检索结果-内蒙古大学图书馆

Functional Analysis of Semi-conserved Transit Peptide Motifs and Mechanistic Implications in Precursor Targeting and Recognition

引用

Molecular Plant 2016年第9期9卷 1286-1301页

作者： Kristen Holbrook Chitra Subramanian Prakitchai Chotewutmontri L. Evan Reddick Sarah Wright Huixia Zhang Lily Moncrief Barry D. Bruce Department of Biochemistry Cellular and Molecular Biology Graduate Program in Plant Physiology and Genetics Graduate School of Genome Science and Technology Department of Botany Department of BotanyUniversity of Tennessee Knoxville TN 37996 USA Present address: Department of Infectious Disease St. Jude Children's Research Hospital Memphis TN 38105 USA Present address: Institute of Molecular Biology University of Oregon Eugene OR 97403 USA present address: Department of Microbiology University of Texas Southwestern Medical Center 5323 Harry Hines Boulevard Dallas TX 75390 USA Present address: Albert R. Mann Library Cornell University Ithaca NY 14850 USA present address: U.S. Food and Drug Administration 10903 New Hampshire Avenue Silver Spring MD 20993 USA

Over 95% of plastid proteins are nuclear-encoded as their precursors containing an N-terminal extension known as the transit peptide （TP）. Although highly variable, TPs direct the precursors through a conserved, posttranslational mechanism involving translocons in the outer （TOC） and inner envelope （TOC）. The organelle import specificity is mediated by one or more components of the Toc complex. However, the high TP diversity creates a paradox on how the sequences can be specifically recognized. An emerging model of TP design is that they contain multiple loosely conserved motifs that are recognized at different steps in the targeting and transport process. Bioinformatics has demonstrated that many TPs contain semiconserved physicochemical motifs, termed FGLK. In order to characterize FGLK motifs in TP recognition and import, we have analyzed two well-studied TPs from the precursor of RuBisCO small subunit （SStp） and ferredoxin （Fdtp）. Both SStp and Fdtp contain two FGLK motifs. Analysis of large set mutations （-85） in these two motifs using in vitro, in organello, and in vivo approaches support a model in which the FGLK domains mediate interaction with TOC34 and possibly other TOC components. In vivo import analysis suggests that multiple FGLK motifs are functionally redundant. Furthermore, we discuss how FGLK motifs are required for efficient precursor protein import and how these elements may permit a convergent function of this highly variable class of targeting sequences.

关键词： chloroplast biology protein translocation Toc34 transit peptide cell biology

来源：评论

学校读者我要写书评

暂无评论

Complete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data

引用

Cell Reports 2025年第6期44卷

作者： Zheng Dong Joanne Whitehead Maggie Fu Julia L. MacIsaac David H. Rehkopf Luis Rosero-Bixby Michael S. Kobor Keegan Korthauer Centre for Molecular Medicine and Therapeutics University of British Columbia 950 West 28th Avenue Vancouver BC V5Z 4H4 Canada BC Children’s Hospital Research Institute University of British Columbia 950 West 28th Avenue Vancouver BC V5Z 4H4 Canada Genome Science and Technology Graduate Program University of British Columbia 100-570 West 7th Avenue Vancouver BC V5Z 4S6 Canada Division of General Medical Disciplines Department of Medicine School of Medicine Stanford University 1070 Arastradero Road Suite 300 Palo Alto CA 94304 USA Centro Centroamericano de Población (CCP) Universidad de Costa Rica San José 2060 Costa Rica Department of Medical Genetics University of British Columbia 950 West 28th Avenue Vancouver BC V5Z 4H4 Canada Edwin S. H. Leong Centre for Healthy Aging University of British Columbia 117-2194 Health Science Mall Vancouver BC V6T 1Z3 Canada Department of Statistics University of British Columbia 2207 Main Mall Vancouver BC V6T 1Z4 Canada

