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Jo SH, Koo J, Park KH. Complete mitochondrial genome of the Korean endemic springtail Tomocerus caputiviolaceus Lee 1975 (Collembola: Tomoceridae). Mitochondrial DNA B Resour 2024; 9:178-181. [PMID: 38288250 PMCID: PMC10823885 DOI: 10.1080/23802359.2024.2305407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024] Open
Abstract
The complete mitochondrial genome of Tomocerus caputiviolaceus was sequenced and assembled. The complete mitochondrial genome is 15,519 bp in length. The mitogenome contained 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. In phylogenetic analysis based on the nucleotide sequences of 13 PCGs, T. caputiviolaceus is closely related to Tomocerus qinae Yu, Yao & Hu, 2016, both of which belong to the genus Tomocerus within the family Tomoceridae.
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Affiliation(s)
- Seon Hwa Jo
- Division of Science Education and Institute of Science Education, Jeonbuk National University, Jeonju, South Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Science Education, Jeonbuk National University, Jeonju, South Korea
| | - Kyung-Hwa Park
- Division of Science Education and Institute of Science Education, Jeonbuk National University, Jeonju, South Korea
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Erdenebaatar K, Park JM, Koo J. The complete chloroplast genome of Spergularia marina (Caryophyllaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1343-1346. [PMID: 38196788 PMCID: PMC10776058 DOI: 10.1080/23802359.2023.2288891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
Spergularia marina (L.) Griseb, 1843 (Caryophyllaceae) is a halophytic plant widely distributed along the southwestern coast of the Korean Peninsula. In this study, the complete chloroplast genome sequence of S. marina was determined using next-generation sequencing (NGS). The chloroplast genome of S. marina is 152,460 bp in length with 36.7% GC content. It comprises a large single-copy (LSC; 83,321), a small single copy (SSC; 17,205 bp), and a pair of inverted repeats (IRs; 25,967 bp) with a typical quadripartite structure. It consists of 131 genes, including 86 protein-coding genes, 8 ribosomal RNAs, and 37 transfer RNAs. Phylogenetic analysis using complete chloroplast genomes showed that among the 17 Caryophyllaceae species, S. marina is most closely related to Spergula arvensis. Since no complete chloroplast genome of the genus Spergularia has been reported to date, our study provides useful genetic information for determining phylogenetic relationships within the Caryophyllaceae.
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Affiliation(s)
- Khongorzul Erdenebaatar
- Division of Science Education and Institute of Fusion Science, Jeonbuk National University, Jeonju, Republic of Korea
| | - Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, Republic of Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, Jeonbuk National University, Jeonju, Republic of Korea
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Tzachor A, Devare M, Richards C, Pypers P, Ghosh A, Koo J, Johal S, King B. Author Correction: Large language models and agricultural extension services. Nat Food 2023; 4:1112. [PMID: 38036702 DOI: 10.1038/s43016-023-00904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Affiliation(s)
- A Tzachor
- CSER, University of Cambridge, Cambridge, UK.
- School of Sustainability, Reichman University, Herzliya, Israel.
| | - M Devare
- International Institute of Tropical Agriculture (IITA), CGIAR, Ibadan, Nigeria
| | - C Richards
- CSER, University of Cambridge, Cambridge, UK
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - P Pypers
- International Institute of Tropical Agriculture (IITA), CGIAR, Ibadan, Nigeria
| | - A Ghosh
- International Center for Tropical Agriculture (CIAT), CGIAR, Nairobi, Kenya
| | - J Koo
- International Food Policy Research Institute (IFPRI), CGIAR, Washington, DC, USA
| | - S Johal
- Agstack Project, Linux Foundation, San Francisco, CA, USA
| | - B King
- Digital and Data Innovation Accelerator, CGIAR, Palmira, Colombia
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Tzachor A, Devare M, Richards C, Pypers P, Ghosh A, Koo J, Johal S, King B. Large language models and agricultural extension services. Nat Food 2023; 4:941-948. [PMID: 37932438 DOI: 10.1038/s43016-023-00867-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Several factors have traditionally hampered the effectiveness of agricultural extension services, including limited institutional capacity and reach. Here we assess the potential of large language models (LLMs), specifically Generative Pre-trained Transformer (GPT), to transform agricultural extension. We focus on the ability of LLMs to simplify scientific knowledge and provide personalized, location-specific and data-driven agricultural recommendations. We emphasize shortcomings of this technology, informed by real-life testing of GPT to generate technical advice for Nigerian cassava farmers. To ensure a safe and responsible dissemination of LLM functionality across farming worldwide, we propose an idealized LLM design process with human experts in the loop.
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Affiliation(s)
- A Tzachor
- CSER, University of Cambridge, Cambridge, UK.
- School of Sustainability, Reichman University, Herzliya, Israel.
| | - M Devare
- International Institute of Tropical Agriculture (IITA), CGIAR, Ibadan, Nigeria
| | - C Richards
- CSER, University of Cambridge, Cambridge, UK
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - P Pypers
- International Institute of Tropical Agriculture (IITA), CGIAR, Ibadan, Nigeria
| | - A Ghosh
- International Center for Tropical Agriculture (CIAT), CGIAR, Nairobi, Kenya
| | - J Koo
- International Food Policy Research Institute (IFPRI), CGIAR, Washington, DC, USA
| | - S Johal
- Agstack Project, Linux Foundation, San Francisco, CA, USA
| | - B King
- Digital and Data Innovation Accelerator, CGIAR, Palmira, Colombia
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Csuzdi C, Koo J, Choi NJ, Szederjesi T, Hong Y. Complete mitochondrial genome of the composting worm Dendrobaena veneta (Clitellata: Oligochaeta, Lumbricidae). Mitochondrial DNA B Resour 2023; 8:1082-1086. [PMID: 37849654 PMCID: PMC10578090 DOI: 10.1080/23802359.2023.2265177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
Dendrobaena veneta (Rosa, 1886) is widely distributed all over Europe due to its use as compost worm. The specimen presented here was collected in Tiranë district, Albania. Currently, only two species' complete or nearly complete mitochondrial genome (mitogenome) sequences have been reported in the genus Dendrobaena; D. octaedra (Savigny, 1826) and D. tellermanica Perel, 1966. In this study, the complete mitogenome of D. veneta was sequenced, assembled, and annotated. The mitogenome of D. veneta is a circular DNA molecule, consisting of 15,475 bp with an A + T content of 61.2%. It contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 non-coding region (control region). Phylogenetic analysis showed that D. veneta is clustered with the other two Dendrobaena species in the well-supported family Lumbricidae.
