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Molecular architecture of mammalian pyruvate dehydrogenase complex

Protein & Cell 2025年第1期16卷 72-78页

作者： Maofei Chen Yutong Song Sensen Zhang Yitang Zhang Xudong Chen Minghui Zhang Meng Han Xin Gao Sai Li Maojun Yang Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological StructureSchool of Life SciencesTsinghua UniversityBeijing 100084China Ministry of Education Key Laboratory of Protein Science Tsinghua UniversityBeijing 100084China State Key Laboratory of Membrane Biology Tsinghua UniversityBeijing 100084China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesShenzhen University Health Science CenterShenzhen 518060China Protein Research Technology Center Protein Chemistry and Omics PlatformSchool of Life SciencesTsinghua UniversityBeijing 100084China Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Kingdom of Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Kingdom of Saudi Arabia Cryo-EM Facility Center Southern University of Science and TechnologyShenzhen 518055China Beijing Life Science Academy Beijing 102209China

Dear Editor,Pyruvate dehydrogenase complex(PDHc) is a large multienzyme assembly(Mr = 4–10 million Daltons) consisting of three essential components: pyruvate dehydrogenase(E1p), dihydrolipoyl transacetylase(E2p), and dihydrolipoyl dehydrogenase(E3). These three enzymes perform distinct functions sequentially to catalyze the oxidative decarboxylation of pyruvate with formation of nicotinamide adenine dinucleotide(NADH) and acetyl-coenzyme A(Patel and Roche, 1990).

关键词： sequentially oxidative Dalton

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Integrating information retrieval techniques with traditional DB methods in a web-based database browser 98

Integrating information retrieval techniques with traditiona...

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1998 ACM Symposium on Applied Computing, SAC 1998

作者： Sabin, Roberta Evans Yap, Tieng K. Computer Science Department Loyola College BaltimoreMD21210 United States Computational Bioscience and Engineering Laboratory National Institutes of Health BethesdaMD20817 United States

ISBN: (纸本)0897919696

A Web-based tool for retrieval of documents containing disparate types of data from a large collection is described. This tool uses a relational database system to implement information retrieval methodologies and allows naive users to query the database using freeform expressions instead of a formal query language such as SQL. The database relations contain both attributes whose values may be compared with relational operations and terms from free text portions of the documents which are stored along with measures of information content that allow the ranking of query results. This paper illustrates an application of this integrated tool to the retrieval of biological sequence information. © 1998 ACM.

关键词： Information retrieval

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TELS: A Novel computational Framework for Identifying Motif Signatures of Transcribed Enhancers

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 332-341页

作者： Dimitrios Kleftogiannis Haitham Ashoor Vladimir B.Bajic Centre for Evolution and Cancer Division of Molecular PathologyThe Institute of Cancer Research(ICR)London SM2 5NGUnited Kingdom The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Computational Bioscience Research Center(CBRC) ComputerElectrical and Mathematical Sciences and Engineering

In mammalian cells, transcribed enhancers(TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers’ DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search(TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of *** a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and *** results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers’ broad activity. TELS codes and material are publicly available at http://***/TELS.

关键词： Sequence analysis Machine learning Transcription regulation Transcribed enhancer Motif identification

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Theoretical study for quercetin/β-cyclodextrin complexes: Quantum chemical calculations based on the PM3 and ONIOM2 method

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Journal of Inclusion Phenomena and Macrocyclic Chemistry 2007年第3-4期58卷 337-344页

作者： Yan, Chunli Xiu, Zhilong Li, Xiaohui Teng, Hu Hao, Ce Department of Bioscience and Biotechnology School of Environmental and Biological Science and Technology Dalian University of Technology Dalian 116024 China Department of Chemistry School of Chemical Science and Engineering Dalian University of Technology Dalian 116024 China Virtual Laboratory of Computational Chemistry CNIC Chinese Academy of Sciences Beijing China

The inclusion interaction between quercetin and β- (β-CD) binding site has been investigated, based on PM3 and ONIOM2 methods. The obtained results clearly indicate that the orientation in which the B ring of the guest molecule located near the secondary hydroxyls of the β-CD cavity is preferred in the binding energy. Moreover, Analyses regarding the complex structures suggest that one hydrogen bond between 7-hydroxy group (OH) of quercetin and 6-OH of β-CD is formed. This hydrogen bond interaction plays an important role in the bound quercetin/β-CD complex. © Springer Science+Business Media B.V. 2007.

