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- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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. |
- Zirn, B, et al.
(författare)
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Expression profiling of Wilms tumors reveals new candidate genes for different clinical parameters
- 2006
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136. ; 118:8, s. 1954-1962
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Tidskriftsartikel (refereegranskat)abstract
- Wilms tumor is the most frequent renal neoplasm in children, but our understanding of its genetic basis is still limited. We performed cDNA microarray experiments using 63 primary Wilms tumors with the aim of detecting new candidate genes associated with malignancy grade and tumor progression. All tumors had received preoperative chemotherapy as mandated by the SIOP protocol, which sets this study apart from related approaches in the Unites States that are based on untreated samples. The stratification of expression data according to clinical criteria allowed a rather clear distinction between different subsets of Wilms tumors. Clear-cut differences in expression patterns were discovered between relapse-free as opposed to relapsed tumors and tumors with intermediate risk as opposed to high risk histology. Several differentially expressed genes, e.g. TRIM22, CENPF, MYCN, CTGF, RARRES3 and EZH2, were associated with Wilms tumor progression. For a subset of differentially expressed genes, microarray data were confirmed by real-time RT-PCR on the original set of tumors. Interestingly, we found the retinoic acid pathway to be deregulated at different levels in advanced tumors suggesting that treatment of these tumors with retinoic acid may represent a promising novel therapeutic approach. (c) 2005 Wiley-Liss, Inc.
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| 4. |
- Barthes, Gilles, et al.
(författare)
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Verifying relational properties using trace logic
- 2019
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Ingår i: Proceedings of the 19th Conference on Formal Methods in Computer-Aided Design, FMCAD 2019. ; , s. 170-178
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Konferensbidrag (refereegranskat)abstract
- We present a logical framework for the verification of relational properties in imperative programs. Our frame-work reduces verification of relational properties of imperative programs to a validity problem in trace logic, an expressive instance of first-order predicate logic. Trace logic draws its expressiveness from its syntax, which allows expressing properties over computation traces. Its axiomatization supports fine-grained reasoning about intermediate steps in program execution, notably loop iterations. We present an algorithm to encode the semantics of programs as well as their relational properties in trace logic, and then show how first-order theorem proving can be used to reason about the resulting trace logic formulas. Our work is implemented in the tool RAPID and evaluated with examples coming from the security field.
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| 8. |
- Xu, Y. H., et al.
(författare)
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Synthesis and characterization of dinuclear ruthenium complexes covalently linked to Ru-II tris-bipyridine : An approach to mimics of the donor side of photosystem II
- 2005
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 11:24, s. 7305-7314
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Tidskriftsartikel (refereegranskat)abstract
- To mimic the electron-donor side of photosystem II (PSII), three trinuclear ruthenium complexes (2, 2a, 2b) were synthesized. In these compl plexes, a mixed-valent dinuclear Ru-2(II,III) moiety with one phenoxy and two acetato bridges is covalently linked to a Ru-II tris-bipyridine photosensitizer. The properties and photoinduced electron/energy transfer of these complexes were studied. The results show that the Ru-2(II,III) moieties in the complexes readily undergo reversible one-electron reduction and one-electron oxidation to give the Ru-2(II,II) and Ru-2(II,III) states, respectively. This could allow for photooxidation of the sensitizer part with an external acceptor and subsequent electron transfer from the dinuclear ruthenium moiety to regenerate the sensitizer. However, all trinuclear ruthenium complexes have a very short excited-state lifetime, in the range of a few nanoseconds to less than 100 ps. Studies by femtosecond time-resolved techniques suggest that a mixture of intramolecular energy and electron transfer between the dinuclear ruthenium moiety and the excited [Ru(bpy)(3)](2+) photosensitizer is responsible for the short lifetimes. This problem is overcome by anchoring the complexes with ester- or carboxyl-substituted bipyridine ligands (2a, 2b) to nanocrystalline TiO2, and the desired electron transfer from the excited state of the [Ru(bPY)(3)](2+) moiety to the conduction band of TiO2, followed by intramolecular electron transfer from the dinuclear Ru-2(II,III) moiety to photogenerated Ru-III was observed. The resulting long-lived Ru-2(III,III) state decays on the millisecond timescale.
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| 9. |
- Zhu, Yongda, et al.
(författare)
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Probing Ultralate Reionization: Direct Measurements of the Mean Free Path over 5 z
- 2023
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 955:2
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Tidskriftsartikel (refereegranskat)abstract
- The mean free path of ionizing photons, lambda(mfp), is a critical parameter for modeling the intergalactic medium (IGM) both during and after reionization. We present direct measurements of lambda(mfp) from QSO spectra over the redshift range 5 < z < 6, including the first measurements at z similar or equal to 5.3 and 5.6. Our sample includes data from the XQR-30 VLT large program, as well as new Keck/ESI observations of QSOs near z similar to 5.5, for which we also acquire new [C II] 158 mu m redshifts with ALMA. By measuring the Lyman continuum transmission profile in stacked QSO spectra, we find lambda(mfp) = 9.33(-1.80)(+2.06), 5.40(-1.40)(+1.47), 3.31(-1.34)(+2.74), and 0.81(-0.48)(+0.73) pMpc at z = 5.08, 5.31, 5.65, and 5.93, respectively. Our results demonstrate that lambda(mfp) increases steadily and rapidly with time over 5 < z < 6. Notably, we find that lambda(mfp) deviates significantly from predictions based on a fully ionized and relaxed IGM as late as z = 5.3. By comparing our results to model predictions and indirect lambda(mfp) constraints based on IGM Ly alpha opacity, we find that the evolution of lambda(mfp) is consistent with scenarios wherein the IGM is still undergoing reionization and/or retains large fluctuations in the ionizing UV background well below redshift 6.
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