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Characterization of the complete mitochondrial genome ofSilurus soldatoviin Korean river

Mitochondrial DNA Part B 2019年第2期4卷 3886-3887页

作者： Md. Jobaidul Alam Mahmoud Aboalyamin Soliman Khalil Kyung Su Kim Sapto Andriyono Chang Geun Choi Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of Korea KOICA-PKNU International Graduate Program of Fisheries Science Graduate School of Global Fisheries Pukyong National University Busan Republic of Korea Gyeongsangnam-do Freshwater Fish Research Center Miryang Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty Universitas Airlangga Surabaya Indonesia Department of Ecological Engineering Pukyong National University Busan Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaKOICA-PKNU International Graduate Program of Fisheries Science Graduate School of Global Fisheries Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome ofSilurus soldatovifirstly collected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 16,525 bp in length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Siluridae. Twenty-eight genes were located on H strand, whereas the remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences, S. soldatovishowed highest identity (99.38%) to the Chinese haplotype ofS. soldatovi(NC022723) followed by the Chinese haplotype ofSilurus asotus(JX087351). Interestingly, intraspecies variations ofS. asotusare higher than those of interspecies and further study should be made to elucidate the evolutional relationship between twoSilurusspecies.

关键词： Next-generation sequencing Silurus soldatovi mitochondrial genome alien species

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An Open-Source Knowledge Graph Ecosystem for the Life sciences

arXiv

引用

arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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Characterization of the complete mitochondrial genome ofOdontobutis platycephalacollected from Nakdong River, South Korea

引用

Mitochondrial DNA Part B 2019年第2期4卷 3908-3909页

作者： Md. Jobaidul Alam Kyung Su Kim Sapto Andriyono Wongyu Park Hae-Ja Baek Jae-Young Je Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of Korea Gyeongsangnam-do Freshwater Fish Research Center Miryang Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty C Campus Jl Universitas Airlangga Surabaya Indonesia Department of Marine Biology Pukyong National University Busan Republic of Korea Department of Marine-Bio Convergence Science Pukyong National University Busan Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome ofOdontobutis platycephalacollected from a native Korean river was determined by the bioinformatics assembly of the next-generation sequencing (NGS) reads. The circular mitogenome was 17,590 bp length which harbored canonical 13 protein-coding genes, 22 tRNAs, and 2 rRNAs, which was identical to those of family Odontobutidae. Twenty-eight genes were located on H strand, whereas remaining nine genes were on L strand. Except for COX1 gene (GTG), other 12 protein-coding genes were predicted typical start codons (ATG). Among the currently known mitogenome sequences,O. platycephalashowed highest identity (96.98%) to Korean haplotype ofO. platycephala(NC010199).

关键词： Next-generation sequencing Odontobutis platycephala mitochondrial genome

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Frontispiece: Visible Light-Driven Molecular Switches and Motors: Recent Developments and Applications

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Chemistry – A European Journal 2022年第18期28卷

作者： Dr. Hao Wang Dr. Hari Krishna Bisoyi Xinfang Zhang Dr. Fathy Hassan Prof. Quan Li Advanced Materials and Liquid Crystal Institute and Chemical Physics Interdisciplinary Program Kent State University Kent Ohio 44242 USA Department of Chemistry Faculty of Science Tanta University Tanta El-Gharbia 31527 Egypt Institute of Advanced Materials School of Chemistry and Chemical Engineering and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research Southeast University Nanjing 211189 China

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Mitochondrial genome of Mola carplet,Amblypharyngodon mola(Hamilton, 1822) and its evolutional relationship in subfamily Danioninae

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Mitochondrial DNA Part B 2019年第1期4卷 650-651页

作者： Md. Jobaidul Alam Sapto Andriyono A. T. M. Eunus Md. Mofizur Rahman Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Fisheries Ministry of Fisheries and Livestock Dhaka Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFaculty of Fisheries and Marine C Campus Jl. Mulyorejo Surabaya Universitas Airlangga East Java Indonesia World Fish Bangladesh and South Asia Office Dhaka Bangladesh Department of Marine Biology Pukyong National University Busan Republic of KoreaDepartment of Fisheries and Marine Science Noakhali Science and Technology University Sonapur Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome in Mola carplet,Amblypharyngodon mola(Hamilton, 1822) was determined by MiSeq platform for the first time in the genus. The mitogenome ofA. molawas circular and 16,545 bp in length, which harbours a canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (D-Loop). Twenty eight genes were encoded on the H strand and the other 9 genes were on the L strand. The incomplete stop codon (TA-/T–) was identified in seven genes (COX2,COX3,ND2,ND3,ND4,ATP6, andCytb). The mitogenome ofA. molashowed highest (82%) sequence identity withRasbora vaterifloris(GenBank No. NC015531), which is endemic to Sri Lanka.