The complete telomere-to-telomere human genome assembly (T2T-CHM13) and the draft human pangenome reference provide unique opportunities to refine DNA methylation (DNAm) studies. Here, we find that T2T-CHM13 calls 7.4% more CpGs genome wide compared to GRCh38 across four widely used short-read DNAm profiling methods and improves the evaluation of probe cross-reactivity and mismatch for Illumina DNAm arrays, yielding new and more reproducible sets of unambiguous probes. The pangenome reference further expands CpG calling by 4.5% in short-read sequencing data and identifies cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These benefits facilitate the discovery of biologically relevant DNAm alterations in epigenome-wide association studies (EWASs). For instance, additional DNAm alterations enriched in cancer-related genes and pathways are identified in cancer EWASs. Together, this study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of DNAm investigations.

关键词： T2T-CHM13 pangenome epigenetics bisulfite sequencing cross-reactive probe Illumina Infinium HumanMethylation BeadChips annotation Illumina HumanMethylationEPIC BeadChip Infinium MethylationEPIC v.2.0 EPICv2 epigenome-wide association study cancer

来源：评论

学校读者我要写书评

暂无评论

Quantum simulation of an extended Dicke model with a magnetic solid

Communications Materials

引用

Communications Materials 2024年第1期5卷 42页

作者： Marquez Peraca, Nicolas Li, Xinwei Moya, Jaime M. Hayashida, Kenji Kim, Dasom Ma, Xiaoxuan Neubauer, Kelly J. Fallas Padilla, Diego Huang, Chien-Lung Dai, Pengcheng Nevidomskyy, Andriy H. Pu, Han Morosan, Emilia Cao, Shixun Bamba, Motoaki Kono, Junichiro Department of Physics and Astronomy Rice University HoustonTX United States Department of Physics California Institute of Technology PasadenaCA United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX United States Division of Applied Physics Graduate School of Engineering Hokkaido University Hokkaido Japan Department of Electrical and Computer Engineering Rice University HoustonTX United States Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University Shanghai China Department of Physics and Center for Quantum Frontiers of Research and Technology National Cheng Kung University Tainan Taiwan Department of Chemistry Rice University HoustonTX United States Department of Physics I Kyoto University Kyoto Japan The Hakubi Center for Advanced Research Kyoto University Kyoto Japan PRESTO Japan Science and Technology Agency Saitama Japan Department of Physics Yokohama National University Yokohama Japan Department of Materials Science and NanoEngineering Rice University HoustonTX United States

The Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO3, where the role of atoms (photons) is played by Er3+ spins (Fe3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems. © The Author(s) 2024.

关键词： Atoms

来源：评论

学校读者我要写书评

暂无评论

Magnetically tuned continuous transition from weak to strong coupling in terahertz magnon polaritons

引用

Physical Review Research 2023年第1期5卷 L012039-L012039页

作者： Andrey Baydin Kenji Hayashida Takuma Makihara Fuyang Tay Xiaoxuan Ma Wei Ren Guohong Ma G. Timothy Noe, II Ikufumi Katayama Jun Takeda Hiroyuki Nojiri Shixun Cao Motoaki Bamba Junichiro Kono Department of Electrical and Computer Engineering Rice University Houston Texas 77005 USA Smalley-Curl Institute Rice University Houston Texas 77005 USA Division of Applied Physics Graduate School of Engineering Hokkaido University Sapporo Hokkaido 060-8628 Japan Department of Physics and Astronomy Rice University Houston Texas 77005 USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas 77005 USA Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University 200444 Shanghai China Department of Physics Graduate School of Engineering Science Yokohama National University Yokohama 240-8501 Japan Institute for Materials Research Tohoku University Sendai 980-8577 Japan The Hakubi Center for Advanced Research Kyoto University Kyoto 606-8502 Japan Department of Physics I Kyoto University Kyoto 606-8502 Japan PRESTO Japan Science and Technology Agency Kawaguchi 332-0012 Japan Department of Materials Science and NanoEngineering Rice University Houston Texas 77005 USA

