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Development and applications of functional gene microarrays in the analysis of the functional diversity

Zhili HE, Joy D. VAN NOSTRAND, Ye DENG, Jizhong ZHOU

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 1-20 doi: 10.1007/s11783-011-0301-y

摘要： Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification, array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration, and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.

关键词： functional gene arrays (FGAs)     GeoChip     microbial communities     functional diversity/composition/structure     environmental factor     ecosystem functioning    

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Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

《医学前沿（英文）》 2024年 第18卷 第1期   页码 109-127 doi: 10.1007/s11684-023-1008-8

摘要： Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer–promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.

关键词： 3D genome     cancer     TADs     loop     gene regulation    

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Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

《医学前沿（英文）》 2007年 第1卷 第1期   页码 93-98 doi: 10.1007/s11684-007-0018-2

摘要： The purpose of this study was to explore the differentially expressed genes in lymph-node cells (LNC) of lymphomas and reactive lymph node hyperplasia, and to perform an initial bioinformatic analysis on a novel gene, KIAA0372, which is highly expressed in the LNC of lymphomas. mRNA extracted from LNC of lymphomas and reactive lymph node hyperplasia were respectively marked with biotin and hybridized with Gene Expression Chips, resulting in differentially expressed genes. Initial bioinformatic analysis was then performed on a novel gene named KIAA0372, whose function has not yet been explored. Its structure and genomic location, its product s physical and chemical properties, subcellular localization and functional domains, were also predicted. Further, a systematic evolution analysis was performed on similar proteins from among several species. Using Gene Expression Chips, many differentially expressed genes were uncovered. Efficient bioinformatic analysis has fundamentally determined that KIAA0372 is an extracellular protein which may be involved in TGF-β signaling. Microarray is an efficient and high throughput strategy for detection of differentially expressed genes. And KIAA0372 is thought to be a potential target for tumor research using bioinformatic analysis.

关键词： bioinformatic analysis     functional     KIAA0372     detection     Microarray    

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FUNCTIONAL GAIN OF FRUIT NETTED-CRACKING IN AN INTROGRESSION LINE OF TOMATO WITH HIGHER EXPRESSION OFTHE FNC GENE

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Fruit cracking is a major disorder that affects the integrity of fruit and reduces the commercial value of tomato and other fleshy fruit. Here, we have found a novel fruit ‘netted-cracking’ (FNC) phenotype in tomato introgression line IL4-4 which is present in neither the donor parent (LA0716) nor the receptor parent (M82). An F2 population was generated by crossing IL4-4 with M82 to genetically characterize the FNC gene and this showed that a single dominant gene determined fruit netted-cracking. Further map-based cloning narrowed down the FNC locus to a 230 kb region on chromosome 4. Sequencing and annotation analysis show that FNC(Solyc04 g082540) was the most likely candidate gene. Functional characterization of FNC by overexpressing FNCAC and FNCIL4-4resulted in the fruit netted-cracking phenotype, suggesting that the FNC transcript level results in the functional gain of fruit netted-cracking. These findings were further confirmed by FNC ortholog in netted-cracking pepper and melon, indicating a common regulatory mechanism in different plant species. Furthermore, cytoplasm and nucleus-localized FNC indicates increased expression of genes involved in suberin, lignin, lipid transport and cell wall metabolism. These findings provide novel genetic insights into fruit netted-cracking and offer a way to promote molecular improvement toward cracking resistant cultivars.

 

关键词： fine mapping / fruit netted-cracking / introgression line / transcript level    

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Engineering the grain boundary: a promising strategy to configure NiCoPO/NiCoP nanowire arrays for ultra-stable

《化学科学与工程前沿（英文）》 2022年 第16卷 第8期   页码 1259-1267 doi: 10.1007/s11705-021-2132-0

摘要： NiCoP4O12/NiCoP nanorod-like arrays with tunable grain boundary density and pores were synthesized by the processes composed of hydrothermal and pyrolysis, in which, the electron structure of Ni and Co atoms characterized by X-ray photoelectron spectroscopy was contemporaneous inverse manipulated. The optimized NiCoP4O12/NiCoP arrays have a high specific capacitance of 507.8 μAh∙cm–2 at 1 mA∙cm–2, and good rate ability of 64.7% retention at 30-folds increased current density. Importantly, an ultra-stable ability, 88.5% of retention after 10000 cycles, was achieved in an asymmetric cell assembled of the NiCoP4O12/NiCoP arrays with activated carbon. In addition, the energy and power densities of an asymmetric cell were higher than those of other work, demonstrating as-prepared NiCoP4O12/NiCoP arrays are promising electrodes for supercapacitors.

