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Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

《农业科学与工程前沿(英文)》 2014年 第1卷 第1期   页码 77-84 doi: 10.15302/J-FASE-2014010

摘要: While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of .

关键词: Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

Identification of molecular markers linked to rice bacterial blight resistance genes from

Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

《农业科学与工程前沿(英文)》 2015年 第2卷 第3期   页码 260-265 doi: 10.15302/J-FASE-2015070

摘要: Y73 is a progeny of asymmetric somatic hybridization between cv. Dalixiang and the wild rice species . Inoculation with a range of strains of pv. showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB) from its wild parent. An F population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.

关键词: Oryza meyeriana     bacterial blight resistance gene     genetic population     linkage molecular marker    

Chinmedomics facilitated quality-marker discovery of Sijunzi decoction to treat spleen qi deficiency

Qiqi Zhao, Xin Gao, Guangli Yan, Aihua Zhang, Hui Sun, Ying Han, Wenxiu Li, Liang Liu, Xijun Wang

《医学前沿(英文)》 2020年 第14卷 第3期   页码 335-356 doi: 10.1007/s11684-019-0705-9

摘要: Sijunzi decoction (SJZD) is a Chinese classical formula to treat spleen qi deficiency syndrome (SQDS) and has been widely used for thousands of years. However, the quality control (QC) standards of SJZD are insufficient. Chinmedomics has been designed to discover and verify bioactive compounds of a variety of formula rapidly. In this study, we used Chinmedomics to evaluate the SJZD’s efficacy against SQDS to discover the potential quality-markers (q-markers) for QC. A total of 56 compounds in SJZD were characterized , and 23 compounds were discovered . A total of 58 biomarkers were related to SQDS, and SJZD can adjust a large proportion of marker metabolites to normal level and then regulate the metabolic profile to the health status. A total of 10 constituents were absorbed as effective ingredients that were associated with overall efficacy. We preliminarily determined malonyl-ginsenoside Rb2 and ginsenoside Ro as the q-markers of ginseng; dehydrotumulosic acid and dihydroxy lanostene-triene-21-acid as the q-markers of poria; glycyrrhizic acid, isoglabrolide, and glycyrrhetnic acid as the q-markers of licorice; and 2-atractylenolide as the q-marker of macrocephala. According to the discovery of the SJZD q-markers, we can establish the quality standard that is related to efficacy.

关键词: traditional Chinese medicine     Sijunzi decoction     spleen qi deficiency syndrome     Chinmedomics     quality-marker    

Protein phosphatase magnesium-dependent 1δ is a novel tumor marker and target in hepatocellular carcinoma

null

《医学前沿(英文)》 2016年 第10卷 第1期   页码 52-60 doi: 10.1007/s11684-016-0433-3

摘要:

Hepatocellular carcinoma (HCC) is a lethal liver malignancy worldwide. In this study, we reported that protein phosphatase magnesium-dependent 1δ (PPM1D) was highly expressed in the majority of HCC cases (approximately 59%) and significantly associated with high serum α-fetoprotein (AFP) level (P= 0.044). Kaplan-Meier and Cox regression data indicated that PPM1D overexpression was an independent predictor of HCC-specific overall survival (HR, 2.799; 95% CI, 1.346–5.818, = 0.006). Overexpressing PPM1D promoted cell viability and invasion, whereas RNA interference-mediated knockdown of PPM1D inhibited proliferation, invasion, and migration of cultured HCC cells. In addition, PPM1D suppression by small interfering RNA decreased the tumorigenicity of HCC cells in vivo. Overall, results suggest that PPM1D is a potential prognostic marker and therapeutic target for HCC.

关键词: PPM1D     hepatocellular carcinoma     prognosis     target therapy    

Novel polymorphic EST-based microsatellite marker isolation and characterization from

Manosh Kumar BISWAS,Peng CHEN,Mohamed Hamdy AMAR,Xiuxin DENG

《农业科学与工程前沿(英文)》 2015年 第2卷 第1期   页码 60-65 doi: 10.15302/J-FASE-2015048

摘要: Novel simple sequence repeat (SSR) markers were developed to evaluate their utility for genetic diversity and breeding studies of and related species. A total of 108 primer pairs were characterized by PCR amplification experiments. Among these, 61 were polymorphic and transferable to other citrus species. The number of alleles per locus ranged from 2 to 6, with an average of 2.37 alleles per locus. The expected heterozygosity and observed heterozygosity ranged from 0 to 0.83 and 0 to 1.00, respectively. These novel polymorphic SSR markers will be useful for citrus cultivar identification and evaluation as well as breeding studies.