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Affiliation(s)
- Csaba Csuzdi
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, Korea
| | - Nak jung Choi
- Crop Foundation Research Division, National Institute of Crop Science, Korea
| | - Tímea Szederjesi
- Department of Systematic Zoology, Eötvös Loránd University, Budapest, Hungary
| | - Yong Hong
- Department of Agricultural Biology, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju, Korea
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Koo J, Hong Y. The complete mitochondrial genome of the Korean endemic earthworm Amynthas deogyusanensis (Clitellata: Megascolecidae). Mitochondrial DNA B Resour 2023; 8:107-109. [PMID: 36643809 PMCID: PMC9833400 DOI: 10.1080/23802359.2022.2161839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Korean endemic earthworm Amynthas deogyusanensis Hong and James, 2001 (Clitellata: Megascolecidae) is found in the forest area of Deogyu Mountain, South Korea. In this study, the complete mitochondrial genome (mitogenome) of A. deogyusanensis was sequenced, assembled, and annotated. The mitogenome of A. deogyusanensis is a circular DNA molecule, consisting of 15,257 bp with an A + T content of 67.9%. It contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding region (control region). Phylogenetic analysis suggested that the family Megascolecidae is a monophyletic group with full support, whereas the genus Amynthas is non-monophyletic with the genera Metaphire and Duplodicodrilus.
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Affiliation(s)
- Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, Republic of Korea
| | - Yong Hong
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea,CONTACT Yong Hong Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju, Republic of Korea
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Park JM, Koo J. The complete chloroplast genome sequence of Berchemia racemosa Siebold & Zucc. (Rhamnaceae), a rare plant species in Korea. Mitochondrial DNA B Resour 2023; 8:69-72. [PMID: 36620322 PMCID: PMC9817123 DOI: 10.1080/23802359.2022.2161329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Berchemia racemosa Siebold & Zucc., 1845 is a rare species distributed in restricted areas in the western Korean peninsula. In this study, the complete chloroplast genome (plastome) of B. racemosa was sequenced and assembled by Illumina paired-end sequencing. The plastome of B. racemosa was 161,187 bp in length and was quadripartite in structure, including a large single-copy (LSC) region of 89,503 bp, a small single-copy (SSC) region of 18,214 bp, and two inverted repeats of 26,735 bp. The GC content was 37.2%. The plastome of B. racemosa contains 130 genes, including eight ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and 85 protein-coding genes. Phylogenetic analysis using complete genome sequences showed that B. racemosa is most closely related to Berchemia flavescens.
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Affiliation(s)
- Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, South Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea,CONTACT Jachoon Koo Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju, South Korea
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Park JM, Oh A, Koo J. Complete chloroplast genome sequence of Eranthis byunsanensis B.Y. Sun (Ranunculaceae), an endemic species in Korea. Mitochondrial DNA B Resour 2023; 8:570-574. [PMID: 37200680 PMCID: PMC10187104 DOI: 10.1080/23802359.2023.2209383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
The Korean endemic Eranthis byunsanensis B.Y. Sun, 1993 (Ranunculaceae) is a rare plant distributed in the southwestern part of the Korean Peninsula. The complete chloroplast (cp) genome of E. byunsanensis was sequenced by next-generation sequencing (NGS) using an Illumina HiSeq X platform. The cp genome of E. byunsanensis is 160,324 bp in length with 37.9% GC content. It showed a typical quadripartite structure consisting of a pair of inverted repeats (IRs; 28,356 bp), a large single-copy region (LSC; 87,671 bp), and a small single-copy region (SSC; 15,941 bp). The cp genome comprises 130 genes including 85 protein-coding genes (PCGs), 37 tRNA genes, and eight rRNA genes. The molecular phylogenetic analysis indicates that E. byunsanensis is closely related to Eranthis stellata, both of which belong to the genus Eranthis.
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Affiliation(s)
- Joon Moh Park
- Forest Resource Research Division, Jeollabuk-do Forest Environment Research Institute, Jinan, Republic of Korea
| | - Ami Oh
- Department of Biology, Chungbuk National University, Cheongju, Republic of Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, Jeonbuk National University, Jeonju, Republic of Korea
- CONTACT Jachoon Koo Division of Science Education and Institute of Fusion Science, Jeonbuk National University, Jeonju, Republic of Korea
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Yang HF, He KY, Koo J, Shen SW, Zhang SH, Liu G, Liu YZ, Chen C, Liang AJ, Huang K, Wang MX, Gao JJ, Luo X, Yang LX, Liu JP, Sun YP, Yan SC, Yan BH, Chen YL, Xi X, Liu ZK. Visualization of Chiral Electronic Structure and Anomalous Optical Response in a Material with Chiral Charge Density Waves. Phys Rev Lett 2022; 129:156401. [PMID: 36269973 DOI: 10.1103/physrevlett.129.156401] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/07/2022] [Indexed: 05/02/2023]
Abstract
Chiral materials have attracted significant research interests as they exhibit intriguing physical properties, such as chiral optical response, spin-momentum locking, and chiral induced spin selectivity. Recently, layered transition metal dichalcogenide 1T-TaS_{2} has been found to host a chiral charge density wave (CDW) order. Nevertheless, the physical consequences of the chiral order, for example, in electronic structures and the optical properties, are yet to be explored. Here, we report the spectroscopic visualization of an emergent chiral electronic band structure in the CDW phase, characterized by windmill-shaped Fermi surfaces. We uncover a remarkable chirality-dependent circularly polarized Raman response due to the salient in-plane chiral symmetry of CDW, although the ordinary circular dichroism vanishes. Chiral Fermi surfaces and anomalous Raman responses coincide with the CDW transition, proving their lattice origin. Our Letter paves a path to manipulate the chiral electronic and optical properties in two-dimensional materials and explore applications in polarization optics and spintronics.
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Affiliation(s)
- H F Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - K Y He
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - J Koo
- Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - S W Shen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - S H Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - G Liu
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
| | - Y Z Liu
- Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - C Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
| | - A J Liang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
| | - K Huang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
| | - M X Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
| | - J J Gao
- Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, HFIPS, Hefei 230031, People's Republic of China
| | - X Luo
- Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, HFIPS, Hefei 230031, People's Republic of China
| | - L X Yang
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing 100084, People's Republic of China
| | - J P Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
| | - Y P Sun
- Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, HFIPS, Hefei 230031, People's Republic of China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, HFIPS, Hefei, 230031, People's Republic of China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - S C Yan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
| | - B H Yan
- Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Y L Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing 100084, People's Republic of China
| | - X Xi
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, People's Republic of China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People's Republic of China
| | - Z K Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, People's Republic of China
- ShanghaiTech Laboratory for Topological Physics, Shanghai 201210, People's Republic of China
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Csuzdi C, Koo J, Hong Y. The complete mitochondrial DNA sequences of two sibling species of lumbricid earthworms, Eiseniafetida (Savigny, 1826) and Eiseniaandrei (Bouché, 1972) (Annelida, Crassiclitellata): comparison of mitogenomes and phylogenetic positioning. Zookeys 2022; 1097:167-181. [PMID: 36761685 PMCID: PMC9848864 DOI: 10.3897/zookeys.1097.80216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/03/2022] [Indexed: 11/12/2022] Open
Abstract
Composting earthworms of the genus Eisenia play an important role in soil ecosystems. However, taxonomic classification of this genus, especially the sibling species Eiseniafetida and Eiseniaandrei, is complicated because of their morphological similarity. In this study, we assessed the utility of the complete mitochondrial genome (mitogenome) for identification and differentiation of the two species. The complete mitogenomes of E.andrei and E.fetida were 15,714 and 16,560 bp, respectively. They contained 37 genes, comprising 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a putative non-coding region, as observed in other earthworms. Sequence comparisons based on the complete nucleotide sequences excluding the non-coding region showed 85.8% similarity, whereas the predicted amino acid sequences of the 13 PCGs were 92.7% similar between the two species. In particular, distinct features were found in the non-coding regions of the mitogenomes. They include a control region associated with putative mitogenome replication and an extended sequence. The extended sequence showed significant differences between the two species and other known earthworm species, suggesting its potential as a feasible molecular marker for species identification. Phylogenetic analysis of the 36 mitogenomes of earthworm species corroborated the monophyly of the genus Eisenia and the taxonomic distinctness of the sibling species pair, E.fetida and E.andrei.
