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The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on IlluminaR ....
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems studied. The McMurdo Dry Valleys of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change predictions. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past and future changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We ident ....
Reverse Transcription Quantitative PCR (RT-qPCR) Following total RNA extraction using TRIzol reagent (Invitrogen), cDNA was synthesized using Mir-X miRNA First-Strand Synthesis Kit (Takara Holdings Inc., Kyoto, Japan) with extracted total RNA (2 μg). The miRNA expression was measured by qPCR with SYBR Advantage qPCR Premix (Takara) on CFX133a Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, CA, USA). Relative expression was determined with a U6 control through the 2 −ΔΔCt method. The primers used are depicted in Table 1. Table 1 Primer Sequences Cell Culture, Transfection and Infection Human lung cancer cell lines, including H522, H460, SK-MES-1, and A549, and a human bronchial epithelial cell line BEAS-2B, were from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (Shanghai, China). Cell lines H522, H460, and A549 were cultivated in RPMI-1640 medium (Gibco; Thermo Fisher Scientific), while SK-MES-1 cells were in m ....
H) CCND1 expression in BC patients revealed by GEPIA website ( I) the β-catenin and GSK3β expression as well as the extent of GSK3β phosphorylation in MCF-7 and T47D parents and resistant cells. Data are displayed in the form of mean ± SD. All experiments were repeated at least three times. In panel ( B) two-way ANOVA along with Tukey’s multiple comparison was applied, while in panel ( D, E and p 0.05, p 0.01. Abbreviations: miR, microRNA; FOXO1, forkhead box O1; CCND1, cyclin D1; SD, standard deviation; ANOVA, analysis of variance. We predicted that FOXO1 could bind to the promoter sequence of CCND1 through the JASPAR website ( ....