关键词: microsatellite     polymorphism     Poncirus trifoliata    

Erratum to “Targeted Genotyping of a Whole-Gene Repertoire by an Ultrahigh-Multiplex and Flexible HD-Marker Erratum

Pingping Liu,Jia Lv,Cen Ma,Tianqi Zhang,Xiaowen Huang,Zhihui Yang,Lingling Zhang,Jingjie Hu,Shi Wang,Zhenmin Bao,

《工程(英文)》 2022年 第18卷 第11期   页码 259-259 doi: 10.1016/j.eng.2022.09.002

关键词: online     THE AUTHORS.Published     repertoire     behalf     Engineering     September     genotyping     Academy     HD-marker approach”     Education Press Limited Company.    

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿(英文)》 2022年 第16卷 第1期   页码 1-3 doi: 10.1007/s11705-021-2134-y

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿(英文)》 2022年 第16卷 第2期   页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要: Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词: computer-aided molecular design     bio-oil additives     molecular signature descriptor    

Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿(英文)》 2013年 第7卷 第2期   页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要:

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词: malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

Molecular classification and molecular targeted therapy of cancer

null

《医学前沿(英文)》 2013年 第7卷 第2期   页码 147-149 doi: 10.1007/s11684-013-0274-2

分子电子学的发展 Review

Paven Thomas Mathew, 房丰洲

《工程(英文)》 2018年 第4卷 第6期   页码 760-771 doi: 10.1016/j.eng.2018.11.001

摘要:

分子电子学(moletronics)是用分子作为单元对分子电子学器件进行装配。这是一个包含物理、化学、材料科学及工程等学科的多学科交叉领域。分子电子学致力于使硅元件尺寸进一步减小。科学家已经在等效分子器件方面进行了诸多探索性研究。分子电子学在电子以及光子应用中逐渐产生影响,如导电聚合物、光色材料、有机超导体、电致变色材料等。为了满足减小硅片尺寸的需求,研究人员有必要将这种新型技术引入到分子层面。虽然分子层面仪器的实验验证和建模分析是一项艰巨的任务,但分子电子学领域依然出现了突破性进展。本文将对不同分子器件和潜在的适用于不同器件的分子应用结合起来进行讨论,如分子晶体管、分子二极管、分子电容、分子导线和分子绝缘体等。本文简要讨论未来的发展趋势以及介绍各种基于石墨烯已取得一定研究成果的分子仪器。

关键词: 分子电子学     分子晶体管     分子二极管     分子电容器     分子导线     石墨烯    

Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

《化学科学与工程前沿(英文)》 2010年 第4卷 第3期   页码 250-256 doi: 10.1007/s11705-009-0281-7

摘要: Two kinds of heavy oils were fractionated into eight fractions by Liquid-Solid Adsorption Chromatography, respectively, and samples were collected to measure properties. According to the elemental analysis, molecular weight and H-NMR data, average molecular structures of polycyclic aromatic and heavy resin were constructed with improved Brown-Ladner (B-L) method and several corrections. And then, the most stable conformations of polycyclic aromatic and heavy resin in vacuum and toluene solution were obtained by molecular dynamic simulation, and the molecular size was gotten via the radius of gyration analysis. The results showed that the radius of gyration of polycyclic aromatic and heavy resin was 0.55–0.70 nm in vacuum and 0.60–0.90 nm in toluene solution. With molecular weight increasing, the molecular size in vacuum and toluene solution also increased. Due to the swelling behavior of solvent, the alkyl side chains of heavy oil molecule in solution were more stretched. Thus, the molecular size in toluene solution was larger than that in vacuum.

关键词: dynamic simulation     molecular dynamic     behavior     molecule     Adsorption Chromatography    

Effect of / molecular structures on pyrolysis performance and heat sink of decalin isomers

《化学科学与工程前沿(英文)》 2023年 第18卷 第1期 doi: 10.1007/s11705-023-2375-z

摘要: Decalin is considered as an important compound of high-energy-density endothermic fuel, which is an ideal on-board coolant for thermal management of advanced aircraft. However, decalin contains two isomers with a tunable composition, and their effects on the pyrolysis performance, such as the heat sink and coking tendency have not been demonstrated. Herein, we investigated the pyrolysis of decalin isomers, i.e., cis-decalin, trans-decalin and their mixtures (denoted as mix-decalin), in order to clarify the effects of the cis-/trans-structures on the pyrolysis performance of decalin fuels. The pyrolysis results confirmed that conversion of the tested fuels (600–725 °C, 4 MPa) decreased in the order cis-decalin > mix-decalin > trans-decalin. Detailed analyses of the pyrolysis products were used to compare the product distributions from cis-decalin, mix-decalin and trans-decalin, and the yields of some typical components (such as cyclohexene, 1-methylcyclohexene, benzene and toluene) showed significant differences, which could be ascribed to deeper cracking of cis-decalin. Additionally, the heat sinks and coking tendencies of the decalins decreased in the order cis-decalin > mix-decalin > trans-decalin. This work demonstrates the relationship between the cis/trans structures and the pyrolysis performance of decalin, which provides a better understanding of the structure-activity relationships of endothermic hydrocarbon fuels.

