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Lu X, Zhu MJH, Risko EF. Semantic partitioning facilitates memory for object location through category-partition cueing. Memory 2024; 32:411-430. [PMID: 38588665 DOI: 10.1080/09658211.2024.2335111] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/02/2024] [Indexed: 04/10/2024]
Abstract
In our lived environments, objects are often semantically organised (e.g., cookware and cutlery are placed close together in the kitchen). Across four experiments, we examined how semantic partitions (that group same-category objects in space) influenced memory for object locations. Participants learned the locations of items in a semantically partitioned display (where each partition contained objects from a single category) as well as a purely visually partitioned display (where each partition contained a scrambled assortment of objects from different categories). Semantic partitions significantly improved location memory accuracy compared to the scrambled display. However, when the correct partition was cued (highlighted) to participants during recall, performance on the semantically partitioned display was similar to the scrambled display. These results suggest that semantic partitions largely benefit memory for location by enhancing the ability to use the given category as a cue for a visually partitioned area (e.g., toys - top left). Our results demonstrate that semantically structured spaces help location memory across partitions, but not items within a partition, providing new insights into the interaction between meaning and memory.
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Affiliation(s)
- Xinyi Lu
- Department of Psychology, University of Waterloo, Waterloo, Canada
| | - Mona J H Zhu
- Department of Psychology, University of Waterloo, Waterloo, Canada
| | - Evan F Risko
- Department of Psychology, University of Waterloo, Waterloo, Canada
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Miura M, Sakaue F, Matsuno H, Morita K, Yoshida A, Hara RI, Nishimura R, Nishida Y, Yokogawa M, Osawa M, Yokota T. TDP-43 N-terminal domain dimerisation or spatial separation by RNA binding decreases its propensity to aggregate. FEBS Lett 2023. [PMID: 37177801 DOI: 10.1002/1873-3468.14635] [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: 11/21/2022] [Revised: 03/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Aggregation of the 43 kDa TAR DNA-binding protein (TDP-43) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RNA binding and TDP-43 N-terminal domain dimerisation have been suggested to ameliorate TDP-43 aggregation. However, the relationship between these factors and solubility of TDP-43 is largely unknown. Therefore, we developed new oligonucleotides which can recruit two TDP-43 molecules and interfere with their intermolecular interactions via spatial separation. Using these oligonucleotides and TDP-43-preferable UG-repeats, we uncovered two distinct mechanisms for modulating TDP-43 solubility by RNA binding: one is N-terminal domain dimerisation and the other is spatial separation of two TDP-43 molecules. This study provides new molecular insights into the regulation of TDP-43 solubility.
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Affiliation(s)
- Motoki Miura
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Fumika Sakaue
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Hirokazu Matsuno
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Kento Morita
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Akiko Yoshida
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
| | - Rintaro Iwata Hara
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
- NucleoTIDE and PepTIDE Drug Discovery Center, Tokyo Medical and Dental University
| | - Ren Nishimura
- Graduate School of Pharmaceutical Sciences, Keio University
| | - Yurika Nishida
- Graduate School of Pharmaceutical Sciences, Keio University
| | | | - Masanori Osawa
- Graduate School of Pharmaceutical Sciences, Keio University
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University
- NucleoTIDE and PepTIDE Drug Discovery Center, Tokyo Medical and Dental University
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Sartor F, Kovács ÁT. Rhythmic Spatial Self-Organization of Bacterial Colonies. mBio 2022;:e0170322. [PMID: 35938723 DOI: 10.1128/mbio.01703-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacteria display a remarkable capacity to organize themselves in space and time within biofilms. Traditionally, the spatial organization of biofilms has been dissected vertically; however, biofilms can exhibit complex, temporally structured, two-dimensional radial patterns while spreading on a surface. Kahl and colleagues report a ring pattern that indicates the alternating redox metabolism of P. aeruginosa biofilms under light/dark cycles. Does the presence of a rhythmic, daily phenotype imply a circadian rhythm? Here, we highlight several examples of rhythmic patterns reported in the literature for surface-colonizing multicellular assemblies and discuss the conceptual requirements for proving the presence of a prokaryotic circadian clock behind pattern formation.