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Affiliation(s)
- Csaba Csuzdi
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Yong Hong
- Division of Science Education and Institute of Fusion Science, College of Education, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Koo J, Latifi K, Caudell J, Jordan P, Shen S, Adamson P, Feygelman V. Development of a Deep Learning-Based Auto-Segmentation of Organs at Risk for Head and Neck Radiotherapy Planning. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2021.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lee I, Koo J, Park KH. Complete mitochondrial genome of the Korean endemic springtail Homidia koreana Lee & Lee, 1981 (Collembola: Entomobryidae). Mitochondrial DNA B Resour 2022; 7:135-137. [PMID: 34993338 PMCID: PMC8725819 DOI: 10.1080/23802359.2021.2015268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The Korean endemic springtail Homidia koreana Lee & Lee, 1981 is popular in the leaf litter of various forests of South Korea, probably widely distributed throughout the Korean Peninsula. The complete mitochondrial genome of H. koreana was sequenced, assembled, and annotated. The mitochondrial genome of H. koreana consists of a circular DNA molecule of 14,846 bp, with 68.4% AT content. It comprises 13 protein-coding genes (PCGs), 22 transfer (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The molecular phylogenetic relationships estimated using MrBayes 3.2 revealed that H. koreana was closely related to Homidia socia Denis, 1929, both of which belong to the genus Homidia.
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Affiliation(s)
- Inae Lee
- Department of Biology Education and Institute of Science Education, Jeonbuk National University, Jeonju, Korea
| | - Jachoon Koo
- Department of Biology Education and Institute of Science Education, Jeonbuk National University, Jeonju, Korea
| | - Kyung-Hwa Park
- Department of Biology Education and Institute of Science Education, Jeonbuk National University, Jeonju, Korea
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Koo J, Nardella L, Degnan M, Andreozzi J, Yu H, Penagaricano J, Johnstone P, Oliver D, Ahmed K, Rosenburg S, Wuthrick E, Diaz R, Feygelman V, Moros E, Redler G. Clinical Implementation and Utility of Triggered kV Imaging During Spine Stereotactic Body Radiotherapy for Intrafraction Motion Management. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Poirier C, Carter A, Kwan Y, Selvanathan C, Koo J, Westlund J, Leblanc K. ATRIAL FIBRILLATION PATIENTS' EXPERIENCES WITH COMBINATION ANTITHROMBOTIC THERAPY POST-PERCUTANEOUS CORONARY INTERVENTION. Can J Cardiol 2021. [DOI: 10.1016/j.cjca.2021.07.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Tada Y, Iversen L, Koo J. Early efficacy and safety data with fixed-dose combination calcipotriol/betamethasone dipropionate foam attributed to mechanism of absorption and steroid potency. J Eur Acad Dermatol Venereol 2021; 35 Suppl 1:5-9. [PMID: 33619779 PMCID: PMC7986689 DOI: 10.1111/jdv.17027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/27/2020] [Indexed: 01/16/2023]
Abstract
Topical therapy is the mainstay of treatment for the majority of patients with psoriasis vulgaris (chronic plaque psoriasis), with combinations of vitamin D analogues and glucocorticoids having been shown to negate many of the negative effects associated with either monocomponent individually. Following the established efficacy of fixed‐dose combination calcipotriol (Cal; 50 µg/g) plus betamethasone dipropionate (BD; 0.5 mg/g) ointment and gel formulations, a novel Cal/BD foam formulation was developed. When applied, Cal/BD foam forms a supersaturated solution on the skin, increasing the penetration and bioavailability of Cal and BD. Early data indicate that this results in improved efficacy outcomes versus Cal/BD ointment, without negatively affecting safety outcomes (such as the incidence/severity of side effects or impacted calcium homeostasis or hypothalamic‐pituitary‐adrenal axis). This article discusses the potency and absorption of fixed‐dose combination Cal/BD foam, as well as the positive early efficacy and safety data associated with its utilisation in the treatment of psoriasis vulgaris. Video abstract
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Affiliation(s)
- Y Tada
- Department of Dermatology, Teikyo University School of Medicine, Tokyo, Japan
| | - L Iversen
- Department of Dermatology, Aarhus University Hospital, Aarhus, Denmark
| | - J Koo
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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Katheria AC, Koo J. Applying the principle 'First Do No Harm' during the pandemic. BJOG 2020; 128:916. [PMID: 33248012 PMCID: PMC7753430 DOI: 10.1111/1471-0528.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 11/27/2022]
Affiliation(s)
- A C Katheria
- Neonatal Research Institute, Sharp Mary Birch Hospital for Women & Newborns, San Diego, CA, USA
| | - J Koo
- Neonatal Research Institute, Sharp Mary Birch Hospital for Women & Newborns, San Diego, CA, USA
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Pandith A, Koo J, Seo YJ. Daphnetin: A novel blue-green photonic switch for disodium phosphates that allows monitoring of polymerase chain reactions. Spectrochim Acta A Mol Biomol Spectrosc 2018; 204:620-628. [PMID: 29980064 DOI: 10.1016/j.saa.2018.06.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/15/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
This paper describes the very simple and robust ratiometric photonic switching properties of daphnetin (DP) toward HPO42- ions selectively in complex biological fluids, without any interference from other relevant anions under physiological conditions. The sensing ability of DP toward HPO42- ions was first demonstrated using UV-Vis and fluorescence spectroscopy, dynamic light scattering (DLS), and one- and two-dimensional NMR spectroscopy. DP can detect HPO42- ions at concentrations up to the sub-micromolar/nanomolar level very effectively, with a ratiometric response resulting from intramolecular charge transfer aided by aggregated-induced emission. The interactions between DP and HPO42- ions resulted in new bands appearing in the UV-Vis (at 385 nm) and emission (at 535 nm) spectra. The noncovalently held HPO42- ions induced pronounced specific aggregation of DP molecules, resulting in the new excimer band at 535 nm while retaining the monomer band centered at 445 nm. In contrast, reciprocal absorptivity changes were observed at 320 and 385 nm, with exponential decrements and increments, respectively. This probe could effectively monitor the consumption of dNTPs during various cycles of the polymerase chain reaction performed with relatively short oligonucleotides as well as genomic DNA from Agrobacterium tumefaciens (AcH5α strain).
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Affiliation(s)
- Anup Pandith
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Jachoon Koo
- Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea.
