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Search Results: 1 - 10 of 27508 matches for " Jinnan Hu "
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A distribution pattern assisted method of transcription factor binding site discovery for both yeast and filamentous fungi  [PDF]
Jinnan Hu, Chenxi Chen, Kun Huang, Thomas K. Mitchell
Advances in Bioscience and Biotechnology (ABB) , 2013, DOI: 10.4236/abb.2013.44067
Abstract: Transcription factors (TFs) are the core sentinels of gene regulation functioning by binding to highly specific DNA sequences to activate or repress the recruitment of RNA polymerase. The ability to identify transcription factor binding sites (TFBSs) is necessary to understand gene regulation and infer regulatory networks. Despite the fact that bioinformatics tools have been developed for years to improve computational identification of TFBSs, the accurate prediction still remains changeling as DNA motifs recognized by TFs are typically short and often lack obvious patterns. In this study we introduced a new attribute-motif distribution pattern (MDP) to assist in TFBS prediction. MDP was developed using a TF distribution pattern curve generated by analyzing 25 yeast TFs and 37 of their experimentally validated binding motifs, followed by calculating a scoring value to quantify the reliability of each motif prediction. Finally, MDP was tested using another set of 7 TFs with known binding sites to in silico validate the approach. The method was further tested in a non-yeast system using the filamentous fungus Magnaporthe oryzae transcription factor MoCRZ1. We demonstrate superior prediction reranking results using MDP over the commonly used program MEME and the other four predictors. The data showed significant improvements in the ranking of validated TFBS and provides a more sensitive statistics based approach for motif discovery.
On Design Inspiration for the Seismic Visitor Center Survey  [PDF]
Jinnan Hu, Ke Jia, Ying Zhang
Open Access Library Journal (OALib Journal) , 2019, DOI: 10.4236/oalib.1105021
The Tangshan earthquake has passed for more than 40 years, but the painful memories still remain in the heart of the Tangshan people, while staying in the ruins that best reflect the current status of the earthquake—National Library of Protection Works “Library Seismic Site” of Xinhua Road Campus, North China University of Science and Technology. In order to bear the heavy pains of the Tangshan people, through the curriculum design of North China University of Technology, an “earthquake-relic site visitor center” was planned. The author conducted preliminary investigations on the Tangshan Earthquake Relics Park and the Tangshan Hero Monument: How the construction and the site environment were integrated and how the earthquake occurred. There is a certain amount of inspiration for how the commemorative nature of the dialogue took place.
Generation and characterization of a recombinant Newcastle disease virus expressing the red fluorescent protein for use in co-infection studies
Li Jinnan,Hu Haixia,Yu Qingzhong,Diel Diego G
Virology Journal , 2012, DOI: 10.1186/1743-422x-9-227
Abstract: Background Many viruses have evolved multiple strategies to prevent super infection of host cells by more than one virion. This phenomenon, known as super infection exclusion, may play an important role on virus evolution because it can affect the frequency of reassortment and/or recombination. Newcastle disease virus (NDV), a negative sense single-stranded RNA virus, is characterized by its continuous evolutionary dynamics and by a low frequency of recombination events. However, the mechanisms that contribute to the low recombination rates on NDV are still not completely understood. Methods In this study we assessed the ability of two NDV strains (LaSota and B1) to super infect host cells in vitro. We generated a recombinant NDV strain LaSota expressing the red fluorescent protein (RFP) and used it in co-infection assays with a related NDV strain B1 expressing the green fluorescent protein (GFP). DF-1 cells were inoculated with both viruses at the same time or at different intervals between primary infection and super infection. Results When both viruses were inoculated at the same time point, a 27% co-infection rate was observed, whereas when they were inoculated at different time points the super infection rates decreased to levels as low as 1.4%. Conclusions These results indicate that although different NDV strains can co-infect host cells in vitro, the super infection rates are low, specially as the time between the primary infection and super infection increases. These results confirm the occurrence of super infection exclusion between different strains of NDV.
Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer
Jinnan Hu, Chenxi Chen, Tobin Peever, Ha Dang, Christopher Lawrence, Thomas Mitchell
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-171
Abstract: To gain a richer understanding of the molecular determinants of virulence and the evolution of pathogenicity, we performed whole genome sequencing of A. arborescens. Here we present the de-novo assembly of the CDC and its predicted gene content. Also presented is hybridization data validating the CDC assembly. Predicted genes were functionally annotated through BLAST. Gene ontology terms were assigned, and conserved domains were identified. Differences in nucleotide usage were found between CDC genes and those on the essential chromosome (EC), including GC3-content, codon usage bias, and repeat region load. Genes carrying PKS and NRPS domains were identified in clusters on the CDC and evidence supporting the origin of the CDC through horizontal transfer from an unrelated fungus was found.We provide evidence supporting the hypothesis that the CDC in A. arborescens was acquired through horizontal transfer, likely from an unrelated fungus. We also identified several predicted CDC genes under positive selection that may serve as candidate virulence factors.
Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus
Soonok Kim,Jinnan Hu,Yeonyee Oh,Jongsun Park,Jinhee Choi,Yong-Hwan Lee,Ralph A. Dean,Thomas K. Mitchell
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000909
Abstract: Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.
RNA-Seq Analysis of the Sclerotinia homoeocarpa – Creeping Bentgrass Pathosystem
Angela M. Orshinsky, Jinnan Hu, Stephen O. Opiyo, Venu Reddyvari-Channarayappa, Thomas K. Mitchell, Michael J. Boehm
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041150
Abstract: Sclerotinia homoeocarpa causes dollar spot disease, the predominate disease on highly-maintained turfgrass. Currently, there are major gaps in our understanding of the molecular interactions between S. homoeocarpa and creeping bentgrass. In this study, 454 sequencing technology was used in the de novo assembly of S. homoeocarpa and creeping bentgrass transcriptomes. Transcript sequence data obtained using Illumina's first generation sequencing-by-synthesis (SBS) were mapped to the transcriptome assemblies to estimate transcript representation in different SBS libraries. SBS libraries included a S. homoeocarpa culture control, a creeping bentgrass uninoculated control, and a library for creeping bentgrass inoculated with S. homoeocarpa and incubated for 96 h. A Fisher's exact test was performed to determine transcripts that were significantly different during creeping bentgrass infection with S. homoeocarpa. Fungal transcripts of interest included glycosyl hydrolases, proteases, and ABC transporters. Of particular interest were the large number of glycosyl hydrolase transcripts that target a wide range of plant cell wall compounds, corroborating the suggested wide host range and saprophytic abilities of S. homoeocarpa. Several of the multidrug resistance ABC transporters may be important for resistance to both fungicides and plant defense compounds. Creeping bentgrass transcripts of interest included germins, ubiquitin transcripts involved in proteasome degradation, and cinnamoyl reductase, which is involved in lignin production. This analysis provides an extensive overview of the S. homoeocarpa-turfgrass pathosystem and provides a starting point for the characterization of potential virulence factors and host defense responses. In particular, determination of important host defense responses may assist in the development of highly resistant creeping bentgrass varieties.
Advance in the study of the Lower Triassic conodonts at Meishan Section, Changxing, Zhejiang Province
Jinnan Tong,Ying Yang
Chinese Science Bulletin , 1998, DOI: 10.1007/BF02883680
Abstract: Meishan Section in Changxing County of Zhejiang Province is one of the four candidates of the global stratotype section and point (GSSP) of the Permian and Triassic boundary (PTB), and currently the conodonts have been widely accepted as the index fossils to define the Permian and Triassic boundary. The previous studies on the Lower Triassic conodonts at Meishan Section are summarized and the recent discovery of the Lower Triassic conodonts there is reported. The recognized data from the section indicate that Meishan is the best selection of the GSSP of PTB.
The conjugate prior for discrete hierarchical log-linear models
Jinnan Liu,Helene Massam
Mathematics , 2006,
Abstract: In the Bayesian analysis of contingency table data, the selection of a prior distribution for either the log-linear parameters or the cell probabilities parameter is a major challenge. Though the conjugate prior on cell probabilities has been defined by Dawid and Lauritzen (1993) for decomposable graphical models, it has not been identified for the larger class of graphical models Markov with respect to an arbitrary undirected graph or for the even wider class of hierarchical log-linear models. In this paper, working with the log-linear parameters used by GLIM, we first define the conjugate prior for these parameters and then derive the induced prior for the cell probabilities: this is done for the general class of hierarchical log-linear models. We show that the conjugate prior has all the properties that one expects from a prior: notational simplicity, ability to reflect either no prior knowledge or a priori expert knowledge, a moderate number of hyperparameters and mathematical convenience. It also has the strong hyper Markov property which allows for local updates within prime components for graphical models.
Stratigraphic succession of the Nanhuan Period in the Shennongjia area in western Hubei and its regional correlation.

