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Jinbiao Ma

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https://www.readbyqxmd.com/read/28317870/structural-and-functional-studies-of-a-noncanonical-dicer-from-entamoeba-histolytica
#1
Xiang Yu, Xuhang Li, Lina Zheng, Jinbiao Ma, Jianhua Gan
RNaseIII proteins are dsRNA-specific endonucleases involved in many important biological processes, such as small RNA processing and maturation in eukaryotes. Various small RNAs have been identified in a protozoan parasite Entamoeba histolytica. EhRNaseIII is the only RNaseIII endonuclease domain (RIIID)-containing protein in E. histolytica. Here, we present three crystal structures that reveal several unique structural features of EhRNaseIII, especially the interactions between the two helixes (α1 and α7) flanking the RIIID core domain...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28245220/unique-5-p-recognition-and-basis-for-dg-dgtp-misincorporation-of-asfv-dna-polymerase-x
#2
Yiqing Chen, Jing Zhang, Hehua Liu, Yanqing Gao, Xuhang Li, Lina Zheng, Ruixue Cui, Qingqing Yao, Liang Rong, Jixi Li, Zhen Huang, Jinbiao Ma, Jianhua Gan
African swine fever virus (ASFV) can cause highly lethal disease in pigs and is becoming a global threat. ASFV DNA Polymerase X (AsfvPolX) is the most distinctive DNA polymerase identified to date; it lacks two DNA-binding domains (the thumb domain and 8-KD domain) conserved in the homologous proteins. AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the ASFV virus genome; it is highly error prone and plays an important role during the strategic mutagenesis of the viral genome. The structural basis underlying the natural substrate binding and the most frequent dG:dGTP misincorporation of AsfvPolX remain poorly understood...
February 2017: PLoS Biology
https://www.readbyqxmd.com/read/28231321/argonaute10-promotes-the-degradation-of-mir165-6-through-the-sdn1-and-sdn2-exonucleases-in-arabidopsis
#3
Yu Yu, Lijuan Ji, Brandon H Le, Jixian Zhai, Jiayi Chen, Elizabeth Luscher, Lei Gao, Chunyan Liu, Xiaofeng Cao, Beixin Mo, Jinbiao Ma, Blake C Meyers, Xuemei Chen
The degradation of small RNAs in plants and animals is associated with small RNA 3' truncation and 3' uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1...
February 2017: PLoS Biology
https://www.readbyqxmd.com/read/28138017/the-histone-chaperone-nrp1-interacts-with-werewolf-to-activate-glabra2-in-arabidopsis-root-hair-development
#4
Yan Zhu, Liang Rong, Qiang Luo, Baihui Wang, Nana Zhou, Yue Yang, Chi Zhang, Haiyang Feng, Lina Zheng, Wen-Hui Shen, Jinbiao Ma, Aiwu Dong
Nucleosome Assembly Protein 1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss-of-function of the Arabidopsis thaliana NAP1-family genes NAP1-RELATED PROTEIN 1 (NRP1) and NRP2 causes abnormal root hair formation. Yet, the underlying molecular mechanisms remain unclear. Here, we show that NRP1 interacts with the transcription factor WEREWOLF (WER) in vitro and in vivo and enriches at the GLABRA2 (GL2) promoter in a WER-dependent manner. Crystallographic analysis indicates that NRP1 forms a dimer via its N-terminal α-helix...
January 30, 2017: Plant Cell
https://www.readbyqxmd.com/read/27998930/flexibility-and-stabilization-of-hgii-mediated-c-t-and-t-t-base-pairs-in-dna-duplex
#5
Hehua Liu, Chen Cai, Phensinee Haruehanroengra, Qingqing Yao, Yiqing Chen, Chun Yang, Qiang Luo, Baixing Wu, Jixi Li, Jinbiao Ma, Jia Sheng, Jianhua Gan
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing Hg(II)-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-Hg(II)-T containing duplex, three T-Hg(II)-T containing duplexes and one native duplex containing T-T pair without Hg(II) Our structures suggest that both C-T and T-T pairs are flexible in interacting with the Hg(II) ion with various binding modes including N3-Hg(II)-N3, N4-Hg(II)-N3, O2-Hg(II)-N3 and N3-Hg(II)-O4...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27877862/an-ir-iii-complex-chemosensor-for-the-detection-of-thiols
#6
Zhifeng Mao, Jinbiao Liu, Tian-Shu Kang, Wanhe Wang, Quan-Bin Han, Chun-Ming Wang, Chung-Hang Leung, Dik-Lung Ma
In this study, we report the use of a cyclometalated luminescent iridium(III) complex for the visualization of thiols. The detection of glutathione (GSH) by complex 1 is achieved through the reduction of its phendione N^N donor, which influences the metal-to-ligand charge-transfer (MLCT) of the complex. Complex 1 produced a maximum threefold luminescence enhancement at 587 nm in response to GSH. The linear detection range of 1 for GSH is between 0.2 and 2 M equivalents of GSH, with a detection limit of 1.67 μM...