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Yimenu SM, Kim JY, Koo J, Kim BS. Predictive modeling for monitoring egg freshness during variable temperature storage conditions. Poult Sci 2018; 96:2811-2819. [PMID: 28340058 DOI: 10.3382/ps/pex038] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 01/18/2017] [Indexed: 11/20/2022] Open
Abstract
The overall aim of this research was to develop egg freshness prediction models in terms of selected quality indices. Six experiments (4 constant temperatures and 2 variable temperatures) were carried out on hen eggs for a total period of 10, 21, 26, 13, and 105 d at storage temperatures of 30, 20, 20 to 10, 30 to 10, and 5 and 10°C, to observe trends in the relative weight loss (RWL), Haugh unit (HU), yolk index (YI), albumin index (AI), yolk pH, and albumin pH. The results showed that there was an increasing trend in the RWL and a decreasing trend in the YI, AI, and HU for all temperature conditions. The changes in the yolk and albumin pH were not uniform. The data from the constant temperature conditions were used to determine the coefficients of the egg quality prediction models, which consisted of the primary model controlling the change rate of the quality indicator at a temperature condition in differential equation form, and the secondary model controlling the change rate with temperature, which was in quadratic polynomial form. The models were applied to the data from the fluctuating temperature conditions, and the zeroth, third, and eighth order kinetic models described the stepwise change in the RWL, HU, and YI, respectively. The accuracy and bias factor values for the RWL, HU, and YI were 1.116 and 0.940, 1.028 and 1.001, and 1.038 and 0.966, respectively. It can be concluded that the models can be used to predict egg freshness in terms of the RWL, HU, and YI at any temperature condition with in the range of 5 to 30°C during storage.
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Affiliation(s)
- S M Yimenu
- Department of Food Biotechnology, University of Science and Technology (UST), Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea.,Department of Food Science and Postharvest Technology, College of Agriculture and Environmental Sciences, Arsi University, P.O. Box 193 Asella, Ethiopia
| | - J Y Kim
- Smart Food Distribution Research Group, Korea Food Research Institute, 1201-62, Anyangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea.,Department of Mechanical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - J Koo
- Department of Mechanical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - B S Kim
- Department of Food Biotechnology, University of Science and Technology (UST), Gajeong-ro, Yuseong-gu, Daejeon, 305-350, Republic of Korea.,Smart Food Distribution Research Group, Korea Food Research Institute, 1201-62, Anyangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
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Abstract
Rat kidney epithelial cells were microencapsulated within alginate-poly(L)lysinealginate membrane. The microencapsulated cells were incubated using a culture media containing cobalt and another without cobalt. The viability was measured by trypan blue exclusion test. Secretion of erythropoietin (EPO) was measured by radioimmunoassay (RIA). Viability of free cells was 53%. The viability of microencapsulated cells increased to 72% after 12 days of incubation and remained at this level. Samples of the culture media were collected every 2 days for RIA. Samples within the microcapsules were collected by breaking the microcapsules open. RIA of these samples showed the following for the media containing cobalt. Between day 16 and day 32 the concentrations of EPO were 5.3 mU/ml inside and 18.3 mU/ml outside the microcapsule. The medium from the same number of free cells contained 21.2 mU/ml of EPO. Culture media without cobalt collected during the same period contained 1.8 mU/ml inside and 9.9 mU/ml outside the microcapsules. The free cell culture with this media during the same period contained 8.3 mU/ml.
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Affiliation(s)
- J. Koo
- Artificial Cells and Organs Research Centre, Faculty of Medicine, McGill University, Montreal - Canada
| | - T.M.S. Chang
- Artificial Cells and Organs Research Centre, Faculty of Medicine, McGill University, Montreal - Canada
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Affiliation(s)
- S. Sekhon
- Department of Dermatology University of California San Francisco CA U.S.A
| | - J. Koo
- Department of Dermatology University of California San Francisco CA U.S.A
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Abstract
AIM The occurrence of mental health comorbidities such as depression, anxiety, and suicidal ideation or behavior is not uncommon in the context of psoriasis. The negative influence of psoriatic disease on a patient's physical and mental well-being, in combination with overlapping pathophysiology, increase the risk for clinically significant psychiatric conditions. These psychiatric conditions, in turn, influence the patient's outlook and potentially, prognosis. Although the healthcare community increasingly recognizes the association of mental health comorbidities with psoriasis, the extent of the correlation is not fully appreciated. To better understand the relationship between mental health comorbidities and psoriasis, including prevalence, risk factors, and response of psychiatric comorbidities to psoriasis treatment, a narrative review of the published literature was conducted. METHODS Data from epidemiologic, observational, and clinical studies demonstrate a substantially greater mental health comorbidity burden in patients with psoriasis compared with those without psoriasis or patients with other dermatologic conditions. RESULT The influence of contemporary drug therapies on measures of depression and anxiety are predominantly positive, although further data are needed to better understand the effects of long-term therapy. CONCLUSION Clinicians should consider the heightened potential for mental health comorbidities when determining an optimal management strategy for their patients with psoriasis.
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Affiliation(s)
- J J Wu
- a Kaiser Permanente Los Angeles Medical Center , Los Angeles , CA , USA
| | - S R Feldman
- b Wake Forest University School of Medicine , Winston-Salem , NC , USA
| | - J Koo
- c University of California San Francisco , San Francisco , CA , USA
| | - L B Marangell
- d The University of Texas McGovern School of Medicine , Houston , TX , USA.,e Brain Health Consultants , Houston , TX , USA
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Moon H, Kim S, Koo J, Nam G. Ethanol Sclerotherapy for the Treatment of Ovarian Endometrioma. J Minim Invasive Gynecol 2017. [DOI: 10.1016/j.jmig.2017.08.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Koo J, Ong C, Han W. SUN-P103: Validation of Modified Nutrition Screening Tools for Childhood Cancer in a Tertiary Hospital in Singapore. Clin Nutr 2017. [DOI: 10.1016/s0261-5614(17)30524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Koo J, Marangell L, Nakamura M, Armstrong A, Jeon C, Bhutani T, Wu J. Depression and suicidality in psoriasis: review of the literature including the cytokine theory of depression. J Eur Acad Dermatol Venereol 2017; 31:1999-2009. [DOI: 10.1111/jdv.14460] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/08/2017] [Indexed: 12/13/2022]
Affiliation(s)
- J. Koo
- San Francisco Medical Center; University of California; San Francisco CA USA
| | | | - M. Nakamura
- San Francisco Medical Center; University of California; San Francisco CA USA
| | - A. Armstrong
- University of Southern California; Los Angeles CA USA
| | - C. Jeon
- San Francisco Medical Center; University of California; San Francisco CA USA
| | - T. Bhutani
- San Francisco Medical Center; University of California; San Francisco CA USA
| | - J.J. Wu
- Kaiser Permanente Los Angeles Medical Center; Los Angeles CA USA
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Abrouk M, Gandy J, Nakamura M, Lee K, Brodsky M, Singh R, Zhu H, Farahnik B, Bhutani T, Koo J. Secukinumab in the Treatment of Psoriasis and Psoriatic Arthritis: A Review of the Literature. Skin Therapy Lett 2017; 22:1-6. [PMID: 28732152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
While there are several commercially available treatment options for psoriasis and psoriatic arthritis, there remains a large number of individuals who are refractory to current modalities. In the recent past, there has been increasing evidence that interleukin (IL)-17 plays a vital role in the pathophysiology of psoriasis. Preclinical, phase II, and phase III studies of secukinumab (Cosentyx®) targeting IL-17 and its receptor have thus far proved to be promising. We reviewed the results of phase II and phase III clinical trials for secukinumab in the treatment of psoriasis and psoriatic arthritis. Only published studies were considered in the present review. We also performed an English language literature search from January 2003 to September 2015 using PubMed with any of the following key words: (secukinumab OR AIN457) AND (psoriasis OR psoriatic arthritis). In our review of the literature, seven phase III and five phase II clinical trials, as well as open-label extension studies with unpublished findings were found. Results from phase III clinical trials indicated secukinumab to be efficacious and safe for the treatment of psoriasis and psoriatic arthritis according to Psoriasis Area and Severity Index (PASI) and American College of Rheumatology (ACR) scores. The safety profile of this agent was similar across all studies, with the most frequently reported adverse events of nasopharyngitis, upper respiratory infections, headache, and injection site reaction. Secukinumab demonstrates rapid and robust clinical improvement accompanied by a favorable short- term safety profile. The results of the phase III trials continue to reinforce the theory that the IL-17 pathway is an essential target in psoriasis and psoriatic arthritis treatment. Additional extension studies of lower level evidence are needed to further understand the safety profile of the drug.
