Genome-wide identification and evolution of TC1/Mariner in the silkworm (Bombyx mori) genome

Li‑Qin Xie,Ping‑Lan Wang,Shen‑Hua Jiang,Ze Zhang,Hua‑Hao Zhang 한국유전학회 2018 Genes & Genomics Vol.40 No.5

TC1/Mariner transposons belong to class II transposable elements (TEs) that use DNA-mediated “cut and paste” mechanism to transpose, and they have been identified in almost all organisms. Although silkworm (Bombyx mori) has a large amount of TC1/Mariner elements, the genome wide information of this superfamily in the silkworm is unknown. In this study, we have identified 2670 TC1/Mariner (Bmmar) elements in the silkworm genome. All the TEs were classified into 22 families by means of fgclust, a tool of repetitive sequence classification, seven of which was first reported in this study. Phylogenetic and structure analyses based on the catalytic domain (DDxD/E) of transposase sequences indicated that all members of TC1/Mariner were grouped into five subgroups: Mariner, Tc1, maT, DD40D and DD41D/E. Of these five subgroups, maT rather than Mariner possessed most members of TC1/Mariner (51.23%) in the silkworm genome. In particular, phylogenetic analysis and structure analysis revealed that Bmmar15 (DD40D) formed a new basal subgroup of TC1/Mariner element in insects, which was referred to as bmori. Furthermore, we concluded that DD40D appeared to intermediate between mariner and Tc1. Finally, we estimated the insertion time for each copy of TC1/Mariner in the silkworm and found that most of members were dramatically amplified during a period from 0 to 1 mya. Moreover, the detailed functional data analysis showed that Bmmar1, Bmmar6 and Bmmar9 had EST evidence and intact transposases. These implied that TC1/Mariner might have potential transpositional activity. In conclusion, this study provides some new insights into the landscape, origin and evolution of TC1/Mariner in the insect genomes.

The chemistry of two-dimensional layered transition metal dichalcogenide nanosheets

Chhowalla, Manish,Shin, Hyeon Suk,Eda, Goki,Li, Lain-Jong,Loh, Kian Ping,Zhang, Hua Nature Publishing Group, a division of Macmillan P 2013 Nature chemistry Vol.5 No.4

Ultrathin two-dimensional nanosheets of layered transition metal dichalcogenides (TMDs) are fundamentally and technologically intriguing. In contrast to the graphene sheet, they are chemically versatile. Mono- or few-layered TMDs — obtained either through exfoliation of bulk materials or bottom-up syntheses — are direct-gap semiconductors whose bandgap energy, as well as carrier type (n- or p-type), varies between compounds depending on their composition, structure and dimensionality. In this Review, we describe how the tunable electronic structure of TMDs makes them attractive for a variety of applications. They have been investigated as chemically active electrocatalysts for hydrogen evolution and hydrosulfurization, as well as electrically active materials in opto-electronics. Their morphologies and properties are also useful for energy storage applications such as electrodes for Li-ion batteries and supercapacitors.

Study on mechanism of macro failure and micro fracture of local nearly horizontal stratum in super-large section and deep buried tunnel

Li, Shu-cai,Wang, Jian-hua,Chen, Wei-zhong,Li, Li-ping,Zhang, Qian-qing,He, Peng Techno-Press 2016 Geomechanics & engineering Vol.11 No.2

The stability of surrounding rock will be poor when the tunnel is excavated through nearly horizontal stratum. In this paper, the instability mechanism of local nearly horizontal stratum in super-large section and deep buried tunnel is revealed by the analysis of the macro failure and micro fracture. A structural model is proposed to explain the mechanics of surrounding rock collapse under the action of stress redistribution and shed light on the macroscopic analytical approach of the stability of surrounding rock. Then, some highly effective formulas applied in the tunnel engineering are developed according to the theory of mixed-mode micro fracture. And well-documented field case is made to demonstrate the effectiveness and accuracy of the proposed analytical methods of mixed-mode fracture. Meanwhile, in order to make the more accurate judgment about yield failure of rock mass, a series of comprehensive failure criteria are formed. In addition, the relationship between the nonlinear failure criterion and $K_I$ and $K_{II}$ of micro fracture is established to make the surrounding rock failure criterion more comprehensive and accurate. Further, the influence of the parameters related to the tension-shear mixed-mode fracture and compression-shear mixed-mode fracture on the propagation of rock crack is analyzed. Results show that ${\sigma}_3$ changes linearly with the change of ${\sigma}_1$. And the change rate is related to ${\beta}$, angle between the cracks and ${\sigma}_1$. The proposed simple analytical approach is economical and efficient, and suitable for the analysis of local nearly horizontal stratum in super-large section and deep buried tunnel.

