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  • 1
    Online Resource
    Online Resource
    Table_3.PDF
    Frontiers Media SA ; 2021
    In:  Frontiers in Genetics Vol. 11 ( 2021-1-13)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 11 ( 2021-1-13)
    Abstract: Assay for transposase-accessible chromatin using sequencing data (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. Most of the current ATAC-seq tools follow chromatin immunoprecipitation sequencing (ChIP-seq) strategies that do not consider ATAC-seq-specific properties. To incorporate specific ATAC-seq quality control and the underlying biology of chromatin accessibility, we developed a bioinformatics software named ATACgraph for analyzing and visualizing ATAC-seq data. ATACgraph profiles accessible chromatin regions and provides ATAC-seq-specific information including definitions of nucleosome-free regions (NFRs) and nucleosome-occupied regions. ATACgraph also allows identification of differentially accessible regions between two ATAC-seq datasets. ATACgraph incorporates the docker image with the Galaxy platform to provide an intuitive user experience via the graphical interface. Without tedious installation processes on a local machine or cloud, users can analyze data through activated websites using pre-designed workflows or customized pipelines composed of ATACgraph modules. Overall, ATACgraph is an effective tool designed for ATAC-seq for biologists with minimal bioinformatics knowledge to analyze chromatin accessibility. ATACgraph can be run on any ATAC-seq data with no limit to specific genomes. As validation, we demonstrated ATACgraph on human genome to showcase its functions for ATAC-seq interpretation. This software is publicly accessible and can be downloaded at https://github.com/RitataLU/ATACgraph .
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2020.618478
    DOI: 10.3389/fgene.2020.618478.s001
    DOI: 10.3389/fgene.2020.618478.s002
    DOI: 10.3389/fgene.2020.618478.s003
    DOI: 10.3389/fgene.2020.618478.s004
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606823-0
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  • 2
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    Image_1.tiff
    Frontiers Media SA ; 2021
    In:  Frontiers in Microbiology Vol. 11 ( 2021-1-22)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 11 ( 2021-1-22)
    Abstract: DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2020.616922
    DOI: 10.3389/fmicb.2020.616922.s001
    DOI: 10.3389/fmicb.2020.616922.s002
    DOI: 10.3389/fmicb.2020.616922.s003
    DOI: 10.3389/fmicb.2020.616922.s004
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2587354-4
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  • 3
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    BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity
    Frontiers Media SA ; 2022
    In:  Frontiers in Bioinformatics Vol. 2 ( 2022-2-10)
    Details
    In: Frontiers in Bioinformatics, Frontiers Media SA, Vol. 2 ( 2022-2-10)
    Abstract: DNA methylation is one of the most studied epigenetic modifications that has applications ranging from transcriptional regulation to aging, and can be assessed by bisulfite sequencing (BS-seq) or enzymatic methyl sequencing (EM-seq) at single base-pair resolution. The permutations of methylation statuses given by aligned reads reflect the methylation patterns of individual cells. These patterns at specific genomic locations are sought to be indicative of cellular heterogeneity within a cellular population, which are predictive of developments and diseases; therefore, methylation heterogeneity has potentials in early detection of these changes. Computational methods have been developed to assess methylation heterogeneity using methylation patterns formed by four consecutive CpGs, but the nature of shotgun sequencing often give partially observed patterns, which makes very limited data available for downstream analysis. While many programs are developed to impute genome-wide methylation levels, currently there is only one method developed for recovering partially observed methylation patterns; however, the program needs lots of data to train and cannot be used directly; therefore, we developed a probabilistic-based imputation method that uses information from neighbouring sites to recover partially observed methylation patterns speedily. It is demonstrated to allow for the evaluation of methylation heterogeneity at 15% more regions genome-wide with high accuracy for data with moderate depth. To make it more user-friendly we also provide a computational pipeline for genome-screening, which can be used in both evaluating methylation levels and profiling methylation patterns genomewide for all cytosine contexts, which is the first of its kind. Our method allows for accurate estimation of methylation levels and makes evaluating methylation heterogeneity available for much more data with reasonable coverage, which has important implications in using methylation heterogeneity for monitoring changes within the cellular populations that were impossible to detect for the assessment of development and diseases.
