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Genome reprogramming for synthetic biology

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Frontiers of Chemical Science and Engineering 2017年第1期11卷 37-45页

作者： Kylie Standage-Beier Xiao Wang School of Life Sciences Arizona State University Tempe AZ 85287 USA School of Biological and Health Systems Engineering Arizona State University Tempe AZ 85287 USA

The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute （JCVI）-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools.

关键词： CRISPR genome engineering syntheticbiology rational design

Excitonic effects in absorption spectra of carbon dioxide reduction photocatalysts

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npj Computational Materials 2021年第1期7卷 1752-1761页

作者： Tathagata Biswas Arunima K.Singh Department of Physics Arizona State UniversityTempeAZ 85287USA

The formation and disassociation of excitons play a crucial role in any photovoltaic or photocatalytic ***,excitonic effects are seldom considered in materials discovery studies due to the monumental computational cost associated with the examination of these ***,we study the excitonic properties of nearly 50 photocatalysts using state-of-the-art Bethe–Salpeter ***~50 materials were recently recognized as promising photocatalysts for CO_(2) reduction through a data-driven screening of 68,860 ***,we propose three screening criteria based on the optical properties of these materials,taking excitonic effects into account,to further down select six ***,we study the correlation between the exciton binding energies obtained from the Bethe–Salpeter formalism and those obtained from the computationally much lessexpensive Wannier–Mott model for these chemically diverse~50 *** work presents a paradigm towards the inclusion of excitonic effects in future materials discovery for solar-energy harvesting applications.

关键词： materials properties dioxide

pyGWBSE:a high throughput workflow package for GW-BSE calculations

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npj Computational Materials 2023年第1期9卷 2127-2136页

作者： Tathagata Biswas Arunima K.Singh Department of Physics Arizona State UniversityTempe 85287 AZUSA

We develop an open-source python workflow package,pyGWBSE to perform automated first-principles calculations within the GW-BSE(Bethe-Salpeter)***-BSE is a many body perturbation theory based approach to explore the quasiparticle(QP)and excitonic properties of *** approximation accurately predicts bandgaps of materials by overcoming the bandgap underestimation issue of the more widely used density functional theory(DFT).BSE formalism produces absorption spectra directly comparable with experimental *** package achieves complete automation of the entire multi-step GW-BSE computation,including the convergence tests of several parameters that are crucial for the accuracy of these *** is integrated with Wannier90,to generate QP bandstructures,interpolated using the maximally-localized wannier *** also enables the automated creation of databases of metadata and data,including QP and excitonic properties,which can be extremely useful for future material discovery studies in the field of ultra-wide bandgap semiconductors,electronics,photovoltaics,and photocatalysis.

关键词： automated python enable

On the effects of landscape configuration on summer diurnal temperatures in urban residential areas: application in Phoenix, AZ

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Frontiers of Earth Science 2019年第3期13卷 445-463页

作者： Yiannis KAMARIANAKIS Xiaoxiao LI B. L. TURNER II Anthony J. BRAZEL School of Mathematical and Statistical Sciences Arizona State UniversityTempe AZ 85287USA School of Geographical Sciences and Urban Planning Arizona State UniversityTempe AZ 85298USA School of Sustainability Arizona State UniversityTempe AZ 85298USA Global Institute of Sustainability Arizona State UniversityTempe AZ 85287USA

The impacts of land-cover composition on urban temperatures, including temperature extremes, are well documented. Much less attention has been devoted to the consequences of land-cover configuration, most of which addresses land surface temperatures. This study explores the role of both composition and configuration—or land system architecture—of residential neighborhoods in the Phoenix metropolitan area, on near-surface air temperature. It addresses two-dimensional, spatial attributes of buildings, impervious surfaces, bare soil/ rock, vegetation and the “urbanscape” at large, from 50 m to 550 m at 100 m increments, for a representative 30-day high sun period. Linear mixed-effects models evaluate the significance of land system architecture metrics at different spatial aggregation levels. The results indicate that, controlling for land-cover composition and geographical variables, land-cover configuration, specifically the fractal dimension of buildings, is significantly associated with near-surface temperatures. In addition, statistically significant predictors related to composition and configuration appear to depend on the adopted level of spatial aggregation.