Isolation, Culture and Identification of Porcine Skeletal Muscle Satellite Cells

Li, Bo-jiang,Li, Ping-hua,Huang, Rui-hua,Sun, Wen-xing,Wang, Han,Li, Qi-fa,Chen, Jie,Wu, Wang-jun,Liu, Hong-lin Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.8

The objective of this study was to establish the optimum protocol for the isolation and culture of porcine muscle satellite cells. Mononuclear muscle satellite cells are a kind of adult stem cell, which is located between the basal lamina and sarcolemma of muscle fibers and is the primary source of myogenic precursor cells in postnatal muscle. Muscle satellite cells are a useful model to investigate the mechanisms of muscle growth and development. Although the isolation and culture protocols of muscle satellite cells in some species (e.g. mouse) have been established successfully, the culture system for porcine muscle satellite cells is very limited. In this study, we optimized the isolation procedure of porcine muscle satellite cells and elaborated the isolation and culture process in detail. Furthermore, we characterized the porcine muscle satellite cells using the immunofluorecence. Our study provides a reference for the isolation of porcine muscle satellite cells and will be useful for studying the molecular mechanisms in these cells.

Cordycepin protects against β–amyloid and ibotenic acid– induced hippocampal CA1 pyramidal neuronal hyperactivity

Li-Hua Yao,Jinxiu Wang,Chao Liu,Shanshan Wei,Guoyin Li,Songhua Wang,Wei Meng,Zhi-Bin Liu,Li-Ping Huang 대한약리학회 2019 The Korean Journal of Physiology & Pharmacology Vol.23 No.6

Cordycepin exerts neuroprotective effects against excitotoxic neuronal death. However, its direct electrophysiological evidence in Alzheimer’s disease (AD) remains unclear. This study aimed to explore the electrophysiological mechanisms underlying the protective effect of cordycepin against the excitotoxic neuronal insult in AD using whole-cell patch clamp techniques. β-Amyloid (Aβ) and ibotenic acid (IBO)–induced injury model in cultured hippocampal neurons was used for the purpose. The results revealed that cordycepin significantly delayed Aβ + IBO–induced excessive neuronal membrane depolarization. It increased the onset time/latency, extended the duration, and reduced the slope in both slow and rapid depolarization. Additionally, cordycepin reversed the neuronal hyperactivity in Aβ + IBO–induced evoked action potential (AP) firing, including increase in repetitive firing frequency, shortening of evoked AP latency, decrease in the amplitude of fast afterhyperpolarization, and increase in membrane depolarization. Further, the suppressive effect of cordycepin against Aβ + IBO–induced excessive neuronal membrane depolarization and neuronal hyperactivity was blocked by DPCPX (8-cyclopentyl-1,3-dipropylxanthine, an adenosine A1 receptor–specific blocker). Collectively, these results revealed the suppressive effect of cordycepin against the Aβ + IBO–induced excitotoxic neuronal insult by attenuating excessive neuronal activity and membrane depolarization, and the mechanism through the activation of A1R is strongly recommended, thus highlighting the therapeutic potential of cordycepin in AD.

