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Construction, characterization and application of a genomewide promoter library in Saccharomyces cerevisiae

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Frontiers of Chemical Science and Engineering 2017年第1期11卷 107-116页

作者： Ting Yuan Yakun Guo Junkai Dong Tianyi Li Tong Zhou Kaiwen Sun Mei Zhang Qingyu Wu Zhen Xie Yizhi Cai Limin Cao Junbiao Dai MOE Key Laboratory of bioinformatics and Centre for Synthetic and Systems Biology School of Life Sciences Tsinghua University Beijing 100084 China College of life Sciences Capital Normal University Beijing 100048 China MOE Key Laboratory of bioinformatics and bioinformatics Division Center for Synthetic and Systems Biology TNLIST/Department of Automation Tsinghua University Beijing 100084 China School of Biological Sciences The King's Buildings University of Edinburgh Edinburgh EH9 3BF UK

Promoters are critical elements to control gene expression but could behave differently under various growth conditions. Here we report the construction of a genome-wide promoter library, in which each native promoter in Saccharomyces cerevisiae was cloned upstream of a yellow fluorescent protein （YFP） reporter gene. Nine libraries were arbitrarily defined and assembled in bacteria. The resulting pools of promoters could be prepared and transformed into a yeast strain either as centromeric plasmids or integrated into a genomic locus upon enzymatic treatment. Using fluorescence activated cell sorting, we classified the yeast strains based on YFP fluorescence intensity and arbitrarily divided the entire library into 12 bins, representing weak to strong promoters. Several strong promoters were identified from the most active bins and their activities were assayed under different growth conditions. Finally, these promoters were applied to drive the expression of genes in xylose utilization to improve fermentation efficiency. Together, this library could provide a quick solution to identify and utilize desired promoters under user-defined growth conditions.

关键词： synthetic biology yeast promoter activity,metabolic engineering xylose utilization

Performance Comparison of Two Efficient Genomic Selection Methods(gsbay & MixP ) applied in Aquacultural Organisms

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Journal of Ocean University of China 2017年第1期16卷 137-144页

作者： SU Hailin LI Hengde WANG Shi WANG Yangfan BAO Zhenmin College of Marine life Science Ocean University of China The center for applied Aquatic Genomics Chinese Academy of Fishery Sciences

Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.

关键词： genomic selection scallop breeding method comparison

Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

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Frontiers of Electrical and Electronic Engineering in China 2018年第3期6卷 239-252页

作者： Jing Gongt Yanyan Jut Di Shao Qiangfeng Cliff Zhang MOE Key Laboratory of bioinformatics Beijing Advanced Innovation Center for Structural BiologyCenter for Synthetic and Systems BiologyTsinghua-Peking Joint Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China

RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions （RRIs） are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs. Results： In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs. Conclusions： The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRls, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.

关键词： RNA-RNA interactions PARIS SPLASH LIGR-seq next generation sequencing

Prediction of sorghum miRNAs and their targets with computational methods

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Chinese Science Bulletin 2010年第13期55卷 1263-1270页

作者： DU JiangFeng WU YongJun FANG XiaoFeng CAO JunXia ZHAO Liang TAO ShiHeng bioinformatics center Northwest Agricultural & Forestry University Yangling 712100 China College of life Sciences Northwest Agricultural & Forestry University Yangling 712100 China

microRNAs 是 21-nt 的一个班在 post-transcriptional 起关键作用的长、非编码、最新识别的 RNA 基因规定。他们的目标涉及各种各样的生物过程，包括开发，新陈代谢，和压力反应。尽管很多 miRNAs 在许多种类被报导了，在蜀黍的 miRNAs... 详细信息