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Affiliation(s)
- M Abrouk
- Irvine School of Medicine, University of California, CA, USA
| | - J Gandy
- Irvine School of Medicine, University of California, CA, USA
| | - M Nakamura
- Department of Dermatology, Psoriasis and Skin Treatment Center, University of California - San Francisco, San Francisco, CA, USA
| | - K Lee
- Department of Dermatology, Psoriasis and Skin Treatment Center, University of California - San Francisco, San Francisco, CA, USA
| | - M Brodsky
- Irvine School of Medicine, University of California, CA, USA
| | - R Singh
- David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
| | - H Zhu
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - B Farahnik
- The Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - T Bhutani
- Department of Dermatology, Psoriasis and Skin Treatment Center, University of California - San Francisco, San Francisco, CA, USA
| | - J Koo
- Department of Dermatology, Psoriasis and Skin Treatment Center, University of California - San Francisco, San Francisco, CA, USA
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Nakamura M, Luber A, Paek S, Koo J, Qureshi A. 345 Assessment of functional impairment in psoriasis. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Savary S, Bregaglio S, Willocquet L, Gustafson D, Mason D’Croz D, Sparks A, Castilla N, Djurle A, Allinne C, Sharma M, Rossi V, Amorim L, Bergamin A, Yuen J, Esker P, McRoberts N, Avelino J, Duveiller E, Koo J, Garrett K. Crop health and its global impacts on the components of food security. Food Secur 2017. [DOI: 10.1007/s12571-017-0659-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kim G, Won J, Kim M, Park S, Lee D, Han K, Joon Ho K, Koo J. Early experience of radioembolization using TheraSphere for the treatment of hepatocellular carcinoma secondary to the hepatitis B virus in Korea. J Vasc Interv Radiol 2017. [DOI: 10.1016/j.jvir.2016.12.1128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Abrouk M, Nakamura M, Zhu TH, Farahnik B, Koo J, Bhutani T. The impact of PASI 75 and PASI 90 on quality of life in moderate to severe psoriasis patients. J DERMATOL TREAT 2017; 28:488-491. [PMID: 28042711 DOI: 10.1080/09546634.2016.1278198] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND It is well known that psoriasis significantly impacts patients' quality of life (QoL). With the introduction of improved treatment modalities with biologic agents, more patients with moderate to severe psoriasis are able to achieve better results as measured by the Psoriasis Area and Severity Index (PASI). PASI 75 indicates a 75% or greater reduction in PASI scores from baseline and is indicative of excellent disease improvement. With newer biologic agents such as secukinumab, ixekizumab and brodalumab, patients are now capable of achieving PASI 90, introducing additional clinical decisions for physicians when considering treatment options. However, little is known regarding how the difference between achieving PASI-75 versus PASI-90 impacts patients' QoL. OBJECTIVES The purpose of this study was to compare how achieving PASI 75 versus PASI 90 impacts QoL for patients with moderate to severe plaque psoriasis by using validated psychometric instruments that have been widely used in both dermatologic and non-dermatologic settings. METHODS Two separate open-label clinical trials were conducted to specifically assess QoL in patients with moderate to severe psoriasis on adalimumab or ustekinumab over 24 weeks. In addition to clinical assessments of psoriasis, patients completed two surveys: The Psychological General Well-Being (PGWB) Index and the Dermatology Life Quality Index (DLQI). Changes in total PGWB score and DLQI score at weeks 12 and 24 compared to baseline were compared between groups achieving PASI 75 and PASI 90. RESULTS There was no statistically significant difference in PGWB scores between patients achieving PASI 75 and patients achieving PASI 90 in the adalimumab treatment group (week 12 p = .21, but there was at week 24 p = .05). There was a statistically significant difference in DLQI between the patients achieving PASI 75 and the patients achieving PASI 90 in the adalimumab treatment group at week 24 (p = .01), but not week 12 (p = .11). There was no statistically significant difference in PGWB scores between patients achieving PASI 75 and patients achieving PASI 90 in the ustekinumab treatment group (week 12 p = .11, week 24 p = .35). There was no statistically significant difference in DLQI between the patients achieving PASI 75 and the patients achieving PASI 90 in the ustekinumab treatment group at week 24 (week 12 p = .49, week 24 p = .11). CONCLUSIONS There has been tremendous attention surrounding newer biologic agents that can achieve PASI 90 and even PASI 100. Although the results are impressive with regard to physical improvement of psoriasis, there may not be a clinically significant difference in QoL when comparing patients who achieve PASI-75 versus PASI 90.
