Abstract:DDX3Y computational catalytic network construction and analysis of human left brain is very useful to identify novel markers and potential targets for the understanding of brain mechanism. By integration of gene regulatory network infer (GRNInfer) and the database for annotation, visualization and integrated discovery (DAVID 2010 version) we identified and constructed significant molecule DDX3Y catalytic network from 15 chimpanzee and 14 human left brain samples in the same GEO Dataset GDS2678. Our result verified DDX3Y catalytic module only in the downstream of chimpanzee left brain (AGL, PDIA2, PPID, RBBP6 activation; ENOSF1, GSTM3, RECQL, RPP14 inhibition) and downstream (DDX19A, ENPP2, RPP14, SPTLC1activation; AGL, ENOSF1, GSTM3, RECQL, HERC2P2, HERC2P3, PCSK6, PDE8A, PDIA2, PPID, RBBP6 inhibition), whereas in the upstream of human left brain (GSTM3, HSD17B6, PCSK6 activation; EGFR, ENOSF1 inhibition) and downstream (AGL, DDX19A, EGFR, HSD17B6 activation; ABCC10, ENPP2, GSTM3, HERC2P3, PCSK6, PDE8A, PDIA2, PPID, RECQL, SPTLC1 inhibition). Importantly, we datamined that DDX3Y catalytic cluster of human left brain is involved in nervous system development, ubl conjugation, response to chemical stimulus, neurogenesis, cell development and cognition, regulation of apoptosis, anatomical structure development, ATPase activity, coupled, endoplasmic reticulum, polysaccharide binding, pyrophosphatase activity, cellular localization, transport and calcium ion binding (only in human left brain terms) without Isomerase and zinc ion binding (only in chimpanzee left brain terms), the condition is vital to central nervous system development and cognition of human left brain. Our result demonstrated that common terms in both chimpanzee and human left brain include phosphoprotein, hydrolase, organelle, metabolic process, nucleic acid binding, metal-binding, acetylation, DNA binding, Golgi apparatus, identical protein binding, homeostatic process, signal transducer activity, membrane, developmental process, glycoprotein, cytoskeletal protein binding, regulation of cellular process and biosynthetic process, and these terms are more relative to development and cognition, therefore we deduced the stronger DDX3Y catalytic network in human left brain consistent with our number computation. It would be necessary of the stronger DDX3Y catalytic function to development and cognition of human left brain.

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	1. DDX3Y Computational Catalytic Network Construction and Analysis between Left Brain of Chimpanzee and Human
	LIU Xiaoxiao,HUANG Juxiang,WANG Lin
	Biology 07 November 2018
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	Abstract:DDX3Y computational catalytic network construction and analysis of human left brain is very useful to identify novel markers and potential targets for the understanding of brain mechanism. By integration of gene regulatory network infer (GRNInfer) and the database for annotation, visualization and integrated discovery (DAVID 2010 version) we identified and constructed significant molecule DDX3Y catalytic network from 15 chimpanzee and 14 human left brain samples in the same GEO Dataset GDS2678. Our result verified DDX3Y catalytic module only in the downstream of chimpanzee left brain (AGL, PDIA2, PPID, RBBP6 activation; ENOSF1, GSTM3, RECQL, RPP14 inhibition) and downstream (DDX19A, ENPP2, RPP14, SPTLC1activation; AGL, ENOSF1, GSTM3, RECQL, HERC2P2, HERC2P3, PCSK6, PDE8A, PDIA2, PPID, RBBP6 inhibition), whereas in the upstream of human left brain (GSTM3, HSD17B6, PCSK6 activation; EGFR, ENOSF1 inhibition) and downstream (AGL, DDX19A, EGFR, HSD17B6 activation; ABCC10, ENPP2, GSTM3, HERC2P3, PCSK6, PDE8A, PDIA2, PPID, RECQL, SPTLC1 inhibition). Importantly, we datamined that DDX3Y catalytic cluster of human left brain is involved in nervous system development, ubl conjugation, response to chemical stimulus, neurogenesis, cell development and cognition, regulation of apoptosis, anatomical structure development, ATPase activity, coupled, endoplasmic reticulum, polysaccharide binding, pyrophosphatase activity, cellular localization, transport and calcium ion binding (only in human left brain terms) without Isomerase and zinc ion binding (only in chimpanzee left brain terms), the condition is vital to central nervous system development and cognition of human left brain. Our result demonstrated that common terms in both chimpanzee and human left brain include phosphoprotein, hydrolase, organelle, metabolic process, nucleic acid binding, metal-binding, acetylation, DNA binding, Golgi apparatus, identical protein binding, homeostatic process, signal transducer activity, membrane, developmental process, glycoprotein, cytoskeletal protein binding, regulation of cellular process and biosynthetic process, and these terms are more relative to development and cognition, therefore we deduced the stronger DDX3Y catalytic network in human left brain consistent with our number computation. It would be necessary of the stronger DDX3Y catalytic function to development and cognition of human left brain.
	TO cite this article:LIU Xiaoxiao,HUANG Juxiang,WANG Lin. DDX3Y Computational Catalytic Network Construction and Analysis between Left Brain of Chimpanzee and Human[OL].[ 7 November 2018] http://en.paper.edu.cn/en_releasepaper/content/4746419