Depending on the relative rates of coupling and dissipation, a light-matter coupled system is either in the weak- or strong-coupling regime. Here, we present a unique system where the coupling rate continuously increases with an externally applied magnetic field while the dissipation rate remains constant, allowing us to monitor a weak-to-strong coupling transition as a function of magnetic field. We observed a Rabi splitting of a terahertz magnon mode in yttrium orthoferrite above a threshold magnetic field of ∼14 T. Based on a microscopic theoretical model, we show that with increasing magnetic field the magnons transition into magnon polaritons through an exceptional point, which will open up new opportunities for in situ control of non-Hermitian systems.

关键词： Antiferromagnetism High magnetic fields Magneto-optics Magnons Polaritons Non-Hermitean systems Terahertz time-domain spectroscopy Transfer matrix method

来源：评论

学校读者我要写书评

暂无评论

Publisher Correction: IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis

引用

Scientific reports 2018年第1期8卷 10367页

作者： Daichi Shigemizu Fuyuki Miya Shintaro Akiyama Shujiro Okuda Keith A Boroevich Akihiro Fujimoto Hidewaki Nakagawa Kouichi Ozaki Shumpei Niida Yonehiro Kanemura Nobuhiko Okamoto Shinji Saitoh Mitsuhiro Kato Mami Yamasaki Tatsuo Matsunaga Hideki Mutai Kenjiro Kosaki Tatsuhiko Tsunoda Department for Medical Genome Sciences Medical Genome Center National Center for Geriatrics and Gerontology Aichi Japan. daichi@ncgg.go.jp. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. daichi@ncgg.go.jp. RIKEN Center for Integrative Medical Sciences Yokohama Japan. daichi@ncgg.go.jp. Medical Sciences Innovation Hub Program Cluster for Science and Technology Hub RIKEN Yokohama Japan. daichi@ncgg.go.jp. CREST JST Japan. daichi@ncgg.go.jp. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department for Medical Genome Sciences Medical Genome Center National Center for Geriatrics and Gerontology Aichi Japan. Niigata University Graduate School of Medical and Dental Sciences Niigata Japan. Department of Drug Discovery Medicine Graduate School of Medicine Kyoto University Kyoto Japan. Division of Regenerative Medicine Institute for Clinical Research Osaka National Hospital National Hospital Organization Osaka Japan. Department of Neurosurgery Osaka National Hospital National Hospital Organization Osaka Japan. Department of Medical Genetics Osaka Medical Center and Research Institute for Maternal and Child Health Osaka Japan. Department of Pediatrics and Neonatology Nagoya City University Graduate School of Medical Sciences Nagoya Japan. Department of Pediatrics Showa University School of Medicine Tokyo Japan. Department of Pediatric Neurosurgery Takatsuki General Hospital Osaka Japan. Division of Hearing and Balance Research National Institute of Sensory Organs National Hospital Organization Tokyo Medical Center Tokyo Japan. Center for Medical Genetics Keio University School of Medicine Tokyo Japan. Department of Medical Science Mathematics Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan. tsunoda.mesm@mri.tmd.a

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Magnetically Tuned Continuous Transition from Weak to Strong Coupling in Terahertz Magnon Polaritons

arXiv

引用

arXiv 2022年

作者： Baydin, Andrey Hayashida, Kenji Makihara, Takuma Tay, Fuyang Ma, Xiaoxuan Ren, Wei Ma, Guohong Noe, G. Timothy Katayama, Ikufumi Takeda, Jun Nojiri, Hiroyuki Cao, Shixun Bamba, Motoaki Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States The Smalley-Curl Institute Rice University HoustonTX77005 United States Division of Applied Physics Graduate School of Engineering Hokkaido University Hokkaido Sapporo060-8628 Japan Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics International Center of Quantum and Molecular Structures Materials Genome Institute Shanghai University Shanghai200444 China Department of Physics Graduate School of Engineering Science Yokohama National University Yokohama240-8501 Japan Institute for Materials Research Tohoku University Sendai980-8577 Japan The Hakubi Center for Advanced Research Kyoto University Kyoto606-8502 Japan Department of Physics I Kyoto University Kyoto606-8502 Japan PRESTO Japan Science and Technology Agency Kawaguchi332-0012 Japan Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