关键词： land system architecture urban heat island effect linear mixed-effects models near-surface air temperature land-cover configuration

Economic reform, open-door policy and changes in spatial development patterns in China

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Journal of Geographical Sciences 2000年第4期10卷 7-19页

作者： WANG Enru1, LU Xiang-xing2 (1.Department of Geography university of Washington Smith Hall, Box 353550 Seattle, WA 98195, USA 2. Department of Geography Kansas state university Manhattan, KS 66506, USA) university of Washington 美国 Kansas state university 美国

The study profiles and explains the significant changes that have taken place in China's spatial development patterns since the inception of its economic reform and opening two decades ago. Principal component analysis is used to delineate spatial patterns. The analyses show that prior to the reform China's spatial development pattern was characterized by the dominance of the three municipalities and the Northeast, as well as by both the coast-interior and the north-south disparities. Northern provinces were generally more industrialized and economically powerful than the southern ones. After two decades of reform, regional development has become multi-centered with South China, the Yangtze Delta and the Beijing-Tianjin area being the three most important regions of the country. The coastal provinces as a whole rose to prominence on China's economic map while the Northeast has diminished its clout. The coast-interior gap not only remains but may have widened. The north-south disparity also still exists but there has been a role reversal with the south now in the lead position. Virtually all inland provinces now find themselves at or near the low end of the development spectrum. We argue that the major reason for the recent shifts in Chinese space economy is the spatially differentiated economic growth resulted from the reform and open door policy and from the new, uneven development strategy adopted by the Chinese government. The paper discusses four specific factors that have reshaped China's spatial development patterns.

关键词： regional development pattern differentiated growth economic reform open door policy

On-chip isotachophoresis separation of functional DNA origami capture nanoarrays from cell lysate

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Nano Research 2013年第10期6卷 712-719页

作者： Qian Mei Roger H. Johnson Xixi Wei Fengyu Su Yan Liu Laimonas Kelbauskas Stuart Lindsay Deirdre R. Meldrum Hao Yan Center for Biosignatures Discovery Automation Arizona State University Tempe AZ 85287 USA Center for Single Molecule Biophysics Arizona State University Tempe AZ 85287 USA Department of Chemistryand Biochemistry Arizona State University Tempe AZ85287 USA Department of Physics Arizona State University Tempe AZ 85287 USA

Scaffolded DNA origami, a versatile method to construct high yield self- assembled DNA nanostructures, has been investigated to develop water-soluble nanoarrays for label free RNA detection, drug delivery, molecular positioning and recognition, and spatially ordered catalysis of single molecule chemical reactions. Its attributes that facilitate these applications suggest DNA origami as a candidate platform for intracellular targeting. After the interaction with targeted proteins in cell lysate, it is critical to separate and concentrate DNA origami nanoarrays from the crude cell lysate for further analysis. The recent development of microchip isotachophoresis （ITP） provides an alternative robust sample preconcentration and electrophoretic separation method. In this study, we present online ITP for stacking, separation and identification of aptamer-functionalized DNA origami and its thrombin complex in a simple cross-channel fused silica microfluidic chip. In particular, the method achieved separation of a binding complex in less than 5 min and 150-fold signal enhancement. We successfully separated and analyzed the thrombin bound origami-aptamer spiked into cell lysate using on-chip ITP. Our results demonstrate that origami/thrombin nanostructures can be effectively separated from cell lysate using this method and that the structural integrity of the concentrated binding complex is maintained as confirmed by atomic force microscopy （AFM）. An ITP-based separation module can be easily coupled to other microchip pre- and post-processing steps to provide an integrated proteomics analysis platform for diagnostic applications.

关键词： DNA origami nanoarray aptamer microfluidics isotachophoresis

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如何增长知识的力量?

