| 1. |
- 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. |
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Lee, Chia-Lin, et al.
(författare)
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Synthesis and Biological Evaluation of Phenanthrenes as Cytotoxic Agents with Pharmacophore Modeling and ChemGPS-NP Prediction as Topo II Inhibitors
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:5, s. e37897-
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Tidskriftsartikel (refereegranskat)abstract
- In a structure-activity relationship (SAR) study, 3-methoxy-1,4-phenanthrenequinones, calanquinone A (6a), denbinobin (6b), 5-OAc-calanquinone A (7a) and 5-OAc-denbinobin (7b), have significantly promising cytotoxicity against various human cancer cell lines (IC50 0.08-1.66 mu g/mL). Moreover, we also established a superior pharmacophore model for cytotoxicity (r = 0.931) containing three hydrogen bond acceptors (HBA1, HBA2 and HBA3) and one hydrophobic feature (HYD) against MCF-7 breast cancer cell line. The pharmacophore model indicates that HBA3 is an essential feature for the oxygen atom of 5-OH in 6a-b and for the carbonyl group of 5-OCOCH3 in 7a-b, important for their cytotoxic properties. The SAR for moderately active 5a-b (5-OCH3), and highly active 6a-b and 7a-b, are also elaborated in a spatial aspect model. Further rational design and synthesis of new cytotoxic phenanthrene analogs can be implemented via this model. Additionally, employing a ChemGPS-NP based model for cytotoxicity mode of action (MOA) provides support for a preliminary classification of compounds 6a-b as topoisomerase II inhibitors.
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| 5. |
- Cha, Shih-Ting, et al.
(författare)
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MicroRNA-519c suppresses hypoxia-inducible factor-1alpha expression and tumor angiogenesis.
- 2010
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Ingår i: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 70:7, s. 2675-2685
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Tidskriftsartikel (refereegranskat)abstract
- Hypoxia-inducible factor-1alpha (HIF-1alpha) is widely considered to be one of the key regulators of tumor angiogenesis. The upstream regulation is complex and involves several growth factors, cytokines, and hypoxia. Herein, we have identified miR-519c as a hypoxia-independent regulator of HIF-1alpha, acting through direct binding to the HIF-1alpha 3' untranslated region and leading to reduced tumor angiogenesis. Overexpression of miR-519c resulted in a significant decrease of HIF-1alpha protein levels and reduced the tube formation of human umbilical vein endothelial cells; similarly, antagomir inhibition of miR-519c increased the level of HIF-1alpha protein and enhanced angiogenic activity, suggesting an important role of miR-519c in HIF-1alpha-mediated angiogenesis. Consistent with the overexpression of miR-519c in cancer patients with better prognosis, mice injected with miR-519c-overexpressing cells exhibited dramatically reduced HIF-1alpha levels, followed by suppressed tumor angiogenesis, growth, and metastasis. In addition, we found that hepatocyte growth factor (HGF), a known HIF-1alpha inducer, reduced the miR-519c levels through an Akt-dependent pathway. This regulation was posttranscriptional and may be mediated by suppression of miR-519c maturation. Taken together, our findings provide the first evidence that miR-519c is a pivotal regulator of tumor angiogenesis and that microenvironmental HGF contributes to regulating miR-519c biogenesis in cancer cells.
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| 6. |
- Hsieh, Yves S-Y, et al.
(författare)
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Structure and bioactivity of the polysaccharides in medicinal plant Dendrobium huoshanense
- 2008
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Ingår i: Bioorganic & Medicinal Chemistry. - : Elsevier. - 0968-0896 .- 1464-3391. ; 16:11, s. 6054-68
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Tidskriftsartikel (refereegranskat)abstract
- Detailed structures of the active polysaccharides extracted from the leaf and stem cell walls and mucilage of Dendrobium huoshanense are determined by using various techniques, including chromatographic, spectroscopic, chemical, and enzymatic methods. The mucilage polysaccharide exhibits specific functions in activating murine splenocytes to produce several cytokines including IFN-gamma, IL-10, IL-6, and IL-1alpha, as well as hematopoietic growth factors GM-CSF and G-CSF. However, the deacetylated mucilage obtained from an alkaline treatment fails to induce cytokine production. The structure and bioactivity of mucilage components are validated by further fractionation. This is the first study that provides clear evidence for the structure and activity relationship of the polysaccharide in D. huoshanense.
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| 7. |
- Chang, Ting-Chia, et al.
(författare)
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Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer
- 2019
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 14:4
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Tidskriftsartikel (refereegranskat)abstract
- Human endogenous retroviruses (HERVs) have been investigated for potential links with human cancer. However, the distribution of somatic nucleotide variations in HERV elements has not been explored in detail. This study aims to identify HERV elements with an over-representation of somatic mutations (hot spots) in cancer patients. Four HERV elements with mutation hotspots were identified that overlap with exons of four human protein coding genes. These hotspots were identified based on the significant over-representation (p<8.62e-4) of non-synonymous single-nucleotide variations (nsSNVs). These genes are TNN (HERV-9/LTR12), OR4K15 (HERV-IP10F/LTR10F), ZNF99 (HERV-W/HERV17/LTR17), and KIR2DL1 (MST/MaLR). In an effort to identify mutations that effect survival, all nsSNVs were further evaluated and it was found that kidney cancer patients with mutation C2270G in ZNF99 have a significantly lower survival rate (hazard ratio = 2.6) compared to those without it. Among HERV elements in the human non-protein coding regions, we found 788 HERVs with significantly elevated numbers of somatic single-nucleotide variations (SNVs) (p<1.60e-5). From this category the top three HERV elements with significantly over-represented SNVs are HERV-H/LTR7, HERV-9/LTR12 and HERV-L/MLT2. Majority of the SNVs in these 788 HERV elements are located in three DNA functional groups: long non-coding RNAs (lncRNAs) (60%), introns (22.2%) and transcriptional factor binding sites (TFBS) (14.8%). This study provides a list of mutational hotspots in HERVs, which could potentially be used as biomarkers and therapeutic targets.
