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Theoretical prediction on the reactivity of the Co-mediated intramolecular Pauson-Khand reaction for constructing bicyclo-skeletons in natural products

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Chinese Chemical Letters 2019年第4期30卷 889-894页

作者： Lei Zhu Zheyuan Wang Song Liu Tao Zhang Zhen Yang Ruopeng Bai Yu Lan School of Chemistry and Chemical Engineering Chongqing Key Laboratory of Theoretical and Computational Chemistry Chongqing University Laboratory of Chemical genomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School College of Chemistry and Molecular Engineering Zhengzhou University

The Co_2(CO)_8-mediated intramolecular Pauson-Khand reaction is an efficient approach for constructing polycyclic skeletons. Recently, some of us reported a series of this type reactions involving stericallyhindered enynes for synthesizing natural products with reasonable reaction rates and yields. However,the reason for the high reactivity of the reaction remains unclear. We employed density functional theory calculations to clarify the mechanism and reactivity for this reaction. In contrast with chain olefin reactants, CO insertion is considered to be the rate-determining step for the overall Pauson-Khand reaction of cyclooctene derivatives. The reduced activation free energy for the alkene insertion step is attributed to: i) the electron-withdrawing group in close proximity to the C—C triple bond enhancing the reactivity of the alkyne moiety; ii) lower steric hindrance during alkene insertion when using the cyclooctene derivative. The effect of the substituent on the Co_2(CO)_8-mediated intramolecular PausonKhand reaction was then investigated. Internal alkenes exhibit lower reactivity than terminal alkenes because of the steric hindrance introduced by the substituted group. The cis internal alkene exhibits higher reactivity than the trans internal alkene. An ester group in close proximity to the C—C triple bond significantly enhances the reactivity.

关键词： Pauson-Khand reaction Bicyclo-skeletons DFT calculations Mechanism Reactivity

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Transcriptional profiling of dental sensory and proprioceptive trigeminal neurons using single-cell RNA sequencing

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International Journal of Oral Science 2023年第3期15卷 513-526页

作者： Pa Reum Lee Jihoon Kim Heather Lynn Rossi Sena Chung Seung Yub Han Junhyong Kim Seog Bae Oh Department of Neurobiology and Physiology School of Dentistry and Dental Research InstituteSeoul National UniversitySeoulRepublic of Korea genomics and computational biology graduate group University of PennsylvaniaPhiladelphiaPAUSA Department of Pathobiology University of PennsylvaniaPhiladelphiaPAUSA Department of biology University of PennsylvaniaPhiladelphiaPAUSA Brain Science Institute Korea Institute of Science and Technology(KIST)SeoulRepublic of Korea

Dental primary afferent(DPA)neurons and proprioceptive mesencephalic trigeminal nucleus(MTN)neurons,located in the trigeminal ganglion and the brainstem,respectively,are essential for controlling masticatory *** extensive transcriptomic studies on various somatosensory neurons,there is still a lack of knowledge about the molecular identities of these populations due to technical challenges in their circuit-validated ***,we employed high-depth single-cell RNA sequencing(scRNA-seq)in combination with retrograde tracing in mice to identify intrinsic transcriptional features of DPA and MTN *** transcriptome analysis revealed five major types of DPA neurons with cell type-specific gene enrichment,some of which exhibit unique mechano-nociceptive properties capable of transmitting nociception in response to innocuous mechanical stimuli in the ***,we discovered cellular heterogeneity within MTN neurons that potentially contribute to their responsiveness to mechanical stretch in the masseter muscle ***,DPA and MTN neurons represented sensory compartments with distinct molecular profiles characterized by various ion channels,receptors,neuropeptides,and ***,our study provides new biological insights regarding the highly specialized mechanosensory functions of DPA and MTN neurons in pain and proprioception.