GUAN Kaiping
,TIAN Li,AN Zhihui,YE Qin,HU Jun,TONG Jinnan

- , 2016, DOI: 10.13745/j.esf.2016.06.016
Abstract: 新元古代是地质历史时期气候变化最为剧烈的时期之一,在全球范围内留下了多次明显的冰川活动记录。以峡东地区为代表的鄂西地区新元古界是国际研究的经典和热点。然而,峡东地区新元古代地层序列并不完整,其毗邻的神农架西部地层序列更具代表性。位于鄂西神农架西部的高桥河剖面,其南华系超覆于中元古界神农架群基底之上,从下而上依次为莲沱组、古城组、大塘坡组和南沱组,上覆震旦系陡山沱组。通过与鄂西峡东地区、长阳地区的代表性剖面的区域地层对比,发现高桥河剖面的南华纪沉积地层序列最为连续,是鄂西地区新元古代最完整和最具代表性的地层序列之一,能够作为该区域新元古代地层划分和对比的参照标准,并为研究这一重大关键地质时期的极端古气候演变提供基础材料。
Application of Discrete Multicriteria Optimization Decision Model (DMODM) in EQDSS

Wang Jinnan,

环境科学 , 1992,
Abstract: DMODM is a model that can solve a sort of decisive optimization problems which are formed by discrete values of a number of decisive variables and have multicriteria for assessment of alternatives. This essay briefly describes the principle, solving methods-dominated approximation method and reference point approach of the model, as well as its application and effect in the National Environmental Quality Decision Support System (NEQDSS).
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