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  • Oxford University Press (OUP)  (19)
  • 1
    Online Resource
    Online Resource
    A simple technology for plastid transformation with fragmented DNA
    Oxford University Press (OUP) ; 2022
    In:  Journal of Experimental Botany Vol. 73, No. 18 ( 2022-10-18), p. 6078-6088
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 73, No. 18 ( 2022-10-18), p. 6078-6088
    Abstract: Plastid engineering has several unique advantages such as high expression of transgenes due to high polyploidy of plastid genomes and environmental biosafety because of maternal inheritance of transgenes, and has become a promising tool for molecular farming, metabolic engineering, and genetic improvement. However, there are no standard vectors available for plastid transformation. Moreover, the construction of plastid transformation vectors containing long operons or genes encoding proteins that are toxic to Escherichia coli was tedious or difficult. Here, we developed a simple plastid transformation technology without the need for in vitro vector construction by using multiple linear DNA fragments which share homologous sequences (HSs) at their ends. The strategy is based on homologous recombination between HSs of DNA fragments via endogenous recombination machinery in plastids, which subsequently are integrated into the plastid genome. We found that HSs of 200 bp or longer were sufficient for mediating the integration into the plastid genome with at least similar efficiency to that of plasmid DNA-based plastid transformation. Furthermore, we successfully used this method to introduce a phage lysin-encoding gene and a long operon into a tobacco plastid genome. The establishment of this technology simplifies the plastid transformation procedure and provides a novel solution for expressing proteins, which are either toxic to the cloning host or large operons in plastids, without need of vector cloning.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erac256
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 2
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    Intraspecific variation in microhabitat selection in reintroduced Chinese giant salamanders
    Oxford University Press (OUP) ; 2023
    In:  Current Zoology Vol. 69, No. 2 ( 2023-04-21), p. 121-127
    Details
    In: Current Zoology, Oxford University Press (OUP), Vol. 69, No. 2 ( 2023-04-21), p. 121-127
    Abstract: Reintroduction of captive-bred Chinese giant salamanders is a primary approach for restoring wild populations. Despite previous studies have investigated the habitat preferences of reintroduced Chinese giant salamanders, the intraspecific variation in their habitat selection has been neglected. In the present study, 30 captive-bred Chinese giant salamanders belonging to 3 groups (i.e., 10 males, 10 females, and 10 juveniles) were released into a montane stream to explore whether intraspecific variation in habitat selection occurred in this species using radiotelemetry. Our results indicated that linear home range and daily movement of males were significantly higher than those of females and juveniles. Male sedentariness was significantly lower than that of females and juveniles. No significant differences were detected between females and juveniles in these measures. Importantly, we found that males preferred microhabitats with low water conductivity and deep water depth. Females preferred microhabitats with high water conductivity, low dissolved oxygen and ammonium-nitrogen, and slow current velocity, while juveniles occupied microhabitats with low ammonium-nitrogen. In addition, males and juveniles exhibited higher niche breadth than females. Niche overlap was high between adults and juveniles but low between males and females. Our study revealed the presence of spatial segregation in reintroduced Chinese giant salamanders. Males, females, and juveniles exhibited variation in microhabitat selection. These results provide important information for use when planning strategies for conservation of Chinese giant salamanders.
    Type of Medium: Online Resource
    ISSN: 1674-5507 , 2396-9814
    URL: Article
    DOI: 10.1093/cz/zoac028
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2628880-1
    SSG: 12
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  • 3
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    Length-dependent accumulation of double-stranded RNAs in plastids affects RNA interference efficiency in the Colorado potato beetle
    Oxford University Press (OUP) ; 2020
    In:  Journal of Experimental Botany Vol. 71, No. 9 ( 2020-05-09), p. 2670-2677
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 71, No. 9 ( 2020-05-09), p. 2670-2677
    Abstract: Transplastomic potato plants expressing double-stranded RNA (dsRNA) targeted against essential genes of the Colorado potato beetle (CPB) can be lethal to larvae by triggering an RNA interference (RNAi) response. High accumulation levels of dsRNAs in plastids are crucial to confer an efficient RNAi response in the insects. However, whether length and sequence of the dsRNA determine the efficacy of RNAi and/or influence the level of dsRNA accumulation in plastids is not known. We compared the RNAi efficacy of different lengths of dsRNA targeted against the CPB β-Actin gene (ACT) by feeding in vitro-synthesized dsRNAs to larvae. We showed that, while the 60 bp dsRNA induced only a relatively low RNAi response in CPB, dsRNAs of 200 bp and longer caused high mortality and similar larval growth retardation. When the dsRNAs were expressed from the plastid (chloroplast) genome of potato plants, we found that their accumulation were negatively correlated with length. The level of dsRNA accumulation was positively associated with the observed mortality, suppression of larval growth, and suppression of target gene expression. Importantly, transplastomic potato plants expressing the 200 bp dsRNA were better protected from CPB than plants expressing the 297 bp dsRNA, the best-performing line in our previous study. Our results suggest that the length of dsRNAs is an important factor that influences their accumulation in plastids and thus determines the strength of the insecticidal RNAi effect. Our findings will aid the design of optimized dsRNA expression constructs for plant protection by plastid-mediated RNAi.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/eraa001