关键词： Polariton

来源：评论

学校读者我要写书评

暂无评论

C-Terminal-Truncating ASXL1 Mutations Induce MDS Via Inhibition Of PRC2

引用

BLOOD 2013年第21期122卷 471-471页

作者： Inoue, Daichi Kitaura, Jiro Togami, Katsuhiro Nishimura, Koutarou Enomoto, Yutaka Uchida, Tomoyuki Kagiyama, Yuki Kawabata, Kimihito Cojin Nakahara, Fumio Oki, Toshihiko Harada, Hironori Ochiya, Takahiro Aburatani, Hiroyuki Kimura, Hiroshi Thol, Felicitas Heuser, Michael Levine, Ross L. Abdel-Wahab, Omar Kitamura, Toshio Division of Cellular Therapy The Institute of Medical Science The University of Tokyo Tokyo Japan Division of Hematological Malignancy National Cancer Center Research Institute Tokyo Japan Department of Hematology Juntendo University School of Medicine Tokyo Japan Sec. Meta. National Cancer Center Research Institute Tokyo Japan Genome Science Division Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Graduate School of Frontier Biosciences Osaka University Suita Japan Department of Hematology Hemostasis Oncology and Stem Cell Transplantation Hannover Medical School Hannover Germany Department of Medicine Memorial Sloan-Kettering Cancer Center New York NY USA Leukemia Service and Human Oncology and Pathogenesis Program Memorial Sloan-Kettering Cancer Center New York City NY USA

471

关键词：

来源：评论

学校读者我要写书评

暂无评论

Two-Step Activated Carbon Cloth Enhances Microbial Interactions and Methane Production During Anaerobic Digestion of Municipal Sludge

SSRN

引用

SSRN 2022年

作者： Kumar, Vikas Kieft, Brandon Devi, Parmila Hallam, Steven J. Eskicioglu, Cigdem UBC Bioreactor Technology Group School of Engineering University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Department of Microbiology and Immunology University of British Columbia VancouverBCV6T 1Z4 Canada Department of Microbiology and Immunology University of British Columbia VancouverBC Canada Graduate Program in Bioinformatics University of British Columbia VancouverBCV6T 1Z4 Canada Genome Science and Technology Program University of British Columbia 2329 West Mall VancouverBCV6T 1Z4 Canada Life Sciences Institute University of British Columbia VancouverBCV6T 1Z3 Canada ECOSCOPE Training Program University of British Columbia VancouverBCV6T 1Z3 Canada

This study investigated the effects of two-step activated carbon cloth (CC) on the syntrophic microbial association during anaerobic digestion (AD) of municipal sludge. A simple two-step activation, acid pretreatment (H2SO4/HNO3) followed by air calcination (550°C), was used to convert commercial untreated CC (U-CC) into high performance activated CC (A-CC). Biochemical methane potential (BMP) assays conducted at different CC dosages indicated that A-CC, at a dose of 0.80 g A-CC {1.48 g A-CC/g-VS (volatile solids)substrate}, enhanced methane yield from by 3.7 times and reduced the lag phase up to 15.6-fold, compared to non-CC control within 3 days. Characterization of CC surfaces and kinetic modeling indicated a 435-times increased A-CC pore size area (Barrett, Joyner, and Halenda, BJH) with the potential to promote electron transfer and accelerate kinetic rates of methane production. Consistent with these results, microbial community structure analysis of CC surfaces indicated rapid adherence of methanogenic archaea and bacterial syntrophs to A-CC within 3 days. Multi-variate statistical analyses indicated that these populations were highly enriched on 0.80 g A-CC dosage compared to controls. Based on these results it can be concluded that A-CC provides a robust selective environment for syntrophic energy metabolism driving enhanced methane production from municipal sludge. © 2022, The Authors. All rights reserved.

