Transcriptome sequencing and characterization of Astragalus membranaceus var. mongholicus root reveals key genes involved in flavonoids biosynthesis

Jianping Liang,Wenqian Li,Xiaoyun Jia,Ying Zhang,Jianping Zhao 한국유전학회 2020 Genes & Genomics Vol.42 No.8

Background Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao is a traditional medicinal herb of Leguminosae since it contains bioactive compounds such as flavonoids, which have significant pharmacological effects on immunity and antioxidant. However, the scanty genomic and transcriptome resources of Astragalus membranaceus have hindered further exploration of its biosynthesis and accumulation mechanism. Objective This project aim to further improve our understanding of the relationship between transcriptional behavior and flavonoids content of A. mongholicus. Methods The accumulation of flavonoids and related gene expression in five different developmental stages (A: vegetative, B: florescence, C: fruiting, D: fruit ripening and E: defoliating stages) of A. mongholicus root were studied by combining UV spectrophotometry and transcriptomic techniques. The de novo assembly, annotation and functional evaluation of the contigs were performed with bioinformatics tools. Results After screening and assembling the raw data, there were a total of 158,123 unigenes with an average length of 644.89 bp were finally obtained, which has 8362 unigenes could be jointly annotated by NR, SwissProt, eggNOG, GO, KEGG and Pfam databases. KEGG enrichment analysis was performed on differentially expressed genes(DEGs)in the four groups (A vs. B, B vs. C, C vs. D, D vs. E). The results showed that many DEGs in each group were significantly enriched to flavonoids biosynthesis related pathways. Among them, a number of 86 were involved in the biosynthesis of isoflavonoid (12), flavonoid (5) and phenylpropanoid (69). Further analysis of these DEGs revealed that the expression levels of key genes such as PAL, 4CL, CCR , COMT, DFR, etc. were all down-regulated at the fruiting stage, and then raised at the fruit ripening stage. This expression pattern was similar to the accumulation trend of total flavonoids content. Conclusions In summary, this comprehensive transcriptome dataset allowed the identification of genes associated with flavonoids metabolic pathways. The results laid a foundation for the biosynthesis and regulation of flavonoids. It also provided a scientific basis for the most suitable harvest time and resource utilization of A. mongholicus.

A Study on Anisotropic Characteristics of Representative Elementary Volumes of Rock Mass

( Jianping Chen ),( Ying Liu ) 대한지질공학회 2019 대한지질공학회 학술발표회논문집 Vol.2019 No.2

Asymmetric, anisotropy, irregular, discontinuity is the basic properties of rock mass due to the fractures extensive universal developed, that gives rise to complicated physical and mechanical behavior of rock mass, strength of rock mass is influenced by size effect, representative elementary volumes (RVE) has a very close relationship with the size effect of the rock mass, RVE value is calculated in different direction, the result shows that the RVE also has the anisotropic characteristics. Field observation value of fractures is obtained by the method of sampling windows during the field geological survey, then, the statistical homogenous zones is demarcated based on Miller’s method, the bias of observed trace length, orientation and spacing of fractures is corrected in each homogenous unit, and then a three dimensional fracture network models for different homogenous unit are established by using Monte-Carlo method. The REV of rock mass is calculated based on the three-dimensional fracture network. Based on the 3D fracture network model, the volume fracture intensity index (P32) and multisampling non-parametric statistical test method are used to analyze the REV characteristics in different sampling directions. With the increase of the number of fracture groups, the anisotropic characteristics of REV become more obvious. Acknowledgments This work was supported by the State key program of National Natural Science Fund of China-Yunnan Joint Fund (Grant No. U1702241).

Lossy Source Compression of Non-Uniform Binary Source via Reinforced Belief Propagation over GQ-LDGM Codes

Jianping Zheng,Baoming Bai,Ying Li 한국전자통신연구원 2010 ETRI Journal Vol.32 No.6

In this letter, we consider the lossy coding of a non-uniform binary source based on GF(q)-quantized low-density generator matrix (LDGM) codes with check degree dc=2. By quantizing the GF(q) LDGM codeword, a non-uniform binary codeword can be obtained, which is suitable for direct quantization of the non-uniform binary source. Encoding is performed by reinforced belief propagation, a variant of belief propagation. Simulation results show that the performance of our method is quite close to the theoretic rate-distortion bounds. For example, when the GF(16)-LDGM code with a rate of 0.4 and block-length of 1,500 is used to compress the non-uniform binary source with probability of 1 being 0.23, the distortion is 0.091, which is very close to the optimal theoretical value of 0.074.