Cordycepin protects against β–amyloid and ibotenic acid– induced hippocampal CA1 pyramidal neuronal hyperactivity

Li-Hua Yao,Jinxiu Wang,Chao Liu,Shanshan Wei,Guoyin Li,Songhua Wang,Wei Meng,Zhi-Bin Liu,Li-Ping Huang 대한약리학회 2019 The Korean Journal of Physiology & Pharmacology Vol.23 No.6

Cordycepin exerts neuroprotective effects against excitotoxic neuronal death. However, its direct electrophysiological evidence in Alzheimer’s disease (AD) remains unclear. This study aimed to explore the electrophysiological mechanisms underlying the protective effect of cordycepin against the excitotoxic neuronal insult in AD using whole-cell patch clamp techniques. β-Amyloid (Aβ) and ibotenic acid (IBO)–induced injury model in cultured hippocampal neurons was used for the purpose. The results revealed that cordycepin significantly delayed Aβ + IBO–induced excessive neuronal membrane depolarization. It increased the onset time/latency, extended the duration, and reduced the slope in both slow and rapid depolarization. Additionally, cordycepin reversed the neuronal hyperactivity in Aβ + IBO–induced evoked action potential (AP) firing, including increase in repetitive firing frequency, shortening of evoked AP latency, decrease in the amplitude of fast afterhyperpolarization, and increase in membrane depolarization. Further, the suppressive effect of cordycepin against Aβ + IBO–induced excessive neuronal membrane depolarization and neuronal hyperactivity was blocked by DPCPX (8-cyclopentyl-1,3-dipropylxanthine, an adenosine A1 receptor–specific blocker). Collectively, these results revealed the suppressive effect of cordycepin against the Aβ + IBO–induced excitotoxic neuronal insult by attenuating excessive neuronal activity and membrane depolarization, and the mechanism through the activation of A1R is strongly recommended, thus highlighting the therapeutic potential of cordycepin in AD.

Expression, Purification, and Biological Characterization of The Amino-Terminal Fragment of Urokinase in Pichia pastoris

( Jian Ping Li ),( Yu Li Lin ),( Hong Qin Zhuang ),( Zi Chun Hua ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.9

Urokinase (uPA) and its receptor (uPAR) play an important role in tumor growth and metastasis. Targeting the excessive activation of this system as well as the proliferation of the tumor vascular endothelial cell would be expected to prevent tumor neovasculature and halt the tumor development. In this regard, the amino-terminal fragment (ATF) of urokinase has been confirmed as effective to inhibit the proliferation, migration, and invasiveness of cancer cells via interrupting the interaction of uPA and uPAR. Previous studies indicated that ATF expressed in Escherichia coli was mainly contained in inclusion bodies and also lacked posttranslational modifications. In this study, the biologically active and soluble ATF was cloned and expressed in Pichia pastoris. The recombinant protein was purified to be homogenous and confirmed to be biologically active. The yield of the active ATF was about 30 mg/l of the P. pastoris culture medium. The recombinant ATF (rATF) could efficiently inhibit angiogenesis, endothelial cell migration, and tumor cell invasion in vitro. Furthermore, it could inhibit in vivo xenograft tumor growth and prolong the survival of tumor-bearing mice significantly by competing with uPA for binding to cell surfaces. Therefore, P. pastoris is a highly efficient and cost-effective expression system for large-scale production of biologically active rATFs for potential therapeutic application.

Combined Expression of Metastasis Related Markers Naa10p, SNCG and PRL-3 and its Prognostic Value in Breast Cancer Patients

Min, Li,Ma, Ruo-Lan,Yuan, Hua,Liu, Cai-Yun,Dong, Bing,Zhang, Cheng,Zeng, Yan,Wang, Li,Guo, Jian-Ping,Qu, Li-Ke,Shou, Cheng-Chao Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.7

Combinations of multiple biomarkers representing distinct aspects of metastasis may have better prognostic value for breast cancer patients, especially those in late stages. In this study, we evaluated the protein levels of N-${\alpha}$-acetyltransferase 10 protein (Naa10p), synuclein-${\gamma}$ (SNCG), and phosphatase of regenerating liver-3 (PRL-3) in 365 patients with breast cancer by immunohistochemistry. Distinct prognostic subgroups of breast cancer were identified by combination of the three biomarkers. The Naa10p+SNCG-PRL-3-subgroup showed best prognosis with a median distant metastasis-free survival (DMFS) of 140 months, while the Naa10p-SNCG+PRL-3+subgroup had the worst prognosis with a median DMFS of 60.5 months. Multivariate analysis indicated Naa10p, SNCG, PRL-3, and the TNM classification were all independent prognostic factors for both DMFS and overall survival (OS). The three biomarker combination of Naa10p, SNCG and PRL-3 performed better in patients with lymph node metastasis, especially those with more advanced tumors than other subgroups. In conclusion, the combined expression profile of Naa10p, SNCG and PRL-3, alone or in combination with the TNM classification system, may provide a precise estimate of prognosis of breast cancer patients.

