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  • 1
    Online Resource
    Online Resource
    Genomic Insights into the Origin and Evolution of Molluscan Red-Bloodedness in the Blood Clam Tegillarca granosa
    Oxford University Press (OUP) ; 2021
    In:  Molecular Biology and Evolution Vol. 38, No. 6 ( 2021-05-19), p. 2351-2365
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 38, No. 6 ( 2021-05-19), p. 2351-2365
    Abstract: Blood clams differ from their molluscan kins by exhibiting a unique red-blood (RB) phenotype; however, the genetic basis and biochemical machinery subserving this evolutionary innovation remain unclear. As a fundamental step toward resolving this mystery, we presented the first chromosome-level genome and comprehensive transcriptomes of the blood clam Tegillarca granosa for an integrated genomic, evolutionary, and functional analyses of clam RB phenotype. We identified blood clam-specific and expanded gene families, as well as gene pathways that are of RB relevant. Clam-specific RB-related hemoglobins (Hbs) showed close phylogenetic relationships with myoglobins (Mbs) of blood clam and other molluscs without the RB phenotype, indicating that clam-specific Hbs were likely evolutionarily derived from the Mb lineage. Strikingly, similar to vertebrate Hbs, blood clam Hbs were present in a form of gene cluster. Despite the convergent evolution of Hb clusters in blood clam and vertebrates, their Hb clusters may have originated from a single ancestral Mb-like gene as evidenced by gene phylogeny and synteny analysis. A full suite of enzyme-encoding genes for heme synthesis was identified in blood clam, with prominent expression in hemolymph and resembling those in vertebrates, suggesting a convergence of both RB-related Hb and heme functions in vertebrates and blood clam. RNA interference experiments confirmed the functional roles of Hbs and key enzyme of heme synthesis in the maintenance of clam RB phenotype. The high-quality genome assembly and comprehensive transcriptomes presented herein serve new genomic resources for the super-diverse phylum Mollusca, and provide deep insights into the origin and evolution of invertebrate RB.
    Type of Medium: Online Resource
    ISSN: 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msab030
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2024221-9
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  • 2
    Online Resource
    Online Resource
    Erratum to: Genomic Insights into the Origin and Evolution of Molluscan Red-Bloodedness in the Blood Clam Tegillarca granosa
    Oxford University Press (OUP) ; 2021
    In:  Molecular Biology and Evolution Vol. 38, No. 8 ( 2021-07-29), p. 3494-3494
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 38, No. 8 ( 2021-07-29), p. 3494-3494
    Type of Medium: Online Resource
    ISSN: 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msab126
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2024221-9
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  • 3
    Online Resource
    Online Resource
    Competition between PAF1 and MLL1/COMPASS confers the opposing function of LEDGF/p75 in HIV latency and proviral reactivation
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Advances Vol. 6, No. 20 ( 2020-05-15)
    Details
    In: Science Advances, American Association for the Advancement of Science (AAAS), Vol. 6, No. 20 ( 2020-05-15)
    Abstract: Transcriptional status determines the HIV replicative state in infected patients. However, the transcriptional mechanisms for proviral replication control remain unclear. In this study, we show that, apart from its function in HIV integration, LEDGF/p75 differentially regulates HIV transcription in latency and proviral reactivation. During latency, LEDGF/p75 suppresses proviral transcription via promoter-proximal pausing of RNA polymerase II (Pol II) by recruiting PAF1 complex to the provirus. Following latency reversal, MLL1 complex competitively displaces PAF1 from the provirus through casein kinase II (CKII)–dependent association with LEDGF/p75. Depleting or pharmacologically inhibiting CKII prevents PAF1 dissociation and abrogates the recruitment of both MLL1 and Super Elongation Complex (SEC) to the provirus, thereby impairing transcriptional reactivation for latency reversal. These findings, therefore, provide a mechanistic understanding of how LEDGF/p75 coordinates its distinct regulatory functions at different stages of the post-integrated HIV life cycles. Targeting these mechanisms may have a therapeutic potential to eradicate HIV infection.
