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Cloning of human XAF1 gene promoter and assay of its transcription activity in a variety of cell lines

Qiong CHEN, Qing YU, Yuhu SONG, Peiyuan Li, Ying CHANG, Zhijun WANG, Lifeng LIU, Wei WU, Jusheng LIN

《医学前沿（英文）》 2009年第3卷第2期页码 148-152 doi: 10.1007/s11684-009-0032-7

摘要： To investigate the regulation of tumor suppressor XAF1 gene expression in digestive system cancers, we studied XAF1 gene promoter transcription activity and mRNA level in digestive system cancer cell lines (human hepatoma cell line HepG2, human colon cancer cell line LoVo, and human gastric cancer cell line AGS) and nontumor cell lines (human embryonic liver cell line L02 (L02 cells) and human embryonic kidney 293 cells [HEK293 cells]) as controls. 1395-bp-promoter fragment of XAF1 gene was amplified by polymerase chain reaction (PCR) and cloned into pGL3-basic vector and pEGFP-1 vector to assay its promoter transcription activity. The plasmids were transfected into a variety of cell lines by lipofectamine 2000. The promoter transcription activity was determined by dual-luciferase report assay, and enhanced green fluorescent protein (EGFP)-positive cells were detected by fluorescence microscope. The expression of XAF1 mRNA in HEK293 and L02 were significantly higher than that in any of the three digestive system cancer cell lines. The dual-luciferase reporter assay showed that the promoter transcription activity in digestive system tumor cell lines transfected with pGL3-XAF1p promoter was apparently lower than that of both HEK293 and L02 cells. Expression of green fluorescent protein (GFP) under the control of XAF1 promoter in the three digestive system cancer cell lines was lower than that of both HEK293 and L02 cells. The activities of pGL3-XAF1p in the three digestive system cancer cell lines after treatment with heat stress were significantly lower than those in the unstressed cells. The results suggested that remarkably down-regulated XAF1 mRNA expression in digestive system cancer cell lines may be due to loss of transcription activity of XAF1 promoter.

关键词： gene X-linked inhibitor of apoptosis protein associated factor-1 (XAF1) promoter transcription regulation

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Hepatitis B virus X protein upregulates tumor necrosis factor-α expression of rat mesangial cell

Hong-Zhu LU MD, Dan LIU BM, Qi-Hong FAN BM, Jian-Hua ZHOU MD,

《医学前沿（英文）》 2010年第4卷第1期页码 106-111 doi: 10.1007/s11684-010-0004-y

摘要： Hepatitis B virus X protein (HBx), a 17-kd protein encoded by X gene of hepatitis B virus (HBV), has been shown to function as a transcriptional trans-activator of a variety of viral and cellular promoter/enhancer elements. The aim of the study is to investigate the extracellular regulated protein kinases (ERKs) pathway of HBx on glomerular mesangial cell (GMC) proliferation and tumor necrosis factor-α (TNF-α) expression. The HBV X gene was amplified by polymerase chain reaction (PCR), inserted into the eukaryotic expression vector pCI-neo and confirmed by restriction endonuclease digestion and sequence analysis. PCI-neo containing HBV X gene (pCI-neo-X) was then transfected into cultured GMC line via liposome. GMC proliferation, TNF-α and its mRNA expression were compared in the condition of with or without U0126 in culture media. HBx, ERK and p-ERK expression in GMCs was assessed by Western blotting. TNF-α mRNA expression was assessed by semi-quantitative reverse transcription-PCR (RT-PCR). TNF-α level in supernatants was measured by ELISA. GMC proliferation was detected by 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide (MTT) kit. The results showed that HBx expression was found in transfected GMCs and became prominent at 36th and 48th h after transfection whether with or without U0126 in culture media. TNF-α mRNA expression was significantly decreased in U0126 group compared with U0126-free group. TNF-α levels in supernatants in PCI-neo-X transfection without U0126 group were (189.0±18.1) and (172.3±24.3) pg/mL at 36th and 48th h after transfection, respectively. In contrast, TNF-α levels in supernatants with U0126 were (65.6±11.6) and (84.0±24.6) pg/mL at 36th and 48th h, respectively. The TNF-α levels in the latter groups were significantly lower than those in the former groups (<0.05). GMCs proliferation was also lower in added U0126 group at 36th and 48th h after transfection. From above, we can conclude that HBx could induce GMC proliferation and increase TNF-α mRNA expression and its protein production. HBx upregulates TNF-α expression and induces cell proliferation of GMC line partly through ERK signal transduction pathway.

