De novo genome assembly and annotation of Holothuria scabra (Jaeger, 1833) from nanopore sequencing reads

Luo Honglin,Huang Guanghua,Li Jianbin,Yang Qiong,Zhu Jiajie,Zhang Bin,Feng Pengfei,Zhang Yongde,Yang Xueming 한국유전학회 2022 Genes & Genomics Vol.44 No.12

Background: Holothuria scabra is a costly gourmet and traditional Chinese tonic medicine. However, the lack of high-quality genome information hinders the genetic, phylogenetic, and bioactivator researches. Objective: To construct high-quality genomic data of H. scabra and conduct genome-wide phylogenetic analysis. Methods: The whole genome of a male H. scabra was sequenced based on Nanopore MinION platform, and the sequence was assembled by wtdbg2. Transcriptome sequencing was used to aid the gene annotation. Repeat sequences, non-coding RNA, pseudogene and gene functional annotation were analyzed. 750 single-copy gene families from ten species were applied to construct phylogenetic tree for evolutionary analysis by using the ML method. Results: The H. scabra genome of 1.18 Gb (N50 = 1557,492 bp) with 500.42 Mb of putative repetitive sequences was assembled from a male H. scabra individual, and 16,642 protein-coding genes, 951 pseudogenes, 1791 motifs and 45,400 domains from the generated assembly were identified. The divergence time between H. scabra and its ancestor was estimated approximately 192.6 million years ago. H. scabra and A. japonicas joined together while sea urchin and sea star diverged about 440 Mya ago. Some key genes involved in notochord and gill slits development, skeleton degeneration and nervous system, as well as homeobox genes differ between H. scabra and Apostichopus japonicas. Conclusion: We report the first whole genome of H. scabra with expectation that this will be a valuable resource for genetic, phylogenetic, breading, molecular biology and bioactivator studies of sea cucumbers and other invertebrates.

Chemical Mechanical Planarization

Xinchun Lu,Jianbin Luo,Dewen Zhao 대한기계학회 2013 대한기계학회 춘추학술대회 Vol.2013 No.5

CXCL-13 Regulates Resistance to 5-Fluorouracil in Colorectal Cancer

Guolin Zhang,Xin Luo,Wei Zhang,Engeng Chen,Jianbin Xu,Fei Wang,Gaoyang Cao,Zhenyu Ju,Dongai Jin,Xuefeng Huang,Wei Zhou,Zhangfa Song 대한암학회 2020 Cancer Research and Treatment Vol.52 No.2

Purpose 5-Fluorouracil (5-Fu) is used as a conventional chemotherapy drug in chemotherapy for patients with advanced colorectal cancer, but many patients still suffer from treatment failure due to 5-Fu resistance. Emerging observations revealed the important role of chemokine (C-X-C motif) ligand 13 (CXCL-13) in tumor microenvironment and its relationship with prognosis in patients with colorectal cancer. This study is designed to reveal the important role of CXCL-13 in causing colorectal cancer resistance to 5-Fu. Materials and Methods CXCL-13 levels of patient's serum or cell culture supernatants were measured separately by enzyme-linked immunosorbent assay. In cell assays, cell viability is detected by Cell Counting Kit-8. Therefore, the recombinant human CXCL-13 was used to simulate its high expression in cells while its antibody and siRNA were used to reduce CXCL-13 expression in cells. Results In this study, we demonstrated that CXCL-13 is associated with 5-Fu resistance by culture medium exchange experiments and cytokine arrays of colorectal cancer resistant and nonresistant cells. Clinical studies showed that CXCL-13 is highly expressed in the serum of 5-Fu–resistant patients. High levels of serum CXCL-13 also predict a worse clinical outcome. The addition of recombinant CXCL-13 cytokine resulted in 5-Fu resistance, while its antibody overcame 5-Fu resistance, and knockdown of CXCL-13 expression by siRNA also reduced 5-Fu resistance, which can be saved by added recombination CXCL-13. Conclusion These results not only identify a CXCL-13 mediated 5-Fu resistance mechanism but also provide a novel target for 5-Fu–resistant colorectal cancer in prevention and treatment strategies.

