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1. Personalized prognostic signature for lung cancer based on 15 transcription-related gene pairs | |||
Liao Zili,Ren Zhihao,Zhang Boxiang,Zhu Ruiyu | |||
Biology 15 February 2023 | |||
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Abstract:Lung cancer is the most aggressive malignancy and the leading cause of cancer deaths worldwide. Currently, reliable biomarkers are lacking in the diagnosis, prognosis and treatment of lung cancer. Given the significant role of transcription factors in tumorigenesis and progression, we aimed to establish a signature based on transcription-related gene pairs for the first time to predict the prognosis of lung cancer patients. The gene expression data and clinical information of 1568 lung cancer patients were obtained from The Cancer Genome Atlas data portal (TCGA) and Gene Expression Omnibus (GEO) as a training cohort and validation cohort, respectively. Through univariate Cox analysis and Least Absolute Shrinkage and Selection Operator (LASSO) analysis, we screened 15 transcription-related gene pairs to construct the transcription-related prognostic signature. Based on this signature, the samples were classified into high-risk group and low-risk group. Kaplan-Meier analysis and independent prognostic analysis showed that transcription-related prognostic signature predicted overall survival in lung cancer patients (p < 0.001). Compared with multiple clinical and pathological factors, the results of multivariate Cox regression analysis indicated that the signature was an independent prognostic factor in patients with lung cancer. Further analysis revealed the cellular pathways associated with this signature and the relationship between this signature and immune cell content. In conclusion, we established for the first time the signature of transcription-related genes on prognosis as an indicator to assess the overall survival in lung cancer patients. Our study provides new ideas for developing cancer prognostic signature and discovering new drug targets. | |||
TO cite this article:Liao Zili,Ren Zhihao,Zhang Boxiang, et al. Personalized prognostic signature for lung cancer based on 15 transcription-related gene pairs[OL].[15 February 2023] http://en.paper.edu.cn/en_releasepaper/content/4759077 |
2. Recombinant expression, fermentation and characterization of a type Ⅲ human like collagen | |||
XIANG Zhixiang,GONG Jingsong,XU Zhenghong,SHI Jingsong | |||
Biology 12 May 2022 | |||
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Abstract:Collagen, the highest content protein in the body, as irreplaceable biological functions, and it is widespread concerned in food, beauty, and medicine with great market demand. The gene encoding hlCOLⅢ α1 chain fragment was integrated into Pichia pastoris genome after partial amino acids were substituted. Combined with promoter engineering and high-density fermentation technology, soluble secretory expression with the highest yield of 1.05 g L-1 was achieved using two-stage feeding method, and the purity could reach 96% after affinity purification. The determination of N/C-terminal protein sequence were consistent with the theoretical expectation, glycine shared 27.02% and proline 23.92% in amino acid analysis, which were in accordance with the characteristics of collagen. Mass spectrometry combined with Fourier transform infrared spectroscopy and circular dichroism revealed that the target product existed as homologous dimer and trimer in the broth , which laid a foundation for exploring the self-assembly of collagen. | |||
TO cite this article:XIANG Zhixiang,GONG Jingsong,XU Zhenghong, et al. Recombinant expression, fermentation and characterization of a type Ⅲ human like collagen[OL].[12 May 2022] http://en.paper.edu.cn/en_releasepaper/content/4757718 |
3. Comparative transcriptome analysis reveals the mechanism of enhanced microbial hyaluronan biosynthesis | |||
Yao Zhiyuan,Gong Jinsong,Su Chang,Li Heng,Xu Zhenghong,Shi Jinsong | |||
Biology 11 May 2022 | |||