	2. GPSM2 Signal Transduction Computational Network Analysis in Human No-Tumor Hepatitis/Cirrhosis and Hepatocellular Carcinoma Transformation
	ZHUANG Jing,HUANG Juxiang,WANG Lin
	Biology 21 August 2018
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	Abstract:LGN protein (GPSM2) is involved in transcription or cell division presented in several papers. However, how the molecular network and interpretation concerning GPSM2 signal transduction between no-tumor hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation remains to be elucidated. Here we constructed and analyzed significant higher expression gene GPSM2 activated & inhibited upstream and downstream signal transduction network from HCC vs no-tumor hepatitis/cirrhosis pateints (viral infection HCV or HBV) in GEO Dataset by using gene regulatory network inference method based on linear programming and decomposition procedure, under covering GPSM2 pathway and matching signal transduction enrichment analysis by the CapitalBio MAS 3.0 integrated of public databases including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, etc. By compared the different activated & inhibited GPSM2 network with GO analysis between no-tumor hepatitis/cirrhosis and HCC transformation, our result showed GPSM2 signal transduction network: (1) more nucleus and cytoplasm but less extracellular space protein binding in no-tumor hepatitis/cirrhosis; (2) more growth factor activity but less cytoplasm enzyme activator activity in HCC; (3) less activation & more inhibition molecular numbers in no-tumor hepatitis/cirrhosis but more activation & less inhibition in HCC. Therefore, we inferred (4) GPSM2 signal transduction network stronger transcription but weaker cell differentiation as a result increasing cytoplasm protein translation in no-tumor hepatitis/cirrhosis; (5) stronger cell proliferation but weaker regulation of muscle contraction as a result inceasing nuclear cell division in HCC.
	TO cite this article:ZHUANG Jing,HUANG Juxiang,WANG Lin. GPSM2 Signal Transduction Computational Network Analysis in Human No-Tumor Hepatitis/Cirrhosis and Hepatocellular Carcinoma Transformation[OL].[21 August 2018] http://en.paper.edu.cn/en_releasepaper/content/4745835

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	3. The research in equilibrium study and diversified models of thifensulfuron methyl in several common pure solvents and mixture organic solvents from (278.15 to 333.15) K
	Yuhao Zhang,Yemin Yu,Yonghong Hu,Renlun Deng,Wenge Yang,Tao Li,Yang Cao
	Biology 10 May 2017
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	Abstract:IThifensulfuron methyl is a kind of herbicide and an important chemical intermediate product, Data on corresponding solid?liquid equilibrium of thifensulfuron methyl in different solvents is essential for a preliminary study of industrial applications. In this study, the solubility of thifensulfuron methyl in water, methanol, ethanol, butyl alcohol, isopropanol, acetone, acetonitrile, hexane and ethyl acetate pure solvents and the solubility in (ethanol + ethyl acetate) mixture solvents was measured in the temperature range from 278.15 K to 328.15 K. We use the gravimetric method get the solubility data, contact with the modified apelblat equation and λh equation. We can calculate and analysis thermodynamic parameters (including enthalpy, entropy, and gibbs energy) by the van't hoff analysis and gibbs equation. Calculations proves that the modified apelblat model has advantages than the other two models. In addition, the calculated thermodynamic parameters indicated that in each studied solvent the dissolution of thermodynamic models is endothermic, nonspontaneous, and an entropy-driven process.
	TO cite this article:Yuhao Zhang,Yemin Yu,Yonghong Hu, et al. The research in equilibrium study and diversified models of thifensulfuron methyl in several common pure solvents and mixture organic solvents from (278.15 to 333.15) K[OL].[10 May 2017] http://en.paper.edu.cn/en_releasepaper/content/4732331


	4. The complete mitogenome and gene organization of the Chinese water dragon (Physignathus cocincinus)
	YAN Long,YAN Peng
	Biology 29 April 2017
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	Abstract:The complete mitochondrial DNA sequence of the Chinese water dragon (Physignathus cocincinus) was determined using PCR and sequenced with a primer walking method. The complete mitochondrial genome is 16,451 bp in length, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region (CR). The gene arrangement and composition of P. cocincinus was similar to most other vertebrate, but the order of the tRNA-Ile and tRNA-Gln was switched and lack of the origin of L-strand replication (OL). Meanwhile, there was only one CR in P. cocincinus mitogenome, where it was located between the tRNA-Pro and tRNA-Phe gene. Duplication of the control region was not found in P. cocincinus, which was often observed in the mitogenomes of Agamidae.
	TO cite this article:YAN Long,YAN Peng. The complete mitogenome and gene organization of the Chinese water dragon (Physignathus cocincinus)[OL].[29 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4730948