关键词： Next generation sequencing Amblypharyngodon mola mitochondrial genome Danioninae Bangladesh

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Topographical pattern of blood-brain barrier impairment in preclinical and clinical Alzheimer’s disease

引用

Alzheimer's & Dementia 2023年第S17期19卷

作者： Dahyun Yi Min Soo Byun Joon Sik Park Gihwan Byeon Hyejin Ahn Gijung Jung Koung Mi Kang Chul-Ho Sohn Jaeseok Park Dong Young Lee Seoul National University Seoul Korea Republic of (South) Institute of Human Behavioral Medicine Medical Research Center Seoul National University Seoul Korea Republic of (South) Correspondece Seoul National University College of Medicine Seoul Korea Republic of (South) Seoul National University Hospital Seoul Korea Republic of (South) Sungkyunkwan University Department of Biomedical Engineering Seoul Korea Republic of (South) Kangwon National University Hospital Chuncheon Korea Republic of (South) Interdisciplinary program of cognitive science Seoul National University College of Humanities Seoul Korea Republic of (South) Sungkyunkwan University Biomedical Institute for Convergence Seoul Korea Republic of (South)

Background While blood-brain barrier (BBB) damage in some brain regions has been suggested in Alzheimer’s disease (AD) dementia and mild cognitive impairment (MCI), the topographical pattern of BBB impairment associated with AD process in whole brain level is still poorly understood. Using high-resolution 3-dimensional (3D) dynamic contrast-enhanced (DCE) scans of BBB permeability ( K trans ) for the whole brain, we aimed to reveal topographical pattern of BBB impairment related to Alzheimer’s disease (AD) including preclinical as well as clinically impaired state. Method Ninety-one participants were included in the study [45 cognitively normal (CN) older adults, 24 individuals with mild cognitive impairment (MCI), and 22 patients with AD dementia]. Comprehensive clinical and neuropsychological assessments were administered to all participants. High-resolution DCE- as well as T 1 -weighted-MRI scans were obtained in addition to amyloid-PET scans. Amyloid-beta (Ab) positivity was obtained using previously established cut-offs. Preprocessing of K trans maps incorporated FreeSurfer-based (v6.0) segmentation to ensure exclusion of the voxels within cerebrospinal fluid (CSF) spaces. Voxel-wise analyses were conducted using SPM12 implemented in MATLAB 2018b. Result Subtle BBB impairment, as measured by K trans map images based on high-resolution 3D DCE-MRI, was observed at multiple brain regions even in preclinical AD (i.e., Ab-positive CN) as well as AD with cognitive impairment (i.e., Ab-positive MCI and AD). The brain regions with impaired K trans closely corresponded to the AD-signature regions (Figure). Compared to Ab-negative CN, Ab-positive CN showed increased breakdown of BBB in the precuneus, posterior-cingulate cortex, and medial temporal lobe. Moreover, compared to Ab-negative CN, Ab-positive MCI and AD patients showed increased breakdown of BBB in more diffuse regions including bilateral frontal, parietal and inferior temporal areas. In contrast, when using lo

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Wisdom of Crowds for Supporting the Safety Evaluation of Nanomaterials