关键词： Binding energy

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Cortical transcriptome analysis after spinal cord injury reveals the regenerative mechanism of central nervous system in CRMP2 knock-in mice

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Neural Regeneration Research 2021年第7期16卷 1258-1265页

作者： Ayaka Sugeno Wenhui Piao Miki Yamazaki Kiyofumi Takahashi Koji Arikawa Hiroko Matsunaga Masahito Hosokawa Daisuke Tominaga Yoshio Goshima Haruko Takeyama Toshio Ohshima Laboratory for Molecular Brain Science Department of Life Science and Medical BioscienceGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Biomolecular Engineering Laboratory Department of Life Science and Medical BioscienceGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Computational Bio Big-Data Open Innovation Laboratory(CBBD-OIL) National Institute of Advanced Industrial Science and Technology(AIST)TokyoJapan Research Organization for Nano and Life Innovation Waseda UniversityTokyoJapan Institute for Advanced Research of Biosystem Dynamics Waseda Research Institute for Science and EngineeringGraduate School of Advanced Science and EngineeringWaseda UniversityTokyoJapan Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology(AIST)TsukubaJapan Department of Molecular Pharmacology and Neurobiology Graduate School of MedicineYokohama City UniversityYokohamaJapan

Recent studies have shown that mutation at Ser522 causes inhibition of collapsin response mediator protein 2(CRMP2) phosphorylation and induces axon elongation and partial recovery of the lost sensorimotor function after spinal cord injury(SCI).We aimed to reveal the intracellular mechanism in axotomized neurons in the CRMP2 knock-in(CRMP2KI) mouse model by performing transcriptome analysis in mouse sensorimotor cortex using micro-dissection punching *** to that, we analyzed the structural pathophysiology in axotomized or neighboring neurons after SCI and found that somatic atrophy and dendritic spine reduction in sensorimotor cortex were suppressed in CRMP2KI *** analysis of the transcriptome has aided in the identification of four hemoglobin genes Hba-a1, Hba-a2, Hbb-bs, and Hbb-bt that are significantly upregulated in wild-type mice with concomitant upregulation of genes involved in the oxidative phosphorylation and ribosomal pathways after ***, we observed substantial upregulation in channel activity genes and downregulation of genes regulating vesicles, synaptic function, glial cell differentiation in CRMP2KI ***, the transcriptome profile of CRMP2KI mice has been discussed wherein energy metabolism and neuronal pathways were found to be differentially *** results showed that CRMP2KI mice displayed improved SCI pathophysiology not only via microtubule stabilization in neurons, but also possibly via the whole metabolic system in the central nervous system, response changes in glial cells, and *** together, we reveal new insights on SCI pathophysiology and the regenerative mechanism of central nervous system by the inhibition of CRMP2 phosphorylation at *** these experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee at Waseda University, Japan(2017-A027 approved on March 21, 2017;2018-A003 approved on March 25, 2018;2019-A026 approved on March

关键词： CNS regeneration cortex CRMP2 hemoglobin metabolic pathway spinal cord injury spine transcriptome

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Information technology applications in biomedical research

Information technology applications in biomedical research

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： R.L. Martino K.M. Kempner C.A. Johnson Computational Bioscience and Engineering Laboratory National Institutes of Health DHHS Bethesda MD USA

High end computer systems, high speed networks, and other advanced information technologies provide the performance needed in today's biomedical research computing environment. NIH participates in the national Computing, Information, and Communications Research and Development (CIC R&D) program by applying these new technologies to problems in biomedicine. We describe a high speed networking example, the Radiology Consultation WorkStation, and a high end computing example, positron emission tomographic (PET) image reconstruction. The NIH Cancer Genome Anatomy Project (CGAP) provides an example of a major biomedical research effort that will require the creative use of information technology in the future. We end with conclusions concerning the impact new technologies have had on biomedical research and a discussion of plans for the future.