关键词： NiCo     array electrode     grain boundary     stability     supercapacitor    

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Erratum to: Polypyrrole@NiCo hybrid nanotube arrays as high performance electrocatalyst for hydrogen

Shenghua Ye, Gaoren Li

《化学科学与工程前沿（英文）》 2019年 第13卷 第4期   页码 845-845 doi: 10.1007/s11705-019-1879-z

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Tuning the electronic structure of NiCoP arrays through V doping for pH-universal hydrogen evolution

Yu Lin, Jinlei Wang, Duanlin Cao, Yaqiong Gong

《化学科学与工程前沿（英文）》 2021年 第15卷 第5期   页码 1134-1146 doi: 10.1007/s11705-020-2014-x

摘要： The exploration of cost-effective, high-performance, and stable electrocatalysts for the hydrogen evolution reaction (HER) over wide pH range (0–14) is of paramount importance for future renewable energy conversion technologies. Regulation of electronic structure through doping vanadium atoms is a feasible construction strategy to enhance catalytic activities, electron transfer capability, and stability of the HER electrode. Herein, V-doped NiCoP nanosheets on carbon fiber paper (CFP) (denoted as V -NiCoP/CFP) were constructed by doping V modulation on NiCoP nanosheets on CFP and used for pH-universal HER. Benefiting from the abundant catalytic sites and optimized hydrogen binding thermodynamics, the resultant V -NiCoP/CFP demonstrates a significantly improved HER catalytic activity, requiring overpotentials of 46.5, 52.4, and 85.3 mV to reach a current density of 10 mA·cm in 1 mol·L KOH, 0.5 mol·L H SO , and 1 mol·L phosphate buffer solution (PBS) electrolytes, respectively. This proposed cation-doping strategy provides a new inspiration to rationally enhance or design new-type nonprecious metal-based, highly efficient, and pH-universal electrocatalysts for various energy conversion systems.

关键词： hydrogen evolution reaction     transition metal phosphides     pH-universal     vanadium doping     carbon fiber paper    

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Nickel nanopore arrays as promising current collectors for constructing solid-state supercapacitors with

Huaping Zhao, Long Liu, Yaoguo Fang, Ranjith Vellacheri, Yong Lei

《化学科学与工程前沿（英文）》 2018年 第12卷 第3期   页码 339-345 doi: 10.1007/s11705-018-1699-6

摘要：

In this work, nickel nanopore arrays with a highly-oriented nanoporous structure inherited from porous alumina membranes were used as nanostructured current collectors for constructing ultrahigh rate solid-state supercapacitors. A thin layer of poly(3,4-ethylenedioxythiophene) (PEDOT) as electroactive materials was conformally coated onto nickel nanopores to form heterostructured electrodes. The as-prepared electrodes have a large specific surface area to ensure a high capacity, and the highly-oriented nanoporous structure of nickel nanopores reduces the ion transport resistance, allowing the ions in the solid-state electrolytes to quickly access the PEDOT surface during the fast charge-discharge process. As a result, the assembled solid-state supercapacitor in a symmetric configuration exhibits an ideal capacitive behavior and a superior rate capability even at an ultrahigh scan rate of 50 V·s−1.

关键词： supercapacitor     ultrahigh rate     metallic nanopore arrays     current collectors     PEDOT    

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Construction of NiCoO nanoflake arrays on cellulose-derived carbon nanofibers as a freestanding electrode

《化学科学与工程前沿（英文）》 2023年 第17卷 第6期   页码 691-703 doi: 10.1007/s11705-022-2268-6

摘要： Cellulose has a wide range of applications in many fields due to their naturally degradable and low-cost characteristics, but few studies can achieve cellulose-nanofibers by conventional electrospinning. Herein, we demonstrate that the freestanding cellulose-based carbon nanofibers are successfully obtained by a special design of electrospinning firstly, pre-oxidation and high-temperature carbonization (1600 °C), which display a superior electrical conductivity of 31.2 S·cm–1 and larger specific surface area of 35.61 m2·g–1 than that of the polyacrylonitrile-based carbon nanofibers (electrical conductivity of 18.5 S·cm–1, specific surface area of 12 m2·g–1). The NiCo2O4 nanoflake arrays are grown uniformly on the cellulose-based carbon nanofibers successfully by a facile one-step solvothermal and calcination method. The as-prepared cellulose-based carbon nanofibers/NiCo2O4 nanoflake arrays are directly used as electrodes to achieve a high specific capacitance of 1010 F·g–1 at 1 A·g–1 and a good cycling stability with 90.84% capacitance retention after 3000 times at 10 A·g–1. Furthermore, the all-solid-state symmetric supercapacitors assembled from the cellulose-based carbon nanofibers/NiCo2O4 deliver a high energy density of 62 W·h·kg–1 at a power density of 1200 W·kg–1. Six all-solid-state symmetric supercapacitors in series can also power a ‘DHU’ logo consisted of 36 light emitting diodes, confirming that the cellulose-based carbon nanofiber is a promising carbon matrix material for energy storage devices.

