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  • 1
    Online Resource
    Online Resource
    Author Correction: Robust estimation of bacterial cell count from optical density
    Springer Science and Business Media LLC ; 2020
    In:  Communications Biology Vol. 3, No. 1 ( 2020-10-27)
    Details
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2020-10-27)
    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    URL: Article
    DOI: 10.1038/s42003-020-01371-9
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2919698-X
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  • 2
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    Online Resource
    Robust estimation of bacterial cell count from optical density
    Springer Science and Business Media LLC ; 2020
    In:  Communications Biology Vol. 3, No. 1 ( 2020-09-17)
    Details
    In: Communications Biology, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2020-09-17)
    Abstract: Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli . Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals   〈 1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
    Type of Medium: Online Resource
    ISSN: 2399-3642
    URL: Article
    DOI: 10.1038/s42003-020-01127-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2919698-X
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  • 3
    Online Resource
    Online Resource
    Effect of foliar spraying of organic and inorganic selenium fertilizers during different growth stages on selenium accumulation and speciation in rice
    Springer Science and Business Media LLC ; 2023
    In:  Plant and Soil Vol. 486, No. 1-2 ( 2023-05), p. 87-101
    Details
    In: Plant and Soil, Springer Science and Business Media LLC, Vol. 486, No. 1-2 ( 2023-05), p. 87-101
    Abstract: Most crops are supplemented with selenium (Se) through the exogenous addition of inorganic Se fertilizer. There is a lack of in-depth research on organic Se fertilizers. Meanwhile, the dosage range between human Se deficiency and Se toxicity is narrow, so the Se content of agricultural products needs to be controlled within a reasonable interval. Methods Se accumulation and speciation in rice were analyzed and compared during three different growth stages (late tillering stage, initiate heading stage, and full heading stage) using three Se fertilizers: selenite, fermented Se, and potassium selenocyanoacetate (Se-AAF) via the foliar application. Results The Se content in rice sprayed with organic Se fertilizer was controlled in the relatively safe range and met the human Se supplement requirement compared to the sprayed sodium selenite, which was too high of a dose. The percentage of organic Se and protein Se in brown rice was found to be similar in all three Se fertilizers. The highest organic Se content of 91.57% was found in the grain of rice at the full heading stage by spraying Se-AAF. The main Se species in the grain was selenomethionine (SeMet), which reached 80% of the total Se. Se-methyl selenocysteine(SeMeCys) was found only in Se-AAF. The grain quality showed that all three Se fertilizers increased the consistency of gelatinization. Conclusions Appropriately delaying the spraying time and selecting organic Se fertilizer as the Se source can help to produce green and safe selenium-rich rice.
    Type of Medium: Online Resource
    ISSN: 0032-079X , 1573-5036
    URL: Article
    DOI: 10.1007/s11104-022-05567-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 1478535-3
    detail.hit.zdb_id: 208908-7
    SSG: 12
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  • 4
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    Circulating tumor DNA as a prognostic marker in high-risk endometrial cancer
    Springer Science and Business Media LLC ; 2021
    In:  Journal of Translational Medicine Vol. 19, No. 1 ( 2021-12)
    Details
    In: Journal of Translational Medicine, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2021-12)
    Abstract: Currently, there is no reliable blood-based marker to track tumor recurrence in endometrial cancer (EC) patients. Liquid biopsies, specifically, circulating tumor DNA (ctDNA) analysis emerged as a way to monitor tumor metastasis. The objective of this study was to examine the feasibility of ctDNA in recurrence surveillance and prognostic evaluation of high-risk EC. Methods Tumor tissues from nine high-risk EC patients were collected during primary surgery and tumor DNA was subjected to next generation sequencing to obtain the initial mutation spectrum using a 78 cancer-associated gene panel. Baseline and serial post-operative plasma samples were collected and droplet digital PCR (ddPCR) assays for patient-specific mutations were developed to track the mutations in the ctDNA in serial plasma samples. Log-rank test was used to assess the association between detection of ctDNA before or after surgery and disease-free survival. Results Somatic mutations were identified in all of the cases. The most frequent mutated genes were PTEN , FAT4 , ARID1A , TP53 , ZFHX3 , ATM , and FBXW7 . For each patient, personalized ddPCR assays were designed for one-to-three high-frequent mutations. DdPCR analysis and tumor panel sequencing had a high level of agreement in the assessment of the mutant allele fractions in baseline tumor tissue DNA. CtDNA was detected in 67% (6 of 9) of baseline plasma samples, which was not predictive of disease-free survival (DFS). CtDNA was detected in serial post-operative plasma samples (ctDNA tracking) of 44% (4 of 9) of the patients, which predicted tumor relapse. The DFS was a median of 9 months (ctDNA detected) versus median DFS undefined (ctDNA not detected), with a hazard ratio of 17.43 (95% CI, 1.616–188.3). The sensitivity of post-operative ctDNA detection in estimating tumor relapse was 100% and specificity was 83.3%, which was superior to CA125 or HE4. Conclusions Personalized ctDNA detection was effective and stable for high-risk EC. CtDNA tracking in post-operative plasma is valuable for predicting tumor recurrence.