关键词： trigeminal specialized Together

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Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations

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Journal of Animal Science and Biotechnology 2020年第2期11卷 316-326页

作者： Xiao Wang Guosheng Su Dan Hao Mogens SandøLund Haja N.Kadarmideen Quantitative genomics Bioinformatics and Computational Biology GroupDepartment of Applied Mathematics and Computer ScienceTechnical University of DenmarkRichard Peterson PladsBuilding 3242800 Kongens LyngbyDenmark Center for Quantitative Genetics and genomics Department of Molecular Biology and GeneticsAarhus University8830 TjeleDenmark Department of Molecular biology and Genetics Aarhus University8000 Aarhus CDenmark College of Animal Science and Technology Northwest A&F UniversityYangling 712100ShannxiChina

Background:Genotyping by sequencing(GBS)still has problems with missing *** is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing *** allele frequency(MAF)is widely used as a marker data editing criteria for genomic *** this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock ***:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before ***,IMPUTE2 and FImpute software were applied to impute the original ***,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS *** results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and *** was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=*** genomic prediction,retaining more SNPs with no MAF limit resulted in higher *** the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS *** and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=*** best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=***:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high *** resulted in larger gains in the reliability of genomic predictions for GBS with lowe

关键词： Genomic prediction Genotyping by sequencing Imputation MAF Simulation

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NPEST： a nonparametric method and a database for transcription start site prediction

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Frontiers of Electrical and Electronic Engineering in China 2013年第4期8卷 261-271页

作者： Tatiana Tatarinova Alona Kryshchenko Martin Triska Mehedi Hassan Denis Murphy Michael Neely Alan Schumitzky Children's Hospital Los Angeles and Keck School of Medicine University of Southern California Los Angeles CA 90027 USA genomics and computational biology research group University of South Wales Treforest Wales UK

In this paper we present NPEST, a novel tool for the analysis of expressed sequence tags （EST） distributions and transcription start site （TSS） prediction. This method estimates an unknown probability distribution of ESTs using a maximum likelihood （ML） approach, which is then used to predict positions of TSS. Accurate identification of TSS is an important genomics task, since the position of regulatory elements with respect to the TSS can have large effects on gene regulation, and performance of promoter motif-finding methods depends on correct identification of TSSs. Our probabilistic approach expands recognition capabilities to multiple TSS per locus that may be a useful tool to enhance the understanding of alternative splicing mechanisms. This paper presents analysis of simulated data as well as statistical analysis of promoter regions of a model dicot plant Arabidopsis thaliana. Using our statistical tool we analyzed 16520 loci and developed a database of TSS, which is now publicly available at ***/NPEST.

关键词： transcription start site (TSS) nonparametric maximum likelihood

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Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development

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genomics, Proteomics & Bioinformatics 2022年第1期20卷 147-162页

作者： Yikai Luo Han Liang graduate Program in Quantitative and computational Biosciences Baylor College of MedicineHoustonTX 77030USA Department of Bioinformatics and computational biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Department of Systems biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

Genome-and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution,but its characteristics and implication in cancer evolution and therapy remain largely ***,we analyzed large-scale transcriptome/proteome profiles,such as The Cancer Genome Atlas(TCGA),the Genotype-Tissue Expression(GTEx),and the Clinical Proteomic Tumor Analysis Consortium(CPTAC),and found that compared to normal tissues,different cancer types showed a convergent pattern toward using biosynthetically low-cost amino *** a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids,termed energy cost per amino acid(ECPA).With this index,we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development,and revealed their reversed ***,focusing on the liver,a tissue with a dramatic increase in ECPA during development,we found that ECPA represents a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts and outperforms any index based on single *** study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.