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Abstract:This study reveals the genetic and biochemical changes underlying the enhanced hyaluronan (HA) biosynthesis in Streptococcus zooepidemicus. The selected mutants performed a steady improvement of HA yield after multiple rounds of atmospheric and room temperature plasma (ARTP) mutagenesis combining with novel bovine serum albumin / cetyltrimethylammonium bromide coupled high-throughput screening assay. Compared to the corresponding wild type strains, the HA yield of the obtained mutant (mutant-A17) greatly increased by 42.9% with concomitant accelerated growth. Transcriptome sequencing exhibits that distinct mutants have similar genetic changes. Regulation in direction of metabolic flow into the HA biosynthesis, by enhancing genes responsible for the biosynthesis of HA including hasB, glmU and glmM, weaking downstream gene (nagA and nagB) of UDP-GlcNAc and significantly down-regulating transcription of wall-synthesizing genes, which could cause accumulation of precursors. These associated regulatory genes may provide control point for the efficient synthesis of HA and engineering of the HA-producing cell factory. | |||
TO cite this article:Yao Zhiyuan,Gong Jinsong,Su Chang, et al. Comparative transcriptome analysis reveals the mechanism of enhanced microbial hyaluronan biosynthesis[OL].[11 May 2022] http://en.paper.edu.cn/en_releasepaper/content/4757714 |
4. Preliminary study on the function of 6mA demethylase in Arabidopsis thaliana | |||
Min Gao,Chongsheng He | |||
Biology 07 April 2022 | |||
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Abstract:N6-methyladenine (6mA) is the most conservative and common epigenetic marker in prokaryotes. The function and distribution of 6mA in eukaryotes, especially in plants, is still a mystery. It has been reported that 6mA does exist in plants and plays a vital role. However, how 6mA affects plant development, high temperature resistance and stress response is still unknown. 6mA has been proved to be a dynamic modification in eukaryotes, mediated by methyltransferase and demethylase. Arabidopsis thaliana is the model organism for plant biology and system biology research. In this study, we used Arabidopsis thaliana as material to identify 6mA demethylase in plants. Through bioinformatics analysis and in vitro enzyme activity experiment, 6mA demethylase in Arabidopsis thaliana has been found, which paved the road for the study of function and mechanism of demethylase in plants. | |||
TO cite this article:Min Gao,Chongsheng He. Preliminary study on the function of 6mA demethylase in Arabidopsis thaliana[OL].[ 7 April 2022] http://en.paper.edu.cn/en_releasepaper/content/4757339 |
5. Research progress of related methods for controlling targeted protein level | |||
MIn Gao,ChongSheng He | |||
Biology 10 August 2021 | |||
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Abstract:In this paper, we reviewed the progress of target protein degradation methods, with special attention to the use of plant hormones to stimulate the degradation. Protein is the key player of many biological processes, interfering the protein level precisely is both important for basic research and clinical application. There are many ways to control the protein level artificially in different levels such as CRISPR-Cas9, RNAi and so on. These methods show different limitations, for example, CRISPR-Cas9 is irreversible, RNAi can cause off-target effect. Targeted protein degradation is one of the ways to regulate the protein level in a post-translational level, it can affect the protein level very fast and reversibly. To achieve targeted protein degradation, different methods have been developed such as small-molecule induced degradation, photo-induced degradation, auxin induced degradation and so on. The core principle is to degrade the target protein in a controllable manner. | |||
TO cite this article:MIn Gao,ChongSheng He. Research progress of related methods for controlling targeted protein level[OL].[10 August 2021] http://en.paper.edu.cn/en_releasepaper/content/4755399 |
6. A 110 nt fragment in the 5\'UTR of STAT2 that determines IRES activity and influences cell proliferation | |||
Zhou Kantian,Liao Zili,Zhu Ruiyu | |||
Biology 30 March 2021 | |||