关键词： Information technology Biomedical computing Computer networks High performance computing High-speed networks Application software Research and development Radiology Workstations Radioactive decay

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Parallel algorithms in molecular biology

Parallel algorithms in molecular biology

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International Conference and Exhibition on High-Performance Computing and Networking, HPCN Europe 1997

作者： Martino, Robert L. Yap, Tieng K. Suh, Edward B. Computational Bioscience and Engineering Laboratory Division of Computer Research and Technology National Institutes of Health Building 12A Room 2033 12 South Drive MSC 5624 BethesdaMD20892 United States

ISBN: (纸本)3540628983

Scalable parallel computer architectures provide the computational performance needed for advanced computing problems in molecular biology. Many scientific challenges in molecular biology have associated with them a computational requirement that must be solved before scientific progress can be made. We have developed a number of parallel algorithms and techniques useful in determining biological structure and function. Two example applications are the alignment of multiple DNA and protein sequences using speculative computation and the calculation of the solvent accessible surface area of proteins used to predict the three-dimensional conformation of these molecules from their primary structure. Timing results demonstrate substantial performance improvements with parallel implementations compared with conventional sequential systems. As the developed methods allow molecular biologists to perform computational tasks that would not otherwise be possible, we continue to develop parallel algorithms useful to this important scientific field. © 1997 Springer-Verlag Berlin Heidelberg.

关键词： Parallel algorithms

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Syntax-ignorant n-gram embeddings for sentiment analysis of arabic dialects 4

Syntax-ignorant n-gram embeddings for sentiment analysis of ...

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4th Arabic Natural Language Processing Workshop, WANLP 2019, held at ACL 2019

作者： Mulki, Hala Haddad, Hatem Gridach, Mourad Babaoǧlu, Ismail Department of Computer Engineering Konya Technical University Turkey Riadi Laboratory National School of Computer Sciences University of Manouba Tunisia Computational Bioscience Program University of Colorado School of Medicine United States ICompass Consulting Tunisia

ISBN: (纸本)9781950737321

Arabic sentiment analysis models have employed compositional embedding features to represent the Arabic dialectal content. These embeddings are usually composed via ordered, syntax-aware composition functions and learned within deep neural frameworks. With the free word order and the varying syntax nature across the different Arabic dialects, a sentiment analysis system developed for one dialect might not be efficient for the others. Here we present syntax-ignorant n-gram embeddings to be used in sentiment analysis of several Arabic dialects. The proposed embeddings were composed and learned using an unordered composition function and a shallow neural model. Five datasets of different dialects were used to evaluate the produced embeddings in the sentiment analysis task. The obtained results revealed that, our syntax-ignorant embeddings could outperform word2vec model and doc2vec both variant models in addition to hand-crafted system baselines, while a competent performance was noticed towards baseline systems that adopted more complicated neural architectures. © ACL *** right reserved.

关键词：

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Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

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Science Bulletin 2016年第15期61卷 1176-1186页

作者： Yong Wang Zhao-Ming Gao Jiang-Tao Li Salim Bougouffa Ren Mao Tian Vladimir B. Bajic Pei-Yuan Qian Sanya Institute of Deep Sea Science and Engineering ChineseAcademy of Sciences Sanya 572000 China Division of Life Science Hong Kong University of Science and Technology Clear Water Bay Hong Kong China State Key Laboratory of Marine Geology Tongji UniversityShanghai 200092 China Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Jeddah 23955-6900 Saudi Arabia

Aerophobetes （or CD12） is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bac- terium TCSI from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS 1 and some thermophilic bac- terial phyla. The genome of TCS1 （at least 1.27 Mbp） contains a full set of genes encoding core metabolic path- ways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved inthe sediment under the microbial mat. Aerophobetes bac- terium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood-Ljung- dahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood-Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aero- phobetes bacterium TCS 1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal trans- duction and cell motility. The metabolic activities of TCS 1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCSI might be a facultative bacterium in anaerobic saline sedi- ments near cold seeps.

关键词： Deep-sea sediment Aerophobetes Metagenome Sugar fermentation Cold seep

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MRI compatible hemodynamic recording system

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Journal of Cardiovascular Magnetic Resonance 2013年第SUPPL 1期15卷 P22-P22页

作者： Bo Xiao John W Kakareka Randall H Pursley Thomas Pohida Robert J Lederman Anthony Faranesh Computational Bioscience and Engineering Laboratory CIT NIH Bethesda MD USA Cardiovascular and Pulmonary Branch NHLBI NIH Bethesda MD USA

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