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Search Results: 1 - 10 of 34413 matches for " Zuhong Lu "
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The Fate of miRNA* Strand through Evolutionary Analysis: Implication for Degradation As Merely Carrier Strand or Potential Regulatory Molecule?
Li Guo,Zuhong Lu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011387
Abstract: During typical microRNA (miRNA) biogenesis, one strand of a ~22 nt RNA duplex is preferentially selected for entry into a silencing complex, whereas the other strand, known as the passenger strand or miRNA* strand, is degraded. Recently, some miRNA* sequences were reported as guide miRNAs with abundant expression. Here, we intended to discover evolutionary implication of the fate of miRNA* strand by analyzing miRNA/miRNA* sequences across vertebrates.
Mini-clusters with mean probabilities for identifying effective siRNAs
Jia Xingang, Zuhong Lu, Qiuhong Han
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-512
Abstract: Here, we try to split effective and ineffective siRNAs into many smaller subclasses by RMP-MiC(the relative mean probabilities of siRNAs with the mini-clusters algorithm). The relative mean probabilities of siRNAs are the modified arithmetic mean value of three probabilities, which come from three Markov chain of effective siRNAs. The mini-clusters algorithm is a modified version of micro-cluster algorithm.When the RMP-MiC was applied to the experimental siRNAs, the result shows that all effective siRNAs can be identified correctly, and no more than 9% ineffective siRNAs are misidentified as effective ones. We observed that the efficiency of those misidentified ineffective siRNAs exceed 70%, which is very closed to the used efficiency threshold. From the analysis of the siRNAs data, we suggest that the mini-clusters algorithm with relative mean probabilities can provide new insights to the applications for distinguishing effective siRNAs from ineffective ones.RNA interference (RNAi) is a cellular process for sequence specific destruction of mRNA [1]. The broad mechanistic details for the pathway have been largely characterized. Long double-stranded RNAs duplex or hairpin precursors are cleaved into small interfering RNAs (siRNAs) by the ribonuclease III enzyme Dicer. The typical siRNAs have a 19-nucleotide paired region followed by a 2-nucleotide 3’ overhang [2]. The siRNAs are used to initiate RNAi [3-6]. Therefore, the distinguishing the effective siRNAs from the ineffective ones is in high demand for gene knockout technology. In order to design effective siRNAs, many computational approaches have been proposed [7-20]. Some approaches focus on finding the common features of effective siRNAs, though they initially and intuitively provide guidelines for siRNAs design, are far from satisfied due to low sensitivity and specificity [8,18]. The other approaches are motivated by statistical learning theory, attempt to classify the siRNAs into effective and ineffective cl
Simulation of ChIP-Seq based on extra-sonication of IPed DNA fragments
Wei Wang,XiaoLong Shi,ZuHong Lu
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-010-3013-y
Abstract: The combination of chromatin immunoprecipitation with sequencing (ChIP-Seq) is an effective method for obtaining an in vivo genome-wide profile of the interaction of a protein with DNA. With the dramatic development of high-throughput short sequencing technologies, several new algorithms have been developed to process ChIP-Seq. However, the reported analytical tools for ChIP-Seq based on size selection of immunoprecipitated (IPed) DNA fragments are mainly adopted on the Solexa system. As a sequencer with the highest throughput, few studies of ChIP-Seq based on SOLiD system have been reported. The main difference of the SOLiD and Solexa systems exists in the length of DNA fragments during preparing sequencing libraries. The SOLiD system has relatively short DNA fragments if it processes a further sonication of IPed DNA fragments in order to meet the length requirement of DNA fragments for emulsion-PCR (ePCR). This work aims to investigate the influences of DNA fragment length on data analysis from ChIP-Seq. Previous studies show that typical bimodal peaks can be observed in Solexa ChIP-Seq data, but based on the analysis of the real SOLiD ChIP-Seq data in this study, we found that there were no double peaks with apparent reads shift in a local enriched region and the local reads distribution of peaks were tested by normal distribution. Using real and simulated ChIP-Seq data, three main ChIP-Seq algorithms (CisGenome, SISSRs and MACS) have been investigated. We found that algorithms developed for processing ChIP-Seq data generated from Solexa library protocol, cannot efficiently capture the feature of the ChIP-Seq data from SOLiD library. Misuse of those analytical tools would be a possible reason for failure of ChIP-Seq on the SOLiD system. Therefore, a new ChIP-Seq analytical strategy for an extra-sonication of IPed DNA fragments needs to be developed.
An all solid-state electrochromic smart window
Su Lianyong,Lu Zuhong,Wei Yu
Chinese Science Bulletin , 1998, DOI: 10.1007/BF02884619
Abstract: An all solid-state electrochromic smart window employing prussian blue and electrodeposited WO3 film with poly (vinyl chloride) (PVC) gel electrolyte that has high conductivity (2 mS/cm) at room temperature has been fabricated for the first time. The smart window has beell found to be excellent for electrochromism and memory characteristics.
An all solid-state electrochromic smart window

Su Lianyong,Lu Zuhong,Wei Yu,

科学通报(英文版) , 1998,
Abstract: An all solid-state electrochromic smart window employing prussian blue and electrodeposited WO3 film with poly (vinyl chloride) (PVC) gel electrolyte that has high conductivity (2 mS/cm) at room temperature has been fabricated for the first time. The smart window has beell found to be excellent for electrochromism and memory characteristics.
