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Bar-On B. The effect of structural curvature on the load-bearing characteristics of biomechanical elements. J Mech Behav Biomed Mater 2023; 138:105569. [PMID: 36549249 DOI: 10.1016/j.jmbbm.2022.105569] [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: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Miniature, sharped-edge, curved-shape biomechanical elements appear in various biological systems and grant them diverse functional capabilities, such as mechanical defense, venom injection, and frictional support. While these biomechanical elements demonstrate diverse curved shapes that span from slightly curved needle-like elements (e.g., stingers), through moderately curved anchor-like elements (e.g., claws), to highly curved hook-like elements (e.g., fangs)-the curvature effect on the load-bearing capabilities of these biomechanical elements are yet mostly unknown. Here, we employ structural-mechanical modeling to explore the relationships between the curved shapes of biomechanical elements on their local deformation mechanisms, overall elastic stiffness, and reaction forces on a target surface. We found that the curvature of the biomechanical element is a prime modulator of its load-bearing characteristics that substantially affect its functional capabilities. Slightly curved elements are preferable for penetration states with optimal load-bearing capabilities parallel to their tips but possess high directional sensitivity and degraded capabilities for scratching states; contrary, highly curved elements are suitable for combined penetration-scratching states with mild directional sensitivity and optimal load-bearing capabilities in specialized angular orientation to their tips. These structural-mechanical principles are tightly linked to the intrinsic functional roles of biomechanical elements in diverse natural systems, and their synthetic realizations may promote new engineering designs of advanced biomedical injections, functional surfaces, and micromechanical devices.
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Affiliation(s)
- Benny Bar-On
- Department of Mechanical Engineering, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
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Spit S, Andringa S, Rispens J, Aboh EO. Kindergarteners Use Cross-Situational Statistics to Infer the Meaning of Grammatical Elements. J Psycholinguist Res 2022; 51:1311-1333. [PMID: 35794402 PMCID: PMC9646556 DOI: 10.1007/s10936-022-09898-0] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Many studies demonstrate that detecting statistical regularities in linguistic input plays a key role in language acquisition. Yet, it is unclear to what extent statistical learning is involved in more naturalistic settings, when young children have to acquire meaningful grammatical elements. In the present study, we address these points, by investigating whether statistical learning is involved in acquiring a morpho-syntactic structure from input that resembles natural languages more closely. We exposed 50 kindergarteners (M = 5 years, 5 months) to a miniature language in which they had to learn a grammatical marker that expressed number, and which could only be acquired on the basis of the distributional properties in the input. Half of the children performed an attention check during the experiment. Results show that young children are able to learn this meaning. We found no clear evidence that facilitating attention to the input increases learning performance.
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Affiliation(s)
- Sybren Spit
- Amsterdam Center for Language and Communication, University of Amsterdam, Spuistraat 134, 1012 VB, Amsterdam, The Netherlands.
| | - Sible Andringa
- Amsterdam Center for Language and Communication, University of Amsterdam, Spuistraat 134, 1012 VB, Amsterdam, The Netherlands
| | - Judith Rispens
- Amsterdam Center for Language and Communication, University of Amsterdam, Spuistraat 134, 1012 VB, Amsterdam, The Netherlands
| | - Enoch O Aboh
- Amsterdam Center for Language and Communication, University of Amsterdam, Spuistraat 134, 1012 VB, Amsterdam, The Netherlands
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Zhang F, Hu H, Wang L, Zhou Q, Huang X. Effects of rare earth and acid rain pollution on plant chloroplast ATP synthase and element contents at different growth stages. Chemosphere 2018; 194:441-449. [PMID: 29227892 DOI: 10.1016/j.chemosphere.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 10/04/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
UNLABELLED Combined rare earth and acid rain pollution has become a new environmental problem, seriously affecting plant survival. The effects of these two kinds of pollutants on plant photosynthesis have been reported, but the micro mechanisms are not very clear. In this research, we studied the effects of lanthanum [La(III), 0.08, 1.20 and 2.40 mM] and acid rain (pH value = 2.5, 3.5 and 4.5) on the ATPase activity and gene transcription level and the functional element contents in rice leaf chloroplasts. The results showed that the combined 0.08 mM La(III) and pH 4.5 acid rain increased the ATPase activity and gene transcription level as well as contents of some functional elements. But other combined treatments of acid rain and La(III) reduced the ATPase activity and gene transcription level as well as functional element contents. The change magnitude of the above indexes at rice booting stage was greater than that in seedling stage or grain filling stage. These results reveal that effects of La(III) and acid rain on ATPase activity and functional element contents in rice leaf chloroplasts are related to the combination of La(III) dose and acid rain intensity and the plant growth stage. In addition, the changes in the ATPase activity were related to ATPase gene transcription level. This study would provide a reference for understanding the microcosmic mechanism of rare earth and acid rain pollution on plant photosynthesis and contribute to evaluate the possible environmental risks associated with combined La(III) and acid rain pollution. ONE SENTENCE SUMMARY The effects of La(III) and acid rain on activity and gene transcription level of rice chloroplast ATPase and contents of functional elements were different at different growth stages.
