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  • Oxford University Press (OUP)  (13)
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  • Oxford University Press (OUP)  (13)
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  • 1
    Online Resource
    Online Resource
    The role of ubiquitination and deubiquitination in the regulation of cell junctions
    Oxford University Press (OUP) ; 2018
    In:  Protein & Cell Vol. 9, No. 9 ( 2018-9), p. 754-769
    Details
    In: Protein & Cell, Oxford University Press (OUP), Vol. 9, No. 9 ( 2018-9), p. 754-769
    Type of Medium: Online Resource
    ISSN: 1674-800X , 1674-8018
    URL: Article
    DOI: 10.1007/s13238-017-0486-3
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2543451-2
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  • 2
    Online Resource
    Online Resource
    Phosphorylated E2F1 is stabilized by nuclear USP11 to drive Peg10 gene expression and activate lung epithelial cells
    Oxford University Press (OUP) ; 2018
    In:  Journal of Molecular Cell Biology Vol. 10, No. 1 ( 2018-02-01), p. 60-73
    Details
    In: Journal of Molecular Cell Biology, Oxford University Press (OUP), Vol. 10, No. 1 ( 2018-02-01), p. 60-73
    Type of Medium: Online Resource
    ISSN: 1759-4685
    URL: Article
    DOI: 10.1093/jmcb/mjx034
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2500949-7
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  • 3
    Online Resource
    Online Resource
    An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans
    Oxford University Press (OUP) ; 2023
    In:  GENETICS Vol. 223, No. 4 ( 2023-04-06)
    Details
    In: GENETICS, Oxford University Press (OUP), Vol. 223, No. 4 ( 2023-04-06)
    Abstract: The auxin-inducible degradation system has been widely adopted in the Caenorhabditis elegans research community for its ability to empirically control the spatiotemporal expression of target proteins. This system can efficiently degrade auxin-inducible degron (AID)-tagged proteins via the expression of a ligand-activatable AtTIR1 protein derived from A. thaliana that adapts target proteins to the endogenous C. elegans proteasome. While broad expression of AtTIR1 using strong, ubiquitous promoters can lead to rapid degradation of AID-tagged proteins, cell type-specific expression of AtTIR1 using spatially restricted promoters often results in less efficient target protein degradation. To circumvent this limitation, we have developed an FLP/FRT3-based system that functions to reanimate a dormant, high-powered promoter that can drive sufficient AtTIR1 expression in a cell type-specific manner. We benchmark the utility of this system by generating a number of tissue-specific FLP-ON::TIR1 drivers to reveal genetically separable cell type-specific phenotypes for several target proteins. We also demonstrate that the FLP-ON::TIR1 system is compatible with enhanced degron epitopes. Finally, we provide an expandable toolkit utilizing the basic FLP-ON::TIR1 system that can be adapted to drive optimized AtTIR1 expression in any tissue or cell type of interest.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1093/genetics/iyad013
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Enhanced Efficiency of flySAM by Optimization of sgRNA Parameters in Drosophila
    Oxford University Press (OUP) ; 2020
    In:  G3 Genes|Genomes|Genetics Vol. 10, No. 12 ( 2020-12-01), p. 4483-4488
    Details
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 10, No. 12 ( 2020-12-01), p. 4483-4488
    Abstract: The flySAM/CRISPRa system has recently emerged as a powerful tool for gain-of-function studies in Drosophila melanogaster. This system includes Gal4/UAS-driven dCas9 activators and U6 promoter-controlled sgRNA. Having established dCas9 activators superior to other combinations, to further enhance the efficiency of the targeting activators we systematically optimized the parameters of the sgRNA. Interestingly, the most efficient sgRNAs were found to accumulate in the region from -150bp to -450bp upstream of the transcription start site (TSS), and the activation efficiency showed a strong positive correlation with the GC content of the sgRNA targeting sequence. In addition, the target region is dominant to the GC content, as sgRNAs targeting areas beyond -600bp from the TSS lose efficiency even when containing 75% GC. Surprisingly, when comparing the activities of sgRNAs targeting to either DNA strand, sgRNAs targeting to the non-template strand outperform those complementary to the template strand, both in cells and in vivo. In summary, we define criteria for sgRNA design which will greatly facilitate the application of CRISPRa in gain-of-function studies.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    URL: Article