关键词： hepatitis B virus X gene glomerular mesangial cell line extracellular regulated protein kinases tumor necrosis factor-α

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing in Chinese patients

《医学前沿（英文）》页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma whole-genome sequencing TMSB4X copy number variation gene mutation

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人类遗传病的家系收集疾病基因定位克隆与疾病基因功能的研究

夏家辉

《中国工程科学》 2000年第2卷第11期页码 1-11

摘要：

介绍了中国医学遗传学国家重点实验室在遗传病家系收集、疾病基因定位、疾病基因克隆和疾病基因功能研究方面的研究工作。用细胞遗传学G显带技术于1975年发现了一条与鼻咽癌相关的标记染色体t（1；3）（q44；p11）；1981年将睾丸决定基因（TDF）定位于Yp11.32带；1991年以来收集遗传病家系345种共590个；1996年用显微切割、PCR、微克隆技术克隆了EXT2基因；1998年用基因家族-候选疾病基因克隆方法克隆了遗传性神经性耳聋基因GJB3；1999年用连锁分析和全基因组扫描将一种遗传性弥漫性浅表性光敏性汗孔角化症定位于12q23.2带，并在基因功能研究中发现了一个新的细胞内转运蛋白。

关键词：遗传病家系基因定位和克隆基因家族-候选疾病基因克隆基因组扫描基因功能研究

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采用白光X射线源和模拟阵列能量色散阵列探测器的高通量粉末衍射技术 Article

汪晓平, 董伟伟, 张鹏, 唐浩琪, 张澜庭, 杨铁莹, 刘鹏, 汪洪, 项晓东

《工程（英文）》 2022年第10卷第3期页码 81-88 doi: 10.1016/j.eng.2021.05.023

摘要： text-align: justify;">在上海同步辐射光源（SSRF）的弯铁光束线上，利用由空间扫描硅漂移探测器（SDD）模拟获得的能量色散阵列探测器，对CeO₂样品进行高通量白光X射线粉末衍射校正后的衍射图谱表明，由能量色散X 射线衍射（EDXRD）获得的不同衍射峰之间的相对强度与来自角度分辨X射线衍射（ARXRD）的相对强度一致，说明EDXRD结果可用于分析未知样品的晶体结构。实验同时采集了X射线荧光（XRF）信号。来自所有像素的XRF计数可直接在能量坐标下叠加，而衍射信号则需在d 空间下叠加，从而大大改善了阵列探测器的峰值强度和信噪比（S/N）。与ARXRD相比，白光X射线衍射信号强度是单色光衍射信号强度的10⁴倍左右。

关键词：高通量实验白光X射线衍射能量色散阵列探测器能量色散X射线衍射角分辨X射线衍射

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Molecular engineering of dendrimer nanovectors for siRNA delivery and gene silencing