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Affiliation(s)
- Fan Zhang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Huiqing Hu
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Lihong Wang
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Qing Zhou
- State Key Laboratory of Food Science and Technology, Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Cooperative Innovation Center of Water Treatment Technology and Materials, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Xiaohua Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210046, China.
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Abstract
Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions.
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Affiliation(s)
- Mirko Ledda
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
- Integrative Genetics and Genomics Graduate Group, UC Davis, 1 Shields Ave, Davis, 95616 USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, UC Davis, 1 Shields Ave, Davis, 95616 USA
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Naidoo T, Sjödin P, Schlebusch C, Jakobsson M. Patterns of variation in cis-regulatory regions: examining evidence of purifying selection. BMC Genomics 2018; 19:95. [PMID: 29373957 PMCID: PMC5787233 DOI: 10.1186/s12864-017-4422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 07/19/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements. RESULTS We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations. CONCLUSIONS In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.
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Affiliation(s)
- Thijessen Naidoo
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Per Sjödin
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Carina Schlebusch
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden. .,Science for Life Lab, Uppsala, Sweden.
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Zhu L, Jiang K, Webber K, Wong L, Liu T, Chen Y, Jarvis JN. Chromatin landscapes and genetic risk for juvenile idiopathic arthritis. Arthritis Res Ther 2017; 19:57. [PMID: 28288683 PMCID: PMC5348874 DOI: 10.1186/s13075-017-1260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 02/07/2023] Open
Abstract
Background The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci. Methods We analyzed RNA sequencing (RNA-Seq) data, H3K27ac and H3K4me1 chromatin immunoprecipitation-sequencing (ChIP-Seq) data, and previously published chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data to characterize the chromatin landscapes within the known JIA-associated risk loci. Results In both neutrophils and primary CD4+ T cells, the majority of the JIA-associated linkage disequilibrium (LD) blocks contained H3K27ac and/or H3K4me1 marks. These LD blocks were also binding sites for a small group of transcription factors, particularly in neutrophils. Furthermore, these regions showed abundant intronic and intergenic transcription in neutrophils. In neutrophils, none of the genes that were differentially expressed between untreated patients with JIA and healthy children were located within the JIA-risk LD blocks. In CD4+ T cells, multiple genes, including HLA-DQA1, HLA-DQB2, TRAF1, and IRF1 were associated with the long-distance interacting regions within the LD regions as determined from ChIA-PET data. Conclusions These findings suggest that genetic risk contributes to the aberrant transcriptional control observed in JIA. Furthermore, these findings demonstrate the challenges of identifying the actual causal variants within complex genomic/chromatin landscapes. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1260-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisha Zhu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kaiyu Jiang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Karstin Webber
- Graduate Program in Biological Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yanmin Chen
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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Hu H, Wang L, Zhou Q, Huang X. Combined effects of simulated acid rain and lanthanum chloride on chloroplast structure and functional elements in rice. Environ Sci Pollut Res Int 2016; 23:8902-8916. [PMID: 26815371 DOI: 10.1007/s11356-015-5962-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/26/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
Acid rain and rare earth element (REE) pollution exist simultaneously in many agricultural regions. However, how REE pollution and acid rain affect plant growth in combination remains largely unknown. In this study, the combined effects of simulated acid rain and lanthanum chloride (LaCl3) on chloroplast morphology, chloroplast ultrastructure, functional element contents, chlorophyll content, and the net photosynthetic rate (P n) in rice (Oryza sativa) were investigated by simulating acid rain and rare earth pollution. Under the combined treatment of simulated acid rain at pH 4.5 and 0.08 mM LaCl3, the chloroplast membrane was smooth, proteins on this membrane were uniform, chloroplast structure was integrated, and the thylakoids were orderly arranged, and simulated acid rain and LaCl3 exhibited a mild antagonistic effect; the Mg, Ca, Mn contents, the chlorophyll content, and the P n increased under this combined treatment, with a synergistic effect of simulated acid rain and LaCl3. Under other combined treatments of simulated acid rain and LaCl3, the chloroplast membrane surface was uneven, a clear "hole" was observed on the surface of chloroplasts, and the thylakoids were dissolved and loose; and the P n and contents of functional elements (P, Mg, K, Ca, Mn, Fe, Ni, Cu, Zn and Mo) and chlorophyll decreased. Under these combined treatments, simulated acid rain and LaCl3 exhibited a synergistic effect. Based on the above results, a model of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis was established in order to reveal the combined effects on plant photosynthesis, especially on the photosynthetic organelle-chloroplast. Our results would provide some references for further understanding the mechanism of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis.
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Affiliation(s)
- Huiqing Hu
- State Key Laboratory of Food Science and Technology, College of Environment and Civil Engineering, Jiangsu Coorperative Innovation Center of Water Treatment Technology and Materials, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Lihong Wang
- State Key Laboratory of Food Science and Technology, College of Environment and Civil Engineering, Jiangsu Coorperative Innovation Center of Water Treatment Technology and Materials, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Qing Zhou
- State Key Laboratory of Food Science and Technology, College of Environment and Civil Engineering, Jiangsu Coorperative Innovation Center of Water Treatment Technology and Materials, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Xiaohua Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210046, China.
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