    DOI: 10.1534/g3.120.401614
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2629978-1
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  • 5
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    A CRISPR-based nucleic acid detection platform (CRISPR-CPA): Application for detection of Nocardia farcinica
    Oxford University Press (OUP) ; 2022
    In:  Journal of Applied Microbiology Vol. 132, No. 5 ( 2022-05-01), p. 3685-3693
    Details
    In: Journal of Applied Microbiology, Oxford University Press (OUP), Vol. 132, No. 5 ( 2022-05-01), p. 3685-3693
    Abstract: To establish a CRISPR-based nucleic acid detection platform and apply it to the detection of Nocardia farcinica. Methods and Results A CRISPR-based nucleic acid detection platform, termed CRISPR-CPA (CRISPR/Cas12a combined with PCR amplification), which employed PCR for pre-amplification of target sequences and CRISPR-Cas12a-based detection for decoding of the PCR amplicons, was developed. To demonstrate its feasibility, CRISPR-CPA was applied to the detection of N. farcinica. A pair of PCR primers and a crRNA, which targeting the conservative and specific part of gyrA of N. farcinica reference strain IFM 10152, were designed according to the principle of CRISPR-CPA. The whole detection process of N. farcinica CRISPR-CPA assay, including sample pre-treatment and DNA extraction (~20 min), PCR pre-amplification (60 min), CRISPR-based detection (10 min), can be completed within 90 min. A total of 62 isolates were used to evaluate the specificity of N. farcinica CRISPR-CPA assay. Clinical specimens were employed to determine the feasibility of the method in practical application. The limit of detection of the N. farcinica CRISPR-CPA assay is 1 pg DNA per reaction in pure cultures and 105 CFU/ml in sputum specimens, which is similar with culture but significantly more timesaving. Conclusions The N. farcinica CRISPR-CPA assay is an economic and specific method to detect N. farcinica and provides a high-efficiency tool for screening of pathogens especially of some hard-to-culture and slow-growth infectious agents. Significance and Impact of the Study In CRISPR-CPA system, the PCR primers are engineered with a protospacer adjacent motif (PAM) site of Cas12a effector and an additional base A was added at the 5′ end of the engineered PCR primer for protecting PAM site, thus the CRISPR-CPA can detect any sequence. Also, we applied CRISPR-CPA to rapidly detect N. farcinica, which is slow-growing bacteria and is firstly detected by a CRISPR-based method.
    Type of Medium: Online Resource
    ISSN: 1365-2672 , 1364-5072
    URL: Article
    DOI: 10.1111/jam.15424
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2020421-8
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  • 6
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    A dual-activity topoisomerase complex regulates mRNA translation and turnover
    Oxford University Press (OUP) ; 2022
    In:  Nucleic Acids Research Vol. 50, No. 12 ( 2022-07-08), p. 7013-7033
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. 12 ( 2022-07-08), p. 7013-7033
    Abstract: Topoisomerase 3β (TOP3B) and TDRD3 form a dual-activity topoisomerase complex that interacts with FMRP and can change the topology of both DNA and RNA. Here, we investigated the post-transcriptional influence of TOP3B and associated proteins on mRNA translation and turnover. First, we discovered that in human HCT116 colon cancer cells, knock-out (KO) of TOP3B had similar effects on mRNA turnover and translation as did TDRD3-KO, while FMRP-KO resulted in rather distinct effects, indicating that TOP3B had stronger coordination with TDRD3 than FMRP in mRNA regulation. Second, we identified TOP3B-bound mRNAs in HCT116 cells; we found that while TOP3B did