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Gao X, Sun R, Jiao N, Liang X, Li G, Gao H, Wu X, Yang M, Chen C, Sun X, Chen L, Wu W, Cong Y, Zhu R, Guo T, Liu Z. Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease. Cell Rep Med 2023:101050. [PMID: 37172588 DOI: 10.1016/j.xcrm.2023.101050] [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] [Received: 12/06/2022] [Revised: 02/07/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.
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Affiliation(s)
- Xiang Gao
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ruicong Sun
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Na Jiao
- National Clinical Research Center for Child Health, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Gengfeng Li
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Han Gao
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiaohan Wu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Muqing Yang
- Center for Difficult and Complicated Abdominal Surgery, The Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Chunqiu Chen
- Center for Difficult and Complicated Abdominal Surgery, The Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Xiaomin Sun
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Liang Chen
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Wei Wu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ruixin Zhu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China.
| | - Zhanju Liu
- Center for Inflammatory Bowel Disease Research and Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
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Wu X, He Z, Li M, Han Z, Huang C. Identifying Learners' Interaction Patterns in an Online Learning Community. Int J Environ Res Public Health 2022; 19:2245. [PMID: 35206442 DOI: 10.3390/ijerph19042245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 12/10/2022]
Abstract
The interactions among all members of an online learning community significantly impact collaborative reflection (co-reflection). Although the relationship between learners’ roles and co-reflection levels has been explored by previous researchers, it remains unclear when and with whom learners at different co-reflection levels tend to interact. This study adopted multiple methods to examine the interaction patterns of diverse roles among learners with different co-reflection levels based on 11,912 posts. First, the deep learning technique was applied to assess learners’ co-reflection levels. Then, a social network analysis (SNA) was conducted to identify the emergent roles of learners. Furthermore, a lag sequence analysis (LSA) was employed to reveal the interaction patterns of the emergent roles among learners with different co-reflection levels. The results showed that most learners in an online learning community reached an upper-middle co-reflection level while playing an inactive role in the co-reflection process. Moreover, higher-level learners were superior in dialog with various roles and were more involved in self-rethinking during the co-reflection process. In particular, they habitually began communication with peers and then with the teacher. Based on these findings, some implications for facilitating online co-reflection from the perspective of roles is also discussed.
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Cao Y, Park SJ, Im W. A systematic analysis of protein-carbohydrate interactions in the Protein Data Bank. Glycobiology 2020; 31:126-136. [PMID: 32614943 DOI: 10.1093/glycob/cwaa062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022] Open
Abstract
Protein-carbohydrate interactions underlie essential biological processes. Elucidating the mechanism of protein-carbohydrate recognition is a prerequisite for modeling and optimizing protein-carbohydrate interactions, which will help in discovery of carbohydrate-derived therapeutics. In this work, we present a survey of a curated database consisting of 6,402 protein-carbohydrate complexes in the Protein Data Bank (PDB). We performed an all-against-all comparison of a subset of nonredundant binding sites, and the result indicates that the interaction pattern similarity is not completely relevant to the binding site structural similarity. Investigation of both binding site and ligand promiscuities reveals that the geometry of chemical feature points is more important than local backbone structure in determining protein-carbohydrate interactions. A further analysis on the frequency and geometry of atomic interactions shows that carbohydrate functional groups are not equally involved in binding interactions. Finally, we discuss the usefulness of protein-carbohydrate complexes in the PDB with acknowledgement that the carbohydrates in many structures are incomplete.
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Affiliation(s)
- Yiwei Cao
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Sciences and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Sang-Jun Park
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Sciences and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Sciences and Engineering, Lehigh University, Bethlehem, PA 18015, USA.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
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Kuppler J, Höfers MK, Wiesmann L, Junker RR. Time-invariant differences between plant individuals in interactions with arthropods correlate with intraspecific variation in plant phenology, morphology and floral scent. New Phytol 2016; 210:1357-68. [PMID: 26840542 DOI: 10.1111/nph.13858] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 07/15/2015] [Accepted: 12/09/2015] [Indexed: 05/10/2023]
Abstract
The basic units of ecological and evolutionary processes are individuals. Network studies aiming to infer mechanisms from complex systems, however, usually focus on interactions between species, not individuals. Accordingly, the structure and underlying mechanisms of individual-based interaction networks remain largely unknown. In a common garden, we recorded all interactions on flowers and leaves of 97 Sinapis arvensis individuals from seedling stage to fruit set and related interindividual differences in interactions to the plant individuals' phenotypes. The plant individuals significantly differed in their quantitative and qualitative interactions with arthropods on flowers and leaves. These differences remained stable over the entire season and thus were time-invariant. Variation in interacting arthropod communities could be explained by a pronounced intraspecific variability in flowering phenology, morphology and flower scent, and translated into variation in reproductive success. Interestingly, plant individuals with a similar composition of flower visitors were also visited by a similar assemblage of interaction partners at leaves. Our results show that the nonuniformity of plant species has pronounced effects in community ecology, potentially with implications for the persistence of communities and populations, and their ability to withstand environmental fluctuations.
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Affiliation(s)
- Jonas Kuppler
- Department Biology, Institute of Sensory Ecology, Heinrich-Heine-University, Universitätstrasse 1, Düsseldorf, 40225, Germany
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
| | - Maren K Höfers
- Department Biology, Institute of Sensory Ecology, Heinrich-Heine-University, Universitätstrasse 1, Düsseldorf, 40225, Germany
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
| | - Lisa Wiesmann
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
| | - Robert R Junker
- Department of Ecology and Evolution, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, 5020, Austria
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Cebollada A, Vellé A, Sanz Miguel PJ. Hirshfeld and DFT analysis of the N-heterocyclic carbene proligand methylenebis(N-butylimidazolium) as the acetonitrile-solvated diiodide salt. Acta Crystallogr C Struct Chem 2016; 72:456-9. [PMID: 27256692 DOI: 10.1107/s2053229616006781] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/21/2016] [Indexed: 02/02/2023]
Abstract
N-Heterocyclic carbene (NHC) based systems are usually exploited in the exploration of catalytic mechanisms and processes in organocatalysis, and homo- and heterogeneous catalysis. However, their molecular structures have not received adequate attention. The NHC proligand methylenebis(N-butylimidazolium) has been synthesized as the acetonitrile solvate of the diiodide salt, C15H26N4(2+)·2I(-)·CH3CN [1,1'-methylenebis(3-butylimidazolium) diiodide acetonitrile monosolvate], and fully characterized. An interesting cation-anion connection pattern has been identified in the crystal lattice, in which three iodide anions interact simultaneously with the cisoid-oriented cation. A Hirshfeld surface analysis reveals the predominance of hydrogen bonding over anion-π interactions. This particular arrangement is observed in different methylene-bridged bis(imidazolium) cations bearing chloride or bromide counter-anions. Density functional theory (DFT) calculations with acetonitrile as solvent reproduce the geometry of the title cation.
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Affiliation(s)
- Andrea Cebollada
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Alba Vellé
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Pablo J Sanz Miguel
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, Zaragoza 50009, Spain
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