Yu Cao, Xiaoxuan Liu, Ling Peng

《化学科学与工程前沿（英文）》 2017年第11卷第4期页码 663-675 doi: 10.1007/s11705-017-1623-5

摘要： Small interfering RNA (siRNA) therapeutics hold great promise to treat a variety of diseases, as long as they can be delivered safely and effectively into cells. Dendrimers are appealing vectors for siRNA delivery by virtue of their well-defined molecular architecture and multivalent cooperativity. However, the clinical translation of RNA therapeutics mediated by dendrimer delivery is hampered by the lack of dendrimers that are of high quality to meet good manufacturing practice standard. In this context, we have developed small amphiphilic dendrimers that self-assemble into supramolecular structures, which mimic high-generation dendrimers synthesized with covalent construction, yet are easy to produce in large amount and superior quality. Indeed, the concept of supramolecular dendrimers has proved to be very promising, and has opened up a new avenue for dendrimer-mediated siRNA delivery. A series of self-assembling supramolecular dendrimers have consequently been established, some of them out-performing the currently available nonviral vectors in delivering siRNA to various cell types and , including human primary cells and stem cells. This short review presents a brief introduction to RNAi therapeutics, the obstacles to their delivery and the advantages of dendrimer delivery vectors as well as our bio-inspired structurally flexible dendrimers for siRNA delivery. We then highlight our efforts in creating self-assembling amphiphilic dendrimers to construct supramolecular dendrimer nanosystems for effective siRNA delivery as well as the related structural alterations to enhance delivery efficiency. The advent of self-assembling supramolecular dendrimer nanovectors holds great promise and heralds a new era of dendrimer-mediated delivery of RNA therapeutics in biomedical applications.

关键词： gene therapy RNAi therapeutics dendrimer nanovectors gene silencing

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生成锁P<G,X,X'>和它的中央加密系统

史开泉,陈泽雄

《中国工程科学》 2000年第2卷第2期页码 41-46

摘要：

利用数据生成技术，提出生成锁P <G ,X, X´>x,x´>的概念和由P <G ,X, X´>x,x´>构成的中央加密系统。这些系统是：生成锁P <G ,X, X´>x,x´>与单齿中央加密系统，生成锁P <G ,X, X´>x,x´>与多齿中央加密系统。x,x´>x,x´>x,x´>x,x´>

关键词：生成锁中央加密系统多齿加密-解密算法 P X X'>存在定理数位签章唯一性定理

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The antibiotic resistome: gene flow in environments, animals and human beings

null

《医学前沿（英文）》 2017年第11卷第2期页码 161-168 doi: 10.1007/s11684-017-0531-x

摘要：

The antibiotic resistance is natural in bacteria and predates the human use of antibiotics. Numerous antibiotic resistance genes (ARGs) have been discovered to confer resistance to a wide range of antibiotics. The ARGs in natural environments are highly integrated and tightly regulated in specific bacterial metabolic networks. However, the antibiotic selection pressure conferred by the use of antibiotics in both human medicine and agriculture practice leads to a significant increase of antibiotic resistance and a steady accumulation of ARGs in bacteria. In this review, we summarized, with an emphasis on an ecological point of view, the important research progress regarding the collective ARGs (antibiotic resistome) in bacterial communities of natural environments, human and animals, i.e., in the one health settings. We propose that the resistance gene flow in nature is “from the natural environments” and “to the natural environments”; human and animals, as intermediate recipients and disseminators, contribute greatly to such a resistance gene “circulation.”

关键词： antibiotic resistance resistome microbiome gene flow

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Reflections on the system of evaluation of gene-edited livestock

Ziyao FAN, Tianwen WU, Kui WU, Yulian MU, Kui LI

《农业科学与工程前沿（英文）》 2020年第7卷第2期页码 211-217 doi: 10.15302/J-FASE-2019303

摘要：

The rapid development of biotechnology has provided a greater understanding of the biological functions of major candidate genes that have important functions regarding economic traits, and new materials for livestock breeding have been obtained through gene editing (GE) and embryo manipulation with the purpose of improving quality and output and reducing the costs and risk of disease. Public concerns, particularly over safety risks and production performance, must be addressed. Evaluation is the most important component of the regulation of gene-edited livestock and is a crucial guarantee of public safety before the marketing of gene-edited animal products. Here, the system of evaluation of gene-edited livestock is discussed in terms of public safety and production performance. The search for safe and ethical applications in the GE of livestock, a case-by-case evaluation strategy, and classification and simplification are used in order to promote a more efficient, objective, comprehensive and operable evaluation system.