关键词： Amino acid usage Tissue development Biosynthetic energy Diagnostic biomarker

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TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance

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Journal of Genetics and genomics 2011年第1期38卷 1-11页

作者： Song Song Qinglan Ge Jinbo Wang Haiyang Chen Sanyuan Tang Junfeng Bi Xia Li Qi Xie Xun Huang Key Laboratory of Molecular and Developmental biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China State Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China graduate School of Chinese Academy of sciences Beijing 100049 China

TRIpartite Motif （TRIM） family proteins are ring finger domain-containing, multi-domain proteins implicated in many biological processes. Members of the TRIM-9/C-I subfamily of TRIM proteins, including TRIM-9, MIDI and MID2, have neuronal functions and are associated with neurological diseases. To explore whether the functions of C-I TRIM proteins are conserved in invertebrates, we analyzed Caenorhabditis elegans and Drosophila trim-9 mutants. C. elegans trim-9 mutants exhibit defects in the ventral guidance of hermaphrodite specific neuron （HSN） and the touch neuron AVM. Further genetic analyses indicate that TRIM-9 participates in the UNC-6-UNC-40 attraction pathway. Asymmetric distribution of UNC-40 during HSN development is normal in trim-9 mutants. However, the asymmetric localization of MIG-10, a downstream effector of UNC-40, is abolished in trim-9 mutants. These results suggest that TRIM-9 functions upstream of MIG- 10 in the UNC- 40 pathway. Moreover, we showed that TRIM-9 exhibits E3 ubiquitin ligase activity in vitro and this activity is important for TRIM-9 function in vivo. Additionally, we found that Drosophila trim-9 is required for the midline attraction of a group of sensory neuron axons. Over-expression of the Netrin/UNC-6 receptor Frazzled suppresses the guidance defects in trim-9 mutants. Our study reveals an evolutionarily conserved function of TRIM-9 in the UNC-40/Frazzled-mediated UNC-6/Netrin attraction pathway.

关键词： TRIM-9 Axon guidance UNC-6/Netrin UNC-40/Frazzled

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A dive into spectral inference networks: improved algorithms for self-supervised learning of continuous spectral representations

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Applied Mathematics and Mechanics(English Edition) 2023年第7期44卷 1199-1224页

作者： J.WU S.F.WANG P.PERDIKARIS graduate group in Applied Mathematics and computational Science University of Pennsylvania PhiladelphiaPA 19104U.S.A. Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania PhiladelphiaPA 19104U.S.A.

We propose a self-supervising learning framework for finding the dominant eigenfunction-eigenvalue pairs of linear and self-adjoint *** represent target eigenfunctions with coordinate-based neural networks and employ the Fourier positional encodings to enable the approximation of high-frequency *** formulate a self-supervised training objective for spectral learning and propose a novel regularization mechanism to ensure that the network finds the exact eigenfunctions instead of a space spanned by the ***,we investigate the effect of weight normalization as a mechanism to alleviate the risk of recovering linear dependent modes,allowing us to accurately recover a large number of *** effectiveness of our methods is demonstrated across a collection of representative benchmarks including both local and non-local diffusion operators,as well as high-dimensional time-series data from a video *** results indicate that the present algorithm can outperform competing approaches in terms of both approximation accuracy and computational cost.

关键词： spectral learning partial differential equation(PDE) neural network slow features analysis

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Developmental systems biology flourishing on new technologies

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Journal of Genetics and genomics 2008年第10期35卷 577-584页

作者： Jing-Dong J. Han Yi Liu Huiling Xue Kai Xia Hong Yu Shanshan Zhu Zhang Chen Wei Zhang Zheng Huang Chunyu Jin Bo Xian Jing Li Lei Hou Yixing Han Chaoqun Niu Timothy C. Alcon Chinese Academy of Sciences Key Laboratory of Molecular Developmental biology Center for Molecular Systems Biology Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Key Laboratory of Machine Perception （Ministry of Education） Peking University Beijing 100871 China Bioinformatics and computational biology graduate Program Iowa State University Ames IA 50011-1040 USA

Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.