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Affiliation(s)
- Michael Abrouk
- a University of California, Irvine School of Medicine , Irvine , CA , USA
| | - M Nakamura
- b UCSF Department of Dermatology , San Francisco , CA , USA
| | - T H Zhu
- c USC School of Medicine , Los Angeles , CA , USA
| | - B Farahnik
- d University of Vermont School of Medicine , Burlington , VT , USA
| | - J Koo
- b UCSF Department of Dermatology , San Francisco , CA , USA
| | - T Bhutani
- b UCSF Department of Dermatology , San Francisco , CA , USA
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Moon H, Kim S, Park G, Koo J. Profuse Vaginal Discharge May Equally Suggest Adenoma Malignum and Lobular Endocervical Glandular Hyperplasia (LEGH), But Same Cover, Different Story. J Minim Invasive Gynecol 2016; 22:S147. [PMID: 27678817 DOI: 10.1016/j.jmig.2015.08.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- H Moon
- Center for Minimally Invasive Surgery, Department of Obstetrics and Gynecology, Good Moonhwa Hospital, Busan, Korea
| | - S Kim
- Center for Minimally Invasive Surgery, Department of Obstetrics and Gynecology, Good Moonhwa Hospital, Busan, Korea
| | - G Park
- Center for Minimally Invasive Surgery, Department of Obstetrics and Gynecology, Good Moonhwa Hospital, Busan, Korea
| | - J Koo
- Center for Minimally Invasive Surgery, Department of Obstetrics and Gynecology, Good Moonhwa Hospital, Busan, Korea
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Koo J, Yoon M, Chung W, Chung M, Kim D. SU-F-T-244: Radiotherapy Risk Estimation Based On Expert Group Survey. Med Phys 2016. [DOI: 10.1118/1.4956384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Diette N, Koo J, Cabarcas-Petroski S, Schramm L. Gender Specific Differences in RNA Polymerase III Transcription. ACTA ACUST UNITED AC 2016; 7. [PMID: 27158556 DOI: 10.4172/2157-2518.1000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND RNA polymerase (pol) III transcribes a variety of untranslated RNAs responsible for regulating cellular growth and is deregulated in a variety of cancers. In this study, we examined gender differences in RNA pol III transcription in vitro and in vivo. METHODS Expression levels of U6 snRNA, tMet, and known modulators of RNA pol III transcription were assayed in male and female derived adenocarcinoma (AC) lung cancer cell lines and male and female C57BL/6J mice using real time quantitative PCR. Methylation status of the U6 snRNA promoter was determined for lung and liver tissue isolated from male and female C57BL/6J mice by digesting genomic DNA with methylation sensitive restriction enzymes and digestion profiles were analyzed by qPCR using primers spanning the U6 promoter. RESULTS Here, we demonstrate that RNA pol III transcription is differentially regulated by EGCG in male and female derived AC lung cancer cell lines. Basal RNA pol III transcript levels are significantly different in male and female derived AC lung cancer cell lines. These data prompted an investigation of gender specific differences in RNA pol III transcription in vivo in lung and liver tissue. Herein, we report that U6 snRNA RNA pol III transcription is significantly stimulated in the liver tissue of male C57BL/6J mice. Further, the increase in U6 transcription correlates with a significant inhibition in the expression of p53, a negative regulator of RNA pol III transcription, and demethylation of the U6 promoter in the liver tissue of male C57BL/6J mice. CONCLUSIONS To the best of our knowledge, this is the first study demonstrating gender specific differences in RNA pol III transcription both in vivo and in vitro and further highlights the need to include both male and female cell lines and animals in experimental design.
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Affiliation(s)
- N Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - J Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - S Cabarcas-Petroski
- Pennsylvania State University, Beaver Campus, Monaca, Pennsylvania, 15061 USA
| | - L Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
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van den Brink A, Vermijs G, Solignac A, Koo J, Kohlhepp JT, Swagten HJM, Koopmans B. Field-free magnetization reversal by spin-Hall effect and exchange bias. Nat Commun 2016; 7:10854. [PMID: 26940861 PMCID: PMC5411711 DOI: 10.1038/ncomms10854] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/27/2016] [Indexed: 11/09/2022] Open
Abstract
As the first magnetic random access memories are finding their way onto the market, an important issue remains to be solved: the current density required to write magnetic bits becomes prohibitively high as bit dimensions are reduced. Recently, spin–orbit torques and the spin-Hall effect in particular have attracted significant interest, as they enable magnetization reversal without high current densities running through the tunnel barrier. For perpendicularly magnetized layers, however, the technological implementation of the spin-Hall effect is hampered by the necessity of an in-plane magnetic field for deterministic switching. Here we interface a thin ferromagnetic layer with an anti-ferromagnetic material. An in-plane exchange bias is created and shown to enable field-free S HE-driven magnetization reversal of a perpendicularly magnetized Pt/Co/IrMn structure. Aside from the potential technological implications, our experiment provides additional insight into the local spin structure at the ferromagnetic/anti-ferromagnetic interface. Future information storage technology may exploit electrical currents to write the states of ferromagnetic nanoelements via spin torque effects. Here, the authors demonstrate such behaviour promoted by exchange bias from an interfaced antiferromagnet, which may help overcome practical device limitations.
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Affiliation(s)
- A van den Brink
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
| | - G Vermijs
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
| | - A Solignac
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands.,SPEC, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
| | - J Koo
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
| | - J T Kohlhepp
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
| | - H J M Swagten
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
| | - B Koopmans
- Eindhoven University of Technology, PO Box 513, Noord-Brabant, 5600 MB Eindhoven, The Netherlands
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YU H, Koo J, Daruwalla, V, Beano H, Patel K, Wlodarski R, Danier S, Harvill M, Kakos R, Critchfield J. Does tumor size correlate with biochemistry marker when evaluating the short-term therapeutic response of liver metastatic neuroendocrine tumor to yttrium-90 radioembolization? J Vasc Interv Radiol 2016. [DOI: 10.1016/j.jvir.2015.12.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Carlson DA, Gluskin AB, Mogni B, Koo J, Sood R, Lin Z, Pandolfino JE. Esophageal diverticula are associated with propagating peristalsis: a study utilizing high-resolution manometry. Neurogastroenterol Motil 2016; 28:392-8. [PMID: 26646704 PMCID: PMC4760883 DOI: 10.1111/nmo.12739] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/30/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND Esophageal diverticula have been associated with esophageal motility disorders, most commonly achalasia. We aimed to evaluate high-resolution manometry (HRM) motility diagnoses and pressurization patterns in patients with esophageal diverticula. METHODS Patients were retrospectively identified for distal esophageal diverticula and previously completed HRM. High-resolution manometries were analyzed according to the Chicago Classification, and the pressure slope of the compartmentalization phase (time between upper esophageal sphincter closure and the transition zone) of esophageal bolus transit was measured. Pressure slopes were also measured in 10 asymptomatic volunteers (controls) for comparison. KEY RESULTS Nineteen patients (ages 31-83) were included. Eight (42%) patients had normal motility, five (26%) had esophagogastric junction outflow obstruction, and two (11%) had jackhammer esophagus; four patients had other motility diagnoses including only one patient with achalasia. A total of six patients (32%) had at least one hypercontractile swallow. Greater compartmentalization phase pressure slopes were observed in patients at the mid-esophageal body in both supine (median [interquartile range]: 1.9 mmHg/s [0.9, 3.6]) and upright (1.1 [0.1, 3.1]) positions than in controls (supine: -1.3 [-2.4, -0.11], p = 0.001; upright; -0.71 [-2.1, -0.02], p = 0.005). CONCLUSIONS & INFERENCES Propagating peristalsis, often with hypercontractility, was commonly seen in our cohort of patients with esophageal diverticula. Abnormal compartmentalization phase pressurization may indicate a relationship of abnormal esophageal wall mechanics and/or compliance with diverticula; however whether these findings are causal or reactionary remains unclear.