关键词： Anaerobic digestion

来源：评论

学校读者我要写书评

暂无评论

Synthesis and Evaluation of Metal-Impregnated Carbon Cloth Supplementation to Improve Anaerobic Digestion Performance from Municipal Sludge

SSRN

引用

SSRN 2023年

作者： Kumar, Vikas Devi, Parmila Patil, Abhishek Santana, Juan Camilo Bobowski, Jake S. Hallam, Steven J. Eskicioglu, Cigdem UBC Bioreactor Technology Group School of Engineering University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Department of Microbiology and Immunology University of British Columbia VancouverBCV6T 1Z4 Canada Department of Physics University of British Columbia Okanagan Campus KelownaBCV1V 1V7 Canada Graduate Program in Bioinformatics University of British Columbia VancouverBCV6T 1Z4 Canada Genome Science and Technology Program University of British Columbia 2329 West Mall VancouverBCV6T 1Z4 Canada Life Sciences Institute University of British Columbia VancouverBCV6T 1Z3 Canada Ecoscope Training Program University of British Columbia VancouverBCV6T 1Z3 Canada

This study investigated the effect of metal-impregnated carbon cloth (CC) supplementation on thermophilic anaerobic digestion (AD) improvement utilizing municipal sludge as a biomass input. Four types of metal-impregnated CC nanocomposites (Fe/CC, Ni/CC, Ni/Fe/CC, NiPcS/Fe/CC) were synthesized from activated CC (A-CC) using hydrothermal synthesis and compared with untreated CC (U-CC) to evaluate their functional significance for enhanced AD. The main factors inspected were electrical conductivity (EC) and Brunauer–Emmett–Teller (BET) surface area. A-CC had the highest surface area of 386.15 m2/g, followed by Fe/CC, NiPcS/Fe/CC, Ni/CC and Ni/Fe/CC with 140.96, 52.27, 43.52 and 36.07 m2/g, respectively. The A-CC and Fe/CC reactors produced 3.45 and 2.70 times more methane than Control (without CC) in the first 9 days. In contrast, the methane production for U-CC, Ni/CC, Ni/Fe/CC and NiPcS/Fe/CC was only 0.87, 1.26, 1.01 and 1.29 times, respectively, compared to Control. At a higher BET surface (>350 m2/g), the surface area becomes a more dominant factor, and the increase of EC value (>2.9*104 1/Ω.m) does not have an impact on methane enhancement. Microbial community analysis revealed that A-CC had the highest abundances of Syntrophomonas, Coprothermobacter and methanogenic populations, including Methanothermobacter and Methanosarcina, within 3 days compared to Control and metal-impregnated CC. There were minimal changes in microbial community composition in metal-impregnated CC compared to the U-CC. The result implies that the efficacy of CC supplementation for AD upgrading largely depends on the higher surface area compared to metal impregnation or conductivity. © 2023, The Authors. All rights reserved.

关键词： Anaerobic digestion

来源：评论

学校读者我要写书评

暂无评论

Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

引用

Nature communications 2023年第1期14卷 6540页

作者： Hitomi Takada Yohei Sasagawa Mika Yoshimura Kaori Tanaka Yoshimi Iwayama Tetsutaro Hayashi Ayako Isomura-Matoba Itoshi Nikaido Akira Kurisaki Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. itoshi.nikaido@riken.jp. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. itoshi.nikaido@riken.jp. Master's/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan. itoshi.nikaido@riken.jp. Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. akikuri@bs.naist.jp.

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：