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Abstract:As a unique member of the STAT (Signal Transducer and Activator of Transcription) proteins family, STAT2 cannot recognize DNA target sites as homodimers like the others, yet it plays a critical role in type I interferon (IFN-I) signaling and many other signaling pathways. It was reported that STAT2 could help cells to cope with stress conditions by promoting antiviral responses in normal cells or drug resistance in carcinoma cells. As IRES (Internal Ribosome Entry Sites) were known to help promoting survival of cells under stress, together with the discovery that the 5\'UTR of STAT2 could form stable stem-loop secondary structures with a length of 203 nt, suggesting that there might be IRES activity. To testify this speculation, bicistronic reporter assay was designed as the main method to find out whether the 5\'-UTR of STAT2 harbors an IRES element or not. During the process, the IRES activity was confirmed, followed by the discovery that IRES active central domain was located at nt 33-142 in the 5\'UTR of STAT2. Afterwards, CRISPR/Cas9 techniques were utilized to construct a knockout cell line with the deletion of sequence between nt 65-129 in 5\'UTR. And it was discovered that knockout cells grew slightly faster than those wild type ones, which meant that the knocked-out fragment had an impact on normal cell proliferation. The exact mechanism behind this result remains to be further investigated. | |||
TO cite this article:Zhou Kantian,Liao Zili,Zhu Ruiyu. A 110 nt fragment in the 5\'UTR of STAT2 that determines IRES activity and influences cell proliferation[OL].[30 March 2021] http://en.paper.edu.cn/en_releasepaper/content/4754243 |
7. Enhancement of cytoplasmic solubility of heparinase I from Flavobacterium heparinum in Escherichia coli by adding charged tag and co-expression of molecular chaperonin from hyperthermophilic archaea. | |||
Guo Yu,Li Huichao,Zhang Hao,Fujiwara Shinsuke,Gao Le | |||
Biology 01 February 2021 | |||
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Abstract:Heparinase is important in the heparin production and application. The most studied heparinase I is HepA which is secreted by Flavobacterium heparinum. Since HepA was hard to obtain as a soluble form in Escherichia coli, many works were tried to increase cytoplasmic solubility of HepA by adding various protein tags to the HepA terminus. Here we designed a positively charged hexapeptide tag (RGRRGG) which was expected to have enhanced affinity to a chaperonin CpkA from hyperthermophilic archaeaon Thermococcus kodakarensis. HepA was first fused with RGRRGG and expressed by plasmid pET21a. Effect of tag addition on cytoplasmic soluble amount of HepA in E. coli were examined, showing that the amount of the tag fused HepA(HepA\') was boosted in comparison with tag-less original one. HepA\' was next co-expressed with a CpkA by another compatible plasmid pACYCDuet-1. By CpkA co-expression, insoluble amount of HepA\' was decreased and soluble amount of HepA\' was increased and reached to 40% of total expressed amount of HepA\'. The specific activity (126 IU/mg) was also comparable to the native HepA (130 IU/mg). The present data indicated that tag-charged HepA was efficiently obtained as an active form by co-expressing CpkA. (10 Points, Times New Roman) | |||
TO cite this article:Guo Yu,Li Huichao,Zhang Hao, et al. Enhancement of cytoplasmic solubility of heparinase I from Flavobacterium heparinum in Escherichia coli by adding charged tag and co-expression of molecular chaperonin from hyperthermophilic archaea.[OL].[ 1 February 2021] http://en.paper.edu.cn/en_releasepaper/content/4753657 |
8. Characterization and isolation of estradiol degrading bacteria Acinetobacter sp. (7-1) Isolated from Changchun, China. | |||
YU Jian,ZHAO yanyang,HOU yue | |||
Biology 15 December 2020 | |||