    Type of Medium: Online Resource
    ISSN: 1479-5876
    URL: Article
    DOI: 10.1186/s12967-021-02722-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2118570-0
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  • 5
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    Improving the fermentable sugar yields of wheat straw by high-temperature pre-hydrolysis with thermophilic enzymes of Malbranchea cinnamomea
    Springer Science and Business Media LLC ; 2020
    In:  Microbial Cell Factories Vol. 19, No. 1 ( 2020-12)
    Details
    In: Microbial Cell Factories, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2020-12)
    Abstract: Enzymatic hydrolysis is a key step in the conversion of lignocellulosic polysaccharides to fermentable sugars for the production of biofuels and high-value chemicals. However, current enzyme preparations from mesophilic fungi are deficient in their thermostability and biomass-hydrolyzing efficiency at high temperatures. Thermophilic fungi represent promising sources of thermostable and highly active enzymes for improving the biomass-to-sugar conversion process. Here we present a comprehensive study on the lignocellulosic biomass-degrading ability and enzyme system of thermophilic fungus Malbranchea cinnamomea N12 and the application of its enzymes in the synergistic hydrolysis of lignocellulosic biomass. Results Malbranchea cinnamomea N12 was capable of utilizing untreated wheat straw to produce high levels of xylanases and efficiently degrading lignocellulose under thermophilic conditions. Temporal analysis of the wheat straw-induced secretome revealed that M. cinnamomea N12 successively degraded the lignocellulosic polysaccharides through sequential secretion of enzymes targeting xylan and cellulose. Xylanase-enriched cocktail from M. cinnamomea N12 was more active on native and alkali‑pretreated wheat straw than the commercial xylanases from Trichoderma reesei over temperatures ranging from 40 to 75 °C. Integration of M. cinnamomea N12 enzymes with the commercial cellulase preparation increased the glucose and xylose yields of alkali‑pretreated wheat straw by 32 and 166%, respectively, with pronounced effects at elevated temperature. Conclusions This study demonstrated the remarkable xylanase-producing ability and strategy of sequential lignocellulose breakdown of M. cinnamomea N12. A new process for the hydrolysis of lignocellulosic biomass was proposed, comprising thermophilic enzymolysis by enzymes of M. cinnamomea N12 followed with mesophilic enzymolysis by commercial cellulases. Developing M. cinnamomea N12 as platforms for thermophilic enzyme mixture production will provide new perspectives for improved conversion yields for current biomass saccharification schemes.
    Type of Medium: Online Resource
    ISSN: 1475-2859
    URL: Article
    DOI: 10.1186/s12934-020-01408-y
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2091377-1
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  • 6
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    What are the actual needs of visually impaired people?
    Elsevier BV ; 2023
    In:  Displays Vol. 78 ( 2023-07), p. 102411-
    Details
    In: Displays, Elsevier BV, Vol. 78 ( 2023-07), p. 102411-
    Type of Medium: Online Resource
    ISSN: 0141-9382
    URL: Article
    DOI: 10.1016/j.displa.2023.102411
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2019693-3
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  • 7
    Online Resource
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    Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)
    MDPI AG ; 2021
    In:  International Journal of Molecular Sciences Vol. 22, No. 14 ( 2021-07-18), p. 7674-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 22, No. 14 ( 2021-07-18), p. 7674-
    Abstract: Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH4NO3 (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH4NO3 (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms22147674
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 8
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    New natural compound inhibitors of PDGFRA (platelet-derived growth factor receptor α) based on computational study for high−grade glioma therapy
    Frontiers Media SA ; 2023
    In:  Frontiers in Neuroscience Vol. 16 ( 2023-1-4)
    Details
    In: Frontiers in Neuroscience, Frontiers Media SA, Vol. 16 ( 2023-1-4)