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Affiliation(s)
- D. A. Carlson
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - A. B. Gluskin
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - B. Mogni
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - J. Koo
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - R. Sood
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - Z. Lin
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - J. E. Pandolfino
- Division of Gastroenterology and Hepatology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
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Lee K, Song K, Koo J. Delayed appearance of diffusion high signal after recanalization. J Neurol Sci 2015. [DOI: 10.1016/j.jns.2015.08.1388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Koo J, Yoon M, Chung W, Kim D. SU-E-T-617: Plan Quality Estimation of Intensity-Modulated Radiotherapy Cases for Lung Cancer. Med Phys 2015. [DOI: 10.1118/1.4924980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Kang Y, Jang H, Kim Y, Choi B, Kim J, Lee J, Shin H, Kim S, Kay C, Park S, Ji S, Koo J, Jeon S, Lee S. The Feasibility Study of MRI-Based Dose Calculation With Look-up Table in Radiation Treatment Planning. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kim H, Kim B, Suk J, Park J, Jung S, Sun S, Koo J, Lee S. Efficacy of adenosylcobalamin in relieving xerotic pruritus symptoms of atopic dermatitis. J Eur Acad Dermatol Venereol 2013; 28:254-5. [DOI: 10.1111/jdv.12149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/26/2013] [Indexed: 11/29/2022]
Affiliation(s)
- H.K. Kim
- Department of Dermatology; Chung-Ang University College of Medicine; Seoul Korea
| | - B.J. Kim
- Department of Dermatology; Chung-Ang University College of Medicine; Seoul Korea
| | - J.M. Suk
- P&K Skin Research Center; Seoul Korea
| | - J.O. Park
- P&K Skin Research Center; Seoul Korea
| | - S.W. Jung
- P&K Skin Research Center; Seoul Korea
| | - S.O. Sun
- Hanall Biopharma Co., Ltd.; Seoul Korea
| | - J. Koo
- Hanall Biopharma Co., Ltd.; Seoul Korea
| | - S.I. Lee
- Hanall Biopharma Co., Ltd.; Seoul Korea
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Koo J, Zavras A. Antiepileptic drugs (AEDs) during pregnancy and risk of congenital jaw and oral malformation. Oral Dis 2013; 19:712-20. [DOI: 10.1111/odi.12061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 10/28/2012] [Accepted: 11/29/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J Koo
- Columbia University College of Dental Medicine New York; New York; NY; USA
| | - A Zavras
- Department of Epidemiology and of Dentistry; Division of Oral Epidemiology & Biostatistics; Dental Public Health; Herbert Irving Comprehensive Cancer Center; Columbia University Medical Center; New York; NY; USA
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Park J, Cho BG, Kim KD, Koo J, Jang H, Ko KT, Park JH, Lee KB, Kim JY, Lee DR, Burns CA, Seo SSA, Lee HN. Oxygen-vacancy-induced orbital reconstruction of Ti ions at the interface of LaAlO3/SrTiO3 heterostructures: a resonant soft-X-ray scattering study. Phys Rev Lett 2013; 110:017401. [PMID: 23383835 DOI: 10.1103/physrevlett.110.017401] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Indexed: 06/01/2023]
Abstract
Resonant soft-x-ray scattering measurements have been performed to investigate interface electronic structures of (LaAlO(3)/SrTiO(3)) superlattices. Resonant scattering intensities at superlattice reflections show clear evidence of degeneracy lifting in t(2g) states of interface Ti ions. Polarization dependence of intensities indicates the energy of d(xy) states is lower by ~1 eV than two other t(2g) states. The energy splitting is insensitive to epitaxial strain. The orbital reconstruction is induced by oxygen vacancies and confined to the interface within two unit cells, indicating charge compensation at the polar interfaces.
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Affiliation(s)
- J Park
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
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Park K, Wu J, Koo J. A randomized, ‘head-to-head’ pilot study comparing the effects of etanercept monotherapy vs. etanercept and narrowband ultraviolet B (NB-UVB) phototherapy in obese psoriasis patients. J Eur Acad Dermatol Venereol 2012; 27:899-906. [DOI: 10.1111/j.1468-3083.2012.04611.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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43
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Tammam S, Sampaleanu LM, Koo J, Sundaram P, Ayers M, Chong PA, Forman-Kay JD, Burrows LL, Howell PL. Characterization of the PilN, PilO and PilP type IVa pilus subcomplex. Mol Microbiol 2011; 82:1496-514. [PMID: 22053789 DOI: 10.1111/j.1365-2958.2011.07903.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Type IVa pili are bacterial nanomachines required for colonization of surfaces, but little is known about the organization of proteins in this system. The Pseudomonas aeruginosa pilMNOPQ operon encodes five key members of the transenvelope complex facilitating pilus function. While PilQ forms the outer membrane secretin pore, the functions of the inner membrane-associated proteins PilM/N/O/P are less well defined. Structural characterization of a stable C-terminal fragment of PilP (PilP(Δ71)) by NMR revealed a modified β-sandwich fold, similar to that of Neisseria meningitidis PilP, although complementation experiments showed that the two proteins are not interchangeable likely due to divergent surface properties. PilP is an inner membrane putative lipoprotein, but mutagenesis of the putative lipobox had no effect on the localization and function of PilP. A larger fragment, PilP(Δ18-6His), co-purified with a PilN(Δ44)/PilO(Δ51) heterodimer as a stable complex that eluted from a size exclusion chromatography column as a single peak with a molecular weight equivalent to two heterotrimers with 1:1:1 stoichiometry. Although PilO forms both homodimers and PilN-PilO heterodimers, PilP(Δ18-6His) did not interact stably with PilO(Δ51) alone. Together these data demonstrate that PilN/PilO/PilP interact directly to form a stable heterotrimeric complex, explaining the dispensability of PilP's lipid anchor for localization and function.
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Affiliation(s)
- S Tammam
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
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Sodhi R, Gallaugher M, Wang Z, Koo J. Proposed ToF-SIMS/XPS standardization methods for bonding wires in electronic packaging applications. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
BACKGROUND Exposure of cryptic, functional sites on fibrinogen upon its adsorption to hydrophobic surfaces of biomaterials has been linked to an inflammatory response and fibrosis. Such adsorption also induces ordered fibrinogen aggregation which is poorly understood. OBJECTIVE To investigate hydrophobic surface-induced fibrinogen aggregation. METHODS Contact and lateral force scanning probe microscopy, yielding topography, image dimensions and fiber elastic modulus measurements were used along with transmission and scanning electron microscopy. Fibrinogen aggregation was induced under non-enzymatic conditions by adsorption on a trioctyl-surface monolayer (trioctylmethylamine) grafted onto silica clay plates. RESULTS A more than one molecule thick coating was generated by adsorption on the plate from 100 to 200 μg mL⁻¹ fibrinogen solutions, and three-dimensional networks formed from 4 mg mL⁻¹ fibrinogen incubated with uncoated or fibrinogen-coated plates. Fibrils appeared laterally assembled into branching and overlapping fibers whose heights from the surface ranged from approximately 3 to 740 nm. The elastic modulus of fibrinogen fibers was 1.55 MPa. No fibrils formed when fibrinogen lacking αC-domains was used as a coating or was incubated with intact fibrinogen-coated plates, or when the latter plates were sequentially incubated with anti-Aα529-539 mAb and intact fibrinogen. When an anti-Aα241-476 mAb was used instead, fine, long fibers formed. Similarly, sequential incubations of fibrinogen-coated plates with recombinant αC-domain (Aα392-610 fragment) or αC-connector (Aα221-372 fragment) and fibrinogen resulted in distinctly fine fiber networks. CONCLUSIONS Adsorption-induced fibrinogen self-assembly is initiated by a more than one molecule-thick surface layer and eventuates in three-dimensional networks whose formation requires fibrinogen with intact αC-domains.