    Type of Medium: Online Resource
    ISSN: 2375-2548
    URL: Article
    DOI: 10.1126/sciadv.aaz8411
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
    detail.hit.zdb_id: 2810933-8
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  • 4
    Online Resource
    Online Resource
    A survey on protein–DNA-binding sites in computational biology
    Oxford University Press (OUP) ; 2022
    In:  Briefings in Functional Genomics Vol. 21, No. 5 ( 2022-09-16), p. 357-375
    Details
    In: Briefings in Functional Genomics, Oxford University Press (OUP), Vol. 21, No. 5 ( 2022-09-16), p. 357-375
    Abstract: Transcription factors are important cellular components of the process of gene expression control. Transcription factor binding sites are locations where transcription factors specifically recognize DNA sequences, targeting gene-specific regions and recruiting transcription factors or chromatin regulators to fine-tune spatiotemporal gene regulation. As the common proteins, transcription factors play a meaningful role in life-related activities. In the face of the increase in the protein sequence, it is urgent how to predict the structure and function of the protein effectively. At present, protein–DNA-binding site prediction methods are based on traditional machine learning algorithms and deep learning algorithms. In the early stage, we usually used the development method based on traditional machine learning algorithm to predict protein–DNA-binding sites. In recent years, methods based on deep learning to predict protein–DNA-binding sites from sequence data have achieved remarkable success. Various statistical and machine learning methods used to predict the function of DNA-binding proteins have been proposed and continuously improved. Existing deep learning methods for predicting protein–DNA-binding sites can be roughly divided into three categories: convolutional neural network (CNN), recursive neural network (RNN) and hybrid neural network based on CNN–RNN. The purpose of this review is to provide an overview of the computational and experimental methods applied in the field of protein–DNA-binding site prediction today. This paper introduces the methods of traditional machine learning and deep learning in protein–DNA-binding site prediction from the aspects of data processing characteristics of existing learning frameworks and differences between basic learning model frameworks. Our existing methods are relatively simple compared with natural language processing, computational vision, computer graphics and other fields. Therefore, the summary of existing protein–DNA-binding site prediction methods will help researchers better understand this field.
    Type of Medium: Online Resource
    ISSN: 2041-2649 , 2041-2657
    URL: Article
    DOI: 10.1093/bfgp/elac009
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2079121-5
    detail.hit.zdb_id: 2540929-3
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  • 5
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    Online Resource
    Bilayer Bismuth Selenide nanoplatelets based saturable absorber for ultra-short pulse generation (Invited)
    Elsevier BV ; 2017
    In:  Optics Communications Vol. 395 ( 2017-07), p. 55-60
    Details
    In: Optics Communications, Elsevier BV, Vol. 395 ( 2017-07), p. 55-60
    Type of Medium: Online Resource
    ISSN: 0030-4018
    URL: Article
    DOI: 10.1016/j.optcom.2015.11.061
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2017
    detail.hit.zdb_id: 1468811-6
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  • 6
    Online Resource
    Online Resource
    American Joint Committee on Cancer Tumor Staging System Predicts the Outcome and Metastasis Pattern in Conjunctival Melanoma
    Elsevier BV ; 2022
    In:  Ophthalmology Vol. 129, No. 7 ( 2022-07), p. 771-780
    Details
    In: Ophthalmology, Elsevier BV, Vol. 129, No. 7 ( 2022-07), p. 771-780
    Type of Medium: Online Resource
    ISSN: 0161-6420
    URL: Article
    DOI: 10.1016/j.ophtha.2022.02.029
    RVK:
    XA 10000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
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  • 7
    Online Resource
    Online Resource
    Integrated cantilever sensors with a torsional resonance mode for ultraresoluble on-the-spot bio/chemical detection
    AIP Publishing ; 2007
    In:  Applied Physics Letters Vol. 90, No. 4 ( 2007-01-22)
    Details
    In: Applied Physics Letters, AIP Publishing, Vol. 90, No. 4 ( 2007-01-22)
    Abstract: Torsion-mode resonance is built in an integrated cantilever sensor for ultraresoluble detection of specifically bio/chemical mass adsorption. The superior mass resolution of the torsion-mode cantilever to a conventional bending-mode one is verified by energy-dissipation analysis and Q-factor simulation. With integrated transverse piezoresistance for frequency-shift signal readout and Lorentz force for resonance excitation, the torsion-mode sensor is optimally designed for high sensitivity. The microfabricated torsion-mode sensor is measured with a high close-loop Q factor in air. By Allan-variance analysis for the measured frequency stability, 23fg resolution is obtained for the torsion-mode sensor, which is much improved compared to the 313fg for the conventional flexure-mode sensor. The torsional sensor is used to recognize biotin-avidin specific combination, resulting in 443Hz frequency shift for 50μM streptavidin solution.