关键词： cellulose     carbon nanofibers     NiCo2O4     supercapacitors    

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Polypyrrole@NiCo hybrid nanotube arrays as high performance electrocatalyst for hydrogen evolution reaction

Shenghua Ye, Gaoren Li

《化学科学与工程前沿（英文）》 2018年 第12卷 第3期   页码 473-480 doi: 10.1007/s11705-018-1724-9

摘要：

The polypyrrole(PPy)@NiCo hybrid nanotube arrays have been successfully fabricated as a high performance electrocatalyst for hydrogen evolution reaction (HER) in alkaline solution. The strong electronic interactions between PPy and NiCo alloy are confirmed by X-ray photoelectron spectroscopy and Raman spectra. Because these interations can remarkably reduce the apparent activation energy (Ea) for HER and enhance the turnover frequency of catalysts, the electrocatalytic performance of PPy@NiCo hybrid nanotube arrays are significantly improved. The electrochemical tests show that the PPy@NiCo hybrid catalysts exhibit a low overpotential of ~186 mV at 10.0 mA·cm−2 and a small tafel slope of 88.6 mV·deg−1 for HER in the alkaline solution. The PPy@NiCo hybrid nanotubes also exhibit high catalytic activity and high stability for HER.

关键词： NiCo alloy     polypyrrole     hybrid nanotube     electrocatalyst     hydrogen evolution reaction    

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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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Fluorescent probes and functional materials for biomedical applications

《化学科学与工程前沿（英文）》 2022年 第16卷 第10期   页码 1425-1437 doi: 10.1007/s11705-022-2163-1

摘要： Due to their simplicity in preparation, sensitivity and selectivity, fluorescent probes have become the analytical tool of choice in a wide range of research and industrial fields, facilitating the rapid detection of chemical substances of interest as well as the study of important physiological and pathological processes at the cellular level. In addition, many long-wavelength fluorescent probes developed have also proven applicable for in vivo biomedical applications including fluorescence-guided disease diagnosis and theranostics (e.g., fluorogenic prodrugs). Impressive progresses have been made in the development of sensing agents and materials for the detection of ions, organic small molecules, and biomacromolecules including enzymes, DNAs/RNAs, lipids, and carbohydrates that play crucial roles in biological and disease-relevant events. Here, we highlight examples of fluorescent probes and functional materials for biological applications selected from the special issues “Fluorescent Probes” and “Molecular Sensors and Logic Gates” recently published in this journal, offering insights into the future development of powerful fluorescence-based chemical tools for basic biological studies and clinical translation.

关键词： fluorescent probes     imaging     cell     biomedicine     biomolecules    

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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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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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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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标题 作者 时间 类型 操作

Development and applications of functional gene microarrays in the analysis of the functional diversity

Zhili HE, Joy D. VAN NOSTRAND, Ye DENG, Jizhong ZHOU

期刊论文

Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

期刊论文

Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

期刊论文

FUNCTIONAL GAIN OF FRUIT NETTED-CRACKING IN AN INTROGRESSION LINE OF TOMATO WITH HIGHER EXPRESSION OFTHE FNC GENE

期刊论文

Engineering the grain boundary: a promising strategy to configure NiCoPO/NiCoP nanowire arrays for ultra-stable

期刊论文

Erratum to: Polypyrrole@NiCo hybrid nanotube arrays as high performance electrocatalyst for hydrogen

Shenghua Ye, Gaoren Li

期刊论文

Tuning the electronic structure of NiCoP arrays through V doping for pH-universal hydrogen evolution

Yu Lin, Jinlei Wang, Duanlin Cao, Yaqiong Gong

期刊论文

Nickel nanopore arrays as promising current collectors for constructing solid-state supercapacitors with

Huaping Zhao, Long Liu, Yaoguo Fang, Ranjith Vellacheri, Yong Lei

期刊论文

Construction of NiCoO nanoflake arrays on cellulose-derived carbon nanofibers as a freestanding electrode

期刊论文

Polypyrrole@NiCo hybrid nanotube arrays as high performance electrocatalyst for hydrogen evolution reaction

Shenghua Ye, Gaoren Li

期刊论文

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

期刊论文

Fluorescent probes and functional materials for biomedical applications

期刊论文

Molecular engineering of dendrimer nanovectors for siRNA delivery and gene silencing

Yu Cao, Xiaoxuan Liu, Ling Peng

期刊论文

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

null

期刊论文

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

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

期刊论文