not directly influence the stability or translation of most TOP3B target mRNAs, it stabilized a subset of target mRNAs but had a more complex effect on translation–enhancing for some mRNAs whereas reducing for others. Interestingly, a point mutation that specifically disrupted TOP3B catalytic activity only partially recapitulated the effects of TOP3B-KO on mRNA stability and translation, suggesting that the impact of TOP3B on target mRNAs is partly linked to its ability to change topology of mRNAs. Collectively, our data suggest that TOP3B–TDRD3 can regulate mRNA translation and turnover by mechanisms that are dependent and independent of topoisomerase activity.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkac538
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 7
    Online Resource
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    Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting
    Oxford University Press (OUP) ; 2020
    In:  Bioinformatics Vol. 36, No. 17 ( 2020-11-01), p. 4576-4582
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 36, No. 17 ( 2020-11-01), p. 4576-4582
    Abstract: RNA secondary structure plays a vital role in fundamental cellular processes, and identification of RNA secondary structure is a key step to understand RNA functions. Recently, a few experimental methods were developed to profile genome-wide RNA secondary structure, i.e. the pairing probability of each nucleotide, through high-throughput sequencing techniques. However, these high-throughput methods have low precision and cannot cover all nucleotides due to limited sequencing coverage. Results Here, we have developed a new method for the prediction of genome-wide RNA secondary structure profile from RNA sequence based on the extreme gradient boosting technique. The method achieves predictions with areas under the receiver operating characteristic curve (AUC) & gt;0.9 on three different datasets, and AUC of 0.888 by another independent test on the recently released Zika virus data. These AUCs are consistently & gt;5% greater than those by the CROSS method recently developed based on a shallow neural network. Further analysis on the 1000 Genome Project data showed that our predicted unpaired probabilities are highly correlated ( & gt;0.8) with the minor allele frequencies at synonymous, non-synonymous mutations, and mutations in untranslated regions, which were higher than those generated by RNAplfold. Moreover, the prediction over all human mRNA indicated a consistent result with previous observation that there is a periodic distribution of unpaired probability on codons. The accurate predictions by our method indicate that such model trained on genome-wide experimental data might be an alternative for analytical methods. Availability and implementation The GRASP is available for academic use at https://github.com/sysu-yanglab/GRASP. Supplementary information Supplementary data are available online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    URL: Article
    DOI: 10.1093/bioinformatics/btaa534
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1468345-3
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  • 8
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    Evidence for marine sedimentary rocks in Utopia Planitia: Zhurong rover observations
    Oxford University Press (OUP) ; 2023
    In:  National Science Review Vol. 10, No. 9 ( 2023-08-09)
    Details
    In: National Science Review, Oxford University Press (OUP), Vol. 10, No. 9 ( 2023-08-09)
    Abstract: Decades of research using remotely sensed data have extracted evidence for the presence of an ocean in the northern lowlands of Mars in the Hesperian (∼3.3 Ga), but these claims have remained controversial due to the lack of in situ analysis of the associated geologic unit, the Vastitas Borealis Formation (VBF). The Tianwen-1/Zhurong rover was targeted to land within the VBF near its southern margin and has traversed almost 2 km southward toward the interpreted shoreline. We report here on the first in situ analysis of the VBF that reveals sedimentary structures and features in surface rocks that suggest that the VBF was deposited in a marine environment, providing direct support for the existence of an ancient (Hesperian) ocean on Mars.