关键词： evaluation gene editing livestock performance safety

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Distinct gene expression pattern of mutations coordinated by target repression and promoter hypermethylation

《医学前沿（英文）》 2022年第16卷第4期页码 627-636 doi: 10.1007/s11684-020-0815-4

摘要： Runt-related transcription factor 1 (RUNX1) is an essential regulator of normal hematopoiesis. Its dysfunction, caused by either fusions or mutations, is frequently reported in acute myeloid leukemia (AML). However, RUNX1 mutations have been largely under-explored compared with RUNX1 fusions mainly due to their elusive genetic characteristics. Here, based on 1741 patients with AML, we report a unique expression pattern associated with RUNX1 mutations in AML. This expression pattern was coordinated by target repression and promoter hypermethylation. We first reanalyzed a joint AML cohort that consisted of three public cohorts and found that RUNX1 mutations were mainly distributed in the Runt domain and almost mutually exclusive with NPM1 mutations. Then, based on RNA-seq data from The Cancer Genome Atlas AML cohort, we developed a 300-gene signature that significantly distinguished the patients with RUNX1 mutations from those with other AML subtypes. Furthermore, we explored the mechanisms underlying this signature from the transcriptional and epigenetic levels. Using chromatin immunoprecipitation sequencing data, we found that RUNX1 target genes tended to be repressed in patients with RUNX1 mutations. Through the integration of DNA methylation array data, we illustrated that hypermethylation on the promoter regions of RUNX1-regulated genes also contributed to dysregulation in RUNX1-mutated AML. This study revealed the distinct gene expression pattern of RUNX1 mutations and the underlying mechanisms in AML development.

关键词： RUNX1 gene mutation acute myeloid leukemia transcriptional repression DNA methylation

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A mini review: Shape memory polymers for biomedical applications

Kaojin Wang, Satu Strandman, X. X. Zhu

《化学科学与工程前沿（英文）》 2017年第11卷第2期页码 143-153 doi: 10.1007/s11705-017-1632-4

摘要： Shape memory polymers (SMPs) are smart materials that can change their shape in a pre-defined manner under a stimulus. The shape memory functionality has gained considerable interest for biomedical applications, which require materials that are biocompatible and sometimes biodegradable. There is a need for SMPs that are prepared from renewable sources to be used as substitutes for conventional SMPs. In this paper, advances in SMPs based on synthetic monomers and bio-compounds are discussed. Materials designed for biomedical applications are highlighted.

关键词： shape memory polymer biodegradability biocompatibility biomedical application bile acids

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Construction of lentiviral vector carrying Rab9 gene and its expression in mouse brain

Youguo HAO, Min ZHANG, Jinzhi XU, Bitao BU, Jiajun WEI

《医学前沿（英文）》 2009年第3卷第2期页码 141-147 doi: 10.1007/s11684-009-0041-6

摘要： Rab proteins and their effectors facilitate vesicular transport by tethering donor vesicles to their respective target membranes. Rab9 mediates late endosome-to- -Golgi-network trafficking. To explore the possibility of Rab9-related gene therapy for neurodegenerative diseases, we packed Lentivirus encoding Rab9. The expressing plasmid pCDH1-MCF1-Rab9-EF1-copGFP was constructed by using molecular biological techniques. The Lentivirus encoding Rab9 cDNA was packed by Lifectamine-2000 mediated co-transfection of the plasmid pPACKH1- , pPACKH1- and pVSV- into 293T cells. DNA sequencing proved the successful construction of pCDH1-MCF1-Rab9-EF1-copGFP. After 72 hours, the expression of GFP could be detected in BV-2 cells. Western blotting revealed that the Rab9 gene expression in BALB/c mice brain was up-regulated significantly 4 weeks after injection with Lentivirus encoding Rab9, which evidenced a satisfactory increasing effect of this virus. Administration of Lenti-Rab9 to postnatal day 3 Niemann-Pick disease type C (NPC) mice reduced motor defects and prevented the weight loss associated with female NPC mice, as well as modulating the death rate of Purkinje neurons. It is concluded that the packaging of Lentivirus encoding Rab9 was successful. Lentivirus encoding Rab9 can increase the expression of Rab9 gene effectively, which might offer a novel means for the treatment of neurodegenerative diseases.