博鳌观察 2012年第2期 142-143页

作者：王宁美国亚利桑那州立大学(arizona state university)政治和全球研究学院

培根说,知识就是力量。知名物理学家戴维·多伊奇用尽量平实的语言,写下这部《无限之始》,期望告诉你我,'解释性知识'对于知识增长的重要性。作者更期待人们相信,坚定一切问题都可解决的信念,是知识得以增加的先决条件。《无限之始—改... 详细信息

培根说,知识就是力量。知名物理学家戴维·多伊奇用尽量平实的语言,写下这部《无限之始》,期望告诉你我,'解释性知识'对于知识增长的重要性。作者更期待人们相信,坚定一切问题都可解决的信念,是知识得以增加的先决条件。《无限之始—改变世界的解释》的作者戴维·多伊奇是牛津大学著名理论物理学家,量子计算和平行宇宙理论的主要权威之一。但是,这部书却是写给普通读者看的。语言朴实、条理清晰、见解独到、论点鲜明有力—一言以蔽之。

关键词：知识的力量理论物理学家多伊奇鲜明有力平行宇宙知识就是力量你我解释性现代科学人能

Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes

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Journal of Genetics and Genomics 2017年第1期44卷 51-61页

作者： Jingzhong Xie Naxin Huo Shenghui Zhou Yi Wang Guanghao Guo Karin R.Deal Shuhong Ouyang Yong Liang Zhenzhong Wang Lichan Xiao Tingting Zhu Tiezhu Hu Vijay Tiwari Jianwei Zhang Hongxia Li Zhongfu Ni Yingyin Yao Huiru Peng Shengli Zhang Olin D.Anderson Patrick E.McGuire Jan Dvorak Ming-Cheng Luo Zhiyong Liu Yong Q.Gu Qixin Sun state Key Laboratory for Agrobiotechnology China Agricultural UniversityBeijing 100193China USDA-ARS West Regional Research Center AlbanyCA 94770USA Department of Plant Sciences University of California at DavisDavisCA 95616USA Department of Plant Pathology Kansas State UniversityManhattanKS 66506USA arizona Genomics Institute School of Plant ScienceUniversity of ArizonaTucsonAZ 85721USA

Bread wheat （Triticum aestivum, AABBDD） is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path （MTP） of 3176 BAC clones from the short arm ofAe. tauschii chromosome 3 （At3DS）. The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B （Ta3BS） is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element （TE） bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D （Ta3DS）, there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.

关键词： Aegilops tauschii Genome sequencing Sequence assembly Comparative genomics Grass evolution

化学合成DFV-紫杉烷类化合物对未分化甲状腺癌细胞的抗肿瘤作用研究

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肿瘤药学 2024年第2期14卷 179-185页

作者：王美晨王昌伟冯超 Iwao Ojima 西安交通大学第一附属医院肿瘤内科陕西西安710061 西安交通大学第一附属医院陕西省肿瘤精准医学重点实验室陕西西安710061 密歇根大学医学院美国密歇根州安娜堡48109-5368 纽约州立大学石溪分校化学生物与药物研究所美国纽约州纽约11749-3400

目的探索化学合成DFV-紫杉烷类化合物对未分化甲状腺癌细胞的抗肿瘤作用及可能机制。方法噻唑蓝(MTT)实验测定DFV-紫杉烷类化合物对肿瘤细胞增殖及细胞活性的影响;紫外分光光度计测定新型紫杉烷类化合物处理后肿瘤细胞的存活情况;克隆... 详细信息

目的探索化学合成DFV-紫杉烷类化合物对未分化甲状腺癌细胞的抗肿瘤作用及可能机制。方法噻唑蓝(MTT)实验测定DFV-紫杉烷类化合物对肿瘤细胞增殖及细胞活性的影响;紫外分光光度计测定新型紫杉烷类化合物处理后肿瘤细胞的存活情况;克隆形成实验评价新型紫杉烷类化合物对肿瘤细胞增殖能力的敏感性;结晶紫染色计数存活克隆数;流式细胞仪检测新型紫杉烷类化合物对肿瘤细胞周期分布的影响。结果甲状腺癌细胞系8505C和8305C经四种不同的DFV-紫杉烷类化合物处理后,IC_(50)在0.5~5.5 nmol·L^(-1)之间;不同药物处理后,甲状腺癌细胞的增殖能力显著降低(P<0.001);不同浓度的DFV-紫杉烷类化合物可不同程度地抑制甲状腺癌细胞的克隆形成能力(P<0.001);DFV-紫杉烷类化合物可诱导甲状腺癌细胞G_(2)/M期周期阻滞(P<0.001),从而抑制甲状腺癌细胞的生长。结论四种化学合成DFV-紫杉烷类化合物对未分化甲状腺癌细胞具有生长抑制和抗肿瘤作用。

关键词： DFV-紫杉烷类化合物未分化甲状腺癌抗肿瘤作用