	5. Mitochondrial genome sequencing of three firefly beetles and phylogenetic analysis of 18 species of beetles
	WANG Kai,HONG Wei,JIAO Hengwu,MU Feng-Juan,ZHAO Huabin
	Biology 24 April 2017
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	Abstract:To validate the phylogenetic inference based on transcriptome data, we employed the traditional Sanger sequencing to obtain two complete mitogenomes (Aquatica ficta and A. wuhana) and one nearly complete mitogenome (Lamprigera yunnana); we also identified the 13 protein coding genes (PCGs) in mitogenomes from each of the four whole-body transcriptomes; and we additionally retrieved 12 published complete mitogenomes from members of Rhagophthalmidae, Lampyridae, Phengodidae, Elateridae, Lycidae, Cantharidae, and Tenebrionidae. Our mitogenome analysis confirmed the distinctiveness of Rhagophthalmidae from Lampyridae, which is consistent to our earlier transcriptome analysis.
	TO cite this article:WANG Kai,HONG Wei,JIAO Hengwu, et al. Mitochondrial genome sequencing of three firefly beetles and phylogenetic analysis of 18 species of beetles[OL].[24 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4727742


	6. Construction of Recombinant Lentivirus Vector Targeting Bovine LXRα mRNA and Its Silencing Effects on Bovine Muscle Satellite Cells
	Liu Yongfeng,Zhao Lu,Ku Ting,Yang Xingbin
	Biology 24 April 2017
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	Abstract:The liver X receptor α (LXRα) is a member of the nuclear hormone receptor superfamily which could regulate the transcription of the genes involved in cholesterol transportation. Recent studies showed that LXRα is considered as a critical regulator in cholesterol homeostasis in macrophages, which could regulate several genes involved in cholesterol transport, such as the ATP-binding cassette trans-porters (ABCs), ABCA1, ABCG1, apolipoprotein E (ApoE) and lipoprotein lipase (LPL). In our study, four pairs of inhibition shRNA were designed to exclusively target bovine LXRα mRNA. Lentiviral vector containing LXRα shRNAs were constructed through BP and LP recombination system, and used to obtained the corresponding lentiviruses in 293T cells. The titers of the Lenti-14MR0054-01, -2, -3 and -04 viruses were 3×108TU/ml, 2×108TU/ml, 2.5×108TU/ml, 3.5×108TU/ml, respectively. The knockdown efficiency of pLenti-03 targeting LXRα reached 88 % in bovine muscle satellite cells. Furthermore, the mRNA expression of RXRα was upregulated in bovine muscle satellite cells, whereas that of PPARα, PPARγ, ABCA1, LPL, ApoE were downregulated at 48 h post-pLenti-03 viruses infection. Therefore, the efficient lentivirus vector inhibiting bovine LXRα expression was obtained in the present study, providing basis for loss-of-function of LXRα in bovine muscle satellite cells
	TO cite this article:Liu Yongfeng,Zhao Lu,Ku Ting, et al. Construction of Recombinant Lentivirus Vector Targeting Bovine LXRα mRNA and Its Silencing Effects on Bovine Muscle Satellite Cells[OL].[24 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4728945


	7. Identification of a Flavonoid Glucosyltransferase Involved in 7-OH Site Glycosylation in Tea plants
	Dai Xinglong,Zhuang Juhua,Wu Yingling,Wang Peiqiang,Zhao Guifu,Liu Yajun,Jiang Xiaolan,Gao Liping,Xia Tao
	Biology 22 April 2017
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	Abstract:Flavonol glycosides, which are often converted from aglycones catalyzed by UDP-glycosyltransferases (UGTs), play important roles for the health of plants and animals. In present study, CsUGT75L12, a gene encoding a flavonoid 7-O-glycosyltransferase, was identified in tea plants. Recombinant CsUGT75L12 protein displayed glycosyltransferase activity with multiple phenolic compounds including flavanone, flavone, flavonol and isoflavone on the 7-OH position. In relative comparison to wild-type seeds, the content of flavonol-glucosides levels increased in seeds of Arabidopsis overexpressing CsUGT75L12. In order to determine the key amino acid residues responsible for the catalytic activity of the protein, a series of site-directed mutagenesises and enzymatic assays were performed based on the 3D structural modeling and docking analysis. These results suggested that residue Q54 was predicted to be a double binding site functioning as a sugar receptor and donor. Residues H56 and T151 corresponding to the basic active residues H20 and D119 of VvGT1, were not irreplaceable for CsUGT75L12. In addition, residues Y182, S223, P238, T239, and F240 were demonstrated to be responsible for a "reversed" sugar receptor binding model. The results of triple substitution confirmed that the function of residues P238, T239 and F240 may substitute or compensate with each other for the flavonoid 7-O-glycosyltransferase active.?????
	TO cite this article:Dai Xinglong,Zhuang Juhua,Wu Yingling, et al. Identification of a Flavonoid Glucosyltransferase Involved in 7-OH Site Glycosylation in Tea plants[OL].[22 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4728169


