| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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.
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| 2. |
- Wang, Xiaoyan, et al.
(author)
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PAHs and PCBs residues and consumption risk assessment in farmed yellow croaker (Larimichthys crocea) from the East China Sea, China.
- 2019
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In: Marine pollution bulletin. - : Elsevier BV. - 1879-3363 .- 0025-326X. ; 140, s. 294-300
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Journal article (peer-reviewed)abstract
- Large yellow croaker (Larimichthys crocea) purchased from five different farming sites in Zhoushan Archipelago and Xiangshan Harbor in the East China Sea, China were analyzed for polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). Concentrations of PAHs and PCBs in the edible muscle of L. crocea ranged from 83.14 to 174.68 ng/g wet weight (or 266.89 to 695.24 ng/g dry weight) and 3.89 to 17.40 ng/g wet weight (or 15.50 to 54.25 ng/g dry weight), respectively. Incremental lifetime cancer risk (ILCR) associated with the dietary intake of PAHs and PCBs in L. crocea was assessed. Results showed that levels of PAHs in L. crocea were high enough to cause potential carcinogenic risks for human consumption, while, levels of PCBs in fish samples were of low significant carcinogenic risk.
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| 3. |
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| 4. |
- Noguchi, S, et al.
(author)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Journal article (peer-reviewed)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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