microRNAs 是 21-nt 的一个班在 post-transcriptional 起关键作用的长、非编码、最新识别的 RNA 基因规定。他们的目标涉及各种各样的生物过程，包括开发，新陈代谢，和压力反应。尽管很多 miRNAs 在许多种类被报导了，在蜀黍的 miRNAs 的报告是有限的。基于 genomic 调查顺序(GSS ) 和 microRNA (miRNA ) 使用相同搜索第二等的结构， 17 新 miRNAs 的一个总数在这个工作被识别。他们被发现在 11 个 miRNA 家庭之中不均匀的分布式。一些 miRNA 基因在多重地点并且在超过一 genomic 上下文被发现。大多数 miRNAs 在一样的王国以内被保存，但是我们在蜀黍发现 sbi-miR127 和 sbi-miR466 与 H 显示出保存。现代人并且 M。musculus 分别地。经由联机软件 miRU 的那些 17 新 miRNAs 的分析证明他们可能调整 64 目标基因，其大多数涉及 RNA 处理，新陈代谢，房间周期，蛋白质降级，压力反应和交通。11 个 miRNA 家庭中的至少 7 个指向在新陈代谢和压力反应是必要的蛋白质，包括 NADPH 细胞色素 P450 reductase， nucleoside diphosphate kinase 和 superoxide dismutase，建议 miRNAs 起在生物过程的一个必要作用。

关键词： miRNA 高粱细胞色素P450 超氧化物歧化酶计算预测应激反应新陈代谢

Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform

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Journal of Integrative Plant Biology 2015年第11期57卷 980-991页

作者： Yang L Xiao Cui Rui Li Piaopiao Huang Jie Zong Danqing Yao Gang Li Dabing Zhang Zheng Yuan State Key Laboratory of Hybrid Rice School of Life Sciences and BiotechnologyShanghai Jiao Tong University Novel bioinformatics Company Shanghai Agricultural Technology Extension and Service center

DNA markers play important roles in plant breed- ing and genetics. The Insertion/Deletion （InDel） marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor- intensive. We developed an end-to-end computational solution （InDel Markers Development Platform, IMDP） to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequen- ces alignment pipeline （AGA-pipe） and next-generation re- sequencing data mapping pipeline （NGS-pipe）. With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA- pipe and NGS-pipe, we developed 2o5,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction （PCR） analysis of subgroup-specific markers indicated that the precision reached 90% （86 of 95）. Finally, to make them available to the public, we have integrated the InDels/markers information into a website （Rice InDel Marker Database, RIMD, http：I/2o2.12o.45.71/）. The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

关键词： Genetic polymorphism genome alignment InDel marker molecular breeding next-generation sequencing

Fatty acid metabolism and cancer development

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Science Bulletin 2016年第19期61卷 1473-1479,1469页

作者：陈元颖李蓬 MOE Key Laboratory of bioinformatics and Tsinghua-Peking center for life Sciences School of Life Sciences Tsinghua University

Although the type and etiology of cancers are different, pathways in glucose metabolism, pentose phosphate pathway(PPP) and glutamine metabolism have been reprogrammed in cancer cells to adapt to their rapid growth and proliferation. Recent research has also shown that multiple lipid metabolic pathways are altered in cancer ***, we provide a brief review for the role of fatty acid metabolism in cancer development with a special focus on fatty acid uptake and de novo synthesis, triglycerides synthesis, storage and degradation. Reprogramming in fatty acid metabolism plays important roles in providing energy,macromolecules for membrane synthesis and lipid signals during cancer development. Understanding the mechanism of deregulated lipid metabolic pathways in cancer cells would reveal novel therapeutic approaches to combat cancer.

关键词： Lipid metabolism TAG Fatty acids Cancer development

Essential role of NbNOG1 in ribosomal RNA processing

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Journal of Integrative Plant Biology 2018年第11期60卷 1018-1022页

作者： Jiangbo Guo Shaojie Han Jinping Zhao Cuihua Xin Xiyin Zheng Yule Liu Yan Wang Feng Qu School of life Science and Technology Inner Mongolia University of Science and Technology MOE Key Laboratory of bioinformatics Center for Plant Biology Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Department of Plant Pathology the Ohio State University

Nucleolar GTP-binding protein 1（NOG1） is a highly conserved GTPase first reported in Trypanosoma as required for ribosome biogenesis. We characterized NbNOG1, a Nicotiana benthamiana NOG1ortholog sharing more than 45% amino acid identity with Trypanosoma,yeast, and human NOG1. N. benthamiana plants silenced for NbNOG1were stunted and produced sterile ***1is functionally interchangeable with yeast NOG1（ScNOG1）, rescuing yeast lethality caused by loss of ScNOG1. Finally, NbNOG1silencing caused overaccumulation of pre-rRNA processing intermediates,and concomitant loss of mature rRNAs. Collectively,these data support a role for NbNOG1in ribosomal RNA processing.