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 4
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    Role of a chalcone isomerase-like protein in flavonoid biosynthesis in Arabidopsis thaliana
    Oxford University Press (OUP) ; 2015
    In:  Journal of Experimental Botany Vol. 66, No. 22 ( 2015-12), p. 7165-7179
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 66, No. 22 ( 2015-12), p. 7165-7179
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erv413
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 5
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    A causal imaging condition for reverse time migration using the Discrete Hilbert transform and its efficient implementation on GPU
    Oxford University Press (OUP) ; 2019
    In:  Journal of Geophysics and Engineering Vol. 16, No. 5 ( 2019-10-01), p. 894-912
    Details
    In: Journal of Geophysics and Engineering, Oxford University Press (OUP), Vol. 16, No. 5 ( 2019-10-01), p. 894-912
    Abstract: Reverse time migration (RTM) has shown a significant advantage over other imaging algorithms for imaging complex subsurface structures. However, low-wavenumber noise severely contaminates the image, which is one of the main issues in the RTM algorithm. To attenuate the undesired low-wavenumber noise, the causal imaging condition based on wavefield decomposition has been proposed. First, wavefield decompositions are performed to separate the wavefields as up-going and down-going wave components, respectively. Then, to preserve causality, it constructs images by correlating wave components that propagate in different directions. We build a causal imaging condition in this paper. Not only does it consider the up/down wavefield decomposition, but it also applies the decomposition on the horizontal direction to enhance the image quality especially for steeply dipping structures. The wavefield decomposition is conventionally achieved by the frequency-wavenumber (F-K) transform that is very computationally intensive compared with the wave propagation process of the RTM algorithm. To improve the efficiency of the algorithm, we propose a fast implementation to perform wavefield separation using the discrete Hilbert transform via the Graphics Processing Unit. Numerical tests on both the synthetic models and a real data example demonstrate the effectiveness of the proposed method and the efficiency of the optimized implementation scheme. This new imaging condition shows its ability to produce high image quality when applied to both the RTM stack image and also the angle domain common image gathers. The comparison of the total elapsed time for different methods verifies the efficiency of the optimized algorithm.
    Type of Medium: Online Resource
    ISSN: 1742-2132 , 1742-2140
    URL: Article
    DOI: 10.1093/jge/gxz055
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2135382-7
    SSG: 16,13
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  • 6
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    Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer
    Oxford University Press (OUP) ; 2019
    In:  Genome Biology and Evolution Vol. 11, No. 4 ( 2019-04-01), p. 1019-1032
    Details
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 11, No. 4 ( 2019-04-01), p. 1019-1032
    Type of Medium: Online Resource
    ISSN: 1759-6653
    URL: Article
    DOI: 10.1093/gbe/evz055
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2495328-3
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  • 7
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    Clinical concept normalization with a hybrid natural language processing system combining multilevel matching and machine learning ranking
    Oxford University Press (OUP) ; 2020
    In:  Journal of the American Medical Informatics Association Vol. 27, No. 10 ( 2020-10-01), p. 1576-1584
    Details
    In: Journal of the American Medical Informatics Association, Oxford University Press (OUP), Vol. 27, No. 10 ( 2020-10-01), p. 1576-1584
    Abstract: Normalizing clinical mentions to concepts in standardized medical terminologies, in general, is challenging due to the complexity and variety of the terms in narrative medical records. In this article, we introduce our work on a clinical natural language processing (NLP) system to automatically normalize clinical mentions to concept unique identifier in the Unified Medical Language System. This work was part of the 2019 n2c2 (National NLP Clinical Challenges) Shared-Task and Workshop on Clinical Concept Normalization. Materials and Methods We developed a hybrid clinical NLP system that combines a generic multilevel matching framework, customizable matching components, and machine learning ranking systems. We explored 2 machine leaning ranking systems based on either ensemble of various similarity features extracted from pretrained encoders or a Siamese attention network, targeting at efficient and fast semantic searching/ranking. Besides, we also evaluated the performance of a general-purpose clinical NLP system based on Unstructured Information Management Architecture. Results The systems were evaluated as part of the 2019 n2c2 challenge, and our original best system in the challenge obtained an accuracy of 0.8101, ranked fifth in the challenge. The improved system with newly designed machine learning ranking based on Siamese attention network improved the accuracy to 0.8209. Conclusions We demonstrate the successful practice of combining multilevel matching and machine learning ranking for clinical concept normalization. Our results indicate the capability and interpretability of our proposed approach, as well as the limitation, suggesting the opportunities of achieving better performance by combining general clinical NLP systems.