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Costa RC, Bertolini M, Costa Oliveira BE, Nagay BE, Dini C, Benso B, Klein MI, Barāo VAR, Souza JGS. Polymicrobial biofilms related to dental implant diseases: unravelling the critical role of extracellular biofilm matrix. Crit Rev Microbiol 2022; 49:370-390. [PMID: 35584310 DOI: 10.1080/1040841x.2022.2062219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/21/2022]
Abstract
Biofilms are complex tri-dimensional structures that encase microbial cells in an extracellular matrix comprising self-produced polymeric substances. The matrix rich in extracellular polymeric substance (EPS) contributes to the unique features of biofilm lifestyle and structure, enhancing microbial accretion, biofilm virulence, and antimicrobial resistance. The role of the EPS matrix of biofilms growing on biotic surfaces, especially dental surfaces, is largely unravelled. To date, there is a lack of a broad overview of existing literature concerning the relationship between the EPS matrix and the dental implant environment and its role in implant-related infections. Here, we discuss recent advances in the critical role of the EPS matrix on biofilm growth and virulence on the dental implant surface and its effect on the etiopathogenesis and progression of implant-related infections. Similar to other biofilms associated with human diseases/conditions, EPS-enriched biofilms on implant surfaces promote microbial accumulation, microbiological shift, cross-kingdom interaction, antimicrobial resistance, biofilm virulence, and, consequently, peri-implant tissue damage. But intriguingly, the protagonism of EPS role on implant-related infections and the development of matrix-target therapeutic strategies has been neglected. Finally, we highlight the need for more in-depth analyses of polymicrobial interactions within EPS matrix and EPS-targeting technologies' rationale for disrupting the complex biofilm microenvironment with more outstanding translation to implant applications in the near future.
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Affiliation(s)
- Raphael C Costa
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Martinna Bertolini
- Department of Oral Health and Diagnostic Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | | | - Bruna E Nagay
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Caroline Dini
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Bruna Benso
- School of Dentistry, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, CA, Chile
| | - Marlise I Klein
- Department of Dental Materials and Prosthodontics, São Paulo State University, São Paulo, Brazil
| | - Valentim A R Barāo
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Joāo Gabriel S Souza
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil.,Dental Science School (Faculdade de Ciências Odontológicas - FCO), Montes Claros, Brazil.,Dental Research Division, Guarulhos University, Sāo Paulo, Brazil
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Kadye WT, Booth AJ. Environmental niche patterns of native and non-native fishes within an invaded African river system. J Fish Biol 2020; 96:1269-1277. [PMID: 31006850 DOI: 10.1111/jfb.13988] [Citation(s) in RCA: 1] [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: 10/10/2018] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
To test ecological niche theory, this study investigated the spatial patterns and the environmental niches of native and non-native fishes within the invaded Great Fish River system, South Africa. For the native fishes, there were contrasting environmental niche breadths that varied from being small to being large and overlapped for most species, except minnows that were restricted to headwater tributaries. In addition, there was high niche overlap in habitat association among fishes with similar distribution. It was therefore inferred that habitat filtering-driven spatial organisation was important in explaining native species distribution patterns. In comparison, most non-native fishes were found to have broad environmental niches and these fishes showed high tolerance to environmental conditions, which generally supported the niche opportunity hypothesis. The proliferation of multiple non-native fishes in the mainstem section suggest that they form a functional assemblage that is probably facilitated by the anthropogenic modification of flow regimes through inter-basin water transfer. Based on the distribution patterns observed in the study, it was inferred that there was a likelihood of negative interactions between native and non-native fishes. Such effects are likely to be exacerbated by altered flow regime that was likely to have negative implications for native ichthyofauna.
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Affiliation(s)
- Wilbert T Kadye
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - Anthony J Booth
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
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