Single-trial EEG-based emotion recognition usingtemporally regularized common spatial pattern
Cheng Minmin, Lu Zuhong, Wang Haixian
- , 2015, DOI: 10.3969/j.issn.1003-7985.2015.01.010
Abstract: This study addresses the problem of classifying emotional words based on recorded electroencephalogram(EEG)signals by the single-trial EEG classification technique. Emotional two-character Chinese words are used as experimental materials. Positive words versus neutral words and negative words versus neutral words are classified, respectively, using the induced EEG signals. The method of temporally regularized common spatial patterns(TRCSP)is chosen to extract features from the EEG trials, and then single-trial EEG classification is achieved by linear discriminant analysis. Classification accuracies are between 55% and 65%. The statistical significance of the classification accuracies is confirmed by permutation tests, which shows the successful identification of emotional words and neutral ones, and also the ability to identify emotional words. In addition, 10 out of 15 subjects obtain significant classification accuracy for negative words versus neutral words while only 4 are significant for positive words versus neutral words, which demonstrate that negative emotions are more easily identified.
Aberrant microRNA expression in the development of breast carcinoma
Qian Wu,HaiLing Li,JiaFeng Lu,QingYu Ge,ZuHong Lu
Chinese Science Bulletin , 2010, DOI: 10.1007/s11434-010-4022-6
Abstract: microRNAs, a class of small non-coding regulatory RNAs, are involved in oncogenesis and cancer development. Studies have shown that aberrant miRNA expression occurs in breast cancer and is associated with specific clinicopathological features. Some miRNAs might act as suppressor genes or oncogenes, which can be considered as novel markers for breast cancer diagnosis and as prognostic factors. Here we present a review of recent discoveries on miRNAs involved in breast cancer tumorigenesis, invasion, and metastasis.
Haplotype Distribution and Evolutionary Pattern of miR-17 and miR-124 Families Based on Population Analysis
Li Guo,Beili Sun,Fei Sang,Wei Wang,Zuhong Lu
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007944
Abstract: MicroRNAs (miRNAs) are small, endogenously expressed non-coding RNAs that regulate mRNAs post-transcriptionally. Previous studies have explored miRNA evolutionary trend, but evolutionary history and pattern in the miRNA world are still not fully clear. In the paper, we intended to analyze miRNA haplotype distribution and evolutionary network by analyzing miRNA sequences of miR-17 and miR-124 families across animal species as special populations.
Fabrication of Unimolecular Double-stranded DNA Microarrays on Solid Surfaces for Probing DNA-Protein/Drug Interactions
Jinke Wang,Tongxiang Li,Yunfei Bai,Yi Zhu,Zuhong Lu
Molecules , 2003, DOI: 10.3390/80100153
Abstract: We present a novel method for fabricating unimole cular double-stranded DNA microarrays on solid surfaces, which were used to probe sequence-specific DNA/protein interactions. For manufacturing the unimolecular double-stranded DNA microarrays, two kinds of special single-stranded oligonucleotides, constant oligonucleotide and target oligonucleotide, were chemically synthesized. The constant oligonucleotides with internal aminated dT were used to capture and immobilize the target oligonucleotides onto the solid surface, and also to provide a primer for later enzymatic extension reactions, while target oligonucleotides took the role of harbouring DNA-binding sites of DNA-binding proteins. The variant target oligonucleotides were annealed and ligated with the constant oligonucleotides to form the new unimolecular oligonucleotides for microspotting. The prepared unimolecular oligonucleotides were microspotted on aldehyde-derivatized glass slides to make partial-dsDNA microarrays. Finally, the partial-dsDNA microarrays were converted into a unimolecular complete-dsDNA microarray by a DNA polymerase extension reaction. The efficiency and accuracy of the polymerase synthesis were demonstrated by the fluorescent-labeled dUTP incorporation in the enzymatic extension reaction and the restriction endonuclease digestion of the fabricated unimolecular complete-dsDNA microarray. The accessibility and specificity of the sequence-specific DNA-binding proteins binding to the immobilized unimolecular dsDNA probes were demonstrated by the binding of Cy3 labeled NF-?B (p50·p50) to the unimolecular dsDNA microarray. This unimolecular dsDNA microarray provides a general technique for high-throughput DNA-protein or DNA-drugs interactions.
An Emulsion System Based on a Chip Polymerase Chain Reaction
Qinyu Ge,Pinfei Yu,Yunfei Bai,Zuhong Lu
Molecules , 2008, DOI: 10.3390/molecules13123057
Abstract: In this paper we describe a novel method for detecting many DNA fragments through efficient amplification by using an emulsion system based on “on-chip” PCR instead of conventional multiplex polymerase chain reaction (PCR). During the preparation of on-chip PCR, a set of primers were immobilized on a slide and other sets were in an emulsion system. Different emulsion phase primers and other related PCR components were dispersed in different droplets of the emulsion system, and then, due to the thermal instability of emulsion droplets, they would be released onto the surface of the slide after preheating in the first PCR step. To test the above method, we used plasma DNAs from pregnant women who was carrying a male fetus for gender identification. Four different Y chromosome DNA fragments were selected. Results showed that different DNA fragments could be simultaneously amplified with satisfactory results. It is suggested that a simple, convenient and inexpensive on-chip PCR method has been developed.
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