Clipping Value Estimate for Iterative Tree Search Detection

Jianping Zheng,Baoming Bai,Ying Li 한국통신학회 2010 Journal of communications and networks Vol.12 No.5

The clipping value, defined as the log-likelihood ratio (LLR) in the case wherein all the list of candidates have the same binary value, is investigated, and an effective method to estimate it is presented for iterative tree search detection. The basic principle behind the method is that the clipping value of a channel bit is equal to the LLR of the maximum probability of correct decision of the bit to the corresponding probability of erroneous decision. In conjunction with multilevel bit mappings, the clipping value can be calculated with the parameters of the number of transmit antennas,Nt; number of bits per constellation point, Mc; and variance of the channel noise, σ2, per real dimension in the Rayleigh fading channel. Analyses and simulations show that the bit error performance of the proposed method is better than that of the conventional fixed-value method.

Denoising Mapping Utilizing Constellation Symmetry in Denoise-and-Forward Two-Way Relay Channels

Jianping Zheng,Baoming Bai,Ying Li 한국전자통신연구원 2012 ETRI Journal Vol.34 No.4

The denoising mapping with the closest-neighbor clustering (CNC) method in denoise-and-forward two-way relay channels is studied. Specifically, the symmetry of the constellations in source terminals A and B is utilized to reduce the complexity of the CNC method. The specific case considered first to illustrate how the constellation symmetry works in the CNC method is the quadrature phase-shift keying constellation in A and B and the single-antenna deployment in all terminals. This case study shows that an enormous complexity reduction can be achieved. Next, the result is extended to multiple-antenna scenarios and square quadrature amplitude modulations.

The influence of the extent of lymph node metastasis on the prognosis for patients with intrahepatic cholangiocarcinoma

Jianping Wang*,Man Shu*,Hong Peng,Shaoqiang Li,Dongming Li,Jingxian Shen,Ming Kuang,Ying Zhang,Zebin Chen 대한외과학회 2023 Annals of Surgical Treatment and Research(ASRT) Vol.104 No.5

Purpose: Reports showed that some of intrahepatic cholangiocarcinoma (ICC) patients with lymph node metastasis (LNM) may also gain survival benefit undergone resection. However, the effect of the extent of LNM on prognosis and surgical indication is barely discussed. Methods: From September 1994 to November 2018, primary ICC patients undergone initial curable surgery were enrolled. Based on the extent of LNM, we divided these patients into 4 groups, including patients with no LNM (group N0), LNM to hepatoduodenal ligament or common hepatic artery (region A, group A), LNM to gastrohepatic lymph nodes for left liver ICC and periduodenal and peripancreatic lymph node for right liver ICC (region B, group B), or LNM beyond these regions (region C, group C). Multivariable Cox regression analysis was performed to identify the prognostic factors for recurrence- free survival (RFS) and overall survival (OS) in all groups. Results: A total of 133 patients were enrolled. There were 56, 21, 17, and 39 patients in groups N0, A, B, and C, respectively. There was significant difference between groups N0 and C in RFS (P < 0.001) and OS (P = 0.002). When we compared group N0 + A + B with group C, we also found that RFS (P < 0.001) and OS (P = 0.007) were significantly different. In multivariable analysis, the extent of LNM was an independent risk factor for RFS (P < 0.050). Conclusion: ICC patients with the LNM to regions A and B could still achieve good prognosis with resection. Surgery should be carefully considered when LNM to region C.