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Abstract:17β- Estradiol, as a major environmental estrogen, is a serious threat to human health and ecological security. The MS medium containing 0.5 mM estradiol as the sole carbon source was used to isolate a new Gram-negative bacteria from the fishing pond. This screening strain can use as the sole carbon source and energy source such as estradiol and testosterone. After 16S rRNA analysis, the bacteria belong to Acinetobacter sp with 99.71% identity. The strain was Gram-negative bacilli, Spherical, Blunt round ends, Scattered or arranged in pairs, No bud, No flagella. Size 2.126μm×0.753μm; Conditions for optimum degradation of estradiol were 27℃, 150 rpm, and substrate concentration was 1 mM/L, pH7.5 and 1% inoculum. The highest degradation rate, the degradation rate can reach 85%. The strain could grow normally in 5 μg/mL auromycin, but not in 100 μg/mL ampicillin,50 μg/mL kanamycin,10 μg/mL streptomycin. The degradation rate of 17β- estradiol was 81.4%, that of testosterone was 64.6%, that of progesterone was 44.6%, and that of 17α- ethinyl estradiol was 62.3% by high performance liquid chromatography. | |||
TO cite this article:YU Jian,ZHAO yanyang,HOU yue. Characterization and isolation of estradiol degrading bacteria Acinetobacter sp. (7-1) Isolated from Changchun, China.[OL].[15 December 2020] http://en.paper.edu.cn/en_releasepaper/content/4753226 |
9. Tyrosine hydroxylase (TH) upstream-inhibited UPF3 regulator of nonsense transcripts homolog A (UPF3A) subnetwork for learning in human left hemisphere|Prostate via nucleus to mitochondrion to cytosol RNA binding | |||
Xi Ruipeng,HUANG Juxiang,WANG Lin | |||
Biology 14 September 2020 | |||
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Abstract:High tyrosine hydroxylase (TH) upstream-inhibited UPF3 regulator of nonsense transcripts homolog A (yeast) (UPF3A) molecular subnetwork was constructed, including upstream hypothetical LOC400642 (LOC400642), retinoblastoma binding protein 6 (RBBP6), ubiquitin protein ligase E3 component n-recognin 5 (UBR5); downstream chromosome 10 open reading frame 10 (C10orf10), sulfotransferase family 1A member 2 (SULT1A2) reported relation with learning in human left hemisphere. The common biology process of TH upstream-inhibited UPF3A subnetwork was identified by DAVID, containing upstream RBBP6, upstream UBR5, downstream SULT1A2, second-core UPF3A, first-core TH as protein binding; upstream RBBP6, upstream UBR5 as ubiquitin protein transferase activity, zinc ion binding, ligase activity, cellular response to DNA damage stimulus, protein ubiquitination involved in ubiquitin dependent protein catabolic process; upstream UBR5, second-core UPF3A as RNA binding; downstream SULT1A2, first-core TH as small molecule metabolic process; The common cellular component of upstream RBBP6, upstream UBR5, second-core UPF3A, first-core TH as cytoplasm; upstream RBBP6, upstream UBR5, second-core UPF3A as nucleoplasm; upstream UBR5, second-core UPF3A, first-core TH as nucleus; downstream SULT1A2, second-core UPF3A, first-core TH as cytosol; downstream C10orf10, first-core TH as mitochondrion; The common tissue distributions as Prostate_3rd maybe exist the same pattern with human left hemisphere. We propose and mutual positively verify tyrosine hydroxylase (TH) upstream-inhibited UPF3 regulator of nonsense transcripts homolog A (yeast) (UPF3A) subnetwork for learning in human left hemisphere|Prostate via nucleus to mitochondrion to cytosol RNA binding. | |||
TO cite this article:Xi Ruipeng,HUANG Juxiang,WANG Lin. Tyrosine hydroxylase (TH) upstream-inhibited UPF3 regulator of nonsense transcripts homolog A (UPF3A) subnetwork for learning in human left hemisphere|Prostate via nucleus to mitochondrion to cytosol RNA binding[OL].[14 September 2020] http://en.paper.edu.cn/en_releasepaper/content/4752808 |
10. Observe the difference of COVID-19 variation in different regions from the type and number of base mutations | |||
LIU Jian-Zhong, Zheng Jeffrey | |||
Biology 06 May 2020 | |||
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Abstract:Collecting Covid-19 genomes from three regions: Shanghai-China, Tbilisi-Georgia and Sydney-Australia, five similar genomes are selected from each region for research in this paper. Applying ”Datum gene sequence” method proposed,our results are shown that variation is immense in Sydney-Australia region, then variation is shown in the second in Tbilisi-Georgia region and it has a minimal value in Shanghai-China region respectively. | |||
TO cite this article:LIU Jian-Zhong, Zheng Jeffrey. Observe the difference of COVID-19 variation in different regions from the type and number of base mutations[OL].[ 6 May 2020] http://en.paper.edu.cn/en_releasepaper/content/4751960 |
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