关键词: endothermic fuel     decalin     pyrolysis     heat sink     molecular structure    

as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait

Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS

《农业科学与工程前沿(英文)》 2019年 第6卷 第3期   页码 296-308 doi: 10.15302/J-FASE-2019269

摘要:

The application of spectral reflectance indices (SRIs) as proxies to screen for yield potential (YP) and heat stress (HS) is emerging in crop breeding programs. Thus, a comparison of SRIs and their associations with grain yield (GY) under YP and HS conditions is important. In this study, we assessed the usefulness of 27 SRIs for indirect selection for agronomic traits by evaluating an elite spring wheat association mapping initiative (WAMI) population comprising 287 elite lines under YP and HS conditions. Genetic and phenotypic analysis identified 11 and 9 SRIs in different developmental stages as efficient indirect selection indices for yield in YP and HS conditions, respectively. We identified enhanced vegetation index (EVI) as the common SRI associated with GY under YP at booting, heading and late heading stages, whereas photochemical reflectance index (PRI) and normalized difference vegetation index (NDVI) were the common SRIs under booting and heading stages in HS. Genome-wide association study (GWAS) using 18704 single nucleotide polymorphisms (SNPs) from Illumina iSelect 90K identified 280 and 43 marker-trait associations for efficient SRIs at different developmental stages under YP and HS, respectively. Common genomic regions for multiple SRIs were identified in 14 regions in 9 chromosomes: 1B (60–62 cM), 3A (15, 85–90, 101–105 cM), 3B (132–134 cM), 4A (47–51 cM), 4B (71–75 cM), 5A (43–49, 56–60, 89–93 cM), 5B (124–125 cM), 6A (80–85 cM), and 6B (57–59, 71 cM). Among them, SNPs in chromosome 5A (89–93 cM) and 6A (80–85 cM) were co-located for yield and yield related traits. Overall, this study highlights the utility of SRIs as proxies for GY under YP and HS. High heritability estimates and identification of marker-trait associations indicate that SRIs are useful tools for understanding the genetic basis of agronomic and physiological traits.

关键词: genome-wide association study (GWAS)     heat tolerance     spectral reflectance     spring wheat    

Enhanced separation of tetrafluoropropanol from water via carbon nanotubes membranes: insights from molecular

《环境科学与工程前沿(英文)》 2023年 第17卷 第11期 doi: 10.1007/s11783-023-1740-y

摘要:

● MD simulations unveil the transport mechanism for TFP-water mixture through CNTs.

关键词: Fluorinated alcohol     Carbon nanotube     Molecular simulation     Fluorine modified    

标题 作者 时间 类型 操作

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

期刊论文

Identification of molecular markers linked to rice bacterial blight resistance genes from

Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

期刊论文

Chinmedomics facilitated quality-marker discovery of Sijunzi decoction to treat spleen qi deficiency

Qiqi Zhao, Xin Gao, Guangli Yan, Aihua Zhang, Hui Sun, Ying Han, Wenxiu Li, Liang Liu, Xijun Wang

期刊论文

Protein phosphatase magnesium-dependent 1δ is a novel tumor marker and target in hepatocellular carcinoma

null

期刊论文

Novel polymorphic EST-based microsatellite marker isolation and characterization from

Manosh Kumar BISWAS,Peng CHEN,Mohamed Hamdy AMAR,Xiuxin DENG

期刊论文

Erratum to “Targeted Genotyping of a Whole-Gene Repertoire by an Ultrahigh-Multiplex and Flexible HD-Marker

Pingping Liu,Jia Lv,Cen Ma,Tianqi Zhang,Xiaowen Huang,Zhihui Yang,Lingling Zhang,Jingjie Hu,Shi Wang,Zhenmin Bao,

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

期刊论文

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文

分子电子学的发展

Paven Thomas Mathew, 房丰洲

期刊论文

Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

期刊论文

Effect of / molecular structures on pyrolysis performance and heat sink of decalin isomers

期刊论文

as proxies for yield potential and heat stress tolerance in spring wheat: heritability estimates and marker-trait

Caiyun LIU, Francisco PINTO, C. Mariano COSSANI, Sivakumar SUKUMARAN, Matthew P. REYNOLDS

期刊论文

Enhanced separation of tetrafluoropropanol from water via carbon nanotubes membranes: insights from molecular

期刊论文