    Type of Medium: Online Resource
    ISSN: 2673-7647
    URL: Article
    DOI: 10.3389/fbinf.2022.815289
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 3091287-8
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  • 4
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    Image4.JPEG
    Frontiers Media SA ; 2023
    In:  Frontiers in Genetics Vol. 14 ( 2023-1-18)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 14 ( 2023-1-18)
    Abstract: The entomopathogenic fungus (EPF), Beauveria bassiana, is an important and commonly used EPF for microbial control. However, the role of DNA methylation has not been thoroughly studied. Therefore, the whole genomic DNA methylome of one promising EPF isolate, B. bassiana NCHU-157 (Bb-NCHU-157), was investigated by Oxford Nanopore Technologies (ONT). First, the whole genome of Bb-NCHU-157 was sequenced by next-generation sequencing (NGS) and ONT. The genome of Bb-NCHU-157 contains 16 contigs with 34.19 Mb and 50% GC content, which are composed of 10,848 putative protein-coding genes. Two putative DNA methyltransferases (DNMTs) were found, including Dim-2 and C-5 cytosine-specific DNA methylases. Both DNMTs showed higher expression levels in the mycelium stage than in the conidia stage, indicating that development of DNA methylation in Bb-NCHU-157 might occur in the mycelium stage. The global methylation level of the mycelium stage (5 mC = 4.56%, CG = 3.33%, CHG = 0.74%, CHH = 0.49%) was higher than that of the conidial stage (5 mC = 2.99%, CG = 1.99%, CHG = 0.63%, CHH = 0.37%) in both the gene and transposable element (TE) regions. Furthermore, the TE regions showed higher methylation frequencies than the gene regions, especially for CHH site methylation, suggesting regulation of genomic stabilization during mycelium development. In the gene regions, high methylation frequencies were found around the transcription start site (TSS) and transcription end site (TES). Moreover, CG and CHG methylation mainly occur in the promoter and intergenic regions, while CHH methylation occurs in the TE region. Among the methylated regions, 371, 661, and 756 differentially DNA methylated regions (DMRs) were hypermethylated in the mycelium in CG, CHG, and CHH, while only 13 and 7 DMRs were hypomethylated in the mycelium in CHG, and CHH, respectively. Genes located in the DMR shared the GO terms, DNA binding (GO: 0003677), and sequence-specific DNA binding (GO: 0043565) for hypermethylation in the mycelium, suggesting that methylation might regulate gene expression from the initial process. Evaluation of the DNA methylome in Bb-NCHU-157 by ONT provided new insight into this field. These data will be further validated, and epigenetic regulation during the development of B. bassiana will be explored.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2023.1085631
    DOI: 10.3389/fgene.2023.1085631.s001
    DOI: 10.3389/fgene.2023.1085631.s002
    DOI: 10.3389/fgene.2023.1085631.s003
    DOI: 10.3389/fgene.2023.1085631.s004
    DOI: 10.3389/fgene.2023.1085631.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2606823-0
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  • 5
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    A new direction for directed mutation?
    PAGEPress Publications ; 2011
    In:  Trends in Evolutionary Biology Vol. 3, No. 1 ( 2011-09-15), p. 3-
    Details
    In: Trends in Evolutionary Biology, PAGEPress Publications, Vol. 3, No. 1 ( 2011-09-15), p. 3-
    Type of Medium: Online Resource
    ISSN: 2036-265X , 2036-2641
    URL: Article
    DOI: 10.4081/eb.2011.e3
    Language: Unknown
    Publisher: PAGEPress Publications
    Publication Date: 2011
    detail.hit.zdb_id: 2555821-3
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  • 6
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    DataSheet_1.docx
    Frontiers Media SA ; 2022
    In:  Frontiers in Immunology Vol. 13 ( 2022-5-4)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 13 ( 2022-5-4)
    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus responsible for the ongoing COVID-19 pandemic. SARS-CoV-2 binds to the human cell receptor angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain in the S1 subunit of the spike protein (S1-RBD). The serum levels of autoantibodies against ACE2 are significantly higher in patients with COVID-19 than in controls and are associated with disease severity. However, the mechanisms through which these anti-ACE2 antibodies are induced during SARS-CoV-2 infection are unclear. In this study, we confirmed the increase in antibodies against ACE2 in patients with COVID-19 and found a positive correlation between the amounts of antibodies against ACE2 and S1-RBD. Moreover, antibody binding to ACE2 was significantly decreased in the sera of some COVID-19 patients after preadsorption of the sera with S1-RBD, which indicated that antibodies against S1-RBD can cross-react with ACE2. To confirm this possibility, two monoclonal antibodies (mAbs 127 and 150) which could bind to both S1-RBD and ACE2 were isolated from S1-RBD-immunized mice. Measurement of the binding affinities by Biacore showed these two mAbs bind to ACE2 much weaker than binding to S1-RBD. Epitope mapping using synthetic overlapping peptides and hydrogen deuterium exchange mass spectrometry (HDX-MS) revealed that the amino acid residues P463, F464, E465, R466, D467 and E471 of S1-RBD are critical for the recognition by mAbs 127 and 150. In addition, Western blotting analysis showed that these mAbs could recognize ACE2 only in native but not denatured form, indicating the ACE2 epitopes recognized by these mAbs were conformation-dependent. The protein–protein interaction between ACE2 and the higher affinity mAb 127 was analyzed by HDX-MS and visualized by negative-stain transmission electron microscopy imaging combined with antigen-antibody docking. Together, our results suggest that ACE2-cross-reactive anti-S1-RBD antibodies can be induced during SARS-CoV-2 infection due to potential antigenic cross-reactivity between S1-RBD and its receptor ACE2.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    URL: Article
