80 research outputs found

    Data_Sheet_2_Challenges in estimating effective population sizes from metagenome-assembled genomes.xlsx

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    Effective population size (Ne) plays a critical role in shaping the relative efficiency between natural selection and genetic drift, thereby serving as a cornerstone for understanding microbial ecological dynamics. Direct Ne estimation relies on neutral genetic diversity within closely related genomes, which is, however, often constrained by the culturing difficulties for the vast majority of prokaryotic lineages. Metagenome-assembled genomes (MAGs) offer a high-throughput alternative for genomic data acquisition, yet their accuracy in Ne estimation has not been fully verified. This study examines the Thermococcus genus, comprising 66 isolated strains and 29 MAGs, to evaluate the reliability of MAGs in Ne estimation. Despite the even distribution across the Thermococcus phylogeny and the comparable internal average nucleotide identity (ANI) between isolate populations and MAG populations, our results reveal consistently lower Ne estimates from MAG populations. This trend of underestimation is also observed in various MAG populations across three other bacterial genera. The underrepresentation of genetic variation in MAGs, including loss of allele frequency data and variable genomic segments, likely contributes to the underestimation of Ne. Our findings underscore the necessity for caution when employing MAGs for evolutionary studies, which often depend on high-quality genome assemblies and nucleotide-level diversity.</p

    Data_Sheet_1_Challenges in estimating effective population sizes from metagenome-assembled genomes.pdf

    No full text
    Effective population size (Ne) plays a critical role in shaping the relative efficiency between natural selection and genetic drift, thereby serving as a cornerstone for understanding microbial ecological dynamics. Direct Ne estimation relies on neutral genetic diversity within closely related genomes, which is, however, often constrained by the culturing difficulties for the vast majority of prokaryotic lineages. Metagenome-assembled genomes (MAGs) offer a high-throughput alternative for genomic data acquisition, yet their accuracy in Ne estimation has not been fully verified. This study examines the Thermococcus genus, comprising 66 isolated strains and 29 MAGs, to evaluate the reliability of MAGs in Ne estimation. Despite the even distribution across the Thermococcus phylogeny and the comparable internal average nucleotide identity (ANI) between isolate populations and MAG populations, our results reveal consistently lower Ne estimates from MAG populations. This trend of underestimation is also observed in various MAG populations across three other bacterial genera. The underrepresentation of genetic variation in MAGs, including loss of allele frequency data and variable genomic segments, likely contributes to the underestimation of Ne. Our findings underscore the necessity for caution when employing MAGs for evolutionary studies, which often depend on high-quality genome assemblies and nucleotide-level diversity.</p

    Average annual precipitation and potential evapotranspiration of 1967–1999 and precipitation in 2013 in the Sanyanjing catchment, Shanxi province, China.

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    <p>Average annual precipitation and potential evapotranspiration of 1967–1999 and precipitation in 2013 in the Sanyanjing catchment, Shanxi province, China.</p

    Vaginoplasty with Acellular Dermal Matrix after Radical Resection for Carcinoma of the Uterine Cervix

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    <p>Various methods are available for vaginoplasty, but many of them have the drawbacks including surgical complexity and postoperative pain at the donor site. We herein evaluated the outcomes of vaginoplasty using tissue-engineered biomaterial graft. This study included 16 early stage cervical cancer patients who received curative surgery in combination with radiotherapy. They underwent vaginoplasty with tissue-engineered biological material, acellular dermal matrix (ADM). After treatment, a vaginal dilator was advised to be used for 6 months to prevent contraction of vagina. The effectiveness of the treatment was evaluated by the anatomic changes of vagina before and after treatment, and the sexual outcomes at 12-month after treatment. The procedure was safe with no intra-operative complications reported. The mean operation time was 1.7 ± 0.3 hours, with 11/16 patients had blood loss < 50 mL during surgery. Generally, epithelialization was observed in 2-week after treatment. At the 1-year follow-up visit, the mean vaginal width was increased significantly from 1.31 ± 0.4 cm before surgery to 4.13 ± 0.43 cm after surgery (p = 0.034). The vaginal length was also increased from 5.97 ± 0.59 cm to 9.25 ± 0.66 cm (p < 0.001). Majority of the patients (12/16) reported satisfactory sexual life. The use of ADM in vaginoplasty was a safe and effective procedure that provided satisfactory sexual function for patients with vaginal abnormalities after cervical cancer treatment.</p

    CEM.NKR is resistant to productive infection by HIV-1.

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    <p>A) CEM.NKR cell surface CD4 and CXCR4 expression determined by flow cytometry and compared with the other indicated cell lines. B) HIV-1 infection kinetics. A total of 5×10<sup>5</sup> of the indicated cells was infected with 100 ng HIV-1 (NL 4-3) and viral growth curves were determined by measuring p24<sup>Gag</sup> in the supernatant. Results shown are one of three independent experiments. The error bars for CEM.NKR represent standard deviation in these three independent experiments.</p

    Single-round HIV-1 replication in human T cell lines.

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    <p>A) Expression of viral protein from multiply spliced RNA species. The simple reference diagram at the top of the figure indicates the position of the reporter gene in the viral genome. The indicated cell lines were infected with pNL-Luc reporter viruses. Twenty-four hours later, intracellular luciferase activity was measured. B) Expression of viral protein from singly spliced RNA species. The indicated cell lines were infected with VSV-G pseudotyped pNL-enCAT reporter viruses followed by intracellular CAT activity assay 24 hours later. A2.01(-) served as a negative control where A2.01 cells were infected by the same virus without VSV-G pseudotying. C) Expression of viral protein from un-spliced RNA species. The indicated cell lines were infected by <i>env</i>-deficient HIV-1 pseudotyed with VSV-G. Six days later the levels of intracellular Gag protein were determined by ELISA. A2.01(-) served as a negative control where A2.01 cells were infected by the same virus without VSV-G pseudotying. D) Levels of viral release. The infection experiment was performed as in C) and levels of viral release were determined by p24<sup>Gag</sup> ELISA. Error bars in these experiments represent standard deviations in three independent experiments.</p

    Background information of 101 soil sampling points in the Sanyanjing catchment study area in Shanxi province, China.

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    <p>Background information of 101 soil sampling points in the Sanyanjing catchment study area in Shanxi province, China.</p

    Vertical soil water profiles in relation to different groups in the Sanyanjing catchment study area before and after the rainy season (a. before the rainy season; and b. after the rainy season).

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    <p>Vertical soil water profiles in relation to different groups in the Sanyanjing catchment study area before and after the rainy season (a. before the rainy season; and b. after the rainy season).</p

    Combined grouping of 101 vertical profiles of soil water content (0–300 cm) in Sanyanjing catchment by cluster analysis of the mean value and regression gradient.

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    <p>Combined grouping of 101 vertical profiles of soil water content (0–300 cm) in Sanyanjing catchment by cluster analysis of the mean value and regression gradient.</p

    Location of Sanyanjing catchment and distribution of 101 sampling points in the Sanyanjing catchment.

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    <p>Location of Sanyanjing catchment and distribution of 101 sampling points in the Sanyanjing catchment.</p
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