Comparative transcriptome profiling of chilling tolerant rice chromosome segment substitution line in response to early chilling stress

Rongbai Li,Jijing Luo,Yongliang Wang,Qigui Jiang,Jianbin Liu,Wei Zeng,Yindi Zeng 한국유전학회 2017 Genes & Genomics Vol.39 No.2

Rice (Oryza sativa L.) is thermophilic crop and all of its growth stages are affected by low temperature stress. However, some populations of common wild rice in Guangxi Province (China) (GXWR) can tolerate low temperature stress. To understand the molecular mechanisms underlying chilling tolerance in these wild rice resources, transcriptome sequencing was performed to study the differentially expressed genes (hereafter referred to as DEGs) between GXWR-derived chilling-tolerant chromosome segment substitution line (hereafter referred to as CSSL), DC90, and its chilling-sensitive recurrent parent 9311 under early chilling stress. Comparative transcriptomic analysis revealed 659 DEGs exclusively identified in DC90 in response to early chilling stress. Functional clustering by CARMO (comprehensive annotation platform for functional exploration of rice multiomics data) showed that majority of the DEGs were enriched in chloroplasts, suggesting a connection between chilling stress tolerance and photosynthesis regulation exists in rice. KEGG analysis of these DEGs presented a complicated chilling responsive regulatory network, including ‘phytohormone signaling’, ‘photosynthesis pathway’, ‘ribosome translation machinery’, ‘phenylpropanoid biosynthesis’, which is coordinately involved in early chilling response. Here, the identified DEGs and unveiled molecular regulatory network sheds light on deep understanding the mechanisms underlying rice chilling stress tolerance. As well, KEGG term-enriched DEGs, chilling tolerant QTLs (quantitative trait loci), and co-localized DEGs in introgression interval, will be focused for further functional investigation of the molecular mechanisms of chilling stress response in rice.

Thermal-mechanical fully coupled analysis of high-speed angular contact ball bearings

Lanwen Wang,Xuanyu Sheng,Jianbin Luo 대한기계학회 2021 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.35 No.2

The thermal and mechanical properties of angular contact ball bearings are critical to their operating accuracy and service life. On the basis of the theory of dynamics and frictional heat generation, this work establishes a thermal-mechanical fully coupled model. The high-speed motion characteristics, temperature, and dynamic stiffness are analyzed, and the simulation results are compared with the theoretical calculation and experimental results. Then, the temperature and axial deformation of the bearings under different rotation speeds are analyzed, and the laws of mechanical and thermal characteristics of the bearings are obtained. Results show that an increase in the rotation speed of the inner ring causes the temperature of each component to increase, with the contact area of the balls showing the greatest increase in temperature. An increase in rotation speed also increases the axial deformation of the inner ring.

Sparsity maximization nonlinear blind deconvolution and its application in identification of satellite microvibration sources

Teng Gong,ZhouSuo Zhang,Xin Luo,Jianbin Cao,Yanfei Guo 대한기계학회 2020 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.34 No.1

In this study, sparsity maximization nonlinear blind deconvolution (NBD) is proposed to identify the vibration sources of satellite systems from mixed vibration signals. The proposed algorithm decomposes NBD into two independent stages, namely, nonlinear compensation and blind deconvolution. Since nonlinear distortion weakens the sparsity of the observed signals, sparsity maximization is introduced to the nonlinear compensation stage. In the blind deconvolution stage, the blind deconvolution algorithm with reference is used to separate the source signals. The proposed algorithm can improve the accuracy of source signal extraction from nonlinear mixed signals of complex mechanical systems. The effectiveness of the proposed method is verified through simulations. An experimental system of aluminum cabin structure is built based on the satellite’s cabin structure. Results show that the proposed algorithm can successfully realize the identification of source signals.