SSRN

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SSRN 2025年

作者： Saarimäki, Laura Aliisa Fratello, Michele del Giudice, Giusy Di Lieto, Emanuele Afantitis, Antreas Alenius, Harri Chiavazzo, Eliodoro Gulumian, Mary Karisola, Piia Lynch, Iseult Mancardi, Giulia Melagraki, Georgia Netti, Paolo A. Papadiamantis, Anastasios G. Peijnenburg, Willie Santos, Hélder A. Serchi, Tommaso Shahbazi, Mohammad-Ali Stoeger, Tobias Valsami-Jones, Eugenia Vivo, Paola Vrček, Ivana Vinković Vogel, Ulla Wick, Peter Winkler, David A. Serra, Angela Greco, Dario Faculty of Medicine and Health Technology Tampere University Tampere33520 Finland Division of Pharmaceutical Biosciences Faculty of Pharmacy University of Helsinki Helsinki00790 Finland NovaMechanics Ltd Nicosia Cyprus Institute of Environmental Medicine Karolinska Institutet Stockholm171 77 Sweden Research Program Medical Faculty University of Helsinki Helsinki00290 Finland Politecnico di Torino Corso Duca degli Abruzzi 24 Torino10129 Italy National Institute for Occupational Health National Health Laboratory Services Johannesburg South Africa School of Geography Earth and Environmental Sciences University of Birmingham Birmingham United Kingdom Division of Physical Sciences and Applications Hellenic Military Academy Vari Greece Interdisciplinary Research Centre on Biomaterials-CRIB University of Napoli Federico II P.le Tecchio 80 Napoli80125 Italy Institute of Environmental Sciences Leiden University Leiden Netherlands National Institute of Public Health and the Environment Center for Safety of Products and Substances Bilthoven Netherlands University of Groningen Groningen Netherlands Drug Research Program Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki Helsinki Finland Luxembourg Institute of Science and Technology 5 Avenue des Hauts Fourneaux Eschsur-Alzette4362 Luxembourg Munich Germany Solar Cells Faculty of Engineering and Natural Sciences Tampere University P.O. Box 541 TampereFI-33014 Finland Institute for Medical Research and Occupational Health Zagreb Croatia National Research Centre for the Working Environment Copenhagen ODK-2100 Denmark Lerchenfeldstrasse 5 St. Gallen9014 Switzerland La Trobe Institute of Molecular Science La Trobe University Bundoora3086 Australia Monash Institute of Pharmaceutical Sciences Monash University Parkville3052 Australia School of Pharmacy University of Nottingham NottinghamNG7 2QL United Kingdom Tampere Institute for Advanced Study

The development of new approach methodologies (NAMs) to replace current in vivo testing for the safety assessment of engineered nanomaterials (ENMs) is hindered by the scarcity of validated experimental data for a broad range of ENMs. We introduce a framework to address this challenge by harnessing the collective expertise of professionals from multiple complementary and related fields (‘wisdom of crowds’ or WoC). By integrating expert insights, we aim to fill data gaps and generate consensus concern scores for diverse ENMs, thereby enhancing the predictive power of nanosafety computational models. Our investigation reveals an alignment between expert opinion and experimental data, providing robust estimations of concern levels. Building upon these findings, we employ predictive machine learning models trained on the newly defined concern scores, ENM descriptors, and gene expression profiles, to quantify potential harm across various toxicity endpoints. These models further revealed key genes potentially involved in underlying toxicity mechanisms. Notably, genes associated with metal ion homeostasis, inflammation, and oxidative stress emerge as predictors of ENM toxicity across diverse endpoints. This study showcases the value of integrating expert knowledge and computational modeling to address the complexity of nanomaterial safety. Our work suggests that this interdisciplinary approach enhances the accuracy and efficiency of safety assessment in the rapidly evolving landscape of nanotechnology. © 2025, The Authors. All rights reserved.

关键词： Nanoclay

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Author Correction: O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine

引用

Nature communications 2022年第1期13卷 6253页

作者： Kibum Kim Hee Chan Yoo Byung Gyu Kim Sulhee Kim Yulseung Sung Ina Yoon Ya Chun Yu Seung Joon Park Jong Hyun Kim Kyungjae Myung Kwang Yeon Hwang Sunghoon Kim Jung Min Han Interdisciplinary Program of Integrated OMICS for Biomedical Science Graduate School Yonsei University Seoul 03722 South Korea. Yonsei Institute of Pharmaceutical Sciences College of Pharmacy Yonsei University Incheon 21983 South Korea. Center for Genomic Integrity Institute for Basic Science Ulsan 44919 South Korea. Department of Biotechnology College of Life Sciences and Biotechnology Korea University Seoul 02841 South Korea. Institute for Artificial Intelligence and Biomedical Research Medicinal Bioconvergence Research Center Yonsei University Incheon 21983 South Korea. College of Medicine Gangnam Severance Hospital Yonsei University Seoul 06273 South Korea. Department of Biochemistry School of Medicine Catholic University of Daegu Daegu 42472 South Korea. Department of Biomedical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 South Korea. Interdisciplinary Program of Integrated OMICS for Biomedical Science Graduate School Yonsei University Seoul 03722 South Korea. jhan74@yonsei.ac.kr. Yonsei Institute of Pharmaceutical Sciences College of Pharmacy Yonsei University Incheon 21983 South Korea. jhan74@yonsei.ac.kr. POSTECH Biotech Center Pohang University of Science and Technology Pohang 37673 South Korea. jhan74@yonsei.ac.kr.