    Type of Medium: Online Resource
    ISSN: 2095-5138 , 2053-714X
    URL: Article
    DOI: 10.1093/nsr/nwad137
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2745465-4
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  • 9
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    Cortical phase-amplitude coupling is key to the occurrence and treatment of freezing of gait
    Oxford University Press (OUP) ; 2022
    In:  Brain Vol. 145, No. 7 ( 2022-07-29), p. 2407-2421
    Details
    In: Brain, Oxford University Press (OUP), Vol. 145, No. 7 ( 2022-07-29), p. 2407-2421
    Abstract: Freezing of gait is a debilitating symptom in advanced Parkinson’s disease and responds heterogeneously to treatments such as deep brain stimulation. Recent studies indicated that cortical dysfunction is involved in the development of freezing, while evidence depicting the specific role of the primary motor cortex in the multi-circuit pathology of freezing is lacking. Since abnormal beta-gamma phase-amplitude coupling recorded from the primary motor cortex in patients with Parkinson’s disease indicates parkinsonian state and responses to therapeutic deep brain stimulation, we hypothesized this metric might reveal unique information on understanding and improving therapy for freezing of gait. Here, we directly recorded potentials in the primary motor cortex using subdural electrocorticography and synchronously captured gait freezing using optoelectronic motion-tracking systems in 16 freely-walking patients with Parkinson’s disease who received subthalamic nucleus deep brain stimulation surgery. Overall, we recorded 451 timed up-and-go walking trials and quantified 7073 s of stable walking and 3384 s of gait freezing in conditions of on/off-stimulation and with/without dual-tasking. We found that (i) high beta-gamma phase-amplitude coupling in the primary motor cortex was detected in freezing trials (i.e. walking trials that contained freezing), but not non-freezing trials, and the high coupling in freezing trials was not caused by dual-tasking or the lack of movement; (ii) non-freezing episodes within freezing trials also demonstrated abnormally high couplings, which predicted freezing severity; (iii) deep brain stimulation of subthalamic nucleus reduced these abnormal couplings and simultaneously improved freezing; and (iv) in trials that were at similar coupling levels, stimulation trials still demonstrated lower freezing severity than no-stimulation trials. These findings suggest that elevated phase-amplitude coupling in the primary motor cortex indicates higher probabilities of freezing. Therapeutic deep brain stimulation alleviates freezing by both decoupling cortical oscillations and enhancing cortical resistance to abnormal coupling. We formalized these findings to a novel ‘bandwidth model,’ which specifies the role of cortical dysfunction, cognitive burden and therapeutic stimulation on the emergence of freezing. By targeting key elements in the model, we may develop next-generation deep brain stimulation approaches for freezing of gait.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    URL: Article
    DOI: 10.1093/brain/awac121
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1474117-9
    SSG: 12
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  • 10
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    Convergence between germline and somatic mutations in pancreatic neuroendocrine tumors
    Oxford University Press (OUP) ; 2022
    In:  European Journal of Endocrinology Vol. 187, No. 1 ( 2022-07-01), p. 85-90
    Details
    In: European Journal of Endocrinology, Oxford University Press (OUP), Vol. 187, No. 1 ( 2022-07-01), p. 85-90
    Abstract: The pancreatic neuroendocrine tumors (PanNETs) are a group of clinically heterogeneous neoplasms. Although previous studies illustrated the somatic mutation pattern for PanNETs, the germline mutation pattern is still unclear. Here, we comprehensively screened the underlying germline mutations in a cohort of multiple endocrine neoplasia type 1 (MEN1)-related and sporadic PanNETs to reveal the characteristics of germline mutation in PanNET patients. Methods Patients diagnosed with PanNETs by biopsy or surgical pathology were enrolled in this study. Peripheral blood samples were used for genomic DNA purification and subsequent sequencing. The following sequencing techniques were used and compared for validation: (1) targeted gene capture with a customized panel; (2) whole exome sequencing data from previous study. Results A total of 184 PanNET patients were enrolled, including 20 MEN1-related and 164 sporadic cases. In this study, MEN1 mutation rate in MEN1-related PanNETs was 60% (12/20), of which 50% were novel mutation sites. For sporadic PanNETs, the overall germline mutation rate was very low. Besides the rare MEN1 mutation, previously unreported germline variant in DAXX was found in one non-functional PanNET. Conclusions This study revealed distinctive germline mutation rates between MEN1-related and sporadic PanNETs. The novel MEN1 mutations contribute to revealing the spectrum of MEN1 mutations in PanNETs. The newly discovered germline variant of DAXX in sporadic PanNET implies a tendency of convergence between germline and somatic mutation genes.
    Type of Medium: Online Resource
    ISSN: 0804-4643 , 1479-683X
    URL: Article
    DOI: 10.1530/EJE-21-0893
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1485160-X
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