2016: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27708644/comparative-analysis-of-immune-activation-markers-of-cd8-t-cells-in-lymph-nodes-of-different-origins-in-siv-infected-chinese-rhesus-macaques
#7
Jinbiao Liu, Qianhao Xiao, Runhong Zhou, Yong Wang, Qiaoyang Xian, Tongcui Ma, Ke Zhuang, Li Zhou, Deyin Guo, Xu Wang, Wen-Zhe Ho, Jieliang Li
Altered T-cell homeostasis, such as expansion of CD8(+) T cells to the secondary lymphatic compartments, has been suggested as a mechanism of HIV/simian immunodeficiency virus (SIV)-pathogenesis. However, the role of immune activation of CD8(+) T cells in the CD4/CD8 turnover and viral replication in these tissues is not completely understood. In this study, we compared the expression of immune activation markers (CD69 and HLA-DR) on CD8(+) T cells in the peripheral blood and lymph nodes (LNs) of SIV-infected/uninfected Chinese rhesus macaques...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27596600/structural-basis-for-single-stranded-rna-recognition-and-cleavage-by-c3po
#8
Jing Zhang, Hehua Liu, Qingqing Yao, Xiang Yu, Yiqing Chen, Ruixue Cui, Baixing Wu, Lina Zheng, Junjun Zuo, Zhen Huang, Jinbiao Ma, Jianhua Gan
Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced silencing complex, the effector complex of RNA interference (RNAi). Here, we report three crystal structures of Nanoarchaeum equitans (Ne) C3PO. The apo-NeC3PO structure adopts an open form and unravels a potential substrates entryway for the first time...
September 4, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27558897/ythdf2-destabilizes-m-6-a-containing-rna-through-direct-recruitment-of-the-ccr4-not-deadenylase-complex
#9
Hao Du, Ya Zhao, Jinqiu He, Yao Zhang, Hairui Xi, Mofang Liu, Jinbiao Ma, Ligang Wu
Methylation at the N6 position of adenosine (m(6)A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions. YT521-B homology domain family (YTHDF) proteins are the readers of m(6)A, the binding of which results in the alteration of the translation efficiency and stability of m(6)A-containing RNAs. However, the mechanism by which YTHDF proteins cause the degradation of m(6)A-containing RNAs is poorly understood...
August 25, 2016: Nature Communications
https://www.readbyqxmd.com/read/27424263/ultrasensitive-electrochemical-detection-of-mirna-21-by-using-an-iridium-iii-complex-as-catalyst
#10
Xiangmin Miao, Wanhe Wang, Tianshu Kang, Jinbiao Liu, Kwok-Keung Shiu, Chung-Hang Leung, Dik-Lung Ma
The ultrasensitive electrochemical detection of miRNA-21 was realized by using a novel redox and catalytic "all-in-one" mechanism with an iridium(III) complex as a catalyst. To construct such a sensor, a capture probe (CP) was firstly immobilized onto the gold electrode surface. In the presence of miRNA-21, a sandwiched DNA complex could form between CP and a methylene blue (MB) labeled G-rich detection probe modified onto a gold nanoparticle (AuNP) surface (DP-AuNPs). Upon addition of K(+), the structure of DP changed to a G-quadruplex...