Constructions of quantum Bose–Chadhuri–Hocquenghem code using spectral techniques

Guo, Ying,Zeng, Guihua,Ho Lee, Moon,Fan, Jianping Royal Swedish Academy of Sciences 2007 Physica scripta Vol.76 No.2

<P>A quantum Bose–Chadhuri–Hocquenghem (BCH) code is constructed over <I>F</I><SUP><I>n</I></SUP><SUB><I>p</I><SUP><I>m</I></SUP></SUB> in the spectrum domain by employing Fourier transform. The constructed code may be employed to describe the characters of the quantum code over <I>F</I><SUP><I>n</I></SUP><SUB><I>p</I></SUB> in the time domain. Each quantum state of the proposed code has certain specified consecutive spectral components equalling zeros, and the error-correcting ability of the code can hence be determined by the number of consecutive zeros in its parity spectrums. Moreover, the decoding process may be performed more efficiently by using the spectrum techniques rather than by using the traditional methods.</P>

Tissue-associated profiling of gene expression in the fifth-instar larvae of Chinese Oak Silkworm, Antheraea pernyi

Duan Jianping,Liang Shimei,Zhu Zhenni,Yang Xinfeng,Li Ying,Xu Xin,Wang Jiazhen,Zhu Xuwei,Yao Lunguang 한국응용곤충학회 2023 Journal of Asia-Pacific Entomology Vol.26 No.2

Antheraea pernyi is an edible insect with important economic value in both traditional and non-traditional ap plications. Elucidating the details of gene expression variation among different A. pernyi larval tissues will greatly improve our knowledge about A. pernyi biology and promote its protection and breeding. Here, tissue-based transcriptome and gene co-expression network analysis were performed for the fifth-instar larval tissues of testis, midgut, Malpighian tubule, head, trachea, silk gland, integument, hemocyte, ovary, and fat body. A total of 1,991 tissue-associated genes, including 62 transcription factor-encoding genes, were correlated with the development and functions of these tissues. Moreover, 10 gene co-expression modules that were highly corre lated with the tissues were also determined. The most important 30 genes with top connectivity in each module were identified as hub genes to form the core co-expression network with important biological functions in the corresponding tissues. Based on these resources, further in-depth studies should be conducted to determine the roles of candidate genes and transcription factors governing tissue development and trait formation in A. pernyi.

Clipping Value Estimate for Iterative Tree Search Detection

Zheng, Jianping,Bai, Baoming,Li, Ying The Korea Institute of Information and Commucation 2010 Journal of communications and networks Vol.12 No.5

The clipping value, defined as the log-likelihood ratio (LLR) in the case wherein all the list of candidates have the same binary value, is investigated, and an effective method to estimate it is presented for iterative tree search detection. The basic principle behind the method is that the clipping value of a channel bit is equal to the LLR of the maximum probability of correct decision of the bit to the corresponding probability of erroneous decision. In conjunction with multilevel bit mappings, the clipping value can be calculated with the parameters of the number of transmit antennas, $N_t$; number of bits per constellation point, $M_c$; and variance of the channel noise, $\sigma^2$, per real dimension in the Rayleigh fading channel. Analyses and simulations show that the bit error performance of the proposed method is better than that of the conventional fixed-value method.

Affinity-Purification of Fibrinogenase with High Proteolytic Activity from Agkistrodon halys (Chinese) Venom

Biao Ma,Ying Zhang,Dan Wu,Jianping Jia,Wentao Xu,Yunbo Luo 대한약학회 2008 Archives of Pharmacal Research Vol.31 No.9

To purify and characterize the fibrinogenase with high proteolytic activity from Agkistrodon halys (Chinese) Venom. Monoclonal antibodies against fibrinogenase were prepared and a novel affinity chromatography equipped with a monoclonal antibody against fibrinogenase was developed and applied for the purification of fibrinogenases. The purified fibrinogenase was identified by fibrinolytic activity assay, and antithrombosis activity assay. HPLC chromatography and SDS-PAGE analysis demonstrated the uniformity and purity of the purified fibrinogenase. In comparison with a conventional A-50 chromatography method, affinity-purified fibrinogenase showed higher activity (3631 U mg-1 vs 501 U mg-1). In addition, the physiological activity of the fibrinogenase both in vitro and ex vivo showed the purified fibrinogenase can specifically degrade β-, γ-fibrinogen and has a high anti-thrombotic activity. In conclusion, the purified fibrinogenase by affinity column were shown to be homogeneous and showed a high and specific proteolytic activity against β-chains of fibrinogen molecules and antithrombosis activity.