	8. A new transgenic mouse model of spinal cord injury
	LI Cheng,LIU Yaobo
	Biology 04 April 2017
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	Abstract:Objective: To explore a new model for the study of spinal cord injury, and to prove the possibility of this model. Methods: The Thy1( thymus cell antigen 1, theta)-YFPH transgenic mice and DiI tracing were employed to observe the distribution of corticospinal tract (CST). And lateral spinal cord hemisection injury model was made using the Thy1-YFPH mice. Results: Pyramidal neurons in cerebral cortex layer Ⅴ was specifically labeled and projected to pyramidal decussation in the medulla. In the spinal cord, the YFP labeled projections were distributed at the same locations as dorsal CST (dCST), dorsolateral CST (dlCST) and ventral CST (vCST). YFP positive axons were mostly colocalized with DiI traced dCST both in the spinal cord of uninjured Thy1-YFPH mice. Conclusion: The Thy1-YFPH mice could label the CST in the mouse spinal cord, and could be used as an easy and convenient model to monitor the degeneration, regeneration and remodeling of CST axons after spinal cord injury.
	TO cite this article:LI Cheng,LIU Yaobo. A new transgenic mouse model of spinal cord injury[OL].[ 4 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4724205


	9. Identification of hybrids in Potamogeton：incongruence between plastid and ITS regions solved by a novel barcoding marker PHYB
	Tao Yang,Tian-lei Zhang,Ming-fang Du,Feng-qin Tian,Xing Liu,Youhao Guo
	Biology 14 June 2016
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	Abstract:Potamogeton is one of the most difficult groups to clarify in aquatic plants, which have an extensive range of interspecific morphological and ecological diversity. Internal transcribed spacer (ITS) of nuclear ribosomal DNA is prevalent for phylogenetic analysis in plants. However, most researches have demonstrated that ITS regions show a high percentage of homoplasy in phylogenetic data sets. In this study, eighteen materials were collected in the genus Potamogeton from China and an incongruence was shown between the rbcL and ITS phylogenies. To solve this discrepancy, we sequenced a novel barcode PHYB gene to improve resolution and accuracy of the phylogenetic relationships. The PHYB phylogenetic analysis successfully resolved the incongruence between the rbcL and ITS phylogenies. In addition, six hybrids were confirmed using the PHYB marker, including P. compressus × P. pusillus, P. octandrus × P. oxyphyllus, P. gramineus × P. lucens, P. distinctus × P. natans, P. distinctus × P. wrightii, and S. pectinata × S. amblyophylla. Whereas, only one hybrid was identified (P. compressus × P. pusillus) for the ITS phylogeny, indicating that ITS homoplasy is present in Potamogeton and ITS regions completely homogenized towards to one parental type. Thus, ITS regions maybe have limited utility in phylogenetic relationships for Potamogeton. It is recommended that a three-locus combination of chloroplast DNA, ITS and PHYB is potential to effectively reveal more robust phylogenetic relationships and species identification.
	TO cite this article:Tao Yang,Tian-lei Zhang,Ming-fang Du, et al. Identification of hybrids in Potamogeton：incongruence between plastid and ITS regions solved by a novel barcoding marker PHYB[OL].[14 June 2016] http://en.paper.edu.cn/en_releasepaper/content/4697545


	10. Comparisons of extraction methods of microbial DNA from fermented grains
	ZHANG Yuhan,LI Guanhua,YUAN Lin
	Biology 19 May 2016
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	Abstract:Microbial populations in fermented grains during fermentation is the key to influence the flavor of Chinese liquor. In this paper, fermented grains samples from Hetao were used for DNA extraction, we studied the effects of six different extraction methods on total DNA extraction from fermented grains. The follow-up experiment showed that the obtained results in the use of the repeated freezing and thawing was the best for DNA extraction and polyacrylamide gel electrophoresis. Comparing with the other methods, the repeated freezing and thawing can reflect better the diversity of microorganism.
	TO cite this article:ZHANG Yuhan,LI Guanhua,YUAN Lin. Comparisons of extraction methods of microbial DNA from fermented grains[OL].[19 May 2016] http://en.paper.edu.cn/en_releasepaper/content/4691595

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