关键词： Essential role of NbNOG1 in ribosomal RNA processing Figure

DIProT:A deep learning based interactive toolkit for efficient and effective Protein design

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Synthetic and Systems Biotechnology 2024年第2期9卷 217-222页

作者： Jieling He Wenxu Wu Xiaowo Wang Ministry of Education Key Laboratory of bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijingChina

The protein inverse folding problem,designing amino acid sequences that fold into desired protein structures,is a critical challenge in biological *** numerous data-driven and knowledge-driven methods,there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein *** this paper,we present DIProT,an interactive protein design *** leverages a non-autoregressive deep generative model to solve the inverse folding problem,combined with a protein structure prediction *** integration allows users to incorporate prior knowledge into the design process,evaluate designs in silico,and form a virtual design loop with human *** inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets,with promising sequence recovery and inference *** studies further illustrate how DIProT can facilitate user-guided protein design.

关键词： Computational Protein design Interactive design toolkit Protein inverse folding Non-autoregressive decoding

Silk-based nerve guidance conduits with macroscopic holes modulate the vascularization of regenerating rat sciatic nerve

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Neural Regeneration Research 2025年第6期20卷 1789-1800页

作者： Carina Hromada Patrick Heimel Markus Kerbl LászlóGál Sylvia Nürnberger Barbara Schaedl James Ferguson Nicole Swiadek Xavier Monforte Johannes C.Heinzel Antal Nógrádi Andreas H.Teuschl-Woller David Hercher Department life Science Engineering University of Applied Sciences Technikum WienViennaAustria Austrian Cluster for Tissue Regeneration ViennaAustria Ludwig Boltzmann Institute for Traumatology The Research Center in Cooperation with AUVAViennaAustria University Clinic of Dentistry Medical University of ViennaViennaAustria Department of Plastic Reconstructive and Aesthetic SurgeryLandesklinikum Wiener Neustadt2700 Wiener NeustadtAustria Department of Anatomy Histology and EmbryologyAlbert Szent-Györgyi Medical SchoolUniversity of SzegedSzegedHungary Medical University of Vienna Department of Orthopedics and Trauma SurgeryDevision of Trauma SurgeryViennaAustria Department of Hand- PlasticReconstructive and Burn SurgeryBG Unfallklinik TuebingenUniversity of TuebingenTuebingenGermany

Peripheral nerve injuries induce a severe motor and sensory deficit. Since the availability of autologous nerve transplants for nerve repair is very limited, alternative treatment strategies are sought, including the use of tubular nerve guidance conduits(tNGCs). However, the use of tNGCs results in poor functional recovery and central necrosis of the regenerating tissue, which limits their application to short nerve lesion defects(typically shorter than 3 cm). Given the importance of vascularization in nerve regeneration, we hypothesized that enabling the growth of blood vessels from the surrounding tissue into the regenerating nerve within the tNGC would help eliminate necrotic processes and lead to improved regeneration. In this study, we reported the application of macroscopic holes into the tubular walls of silk-based tNGCs and compared the various features of these improved silk^(+) tNGCs with the tubes without holes(silk^(–) tNGCs) and autologous nerve transplants in an 8-mm sciatic nerve defect in rats. Using a combination of micro-computed tomography and histological analyses, we were able to prove that the use of silk^(+) tNGCs induced the growth of blood vessels from the adjacent tissue to the intraluminal neovascular formation. A significantly higher number of blood vessels in the silk^(+) group was found compared with autologous nerve transplants and silk^(–), accompanied by improved axon regeneration at the distal coaptation point compared with the silk^(–) tNGCs at 7 weeks postoperatively. In the 15-mm(critical size) sciatic nerve defect model, we again observed a distinct ingrowth of blood vessels through the tubular walls of silk^(+) tNGCs, but without improved functional recovery at 12 weeks postoperatively. Our data proves that macroporous tNGCs increase the vascular supply of regenerating nerves and facilitate improved axonal regeneration in a short-defect model but not in a critical-size defect model. This study suggests that further optimizatio

关键词： axon regeneration blood vessel functional recovery macroporous nerve lesion peripheral nerve repair sciatic nerve silk-based nerve guidance conduit vascularization