    Type of Medium: Online Resource
    ISSN: 0003-6951 , 1077-3118
    URL: Article
    DOI: 10.1063/1.2433753
    RVK:
    UA 1000
    Language: English
    Publisher: AIP Publishing
    Publication Date: 2007
    detail.hit.zdb_id: 211245-0
    detail.hit.zdb_id: 1469436-0
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  • 8
    Online Resource
    Online Resource
    Molecular Characterization and Expression of the LAP3 Gene and Its Association with Growth Traits in the Blood Clam Tegillarca granosa
    MDPI AG ; 2021
    In:  Fishes Vol. 6, No. 4 ( 2021-10-29), p. 54-
    Details
    In: Fishes, MDPI AG, Vol. 6, No. 4 ( 2021-10-29), p. 54-
    Abstract: Leucine aminopeptidase 3 (LAP3) is a metallopeptidase that cleaves N-terminal residues and is involved in protein maturation and degradation. In this study, we characterized the leucine aminopeptidase 3 (LAP3) gene from Tegillarca granosa (Tg-LAP3 for short), which appeared to consist of 15,731 nucleotides encoding 530 amino acids. We identified 12 introns and 13 exons in the Tg-LAP3 gene, suggesting a highly conserved genomic structure. The proximal promoter sequence consists of 1922 bps with a typical TATA box structure, which is the general structural characteristic of core promoters in eukaryotes. We found two functional domains in the Tg-LAP3 protein, including an N-terminal domain (41–174aa) and a peptidase_M17 catalytic domain (209–522aa). Multiple alignment showed that Tg-LAP3 shares 73.4% identity with LAP3 of Mizuhopecten yessoensis and 55.2–70.7% identity with LAP3 of other species. Quantitative analysis of Tg-LAP3 in embryos/larvae and adult tissues indicated that the highest expression occurred in eyebot larva, with limited expression in other stages; among tissues, the highest expression was found in the liver (p 〈 0.05). Association analysis found that three single-nucleotide polymorphisms (SNPs) (g.-488A 〉 G, g.-1123C 〉 T, and g.-1304C 〉 A) in the proximal promoter were successfully typed, but there was no significant difference in growth traits (body weight, shell length, shell width, and shell height) among these genotypes. The results of our study demonstrate the functional roles of the Tg-LAP3 gene and provide valuable information for molecular marker-assisted selection (MAS) of the blood clam.
    Type of Medium: Online Resource
    ISSN: 2410-3888
    URL: Article
    DOI: 10.3390/fishes6040054
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2932929-2
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  • 9
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    Online Resource
    Flavonoids intake and weight-adjusted waist index: insights from a cross-sectional study of NHANES
    Frontiers Media SA ; 2024
    In:  Frontiers in Nutrition Vol. 11 ( 2024-6-18)
    Details
    In: Frontiers in Nutrition, Frontiers Media SA, Vol. 11 ( 2024-6-18)
    Abstract: This study conducted data on 15,446 adults to explore the impact of flavonoids on weight-adjusted waist index (WWI). This was a nationwide cross-sectional study among US adults aged 20 years or older. Dietary intake of flavonoids was assessed through 24-h recall questionnaire. WWI was calculated by dividing waist circumference (WC) by the square root of weight. We utilized weighted generalized linear regression to evaluate the association between flavonoids intake and WWI, and restricted cubic splines (RCS) to explore potential non-linear relationships. Our findings indicated that individuals with lower WWI experienced a notable increase in their consumption of total flavonoids, flavanones, flavones, flavan-3-ols, and anthocyanidins intake ( β (95% CI); −0.05(−0.09, −0.01); −0.07(−0.13, 0.00); −0.07(−0.11, −0.02); −0.06(−0.11, 0.00); −0.13(−0.18, −0.08), respectively), with the exception of flavonols and isoflavones. Additionally, consumption of total flavonoids, flavonols, flavanones, isoflavones, and flavan-3-ols had a non-linear relationship with WWI (all P for non-linearity & lt; 0.05). Furthermore, the effect of total flavonoids on WWI varied in race ( P for interaction = 0.011), gender ( P for interaction = 0.038), and poverty status ( P for interaction = 0.002). These findings suggested that increase the intake of flavonoids might prevent abdominal obesity, but further prospective studies are requested before dietary recommendation.
    Type of Medium: Online Resource
    ISSN: 2296-861X
    URL: Article
    DOI: 10.3389/fnut.2024.1400726
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2024
    detail.hit.zdb_id: 2776676-7
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  • 10
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    Online Resource
    A novel fluorescent probe based on triphenylamine for detecting sulfur dioxide derivatives
    Royal Society of Chemistry (RSC) ; 2022
    In:  New Journal of Chemistry Vol. 46, No. 12 ( 2022), p. 5526-5533
    Details
    In: New Journal of Chemistry, Royal Society of Chemistry (RSC), Vol. 46, No. 12 ( 2022), p. 5526-5533
    Abstract: According to the nucleophilicity of sulfur dioxide derivatives, a reactive fluorescent probe was designed and synthesized by linking triphenylamine with benzoindole. When the probe reacts with sulfur dioxide derivatives, the two fluorophores of the probe are disconnected to release strong blue fluorescence, and the fluorescence signal at 475 nm is significantly enhanced. The probe can rapidly identify sulfur dioxide derivatives (within 300 s), and has the advantages of strong selectivity and low detection limit (2.75 × 10 −6 M). The probe with low toxicity can be used to detect sulfur dioxide derivatives in HepG-2 cells. In addition, detection test paper and silica functional materials prepared based on the probe also achieved excellent results in the detection of sulfur dioxide derivatives, which provides a potential direction for the further commercialization of the probe.
    Type of Medium: Online Resource
    ISSN: 1144-0546 , 1369-9261
    URL: Article
    DOI: 10.1039/D1NJ06099F
    Language: English
    Publisher: Royal Society of Chemistry (RSC)
    Publication Date: 2022
    detail.hit.zdb_id: 1472933-7
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