    DOI: 10.3389/fimmu.2022.868724
    DOI: 10.3389/fimmu.2022.868724.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606827-8
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  • 7
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    An 8b-Precision 6T SRAM Computing-in-Memory Macro Using Time-Domain Incremental Accumulation for AI Edge Chips
    Institute of Electrical and Electronics Engineers (IEEE) ; 2024
    In:  IEEE Journal of Solid-State Circuits Vol. 59, No. 7 ( 2024-7), p. 2297-2309
    Details
    In: IEEE Journal of Solid-State Circuits, Institute of Electrical and Electronics Engineers (IEEE), Vol. 59, No. 7 ( 2024-7), p. 2297-2309
    Type of Medium: Online Resource
    ISSN: 0018-9200 , 1558-173X
    URL: Article
    DOI: 10.1109/JSSC.2023.3343669
    Language: Unknown
    Publisher: Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2024
    detail.hit.zdb_id: 240580-5
    detail.hit.zdb_id: 2040287-9
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  • 8
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    Improved SPM tolerance and cost-effective phase-modulation duobinary transmission over 230-km standard single-mode fiber using a single Mach-Zehnder modulator
    Institute of Electrical and Electronics Engineers (IEEE) ; 2005
    In:  IEEE Photonics Technology Letters Vol. 17, No. 12 ( 2005-12), p. 2754-2756
    Details
    In: IEEE Photonics Technology Letters, Institute of Electrical and Electronics Engineers (IEEE), Vol. 17, No. 12 ( 2005-12), p. 2754-2756
    Type of Medium: Online Resource
    ISSN: 1041-1135
    URL: Article
    DOI: 10.1109/LPT.2005.859433
    Language: Unknown
    Publisher: Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2005
    detail.hit.zdb_id: 2025386-2
    detail.hit.zdb_id: 246805-0
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  • 9
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    A Flat Panel Display Combining a Polymer-Dispersed Liquid Crystal Film with an Electroluminescent Device
    IOP Publishing ; 1994
    In:  Japanese Journal of Applied Physics Vol. 33, No. 6B ( 1994-06-01), p. L870-
    Details
    In: Japanese Journal of Applied Physics, IOP Publishing, Vol. 33, No. 6B ( 1994-06-01), p. L870-
    Abstract: A novel display device combining a polymer-dispersed liquid crystal (PDLC) film and a thin-film electroluminescent (TFEL) device was fabricated. This device may be used as a liquid crystal display (LCD) in strong light ambient. In the dark, it can be switched to become an electroluminescent display, providing high viewability. Measurements of its electrooptical characteristics showed that the breakdown voltage of the TFEL device did not change significantly with the addition of a LC layer. It implies that the cured polymer could provide an intrinsic barrier preventing LC material from diffusing into the TFEL device.
    Type of Medium: Online Resource
    ISSN: 0021-4922 , 1347-4065
    URL: Article
    DOI: 10.1143/JJAP.33.L870
    RVK:
    UA 4210.1
    RVK:
    UA 4210.2
    RVK:
    UA 4210
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 1994
    detail.hit.zdb_id: 218223-3
    detail.hit.zdb_id: 797294-5
    detail.hit.zdb_id: 2006801-3
    detail.hit.zdb_id: 797295-7
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  • 10
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    A new calibration method for charm jet identification validated with proton-proton collision events at √s = 13 TeV
    IOP Publishing ; 2022
    In:  Journal of Instrumentation Vol. 17, No. 03 ( 2022-03-01), p. P03014-
    Details
    In: Journal of Instrumentation, IOP Publishing, Vol. 17, No. 03 ( 2022-03-01), p. P03014-
    Abstract: Many measurements at the LHC require efficient identification of heavy-flavour jets, i.e. jets originating from bottom (b) or charm (c) quarks. An overview of the algorithms used to identify c jets is described and a novel method to calibrate them is presented. This new method adjusts the entire distributions of the outputs obtained when the algorithms are applied to jets of different flavours. It is based on an iterative approach exploiting three distinct control regions that are enriched with either b jets, c jets, or light-flavour and gluon jets. Results are presented in the form of correction factors evaluated using proton-proton collision data with an integrated luminosity of 41.5 fb -1 at  √s = 13 TeV, collected by the CMS experiment in 2017. The closure of the method is tested by applying the measured correction factors on simulated data sets and checking the agreement between the adjusted simulation and collision data. Furthermore, a validation is performed by testing the method on pseudodata, which emulate various mismodelling conditions. The calibrated results enable the use of the full distributions of heavy-flavour identification algorithm outputs, e.g. as inputs to machine-learning models. Thus, they are expected to increase the sensitivity of future physics analyses.
    Type of Medium: Online Resource
    ISSN: 1748-0221
    URL: Article
    DOI: 10.1088/1748-0221/17/03/P03014
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2022
    detail.hit.zdb_id: 2235672-1
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