearch for Xiaoju Wang in:Nature Research journals • PubMed • Google ScholarSearch for Meng Zhao in:Nature Research journals • PubMed • Google ScholarSearch for Rendong Yang

Aquaporin3 Is Required for FGF-2-Induced Migration of Human Breast Cancers

Purpose The aquaporin (AQP) family consists of a number of small integral membrane proteins that transport water and glycerol. AQPs are critical for trans-epithelial fluid transport. Recent reports demonstrated that AQPs, particularly AQP1 and AQP5, are expressed in high grade tumor cells of a variety of tissue origins, and that AQPs are involved in cell migration and metastasis...

Screening for Differentially Expressed Proteins Relevant to the Differential Diagnosis of Sarcoidosis and Tuberculosis

Background In this study, we sought to identify differentially expressed proteins in the serum of patients with sarcoidosis or tuberculosis and to evaluate these proteins as markers for the differential diagnosis of sarcoidosis and sputum-negative tuberculosis. Methods Using protein microarrays, we identified 3 proteins exhibiting differential expression between patients with...

Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature

Background Antigen-antibody interactions are key events in immune system, which provide important clues to the immune processes and responses. In Antigen-antibody interactions, the specific sites on the antigens that are directly bound by the B-cell produced antibodies are well known as B-cell epitopes. The identification of epitopes is a hot topic in bioinformatics because of...

Cloning and Characterization of Maize miRNAs Involved in Responses to Nitrogen Deficiency

Although recent studies indicated that miRNAs regulate plant adaptive responses to nutrient deprivation, the functional significance of miRNAs in adaptive responses to nitrogen (N) limitation remains to be explored. To elucidate the molecular biology underlying N sensing/signaling in maize, we constructed four small RNA libraries and one degradome from maize seedlings exposed to...

LlSR28 Is Involved in Pollen Germination by Affecting Filamentous Actin Dynamics

Alternative splicing plays important roles in gene regulation and contributes to protein complexity. Previous studies suggest that alternative splicing exists in members of the villin/gelsolin/fragmin superfamily. In this study, a serine/argine-rich (SR) protein cDNA with 28kDa protein (LlSR28) was isolated from a lily (Lilium longiflorum) expression library. Protein domain...

A semantic proteomics dashboard (SemPoD) for data management in translational research

Background One of the primary challenges in translational research data management is breaking down the barriers between the multiple data silos and the integration of 'omics data with clinical information to complete the cycle from the bench to the bedside. The role of contextual metadata, also called provenance information, is a key factor ineffective data integration...

Computational Prediction of Conformational B-Cell Epitopes from Antigen Primary Structures by Ensemble Learning

Motivation The conformational B-cell epitopes are the specific sites on the antigens that have immune functions. The identification of conformational B-cell epitopes is of great importance to immunologists for facilitating the design of peptide-based vaccines. As an attempt to narrow the search for experimental validation, various computational models have been developed for the...

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo. However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on...

Regulation of OsmiR156h through Alternative Polyadenylation Improves Grain Yield in Rice

Substantial increases in grain yield of cereal crops are required to feed a growing human population. Here we show that a natural variant of SEMIDWARF AND HIGH-TILLERING (SDT) increases harvest index and grain productivity in rice. Gain-of-function sdt mutation has a shortened polyadenylation tail on the OsmiR156h microRNA precursor, which cause the up-regulation of OsmiR156h...

RA-XII inhibits tumour growth and metastasis in breast tumour-bearing mice via reducing cell adhesion and invasion and promoting matrix degradation

information Author notesHoi-Wing Leung & Si-Meng Zhao These authors contributed equally to this work. AffiliationsInstitute of Chinese MedicineHoi-Wing Leung, Grace Gar-Lee Yue, Julia Kin-Ming Lee, Kwok-Pui ... Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaSi-Meng Zhao & Ning-Hua TanUniversity of Chinese Academy of Sciences, Beijing 100049, ChinaSi

Phylogenetic assessment of Chaetomium indicum and allied species, with the introduction of three new species and epitypification of C. funicola and C. indicum

Xue-Wei Wang Xiao-Liang Wang Fu-Jiang Liu Xiao-Meng Zhao Jing Li Lei Cai Historically, the Chaetomium indicum group contained six species with similar ascus and ascospore morphology. Large

Identification and characterization of phosphodiesterases that specifically degrade 3′3′-cyclic GMP-AMP

Cyclic dinucleotides act as intracellular second messengers, modulating a variety of cellular activities including innate immune activation. Although phosphodiesterases (PDEs) hydrolyzing c-di-GMP and c-di-AMP have been identified, no PDEs for cGAMPs have been reported. Here we identified the first three cGAMP-specific PDEs in V. cholerae (herein designated as V-cGAP1/2/3). V...

Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin–focal adhesion kinase signal transduction

Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin–focal adhesion kinase signal transduction Yu-ting Huang,1,* Lan Zhao,1,* Zheng Fu,1 Meng Zhao,1

Enantioselective Hydrolysis of Amino Acid Esters Promoted by Bis(β-cyclodextrin) Copper Complexes

-Shan Xue, Meng Zhao, Zhuo-Feng Ke, Bei-Chen Cheng, Hua Su, Qian Cao, Zhen-Kun Cao, Jun Wang, Liang-Nian Ji & Zong-Wan Mao AuthorsSearch for Shan-Shan Xue in:Nature Research journals • PubMed • Google ... ScholarSearch for Meng Zhao in:Nature Research journals • PubMed • Google ScholarSearch for Zhuo-Feng Ke in:Nature Research journals • PubMed • Google ScholarSearch for Bei-Chen Cheng in:Nature Research journals