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Jinbiao Ma

Jinbiao Shi, Dan Shao, Jianling Zhang, Dongxing Tan, Xiuniang Tan, Bingxing Zhang, Buxing Han, Fanyu Zhang, Lifei Liu, Xiuyan Cheng
A non-noble cadmium electrode was synthesized via an electrolysis strategy, which can electroreduce carbon dioxide into carbon monoxide with high selectivity and efficiency. The partial current density for CO can reach up to 59.0 mA cm-2 at a Faradaic efficiency of 99.2% using 1-butyl-3-methylimidazolium hexafluorophosphate/acetonitrile as the electrolyte.
May 10, 2018: Chemical Communications: Chem Comm
Baixing Wu, Mengmeng Zhang, Shichen Su, Hehua Liu, Jianhua Gan, Jinbiao Ma
Vernalization is a pivotal stage for some plants involving many epigenetic changes during cold exposure. In Arabidopsis, an essential step in vernalization for further flowering is successful silence the potent floral repressor Flowering Locus C (FLC) by repressing histone mark. AtVal1 is a multi-function protein containing five domains that participate into many recognition processes and is validated to recruit the repress histone modifier PHD-PRC2 complex and interact with components of the ASAP complex target to the FLC nucleation region through recognizing a cis element known as CME (cold memory element) by its plant-specific B3 domain...
May 9, 2018: Biochemical and Biophysical Research Communications
Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J Hannon, Yang Yu
Protein-RNA interaction networks are essential to understand gene regulation control. Identifying binding sites of RNA-binding proteins (RBPs) by the UV-crosslinking and immunoprecipitation (CLIP) represents one of the most powerful methods to map protein-RNA interactions in vivo. However, the traditional CLIP protocol is technically challenging, which requires radioactive labeling and suffers from material loss during PAGE-membrane transfer procedures. Here we introduce a super-efficient CLIP method (GoldCLIP) that omits all gel purification steps...
April 27, 2018: Genomics, Proteomics & Bioinformatics
Ling Peng, Fengjuan Zhang, Renfu Shang, Xueyan Wang, Jiayi Chen, James J Chou, Jinbiao Ma, Ligang Wu, Ying Huang
Small noncoding RNAs (sncRNAs) regulate many genes in eukaryotic cells. Hua enhancer 1 (Hen1) is a 2'-O-methyltransferase that adds a methyl group to the 2'-OH of 3'-terminal nucleotide of sncRNAs. The types and properties of sncRNAs may vary among different species, and the domain composition, structure, and function of Hen1 proteins differ accordingly. In mammals, Hen1 specifically methylates sncRNAs called p-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs). However, other types of sncRNAs that are methylated by Hen1 have not yet been reported, and the structures and the substrates of mammalian Hen1 remain unknown...
April 27, 2018: Journal of Biological Chemistry
Jie Zhang, Xiyue Chen, Ping Liu, Jinbiao Zhao, Jian Sun, Wenyi Guan, Lee J Johnston, Crystal L Levesque, Peixin Fan, Ting He, Guolong Zhang, Xi Ma
Clostridium butyricum (C. butyricum) is known as a butyrate producer and a regulator of gut health,but whether it exerts beneficial effect as a dietary supplement via modulating the intestinal microbiota remains elusive. This study investigated the impact of C. butyricum on the fecal microbiota composition and their metabolites on d 14 and d 28 after weaned with 10 g/kg dietary supplementation of C. butyricum. Dynamic changes of microbial compositions showed dramatically increasing Selenomonadales and decreasing Clostridiales on d 14 and d 28...
April 23, 2018: Journal of Agricultural and Food Chemistry
Yuhan Zhang, Weiwei Liu, Ronghong Li, Jiaqi Gu, Ping Wu, Chao Peng, Jinbiao Ma, Ligang Wu, Yang Yu, Ying Huang
The Tudor domain-containing (Tdrd) family proteins play a critical role in transposon silencing in animal gonads by recognizing the symmetrically dimethylated arginine (sDMA) on the (G/A)R motif of the N-terminal of PIWI family proteins via the eTud domains. Papi, also known as "Tdrd2," is involved in Zucchini-mediated PIWI-interacting RNA (piRNA) 3'-end maturation. Intriguingly, a recent study showed that, in papi mutant flies, only Piwi-bound piRNAs increased in length, and not Ago3-bound or Aub-bound piRNAs...
March 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
Li Li, Osama Abdalla Abdelshafy Mohamad, Jinbiao Ma, Ariel D Friel, Yangui Su, Yun Wang, Zulpiya Musa, Yonghong Liu, Brian P Hedlund, Wenjun Li
Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue...
March 7, 2018: Antonie Van Leeuwenhoek
Baixing Wu, Shichen Su, Deepak P Patil, Hehua Liu, Jianhua Gan, Samie R Jaffrey, Jinbiao Ma
Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m6 A "reader." hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively...