关键词： Rab9 lentivirus gene therapy gene transfer

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A study on quality evaluation for bituminous mixture using X-ray CT

Satoshi TANIGUCHI, Keiichiro OGAWA, Jun OTANI, Itaru NISHIZAKI

《结构与土木工程前沿（英文）》 2013年第7卷第2期页码 89-101 doi: 10.1007/s11709-013-0197-7

摘要： The objective of this paper is to propose a new quality evaluation method for asphalt concrete mixture using X-ray CT scanner. To achieve this aim, asphalt mixtures should be subjected to the X-ray CT scanning and its characteristics should be clarified. The approach employed in this study was as follows: 1) Coarse aggregate, fine aggregate, filler and bitumen were prepared; 2) dense-graded, coarse-graded and porous asphalt mixtures were made; 3) materials and mixtures were subjected to the X-ray CT scanning; 4) frequency of CT-value, threshold value, average slice CT-value, average segment CT-value were computed. In the material examination, CT-value of aggregate becomes smaller in the order of coarse aggregate, fine aggregate and filler and CT image of bitumen was nearly homogeneous. In the mixture examination, histograms of CT-value and four segmentation images made from CT images expressed the material and mixture characterization such as particle size and the difference in bitumen content and mixture type visibly and the bitumen content varies with the threshold values. In addition, the average segment CT-value without threshold value by dividing the fine aggregate from the coarse aggregate and average CT-value of the coarse aggregate, especially is highly correlated with average CT-value of the bitumen.

关键词： asphalt concrete mixture aggregate bitumen bitumen content quality evaluation X-ray CT

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Adsorption of fluoride on clay minerals and their mechanisms using X-ray photoelectron spectroscopy

Junyi DU, Daishe WU, Huayun XIAO, Ping LI

《环境科学与工程前沿（英文）》 2011年第5卷第2期页码 212-226 doi: 10.1007/s11783-010-0255-5

摘要： This research investigates the adsorption mechanisms of fluoride (F) on four clay minerals (kaolinite, montmorillonite, chlorite, and illite) under different F concentrations and reaction times by probing their fluoride superficial layer binding energies and element compositions using X-ray photoelectron spectroscopy (XPS). At high F concentrations ( = 5–1000 mg·L ), the amount of F adsorbed ( ), amount of hydroxide released by clay minerals, solution F concentration, and the pH increase with increasing . The increases are remarkable at >50 mg·L . The increases significantly by continuously modifying the pH level. At <5–100 mg·L , clay minerals adsorb H to protonate aluminum-bound surface-active hydroxyl sites in the superficial layers and induce F binding. As the increases, F , along with other cations, is adsorbed to form a quasi-cryolite structure. At >100 mg·L , new minerals precipitate and the product depends on the critical Al concentration. At [Al ]>10 mol·L , cryolite forms, while at [Al ]<10 mol·L , AlF is formed. At low (0.3–1.5 mg·L ), proton transfer occurs, and the F adsorption capabilities of the clay minerals increase with time.

关键词： clay mineral fluoride (F) adsorption mechanism X-ray photoelectron spectroscopy (XPS)

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Purification of ice structuring protein complexes from winter wheat using Triton X-114 phase partitioning

Huaneng XU, Haiying CHEN, Weining HUANG,

《化学科学与工程前沿（英文）》 2009年第3卷第4期页码 383-385 doi: 10.1007/s11705-009-0249-7

摘要： Ice structuring proteins (ISPs) isolated from the cold-acclimated plants have a great potential in improving the quality of frozen foods. The purification of ISP complexes from winter wheat was achieved using an aqueous two-phase system of Triton X-114. The highly reactive phenols were removed, and the ISP complexes remained in the aqueous phase after phase separation. The ISP complexes treated by this procedure retained higher thermal hysteresis activity than those treated by ammonium sulfate method. The phase separation technique provides a simple and mild way for removing phenols from ISP complexes.

关键词： separation technique thermal hysteresis cold-acclimated purification X-114