December 15, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27119725/structural-and-molecular-mechanism-of-cdpr-involved-in-quorum-sensing-and-bacterial-virulence-in-pseudomonas-aeruginosa
#11
Jingru Zhao, Xiang Yu, Miao Zhu, Huaping Kang, Jinbiao Ma, Min Wu, Jianhua Gan, Xin Deng, Haihua Liang
Although quorum-sensing (QS) systems are important regulators of virulence gene expression in the opportunistic human pathogen Pseudomonas aeruginosa, their detailed regulatory mechanisms have not been fully characterized. Here, we show that deletion of PA2588 resulted in increased production of pyocyanin and biofilm, as well as enhanced pathogenicity in a mouse model. To gain insights into the function of PA2588, we performed a ChIP-seq assay and identified 28 targets of PA2588, including the intergenic region between PA2588 and pqsH, which encodes the key synthase of Pseudomonas quinolone signal (PQS)...
April 2016: PLoS Biology
https://www.readbyqxmd.com/read/27111035/ref6-recognizes-a-specific-dna-sequence-to-demethylate-h3k27me3-and-regulate-organ-boundary-formation-in-arabidopsis
#12
Xia Cui, Falong Lu, Qi Qiu, Bing Zhou, Lianfeng Gu, Shuaibin Zhang, Yanyuan Kang, Xiekui Cui, Xuan Ma, Qingqing Yao, Jinbiao Ma, Xiaoyu Zhang, Xiaofeng Cao
RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb-mediated gene silencing by removing methyl groups from trimethylated histone H3 lysine 27 (H3K27me3) in hundreds of genes in Arabidopsis thaliana. Here we show that REF6 function and genome-wide targeting require its four Cys2His2 zinc fingers, which directly recognize a CTCTGYTY motif. Motifs bound by REF6 tend to cluster and reside in loci with active chromatin states. Furthermore, REF6 targets CUP-SHAPED COTYLEDON 1 (CUC1), which harbors CTCTGYTY motifs, to modulate H3K27me3 levels and activate CUC1 expression...
June 2016: Nature Genetics
https://www.readbyqxmd.com/read/26899271/a-long-lifetime-switch-on-iridium-iii-chemosensor-for-the-visualization-of-cysteine-in-live-zebrafish
#13
Zhifeng Mao, Modi Wang, Jinbiao Liu, Li-Juan Liu, Simon Ming-Yuen Lee, Chung-Hang Leung, Dik-Lung Ma
A long lifetime iridium(III) complex chemosensor 1 for cysteine detection has been synthesized. The luminescence signal of 1 could be recognized in strongly fluorescent media through time-resolved emission spectroscopy (TRES). The detection of cysteine in a living zebrafish was demonstrated.
March 25, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/26528307/a-method-for-the-further-assembly-of-targeted-unigenes-in-a-transcriptome-after-assembly-by-trinity
#14
Xinlong Xiao, Jinbiao Ma, Yufang Sun, Yinan Yao
RNA-sequencing has been widely used to obtain high throughput transcriptome sequences in various species, but the assembly of a full set of complete transcripts is still a significant challenge. Judging by the number of expected transcripts and assembled unigenes in a transcriptome library, we believe that some unigenes could be reassembled. In this study, using the nitrate transporter (NRT) gene family and phosphate transporter (PHT) gene family in Salicornia europaea as examples, we introduced an approach to further assemble unigenes found in transcriptome libraries which had been previously generated by Trinity...
2015: Frontiers in Plant Science
https://www.readbyqxmd.com/read/26472911/panoramix-enforces-pirna-dependent-cotranscriptional-silencing
#15
Yang Yu, Jiaqi Gu, Ying Jin, Yicheng Luo, Jonathan B Preall, Jinbiao Ma, Benjamin Czech, Gregory J Hannon
The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. Here we show that the CG9754 protein is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. Enforced tethering of CG9754 to nascent messenger RNA transcripts causes cotranscriptional silencing of the source locus and the deposition of repressive chromatin marks...
October 16, 2015: Science
https://www.readbyqxmd.com/read/26378374/double-balanced-graphene-integrated-mixer-with-outstanding-linearity
#16
Hongming Lyu, Huaqiang Wu, Jinbiao Liu, Qi Lu, Jinyu Zhang, Xiaoming Wu, Junfeng Li, Teng Ma, Jiebin Niu, Wencai Ren, Huiming Cheng, Zhiping Yu, He Qian
A monolithic double-balanced graphene mixer integrated circuit (IC) has been successfully designed and fabricated. The IC adopted the cross-coupled resistive mixer topology, integrating four 500 nm-gate-length graphene field-effect transistors (GFETs), four on-chip inductors, and four on-chip capacitors. Passive-first-active-last fabrication flow was developed on 200 mm CMOS wafers. CMOS back-end-of-line processes were utilized to realize most fabrication steps followed by GFET-customized processes. Test results show excellent output spectrum purity with suppressed radio frequency (RF) and local oscillation (LO) signals feedthroughs, and third-order input intercept (IIP3) reaches as high as 21 dBm...