Transmembrane Helix of Novel Oncogene with Kinase-Domain (NOK) Influences Its Oligomerization and Limits the Activation of RAS/MAPK Signaling

Ying-Hua Li,Yin-Yin Wang,Shan Zhong,Zhi-Li Rong,Yong-Ming Ren,Zhi-Yong Li,Shu-Ping Zhang,Zhi-Jie Chang,Li Liu 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.1

Ligand-dependent or independent oligomerization of receptor protein tyrosine kinase (RPTK) is often an essential step for receptor activation and intracellular signaling. The novel oncogene with kinase-domain (NOK) is a unique RPTK that almost completely lacks an ectodomain, expresses intracellularly and activates constitutively. However, it is unknown whether NOK can form oligomer or what function oligomerization would have. In this study, two NOK deletion mutants were generated by either removing the ectodomain (NOKECD) or including the endodomain (NOK-ICD). Co-immunoprecipitation demonstrated that the transmembrane (TM) domain of NOK was essential for its intermolecular interaction. The results further showed that NOK aggregated more closely as lower order oligomers (the dimer- and trimer-sized) than either deletion mutant did since NOK could be cross-linked by both Sulfo-EGS and formaldehyde, whereas either deletion mutant was only sensitive to Sulfo-EGS. Removing the NOK TM domain (NOK-ICD) not only markedly promoted higher order oligomerization, but also altered the subcellular localization of NOK and dramatically elevated the NOK-mediated constitutive activation of extracellular signal-regulated kinase (ERK). Moreover, NOK-ICD but not NOK or NOKECD was co-localized with the upstream signaling molecule RAS on cell membrane. Thus, TM-mediated intermolecular contacting may be mainly responsible for the constitutive activation of NOK and contribute to the autoinhibitory effect on RAS/MAPK signaling.

De novo transcriptome analysis of an albino mutant Pasphiopedilum pacific shamrock reveals reduced expression of genes related to chloroplast biosynthesis and division

Han Li,Hua Cao,Rong‑pei Yu,Zhen Miao,Ji‑hua Wang,Su‑Ping Qu,Qiang Yuan,Shenchong Li 한국원예학회 2018 Horticulture, Environment, and Biotechnology Vol.59 No.3

Paphiopedilum pacific shamrock is an orchid with high ornamental value. Understanding the mechanisms responsible for leaf color in albino mutants is important for ornamental development and breeding. In this study, we compared the leaf photosynthetic pigment content and transcriptome of albino mutants ppa01 and wild-type P. pacific shamrock. Photosynthetic pigment in mutants was less than 2% of the wild type and chl a/b was 60% less than the wild type. Transcriptome sequencing yielded 6.27 Gb and 5.67 Gb clean data from the mutant and wild-type leaves, respectively. De novo assembly yielded 104,763 unigenes with 15,400 greater than 1 kb in length. In unigene expression analysis, 3170 differentially expressed genes (DEGs) were identified with 2231 (70.38% of total DEGs) down-regulated. Results from GO and KEGG enrichment analysis, KEGG pathway analysis and qPCR suggest that the reduction of chloroplast biosynthesis and division in the mutant was due to low expression levels of ppGLK1 and ppFtsz. Mutants were associated with fewer chloroplasts in leaf cells, abnormal chloroplast structures, impaired chlorophyll biosynthesis, and thus reduced total chlorophyll and carotenoid contents. Furthermore, down-regulated expression of ppNYC1 reduced transformation of chlorophyll b into chlorophyll a, leading to a chl a/b decline. The research will guide future studies of leaf pigment mutations and the breeding of P. pacific shamrock.