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Affiliation(s)
- J Koo
- Department of Materials Science and Engineering, SUNY at Stony Brook, Stony Brook, NY, USA
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46
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Ahn J, Jung M, Koo J, Moon Y, Park B, Kim S, Park S, Hong S, Kim J, Sohn J. Prediction of response in advanced breast cancer (ABC) patients who received trastuzumab-paclitaxel (TP): HER2 FISH ratio, expression of class III beta tubulin (bTubIII), and immunoglobulin G fragment C receptor (FCGR) polymorphisms. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.1101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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47
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Koga T, Li C, Endoh MK, Koo J, Rafailovich M, Narayanan S, Lee DR, Lurio LB, Sinha SK. Reduced viscosity of the free surface in entangled polymer melt films. Phys Rev Lett 2010; 104:066101. [PMID: 20366832 DOI: 10.1103/physrevlett.104.066101] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Indexed: 05/29/2023]
Abstract
By embedding "dilute" gold nanoparticles in single polystyrene thin films as "markers", we probe the local viscosity of the free surface at temperatures far above the glass transition temperature (T(g)). The technique used was x-ray photon correlation spectroscopy with resonance-enhanced x-ray scattering. The results clearly showed the surface viscosity is about 30% lower than the rest of the film. We found that this reduction is strongly associated with chain entanglements at the free surface rather than the reduction in T(g).
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Affiliation(s)
- Tadanori Koga
- Chemical and Molecular Engineering Program, Department of Materials Science and Engineering, Stony Brook University, Stony Brook, New York 11794-2275, USA.
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Ayers M, Sampaleanu LM, Tammam S, Koo J, Harvey H, Howell PL, Burrows LL. PilM/N/O/P proteins form an inner membrane complex that affects the stability of the Pseudomonas aeruginosa type IV pilus secretin. J Mol Biol 2009; 394:128-42. [PMID: 19857645 DOI: 10.1016/j.jmb.2009.09.034] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/09/2009] [Accepted: 09/12/2009] [Indexed: 01/16/2023]
Abstract
The highly conserved pilM/N/O/P/Q gene cluster is among the core set of genes required for cell surface expression of type IV pili and associated twitching motility. With the exception of the outer membrane secretin, a multimer of PilQ subunits, the specific functions of the products encoded by this gene cluster are poorly characterized. Orthologous proteins in the related bacterial type II secretion system have been shown to interact to form an inner membrane complex required for protein secretion. In this study, we provide evidence that the PilM/N/O/P proteins form a functionally equivalent type IVa pilus complex. Using Pseudomonas aeruginosa as model organism, we found that all four proteins, including the nominally cytoplasmic PilM, colocalized to the inner membrane. Stability studies via Western blot analyses revealed that loss of one component has a negative impact on the levels of other members of the putative complex. Furthermore, complementation studies revealed that the stoichiometry of the components is important for the correct formation of a stable complex in vivo. We provide evidence that an intact inner membrane complex is required for optimal formation of the outer membrane complex of the type IVa pilus system in P. aeruginosa, as PilQ stability is negatively affected in its absence. Finally, we show that, in the absence of the pilin subunit, the levels of membrane-bound components of the inner membrane complex are negatively regulated by the PilR/S two-component system, suggesting a role for PilR/S in sensing the piliation status of the cell.
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Affiliation(s)
- M Ayers
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada L8N 3Z5
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Sampaleanu LM, Bonanno JB, Ayers M, Koo J, Tammam S, Burley SK, Almo SC, Burrows LL, Howell PL. Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex. J Mol Biol 2009; 394:143-59. [PMID: 19857646 DOI: 10.1016/j.jmb.2009.09.037] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/09/2009] [Accepted: 09/17/2009] [Indexed: 11/18/2022]
Abstract
Type IV pili (T4P) are bacterial virulence factors responsible for attachment to surfaces and for twitching motility, a motion that involves a succession of pilus extension and retraction cycles. In the opportunistic pathogen Pseudomonas aeruginosa, the PilM/N/O/P proteins are essential for T4P biogenesis, and genetic and biochemical analyses strongly suggest that they form an inner-membrane complex. Here, we show through co-expression and biochemical analysis that the periplasmic domains of PilN and PilO interact to form a heterodimer. The structure of residues 69-201 of the periplasmic domain of PilO was determined to 2.2 A resolution and reveals the presence of a homodimer in the asymmetric unit. Each monomer consists of two N-terminal coiled coils and a C-terminal ferredoxin-like domain. This structure was used to generate homology models of PilN and the PilN/O heterodimer. Our structural analysis suggests that in vivo PilN/O heterodimerization would require changes in the orientation of the first N-terminal coiled coil, which leads to two alternative models for the role of the transmembrane domains in the PilN/O interaction. Analysis of PilN/O orthologues in the type II secretion system EpsL/M revealed significant similarities in their secondary structures and the tertiary structures of PilO and EpsM, although the way these proteins interact to form inner-membrane complexes appears to be different in T4P and type II secretion. Our analysis suggests that PilN interacts directly, via its N-terminal tail, with the cytoplasmic protein PilM. This work shows a direct interaction between the periplasmic domains of PilN and PilO, with PilO playing a key role in the proper folding of PilN. Our results suggest that PilN/O heterodimers form the foundation of the inner-membrane PilM/N/O/P complex, which is critical for the assembly of a functional T4P complex.
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Affiliation(s)
- L M Sampaleanu
- Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
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Abstract
BACKGROUND To investigate the clinicopathological significance of androgen receptor (AR) expression in primary breast cancers. PATIENTS AND METHODS We evaluated AR using immunohistochemistry from 413 whole sections from January 2008 to March 2009 and analyzed the relationship between AR and clinicopathological parameters. Tumors with >/=10% nuclear-stained cells were considered to be positive for AR. The differences among variables were calculated by chi-square test. RESULTS The expression rate of AR was 72.9% higher than those of estrogen receptors (ER) and progesterone receptors. AR expression was significant in patients with no elevated preoperative serum cancer antigen 15-3 levels, smaller tumor size, lower histologic grade and hormone receptor-positive and non-triple-negative breast cancer. However, AR expression was observed in 35% of triple-negative cancers. Metaplastic, medullary and mucinous types of carcinomas showed less AR expression. In the ER-negative subgroup, AR was significantly correlated with human epidermal growth factor receptor type 2 (HER-2) overexpression. CONCLUSIONS AR is expressed in a significant number of breast cancers and is associated with lower tumor burden and favorable differentiation. There are many issues to be further investigated such as whether AR is an independent prognostic factor, whether it is a therapeutic target for the triple-negative breast cancers and whether it is associated with HER-2 signaling in ER-negative tumors.
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Affiliation(s)
| | | | | | | | | | | | - B-W Park
- Department of Surgery; Department of Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul.
| | - K S Lee
- Department of Surgery, Pochon CHA University College of Medicine, Seongnam, Korea
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