October 14, 2015: Nano Letters
https://www.readbyqxmd.com/read/25985527/-assembling-of-an-ammonium-transporter-gene-in-salicornia-europaea-by-expression-pattern-analysis-of-unigene-in-transcriptome
#17
Xinlong Xiao, Xuan Zhang, Xiaomeng Wu, Jinbiao Ma, Yin'an Yao
RNA-seq can help us quickly obtain the whole transcriptome sequences of species under different conditions. Many Unigenes that are assembled by raw reads always do not contain complete open reading frame (ORF). In addition, it also has some redundancy in transcriptome library. Some Unigenes in the library, although belong to one transcript, cannot be assembled without overlapping. We found five incomplete Unigenes annotated ammonium transporter (AMT) from Salicornia europaea transcriptome, in which two Unigenes (Uni4 and Uni5) had identical expression patterns across four transcriptomes...
November 2014: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/25832737/the-chromatin-remodeling-factor-atino80-plays-crucial-roles-in-genome-stability-maintenance-and-in-plant-development
#18
Chi Zhang, Lin Cao, Liang Rong, Zengxuan An, Wangbin Zhou, Jinbiao Ma, Wen-Hui Shen, Yan Zhu, Aiwu Dong
INO80 is a conserved chromatin-remodeling factor in eukaryotes. While a previous study reported that the Arabidopsis thaliana INO80 (AtINO80) is required for somatic homologous recombination (HR), the role of AtINO80 in plant growth and development remains obscure. Here, we identified and characterized two independent atino80 mutant alleles, atino80-5 and atino80-6, which display similar and pleiotropic phenotypes, including smaller plant and organ size, and late flowering. Under standard growth conditions, atino80-5 showed decreased HR; however, after genotoxic treatment, HR in the mutant increased, accompanied by more DNA double-strand breaks and stronger cellular responses...
May 2015: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/25749732/ultraviolet-b-protection-of-ascorbate-and-tocopherol-in-plants-related-with-their-function-on-the-stability-on-carotenoid-and-phenylpropanoid-compounds
#19
Yinan Yao, Jingjing You, Yongbin Ou, Jinbiao Ma, Xiuli Wu, Gang Xu
Ascorbate and tocopherol are important hydrophilic or lipophilic antioxidants in plants, while their crucial roles in the antioxidant defense system under ultraviolet B radiation were not well understood. The mutants of Arabidopsis thaliana deficient in ascorbate (vtc1 and vtc2) or tocopherol (vte1) were used to analyze their physiological, biochemical and metabolic change in responses to Ultraviolet B radiation. Results showed that loss of either ascorbate or tocopherol caused reduction in phenylpropanoid and flavonol glycosides compounds, as well as reduction in superoxide dismutase activity and total cellular antioxidant capacity...
May 2015: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/25653658/validation-of-suitable-reference-genes-for-gene-expression-analysis-in-the-halophyte-salicornia-europaea-by-real-time-quantitative-pcr
#20
Xinlong Xiao, Jinbiao Ma, Junru Wang, Xiaomeng Wu, Pengbo Li, Yinan Yao
Real-time quantitative polymerase chain reaction (RT-qPCR), a reliable technique for quantifying gene expression, requires stable reference genes to normalize its data. Salicornia europaea, a stem succulent halophyte with remarkable salt resistance and high capacity for ion accumulation, has not been investigated with regards to the selection of appropriate reference genes for RT-qPCR. In this study, the expression of 11 candidate reference genes, GAPDH (Glyceraldehyde 3-phosphate dehydrogenase), Actin, α-Tub (α-tubulin), β-Tub (β-tubulin), EF1-α (Elongation factor 1-α), UBC (Ubiquitin-conjugating enzyme), UBQ (Polyubiquitin), CYP (Cyclophilin), TIP41 (TIP41-like protein), CAC (Clathrin adaptor complexes), and DNAJ (DnaJ-like protein), was analyzed in S...
2014: Frontiers in Plant Science
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