关键词： developmental systems biology new technologies symposium

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Economic contribution of participatory agroforestry program to poverty alleviation: a case from Sal forests, Bangladesh

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Journal of Forestry Research 2012年第2期23卷 323-332页

作者： K. K. Islam Marjanke Hoogstra M.O. Ullah Noriko Sato Forest Policy Laboratory Graduate School of Bioresource and Bioenvironmental Sciences Kyushu University Japan Forest and Nature Conservation Policy group Wageningen University the Netherlands Nutrition Metabolism and Genomics Group Wageningen University the Netherlands

In the Forest Department of Bangladesh, a Participatory Agroforestry Program （PAP） was initiated at a denuded Sal forests area to protect the forest resources and to alleviate poverty amongst the local poor population. We explored whether the PAP reduced poverty and what factors might be responsible for poverty alleviation. We used three poverty measurement methods： the Head Count Index, the Poverty Gap Index and the Foster-Greer-Thorbecke index to determine the extent poverty reduction. We used a linear regression model to determine the possible differences among factors in poverty reduction. Data were collected through semi structured questionnaires and face to face interviews within the study area. PAP proved effective at poverty alleviation, considerably improving the local situation. The linear regression model showed that PAP output explained the income differences in poverty reduction. Participants identified bureaucracy and illegal money demands by forest department officials, an uncontrolled market system, and underdeveloped road infrastructure as the main obstacles to reduction of poverty. Overall, PAP is quite successful in alleviating poverty. So this program might be of interest at other degraded forest areas as a tool to alleviate poverty.

关键词： Poverty agroforestry model Sal forests linear regression constraints

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MicroRNA bta-miR-365-3p inhibits proliferation but promotes differentiation of primary bovine myoblasts by targeting the activin A receptor type Ⅰ

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Journal of Animal Science and Biotechnology 2021年第1期12卷 141-154页

作者： Dan Hao Xiaogang Wang Xiao Wang Bo Thomsen Yu Yang Xianyong Lan Yongzhen Huang Hong Chen College of Animal Science and Technology Northwest A&F UniversityShaanxi Key Laboratory of Animal GeneticsBreeding and ReproductionYangling 712100ShaanxiChina Department of Molecular biology and Genetics Aarhus University8000 Aarhus CDenmark Quantitative genomics Bioinformatics and Computational Biology GroupDepartment of Applied Mathematics and Computer ScienceTechnical University of DenmarkRichard Petersens PladsBuilding 3242800 Kongens LyngbyDenmark.

Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA *** microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscles express a plethora of microRNA genes that regulate muscle development and function by controlling the expression of protein-coding target genes. To expand our understanding of the role of microRNA, specifically btamiR-365-3 p, in muscle biology, we investigated its functions in regulating primary bovine myoblast proliferation and ***: Firstly, we found that bta-miR-365-3 p was predominantly expressed in skeletal muscle and heart tissue in Chinese Qinchuan beef cattle. Quantitative PCR and western blotting results showed that overexpression of btamiR-365-3 p significantly reduced the expression levels of cyclin D1(CCND1), cyclin dependent kinase 2(CDK2) and proliferating cell nuclear antigen(PCNA) but stimulated the expression levels of muscle differentiation markers, i.e.,MYOD1, MYOG at both mRNA and protein level. Moreover, downregulation of bta-miR-365-3 p increased the expression of CCND1, CDK2 and PCNA but decreased the expression of MYOD1 and MYOG at both mRNA and protein levels. Furthermore, flow cytometry, EdU proliferation assays and immunostaining results showed that increased levels of bta-miR-365-3 p suppressed cell proliferation but promoted myotube formation, whereas decreased levels of bta-miR-365-3 p resulted in the opposite consequences. Finally, we identified that activin A receptor type I(ACVR1) could be a direct target of bta-miR-365-3 p. It was demonstrated that bta-miR-365-3 p can bind to the 3'UTR of ACVR1 gene to regulate its expression based on dual luciferase gene reporter ***, knock-down of ACVR1 was associated with decreased expressions of CDK2, CCND1 and PCNA but increased expression of MYOG and MYOD1 both at mRNA and protein ***: Collectively, these data suggested that bta-m

关键词： ACVR1 Bta-miR-365-3p Cattle Primary bovine myoblast

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