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| 8. |
- Elsayed, Mohamed Hammad, et al.
(författare)
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Visible-light-driven hydrogen evolution using nitrogen-doped carbon quantum dot-implanted polymer dots as metal-free photocatalysts
- 2021
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Ingår i: Applied Catalysis B: Environmental. - : Elsevier BV. - 0926-3373. ; 283
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Tidskriftsartikel (refereegranskat)abstract
- Given the photocatalytic properties of semiconducting polymers and carbon quantum dots (CQDs), we report a new structure for a metal-free photocatalytic system with a promising efficiency for hydrogen production through the combination of an organic semiconducting polymer (PFTBTA) and N-doped carbon quantum dots (NCQDs) covered by PS-PEGCOOH to produce heterostructured photocatalysts in the form of polymer dots (Pdots). This design could provide strong interactions between the two materials owing to the space confinement effect in nanometer-sized Pdots. Small particle size NCQDs are easy to insert inside the Pdot, which leads to an increase in the stability of the Pdot structure and enhances the hydrogen evolution rate by approximately 5-fold over that of pure PFTBTA Pdots. The photophysics and the mechanism behind the catalytic activity of our design are investigated by transient absorption measurement, demonstrating the role of NCQDs to enhance the charge separation and the photocatalytic efficiency of the PFTBTA Pdot.
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| 9. |
- Lin, Chang, et al.
(författare)
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Visualizing Conduit Flows around Solitary Air Pockets
- 2014
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Ingår i: Journal of engineering mechanics. - : American Society of Civil Engineers (ASCE). - 0733-9399 .- 1943-7889. ; 141:5
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Tidskriftsartikel (refereegranskat)abstract
- Understanding flow characteristics around air pockets is fundamental in the study of air entrainment and transport in pipelines. This study deals with the use of flow visualization technique (FVT) and high-speed particle image velocimetry (HSPIV) in exploration of the characteristics around stationary air pockets in horizontal-pipe flow. The air-pocket volume varies from 0 to 10.0 mL, and the air pocket is injected into a fully developed turbulent flow with Reynolds numbers between 17,000 and 18,400. In the plane of symmetry, the main flow features include (1) a horseshoe vortex upstream, (2) a stagnation point on the frontal interface, (3) a separation point and a separated shear layer beneath, (4) a reattached shear layer downstream of the reattachment point (for air-pocket volumes greater than 2.0 mL), and (5) a reverse-flow region downstream. The deformable air pocket in the turbulent flow causes streamwise random movements of both the stagnation and separation points around their mean positions. The flow pattern is categorized based on the occurrence of either separated flow or flow reattachment. Fully separated flow (Mode I) occurs at air-pocket volumes less than 2.0 mL. Intermittently reattached flow (Mode II) occurs if the volume is within 2.0–5.0 mL. Fully reattached flow (Mode III) is evident at volumes greater than 5.0 mL. Water particles on the air-pocket surface move with the adjacent flow, thus forming a slip boundary. The evolution of mean streamwise velocity beneath the air pocket demonstrates the formation of either a separated or a reattached shear layer. Using nonlinear regression analysis, appropriate characteristic velocity and length scales are determined to obtain similarity profiles in the separated shear layer beneath.
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| 10. |
- Lin, Wei Cheng, et al.
(författare)
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Effect of energy bandgap and sacrificial agents of cyclopentadithiophene-based polymers for enhanced photocatalytic hydrogen evolution
- 2021
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Ingår i: Applied Catalysis B: Environmental. - : Elsevier BV. - 0926-3373. ; 298
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Tidskriftsartikel (refereegranskat)abstract
- A library of donor-acceptor system consisting of cyclopentadithiophene-based polymer photocatalysts have been designed and synthesized. Among all photocatalysts, the active PCPDTBSO achieved hydrogen evolution rates of 24.6 mmol h–1 g–1 with apparent quantum yields of 8.7 % at 500 nm. More importantly, combined the results of photocatalytic efficiency, apparent quantum yield, the time-resolved fluorescence decay spectra, the steady-state photoluminescence spectra, and the transient absorption spectroscopy, and the oxidation potentials of sacrificial donors and protons reduction potentials in different pH values, we confirmed the concept that ascorbic acid is a suitable sacrificial donor for narrow bandgap polymers and triethylamine is a suitable sacrificial donor for wide bandgap polymers owing to the existence of the optimal thermodynamic driving force. We believed this study would be advantageous for the selection of photocatalysts and sacrificial donors for hydrogen production.
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