    Abstract: High-grade glioma (HGG) is a malignant brain tumor that is common and aggressive in children and adults. In the current medical paradigm, surgery and radiotherapy are the standard treatments for HGG patients. Despite this, the overall prognosis is still very bleak. Studies have shown that platelet-derived growth factor receptor α (PDGFRA) is an essential target to treat tumors and inhibiting the activity of PDGFRA can improve the prognosis of HGG. Thus, PDGFRA inhibitors are critical to developing drugs and cancer treatment. Objective The purpose of this study was to screen lead compounds and candidate drugs with potential inhibitors against platelet-derived growth factor receptor α (PDGFRA) from the drug library (ZINC database) in order to improve the prognosis of patients with high-grade glioma (HGG). Materials and methods In our study, we selected Imatinib as the reference drug. A series of computer-aided technologies, such as Discovery Studio 2019 and Schrodinger, were used to screen and assess potential inhibitors of PDGFRA. The first step was to calculate the LibDock scores and then analyze the pharmacological and toxicological properties. Following this, we docked the small molecules selected in the previous steps with PDGFRA to study their docking mechanism and affinity. In addition, molecular dynamics simulation was used to determine whether the ligand-PDGFRA complex was stable in nature. Results Two novel natural compounds 1 and 2 (ZINC000008829785 and ZINC000013377891) from the ZINC database were found binding to PDGFRA with more favorable interaction energy. Also, they were predicted with less Ames mutagenicity, rodent carcinogenicity, non-developmental toxic potential, and tolerant with cytochrome P450 2D6 (CYP2D6). The dynamic simulation analysis demonstrated that ZINC000008829785-PDGFRA and ZINC000013377891-PDGFRA dimer complex had more favorable potential energy compared with Imatinib, and they can exist in natural environments stably. Conclusion ZINC000008829785 and ZINC000013377891 might provide a solid foundation for drugs that inhibit PDGFRA in HGG. In addition to being safe drug candidates, these compounds had important implications for improving drugs targeting PDGFRA.
    Type of Medium: Online Resource
    ISSN: 1662-453X
    URL: Article
    DOI: 10.3389/fnins.2022.1060012
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2411902-7
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  • 9
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    Effects of durable antibacterial, UV-resistant cotton fabrics with differentiated polydopamine metal complexes
    Elsevier BV ; 2024
    In:  Materials Letters Vol. 355 ( 2024-01), p. 135495-
    Details
    In: Materials Letters, Elsevier BV, Vol. 355 ( 2024-01), p. 135495-
    Type of Medium: Online Resource
    ISSN: 0167-577X
    URL: Article
    DOI: 10.1016/j.matlet.2023.135495
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 1491964-3
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  • 10
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    Prevalence of BRCA1 and BRCA2 gene mutations in Chinese patients with high‐risk breast cancer
    Wiley ; 2019
    In:  Molecular Genetics & Genomic Medicine Vol. 7, No. 6 ( 2019-06)
    Details
    In: Molecular Genetics & Genomic Medicine, Wiley, Vol. 7, No. 6 ( 2019-06)
    Abstract: Breast cancer is the most common cancer among women worldwide. Here, we report the prevalence of BRCA1/2 mutations in patients with high‐risk breast cancer from Inner Mongolia and Jilin, China, which was a part of a nationwide project on the detection of BRCA1/2 mutations in Chinese patients with hereditary breast cancer. Methods According to the criteria, index patients from a total of 245 independent families were initially recruited. All 49 exons of BRCA1 and BRCA2 and adjacent noncoding regions were screened for mutations based on next‐generation sequencing from collected saliva. Results We detected 17 BRCA1/2 variants in 18 of 216 (8.3%) index patients with high‐risk breast cancer. Among these, seven mutations were novel, including four BRCA1 mutations (c.123_124delCAinsAT, c.5093_5096delCTAA, c.5396‐2A 〉 G, and c.2054delinsGAAGAGTAACAAGTAAGAAGAGTAACAAGAAG), and three BRCA2 mutations (c.304A 〉 T, c.7552_7553insT, and c.9548_9549insA). The BRCA1/2 variants were identified in 14% (8/57) of the patients with triple‐negative breast cancer and in 6.3% (10/159) of the patients with non‐triple‐negative breast cancer. There was no significant difference between the two groups ( p  = 0.07). A higher frequency for BRCA1 mutations was observed in patients with triple‐negative breast cancer than in those with non‐triple‐negative breast cancer (12.3% vs. 2.5%, p  = 0.004). The frequencies of the BRCA2 mutations were not significantly different between patients with triple‐negative breast cancer and those with non‐triple‐negative breast cancer (1.8% vs. 3.8%, p  = 0.46). Conclusion We found that patients with triple‐negative breast cancer had a higher frequency of BRCA1 mutations than those with non‐triple‐negative breast cancer. In this study, no significant associations between the BRCA1/2 mutation status and age, family history of breast cancer, ovarian cancer, pancreatic cancer and prostate cancer, number of primary lesions, tumor size, or lymph node metastasis were observed.
    Type of Medium: Online Resource
    ISSN: 2324-9269 , 2324-9269
    URL: Issue
    URL: Article
    DOI: 10.1002/mgg3.2019.7.issue-6
    DOI: 10.1002/mgg3.677
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2734884-2
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