    Type of Medium: Online Resource
    ISSN: 1067-5027 , 1527-974X
    URL: Article
    DOI: 10.1093/jamia/ocaa155
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2018371-9
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  • 8
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    Functionalized TiCu/TiCuN coating promotes osteoporotic fracture healing by upregulating the Wnt/β-catenin pathway
    Oxford University Press (OUP) ; 2023
    In:  Regenerative Biomaterials Vol. 10 ( 2023-01-17)
    Details
    In: Regenerative Biomaterials, Oxford University Press (OUP), Vol. 10 ( 2023-01-17)
    Abstract: Osteoporosis results in decreased bone mass and insufficient osteogenic function. Existing titanium alloy implants have insufficient osteoinductivity and delayed/incomplete fracture union can occur when used to treat osteoporotic fractures. Copper ions have good osteogenic activity, but their dose-dependent cytotoxicity limits their clinical use for bone implants. In this study, titanium alloy implants functionalized with a TiCu/TiCuN coating by arc ion plating achieved a controlled release of copper ions in vitro for 28 days. The coated alloy was co-cultured with bone marrow mesenchymal stem cells and showed excellent biocompatibility and osteoinductivity in vitro. A further exploration of the underlying mechanism by quantitative real-time polymerase chain reaction and western blotting revealed that the enhancement effects are related to the upregulation of genes and proteins (such as axin2, β-catenin, GSK-3β, p-GSK-3β, LEF1 and TCF1/TCF7) involved in the Wnt/β-catenin pathway. In vivo experiments showed that the TiCu/TiCuN coating significantly promoted osteoporotic fracture healing in a rat femur fracture model, and has good in vivo biocompatibility based on various staining results. Our study confirmed that TiCu/TiCuN-coated Ti promotes osteoporotic fracture healing associated with the Wnt pathway. Because the coating effectively accelerates the healing of osteoporotic fractures and improves bone quality, it has significant clinical application prospects.
    Type of Medium: Online Resource
    ISSN: 2056-3426
    URL: Article
    DOI: 10.1093/rb/rbac092
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2799042-4
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  • 9
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    Premigratory neural crest stem cells generate enteric neurons populating the mouse colon and regulating peristalsis in tissue-engineered intestine
    Oxford University Press (OUP) ; 2021
    In:  Stem Cells Translational Medicine Vol. 10, No. 6 ( 2021-06-01), p. 922-938
    Details
    In: Stem Cells Translational Medicine, Oxford University Press (OUP), Vol. 10, No. 6 ( 2021-06-01), p. 922-938
    Abstract: Hirschsprung's disease (HSCR) is a common congenital defect. It occurs when bowel colonization by neural crest-derived enteric nervous system (ENS) precursors is incomplete during the first trimester of pregnancy. Several sources of candidate cells have been previously studied for their capacity to regenerate the ENS, including enteric neural crest stem cells (En-NCSCs) derived from native intestine or those simulated from human pluripotent stem cells (hPSCs). However, it is not yet known whether the native NCSCs other than En-NCSCs would have the potential of regenerating functional enteric neurons and producing neuron dependent motility under the intestinal environment. The present study was designed to determine whether premigratory NCSCs (pNCSCs), as a type of the nonenteric NCSCs, could form enteric neurons and mediate the motility. pNCSCs were firstly transplanted into the colon of adult mice, and were found to survive, migrate, differentiate into enteric neurons, and successfully integrate into the adult mouse colon. When the mixture of pNCSCs and human intestinal organoids was implanted into the subrenal capsule of nude mice and grown into the mature tissue-engineered intestine (TEI), the pNCSCs-derived neurons mediated neuron-dependent peristalsis of TEI. These results show that the pNCSCs that were previously assumed to not be induced by intestinal environment or cues can innervate the intestine and establish neuron-dependent motility. Future cell candidates for ENS regeneration may include nonenteric NCSCs.
    Type of Medium: Online Resource
    ISSN: 2157-6564 , 2157-6580
    URL: Article
    DOI: 10.1002/sctm.20-0469
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2642270-0
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  • 10
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    DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry
    Oxford University Press (OUP) ; 2023
    In:  Horticulture Research Vol. 10, No. 8 ( 2023-08-04)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 10, No. 8 ( 2023-08-04)
    Abstract: Recently, increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening. However, the role of DNA methylation in regulating specific traits, such as flavor, remains unclear. Here, we report a role of DNA methylation in affecting furanone biosynthesis in strawberry. Strawberry quinone oxidoreductase (FaQR) is a key enzyme in furanone biosynthesis. There are four FaQR homologs in strawberry cultivar ‘Yuexin’, and one of them, FaQR3, contributes ~50% of FaQR transcripts, indicating a major role of FaQR3 in furanone biosynthesis. Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor, we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation, suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression, and responded to different temperatures consistently. In addition, transient expression of a gene in the RNA-directed DNA methylation (RdDM) pathway, FaAGO4, and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway. Transient RNA interference (RNAi) of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation. These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhad131
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2781828-7
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