January 29, 2018: Nature Communications
Li Li, Ghenijan Osman, Nimaichand Salam, Osama Abdalla Mohamed, Jianyu Jiao, Jinbiao Ma, Mipeshwaree Devi Asem, Min Xiao, Wen-Jun Li
A Gram-negative bacterium, designated as strain YIM 690229T , was isolated from the roots of Limonium otolepis. The strain was able to grow at 10-40 °C (optimum, 28-37 °C), pH 6.0-8.0 (optimum, 7.0) and in the presence of up to 7% NaCl (w/v) (optimum, up to 2.5%). Comparative 16S rRNA gene sequence analysis revealed that strain YIM 690229T shared less than 93.9% sequence similarities with members within the order Rhizobiales, and was remotely related to members of the family Hyphomicrobiaceae. Strain YIM 690229T was characterized by the presence of Q-10 as the predominant respiratory lipoquinone...
May 2018: Archives of Microbiology
Hehua Liu, Xiang Yu, Yiqing Chen, Jing Zhang, Baixing Wu, Lina Zheng, Phensinee Haruehanroengra, Rui Wang, Suhua Li, Jinzhong Lin, Jixi Li, Jia Sheng, Zhen Huang, Jinbiao Ma, Jianhua Gan
In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8-17 DNAzyme crystal structures...
December 8, 2017: Nature Communications
Luqian Zheng, Elisabeth Mairhofer, Marianna Teplova, Ye Zhang, Jinbiao Ma, Dinshaw J Patel, Ronald Micura, Aiming Ren
Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme...
October 30, 2017: Nature Communications
Mulugeta Seyoum Ademe, Shoupu He, Zhaoe Pan, Junling Sun, Qinglian Wang, Hongde Qin, Jinhai Liu, Hui Liu, Jun Yang, Dongyong Xu, Jinlong Yang, Zhiying Ma, Jinbiao Zhang, Zhikun Li, Zhongmin Cai, Xuelin Zhang, Xin Zhang, Aifen Huang, Xianda Yi, Guanyin Zhou, Lin Li, Haiyong Zhu, Baoyin Pang, Liru Wang, Yinhua Jia, Xiongming Du
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China...
December 2017: Molecular Genetics and Genomics: MGG
Baixing Wu, Jinhao Xu, Shichen Su, Hehua Liu, Jianhua Gan, Jinbiao Ma
Meiosis is one of the most dramatic differentiation programs accompanied by a striking change in gene expression profiles in fission yeast Schizosaccharomyces pombe. Whereas a number of meiosis-specific transcripts are expressed untimely in mitotic cells, and the entry of meiosis will be blocked as the accumulation of meiosis-specific mRNAs in the mitotic cells. A YTH domain containing protein Mmi1 was identified as a pivotal effector in a post-transcriptional event termed selective elimination of meiosis-specific mRNAs...
September 16, 2017: Biochemical and Biophysical Research Communications
Hehua Liu, Fusheng Shen, Phensinee Haruehanroengra, Qingqing Yao, Yunshan Cheng, Yiqing Chen, Chun Yang, Jing Zhang, Baixing Wu, Qiang Luo, Ruixue Cui, Jixi Li, Jinbiao Ma, Jia Sheng, Jianhua Gan
Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag(I) is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-Ag(I) -C pairs and the first reported G-Ag(I) -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag(I) -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA...
August 1, 2017: Angewandte Chemie
Baixing Wu, Li Li, Ying Huang, Jinbiao Ma, Jinrong Min
N6 -methyladenosine (m6 A) as the most prevalent internal modification in mammalian RNAs has been increasingly realized as an important reversible mark that participates in various biological processes and cancer pathogenesis. In this review, we discuss the catalytic mechanisms of MT-A70 domain family proteins for mediating adenosine N6 -methylation, the removal of this RNA mark by members of ALKB homologue domain family proteins, and the recognition of these m6 A-modified RNAs by YTH domain family proteins...
December 2017: Current Opinion in Structural Biology
Chung-Nga Ko, Chao Yang, Sheng Lin, Shengnan Li, Zhenzhen Dong, Jinbiao Liu, Simon Ming-Yuen Lee, Chung-Hang Leung, Dik-Lung Ma
In this work, we report a novel iridium(III)-based luminescent switch on-off-on probe, for the in vitro and in vivo detection of sulfide ion. The mechanism of this platform is based on the effective charge transfer quenching of the iridium(III) complex 1 by Fe3+ , followed by the restoration of luminescence upon the addition of Na2 S. The probe, hereinafter referred to as 1-Fe3+ , exhibited a linear range of detection for Na2 S from 0.01 to 1.5mM, with a detection limit of 2.9μM at signal-to-noise ratio (S/N) of 3...
August 15, 2017: Biosensors & Bioelectronics
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
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
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
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 PROTEIN1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss of function of the Arabidopsis thaliana NAP1 family genes NAP1-RELATED PROTEIN1 ( 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...
February 2017: Plant Cell
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