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Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2

arXiv

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arXiv 2020年

作者： Law, Jeffrey N. Akers, Kyle Tasnina, Nure Della Santina, Catherine M. Deutsch, Shay Kshirsagar, Meghana Klein-Seetharaman, Judith Crovella, Mark Rajagopalan, Padmavathy Kasif, Simon Murali, T.M. Interdisciplinary Ph.D. Program in Genetics Bioinformatics and Computational Biology BlacksburgVA United States Department of Computer Science Virginia Tech BlacksburgVA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Mathematics University of California Los AngelesCA United States AI for Good Lab Microsoft RedmondWA United States Department of Chemistry Colorado School of Mines GoldenCO United States Department of Computer Science Boston University BostonMA United States Department of Chemical Engineering Virginia Tech BlacksburgVA United States

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. Results: We design a network propagation framework with two novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. Conclusions: We examine how our provenance tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly-emerging viruses. © 2020, CC BY-NC-SA.

关键词： SARS

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Phase-change metal ink with pH-controlled chemical sintering for versatile and scalable fabrication of variable stiffness electronics

引用

science Advances 2025年第22期11卷 eadv4921页

作者： Simok Lee Gun-Hee Lee Inho Kang Woojin Jeon Semin Kim Yejin Ahn Choong Yeon Kim Do A Kwon Michael D. Dickey Steve Park Seongjun Park Jae-Woong Jeong School of Electrical Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. Medical Research Center Seoul National University Seoul 03080 Republic of Korea. Departments of Cogno-Mechatronics Engineering and Optics and Mechatronics Engineering Pusan National University Busan 46241 Republic of Korea. Graduate School of Semiconductor Technology Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Information and Electronics Research Institute Daejeon 34141 Republic of Korea. Research Laboratory of Electronics Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Mechanical Engineering Massachusetts Institute of Technology (MIT) Cambridge MA 02139 USA. Department of Chemical and Biomolecular Engineering North Carolina State University (NCSU) Raleigh NC 27606 USA. Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) 291 Daehak-ro Yuseong-gu Daejeon 34141 Republic of Korea. KAIST Institute for NanoCentury Daejeon 34141 Republic of Korea. Department of Biomedical Sciences College of Medicine Seoul National University Seoul 03080 Republic of Korea. School of Transdisciplinary Innovations Seoul National University Seoul 03080 Republic of Korea. Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Seoul 08826 Republic of Korea. Department of Transdisciplinary Medicine Seoul National University Hospital Seoul 03080 Republic of Korea. KAIST Institute for Health Science and Technology Daejeon 34141 Republic of Korea.

Variable stiffness electronics represent the forefront of adaptive technology, integrating rigid and soft electronics in a single system through dynamic mechanical modulation. While gallium’s high modulus tuning ratio and rapid phase transitions make it ideal for transformative electronic systems (TES), its liquid-state instability, high surface tension, and unintended phase transitions during processing pose substantial challenges. Here, we introduce STiffness-Adjustable temperature-Responsive ink (STAR ink), a chemically sinterable gallium composite electronic ink designed to overcome these obstacles. STAR ink enables high-resolution (~50 micrometers) circuit patterning, large-scale batch fabrication, and three-dimensional structure coating at room temperature. Through pH-controlled chemical sintering, STAR ink–based TES exhibits exceptional mechanical tunability (tuning ratio: 1465) and electrical conductivity (2.27 × 106 siemens per meter). Demonstrated applications—from multilayered variable stiffness printed circuit boards (PCBs) matching standard PCBs’ complexity to body-temperature responsive neural probe—underscore STAR ink’s potential for reconfigurable electronics across consumer electronics and biomedical devices.

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